Scrapie Program Standards 

Volume 1: 

National Scrapie Eradication 

Program 

 

Effective April 25 2019 

United States

Department of 

Agriculture 

Animal and 

Plant Health 

Inspection 

Service 

APHIS 91-55-079 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 

The U.S. Department of Agriculture (USDA) prohibits discrimination in all its programs and 

activities on the basis of race, color, national origin, sex, religion, age, disability, political beliefs, 

sexual orientation, or marital or family status. (Not all prohibited bases apply to all programs.) 

Persons with disabilities who require alternative means for communication of program 

information (Braille, large print, audiotape, etc.) should contact USDA’s TARGET Center at 

(202) 720–2600 (voice and TDD).

To file a complaint of discrimination, write USDA, Director, Office of Civil Rights, Room 326–

W, Whitten Building, 14th and Independence Avenue, SW, Washington, DC 20250–9410 or call 

(202) 720–5964 (voice and TDD). USDA is an equal opportunity provider and employer. 

Mention of companies or commercial products does not imply recommendation or endorsement 

by USDA over others not mentioned. USDA neither guarantees nor warrants the standard of any 

product mentioned. Product names are mentioned solely to report factually on available data and 

to provide specific information. 

Issued April 25, 2019 

A Note on Navigation 

This document has bookmarks for each section and subsection for easier navigation. If the 

bookmarks panel is not already activated, use the following instructions to open it. 

Windows: right-click anywhere on the screen, select “Show Navigation Pane Buttons” 

from the drop-down menu, and then click on the bookmarks icon. 

The bookmarks icon is shown as follows: . 

Mac users: control-click anywhere on the screen, select “Open with Preview,” click on 

the Preview menu icon and then click on “Table of Contents.” 

The Preview menu icon is shown as follows: . 

Additionally, these standards have links to external information as well as internal links for 

easier navigation. Text in blue indicates a link: click on the text to navigate to the webpage 

or section referenced. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 1 

Table of Contents 

Table of Contents .......................................................................................................................... 1

Introduction 5

List of Acronyms ........................................................................................................................... 8

Part I: Definitions ......................................................................................................................... 9

Accredited veterinarian ............................................................................................................... 9

Administrator .............................................................................................................................. 9

Animal.......... ........................................................................................................................... 9

APHIS.......... ............................................................................................................................ 9

APHIS representative ................................................................................................................. 9

Approved laboratory ................................................................................................................... 9

Area Veterinarian in Charge (AVIC) .......................................................................................... 9

Blackfaced sheep ........................................................................................................................ 9

Breed associations and registries .............................................................................................. 10

Breeding sheep or goat ............................................................................................................. 10

Classification or reclassification investigation ......................................................................... 10

Commercial sheep or goat ........................................................................................................ 10

Commingle, commingled, commingling .................................................................................. 10

Consistent State ......................................................................................................................... 10

Deputy Administrator ............................................................................................................... 10

Designated Scrapie Epidemiologist (DSE) ............................................................................... 11

Designation of a flock or animal ............................................................................................... 11

Destroyed .................................................................................................................................. 11

Direct movement to slaughter ................................................................................................... 11

Electronic implant ..................................................................................................................... 11

Exposed animal ......................................................................................................................... 11

Exposed embryo ....................................................................................................................... 12

Exposed flock ........................................................................................................................... 12

Female animal ........................................................................................................................... 12

Flock or herd ............................................................................................................................. 12

Flock identification (ID) number .............................................................................................. 12

Flock of origin .......................................................................................................................... 13

Flock plan ................................................................................................................................. 13

Flock under investigation .......................................................................................................... 13

Found dead ................................................................................................................................ 13

Genetically less susceptible exposed sheep .............................................................................. 13

Genetically resistant exposed sheep ......................................................................................... 14

Genetically susceptible animal ................................................................................................. 14

Genetically susceptible exposed animal ................................................................................... 14

Genotypes of sheep ................................................................................................................... 15

Group/lot identification number (GIN) ..................................................................................... 16

High-risk animal ....................................................................................................................... 16
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 2 

Inconsistent State ...................................................................................................................... 16

Infected flock ............................................................................................................................ 16

Interstate certificate of veterinary inspection (ICVI) ................................................................ 17

Interstate commerce .................................................................................................................. 17

Limited contact ......................................................................................................................... 17

Live-animal test ........................................................................................................................ 17

Low-risk commercial flock ....................................................................................................... 17

Low-risk exposed animal .......................................................................................................... 18

Male animal .............................................................................................................................. 18

Mortgage ................................................................................................................................... 18

National Scrapie Database (NSD) ............................................................................................ 18

National Scrapie Eradication Program (NSEP) ........................................................................ 18

National Scrapie Eradication Program Standards (NSEPS) ..................................................... 18

National Veterinary Services Laboratories (NVSL) ................................................................. 18

Noncompliant flock .................................................................................................................. 19

Official eartag ........................................................................................................................... 19

Official genotype test ................................................................................................................ 19

Official identification device or method ................................................................................... 19

Official identification number .................................................................................................. 20

Official test ............................................................................................................................... 20

Officially identified ................................................................................................................... 20

Owner..... .................................................................................................................................. 20

Owner/hauler statement ............................................................................................................ 20

Permit..... .................................................................................................................................. 20

Person..... .................................................................................................................................. 21

Person number .......................................................................................................................... 21

Post-exposure management and monitoring plan (PEMMP) ................................................... 21

Premises .................................................................................................................................... 21

Premises identification number (PIN) ...................................................................................... 21

Program ..................................................................................................................................... 21

Program-approved test .............................................................................................................. 22

Restricted animal sale or restricted livestock facility ............................................................... 22

Scrapie..... ................................................................................................................................ 22

Scrapie control pilot project ...................................................................................................... 22

Scrapie Free Flock Certification Program (SFCP) ................................................................... 22

Scrapie Free Flock Certification Program Standards (SFCPS) ................................................ 22

Scrapie-positive animal ............................................................................................................. 23

Slaughter channels .................................................................................................................... 23

Source flock .............................................................................................................................. 23

State..... .................................................................................................................................... 24

State Animal Health Official (SAHO) ...................................................................................... 24

State representative ................................................................................................................... 24

Suspect animal .......................................................................................................................... 24

Tamper-resistant sampling kit .................................................................................................. 25
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 3 

Terminal feedlot ........................................................................................................................ 25

Trace..... ................................................................................................................................... 26

Unofficial test ........................................................................................................................... 26

Veterinary Medical Officer (VMO) .......................................................................................... 26

Part II: Administrative Procedures .......................................................................................... 27

A. Supervision of the Cooperative State-Federal-Industry National Scrapie Eradication 

Program (NSEP) ............................................................................................................ 27

B. Appointing DSEs............................................................................................................ 27

C. Administrative Review of Program Activities and Progress ......................................... 27

D. Inspection of Slaughter Establishments, Livestock Markets, Dealers, and Other 

Concentration Points for Identification and Sampling Compliance .............................. 27

E. Identification and Recordkeeping Compliance .............................................................. 30

F. Requirements for Program Personnel Entering Premises .............................................. 33

G. Providing Services to Livestock Owners ....................................................................... 33

H. Exceptions to the Deadlines for Flock Plans, Investigations, and Testing .................... 34

I. Depopulation of All Sexually Intact Sheep and Goats in a Flock (Whole Flock 

Depopulation) ................................................................................................................ 34

J. Indemnity ....................................................................................................................... 34

K. Interstate Certificates of Veterinary Inspection (ICVI) for Sheep and Goats in 

Interstate Commerce ................................................................................................... 41

L. Permits ............................................................................................................................ 43

M. Terminal Feedlots ........................................................................................................... 43

N. Movement Restrictions, Release Procedures, and Criteria for Releasing Movement 

Restrictions on Infected or Source Flocks, Animals Required for Testing, and Exposed 

Animals .......................................................................................................................... 44

O. Procedures for Sheep and Goats Transiting or Temporarily Residing in Inconsistent 

States .............................................................................................................................. 46

P. National Scrapie Database (NSD) – Data Entry Requirements ..................................... 47

Q. Genotyping Administrative Procedures ......................................................................... 48

R. Appeals of APHIS Actions ............................................................................................ 49

Part III: Identification Requirements ....................................................................................... 51

A. Identification of Sheep and Goats in Commerce ........................................................... 51

B. Records of Animals Handled ......................................................................................... 61

Part IV: Shows and Sales ........................................................................................................... 64

Part V: Consistent State Status in the National Scrapie Eradication Program .................... 65

A. State Status in the NSEP ................................................................................................ 65

B. Standards for State Programs to Qualify as Consistent.................................................. 65

C. Scrapie Classification, Renewal, or Reclassification of a State or Zone ....................... 67

Part VI: Surveillance and Monitoring ........................................................................................ 68

Part VII: Epidemiology................................................................................................................ 70

A. Introduction .................................................................................................................... 70

B. Reclassification Procedures: Redesignation of Suspect, High-Risk, and Exposed 

Animals and Exposed, Infected, Source, Under Investigation, and Noncompliant Flocks

........................................................................................................................................ 70
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 4 

C. Procedures for Investigating a Report of a Clinically Suspicious Animal ..................... 74

D. Procedures for Investigating a Report of a Live Test-Positive Animal ......................... 75

E. Procedures for Conducting an Epidemiological Investigation, Managing Flocks, and 

Reporting Results Following Receipt of NVSL Confirmation of a Scrapie-Positive 

Animal Either Through Necropsy Samples or a Live Animal Test ............................... 76

F. Procedures for Investigating and Monitoring a Flock that Received a High-Risk Animal

........................................................................................................................................ 82

G. Testing a Flock Pending Designation as a Source or Infected Flock to Determine 

Whether the Flock is Infected ........................................................................................ 87

Part VIII: Flock Cleanup Plans and PEMMPs ........................................................................ 90

A. Movement Restrictions on Animals in Flocks on a Flock Plan or PEMMP .................. 90

B. Requirements for Flock Plans and Post Exposure Management and Monitoring Plans 

(PEMMPs) ..................................................................................................................... 90

Part IX: Diagnostic Laboratory Approval Procedures and Test Interpretation .................. 96

Part X: Reports ........................................................................................................................... 96

A. Epidemiological Investigation Report ............................................................................ 96

B. Monthly Epidemiology and Compliance Report ........................................................... 98

C. End-of-Year Epidemiology and Compliance Report ..................................................... 98

D. VS Form 5-24, Application for Scrapie Classification, Classification Renewal, or 

Reclassification of a State .............................................................................................. 99

Appendix A: Approval of Laboratories to Conduct Official Genotype Tests ..................... 100

Appendix B: Approval of Laboratories to Conduct Official Program-Approved Diagnostic 

Tests for Scrapie in Sheep and Goats .............................................................. 104

Appendix C: Program Approval of Diagnostic Tests for Scrapie in Sheep and Goats ...... 110

Appendix D: Scrapie Surveillance ........................................................................................... 117

A. General ......................................................................................................................... 117

B. Animals Targeted for Surveillance Sampling .............................................................. 117

C. Surveillance Minimums ............................................................................................... 119

D. Surveillance at Sources Other Than Slaughter ............................................................. 119

E. Sampling Procedures and Forms .................................................................................. 120

Appendix E: Scrapie Cleaning and Disinfection Guidelines ................................................ 123

Pastures ................................................................................................................................... 123

Drylots .................................................................................................................................... 123

Earth Surfaces Inside Structures or Used for Confined Lambing Pens .................................. 123

Non-Earth Surfaces ................................................................................................................. 123
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 5 

Introduction

The objective of the National Scrapie Eradication Program (NSEP) is to achieve classical scrapie 

freedom by identifying and cleaning up the remaining scrapie-infected and source flocks in the 

United States. Eradication will improve the overall health of the national sheep flock and goat 

herd, relieve sheep and goat producers of scrapie-associated economic losses, and increase 

international marketing opportunities. 

The National Scrapie Eradication Program Standards (NSEPS) contain cooperative procedures 

and standards adopted by the USDA Animal and Plant Health Inspection Service (APHIS) and 

Consistent States for eradicating classical scrapie from the United States. These standards are 

intended to assist State and Federal animal health personnel in implementing the NSEP 

consistently and equitably throughout the United States. They are designed to prevent, monitor, 

and eradicate classical scrapie disease from domestic sheep flocks and goat herds and maintain 

Consistent State status. 

These standards replace the Scrapie Eradication Uniform Methods and Rules (UM&R) dated 

June 1, 2005. Flock plan agreements and post-exposure management and monitoring plan 

(PEMMP) agreements made before the effective date of these standards will remain in force, 

unless changed by mutual agreement between APHIS, the State, and the owner. 

 

These standards will be reviewed periodically by representatives of the livestock industry and 

appropriate State and Federal agencies, and APHIS will revise them as needed. APHIS will post 

future revisions of the standards at the National Scrapie Eradication webpage, here.

1

 Substantive 

changes will be made through Federal Register notice and comment. We will also provide email 

notification to stakeholders through GovDelivery, a free email subscription service. To subscribe 

to this free service go here 2 and select “Animal Health - Sheep and Goats” and “Federal Register 

Publications – Notices Regarding Animal Health.” 

Additional information (such as sample formats, detailed instructions on data entry and tissue 

collection, and calculators) is available to State and Federal animal health employees on the 

APHIS-NSEP Scrapie SharePoint site3 This information is also available on CD for Federal and 

State employees who cannot access the Scrapie SharePoint site, and can be obtained by emailing scrapie@aphis.usda.gov. 

 

1 http://www.aphis.usda.gov/animal-health/scrapie.

2 https://public.govdelivery.com/accounts/USDAAPHIS/subscriber/new.

3 https://share.aphis.usda.gov/sites/vs-sgh/
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 6 

Note: as of April 25, 2019, the VS Memoranda listed in the table below are canceled and should 

no longer be referenced. The information and guidance in these memoranda have been updated 

and incorporated into these standards.

Memo4 Title Location within these 

standards 

557.2 Scrapie Reports part X (p. 96)

557.6 Approval of Laboratories to Conduct Official Genotype 

Tests in Sheep 

Appendix A (p. 100)

557.7 Identification Requirements for Captive Sheep and 

Goats, both Domestic and Exotic 

part III.A.4 (p. 57)

557.11 Animal Identification and Sampling for Scrapie 

Surveillance 

part II.D (p. 27), part II.E (p. 30), 

part III.A (p. 51), and Appendix B

(p. 104)

557.13 Requirements for Use of Electronic Implant Devices 

(EID) in Registered Sheep and Goats as Official 

Identification in the Scrapie Eradication Program 

part III.A.3(e) (p. 56)

557.14 Indemnity for Third Trimester Gestation Ewes/Does and 

Early Lambing Ewes/Does 

part II.J.4(a)(4) (p.37 )

557.15 Sheep or Goats from Consistent States Transiting or 

Temporarily Residing in Inconsistent States 

part II.O (p. 46)

557.17 Identification of Animals and Use of RFID for Scrapie 

Program Regulatory Work 

part III.A.11 (p. 61)

557.18 Approval of Laboratories to Conduct Official 

Diagnostic Tests for Scrapie in Sheep and Goats 

Appendix B (p. 104)

557.19 Program Approval of Diagnostic Tests for Scrapie in 

Sheep and Goats 

Appendix C (p. 110)

557.21 Revision of Scrapie Flock Certification Program 

Standards for Export Monitored Flocks 

Scrapie Program Standards 

Volume 2 (SFCP), part III

557.22 Scrapie Control Pilot Project for Flocks Affected by 

Nor98-like Scrapie 

part VIII.B.1 (p. 90)

 

4

 VS Memos 557.12 and 557.16 are historical documents and are still active. VS Memos 557.1, 557.3, 557.4, 557.5, 

557.8, 557.9, 557.10 and 557.20 were either cancelled previously or never published. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 7 

Note: This document replaces the June 2, 2005 Scrapie Eradication Uniform Methods and Rules 

(UMR). Any State law or regulations that incorporate the Scrapie UMR now reference this 

document unless the State law or regulations specifically indicate otherwise.
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 8 

List of Acronyms 

AIMS Animal Identification Management System 

APHIS Animal and Plant Health Inspection Service

AVIC Area Veterinarian in Charge

AZA Association of Zoos and Aquariums 

CFR Code of Federal Regulations

CNS Central nervous system

DSE Designated Scrapie Epidemiologist 

EID Electronic implantable device

EMRS Emergency Management and Response System

EPA Environmental Protection Agency 

FSIS Food Safety and Inspection Service 

GIN Group Identification Number 

ID Identification 

MIM Mobile Information Management 

NASS National Agricultural Statistics Service

NSD National Scrapie Database 

NSEP National Scrapie Eradication Program 

NVSL National Veterinary Services Laboratories 

PEMMP Post-Exposure Management and Monitoring Plan 

PIN Premises Identification Number 

RSSS Regulatory Scrapie Slaughter Surveillance 

SAHO State animal health official 

SCS SCR Surveillance Collaboration Services Scrapie 

SFCP Scrapie Free Flock Certification Program 

SGHSE Sheep and Goat Health Specialist for Epidemiology

SOP Standard operating procedure 

VMO Veterinary Medical Officer

VS Veterinary Services 

VSLS Veterinary Services Laboratory Submissions 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 9 

Part I: Definitions 

Accredited veterinarian 

A veterinarian approved by the APHIS Administrator to perform functions required by 

cooperative State-Federal animal disease control and eradication programs. 

Administrator 

The Administrator of the Animal and Plant Health Inspection Service (APHIS) or any employee 

of the U.S. Department of Agriculture authorized to act for the Administrator. 

Animal.......... 

Any sheep or goat (animals in the genus Ovis or Capra respectively). 

APHIS.......... 

The Animal and Plant Health Inspection Service of the U.S. Department of Agriculture. 

APHIS representative 

An individual employed by APHIS in animal health activities, who is authorized by the 

Administrator to perform specific functions and duties. 

Approved laboratory 

A laboratory approved by the Administrator in accordance with title 9, Code of Federal 

Regulations (9 CFR) 54.11 to conduct one or more scrapie tests, or genotype tests, on one or 

more tissues.5 

Area Veterinarian in Charge (AVIC) 

The veterinary official of APHIS assigned by the Administrator to supervise and perform the 

official animal health work of APHIS in the State concerned. 

Blackfaced sheep 

Any purebred Suffolk, Hampshire, Shropshire, or cross thereof; any nonpurebred sheep known 

to have Suffolk, Hampshire, or Shropshire ancestors; and any nonpurebred sheep of unknown 

ancestry with a black face, except for commercial hair sheep. Note: Nonpurebred hair sheep 

known to have Suffolk, Hampshire, or Shropshire ancestors are not considered commercial hair 

sheep; they are considered blackfaced sheep. 

 

5 See Appendix A: Approval of Laboratories to Conduct Official Genotype Tests for Sheep, and Appendix B: 

Approval of Laboratories to Conduct Official Diagnostic Tests for Scrapie in Sheep and Goats. For a list of 

approved laboratories for genotype testing, go to 

http://www.aphis.usda.gov/animal_health/animal_diseases/scrapie/app-labs-genotype-test.shtml. For a list of 

approved laboratories for scrapie testing, go to 

http://www.aphis.usda.gov/animal_health/nahln/downloads/cwd_scrapie_lab_list.pdf. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 10 

Breed associations and registries 

Organizations that maintain the permanent records of ancestry or pedigrees of animals (including 

the animal's sire and dam), individual identification of animals, and ownership of animals. 

Breeding sheep or goat 

Any sexually intact sheep or goat not moving directly to slaughter, through slaughter channels to 

slaughter, or to a terminal feedlot to enhance its condition for movement to slaughter. 

Classification or reclassification investigation 

An epidemiological investigation conducted or directed by a Designated Scrapie Epidemiologist 

(DSE) for the purpose of designating or redesignating the status of a flock or animal. In 

conducting such an investigation, the DSE will evaluate the available records for flocks and 

individual animals and conduct or direct any testing needed to assess the status of a flock or 

animal. The status of an animal or flock will be determined based on the applicable definitions in 

this section and, when needed to make a designation under 9 CFR 79.4 (see part VII.B for 

additional guidance), official genotype test results, exposure risk, scrapie type involved, results 

of official scrapie testing on live or dead animals, or any combination of these. 

Commercial sheep or goat 

Any animal from a flock from which animals are moved only directly to slaughter or through 

slaughter channels to slaughter, or any animal raised only for meat or fiber production and not 

registered with a sheep or goat registry or used for exhibition. 

Commingle, commingled, commingling 

Animals grouped together having physical contact with each other, including contact through a 

fence with a confined lambing area or lambing animals, but not limited contact (as defined 

below). Commingling includes sharing the same section in a transportation unit where physical 

contact can occur. In cases of shared fence lines, the DSE will determine whether commingling 

has occurred through the fence based on relevant factors such as the type, integrity, and location 

of the fence, the proximity of lambing, and the stocking density. 

Consistent State 

A State that the Administrator has determined conducts an active State scrapie control program 

that meets the requirements of 9 CFR 79.6 or effectively enforces a State-designated plan that the 

Administrator determines is at least as effective in controlling scrapie as the requirements of 9 

CFR 79.6. The list of Consistent States includes all 50 U.S. States: Alabama, Alaska, Arizona, 

Arkansas, California, Colorado, Connecticut, Delaware, Florida, Georgia, Hawaii, Idaho, 

Illinois, Indiana, Iowa, Kansas, Kentucky, Louisiana, Maine, Maryland, Massachusetts, 

Michigan, Minnesota, Mississippi, Missouri, Montana, Nebraska, Nevada, New Hampshire, New 

Jersey, New Mexico, New York, North Carolina, North Dakota, Ohio, Oklahoma, Oregon, 

Pennsylvania, Rhode Island, South Carolina, South Dakota, Tennessee, Texas, Utah, Vermont, 

Virginia, Washington, West Virginia, Wisconsin, and Wyoming. 

Deputy Administrator 

The Deputy Administrator for APHIS Veterinary Services or any employee of the U.S. 

Department of Agriculture authorized to act for the Deputy Administrator. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 11 

 

Designated Scrapie Epidemiologist (DSE) 

An epidemiologist who has demonstrated the knowledge and ability to perform the functions 

required and who has been selected by the SAHO and the AVIC. The Sheep and Goat Health 

Specialist for Epidemiology (SGHSE) and the APHIS National Scrapie Program Coordinator 

must concur in the selection and appointment of the DSE. The DSE must satisfactorily complete 

training designated by APHIS. 

Designation of a flock or animal 

The official determination by the DSE that an animal or flock has a particular disease status or 

classification. 

Destroyed 

Euthanized and the carcass disposed of by burial, landfill, alkaline digestion, incineration, or 

other means authorized by the Administrator that will prevent its use as feed or food. Note: (1) 

Euthanasia may occur at a slaughter facility if the carcass is disposed of as required. (2) 9 CFR 

54.7(a)(3) provides for the movement of scrapie-positive and suspect animals for which 

indemnification is sought to an approved research facility. 

Direct movement to slaughter 

Animals transported to a facility for slaughter without stops or unloading en route, other than for 

food and water, and that are not commingled with any other animals during transport or at such 

food and water stops. 

Electronic implant 

Any radio frequency identification implant device approved for use in the scrapie program by the 

Administrator. 

Exposed animal 

Any animal or embryo that: 

(1) Has been in a flock with a scrapie-positive female animal; 

(2) Has been in an enclosure with a scrapie-positive female animal at any location; 

(3) Resides in a noncompliant flock; or 

(4) Has resided on the premises of a flock before or while it was designated by a DSE an infected 

or source flock and before a flock plan was completed. An animal shall not be designated an 

exposed animal if it only resided on the premises before the date that infection was most likely 

introduced to the premises as determined by a Federal or State representative. If the probable 

date of infection cannot be determined based on the epidemiological investigation, a date 2 years 

before the birth of the oldest scrapie-positive animal born in that flock will be used. If the actual 

birth date is unknown, the date of birth will be estimated based on examination of the teeth and 

any available records. If an age estimate cannot be made, the animal will be assumed to have 

been 48 months of age on the date samples were collected for scrapie diagnosis. Exposed 

animals will be further designated as genetically resistant exposed sheep, genetically less 

susceptible exposed sheep, genetically susceptible exposed animals, or low-risk exposed 

animals. An animal will no longer be an exposed animal if it is redesignated in accordance with 9 

CFR 79.4 (see part VII.B for additional guidance). 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 12 

Exposed embryo 

See exposed animal definition. 

Exposed flock 

1. Any flock that was designated by a DSE an infected or source flock that has completed a 

flock plan, and that retained a female genetically susceptible exposed animal; 

2. Any flock under investigation that retains a female genetically susceptible exposed animal or 

a suspect animal, or whose owner declines to complete genotyping and live-animal and/or 

post-mortem scrapie testing required by the APHIS or State representative investigating the 

flock; or 

3. Any noncompliant flock or any flock for which a PEMMP is required that is not in 

compliance with the conditions of the PEMMP. 

4. A flock will no longer be an exposed flock if it is redesignated in accordance with 9 CFR 

79.4 (see part VII.B for additional guidance). 

Female animal 

A sexually intact female sheep or goat. 

Flock or herd 

All animals maintained on a single premises and all animals under common ownership or 

supervision on two or more premises with animal interchange between the premises. Changes in 

ownership of part or all of a flock do not change the identity of the flock or the regulatory 

requirements applicable to the flock. Animals maintained temporarily on a premises for activities 

such as shows and sales or while in marketing channels are not a flock. More than one flock may 

be maintained on a single premises if: 

1. The flocks are enrolled as separate flocks in the Scrapie Free Flock Certification Program

(SFCP); or 

2. A State or APHIS representative determines, based on examination of flock records, that: 

a. No female animals have moved between the flocks; 

b. The flocks never commingle and are kept at least 30 feet apart at all times or are 

separated by a solid wall through, over, or under which fluids cannot pass and through 

which contact cannot occur; 

c. The flocks have separate flock records and identification ; 

d. The flocks have separate lambing facilities, including buildings and pastures, and a 

pasture or building used for lambing by one flock is not used by the other flock at any 

time; and 

e. The flocks do not share equipment without cleaning and disinfection in accordance with 

the guidelines published in 9 CFR 54.7.6

Flock identification (ID) number 

A nationally unique number assigned by a State, federally recognized Tribal or Federal animal 

health authority to a group of animals managed as a unit on one or more premises and under the 

same ownership. The flock ID number must begin with the State postal abbreviation or APHISassigned Tribal code, must have no more than nine alphanumeric characters, and must not 

 

6

 See Appendix G: Scrapie Disinfection Guidelines for cleaning and disinfection guidance.
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 13 

contain the characters “I”, “O”, or "Q" other than as part of the State postal abbreviation or 

another standardized format authorized by the Administrator and recorded in the National 

Scrapie Database. APHIS may assign Tribal codes to any federally recognized Tribe that 

maintains sheep or goats on Tribal lands. The flock ID number must be recorded in and linked to 

one or more PINs or LIDs in the National Scrapie Database. Note: Flock IDs may be used with 

an animal number unique within the flock to provide a unique official identification number for 

an animal, or may be used with the date and a sequence number to provide a Group/lot 

identification number (GIN) for a group of animals when group identification is permitted. 

Flock of origin 

The flock in which an animal most recently resided in which it either was born, gave birth, or 

was used for breeding purposes. The determination of an animal's flock of origin may be based 

either on the physical presence of the animal in the flock, the presence of official identification 

on the animal traceable to the flock, the presence of other identification on the animal listed on 

the bill of sale, or other evidence, such as registry records. 

 

Flock plan 

A written flock management agreement signed by the owner of a flock, the accredited 

veterinarian (if one is employed by the owner), and a State or APHIS representative in which 

each participant agrees to undertake actions specified in the flock plan to control the spread of 

scrapie from, and eradicate scrapie in, an infected flock or source flock or to reduce the risk of 

the occurrence of scrapie in a flock that contains a high-risk or an exposed animal. As part of a 

flock plan, the flock owner must provide the facilities and personnel needed to carry out the 

requirements of the flock plan. The flock plan must include the requirements in 9 CFR 54.8(a) to 

(i) (see part VIII.B for additional guidance).

Flock under investigation 

Any flock in which an APHIS or State representative has determined a scrapie suspect animal, 

high-risk animal, or scrapie-positive animal resides or may have resided. A flock will no longer 

be a flock under investigation if it is redesignated in accordance with 9 CFR 79.4 (see part VII.B

for additional guidance). 

Found dead 

Any sheep or goat over 14 months of age meeting any of the following criteria: 

1. The animal was discovered on the premises after death, or reasonably should have been 

located after death, in a condition in which a suitable sample could be collected; 

2. The animal died off the premises while still owned by the flock owner (such as animals in 

transit or at a veterinary clinic); or 

3. The animal was euthanized due to illness. 

4. The category includes animals that are home slaughtered or euthanized for reasons other than 

illness if 30 animals have not been tested for scrapie since the start of a PEMMP or the 

animal was designated for testing.

Genetically less susceptible exposed sheep 

Any sheep or sheep embryo that is: 

1. An exposed sheep or sheep embryo of genotype AA QR, unless the Administrator determines 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 14 

that it is epidemiologically linked to a scrapie-positive RR or AA QR sheep or to a scrapie 

type to which the Administrator has determined AA QR sheep are not less susceptible; or 

2. An exposed sheep or sheep embryo of genotype AV QR, unless the Administrator determines 

that it is epidemiologically linked to a scrapie-positive RR or QR sheep, to a flock that the 

Administrator has determined may be affected by valine-associated scrapie (based on an 

evaluation of the genotypes of the scrapie-positive animals linked to the flock), or to another 

scrapie type to which the Administrator has determined AV QR sheep are not less 

susceptible; or 

3. An exposed sheep or sheep embryo of a genotype that has been exposed to a scrapie type to 

which the Administrator has determined that genotype is less susceptible. 

In this definition R or Q refers to codon 171 and A or V refers to codon 136, and Q represents 

any genotype other than R at codon 171 and V represents any genotype other than A at codon 

136. 

Genetically resistant exposed sheep 

Any exposed sheep or sheep embryo of genotype RR, unless the Administrator determines it is 

epidemiologically linked to a scrapie-positive RR sheep or to a scrapie type to which RR sheep 

are not resistant.

Genetically susceptible animal 

Any goat or goat embryo, sheep or sheep embryo of a genotype other than RR or QR, where Q 

represents any genotype other than R at codon 171 or sheep or sheep embryo of undetermined 

genotype. 

Genetically susceptible exposed animal 

Excluding low-risk exposed animals, any exposed animal or embryo that is also: 

1. A genetically susceptible animal; 

2. A sheep or sheep embryo of genotype AV QR that the Administrator determines is 

epidemiologically linked to a scrapie-positive RR or QR sheep, to a flock that the 

Administrator has determined may be affected by valine-associated scrapie (based on an 

evaluation of the genotypes of the scrapie-positive animals linked to the flock), or to a 

scrapie type to which AV QR sheep are susceptible; 

3. A sheep or sheep embryo of genotype AA QR the Administrator determines is 

epidemiologically linked to a scrapie-positive RR or AA QR sheep or to a scrapie type to 

which AA QR sheep are susceptible; or 

4. A sheep or sheep embryo of genotype RR the Administrator determines is epidemiologically 

linked to a scrapie-positive RR sheep or to a scrapie type to which RR sheep are susceptible. 

In this definition R or Q refers to codon 171 and A or V refers to codon 136, and Q represents 

any genotype other than R at codon 171 and V represents any genotype other than A at codon 

136. 

Note: AV QR sheep or sheep embryos epidemiologically linked to a positive animal for which 

the 136 codon type either cannot be determined or is unavailable at the time of depopulation may 

also be removed with the concurrence of the owner. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 15 

Genotypes of sheep 

Two locations on DNA that code for prion protein are particularly important for classical scrapie 

susceptibility: Codons 136 and 171. Codon 136 may code for the amino acids alanine (A) or 

valine (V), and rarely threonine (T). Codon 171 may code for the amino acids arginine (R), 

glutamine (Q), histidine (H), or lysine (K). For the purposes of these standards, H, K, or any 

amino acid other than R at codon 171 will be treated as equivalent to Q at codon 171 and T or 

any amino acid other than A at codon 136 will be treated as V. Sheep that are VV or AV at 

codon 136 and RR at codon 171 are very rare and have not been identified in the United States. 

QQ sheep 

Any sheep that has tested QQ, QK, QH, HK, KK, or HH at codon 171 on an official 

genotype test. APHIS may require confirmatory testing before designating a sheep as QQ. 

QR sheep 

Any sheep that has tested QR, KR, or HR at codon 171 on an official genotype test. APHIS 

may require confirmatory testing before designating a sheep as QR. 

RR sheep 

Any sheep that has tested RR at codon 171 on an official genotype test. APHIS may require 

confirmatory testing before designating a sheep as RR. 

AA sheep 

Any sheep that has tested AA at codon 136 on an official genotype test. APHIS may require 

confirmatory testing before designating a sheep as AA. 

AV sheep 

Any sheep that has tested AV or AT at codon 136 on an official genotype test. APHIS may 

require confirmatory testing before designating a sheep as AV. 

VV sheep 

Any sheep that has tested VV, VT, or TT at codon 136 on an official genotype test. APHIS 

may require confirmatory testing before designating a sheep as VV. 

AA QQ sheep 

Any sheep that has tested QQ, QK, QH, HK, KK, or HH at codon 171 and AA at codon 136 

on an official genotype test. APHIS may require confirmatory testing before designating a 

sheep as AA QQ. 

AV QQ sheep 

Any sheep that has tested QQ, QK, QH, HK, KK, or HH at codon 171 and AV or AT at 

codon 136 on an official genotype test. APHIS may require confirmatory testing before 

designating a sheep as AV QQ. 

VV QQ sheep 

Any sheep that has tested QQ, QK, QH, HK, KK, or HH at codon 171 and VV, VT, or TT at 

codon 136 on an official genotype test. APHIS may require confirmatory testing before 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 16 

designating a sheep as VV QQ. 

AA QR sheep 

Any sheep that has tested QR, KR, or HR at codon 171 and AA at codon 136 on an official 

genotype test. APHIS may require confirmatory testing before designating a sheep as AA 

QR. 

AV QR sheep 

Any sheep that has tested QR, KR, or HR at codon 171 and AV or AT at codon 136 on an 

official genotype test. APHIS may require confirmatory testing before designating a sheep as 

AV QR. 

Group/lot identification number (GIN) 

The identification number used to uniquely identify a unit of animals managed together as one 

group. The format of the GIN may be either as defined in 9 CFR 86.1 or the flock identification 

number followed by a 6-digit representation of the date on which the group or lot of animals was 

assembled (MM/DD/YY). If more than one group is created on the same date a sequential 

number will be added to the end of the GIN (example: XX1234-MMDDYY-1). A group lot 

comprised of animals from a single flock of origin may be subdivided after leaving the premises 

on which the group was formed by adding an S followed by a sequential number to the end of 

the GIN to create a GIN for each subgroup. If a flock identification number is used, the flock 

identification number, date, and sequential number will be separated by hyphens. 

High-risk animal 

The female offspring or embryo of a scrapie-positive female animal, or any suspect animal, or a 

female genetically susceptible exposed animal, or any exposed animal that the Administrator 

determines to be a potential risk. The Administrator may base the determination that an exposed 

animal poses a potential risk on the scrapie type; the epidemiology of the flock or flocks with which 

it is epidemiologically linked, including genetics of the positive sheep; the prevalence of scrapie in 

the flock; any history of recurrent infection; and other flock characteristics. An animal will no 

longer be a high-risk animal if it is redesignated in accordance with 9 CFR 79.4 (see part VII.B for 

additional guidance). 

Inconsistent State 

Any State other than a Consistent State. 

Infected flock 

The flock of origin of a female animal that a State or APHIS representative has determined to be 

a scrapie-positive animal; or any flock in which a State or APHIS representative has determined 

that a scrapie-positive female animal has resided unless an epidemiological investigation 

conducted by a State or APHIS representative shows that the animal did not lamb or abort in the 

flock. A flock will no longer be considered an infected flock after it has completed the 

requirements of a flock plan. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 17 

Interstate certificate of veterinary inspection (ICVI) 

An official document issued by a Federal, State, Tribal, or accredited veterinarian certifying the 

inspection of animals in preparation for interstate movement or other uses as described in this 

part and in accordance with 9 CFR 79.5. 

Interstate commerce 

Trade, traffic, transportation, or other commerce between a place in a State and any place outside 

of that State or between points within a State but through any place outside that State. 

Limited contact 

Any contact with a male animal or brief contact with a female animal off the flock’s premises, 

such as occurs in the show or sales ring at fairs, shows, exhibitions, markets, and sales; between 

ewes being inseminated, flushed, or implanted; or between rams at ram test or collection stations. 

Embryo transfer and artificial insemination equipment and surgical tools must be disinfected 

between animals from different flocks by soaking the tools in either a 2 percent available 

chlorine bleach solution or a 2-molar solution of sodium hydroxide for 1 hour, or another 

disinfectant labeled or exempted by the EPA for this use for these contacts to be considered 

limited. Limited contacts do not include any contact, brief, or otherwise, including contacts 

through a fence, or with an animal during or up to 30 days after she lambed, kidded, or aborted 

or when there is any visible vaginal discharge other than that associated with estrus. Limited 

contacts do not include any activity where uninhibited contact occurs with a female animal, such 

as sharing an enclosure, sharing a section of a transport vehicle, or residing in other flocks for 

breeding or other purposes. 

Live-animal test 

Any test for the diagnosis of scrapie in a live animal approved by the Administrator for 

diagnosing scrapie as specified in the approval and conducted in a laboratory approved by the 

Administrator.7

Low-risk commercial flock 

A flock composed of commercial whitefaced, whitefaced cross, or commercial hair sheep or 

commercial goats that were born in, and have resided throughout their lives in, flocks with no 

known risk factors for scrapie, including any exposure to female blackfaced sheep other than 

whiteface crosses born on the premises; that has never contained a scrapie-positive female, 

suspect female, or high-risk animal; and that has never been an infected, exposed, or source flock 

or a flock under investigation. The animals are identified with a legible permanent brand or ear 

notch pattern registered with an official brand registry or with an official flock identification 

eartag. The term “brand” includes official brand registry brands on eartags in those States whose 

brand law or regulation recognizes brands placed on eartags as official brands. Low-risk 

commercial flocks may exist only in a State where in the previous 10 years no flock that had met 

the definition of a low-risk commercial flock before a classification investigation was designated 

a source or infected flock. 

 

7 See Appendix C: Program Approval of Diagnostic Tests for Scrapie in Sheep and Goats. Additionally, VS 

Memorandum 557.12, Approval of Lymphoid Tissue Testing for Scrapie, and VS Memorandum 557.16, Approval of 

Rectal Biopsy Derived-Lymphoid Tissue Testing for Scrapie, document APHIS’ authorization of these specific tests 

for scrapie. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 18 

Low-risk exposed animal 

Any exposed animal to which the Administrator has determined one or more of the following 

applies: 

1. The positive animal that was the source of exposure was not born in the flock and did not 

lamb in the flock or in an enclosure where the exposed animal resided; 

2. The Administrator and SAHO concur that the animal is unlikely to be infected due to factors 

such as, but not limited to, where the animal resided or the time period the animal resided in 

the flock; 

3. The exposed animal is male and was not born in an infected or source flock; 

4. The exposed animal is a castrated male; 

5. The exposed animal is an embryo of a genetically resistant exposed sheep or a genetically 

less susceptible exposed sheep unless placed in a recipient that was a genetically susceptible 

exposed animal; or, 

6. The animal was exposed to a scrapie type and/or is of a genotype that the Administrator has 

determined poses a low risk of scrapie transmission. 

Note: The Administrator has determined that Nor98-like scrapie poses a low risk of scrapie 

transmission. 

Male animal 

A sexually intact male sheep or goat. 

Mortgage 

Any mortgage, lien, or other security or beneficial interest held by any person other than the one 

claiming indemnity. 

National Scrapie Database (NSD) 

A database designated by the Administrator in which APHIS and State animal health agencies 

cooperatively enter data concerning scrapie outbreaks, flocks, and premises affected by scrapie, 

individual animal identification and premises identification data, and other data to support the 

Scrapie Eradication Program and the Scrapie Flock Certification Program. 

Note: the designated database was comprised of the following applications: SCS SCR, VSLS, 

MIM, EMRS, and the scrapie program utility of AIMS at time of publication. 

National Scrapie Eradication Program (NSEP) 

The cooperative State-Federal-industry program administered by APHIS and Consistent States to 

control and eradicate scrapie. The NSEP is also referred to in these standards as the “Program”. 

National Scrapie Eradication Program Standards (NSEPS) 

Volume 1 of the Scrapie Program Standards, NSEPS is the set of cooperative procedures and 

standards adopted by APHIS and Consistent States for eradicating scrapie. 

National Veterinary Services Laboratories (NVSL) 

The APHIS National Veterinary Services Laboratories and their cooperating and contract 

laboratories. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 19 

Noncompliant flock 

1. Any source, infected, or exposed flock or flock under investigation whose owner declines to 

enter into a flock plan or PEMMP agreement within 60 days of being so designated or whose 

owner is not in compliance with either agreement; 

2. Any exposed flock or flock under investigation whose owner fails to make animals available 

for testing within 60 days of notification, or as mutually agreed by the DSE and the owner, or 

whose owner fails to submit required postmortem samples as directed in the PEMMP; 

3. Any flock whose owner has misrepresented, or who employs a person who has 

misrepresented, the scrapie status of an animal or any other information on a certificate, 

permit, owner statement, or other official document within the last 5 years; or 

4. Any flock whose owner or manager has moved, or who employs a person who has moved, an 

animal in violation of 9 CFR part 79, within the last 5 years. 

Official eartag 

An identification tag approved by APHIS that bears an official identification number for 

individual animals. All official eartags manufactured must bear an official eartag shield. The 

design, size, shape, color, and other characteristics of the official eartag will depend on the needs 

of the users, subject to the approval of the Administrator. The official eartag must be tamperresistant, have a high retention rate in the animal, and be approved in accordance with 9 CFR 

79.2(k) for use in sheep or goats.8 

Official genotype test 

A test to determine the genotype of a live or dead animal conducted at either the NVSL or at an 

approved laboratory.9 The test subject must be an animal that is officially identified and the test 

accurately recorded on an official form supplied or approved by APHIS, with the samples 

collected and shipped to the laboratory using a shipping method specified by the laboratory by: 

1. An accredited veterinarian; 

2. A State or APHIS representative; or 

3. The animal’s owner or owner’s agent, using a tamper-resistant sampling kit approved by 

APHIS for this purpose. 

Official identification device or method 

A means approved by the Administrator of applying an official identification number to an 

animal of a specific species or associating an official identification number with an animal or 

group of animals of a specific species or otherwise officially identifying an animal or group of 

animals; except that, only devices approved and distributed for use in sheep and goats in 

accordance with 9 CFR 79.2 (k) and methods approved for use in sheep and goats in accordance 

with 9 CFR 79.2(a)(2) are included. 

 

 

8 Official eartags approved for use in sheep and goats may be found at 

https://vsapps.aphis.usda.gov/aims/AllProductSelect.do Select Scrapie Program Tags from the drop down and click 

on “Get Approved Devices.” 

9

 See Appendix A: Approval of Laboratories to Conduct Official Genotype Tests in Sheep. Approved laboratories 

are listed at http://www.aphis.usda.gov/animal_health/lab_info_services/downloads/ApprovedLabs_genotyping.pdf
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 20 

Official identification number 

A nationally unique number that is permanently associated with an animal or group of animals 

and adheres to one of the following systems: 

1. National Uniform Eartagging System (NUES) (for sheep and goats this is the State postal 

abbreviation followed by two alphanumeric characters and four digits); 

2. Animal identification number (AIN); 

3. Location-based number system; 

4. Flock-based number system; or 

5. Any other numbering system approved by the Administrator for the official identification of 

animals. 

Note: Official identification numbers for sheep and goats are limited to those distributed through 

the Scrapie Program application in AIMS or its predecessor TAGMAN, flock ID production 

number tattoos, and grandfathered non-840 RFID implants. 

Official test 

Any test for the diagnosis of scrapie in a live or dead animal approved by the Administrator for 

that use and conducted either at an approved laboratory or at NVSL. 

Officially identified 

Identified by means of an official identification device or method approved by the Administrator 

for use in sheep and goats in accordance with 9 CFR 79.2 (k) or 9 CFR 79.2(a)(2) respectively. 

Owner..... 

A person, partnership, company, corporation, or any other legal entity that has legal or rightful 

title to animals, whether or not they are subject to a mortgage. 

Owner/hauler statement 

A signed written statement by the owner or hauler that includes: 

1. The name, address, and phone number of the owner and, if different, the hauler; 

2. The date the animals were moved; 

3. The flock identification number or PIN assigned to the flock or premises of the animals; 

4. If moving individually unidentified animals, the group/lot identification number and any 

information required to officially identify the animals; 

5. The number of animals; 

6. The species, breed, and class of animals. If breed is unknown, for sheep the face color and 

for goats the type (milk, fiber, or meat) must be recorded instead; and 

7. The name and address of point of origin, if different from the owner’s address, and the 

destination. 

An existing document that includes the same information that is signed by the owner or the 

hauler meets this definition. 

Permit..... 

An official document issued in connection with the interstate movement of animals (VS Form 1-

27 or a State form that contains the same information) by an APHIS representative, State 

representative, or an accredited veterinarian authorized to sign such permits. A new permit is 

required for each change in destination for an animal. A permit lists the owner’s name and 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 21 

address; points of origin and destination; number of animals covered; purpose of the movement; 

whether the animals are from an exposed flock, flock under investigation, noncompliant, 

infected, or source flock; whether the animal is a high-risk, exposed, scrapie-positive, or scrapie 

suspect animal; transportation vehicle license number or other identification number; and seal 

number (if a seal is used). A permit also lists all official identifications on the animals covered. 

Official identifications may include: The eartag number; a registered breed association’s 

registration tattoo, brand, or number; a USDA backtag (when applied serially, only the beginning 

and ending numbers need to be recorded); or any other form of official identification present on 

the animal. 

Person..... 

An individual, partnership, company, corporation, or any other legal entity. 

Person number 

A unique number assigned to an accredited veterinarian, a person authorized to redistribute tags, 

or an APHIS or State representative recorded in the NSD for tag allocation, data entry in VSLS, 

and identification on documents such as test charts. 

Post-exposure management and monitoring plan (PEMMP) 

A written agreement signed by the owner of a flock, any accredited veterinarian employed by the 

owner, and a State or APHIS representative in which each participant agrees to undertake actions 

specified in the agreement to reduce the risk of the occurrence of scrapie. The signers also agree 

to monitor for the occurrence of scrapie in the flock for at least 5 years after the last high-risk or 

scrapie-positive animal is removed or after the last exposure of the flock to a scrapie-positive 

animal, unless the monitoring time is otherwise specified by a State or APHIS representative. As 

part of a PEMMP, the flock owner must provide the facilities and personnel needed to carry out 

the required elements listed in the plan. The plan must include the requirements in 9 CFR 54.8. 

Premises 

The ground, area, buildings, and equipment occupied by, or used for, one or more flocks of 

animals. 

Premises identification number (PIN) 

A nationally unique number assigned by a State, Tribal, and/or Federal animal health authority to 

a premises that is, in the judgment of the State, Tribal, and/or Federal animal health authority, a 

geographically distinct location from other premises. The PIN may be used with a producer's 

own livestock production numbering system to provide a nationally unique and herd-unique 

identification number for an animal. It may be used as a component of a group/lot identification 

number (GIN). APHIS may also maintain historical or State premises numbers and link them to 

the PIN in records and databases. Such secondary or historical numbers are typically the State’s 

2-letter postal abbreviation followed by a number assigned by the State.

Program 

The cooperative State-Federal-industry program administered by APHIS and Consistent States to 

control and eradicate scrapie. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 22 

Program-approved test 

A test for the diagnosis of scrapie approved by the Administrator for use in the scrapie 

eradication or certification program or both.10 

Restricted animal sale or restricted livestock facility 

A sale where any animals in slaughter channels are maintained separate from other animals not 

in slaughter channels unless they are from the same flock of origin and are sold in lots that 

consist entirely of animals sold for slaughter only, or a livestock facility at which all animals are 

in slaughter channels and where the sale or facility manager maintains a copy of, or maintains a 

record of, the information from the owner/hauler statement for all animals entering and leaving 

the sale or facility. A restricted sale may be held at a livestock facility that is not restricted. 

Scrapie..... 

A nonfebrile, transmissible, insidious, degenerative disease affecting the central nervous system 

(CNS) of sheep and goats. 

Scrapie control pilot project 

A pilot project authorized by the Administrator in writing, designed to test or improve program 

procedures or to facilitate research to control and eradicate scrapie. In addition to APHIS, 

participants may include State animal health agencies, flock owners, and other parties as 

necessary. (Pilot projects are often established through a memorandum of understanding between 

a State and APHIS; they may also be implemented nationally through amendments to these 

program standards or as an interim measure through changes to a flock plan or PEMMP 

template. Such templates must be approved by the National Scrapie Program Coordinator and the 

plans signed by the State Veterinarian and the AVIC.) 

Scrapie Free Flock Certification Program (SFCP) 

A voluntary State-Federal-industry cooperative effort established under 9 CFR part 54 subpart B 

to meet the following objectives: 

1. Reduce the occurrence and spread of classical scrapie; 

2. Identify flocks that have been free of evidence of classical scrapie over specified time 

periods; 

3. Contribute to the eventual eradication of classical scrapie; and 

4. Enhance the marketability of enrolled animals. 

Scrapie Free Flock Certification Program Standards (SFCPS) 

Volume 2 of the Scrapie Program Standards, SFCPS are the set of cooperative procedures and 

standards adopted by APHIS and State scrapie certification boards for reducing the incidence 

and controlling the spread of classical scrapie. 

 

10 See Appendix C: Program Approval of Diagnostic Tests for Scrapie in Sheep and Goats. Additionally, VS 

Memorandum 557.12, Approval of Lymphoid Tissue Testing for Scrapie, and VS Memorandum 557.16, Approval of 

Rectal Biopsy-Derived Lymphoid Tissue Testing for Scrapie, document APHIS’ authorization of these specific tests 

for scrapie. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 23 

Scrapie-positive animal 

An animal for which a diagnosis of scrapie has been made by the National Veterinary Services 

Laboratories or another laboratory authorized by the Administrator to conduct scrapie tests in 

accordance with this chapter, through: 

(1) Histopathological examination of central nervous system (CNS) tissues from the animal for 

characteristic microscopic lesions of scrapie; 

(2) The use of proteinase-resistant protein analysis methods including but not limited to 

immunohistochemistry, ELISA and/or western blotting on CNS and/or peripheral tissue samples 

from a live or a dead animal for which a given method has been approved by the Administrator 

for use on that tissue; 

(3) Bioassay; 

(4) Scrapie associated fibrils (SAF) detected by electron microscopy; or 

(5) Any other method or combination of methods approved by the Administrator in accordance 

with 9 CFR 54.10. 11

Slaughter channels 

Animals in slaughter channels include any animal that is sold, transferred, or moved either 

directly to or through a restricted animal sale or restricted livestock facility to an official 

slaughter establishment that is under Food Safety and Inspection Service (FSIS) jurisdiction per 

the Federal Meat Inspection Act (FMIA) or under State inspection that FSIS has recognized as at 

least equal to Federal inspection; to a custom exempt slaughter establishment as defined by FSIS 

(9 CFR 303.1) for immediate slaughter; or to an individual for immediate slaughter for personal 

use or to a terminal feedlot. Animals in slaughter channels before arriving at a sale and animals 

that cannot meet the ID and ICVI requirements for unrestricted movement prior to leaving a sale 

may not be sold at an unrestricted sale. This does not preclude animals sold at an unrestricted 

sale from being moved in slaughter channels after sale if identified as required for animals in 

slaughter channels. Animals in slaughter channels must be accompanied by an owner/hauler 

statement completed in accordance with 9 CFR 79.3(g). Animals in slaughter channels may not 

be held in the same enclosure with sexually intact animals from another flock of origin that are 

not in slaughter channels. When selling animals that do not meet the requirements to move as 

breeding animals, owners must note on the bill of sale that the animals are sold only for 

slaughter. 

Source flock 

A flock in which a State or APHIS representative has determined that at least one animal was 

born that was diagnosed as scrapie positive at an age of 72 months or less. The determination 

that an animal was born in a flock must be based either on the presence of official identification 

on the animal traceable to the flock, the presence of other identification on the animal that is 

listed on the bill of sale, or other evidence, such as registry records, to show that a scrapie-

 

11 See Appendix C: Program Approval of Diagnostic Tests for Scrapie in Sheep and Goats for additional guidance. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 24 

positive animal originated from the flock combined with the absence of records indicating that 

the animal was purchased and added to the flock. If DNA from the animal was collected when 

the animal resided in the flock of birth by an accredited veterinarian and stored at an approved 

genotyping laboratory, or if DNA collection and storage is required for breed registration and the 

breed registration has appropriate safeguards in place to ensure the integrity of the banking 

process, the owner may request verification of the animal’s identity based on DNA comparison if 

adequate records and identification have been maintained by the owner and the repository to 

show that the archived DNA is that of the animal that has been traced to the flock. A flock will 

no longer be a source flock after it has completed the requirements of a flock plan. 

State..... 

Each of the 50 States, the District of Columbia, the Northern Mariana Islands, Puerto Rico, and 

all territories or possessions of the United States. 

State Animal Health Official (SAHO) 

An individual employed by the State as the chief animal health official of the State, often but not 

always the State veterinarian. 

State representative 

An individual employed in animal health activities by a State or a political subdivision of a State 

who is authorized by the State or political subdivision to perform the function involved. 

Suspect animal 

1. A mature sheep or goat (as evidenced by eruption of the first incisor) that has been 

condemned by FSIS or a State inspection authority for CNS signs, or that exhibits any of the 

following clinical signs of scrapie and has been determined to be suspicious for scrapie by an 

accredited veterinarian or a State or USDA representative, based on one or more of the 

following signs and the severity of the signs:

a. Weakness of any kind including, but not limited to, stumbling, falling down, or having 

difficulty rising, not including those with visible traumatic injuries and no other signs of 

scrapie;

b. Behavioral abnormalities;

c. Significant weight loss despite retention of appetite or in an animal with adequate 

dentition;

d. Increased sensitivity to noise and sudden movement;

e. Tremors;

f. Star gazing;

g. Head pressing;

h. Bilateral gait abnormalities such as but not limited to incoordination, ataxia, high 

stepping gait of forelimbs, bunny-hop movement of rear legs, or swaying of back end, but 

not including abnormalities involving only one leg or one front and one back leg;

i. Repeated intense rubbing with bare areas or damaged wool in similar locations on both 

sides of the animal’s body or, if on the head, both sides of the poll;

j. Abraded, rough, thickened, or hyperpigmented areas of skin in areas of wool/hair loss in 

similar locations on both sides of the animal’s body or, if on the head, both sides of the 

poll; or
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 25 

k. Other signs of CNS disease. An animal will no longer be a suspect animal if it is 

redesignated in accordance with 9 CFR 79.4 (see part VII.B for additional guidance).

2. A sheep or goat that has tested positive for scrapie or for the proteinase resistant protein 

associated with scrapie on a live-animal screening test or any other test, unless the animal 

is designated a scrapie-positive animal.

3. A sheep or goat that has tested inconclusive or suggestive on an official test for scrapie.

Tamper-resistant sampling kit 

A device or method for collecting DNA samples from sheep or goats approved by the 

Administrator and that identifies both the sample and the animal at the time the sample is 

collected. These devices or methods must ensure that the sample, its corresponding label, and the 

official ID device or method applied to the animal meet the requirements of 9 CFR 79.2(k) and 

that the sample is from the same animal to which the official ID device or method was applied. 

The kit must include an APHIS-approved official form or another form, device, or method 

acceptable to APHIS for transmitting the information required to APHIS and the approved 

laboratory.

Note: As of the publication of these standards no tamper-resistant sampling kits had been 

approved. If approved kit manufacturers will be listed here.

12

 

Terminal feedlot 

1. A drylot approved by a State or APHIS representative or an accredited veterinarian 

authorized to perform this function where animals in the terminal feedlot are separated from 

all other animals by at least 30 feet at all times or are separated by a solid wall through, over, 

or under which fluids cannot pass and contact cannot occur. The lot must be cleaned of all 

organic material before being used to contain sheep or goats not in slaughter channels. 

Further, only castrated males can be maintained with female animals and animals may move 

only to another terminal feedlot or directly to slaughter; or 

2. A drylot approved by a State or APHIS representative or an accredited veterinarian 

authorized to perform this function where only animals that are not pregnant based on the 

animal being male, an owner certification that any female animals have not been exposed to a 

male in the preceding 6 months, a certificate issued by an accredited veterinarian stating the 

animals are open, or the animals are under 6 months of age at time of receipt. Only castrated 

males may be maintained with female animals, and all animals in the terminal feedlot must 

be separated from all other animals such that physical contact cannot occur. Animals may 

move only to another terminal feedlot or directly to slaughter. 

3. A pasture when approved by and maintained under the supervision of the State and in which 

only nonpregnant animals are permitted based on the animal being male, an owner 

certification that any female animals have not been exposed to a male in the preceding 6 

months, or a certificate issued by an accredited veterinarian stating the animals are open or 

the animals are under 6 months of age at time of receipt. Only castrated males may be 

maintained with female animals. There is no direct fence-to-fence contact with another flock, 

and animals may move only to another terminal feedlot or directly to slaughter. 

4. Records of all animals entering and leaving a terminal feedlot must be maintained for 5 years 

after the animal leaves the feedlot and must meet the requirements of 9 CFR 79.2, including 

 

12 https://www.aphis.usda.gov/aphis/ourfocus/animalhealth/animal-disease-information/sheep-and-goathealth/national-scrapie-eradication-program/ct_to_order_ear_tags.
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 26 

either a copy of the required owner/hauler statements for animals entering and leaving the 

facility or the information required to be on the statements. Records must be made available 

for inspection and copying by an APHIS or State representative on request. 

Test eligible 

An animal that meets a test protocol’s age and post-exposure elapsed time requirements for the 

test to be meaningfully applied. 

Trace..... 

All actions required to identify the flock of origin or destination of an animal. 

Unofficial test 

Any test for the diagnosis of scrapie or for the detection of the protease-resistant protein 

associated with scrapie in a live or dead animal that either has not been approved by the 

Administrator or that was not conducted at an approved diagnostic laboratory. 

Veterinary Medical Officer (VMO) 

A veterinarian employed by the State or APHIS. Note: This may include accredited veterinarians 

when paid by APHIS or the State to perform the specified function. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 27 

Part II: Administrative Procedures 

A. Supervision of the Cooperative State-Federal-Industry National Scrapie Eradication 

Program (NSEP) 

Animal health officials employed by the State or the Federal government will supervise the 

cooperative State-Federal-industry scrapie eradication program, commonly known as the 

NSEP. In each State, APHIS and the animal health agency of the State will sign a 

memorandum of understanding (MOU) delineating the respective roles of each in NSEP 

implementation. Additionally, APHIS may include administration of the NSEP within a 

State as part of an umbrella cooperative agreement with the animal health agency of that 

State. 

B. Appointing DSEs

The selection and appointment of DSEs will be made jointly by the SAHO and AVIC 

with the concurrence of the APHIS SGHSE and the APHIS National Scrapie Program 

Coordinator (see VS Memorandum No. 570.9). 

C. Administrative Review of Program Activities and Progress 

Administrative review of a State's scrapie program will consist of the following: 

1. Ongoing review of program activities and records by VS personnel at the local, 

district, and national levels, including but not limited to: 

a. Evaluation of information entered into the NSD by State or Federal animal health 

officials, or both, in each of the States; 

b. Review of epidemiological and ID compliance reports submitted by the DSEs for 

the State to the SGHSE and National Scrapie Program Coordinator; and 

c. Review of applications for renewal or reclassification of a State as described in 

part IV. 

2. Site visits conducted in accordance with VS Memorandum No. 515.1. 

D. Inspection of Slaughter Establishments, Livestock Markets, Dealers, and Other 

Concentration Points for Identification and Sampling Compliance 

A key component of scrapie surveillance is the ability to trace positive animals to the 

correct flock of origin, which requires accurate individual animal or lot identification. 

The goal of scrapie surveillance is to successfully trace 100 percent of positive animals. 

Routine inspection of sheep and goat concentration points is essential to meeting this 

goal. 

1. Sites to inspect are: 

a. Slaughter establishments; 

b. Markets; 

c. Dealers; and 

d. Any other concentration points handling mature sheep or goats, or both. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 28 

2. Sites may be inspected by State or Federal employees or accredited veterinarians who 

have been authorized by the AVIC to conduct such inspections. 

3. Recommendations for frequency of inspections: 

a. Markets. 

1) If handling more than 100 head per sale, at least once every quarter. 

2) If handling fewer than 100 head per sale, at least once every 6 months. 

b. Public sales of sheep seed stock (purebred sales and sales specifically for breeding 

animals such as bred ewe or replacement ewe sales not held at markets). 

1) If handling more than 500 head per sale, at least 75 percent of the sales 

conducted during the year. 

2) If handling 100 to 500 head per sale, at least 50 percent of the sales conducted 

during the year. 

3) If handling 50 to 99 head per sale, at least 25 percent of the sales conducted 

during the year. 

4) Smaller sales should also be inspected if noncompliance is suspected or 

resources permit. 

5) Alternatively, seed stock sales conducted multiple times a year by the same 

management may be inspected on the same schedule as markets. 

c. Dealers and other concentration points. 

1) If handling more than 500 head per month, at least once every quarter. 

2) If handling 100 to 499 head per month, at least once every 6 months. 

3) If handling 50 to 99 head per month, at least once every year. 

4) Lower volume dealers should also be inspected if noncompliance is suspected 

or resources permit. 

d. Slaughter establishments. 

All slaughter establishments handling mature sheep or goats that are in or have 

been in interstate commerce are required to be Regulatory Scrapie Slaughter 

Surveillance (RSSS) collections sites. At sites where the establishment or a 

contractor collects specimens for RSSS, ID compliance and inspection of 

sampling protocol should be conducted at least quarterly. At sites where samples 

are collected by VS or State employees, ID compliance is to be informally 

monitored each time collections are made. If inspectors observe problems with ID 

compliance, they will conduct and document a formal inspection. Slaughter 

establishments should be formally inspected according to the following schedule: 

1) If handling more than 500 mature animals per month, at least once every 

quarter. 

2) If handling 100 to 499 mature animals per month, at least once every 6 

months. 

3) If handling 2 to 99 mature animals per month, at least once every year. 

e. The AVIC may reduce the frequency of visits once compliance is documented, 

but visits should be at least once every 6 months if the facility handles more than 

50 animals per month and at least once every year for all others. If a site is 

noncompliant, maintain the original schedule until compliance is documented for 

at least 6 months. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 29 

f. New facilities and facilities under new ownership or management should be 

inspected as soon as practical and no later than 30 days after the VS Area Office 

becomes aware of the change. 

4. Information to record during inspections 

a. Markets, dealers, seed stock sales, and other concentration points. 

1) Record the total number of sheep and the total number of goats present at the 

time of inspection that require official ID in accordance with 9 CFR 79.3. 

2) Of the sheep requiring identification, record the number of sheep with official 

ID (including those tagged to flock of origin at the inspection site). 

3) Of the goats requiring identification, record the number of goats with official 

ID (including those tagged to flock of origin at the inspection site). 

4) Indicate whether numbers recorded in 1), 2), or 3) are actual counts or 

estimates. 

5) Document the following information for any consignment not in compliance: 

a) Name and address of the source; 

b) Number of animals on the load that require official identification; 

c) When practicable, photos of ears showing absence of official ID and teeth 

for estimating age (if a camera is not available, the basis for age 

determination should be documented in writing); 

d) Absence of other allowed ID, such as tattoos and brands; and 

e) Presence or absence of required records as described in part III.B. 

6) Review records for compliance, and record any deficiencies. 

Note: 

a) If sheep are from a single flock of origin, markets may tag them on arrival 

or pen them separately until they are identified.

b) Ideally, animals at the market should be identified on unloading or shortly 

thereafter, but must be identified before being commingled or sold. 

c) The count of sheep or goats or both with and without official ID should 

only include those animals ready for sale or already sold. Animals that are 

not tagged when the inspection begins must be penned separately from 

sheep or goats from any other flock of origin and must be correctly tagged 

to their flock of origin prior to commingling and prior to sale. At the time 

the inspection begins, unidentified animals commingled with other 

unidentified animals from a different flock of origin should be counted as 

animals without official ID on the inspection report.

b. Slaughter establishments. 

1) On the day of inspection, as the sheep or goats, or both, are unloaded, record 

the following information for each load of sheep or goats (or both) that require 

official ID: 

a) Name and address of the source; 

b) Number of animals by species on the load requiring identification; 

c) Number of animals by species with official ID; 

d) Indicate if counts are actual or estimates; 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 30 

e) When practicable, photos of ears showing absence of official ID and teeth 

for estimating age (if a camera is not available, the basis for age 

determination should be documented in writing); 

f) Absence of other allowed ID, such as tattoos and brands; and 

g) Presence or absence of required records as described in part III.B. 

2) Review establishment records for compliance, and record deficiencies. 

Note:

a) If the animals are unloaded before the inspector arrives, the inspector will 

make every attempt to determine the above information for each load. 

b) Alternative methods such as having the establishment place the heads 

from each consignment in separate containers for later inspection may be 

used. 

5. Inspection reporting procedures are outlined in part X.B. 

E. Identification and Recordkeeping Compliance 

 

1. Federal Responsibilities: 

AVICs are responsible for initiating education or compliance actions (or both) for 

alleged violators of Federal regulations with business addresses in the State or States 

for which they have responsibility. If a noncompliant supplier’s business is outside 

the AVIC’s area of responsibility, the AVIC will provide a report detailing the 

alleged violations to the AVIC for the State where the alleged violator’s business is 

located and to the SGHSE for the States involved. 

a. If fewer than 95 percent of the animals required to be officially identified 

(described in 9 CFR 79.3) are properly identified in any consignment at a 

slaughter establishment, market, or other site where sheep or goats are in or were 

in interstate commerce, and the animals either were not or could not be officially 

identified at the site to the flock of origin or, when permitted by 9 CFR 79.3, to 

the owner before commingling with other animals, the AVIC will ensure that the 

following steps are taken: 

1) Educate the consignor who supplied the consignment about the ID 

requirements in in 9 CFR 79.2 and the NSEPS. 

2) Inform the establishment or market management that in accordance with 9 

CFR 79.2(a), no one, including establishments and markets, may receive or 

transport unidentified animals required to be identified by 9 CFR 79.3 unless 

they identify the animals to their flock of origin (flock in which an animal 

most recently resided, in which it was born, gave birth, or was used for 

breeding purposes) before commingling. Under certain circumstances, 

animals can be identified to the owner of the current flock, even if this flock is 

not the flock of origin (for example, certain commercial whitefaced or hair 

sheep, or goats if the State has exempted them from intrastate identification 

requirements per 9 CFR 79.6(10)(i)). Regulations in 9 CFR 79.3 and 9 CFR 

79.6 specify 18 months as the age of eruption of the second permanent incisor. 

Eighteen months is the maximum age at which a sheep or goat may move 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 31 

unidentified in slaughter channels. 

3) If not contrary to State ID regulations, as an alternative to refusing an animal 

whose flock of origin is undeterminable, markets and dealers may enter into a 

compliance agreement with APHIS to identify the animal with a slaughteronly tag, listing the consignor or, in the case of dealers, the market where 

acquired rather than the flock of origin on the tagging record. Markets and 

dealers must provide a list of all such occurrences to the AVIC within 15 

days, so that the AVIC can follow up with the person who sold them the 

animal to provide education and to initiate a compliance action if the 

infraction meets the criteria in D.1.b. A similar agreement may be made with 

slaughter establishments, except a slaughter-only tag would not be required. A 

compliance agreement template is available in the National Scrapie Reference 

Library on the Scrapie SharePoint site. 

4) Document the infraction and the education provided. 

b. On the first occurrence of any of the infractions listed in 1)–4) below, the 

responsible AVIC will, at a minimum, issue a warning letter. Any subsequent 

occurrence, or individuals or other legal entities that fall under 5), should be 

referred to Investigation and Enforcement Services (IES) for compliance action 

unless there are significant mitigating circumstances. 

1) Any consignor that supplies a single consignment with less than 90 percent of 

the animals identified as required. 

a) This does not include consignments where the unidentified animals were 

officially identified to the flock of origin or, when permitted by 9 CFR 

79.3, to the owner, at sites permitted to officially identify animals as an 

agent for the owner in accordance with 9 CFR 79.2(a). 

b) When evaluating compliance in lots of fewer than 10 animals, more than 1 

animal unidentified should be used as the standard rather than 90 percent 

unless there is a pattern of noncompliance. 

2) Any slaughter establishment, market or other concentration point where fewer 

than 90 percent of the animals present are identified as required during any 

inspection. 

3) Any noncompliance that impedes a disease investigation. 

4) Any person or legal entity (dealer, market, slaughter establishment, etc.) who 

has tagged animals with blue “MEAT” or “SLAUGHTER ONLY” tags due to 

lack of flock of origin information but who has not provided records to the VS 

Area Office indicating the source (producer, market, dealer, or other legal 

entity) of each individual blue “MEAT” or “SLAUGHTER ONLY” tagged 

animal. Tags lost after receipt of an animal are an exception; in this case all 

possible sources should be recorded as provided in 9 CFR 79.3 along with the 

new official ID number applied. 

5) Any person, market, slaughter establishment, or other legal entity whose 

compliance level is habitually below 95 percent. 

c. If the AVIC is aware of any alleged violation of State ID regulations, the AVIC 

for the State where the alleged violation was identified will notify and provide a 

detailed report to the SAHO and to the AVIC with responsibility for the State (if 

different). 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 32 

d. If an AVIC or SAHO becomes aware of any State that habitually does not enforce 

the Consistent State requirements in 9 CFR 79.6, he or she will notify the SGHSE 

for the districts involved, so the alleged deficiency can be investigated and an 

action plan developed to address any deficiency identified. Failure by a State to 

address significant deficiencies will result in removal of Consistent State status. 

e. The AVIC or SAHO must provide a compliance summary as part of the 

Epidemiology and Compliance Report as described in part X to the SGHSE using 

the spreadsheet provided on the Scrapie SharePoint site. 

2. State Responsibilities: 

a. States must have legal authorities (laws and regulations) such that the SAHO can 

institute any action necessary to enforce compliance with State animal ID 

requirements, recordkeeping requirements, and other animal health regulations 

required to meet Consistent State requirements as provided in 9 CFR 79.6. 

b. The SAHO must have the authority and take regulatory action to ensure that the 

following persons maintain records and officially identify animals to enable State 

or APHIS authorities to trace exposed, high-risk, scrapie-positive, and suspect 

animals to all flocks in which they have resided and to determine their final 

disposition: 

1) Persons who purchase, deal in, or sell or otherwise dispose of sheep or goats 

over 18 months of age as well as sexually intact sheep or goats of any age that 

are not in slaughter channels; 

2) Persons who act as commission representatives or brokers of such animals; 

and 

3) Persons who operate or conduct an auction at which sheep or goats are sold. 

c. Action must be taken by the State if there is adequate evidence to establish that a 

person violated or circumvented State recordkeeping, ID, or movement 

requirements for sheep or goats, other State animal health regulations pertaining 

to scrapie, or both. At a minimum, the State will issue a warning on the first 

occurrence and apply penalties as provided under State law or regulation for 

repeat offenses. If not specifically addressed by State law or regulation, States 

will at a minimum apply the same action levels listed under Federal 

responsibilities. If the SAHO is aware of any alleged violation of Federal 

regulations, he or she should notify and provide a detailed report to the AVIC for 

the area involved. 

3. Issuance of Enforcement Actions to Cooperating RSSS Sites, Markets, and Dealers: 

a. APHIS will not pursue an enforcement action for not identifying sheep or goats to 

their flock of origin, including issuing official warnings, to subjects of 

investigations who have cooperated substantially with VS. This includes: 

1) Persons or other legal entities who have signed a compliance agreement with 

APHIS and were acting in compliance with that agreement at the time the 

violation occurred. 

2) Persons or other legal entities who have not signed a compliance agreement 

but were acting in compliance with the requirements of a compliance 

agreement at the time the violation occurred—e.g., if they have received 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 33 

unidentified animals that required official identification to their flock of origin 

but that could not be identified to their flock of origin, and they have 

identified them using official slaughter-only eartags to the consignor and have 

given VS the required information. 

3) Persons or other legal entities who self-reported the violation and for whom 

there have been no subsequent violations or who have subsequently signed a 

compliance agreement with APHIS and are in compliance with that 

agreement. 

4) Persons or other legal entities who did not self-report for which there have 

been no subsequent violations and who signed a compliance agreement with 

APHIS when the violation was brought to their attention and who have been 

and are in compliance with that agreement. 

5) Persons or other legal entities who have provided tissues or heads to APHIS 

for scrapie testing, voluntarily or in accordance with 9 CFR 71.21, where the 

violation would not have been discovered other than through their cooperation 

or compliance, and who have had no subsequent violations or have 

subsequently signed a compliance agreement with APHIS and are in 

compliance with that agreement. 

b. To ensure that these mitigating circumstances are considered: 

1) The APHIS Investigative and Enforcement Services Animal Health and 

Welfare Enforcement Branch (AHWEB) will review the case to determine 

whether the subject meets the criteria, and if necessary, will contact the AVIC 

for the State in which the subject does business and request information to 

document whether the subject meets the criteria. 

2) The AHWEB will request concurrence from the AVIC who requested the 

investigation (the concurring AVIC) before pursuing an enforcement action. If 

the concurring AVIC is the AVIC for the State in which the subject does 

business, the concurring AVIC will verify whether the subject meets the 

criteria. If the concurring AVIC is not the AVIC for the State in which the 

subject does business, the concurring AVIC will ask the SGHSE to verify the 

determination after consulting with the AVIC in the State where the subject 

maintains his, her, or its business and the concurring AVIC. 

F. Requirements for Program Personnel Entering Premises 

Persons entering a premises to perform activities on behalf of the NSEP must be 

employees of the State or APHIS or be authorized by the State or APHIS to carry out 

program procedures. While on those premises, they must use established biosecurity 

practices to minimize the risk of physically transmitting scrapie and other diseases to the 

premises or other premises. 

G. Providing Services to Livestock Owners 

Program services such as collecting blood or tissue samples, identifying animals, and 

other specified activities may be rendered without charge to the livestock owner. 

However, owners are responsible for providing facilities and for handling their animals. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 34 

Program administrators may contract with accredited veterinarians, paraprofessionals, 

other State and Federal agencies, or the management of privately owned firms, as needed, 

to assist State and Federal animal health officials in performing program services. 

H. Exceptions to the Deadlines for Flock Plans, Investigations, and Testing 

Program officials must follow deadlines for flock plans, investigations, and testing except 

when a DSE determines that there are extenuating circumstances. The extenuating 

circumstances must make it impossible to meet the deadline established for a particular 

flock. The DSE must immediately set a new deadline in consultation with the flock 

owner or his or her representative. The new deadline must be consistent with the 

principles of the NSEP. The SGHSE must approve extensions to deadlines established in 

9 CFR part 54. 

I. Depopulation of All Sexually Intact Sheep and Goats in a Flock (Whole Flock 

Depopulation) 

When requested by the DSE, the SGHSE will review sheep and goat flocks for wholeflock depopulation, with indemnity. A recommendation will then be made to the National 

Scrapie Program Coordinator, based on the prevalence and epidemiology of the infection, 

the relative cost of whole flock depopulation versus testing, and ongoing monitoring 

costs associated with a genetic-based flock plan. The National Scrapie Program 

Coordinator will make the final determination on offering whole-flock depopulation to 

the producer based on disease risk, availability of funds, and cost to the government. 

Examples of when a whole flock depopulation may be authorized are listed in part 

VIII.B.3.b. 

J. Indemnity 

1. Animals eligible for Federal indemnity payments: 

Federal indemnity may be paid for an animal only after its owner has applied for 

indemnification and been approved (9 CFR 54.4). Federal indemnity may be paid 

only for the following: 

a. Destruction of high-risk animals and male genetically susceptible exposed 

animals of known genotype; 

b. Destruction of high-risk animals of unknown genotype, if: 

1) The animal resides in a flock that has not been designated an infected or 

source flock; 

2) The animal is the offspring of a scrapie-positive female animal; 

3) The animal is the offspring of an indemnified ewe too young to wean on the 

date the dam is destroyed, or 

4) The National Scrapie Program Coordinator has approved a whole-flock 

depopulation. 

c. Destruction of animals requested for postmortem sampling by the DSE as part of 

an epidemiologic investigation; 

d. Destruction of live scrapie-positive animals; 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 35 

e. Destruction of suspect animals destroyed at the request of an APHIS 

representative; and 

f. Destruction of animals based on an epidemiological investigation when the 

Administrator determines that destroying these animals will contribute to 

eradicating scrapie. 

 

2. Requirements of flock owners to receive indemnity: 

When these standards require a flock to be on a flock plan or PEMMP or both, the 

owner must sign and be in compliance with the approved flock plan and/or PEMMP 

before receiving indemnity, including the provision of records. The owner must also 

sign a request for release of all records from any breed association with which they 

have registered animals. No indemnity will be paid until the animals have been 

destroyed and the premises, including all structures, holding facilities, conveyances, 

and materials contaminated because of occupation or use by the depopulated animals, 

have been properly cleaned and disinfected in accordance with 9 CFR 54.7(e)13; 

except that, partial indemnity may be paid when the National Scrapie Program 

Coordinator determines that weather or other factors outside the owner’s control 

make immediate disinfection impractical. Premises or portions of premises may be 

exempted from the cleaning and disinfecting requirements if a designated scrapie 

epidemiologist determines, based on epidemiological investigation, that cleaning and 

disinfection of such buildings, holding facilities, conveyances, or other materials on 

the premises will not significantly reduce the risk of the spread of scrapie, either 

because effective disinfection is not possible or because normal operations on the 

premises prevent transmission of scrapie. 

3. Notifying owners of their eligibility for indemnity: 

If funds are available14, VS will offer indemnity in writing when VS or the State 

informs the owner that the owner's flock is an infected or source flock or that the 

flock contains an animal eligible for indemnity. If funds are not available, VS will 

offer indemnity as soon as funds become available. Such an offer will include a copy 

of the applicable indemnity calculator and which categories of animals are eligible for 

indemnity. Owners will also be informed of the following at the time the offer is 

made: 

a. Females not made available for inventory, assessment of late gestational status, and 

testing within 30 days of first notice will not qualify for the late gestational premium. 

An extension may be granted by the SGHSE or the National Scrapie Coordinator 

when severe weather or other conditions beyond the owner’s control prevent a timely 

evaluation. 

b. Offspring born more than 60 days after a written offer of indemnity will not be 

indemnified unless the SGHSE or the National Scrapie Program Coordinator 

determines that severe weather or other conditions beyond the control of the owner 

prevent the timely removal of the animals. 

 

13 See Appendix G: Scrapie Disinfection Guidelines for cleaning and disinfection guidance. 

14 Provision of Federal indemnity is contingent on the availability of funding.
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 36 

4. Amount of indemnity payments: 

a. Federal indemnity. Indemnity paid for sheep and goats (9 CFR 54.3 to 9 CFR 

54.6) will be set as follows. 

1) Sheep and goat classes covered by price reports. Indemnity paid for sheep or 

goats will be based on available price report data that most accurately reflect 

the type of animal being indemnified and the time at which the animal was 

indemnified. To calculate indemnity, APHIS may use price information 

provided by the Agricultural Marketing Service (AMS) or other available 

price information for animals sold during the calendar month before the 

calendar month in which APHIS offers to pay an owner; except that, if an 

applicable price report is not available during any period for any class, APHIS 

will use the price established for animals for the most recent month for which 

price information was available. For categories for which price reports are 

discontinued or have remained unavailable or contain insufficient information 

to determine a valid price for more than 3 months, the Administrator may 

establish an alternate method for calculating indemnity for the category. The 

following report categories will be used in calculating the indemnity that may 

be paid: 

a) Slaughter lamb per pound; 

b) Slaughter ewe per pound; 

c) Commercial ewe lamb replacement price per pound; 

d) Commercial yearling ewe replacement price per head; 

e) Commercial running age (young and middle age) ewe price per head; 

f) Aged ewe price per head; 

g) Slaughter kids per pound; 

h) Slaughter does/nannies per pound; 

i) Slaughter bucks/billies per pound; and 

j) Replacement does/nannies per pound. 

2) Other classes of sheep or goats. When the animals to be indemnified are 

goats or sheep that fall outside the classes covered elsewhere in this paragraph 

such as club lambs or kids, or if the animals entered the flock through 

purchase, the DSE may take into consideration the producer's purchase 

records and sales records for the preceding 12 to 24 months or, in the case of 

purchased animals, records showing the purchase price of the animal in 

determining the indemnity amount. The indemnity will not exceed the 

maximum indemnity calculated for a registered animal of the same species, 

weight, and age in accordance with this section. In cases where the owner can 

show that a class of animals increased in value rather than decreased in value 

after age 2, as may be the case with rams bred for their horns, the animals in 

the classes over 2 years may be counted as animals over 1 year and under 2 

years of age for indemnity purposes. For purchased animals the price will be 

adjusted for the animal’s current age if the purchase was more than 12 months 

before indemnity is offered. A spreadsheet is posted on the Scrapie SharePoint

site to assist Federal and State representatives with calculation of indemnity 

for club lamb/kid flocks. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 37 

3) Calculating indemnity. For animals under 1 year of age, the owner may be 

indemnified for the price per pound from paragraph a(1)(a) or a(1)(g) of this 

section for sheep and goats respectively times the greater of 50 pounds or the 

actual weight of the animal as determined at a public scale, or an estimate 

made using a weight tape or other method acceptable to the owner and 

APHIS; except that, for females under 1 year of age not in slaughter channels 

when indemnity was offered and were not being fed or raised for slaughter, 

the indemnity will equal the per-pound price from paragraph a(1)(c) or a(1)(j)

of this section for sheep and goats respectively if that price is higher. For 

sexually intact sheep at least 1 year of age and under 2 years of age, the 

indemnity will equal the greater of the price per head from paragraph a(1)(d)

of this section, or the price per pound from paragraph a(1)(b) of this section 

times the average mature slaughter weight as reported by NASS. 

For sexually intact sheep at least 2 years of age and under 6 years of age, the 

basic indemnity will equal the greater of the price per head from paragraph 

a(1)(e) of this section or the price per pound from paragraph a(1)(b) of this 

section times the average mature slaughter weight as reported by NASS. For 

sexually intact sheep at least 6 years of age and under 8 years of age, the basic 

indemnity will equal the greater of the price per head from paragraph a(1)(f)

of this section or the price per pound from paragraph a(1)(b) of this section 

times the average mature slaughter weight as reported by NASS. 

For sexually intact sheep 8 years of age or older and castrated animals 1 year 

of age or older, the basic indemnity will equal the price per pound from 

paragraph a(1)(b) of this section times the average mature slaughter weight as 

reported by NASS. 

For goats over 1 year of age that are castrated or that were in slaughter 

channels at the time indemnity was offered, the owner may be indemnified for 

the price per pound from paragraph a(1)(h) or (i) as applicable times the 

actual weight determined at a public scale or a weight estimate made using a 

weight tape or other method acceptable to the owner and APHIS. For sexually 

intact goats over 1 year of age not in slaughter channels at the time indemnity 

is offered and were not being fed or raised for slaughter the owner may be 

indemnified for the price per pound from paragraph a(1)(h) or (i) as applicable 

or the price from (a)(1)(j), whichever is more, times the actual weight 

determined at a public scale or a weight estimate made using a weight tape or 

other method acceptable to the owner and APHIS.

4) Premiums in addition to basic indemnity. A premium will be added to the 

basic indemnity for certain animals as described in this paragraph; except that, 

no premium will be added for animals of any age that were in slaughter 

channels or were being fed or raised for slaughter when indemnity was 

offered. 

a) Premium for registered animals and flock sires. A premium will be 

added for each registered animal, equal to $100 for each registered animal 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 38 

under 1 year of age, $200 for each registered animal at least 1 year of age 

and under 4 years of age, and $100 for each registered animal at least 4 

years of age and under 10 years of age. An additional $50 premium will be 

added to the basic indemnity for each flock sire. The owner must provide 

adequate records to qualify for these premiums. Any animal owned by the 

current owner for less than 12 months and not registered to the current 

owner at the time indemnity is first offered, but eligible to be registered in 

the current owner’s name, will receive the registered animal premium 

reduced by $50. Any animal owned by the current owner for 12 months or 

more and not registered to the current owner at the time indemnity is first 

offered does not qualify for the premium. 

b) Premium for pregnant animals. For animals in late pregnancy, the owner 

may be indemnified for three-fourths of the price of the potential 

offspring’s value in paragraphs a(2), a(3) or a(4)(a) of this section for a 

50-pound lamb or kid as applicable depending on the type of offspring 

(i.e., registerable or not) that would be produced by that animal. A female 

animal will be considered to be in late pregnancy if it was exposed to a 

ram and has udder development associated with impending lactation. To 

estimate the number of offspring the animal is likely carrying, the 

documented weaned-offspring rate for the flock’s previous year will be 

used to calculate the average number of fetuses being carried by each of 

the pregnant animals; however, if this number is unknown, the national 

average of lambs born per ewe from NASS will be used. The calculated 

weaned-offspring rate will be determined by dividing the number of 

offspring weaned by the total number of females exposed to a breeding 

male. A 1:1 ratio of male to female offspring will be assumed for 

calculating the average value of each lamb. Females not made available 

for inventory, assessment of late gestational status, and testing within 30 

days of first notice will not qualify for the premium; except that, the 

SGHSE or the National Scrapie Program Coordinator may grant an 

extension when severe weather or other conditions beyond the owner’s 

control prevent a timely evaluation. 

Offspring born within 60 days after a written offer of indemnity will be 

indemnified at three-fourths of the 50-pound lamb or kid price as 

applicable calculated in accordance with paragraphs a(2), a(3) or a(4)(a)

in lieu of receiving the late gestation premium for the dam. Offspring born 

more than 60 days after a written offer of indemnity will not be 

indemnified unless the SGHSE or the National Scrapie Program 

Coordinator determines that severe weather or other conditions beyond the 

owner’s control prevent the timely removal of the animals. In such cases 

the DSE will provide a written justification for granting an extension to 

the SGHSE for consideration. Offspring born after the initial inventory 

and before completion of the flock plan must be inventoried at the time of 

removal or 60 days after the indemnity offer, whichever occurs first, to 

document the animals eligible for indemnity. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 39 

c) Calculating late gestational premium

 A spreadsheet is posted on the Scrapie SharePoint site to assist Federal 

and State representatives with this calculation. 

 Determine which ewes are in late gestation. A “late gestation ewe” 

has been exposed to a ram at least 2 months before the date on 

which indemnity was first offered, and there is visual evidence of 

pregnancy. Visual evidence of third trimester pregnancy, which 

must be present within 30 days of when indemnity is first offered, is 

marked udder development, enlargement and relaxation of the 

vulva, and relaxation of the pelvic ligaments upon inspection.

 To calculate the average number of lambs being carried by the 

indemnified, pregnant ewes, use the documented annual weaned 

lamb rate for the flock's previous year:

 Number of lambs weaned/number of ewes exposed to a ram= 

annual weaned lamb rate.

 If the data needed to calculate the rate are unknown, use the 

current national lambing average as reported by NASS.

 To calculate the value of a pregnancy:

 Using the scrapie indemnity calculator current when indemnity 

is offered, find the value of both a male and a female lamb 

weighing 50 pounds for the appropriate type (registrationeligible, nonregistered, or club lamb/kid).

 The value of the club lamb/kid price cannot exceed the 

registration-eligible lamb/kid price as applicable.

 The value for a registration-eligible lamb is the registered 

price less $50.

 Then, calculate the average male and female value:

i. (male 50-pound lamb value+ female 50-pound lamb 

value)/2 = averaged male and female value.

ii. Since the gender of the lamb that would be produced is 

unknown, a 1:1 male-to-female ratio is assumed.

 Calculate the gestational premium as follows:

 0.75(averaged male and female value)(annual weaned lamb rate) 

= gestational premium.

 Add the gestational premium to the indemnity value of each ewe 

determined to be in late gestation. Do not add the gestational 

premium value to the value of other ewes.  If a dam eligible for the gestational premium when indemnity was 

first offered gives birth before removal, indemnity will be 

calculated for the live offspring as described below, and a gestational 

premium will not be paid for that ewe. 

 Using the scrapie indemnity calculator current when 

indemnity is offered, find the dollar value of a 50-pound 

lamb based on gender and type of lamb for which 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 40 

indemnity is being calculated.

 Multiply the dollar value by 75 percent (0.75).

Premium for early maturing ewes. Any ewe lamb or doe kid nursing a 

lamb or kid or that meets the requirements for a late pregnancy animal will 

be considered a yearling if that results in a higher valuation. 

5) Age and number of animals. If records and identification are inadequate to 

determine the actual age of animals, an APHIS or State representative will 

count all sexually intact animals that are apparently under 1 year of age, and 

those that are apparently at least 1 and under 2 years of age, based on 

examination of their teeth, and the indemnity for these animals will be 

calculated. The total number of these animals will be subtracted from the total 

number of sexually intact animals in the group to be indemnified, and 

indemnity for the remainder will be calculated based on the assumption that 

the remainder of the flock is 80 percent aged 2 to 6 years and 20 percent aged 

6 to 8 years. 

6) Animal weights. If the owner disagrees with the average weight estimate, he 

may have the animals weighed at a public scale at his own expense, provided 

that the animals may not come in contact with other sheep or goats during 

movement to the public scales. Indemnity will be paid based on the actual 

weight times the price per pound for the class of animal as reported in the 

appropriate price report. 

7) Eligibility for indemnity. Indemnity will be paid to an owner only for animals 

actually in a flock at the time indemnity is first offered in writing, and for 

offspring born to animals in that flock within 60 days after the time indemnity 

is first offered in writing. Animals removed from the flock as part of an 

investigation or a PEMMP will be paid indemnity based on the average prices 

at the time an APHIS representative designates, in writing, the animals for 

removal. If an owner declines to remove an animal within 60 days of when 

indemnity is first offered, the owner will receive the lower value of when 

indemnity was first offered in writing or when the animal was actually 

removed. APHIS may withdraw an indemnity offer if an owner does not make 

animals available for inventory, gestational assessment, and testing within 30 

days or does not remove an animal within 60 days of the written indemnity 

offer or by the date specified in a flock plan or PEMMP. 

8) Additional information and assistance. Spreadsheets are posted on the Scrapie 

SharePoint site to assist Federal and State representatives with calculating 

indemnity. 

9) Denial of an indemnity request. Indemnity will be denied in the following 

cases: 

a) Animals do not meet any of the criteria listed in J.1. 

b) The animal, or the animal’s dam or sire, has been moved or handled by the 

owner in violation of the requirements of the Animal Health Protection 

Act or the regulations promulgated thereunder. 

c) The animal was added to the premises while the flock was under 

investigation or while it was an infected or source flock, other than natural 

additions. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 41 

d) The animal is a natural addition born more than 60 days after the owner 

was notified he or she is eligible for indemnity, unless the SGHSE or the 

National Scrapie Program Coordinator determines the dam could not be 

removed within the allowed time as a result of conditions outside the 

owner’s control. 

e) Animals otherwise eligible for indemnity that die before the owner signs 

VS Form 1-23, Appraisal and Indemnity Claim Form. 

f) If the owner established or increased his flock for the purpose of collecting 

or increasing indemnity. 

g) The animals are State or federally owned captive wild/exotic sheep and 

goats. 

h) Lack of available funds. In this case indemnity may be provided later if 

funds become available. 

b. State-industry indemnity: 

State or industry indemnity, or both, may be paid in addition to Federal indemnity 

in accordance with State regulations, industry guidelines, or both as applicable up 

to the fair market value of the animal. 

5. Indemnity procedures for animals destroyed: 

a. Animals for which indemnification is sought must be destroyed. 

b. An APHIS representative must monitor the destruction of animals and disposition 

of their carcasses and must ensure the carcasses are disposed of in a manner that 

prevents their use as feed or food. State personnel may conduct or supervise these 

activities, including signing the valuation portion of the VS Form 1–23, Appraisal 

and Indemnity Claim Form, when authorized and monitored by APHIS. The 

AVIC must review and sign VS Form 1-23. Before the destruction of any animal 

for which indemnity will be claimed, the AVIC must submit a request for 

indemnity and any associated disposal or other costs and obtain approval from the 

SGHSE and have an accounting code assigned. The owner must complete and 

sign VS Form 1-23. APHIS may pay, when approved in advance in writing, the 

reasonable and customary costs of euthanasia, disposal, or both for indemnified 

animals including transport of the animal for euthanasia or of the carcass for 

disposal or both. The owner may provide these services if the cost is within 

APHIS guidelines or represents the best value bid. If the owner provides these 

services, the owner must present to APHIS a copy of either a receipt for expenses 

paid or a bill for services rendered. 

K. Interstate Certificates of Veterinary Inspection (ICVI) for Sheep and Goats in 

Interstate Commerce 

1. Accredited veterinarians are responsible for ensuring both Federal and State ICVI 

requirements are met and that the certificate is correctly filled out before signing the 

ICVI. As State importation requirements may vary, APHIS advises checking with the 

SAHO for importation requirements before signing the ICVI. APHIS requires ICVIs for 

sexually intact sheep and goats not in slaughter channels that cross State lines, except for 

sheep and goats moving in either of the following circumstances: 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 42 

a. The animals are moving without a change of ownership for grazing or other 

management purposes provided:

1) The movement is between two premises both owned or leased by the flock 

owner;

2) Both premises are recorded in the NSD as additional flock premises; and

3) Commingling will not occur with unidentified animals born in another flock or 

any animal not part of the flock.

b. The animals have been in the same flock in which they were born and have not been 

maintained in the same enclosure with unidentified animals born in another flock at 

any time and are moving to a facility approved in accordance with 9 CFR 71.20.

2. ICVIs must include:

a. The number of animals covered by the certificate.

b. The purpose for which the animals are to be moved.

c. The species and breed or, if breed is unknown, in the case of sheep the face color 

and for goats the type (milk, fiber, or meat).

d. Class of animal such as replacement ewe lambs, slaughter lambs or kids, cull ewes, 

club lambs, bred ewes, etc.

e. The names and addresses of the points of origin and destination, and, if different, the 

names and addresses of the consignor, the consignee, and the current owner.

f. Each animal’s official individual ID numbers (provided that, in the case of animals 

identified with flock ID assigned to the flock of origin and meeting the requirements 

for individual animal ID, the flock ID number may be recorded instead of the 

individual ID numbers. For animals allowed by 9 CFR 79.3 to move with group/lot 

identification, the group/lot number may be recorded instead of the individual ID 

numbers).

g. A statement by the issuing accredited, State, Tribal, or Federal veterinarian to the 

effect that on the date of issuance the animals were free of evidence of infectious or 

contagious disease and insofar as can be determined, exposure thereto. This 

statement may be made with respect to scrapie for animals exposed to scrapie if their 

movement is not restricted and they have been designated genetically resistant or 

less susceptible sheep or low-risk exposed animals.

h. Except as provided in 9 CFR 79.5 paragraphs (b) and (c) (“Animal identification 

documents attached to certificates” and “Ownership brands documents attached to 

certificates” respectively), all information required by this paragraph must be typed 

or legibly written on the certificate.

3. Note:

a. In accordance with paragraphs (b), (c), and (e) of 9 CFR 79.3, scrapie-positive, 

suspect, and high-risk animals, sexually intact genetically susceptible exposed male 

animals, and some animals that originated in an infected or source flock require 

permits rather than certificates (see section N).

b. These requirements apply only to the classes of animals APHIS requires to have 

ICVIs.
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 43 

L. Permits 

A permit (VS Form 1–27 or State equivalent) is required for movement of high-risk, 

suspect, scrapie-positive, and sexually intact genetically susceptible exposed male 

animals. (See section N of this part for exposed animals that require a permit to move.) 

Such animals moving intrastate may move under permit or under conditions specified by 

the SAHO that ensure that these animals are destroyed or maintained under restriction. 

M. Terminal Feedlots 

 

1. Approval: 

a. Terminal feedlots may be approved by APHIS, the State, or an accredited 

veterinarian authorized to perform this function by APHIS or the State if: 

1) The facility is a drylot where animals in the terminal feedlot are separated 

from all other animals by at least 30 feet at all times or are separated by a 

solid wall through, over, or under which fluids cannot pass and contact cannot 

occur and which can be cleaned of all organic material. The owner agrees to 

remove and dispose of all organic material from the terminal feedlot before 

using it to contain sheep or goats not in slaughter channels and to only 

maintain castrated male animals with female animals, and to move the animals 

only to another terminal feedlot or directly to slaughter; or 

2) The facility is a drylot where all animals in the terminal feedlot are separated 

from all other animals such that physical contact cannot occur, and where the 

owner has agreed to all of the requirements listed below. 

a) The only animals permitted in the terminal feedlot meet at least one of the 

following criteria: 

 They are not pregnant based on the animal being male, an owner 

certification that any female animals have not been exposed to a male 

in the preceding 6 months, or a certificate issued by an accredited 

veterinarian stating the animals are open; or 

 The animals are under 6 months of age at time of receipt. 

b) Only castrated males will be maintained with female animals. 

c) Animals will be moved only to another terminal feedlot or directly to 

slaughter. 

d) All required records will be maintained. 

b. A State may approve terminal feedlots that are pastures if it has adequate 

resources to supervise the facility and ensures compliance with all of the 

requirements listed below. 

1) The only animals permitted in the terminal feedlot meet at least one of the 

following criteria: 

a) They are nonpregnant animals based on the animal being male, an owner 

certification that any female animals have not been exposed to a male in 

the preceding 6 months, or a certificate issued by an accredited 

veterinarian stating the animals are open; or 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 44 

b) The animals are under 6 months of age at time of receipt. 

2) Only castrated males are maintained with female animals. 

3) There is no direct fence-to-fence contact with another flock. 

4) Animals are moved only to another terminal feedlot or directly to slaughter. 

5) The owner has agreed to comply with these conditions and the recordkeeping 

requirements. 

2. Records: 

Records of all animals entering and leaving a terminal feedlot must be maintained for 

5 years after the animal leaves the feedlot and must meet the requirements of 9 CFR 

79.2, including either a copy of the required owner/hauler statements for animals 

entering and leaving the facility or the information required to be on the statements. 

Records must be made available for inspection and copying by an APHIS or State 

representative on request. 

N. Movement Restrictions, Release Procedures, and Criteria for Releasing Movement 

Restrictions on Infected or Source Flocks, Animals Required for Testing, and 

Exposed Animals 

The movement restrictions are summarized in Table 1. 

1. Suspect animals may not be moved from the premises where identified, except under 

permit, to a research facility designated by APHIS, to a site for destruction, or, when 

appropriate, to the flock of origin for quarantine. Such animals will be placed under 

movement restriction until an investigation is completed. If the investigation concludes 

the animal is a scrapie suspect, the animal will either be indemnified for diagnostic 

purposes and necropsied and tested for scrapie or maintained under restriction until it 

either recovers and is released, or dies and is necropsied and tested for scrapie (see part 

VII.C). 

2. No sexually intact animal will be permitted to move from an infected or source flock 

until a flock plan agreement has been signed and the owner is in compliance; an 

exception is made for animals moving under permit to an APHIS-approved research 

or quarantine facility or for destruction at another site. The movement restrictions on 

the flock and criteria for release of these restrictions will be specified as part of the 

flock plan or PEMMP. 

3. The following animals may be moved unrestricted once they have been officially 

individually identified and entered into the National Scrapie Database (directly in 

SCS SCR or through VSLS), if not restricted by the DSE and if they originate from 

flocks in compliance with a plan or not required to be on a plan: 

a. Genetically resistant exposed sheep; 

b. Genetically less susceptible exposed sheep; and 

c. Low-risk exposed animals. 

4. Genetically less susceptible exposed female sheep restricted by the DSE may move 

only as permitted in the flock plan or PEMMP. The DSE, with the concurrence of the 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 45 

AVIC, SAHO, and the SGHSE, may also require the removal or restriction of some 

or all genetically less susceptible female animals in flocks based on the epidemiology 

of the flock including genetics of the positive sheep, the prevalence of scrapie in the 

flock, any history of recurrent infection, or other characteristics that may make these 

sheep a potential risk. If removal with indemnity is being considered, the SGHSE 

must be consulted to determine if indemnity is available. 

5. High-risk animals and sexually intact genetically susceptible exposed male animals 

must be restricted to the premises where found or moved under permit to an APHISapproved research or quarantine facility or for destruction at another site. Such 

animals not indemnified may be moved under permit to slaughter. Animals old 

enough to test will have tissues submitted for testing when they die or are euthanized 

in accordance with the instructions available in the National Scrapie Reference 

Library on the Scrapie SharePoint site. When requested by the SGHSE, tissues from 

these animals are to be collected as specified for research and developmental work. If 

the number of animals to be euthanized is too large for available resources to sample, 

contact the SGHSE to establish an appropriate sampling plan. Such plans must 

include sampling of all animals where such testing could change the status of a flock 

including all purchased animals over 14 months of age or that have given birth in the 

flock.

6. Scrapie-positive animals must be restricted to the premises where found or moved 

under permit to an APHIS-approved research or quarantine facility or for destruction 

at another site. Tissues from these animals are to be collected as specified by the 

SGHSE for research and developmental work.

7. Animals from noncompliant flocks are considered exposed animals under 9 CFR part 

79 and may be moved only as allowed for exposed animals. Note: This means female 

animals and sexually intact male animals from these flocks are restricted to 

movement under permit for slaughter only unless they are officially genotyped by the 

owner and determined to be genetically resistant or less susceptible. 

8. Animals designated for testing as part of a flock investigation must be restricted to the 

premises where found until the required testing is completed, unless moved under 

permit to slaughter or to an APHIS-approved research or quarantine facility or for 

destruction at another site. These animals will be submitted for testing if they are 

slaughtered, die, or are euthanized before completion of the required testing and are 

old enough for a scrapie test to be meaningfully applied. Note: Animals for which 

indemnity is provided may not be slaughtered for human or animal food. 

9. Exposed wethers of any species or genotype may move unrestricted once they have 

been officially individually identified and entered into the NSD. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 46 

Table 1—Restrictions on Classical Scrapie Exposed Animals 

_ 

Positive 

Animals 

Exposed Animals 

Goats QQ Sheep AVQR 

Sheep 

AAQR 

Sheep 

RR Sheep 

AAQQ sheep 

and goats 

X X Free Free Free 

AVQQ & 

VVQQ 

Sheep 

X X X* Free Free 

AVQR 

Sheep 

X X X Free Free 

AAQR 

Sheep 

X X X X Free 

RR Sheep X X X X X 

Positive animals = Classical scrapie positive animals found in or traced to or from the flock in 

which the exposed animal was exposed. If there is more than one type of positive animal, use the 

genotype for the positive animal listed lowest on the chart to determine which animals to remove 

or restrict. All positive animals are to be destroyed or permanently restricted. 

*If the DSE has determined that the flock is unlikely to be affected by valine-associated scrapie, 

these animals may be reclassified as genetically less susceptible sheep and be allowed to move 

unrestricted. 

Free = Move unrestricted (rare exceptions to this general class are listed in part II N.3 and 4.) 

X = Destroyed or permanently restricted. 

Note: Nor98-like scrapie exposed animals are treated as low-risk exposed animals and may move 

unrestricted once they are officially identified. APHIS, with the concurrence of the involved 

SAHO, may conduct genetics-based pilot projects for goats and release goats determined to be 

genetically resistant or less susceptible.

O. Procedures for Sheep and Goats Transiting or Temporarily Residing in Inconsistent 

States 

1. Sheep and goat producers whose animals reside in an Inconsistent State must comply 

with the requirements in 9 CFR 79.3 for Inconsistent States to move animals 

interstate: 

a. Sheep and goats not in slaughter channels must be enrolled in the SFCP and be in 

compliance with the requirements for such flocks or an equivalent APHISrecognized program. They may also be sheep that are officially genotyped and 

determined to be AA QR or AA RR, officially identified, and accompanied by an 

ICVI that also states the individual animal identification numbers, the flock of 

origin and, for any animal born after January 1, 2002, the flock of birth, if 

different. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 47 

b. Animals in slaughter channels must be officially identified with an official blue 

eartag marked with the words “MEAT” or “SLAUGHTER ONLY” and may 

move only directly to slaughter or to a terminal feedlot. Animals 18 months of age 

and older (as evidenced by the eruption of the second incisor) in slaughter 

channels must also be accompanied by an ICVI that states the individual animal 

identification numbers and, for any animal born after January 1, 2002, the flock of 

birth (and the flock of origin, if different). 

2. For sheep and goats temporarily residing in an Inconsistent State at the time the State 

becomes inconsistent: 

a. The animals must return to their flock of origin’s State within 30 days of the 

State’s inconsistent designation. 

b. If the animals are moved within the required time period, their movement from 

the Inconsistent State may follow the regulatory requirements for sheep and goats 

from Consistent States. 

c. If the animals are not moved within the required time period, their movement 

from the Inconsistent State must follow the regulatory requirements for sheep or 

goats from Inconsistent States. 

3. Sheep and goats transiting an Inconsistent State: 

a. If the animals transit the Inconsistent State without unloading, they may move 

under the movement requirements applicable to their State of origin. 

b. If the animals are unloaded in the Inconsistent State they may thereafter be moved 

interstate only under the requirements for animals moved from an Inconsistent 

State. Exception: Rest stops of less than 24 hours for food and water. Animals 

attending an exhibit, receiving veterinary care, or maintained in an artificial 

insemination collection center or other site where only limited contact will occur 

and where the animals will not reside on the premises of a flock may be moved 

interstate from the Inconsistent State back to their flock of origin if they are 

moved directly to and from the site in accordance with a valid certificate issued in 

a Consistent State under 9 CFR 79.5 and reside in the Inconsistent State for less 

than 30 days unless the AVIC, with the State of origin SAHO’s concurrence, 

approves an extension. 

P. National Scrapie Database (NSD) – Data Entry Requirements 

1. The NSD includes SCS SCR, VSLS, the scrapie investigation records in EMRS, the 

scrapie program tag function of AIMS, and any subsequent applications that replace 

or augment these. Complete information on data entry is available in the National 

Scrapie Reference Library on the Scrapie SharePoint site. Data must be entered as 

provided in the User Guides published on this site. 

2. Information that must be entered by State or APHIS animal health personnel: 

a. Accurate and complete information for each premises, flock or person that meets 

any of the following criteria: 

1) Is or has participated in the SFCP; 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 48 

2) Is or has been designated an infected, source, exposed, or noncompliant flock 

or a flock under investigation, or owned or managed such a flock or the 

premises on which such a flock resided; 

3) Owns or owned an exposed, scrapie suspect, or scrapie-positive animal, or 

such an animal currently resides or previously resided on their premises; or 

4) Has been issued official ID devices or numbers. 

b. Each animal that has been designated scrapie-positive, scrapie-suspect, high-risk, 

or exposed or that resides in an infected or source flock, or that has been 

restricted, or tested or designated for test must have an individual animal record 

completed and maintained in SCS SCR. 

c. Individual records, including movement records, must be completed and 

maintained in SCS SCR for animals in SFCP Export flocks as described in the 

SCS SCR User Guide. 

d. A test record must be entered in VSLS for each animal tested for scrapie or for 

genetic resistance to scrapie. Test records are not entered in SCS SCR. These 

records will automatically be transferred to SCS SCR. 

e. Official eartags for use on sheep and goats must be ordered and distributed to the 

end user through the scrapie program tag function of AIMS or as provided in the 

User Guides for SCS SCR. 

f. Each animal involved in a trace out or trace back investigation must be entered in 

accordance with the applicable SOPs available on the Scrapie SharePoint site. 

Q. Genotyping Administrative Procedures 

1. Authorization from the Sheep and Goat Commodity Team must be obtained before 

submitting genotype samples to a laboratory for testing under the APHIS contract. 

Send an email with the following information: Name of flock, flock identification 

number (flock ID), type of test requested, reason for test (provide narrative such as 

flock plan, trace exposed animals, missing ewe investigation, etc.), genotype of the 

associated positive animals, any previous official genotype tests performed on the 

sheep and laboratory that conducted the test, number of sheep to be tested, sample 

collection medium (Flinders Technology Associates (FTA) card, tissue, tissue swab, 

or blood tubes), flock status, 10-day/5-day turnaround requested. If requesting a 5-day 

turnaround, provide justification. APHIS will email back approval for the codon 

testing to the requestor, as well as which laboratory to send the samples. Further 

information on this procedure is available on the Scrapie SharePoint site. 

2. The genotype of high-risk and exposed sheep the owner wants to keep will be 

determined at two different approved laboratories or at NVSL. Ideally, samples 

should be collected on two separate dates unless one of the following applies: 

a. Radio frequency ID is used with the Mobile Information Module (MIM); or 

b. Three or fewer animals are being sampled. 

In the case of infected or source flocks, the second collection should occur after the 

genetically susceptible animals have been removed. When separate collection cannot 

reasonably be done, the eartag numbers and sample labels must be read and checked 

for accuracy by both the owner or owner’s representative and a State or APHIS 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 49 

representative. 

R. Appeals of APHIS Actions 

1. The following APHIS actions may be appealed by an owner or authorized 

representative of a laboratory, test manufacturer, or eartag manufacturer (9 CFR 

79.4(c)(3)): 

a. The designation of an animal as a scrapie-positive animal, high-risk animal, 

exposed animal, genetically susceptible exposed animal, genetically resistant 

exposed sheep, genetically less susceptible exposed sheep, low-risk exposed 

animal, or suspect animal. 

b. The designation of a flock as an exposed flock, an infected flock, a source flock, a 

flock under investigation, or a noncompliant flock. 

c. Withdrawal of assigned official ID numbers or denial of a request to issue official 

ID numbers. 

d. Withdrawal of laboratory or test approval. 

e. Withdrawal of identification device approval. 

2. Appeal process 

a. The owner must appeal, in writing, to the National Scrapie Program Coordinator 

within 10 days after being informed of the reasons for the proposed action: 

National Scrapie Program Coordinator 

USDA, APHIS, Veterinary Services 

4700 River Road, Unit 43 

Riverdale, MD 20737 

b. The appeal must include all of the facts and reasons on which the owner relies to 

show that the reasons for the proposed action are incorrect or do not support the 

action. 

c. The action under appeal will remain effective pending final determination in the 

proceeding unless the National Scrapie Program Coordinator determines such 

action is not necessary to prevent the possible spread of scrapie. 

d. The National Scrapie Program Coordinator will review the appeal and grant or 

deny the appeal in writing as promptly as circumstances permit, and the written 

decision will include the reasons for the decision. In the event that the National 

Scrapie Program Coordinator made the initial decision the appeal will be 

reviewed by the National Scrapie Program Coordinator’s supervisor or his or her 

designee. 

e. If an owner disputes a material fact or facts leading to the decision on an appeal, 

the owner may submit a written request for reconsideration specifying the 

material fact or facts in dispute and the basis for disputing the facts to the 

National Scrapie Program Coordinator or National Scrapie Program Coordinator’s 

supervisor as appropriate within 10 days after being informed of a denied appeal. 

f. The National Scrapie Program Coordinator or National Scrapie Program 

Coordinator’s supervisor, as appropriate, will review any information regarding 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 50 

the material fact or facts in dispute, including the owner’s written argument and 

supporting documentation, and make a determination with respect to the material 

fact or facts as promptly as circumstances permit. 

g. The National Scrapie Program Coordinator's or National Scrapie Program 

Coordinator’s supervisor decision constitutes final agency action. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 51 

Part III: Identification Requirements 

A. Identification of Sheep and Goats in Commerce 

1. Identification requirements: 

a. Animals required to be identified in 9 CFR 79.3, or 9 CFR 79.6 for Consistent 

States, must be officially identified to the flock of birth or origin on change of 

ownership as required by State regulations or before entering interstate 

commerce. No sheep or goat required to be individually identified or group 

identified may be sold, disposed of, acquired, exhibited, transported, received for 

transportation, offered for sale or transportation, loaded, unloaded, or otherwise 

handled in interstate commerce or commingled with any animals that fall into 

these categories or be loaded or unloaded at a premises or animal concentration 

point (including premises that exhibit animals) where animals have been received 

that have been in interstate commerce or from which animals have moved in 

interstate commerce or leave the premises on which they currently reside if they 

are owned by a person who engages in the interstate commerce of animals unless 

each sheep or goat has been officially identified to the flock of birth or, when 

allowed, flock of origin. Unless prohibited by State law or regulation, this does 

not preclude a person from moving animals as part of a group/lot directly to 

another site in the same State where official eartags that have been assigned to the 

animal’s flock of origin in the NSD will be applied to the animals, or to an 

approved market were the animals will be officially identified. 

b. In cases where the flock of birth cannot be determined, the animal must be 

officially identified to the flock of origin (flock in which an animal most recently 

resided for breeding). Allowed identification methods are listed in paragraph A.3. 

Note: Check with the receiving State to ensure that both State and Federal 

requirements are met. 

c. Sheep and goats required to be officially identified (see d. for exceptions) include: 

1) All sexually intact sheep and goats not in slaughter channels; 

2) All sheep and goats over 18 months of age as evidenced by eruption of the 

second incisor; 

3) Animals for exhibition, including sexually intact sheep and goats of any age 

and wethers 18 months of age and older. There is an exclusion which would 

rarely apply for animals that have never been in interstate commerce, that 

have not resided on premises where animals have been received that have 

been in interstate commerce or from which animals have moved in interstate 

commerce and are not owned by persons who engage in the interstate 

commerce of animals, that are moved to exhibitions conducted at premises 

where animals have not been received that have been in interstate commerce 

or from which animals have moved in interstate commerce and where none of 

the animals exhibited has been in interstate commerce and where the State and 

the exhibit do not require the animals to be identified. Note: Many States and 

exhibitions require official identification of all sheep and goats. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 52 

4) All exposed and high-risk animals, including all low-risk exposed animals, 

genetically susceptible exposed animals, genetically less susceptible exposed 

sheep, and genetically resistant exposed sheep. 

5) All suspect and test-positive animals. 

6) Sheep and goats from noncompliant flocks. 

d. Sheep and goats not required to be individually identified for interstate commerce 

that may move with a group/lot ID and an owner hauler statement include (Note: 

some States require all sheep and goats to be identified): 

1) Sheep and goats under 18 months of age that are in slaughter channels (Note: 

The market or seller must note on the bill of sale that the animal was sold for 

slaughter and must retain a copy of an owner/hauler statement from the buyer 

listing the slaughter establishment, restricted animal sale, restricted livestock 

facility, or terminal feedlot where the animal is being moved, or indicating 

that the animal was purchased for slaughter for personal use). 

2) Wethers under 18 months of age. 

3) Sheep and goats of any age shipped directly to a slaughter establishment or an 

approved market (9 CFR 71.20) that has agreed to act as an agent for the 

owner to apply official ID and when all the animals in a section of a truck are 

from the same flock of origin and are accompanied by an owner/hauler 

statement. (Note: The owner/hauler statement must contain the information 

needed for the establishment or market to officially identify the animals. 

Slaughter establishments may maintain the identity of the animals to the flock 

of origin by slaughtering them by flock of origin in group/lots rather than by 

applying eartags if the flock of origin number is correlated with the heads or 

samples collected for scrapie testing.) 

This includes animals in slaughter channels at 18 months and older (as 

evidenced by the eruption of the second incisor) if the animals were kept as a 

group on the same premises on which they were born and have not been 

maintained in the same enclosure with unidentified animals from another 

flock at any time, including throughout the feeding, marketing, and slaughter 

process. Such groups must have a group/lot ID that includes the flock of 

origin flock ID or PIN/LID. If such a group is subdivided such subdivision 

must be noted by adding a hyphen, an “S”, and a sequential number starting 

with 1 to the end of the group/lot ID. 

4) Sheep or goats moved for grazing or similar management reasons without a 

change of ownership when the animals are moved from a premises owned or 

leased by the owner of the animals to another premises owned or leased by the 

owner of the animals. The premises must be recorded in the National Scrapie 

Database as additional flock premises and commingling must not occur with 

unidentified animals born in another flock or any animal not part of the flock. 

e. Sheep and goats not required to be officially identified: Sheep or goats that have 

only resided on premises and in flocks in the same State and where the animals 

and premises are owned by persons who do not engage in the interstate commerce 

of sheep or goats and where the sheep or goats are of a class exempted from 

official ID by the State while in intrastate commerce. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 53 

2. Issuance of premises and flock ID numbers: 

a. The VS Area Office or the SAHO’s office will issue a PIN to each sheep or goat 

owner who requests one. 

1) The office will enter premises and flock information in the NSD and 

permanently assign a PIN and a flock ID number that in the case of breeding 

flocks can be used on official tags or as the flock ID portion of a tattoo. 

2) In some States, the numbers will be the same. 

b. All 2- and 3-character alphabetical sequences not currently assigned must be 

reserved for use by producers who use registered tattoo prefixes. 

c. All 2- and 3-character numeric and alphanumeric sequences not currently 

assigned must be reserved for producers using flock ID tattoos. 

d. When possible, the flock ID number for flocks with registered tattoo prefixes will 

be the State postal abbreviation followed by the producer’s registered tattoo 

prefix. 

e. Alphabetical and alphanumeric sequences that contain I, O, or Q other than as 

part of a State postal abbreviation may not be assigned. 

3. Allowed identification devices and methods and restrictions on their use: 

a. Official identification devices approved for use in sheep and goats may be found 

here.

15 Select “List ID Devices” from Public Tools, then “Scrapie Program Tags” 

from the drop-down menu, and click on “Get Approved Devices”. APHIS adds 

new devices to this site on approval. 

1) Restricted use of colored tags: Official red, yellow, and blue metal or blue plastic 

eartags may only be used for the following purposes:

a) Official red metal eartags are only to be used for animals that have tested 

positive for scrapie on an official program approved test. 

b) Official yellow metal eartags are only to be used for exposed animals 

permanently restricted to a premises. 

c) Official blue eartags (metal or plastic) produced after [Insert effective date of 

final rule] are to be imprinted with “Slaughter Only” or “MEAT.” Such 

eartags are only to be applied to animals in slaughter channels. 

2) Official eartag placement: 

a) Recommendation for wool sheep and fiber producing goats: To aid in 

shearing place eartags in the animal’s left ear in the middle of the ear halfway 

between base and tip of ear. If a one-piece tag is used place it around the 

lower edge of the ear. Use of metal tags in animals that may be sheared may 

pose a hazard; consider this when selecting the type of tag to use. 

b) Official eartags may not be placed in any tissue other than the ear. 

c) Animals that cannot be ear tagged because of absent or injured ears, or 

because the application of an eartag would obscure an official tattoo, may 

have the official eartag attached to a durable neck strap or collar that can only 

be removed by cutting the strap, collar, or eartag and which must 

accommodate the expected growth of the animal. When a neck strap or collar 

 

15 https://vsapps.aphis.usda.gov/aims/.
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 54 

is used in this manner, the neck strap or collar with eartag must be treated the 

same as an eartag and may not be removed or replaced other than as allowed 

in 9 CFR 79.2(h). If moving directly to slaughter, an APHIS approvedbacktag may be applied instead within 3 inches of the poll. 

3) Use of backtags: 

a) The SAHO, with concurrence of the AVIC for the State involved, may allow 

in a compliance agreement or an approved market agreement the use of 

APHIS-approved backtags applied to the back for mature sexually intact male 

goats with horns moving direct to slaughter that are considered unsafe to 

eartag at a livestock facility or other site. Note: Animals in lots consisting 

only of animals from the same flock of origin may be moved through a 

restricted sale without individual ID for movement to slaughter as a group/lot 

using the flock of origin group/lot ID followed by a dash and an S and a 

sequential number indicating any subdivision of the original group/lot. (Note: 

The market or seller must note on the bill of sale that the animal was sold for 

slaughter and must retain a copy of an owner/hauler statement from the buyer 

listing the group lot ID and the slaughter establishment, restricted animal sale, 

restricted livestock facility, or terminal feedlot where the animal is being 

moved, or indicating that the animal was purchased for slaughter for personal 

use). 

b) Animals moving direct to slaughter that cannot be ear tagged because of 

absent or injured ears, or because the application of an eartag would obscure 

an official tattoo, may be officially identified with an APHIS-approved 

backtag applied within 3 inches of the poll. 

c) The SAHO and AVIC for the State involved, with concurrence of the National 

Scrapie Program Coordinator, may approve other uses of backtags for direct 

to slaughter movements on a case-by-case basis in a compliance or approved 

market agreement. 

b. Allowed official identification methods and restrictions on their use: 

1) Permanent brands and ear notches, registered with an official brand registry, are 

allowed for the official identification of sheep and goats allowed to move with 

group/lot identification by 9 CFR 79.3 as described in III.A.3.e when 

accompanied by: 

a) A brand inspection certificate and an owner statement dated within 30 days, 

stating that the animals were born in and have resided throughout their lives in 

low-risk commercial flocks, and 

b) A veterinarian’s statement issued within 12 months of the movement 

indicating that the flock of origin identified in the owner statement was 

inspected and met the requirements of a low-risk commercial flock on the date 

of issuance. 

2) Registration tattoos, recorded in the book of record of a sheep or goat registry, 

may be used to officially identify sheep or goats required to be individually 

identified by 9 CFR 79.3, moving without a transfer of ownership or moving after 

a transfer of ownership if an application for transfer of registration is completed 

and accompanies the animal when it leaves the sale or premises of origin if: 

b) The association registry premises or flock tattoo prefix has been linked in the 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 55 

NSD to the APHIS-assigned PIN and flock ID number of the flock of birth, 

and documentation of such accompanies the animal; or the breed registry has 

been approved based on information provided to APHIS indicating that the 

tattoos are unique within the registry, retrievable, traceable, and that the 

registry rules allow for release of information to APHIS for regulatory disease 

purposes such as the tracing of scrapie-positive and scrapie-exposed animals 

and that the registry agrees to provide such information (approved registries 

can be found here.

16The tattoo is legible; and 

c) The animal is accompanied by: 

 A copy of the registration certificate or temporary registration certificate 

before its expiration date, and, if not in the name of the current owner, a 

copy of the completed application for transfer of ownership in the name of 

the current owner where the sale occurred within 60 days, or 

 For animals under 60 days of age, a copy of a completed application for 

registration, or 

 An interstate certificate of veterinary inspection that lists the flocks of 

origin and birth, the registry, and the registry tattoo. 

3) Official flock identification tattoos, a combination of the flock identification 

number assigned to the flock of birth or origin in the NSD and an individual 

number unique within the flock, may be used to officially identify sheep or goats 

required to be individually identified by 9 CFR 79.3 if: 

a) The tattoo is legible. 

b) The animals are not in slaughter channels or moving through a concentration 

point where a transfer of ownership may occur, such as a livestock market or 

buying station. This excludes sales of breeding or show stock at a livestock 

show, seed stock sale, or similar event when the flock ID and individual 

number tattoo of each animal is read and recorded with the name and address 

of the seller and the buyer of each animal and the record maintained for 5 

years by the seller or sale management. 

c) The animals are accompanied by an owner/hauler statement that contains the 

information needed to officially identify the animals to their flock of origin 

and, when required, their flock of birth. 

d) The numbers are placed in different ears or in the same ear with the flock 

identification number above the individual number or, in the case of animals 

with absent or injured ears, the tail fold or in animals where the tail fold is too 

small, the flank. 

c. Electronic implantable identification (EID) 

1) Registered sheep or goats and animals from flocks listed in the NSD required to 

be individually identified by 9 CFR 79.3, may be identified with an EID if: 

a) The implant is placed between the skin and the cartilage of the back side of 

the ear near where the ear joins the head or between the skin and the bone of 

the tail near the base of the tail; 

b) The animal is tattooed with a legible “E” if the implant is at the base of the 

ear, or “ET” if the implant is in the tail fold; 

 

16 www.aphis.usda.gov/animal-health/scrapie
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 56 

c) The tattoo is at least 0.3 inches high in the ear or, in the case of earless 

animals, the tail fold; 

d) The animal is not in slaughter channels or moving through a concentration 

point where a transfer of ownership will occur, such as a livestock market or 

buying station, excluding sales of registered animals where an application for 

transfer of registration is completed and accompanies the animal when it 

leaves the sale or premises of origin; 

e) For registered animals: 

 The electronic implant number has been recorded in the book of record of 

a sheep or goat registry association and on the registration certificate; and 

 The animal is accompanied by a copy of the registration certificate and, if 

not in the name of the current owner, a copy of the completed application 

for transfer of ownership in the name of the current owner where the sale 

occurred within 60 days, or for animals under 60 days of age, a copy of a 

completed application for registration. 

f) For animals from flocks listed in the NSD (which may also be used for 

registered animals that originate from flocks listed in the NSD): 

 The animal is legibly tattooed with the flock identification number in the 

ear, or, in the case of earless animals, the tail fold; or, in animals where the 

tail fold is too small, the flank; 

 The animal is accompanied by an ICVI or, if an ICVI is not otherwise 

required, an owner/hauler statement that lists the flock of origin, the flock 

ID number, the electronic implant number, and, if required by 9 CFR 

79.2(a)(1), the flock of birth. 

g) The animal is accompanied by an implant reader that can read the implant in 

the animal and is made available for use by APHIS or State authorities to 

verify the implant number in the animal; 

h) The movement is either for exhibition purposes or other movement without 

change in ownership, or for change in ownership that includes transfer of the 

registration papers, or for change in ownership that may not include transfer 

of registration papers but is directly to a flock listed in the NSD and the 

animal is tattooed as required in paragraph f) of this section and where the 

new owner has a reader that can read the implant in the animal; 

i) The implant is used in accordance with other applicable laws and regulations; 

and 

j) The implant complies with ISO 11784 and ISO 11785, or has been approved 

as a new device type as described above, and the device was approved under 

9 CFR 79.2(k). The implant number must be an Animal Identification Number 

(840) issued to the flock of origin in the AIMS module of the NSD or applied 

to the animal before March 11, 2015. 

d. Animals may be identified with any other official identification method or device 

approved by the Administrator for particular circumstances. 

e. Group/lot identification: Animals may be identified with a GIN when group/lot 

identification is allowed by 9 CFR 79.3 in lieu of individual identification and the 

animals are accompanied by an owner/hauler statement. Group/lot identification may 

be used for:
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 57 

1) Animals in slaughter channels under 18 months of age. 

2) Animals in slaughter channels at 18 months and older (as evidenced by the 

eruption of the second incisor) if the animals were kept as a group on the same 

premises on which they were born and have not been maintained in the same 

enclosure with unidentified animals from another flock at any time, including 

throughout the feeding, marketing, and slaughter process. 

3) Animals in slaughter channels 18 months of age and older (as evidenced by the 

eruption of the second incisor) identified with official individual ID or, in the case 

of animals from flocks that are low-risk commercial flocks, identified using 

identification methods or devices approved for this purpose. (Note: This provision 

exists in 9 CFR 79.3(a) to allow these animals to move with an owner/hauler 

statement rather than an ICVI.). 

4) Animals moving for grazing or other management purposes between two 

premises both owned or leased by the flock owner and recorded in the NSD as 

additional flock premises and where commingling will not occur with unidentified 

animals that were born in another flock or any animal that is not part of the flock. 

A request to APHIS to enter additional flock premises in the NSD is required 

before animals are first moved to the premises. Notification is not required for 

each movement of animals to that premises. Neither group/lot ID nor an ownerhauler statement is required for movements of a flock or its members for flock 

management purposes within a contiguous premises spanning two or more States. 

This provision does not include the transiting or sale of animals through such a 

premises in circumvention of the other 9 CFR part 79 requirements. 

5) Animals moving to a livestock facility approved in accordance with 9 CFR 71.20; 

if facility management has agreed to act as an agent for the owner to apply official 

identification and if the animals have been in the same flock in which they were 

born and have not been maintained in the same enclosure with unidentified 

animals born in another flock at any time. The owner/hauler statement must 

contain the information needed to officially identify the animals to their flock of 

origin and, when required, their flock of birth. 

f. Only APHIS provided or approved devices for sheep and goats will be used. APHISprovided tags will have a unique alphanumeric sequence or flock ID number and a 

production (animal) number unique within a flock. The flock ID number will be the 

Postal Service State abbreviation followed by up to 7 alphanumeric characters. States 

may allow producers to use a national premises (NPIN) or location identification 

number (LID) in place of a flock ID. All tags must have the U.S. shield. 

Premises/flock ID tags produced by approved tag companies will have the 

premises/flock ID number and a unique production number. Series of alphanumeric 

USDA sheep and goat eartags may be assigned to premises or flocks if they are 

linked to the premises or flock in the NSD. Premises/flock ID eartags may only be 

assigned to breeding flocks. 

g. Animals may be identified with any other official identification method or device 

approved by the Administrator for particular circumstances. Device manufacturers 

may contact the National Scrapie Program Coordinator at scrapie@aphis.usda.gov to 

request approval. For additional information see 9 CFR 79.2 (k).
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 58 

4. Identification requirements for captive exotic sheep and goats, and domestic sheep and 

goats maintained in AZA-accredited facilities: 

a. For the purposes of 9 CFR parts 54 and 79, all captive animals of the genus Ovis are 

considered to be sheep and all captive animals of the genus Capra are considered to 

be goats. Therefore, all nontraditional livestock species and captive exotic species in 

the genus Ovis and genus Capra are subject to the requirements for sheep and goats 

in 9 CFR parts 54 and 79.17

b. Exceptions to identification requirements for sheep and goats housed at AZAaccredited zoological parks (zoos): 

1) Domestic and exotic sheep and goats housed in AZA-accredited zoos may be 

identified in accordance with AZA accreditation standards while on exhibit in or 

while in transit between AZA-accredited facilities, if the records required in 9 

CFR 79.2 are properly maintained and linked to the facilities’ internal 

identification systems. 

2) Sheep or goats required to be officially identified per 9 CFR 79.3 or the State 

moved to or from a facility not AZA-accredited must have official ID. 

5. Issuance of official identification devices or numbers: 

a. The State or APHIS official responsible for issuing official sheep and goat eartags or 

official ID numbers in a State may assign serial numbers of official eartags to 

accredited veterinarians, State and APHIS representatives, and persons who own or 

handle sheep or goats and may only assign flock ID and production numbers of 

official eartags to persons who own breeding flocks. The SAHO or the Administrator 

may limit the assignment of official identification devices or numbers to persons for 

use on animals that did not originate in a breeding flock owned by them to slaughteronly devices or numbers. 

b. The State or APHIS official responsible for issuing official sheep and goat eartags or 

official ID numbers in a State may assign serial numbers of official eartags to other 

responsible persons if the SAHO and the AVIC agree that such assignments will 

improve scrapie control and eradication within the State, and if appropriate records 

are maintained and submitted to the VS Area Office to permit traceback of animals to 

the flock of origin and flock of birth. Such serial numbers must be redistributed in 

AIMS or SCS SCR. 

c. Accredited veterinarians, State and APHIS representatives, and other responsible 

persons assigned official identification devices or numbers must have a person record 

and be assigned a person number in the NSD. 

d. Persons who handle sheep or goats who are assigned official identification devices or 

numbers must be assigned premises numbers in the NSD. 

e. Persons who own breeding flocks who are assigned official identification devices or 

numbers must be assigned premises and flock ID numbers in the NSD. 

 

 

17 Mouflon are known to be susceptible to scrapie. Other exotic sheep and goats may also be susceptible to scrapie, 

and could transmit the disease to domestic sheep and goats when they are maintained together. Therefore, it is 

important to individually identify all animals in the genus Ovis and genus Capra when they are moved or exhibited, 

including nontraditional sheep and goat livestock species and sheep and goat species kept at zoos. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 59 

f. Persons assigned official identification devices or numbers for use on animals not 

born in a flock owned by them must provide, if requested, in a manner acceptable to 

APHIS, assignment data associating assigned serial sequences to the flock of origin 

and, when required, the flock of birth. One such method would be to enter the data 

into the online animal identification management system module of the NSD. 

g. All official devices must be distributed through the scrapie program application of 

AIMS and, if redistributed, redistributed through the scrapie program application of 

AIMS or as provided in the User Guides for SCS SCR or a successor APHIS system. 

6. Responsibility of the owner of the flock of origin for officially identifying animals: 

a. The owner of the flock of origin or his or her agent is primarily responsible for and 

must officially identify any animal that requires official identification. This will 

enable sheep or goats to be identified to their flock of birth. Animals born on a 

premises do not have to be identified when officially identified animals from another 

flock of birth are added to the premises. 

b. Producers are strongly encouraged to officially identify their animals before the 

animals leave their premises to prevent any error from occurring in the later 

identification of the animals and to ensure they will meet intra- and interstate 

movement requirements. 

c. If official identification is required and has not been placed on the animal by the 

owner before leaving the flock of origin, the owner must ensure the animal is 

officially identified before it is put in the same enclosure with animals from a 

different flock of origin and before a change of ownership. 

7. Responsibility of persons handling sheep and goats in commerce to identify animals: 

a. Although the owner of the flock of origin is the primary person responsible for 

officially identifying animals, no person may handle sheep or goats at any point in 

interstate commerce before ensuring that all animals requiring identification have 

been officially identified to their flock of origin or birth. 

b. A person must not buy, transport, receive, deliver or otherwise handle in commerce 

an animal required to be identified by 9 CFR or the State that has not been officially 

identified. 

c. If a person transporting animals is aware of any animal in the shipment that loses its 

identification to its flock of origin while in interstate commerce, the person 

transporting the animal is required to inform the receiving party of this fact, and it is 

the responsibility of the person who has control or possession of the animal on 

unloading or delivery to identify the animal or have the animal identified before 

commingling it with any other animals. 

d. A person who engages in interstate commerce of sheep and goats may not receive a 

sheep or goat required to be identified that has not been officially identified, or, when 

allowed, officially identified upon unloading, regardless of whether that animal 

moved interstate. 

 

8. Restrictions on the application of official identification assigned to flocks: 

a. No person will apply a premises or flock ID number, a brand, or an ear notch pattern 

to an animal not from the flock of origin to which the number or the brand or the ear 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 60 

notch pattern was assigned by a State or APHIS representative. This prohibition 

includes individual identification (such as USDA tags) that has been assigned to a 

premises or flock and registration tattoos that contain prefixes that have been assigned 

to a premises or flock. This procedural requirement does not prevent an owner from 

applying individual animal official identification assigned to his or her premises or 

flock to an owned animal that resides on the premises or that is part of the flock, as 

long as a record is maintained linking the individual animal official identification to 

the animal’s flock of origin or birth. 

b. No person will use an official identification device or number provided for the 

identification of sheep and goats other than for the identification of a sheep or goat. 

9. Removal or loss of official identification devices: Official identification devices are 

intended to provide permanent identification of livestock and to ensure the ability to find 

the source of animal disease outbreaks and locate exposed animals. Removal of these 

devices, including devices applied to imported animals in their countries of origin and 

recognized by the Administrator as official, is prohibited except at the time of slaughter, 

at any other location on the death of the animal, or as otherwise approved by the State or 

Tribal animal health official or an AVIC when a device needs to be replaced as allowed 

in 9 CFR 79.2(i). 

a. All man-made identification devices affixed to sheep or goats moved interstate must 

be removed at slaughter and correlated with the carcasses through final inspection by 

means approved by FSIS. If diagnostic samples, including whole heads, are taken, the 

identification devices must be packaged with the samples and must be left attached to 

approximately 1 inch of tissue or to the whole head to allow for identity testing. 

Devices collected at slaughter must be made available to APHIS and FSIS. 

b. All official identification devices affixed to sheep or goat carcasses moved interstate 

for rendering must be removed at the rendering facility and made available to APHIS. 

c. If a sheep or goat loses an official identification device, the person applying the new 

official identification device must record the official ID number on the old device, if 

known, in addition to the information required to be recorded in accordance with B.2

of this part. If the person transporting animals is aware of any animal in the shipment 

that loses its identification to its flock of origin while in interstate commerce, the 

person transporting the animal is required to inform the receiving party of this fact. It 

is the responsibility of the person who has control or possession of the animal on 

unloading or delivery to identify the animal or have the animal identified before 

commingling with any other animals. This will be done by applying official 

individual animal identification to the animal and recording the means of 

identification and the corresponding animal identification number on the waybill or 

other shipping document. A record must be kept linking the identification number to 

the flock of origin. In the case of animals in interstate commerce, if the flock of origin 

cannot be determined, all possible flocks of origin will be listed on the record of 

official identification applied. If this cannot be done, the animal must be identified 

with a slaughter-only eartag and may only move in slaughter channels. In the case of 

sheep, the animal may move for other purposes if it is inspected by an accredited 

veterinarian, found free of evidence of infectious or contagious disease, and officially 

genotyped as AA QR or AA RR. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 61 

10. Loss of ability to apply official identification: Any person who fails to comply with Part 

III, Identification Requirements, will no longer be assigned serial numbers of USDA 

backtags, official sheep and goat tattoos, official eartags, or flock ID numbers for use as 

official identification or any official identification device. 

11. Identification of scrapie suspect, scrapie-positive, scrapie-exposed, and high-risk animals 

including all low-risk exposed animals, genetically susceptible exposed animals, 

genetically less-susceptible exposed animals, and genetically resistant exposed sheep: 

a. The identification device required is an official tamper-resistant or tamper-evident 

metal or plastic eartag or another official identification device approved for this use 

by APHIS. Other official identification may be used when eartags cannot be used due 

to the absence or deformation of the ears. These animals will be identified with at 

least two forms of official identification unless there is an existing unique unofficial 

flock tag or tattoo that would preclude the application of more than one official 

eartag. RFIDs will be used as one form of official ID when such use will facilitate the 

inventory or testing of these animals. 

b. Animals that are positive on an official live-animal test will be identified with a red 

metal tag on each ear. Only APHIS or State representatives may acquire official red 

metal tags. 

c. High-risk animals and sexually intact genetically susceptible exposed male animals 

not removed will be identified with both official yellow metal eartags and with a 

secondary official permanent identification method or device such as an RFID 

implant or official tattoo. 

d. Other animals may be identified with an official eartag of any other approved 

color/material combination approved for the intended use (blue is restricted to 

slaughter only eartags). 

e. Tag application must be done by, under the supervision of, or verified by an APHIS 

or State representative or an accredited veterinarian authorized by APHIS or the State 

to perform this function. 

f. All identification applied to these animals will be recorded in the NSD. 

Note: All forms of identification on suspect, positive, exposed, and high-risk animals 

(including low-risk exposed animals, genetically susceptible exposed animals, 

genetically less susceptible exposed animals, and genetically resistant exposed sheep) 

must be recorded on VS Form 5-20 or equivalent and forwarded to the DSE and the 

VS Area Office. The AVIC must ensure that an individual animal record is created 

for each animal in the NSD. 

B. Records of Animals Handled 

1. General requirements: 

a. Persons who sell, dispose of, acquire, exhibit, transport, receive for transport, offer 

for sale or transportation, load, unload, or otherwise handle sheep or goats in 

interstate commerce or commingle sheep or goats with sheep or goats in interstate 

commerce and required to be identified by 9 CFR 79.3 must officially identify the 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 62 

animals and maintain records linking the official identification to their premises of 

birth or origin if they are not already officially identified. (Persons may not sell or 

dispose of unidentified animals required to be identified unless arrangements have 

been made with the person acquiring the animals to act as his or her agent to identify 

the animals, including maintaining records linking the official ID to their premises of 

birth or origin. Persons may not purchase or acquire unidentified animals required to 

be identified unless they identify them and maintain the required records while acting 

as an agent for the person disposing of the animals.) 

b. Persons who purchase, acquire, sell, or dispose of sheep and goats, whether or not the 

animals are required to be identified, must maintain business records (such as 

yarding receipts, sale tickets, invoices, and waybills) for 5 years. These records 

must include the information described in B.3, “Records required of persons who 

purchase, acquire, sell, or dispose of animals.” 

c. The original tag number or all possible flocks of origin and the new official ID 

number must be listed in the record of official identification applied when an animal 

loses an eartag while in interstate commerce. 

2. Records required of persons who apply official identification to animals: 

Persons who apply official individual or group/lot identification to animals must 

maintain records for 5 years. The records must include the following information: 

a. The flock ID number of the flock of origin, the name and address of the person who 

currently owns the animals, and the name and address of the owner of the flock of 

origin if different; 

b. The name and address of the owner of the flock of birth, if known, for animals born 

after January 1, 2002, in another flock and not already identified to flock of birth; 

c. The date the animals were officially identified; 

d. The number of sheep and the number of goats identified; 

e. The breed and class of the animals. If breed is unknown, for sheep the face color 

and for goats the type (milk, fiber, or meat) must be recorded instead; 

f. The official ID numbers applied to animals by species or the GIN applied in the 

case of a group/lot; 

g. Whether the animals were identified with “Slaughter Only” or “MEAT” 

identification devices; and 

h. Any GIN with which the animal was previously identified. 

3. Records required of persons who purchase, acquire, sell, or dispose of animals: 

Persons who purchase, sell, or transfer without sale sheep or goats must maintain normal 

business records that include the following information: 

a. The number of animals purchased, sold, or transferred without sale; 

b. The date of purchase, sale, or other transfer; 

c. The name and address of the person from whom the animals were purchased or 

otherwise acquired, or to whom they were sold or otherwise transferred; 

d. The species, breed, and class of animal, and if breed is unknown, for sheep the face 

color and for goats the type (milk, fiber, or meat) must be recorded instead; 

e. A copy of the brand inspection certificate for animals officially identified with brands 

or ear notches; 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 63 

f. A copy of any certificate or owner/hauler statement required for movement of the 

animals purchased, sold, or otherwise transferred; and 

g. If the flock of origin or the receiving flock is under a flock plan or PEMMP, any 

additional records required by the plan. 

4. Keeping of records/making records available: 

Each person required to keep records under Part III must maintain the records for at least 

5 years after the person has sold or otherwise disposed of the sheep or goat to another 

person. This record retention requirement may be extended for such further period as the 

Administrator (through the DSE) may require by written notice to the person, for 

purposes of any investigation or action involving the sheep or goat identified in the 

records. The person must make the records available for inspection and copying during 

ordinary business hours (8 a.m. to 5:30 p.m., Monday through Friday) by any authorized 

APHIS or State employee on that employee’s request and presentation of his or her 

official credentials. 

 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 64 

Part IV: Shows and Sales 

A. For practical purposes sexually intact sheep and goats of any age and wethers 18 months 

of age and older that are exhibited require official ID. There is an exclusion which would 

rarely apply for animals that have never been in interstate commerce, that do not reside 

on premises that engage in interstate commerce of animals, and are not owned by persons 

who engage in interstate commerce of animals that are moved to exhibitions conducted at 

premises where animals are not received that have been in interstate commerce or from 

which animals are moved in interstate commerce and where none of the animals 

exhibited has been in interstate commerce. Note: Many States and exhibitions require 

official identification of all sheep and goats. 

B. Whenever practical, ewes over 12 months of age (as evidenced by eruption of the first 

permanent incisor) should be housed in separate enclosures from animals from different 

flocks. Pens used by mature female sheep and goats should be thoroughly cleaned and all 

organic material removed before use by an animal from another flock. 

C. All sheep and goats from SFCP-enrolled flocks must be housed and handled to prevent 

direct contact with female sheep and female goats from flocks of lower status. Spacing 

sufficient to prevent contact or solid partitions may be used to maintain separation. Pens 

must be thoroughly cleaned and all organic material removed before use by an animal 

from an SFCP flock. 

D. Special arrangements should be made to keep the following animals separate from sheep 

and goats from different flocks such that direct contact does not occur and to keep them 

in an area that will be properly cleaned and disinfected, if such animals are allowed at a 

show: 

1. Sheep or goats that are within 30 days of parturition; 

2. Sheep or goats that are within 30 days postpartum or since having aborted; and 

3. Pregnant sheep and goats that have a vaginal discharge. 

E. Should a lambing or kidding occur at the show, the placenta, placental fluids, and soiled 

bedding should be removed immediately and disposed of in a sanitary landfill or by 

another method approved by the State. The dam and her offspring should be removed 

from the show grounds or separated from sheep and goats from different flocks using 

spacing or solid partitions such that direct contact does not occur. The pen should be 

thoroughly cleaned and disinfected before use by another animal. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 65 

Part V: Consistent State Status in the National Scrapie Eradication 

Program 

A. State Status in the NSEP 

1. States are classified as Consistent or Inconsistent in the NSEP. 

a. A Consistent State is a U.S. State, Territory, or possession the Administrator has 

determined conducts an active State scrapie control program that meets the 

requirements of 9 CFR 79.6 or effectively enforces a State-designed plan the 

Administrator determines is at least as effective in controlling scrapie as the 

requirements of 9 CFR 79.6. 

b. Sheep and goats from Inconsistent States have more restrictive interstate 

movement requirements than animals from Consistent States. 

2. See the definition for Consistent State for a current list of States with Consistent 

status. 

B. Standards for State Programs to Qualify as Consistent 

Consistent State status is granted to qualified States by the Administrator in accordance 

with 9 CFR 79.6. A Consistent State meets all elements of the 10 requirements listed 

below. 

1. The State has the authority to restrict the movement of all scrapie-infected and source 

flocks. 

2. The State has the authority to require the reporting of all scrapie-suspect animals and 

the results of all scrapie tests to State or Federal authorities. 

3. The State has signed a memorandum of understanding with APHIS delineating the 

respective role of each in implementing the NSEP. 

4. The State has placed all known scrapie-infected and source flocks under the required 

movement restrictions. 

5. The State has effectively implemented policies to: 

a. Investigate all scrapie suspects reported within 7 days; 

b. Designate a flock’s status within 15 days of notification that the flock contains or 

contained a scrapie-positive animal; 

c. Restrict the movement of newly designated scrapie-infected and source flocks 

within 7 days after they are designated; 

d. Maintain movement restrictions on infected and source flocks until the flocks 

have completed a flock plan and the flock owner has agreed to comply with a 5-

year PEMMP; 

e. Conduct epidemiological investigations of source and infected flocks; 

f. Conduct trace backs of scrapie-positive animals and trace outs of high-risk and 

exposed animals and report any out-of-State traces to the appropriate State within 

45 days of receipt of notification of a scrapie-positive animal; 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 66 

g. Conduct trace backs based on slaughter sampling within 15 days of receiving 

notification of a scrapie positive animal at slaughter. 

6. The State effectively monitors and enforces quarantines. 

7. The State effectively enforces State reporting laws and scrapie regulations. 

8. The State has designated at least one APHIS or State animal health employee to serve 

as the DSE for that State. 

9. The State has educated those engaged in the interstate movement of sheep and goats 

regarding identification and recordkeeping requirements in 9 CFR 79.2. 

10. The State meets the following additional requirements: 

a. It requires and effectively enforces official identification on change of ownership 

of all animals of any age not in slaughter channels and any sheep over 18 months 

of age such that the animal may be traced back to its flock of birth. Commercial 

goats and commercial whiteface or hair sheep under 18 months of age may be 

exempted by State regulation when allowed in 9 CFR 79.6(10)(i). 

b. It maintains required information in the NSD. 

c. It requires official individual identification, even if the animal does not live in an 

infected or source flock, of: 

1) Any live scrapie-positive, suspect, or high-risk animal of any age; 

2) Any sexually intact exposed animal greater than 1 year of age; 

3) Any sexually intact exposed animal of less than 1 year of age on change of 

ownership (except for exposed animals moving in slaughter channels at less 

than 1 year of age). 

d. It effectively enforces movement restrictions on all scrapie-positive, suspect, and 

high-risk animals throughout their lives unless they are moved in compliance with 

9 CFR 79.3. 

e. It requires that tissues from all scrapie-positive or suspect animals and female 

high-risk animals that have lambed (when they have died or are destroyed) be 

submitted to an authorized laboratory to conduct scrapie tests, and it requires the 

complete destruction of the carcass of scrapie-positive and scrapie-suspect 

animals. 

f. It prohibits any animal from being removed from slaughter channels unless it is 

identified to the flock of birth, is not from an Inconsistent State, and is not 

scrapie-exposed or from an infected or source flock. 

g. Additionally, the State has effectively implemented ongoing scrapie surveillance 

that meets the following criteria: 

1) Collects and submits surveillance samples from targeted animals slaughtered 

in State-inspected establishments and from slaughter establishments within the 

State not covered under 9 CFR 71.21, or allows and facilitates the collection 

of such samples by APHIS personnel or contractors; 

2) Transmits required submission and epidemiological information for all scrapie 

samples using the electronic submission system provided by APHIS for 

inclusion in the NSD and for transmission of the submission information to an 

approved laboratory; and 

3) Achieves the annual State-level scrapie surveillance targets for sheep and 

goats originating from the State as determined annually with input from the 

States and made available to the public at the National Scrapie Eradication 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 67 

webpage at least 6 months before the start of the collection period; or 

4) Conducts annual surveillance at a level that will detect scrapie if it is present 

at a prevalence of 0.1 percent in the population of targeted animals originating 

in the State, with a 95 percent confidence. 

C. Scrapie Classification, Renewal, or Reclassification of a State or Zone 

1. Each Consistent State is evaluated annually for renewal of its Consistent State status. 

See Part X.D for the protocol for completing the renewal application, VS Form 5-24. 

2. Each Consistent State undergoes a Consistent State Review at least once every 10 

years, to determine if the State’s laws, regulations, and enforcement mechanisms are 

effectively meeting the requirements of 9 CFR 79.6. 

3. Reclassification 

a. If the Administrator determines that statutory changes are needed to bring a State 

into full compliance with 9 CFR 79.6, the Administrator may grant up to a 2-year 

extension to allow the State to acquire additional authorities before removing its 

Consistent State Status. 

b. If the Administrator determines that a State is Inconsistent, APHIS will publish a 

notice in the Federal Register announcing the State’s Inconsistent status, and will 

remove the State from the list of Consistent States on the APHIS Web site. 

c. An Inconsistent State may request that the Administrator review it for 

reclassification to Consistent State status once it has demonstrated that it meets 

the requirements for Consistent State Status. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 68 

Part VI: Surveillance and Monitoring 

A. Identifying scrapie infected and source flocks is a fundamental component of the NSEP. 

APHIS has implemented a National Scrapie Surveillance Plan (NSSP) that provides a 

framework for identifying scrapie-positive animals through slaughter and non-slaughter 

surveillance. The NSSP is available on the Internet here.

18

 

Surveillance methods include: 

1. Regulatory Scrapie Slaughter Surveillance (RSSS): 

APHIS coordinates sampling and testing of mature sheep and goats at slaughter that 

have a higher than average probability of being scrapie infected. See Appendix D for 

how sampling minimums are determined and the RSSS targeted selection criteria, and 

the RSSS Handbook for detailed sample collection instructions. 

2. Non-slaughter surveillance: 

In addition to slaughter surveillance, VS collects sheep and goat samples for scrapie 

testing from a diverse set of sample streams. 

a. On-farm scrapie surveillance. Sheep and goats over 18 months of age that are 

down or disabled or that die from causes other than slaughter should be sampled 

when it is practical to do so. Sheep and goats slaughtered at home, or at other sites 

that do not qualify as RSSS sites, should be sampled if they meet the RSSS 

sampling criteria (up to 30 per flock). 

b. Suspect animals. Clinically suspicious sheep or goats (see part VII.C). 

c. Mature traceable dead or disabled sheep or goats at markets and slaughter facilities 

that do not participate in RSSS, and other off-farm sites will be sampled and tested 

when practical to do so. 

d. Live animal surveillance testing. Live-animal sampling programs may be used for 

at-risk populations on farms, at markets, or other locations in areas of high scrapie 

prevalence or in high-prevalence classes within an area or for other appropriate 

reasons. If testing will be done at Federal expense, the plan must be a part of a 

cooperative agreement or must be approved by the SGHSE. 

e. Scrapie Free Flock Certification Program (SFCP). Sheep and goat producers 

participating in the SFCP must meet animal sampling requirements. Details of these 

requirements are available in the SFCP standards, which may be obtained on the 

Internet here.

19 or from APHIS VS Sheep, Goat, Cervid and Equine Health, 4700 

River Road, Unit 43, Riverdale, MD 20737–1235. 

f. Laboratories. Diagnostic laboratories should be reminded and encouraged to 

forward appropriate tissues for scrapie testing from all mature sheep and goats 

presented for necropsy; similarly, public health laboratories should be reminded 

and encouraged to forward appropriate tissues from sheep and goats of any age 

 

18 https://www.aphis.usda.gov/animal_health/animal_diseases/scrapie/downloads/national_scrapie_surv_plan.pdf 

19 http://www.aphis.usda.gov/animal_health/animal_diseases/scrapie/
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 69 

that test negative for rabies. 

g. Animals sampled as part of a disease investigation other than natural additions in 

an infected or source flock. 

B. Monitoring 

APHIS must to be able to trace all infected and exposed animals. As a part of 

surveillance activities, ID and recordkeeping compliance must be monitored and when 

deficiencies are identified compliance action must be taken as described in Part II.E. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 70 

Part VII: Epidemiology 

A. Introduction 

The designations QQ, QR, and RR refer to the results of an official genotype test 

conducted at codon 171; AA, AV, and VV refer to the results of an official genotype test 

conducted at codon 136. For the purposes of these standards, H, K, or any amino acid 

other than R at codon 171 is considered the same as Q at codon 171; likewise T or any 

other amino acid other than A at codon 136 is considered the same as V at codon 136. 

Research indicates that QQ sheep are the most susceptible to scrapie infection, whereas 

QR sheep are much less susceptible and RR sheep are resistant. For scrapie testing 

purposes all goats are considered genetically susceptible20. Therefore, when determining 

the status of the flock, in most cases it is only necessary to test the QQ sheep and goats 

for scrapie. When the number of QQ sheep and goats in the flock is insufficient to 

conduct a reliable flock test either through live animal or necropsy testing or a 

combination thereof, or when valine-associated scrapie is suspected, the DSE may 

require testing of other genetically susceptible exposed female animals in the flock by 

IHC on necropsy samples. (Note: Very few flocks will have genetically susceptible 

exposed female animals that are not QQ sheep or goats.) 

Additional guidance on NSD statuses and codes is available on the Scrapie SharePoint

site. 

B. Reclassification Procedures: Redesignation of Suspect, High-Risk, and Exposed 

Animals and Exposed, Infected, Source, Under Investigation, and Noncompliant 

Flocks 

A reclassification investigation may be conducted or directed by the DSE, the SGHSE, or 

the National Scrapie Program Coordinator to determine whether the current designated 

status of a flock or animal may be changed or removed as described in the following 

table. 

 

20 There is evidence that genetic resistance to scrapie may exist in goats similar to sheep, with a similar level of 

certainty as genetic resistance in sheep when it was first piloted by APHIS for flock cleanup in sheep. APHIS may 

pilot the use of genetic resistance in goats to determine the designation of scrapie-exposed goats.
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 71 

Who may 

redesignate21

Animals that 

may be 

redesignated 

Conditions for redesignation

New designation 

SGHSE High-risk 

animal 

1. A determination that the 

animal meets the 

definition of a low-risk 

exposed animal. 

Low-risk 

exposed animal 

DSE High-risk 

animal 

2. Necropsy testing is done, 

including official testing 

of obex and lymph node 

or tonsil, and no PrPsc is 

detected. 

3. The animal’s high-risk 

status is waived in 

accordance with 9 CFR 

 79.7(a)(1) for animals in 

an approved Scrapie 

Control Pilot Project. 

Low-risk 

exposed animal 

DSE (except 

that the 

SGHSE must 

approve any 

that are based 

on a 

determination 

of the 

Administrator) 

High-risk 

animal 

1. The animal meets the 

definition of a 

genetically resistant or 

less susceptible exposed 

sheep and there are no 

additional risk factors 

that would preclude 

redesignation; or 

2. The animal’s high-risk 

status is waived in 

accordance with 9 CFR 

 79.7(a)(1) for animals in 

an approved Scrapie 

Control Pilot Project. 

Genetically 

resistant exposed 

sheep or 

genetically less 

susceptible 

exposed sheep 

DSE Live suspect 

animal that 

was classified 

suspect based 

on clinical 

signs of scrapie 

1. Tested with an official 

live animal scrapie test 

with no PrPsc detected 

or there were insufficient 

follicles to conduct a 

valid test; and 

2. The live animal no 

longer exhibits clinical 

signs, or it was 

No designation 

 

21 If a DSE has not been selected or is temporarily unavailable, a SGHSE, the National Scrapie Program 

Coordinator, or the Associate National Scrapie Program Coordinator may perform any of the duties assigned to the 

DSE. If a SGHSE has not been selected or is temporarily unavailable, another SGHSE, the National Scrapie 

Program Coordinator, or the Associate National Scrapie Program Coordinator may perform any of the duties 

assigned to the SGHSE. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 72 

determined that the signs 

were not caused by 

scrapie. 

SGHSE Live suspect 

animal 

classified 

suspect based 

on an 

unofficial live 

animal test 

1. Tested with an official 

live animal scrapie test 

with no PrPsc detected; 

and 

2. The live animal did not 

or no longer exhibits 

clinical signs, or it was 

determined that the signs 

were not caused by 

scrapie. 

No designation 

SGHSE Dead suspect 

animal 

The animal was 

unavailable for testing 

and a reclassification 

investigation showed the 

animal was not likely to 

have been infected. 

No designation 

DSE Dead suspect 

animal 

No PrPsc detected results 

from necropsy testing 

which included official 

testing of obex and 

lymph node or tonsil. 

No designation 

DSE Exposed flock 

(including 

those that are 

also a 

noncompliant 

flock) or flock 

under 

investigation 

1. The flock has 

successfully completed a 

PEMMP and when 

required a flock plan 

following the exposure 

and all high-risk animals 

have been removed; or 

2. A flock reclassification 

investigation shows the 

flock is not likely to be 

infected and all high-risk 

animals have been 

removed.22

No designation 

DSE Exposed flock 

or flock under 

investigation 

A flock reclassification 

investigation shows the 

flock to be infected or 

source. 

Infected or 

source flock 

 

22 However, the DSE shall also designate the flock as a noncompliant flock if the owner does any of the following: 

Fails to make his or her records available when requested; fails to make animals available for testing within 60 days 

of notification, within 60 days of becoming test eligible, or as mutually agreed by the DSE and the owner; or fails to 

submit required postmortem samples. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 73 

DSE or 

SGHSE 

Exposed flock 

or flock under 

investigation 

A flock reclassification 

investigation could not be 

conducted because the 

owner did not provide the 

necessary records or did not 

make the selected animals 

available for testing within 

60 days of becoming test 

eligible. 

Noncompliant 

and exposed 

flock 

SGHSE Infected flock 

or source flock 

or a flock 

pending 

designation as 

a source or 

infected flock 

The SGHSE for the States 

involved or the National 

Scrapie Program 

Coordinator may authorize 

a DSE to conduct a 

classification or 

reclassification 

investigation of a source or 

infected flock or a flock 

pending designation as a 

source or infected flock. If 

the reclassification 

investigation reveals, based 

on epidemiology or testing23

in the flock, that the flock is 

not an infected or source 

flock, it may be 

redesignated or not 

designated. 

No designation 

unless female 

genetically 

susceptible 

exposed animals 

have been 

retained, in 

which case the 

flock is an 

exposed flock. 

DSE Noncompliant 

flock 

The flock has complied with 

any pending required testing 

or no longer meets the 

definition of a noncompliant 

flock. 

Former flock 

designation, or 

new flock 

designation if 

indicated by test 

results. 

DSE Exposed 

animal, 

exposed flock, 

or infected 

flock 

An epidemiological 

investigation determines the 

exposure was limited to a 

scrapie-positive male 

animal not born in the flock, 

No designation 

 

23 The DSE will select all exposed sheep for scrapie susceptibility genotyping. All genetically susceptible exposed 

animals will be tested for scrapie unless a 95 percent confidence of detecting scrapie at a prevalence of 1 percent can 

be achieved by testing fewer animals. In this situation, the DSE will preferentially select those animals at greatest 

risk of being scrapie infected. If there are insufficient genetically susceptible exposed animals to provide this level 

of confidence with live animal testing, those animals that cannot be tested using a live animal test or that do not give 

a valid result will be selected for necropsy testing. If 95 percent confidence at a prevalence of 1 percent cannot be 

achieved in this manner, the DSE may require necropsy testing of all genetically susceptible exposed animals. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 74 

and the owner has adequate 

records and animal 

identification to show that 

the scrapie-positive male 

animal was acquired from 

outside the flock. 

More detailed instructions on conducting classification/reclassification investigations and 

designating and redesignating animals and flocks are provided in the following sections. 

C. Procedures for Investigating a Report of a Clinically Suspicious Animal 

1. Accredited veterinarians are required to immediately report scrapie suspects to the 

AVIC and SAHO per 9 CFR 161.4(f). 

2. APHIS and State representatives will notify each other of a report of a clinically 

suspicious animal. 

3. If the flock does not already have an assigned premises and flock number, it will be 

assigned a number in the NSD. A “Flock Under Investigation (Sheep)” or “Flock 

Under Investigation (Goats)” program will be opened with a relevant status (reason 

for the investigation). 

4. A VMO will contact the flock owner. The suspect animal and, when determined to be 

appropriate by the DSE with the concurrence of the SAHO, the flock, will be placed 

under a hold order or other appropriate restrictions until the animals’ status is 

determined. 

5. The flock owner will be provided with information about scrapie. 

6. A premises visit will be scheduled as soon as possible but within 7 days of initial 

notification. The purpose of the visit is to examine the suspect animal and conduct an 

investigation. 

7. The owner will be advised not to remove or dispose of the suspect animal (or other 

animals that may display evidence of disease) and to notify the VMO immediately if 

its condition worsens or it dies. 

8. If on examining the animal the VMO determines that clinical signs are compatible 

with scrapie, euthanasia and necropsy will be arranged with the owner’s consent. The 

animal may be purchased for diagnostic purposes if funds are available. If the DSE 

determines that the clinical signs and history make scrapie a likely rather than 

possible diagnosis and the SAHO concurs, the State will maintain movement 

restrictions on potentially exposed susceptible animals in the flock until the animal’s 

status has been determined. 

9. Fresh and formalin-fixed tissues from clinical suspects should be submitted to NVSL for 

testing in accordance with the guidance provided on the Scrapie SharePoint site. 

10. If the owner declines euthanasia of the suspect animal, the VMO will require the 

animal to be held on the premises for observation; except that, the VMO may permit 

the animal to be returned to and held at the flock of origin if the animal is designated 

a suspect animal while off the flock premises. The owner will be advised to isolate 

the suspect animal from other animals in an area that can be cleaned and disinfected, 

and to notify the VMO immediately if its condition worsens or it dies. If the animal 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 75 

dies, it must be necropsied, and tissues must be submitted for testing at NVSL. 

Movement restrictions will be maintained on the animal until the animal’s status has 

been determined. If the DSE determines that the clinical signs and history make 

scrapie a likely rather than possible diagnosis and the SAHO concurs, movement 

restrictions will also be maintained on potentially exposed susceptible animals in the 

flock until the animal’s status has been determined. Failure by the owner to make the 

animal and, if the animal dies, the carcass available for testing in a condition in which 

it can be tested will result in the flock being designated noncompliant or placed under 

a PEMMP. 

11. Suspect sheep and goats not euthanized will be live animal tested and sheep 

genotyped at codons 171 and 136 with the owner’s consent. (Note: If the owner 

refuses to test, the flock will be designated noncompliant.) 

12. Written instructions will be given to the owner regarding the restrictions and contact 

information will be provided for use if the animal’s condition worsens or it dies. 

Prompt reporting by the owner is required to ensure that appropriate samples can be 

collected for diagnostic testing. The owner must be advised, in writing, that flock 

status will be jeopardized if he or she fails to promptly request a necropsy at the 

animal’s death and maintain the head chilled such that diagnostic specimens can be 

obtained, or if he or she moves the animal without a permit. 

13. The animal will be inspected at a minimum of every 4 weeks until scrapie is 

confirmed or ruled out and to monitor compliance with movement restrictions. 

Severely affected animals will be observed more frequently. 

14. If the DSE determines the animal does not have scrapie, movement restrictions will 

be lifted and the investigation status will be closed in the NSD. 

15. An individual animal record and restriction will be created in the NSD; if scrapie or 

genetic testing is done, a test submission must be completed in VSLS. (Additional 

data entry and tissue collection instructions are available on the Scrapie SharePoint

site.) 

16. Clinically suspect animals at slaughter facilities must be condemned in accordance with 

FSIS regulations and FSIS must report them to the AVIC so samples can be collected 

for diagnosis and the carcass can be removed from the food chain. 

D. Procedures for Investigating a Report of a Live Test-Positive Animal

1. APHIS and SAHOs will be notified by the veterinarian or laboratory that conducted 

the test; the first notified will notify his or her counterpart. 

2. If the flock does not already have an assigned premises and flock number, it will be 

assigned a number in the NSD. A program record, with program “Scrapie – Flock 

Under Investigation (sheep) or (goat) as appropriate, will be created. (See the Scrapie 

SharePoint site for data entry instructions.) 

3. If the test was an official program-approved test, the flock will be handled as in part 

VII.E of this document. 

4. If the test was an unofficial test, the animal will be classified as suspect in accordance 

with 9 CFR 79. 

a. If the animal is exhibiting clinical signs, it should be handled as in part VII.C. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 76 

b. The animal will be live animal tested and, if it is a sheep, genotyped at codons 

171 and 136 with the owner’s consent. (Note: If the owner refuses to test, the 

flock will be designated noncompliant and all genetically susceptible female 

animals restricted to movement for slaughter only.) 

c. The suspect designation of an animal may be removed by the DSE if: 

1) The animal is not showing clinical signs of scrapie, it is over 18 months of 

age, and it is negative on an official program-approved test; or 

2) The animal is not showing clinical signs of scrapie and an epidemiological 

investigation shows the animal is not likely to be infected and an official live 

animal test cannot be done due to lack of sufficient tissue. (Note: If the 

unofficial test has a reasonable scientific basis, such as IHC on rectal or third 

eyelid biopsy, lymph node or tonsil, at a laboratory that has not been 

approved, the animal should not be redesignated unless prion protein scrapie 

(PrPsc) cannot be detected in any tissue at necropsy or unless NVSL was able 

to run a confirmatory test on the tissue used for the live animal test with not 

detected results. Restrictions should be placed on the flock pending the results 

of the necropsy.) 

d. After all factors are weighed, if there is significant concern that the animal may be 

at risk of having scrapie, the animal will either be purchased for diagnostic 

reasons and necropsied or held for observation. 

5. An individual animal record and restriction will be created in the NSD. If the animal 

is necropsied or live animal tested, a test submission will be created in VSLS by the 

collector or Federal or State data entry personnel. (See the Scrapie SharePoint site for 

additional data entry and necropsy tissue collection instructions.) 

6. The DSE will submit a summary report to the SGHSE of suspect animals investigated 

each month by the 15th of the following month or as instructed by the SGHSE as part 

of the Monthly Epidemiology and Compliance Report. The report will include the 

number of suspects investigated and the number of infected animals found. 

E. Procedures for Conducting an Epidemiological Investigation, Managing Flocks, and 

Reporting Results Following Receipt of NVSL Confirmation of a Scrapie-Positive 

Animal Either Through Necropsy Samples or a Live Animal Test 

1. Responsibilities of NVSL: 

a. Notify the AVIC, the SGHSE for the States involved, and the National Scrapie 

Program Coordinator that a tissue submitted for scrapie testing was positive by an 

official scrapie test. 

b. Conduct genotyping at codons 112, 136, 141, 154, and 171 for sheep and codons 

146, 211, 222 for goats and report results to the AD, the SGHSE for the States 

involved, and the National Scrapie Program Coordinator. 

c. Conduct identity testing for all slaughter samples submitted with eartags and for 

on-farm samples when the result may implicate another flock. 

2. Responsibilities of the AVIC/VS Area Office: 

a. Keep State officials informed. 

b. Ensure that the deadlines listed in this section and in part V.B are met. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 77 

c. Ensure that a field VMO is assigned to the investigation. 

d. Request approval for indemnity from the SGHSE for the State involved. 

e. Ensure that the NSD is updated with accurate flock status, restrictions, event, and 

animal data and that test submissions are submitted through VSLS (see part II.N, 

NSD) and that all traces are entered into EMRS. 

f. Provide the SGHSE with a list of traces and provide updates as needed during the 

investigation. 

g. Provide trace out information to other VS Area Offices as soon as possible but no 

later than 45 days after determination that an out-of-area trace exists. The 

notification should include, when known: 

1) Information about the positive animal or animals, including date of birth, sex, 

date of death, date of diagnosis, genotype at codons 171 and 136 for sheep and 

146 and 222 for goats or that the genotype couldn’t be determined, the flock 

of origin and date of entry into the flock if purchased, and whether the animal 

or animals was or were born on or lambed on the premises where the exposed 

animal resided and the date of each lambing; 

2) Information about the flock, including the prevalence of scrapie in the flock, 

the genotypes affected, the genotype of the animal being traced, the 

prevalence of scrapie in the birth cohort of the animal being traced, date of 

birth of all positive animals in the flock, and whether the DSE determined that 

some or all QR sheep should be removed or restricted, which ones, and why; 

and 

3) Information about the exposed animal being traced, including identifying 

marks or numbers, the name and address of the person to whom it was sold or 

otherwise disposed, date of birth, breed, sex, genotype at codons 171 and 136 

for sheep and 146 and 222 for goats, the flock of origin and date of entry into 

the flock if purchased, date the animal left the flock, and whether the animal 

was a part of any distinct group that would affect its exposure risk, such as 

offspring of a female positive animal, twin of a positive, or maintained in a 

separate group. 

4) If additional information is obtained after the trace is initiated, it should be 

forwarded to the AVIC in the receiving State. Once notified, the AVIC is 

responsible for the steps listed in VII.F. 

Note: the SGHSE must be copied on all trace out information sent to other VS 

Area Offices. 

h. Assign additional field VMOs if needed to investigate within-area trace outs. 

i. Request records from breed registries. 

j. Officially notify the owner of the flock under investigation of infected or source 

status designation as required by 9 CFR part 79. 

k. If the positive animal was not born into the flock and was diagnosed as scrapie 

positive at an age of 72 months or less, an investigation will be initiated to 

determine the source flock. 

1) If the flock of birth is in the AVIC’s area of responsibility, a pending 

designation status will be opened for the birth flock, and an investigation will 

be initiated. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 78 

2) If the birth flock is out of the AVIC’s area of responsibility, notification must 

be made to the AVIC and the SGHSE for the birth flock’s State as soon as 

possible, but within 45 days. The VS Area Office for the receiving State will 

notify the SAHO, and initiate data entry and the investigation of the birth 

flock. The receiving VS Area Office will notify the SGHSE and the VS Area 

Office for the sending State of the outcome of the investigation. 

3) Based on the epidemiological investigation (including testing in the infected 

flock) the DSE, with concurrence of the AVIC, SAHO, and the SGHSE and 

National Scrapie Program Coordinator, may decide to conduct testing in the 

flock of birth to determine if it is a source flock. It is appropriate to consider 

the following in determining whether to conduct testing in the positive 

animal’s flock of birth to determine if it is the source flock: 

a) The age of the animal at the time of diagnosis; 

b) The age of the animal when it left the birth flock; 

c) The scrapie history of other flocks in which it resided; 

d) The duration and timing of its residence; and 

e) The genotype of the positive animal (this factor should always be 

considered if the positive sheep traced back had valine at codon 136 and 

had been in the other flock for at least 12 months). 

4) If the flock meets the definition of a source flock it will be designated a source 

flock in the NSD. 

l. If the positive animal is a female over 12 months of age that has not resided in the 

flock for its entire adult life, an investigation must be conducted to determine if it 

has lambed in any other flock. If such a flock is identified, that flock must be 

designated infected and handled as such. Notification of AVICs and the SGHSE 

of out-of-area potentially infected flocks will be handled the same as out-of-area 

potential birth flocks described above. Flocks where a positive female animal over 

12 months of age resided, where there is reason to believe she may not have 

lambed but insufficient evidence to show that she did not lamb, should be tested 

as required for flocks pending designation as an infected flock. 

m. If the flock is found not to be in compliance with the flock plan or PEMMP, 

including completion of all actions required by the flock plan that are under the 

control of the flock owner, within 60 days, the infected or source status will be 

reopened and a noncompliant status opened. 

3. Responsibilities of the SAHO: 

a. Issue and enforce a hold order for all sexually intact sheep and goats on the 

premises, and when appropriate, for all sheep and goats owned by the owner of 

the flock or premises or both until the owner has signed and is in compliance with 

a flock plan. Once an owner is in compliance with a flock plan, the SAHO may 

modify the order to include only those sheep or goats required to be restricted or 

destroyed under the flock plan. 

b. If a flock is found not to be in compliance with the flock plan or PEMMP, issue 

and enforce a hold order for all sheep and goats that meet the definition of highrisk animals. 

c. Ensure the deadlines listed in this section and in part V.B are met. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 79 

d. Other responsibilities as mutually agreed by the State and APHIS or as provided 

for in an MOU or cooperative agreement. 

4. Responsibilities of the field VMO: 

a. The VMO will contact the owner and schedule a visit within 7 days of receiving 

the NVSL report. Before the initial visit the VMO should: 

1) Review the flock cleanup plans in part VIII and the flock plan and PEMMP 

templates so he or she can advise the producer of the available options. The 

species and genotype of the positive animal and the epidemiology of the flock 

will determine the flock plans that may be offered to the producer. (Note: In 

nearly all cases, a standard genetic-based flock cleanup plan will be the best 

option for the producer to maintain a viable business.) 

2) Verify that indemnity funds are available. 

3) Review requirements and procedures for approval of plans with the DSE. 

b. During the initial visit, the VMO will complete items c through f 6). If this is not 

possible, the reasons for the delay must be reported to the DSE and a timeline for 

completing the tasks must be provided to and approved by the DSE. 

c. Confirm the identity of the positive animal. 

d. Inform the owner about the results of the diagnostic tests and about his or her 

responsibilities under the program. 

e. Provide the owner information about scrapie and its control. 

f. Determine if the flock is an infected or source flock. If the flock is determined to 

be an infected or source flock: 

1) Work with the State to make sure a hold order is issued for all sexually intact 

sheep and goats and sheep and goat embryos on the premises and, when 

appropriate, for all sheep and goats (including embryos) owned by the owner 

of the flock or premises, or both. 

2) Inventory all sheep and goats and sheep and goat embryos on the premises 

and apply two official eartags to the animals if they do not already have 

official ID (only one official ID may be used if the animal has another form of 

ID unique within the flock). The inventory will list all identification present 

on the animal, the sex, age, and the breed or, if breed is unknown, the color 

and any other identifying marks (the inventory should be documented in the 

NSD with an activity record and individual animal records created). 

3) If indemnity funds are available, provide a copy of the indemnity spreadsheet 

to the owner. 

4) Advise the producer of the available cleanup plan options. 

5) Confirm the status with the DSE and enter or report the information to the VS 

Area Office for entry into the NSD. If the status cannot be immediately 

determined, a Flock Under Investigation program should be opened in SCS 

SCR. 

6) Collect the additional information needed to complete the epidemiological 

investigation report (see epidemiological report described in part X). 

7) Prepare a flock cleanup plan and PEMMP using one of the standard templates 

available on the Scrapie SharePoint site, and have the DSE approve the plans. 

Once the DSE has approved the plans, the VMO will review them with the 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 80 

producer and have the producer sign them. If the producer has owned any 

registered sheep or goats, he or she must also sign a record release request for 

each registry. 

8) Once the flock plan and PEMMP are signed, follow the steps outlined in part 

VIII for the plan selected and have a flock plan and PEMMP program and 

status entered in NSD. 

9) Determine whether each animal is a suspect, high-risk, scrapie positive, or 

low-risk exposed animal or a genetically susceptible, genetically less 

susceptible, or resistant exposed sheep. Sheep no longer in the flock that 

cannot be further designated due to insufficient information will be treated as 

genetically susceptible exposed animals until they are genotyped. 

10) Prepare an indemnity request. 

11) In consultation with the DSE, determine the likely date on which the premises 

was infected. In the case of infected flocks, it is the first date on which the 

infected animal could have lambed in the flock. In source flocks, it is the 

beginning of the lambing season 2 years before the positive animal was born. 

If the age of the positive cannot be determined from the records or estimated 

from examination of the teeth, the positive animal will be assumed to have 

been 48 months of age on the date samples were collected for scrapie testing. 

12) VS Form 5–19D, or an electronic equivalent, will be completed, and 

additional information, as listed in part X, will be collected for the 

epidemiological investigation report. Record all sales of animals after the date 

of infection including, when known, the tag numbers, brands, tattoos, and any 

other form of identification or identifying marks or characteristics including 

age, sex, breed, color, registration information, and the name and address of 

the person who acquired the animal. Document all steps. Provide this 

documentation, copies of all documents (either the completed epidemiological 

investigation report or the information needed to complete the 

epidemiological investigation report, as directed by the DSE), the signed 

original flock plan, the signed PEMMP, and the requests for registration 

records to the VS Area Office with a copy to the DSE. 

g. If the flock does not meet the definition of an infected or source flock, the Flock 

Under Investigation program in the database will be closed. If the flock meets the 

definition of a source or infected flock, the investigation program will be closed, 

and an infected or source program and status and a restriction will be opened in 

the database. All documents are to be attached to the flock record in SCS SCR. 

5. Responsibilities of the DSE: 

a. Ensure that the VMO assigned to conduct an investigation understands the 

process. 

b. Ensure that the deadlines listed in this section and in part V.B are met. 

c. Review and approve the following: 

1) The status of flocks (Note: A flock’s status must be designated within 15 days 

of notification that the flock contains or contained a scrapie-positive animal); 

2) Flock plans; 

3) PEMMPs; 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 81 

4) Designation and redesignation of animals; and 

5) Release of exposed, infected, or source flock programs with the appropriate 

status. 

d. If the DSE believes that genetically less susceptible ewes should be restricted, the 

DSE must consult with the SAHO, the AVIC, and the SGHSE before taking 

action. With their concurrence, the DSE may require the restriction of some or all 

of the exposed QR ewes in the flock. The SGHSE must approve removal with 

indemnity. Following such a discussion, the DSE will prepare a memorandum 

giving the history of the flock, the decision, and the basis of the decision. 

Following review by all parties, the memorandum will be distributed to all States 

receiving traceout animals from the flock and will be posted on the Scrapie 

SharePoint site. (Note: If the codon 136 genotype of the positive animals cannot 

be determined, AVQR sheep may be removed at the discretion of the DSE with 

the owner’s concurrence.) 

e. Animals that meet the definition of high-risk or exposed animals and that also 

meet the definition of a low-risk exposed animal may be redesignated low-risk 

exposed animals by the DSE; or, in cases requiring a determination by the 

Administrator, the SGHSE will make the redesignation decision. (See definition 

of low-risk exposed animal.) 

f. If the DSE determines that additional testing is needed to designate the flock, the 

Flock Under Investigation program will remain open until testing is completed, 

and the flock will be tested as described in part VII.G. (Note: The DSE may use 

this option only in cases where the SGHSE concurs that the scrapie exposure was 

minor or could not be confirmed.) 

g. Review the NSD record to ensure that flock programs and statuses were 

accurately entered and released and animal designations and information were 

correctly entered. 

h. Prepare or review indemnity requests for transmittal through the AVIC to the 

SGHSE. 

i. Prepare or approve the epidemiological investigation report and summary for each 

infected, source, and exposed flock (see part X) and transmit them to the SGHSE. 

6. Responsibilities of SGHSE for infected and source flocks: 

a. Monitor States for compliance with Consistent State status requirements and take 

action to correct shortfalls. 

b. Ensure that all DSEs in their area of responsibility are properly trained. 

c. Review all epidemiological investigations for compliance with policy and 

maintain an electronic copy of the reports on the Scrapie SharePoint site for the 

national program staff. 

d. Review and approve indemnity requests. 

e. Identify animals to be moved to research facilities or sampled for developmental 

work or research. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 82 

F. Procedures for Investigating and Monitoring a Flock that Received a High-Risk 

Animal

(See flowchart in Figure 1.) 

1. The receiving VS Area Office will create a premises and flock record in the NSD if 

the flock has not already been entered. A “Flock Under Investigation (Sheep)” or 

“Flock Under Investigation (Goats)” Program must be opened with a relevant status 

(reason for the investigation). Trace forward investigations must be linked to the 

index case epidemiological case number using Activities. Any out-of-state traces and 

the outcome of the trace investigation will be entered in EMRS or other system 

determined by APHIS. 

 

2. APHIS and SAHOs will notify their State or Federal counterpart. 

3. The flock owner will be contacted by a State or Federal VMO. 

a. The high-risk animals, any other animals required for testing as part of the 

investigation, and, when the SAHO determines the circumstances warrant it, the 

flock will be restricted by an authorized representative of the State. Animals may 

be released if all required testing has been completed and the results indicate the 

animals are not high-risk or scrapie-positive animals and that the flock is unlikely 

to infected as determined by the DSE or SGHSE (see Table in VII.B for who can 

re-designate animals). 

b. The VMO will give the owner information about scrapie. He or she will schedule 

a premises visit to examine the animal or animals and conduct an inventory and 

investigation as soon as possible but within 7 days of notification to the VS Area 

Office. 

c. The owner will be advised to report immediately if the animal dies or is in danger 

of dying. 

4. If the high-risk animal or animals traced to the flock can be positively identified and 

are present in the flock, they will be officially identified and: 

a. High-risk sheep: 

1) Genotyped at codon 171 if exposure is not linked to an AV or VV positive 

sheep; 

2) Genotyped at both codon 171 and codon 136 if exposure is linked to an AV 

or VV positive sheep (see part II.P for genotyping procedures); or 

3) When the owner requests it, ewes may be indemnified and tested for scrapie at 

necropsy without genotyping to minimize the risk of exposing the flock to 

scrapie if there is a risk the exposed ewe will lamb before genotyping and 

disposal can be completed. 

b. High-risk goats should be indemnified and tested at necropsy. 

c. High-risk animals due to lamb should be isolated in an area that can be readily 

cleaned and disinfected until genotyping and necropsy and scrapie testing of ewes 

determined to be genetically susceptible animals is completed. Failure to isolate 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 83 

such animals may be grounds for denial of indemnity for any animals later 

designated high-risk as a result. 

5. Animals that meet the definition of genetically resistant exposed sheep, genetically 

less-susceptible exposed sheep, genetically susceptible exposed animals, or low-risk 

exposed sheep will be designated as such and may move only as allowed in part II.N

of this document. 

6. The presence of an exposed male animal or exposed wether in a flock will not affect 

the status of the flock. A PEMMP is not required for these flocks if the only exposed 

animals they received were male. Once this is verified, the investigation program is 

closed with the appropriate status. If the animal is a sexually intact genetically 

susceptible exposed male animal, it will be restricted to movement by permit only for 

destruction or research or, when requested by the owner, indemnified and destroyed. 

If retained, sexually intact genetically susceptible exposed male animals must be 

entered as restricted animals in CSC SCR and must be accounted for until they die 

and are tested. 

7. The Flock Under Investigation program can be closed and no PEMMP is required if: 

a. All female exposed animals traced to the flock can be positively identified and are 

present in the flock; and 

b. All exposed female sheep that cannot be redesignated as genetically resistant 

exposed sheep or genetically less susceptible exposed sheep, all female offspring 

of a scrapie-positive female animal, and all high-risk goats are tested by IHC at 

necropsy and found negative on brain and lymphoid tissue. 

8. A PEMMP is required for flocks that received high-risk female animals that could not 

be tested (missing or not identifiable) or that retain high-risk animals. 

9. The Flock Under Investigation program will be closed, an exposed flock program will 

be opened, and a retained susceptible animal PEMMP will be done if a high-risk 

animal is retained. 

a. The PEMMP will require: 

1) Permanent restriction of the high-risk animals. 

2) The immediate testing of all the genetically susceptible exposed female 

animals over 14 months of age, or when they reach 14 months of age, using a 

live animal test for scrapie. When the animal subsequently dies or is culled, it 

must be tested using brain and lymph node. 

3) All animals live animal tested must be identified with two official 

identification devices or methods before being tested. All retained high-risk 

animals must be identified with an official tattoo, RFID implant, or other 

official permanent identification to decrease the risk of their identity being 

lost over time. 

4) Animals that have an invalid test result such as insufficient follicles will be 

retested using a live animal test or necropsied and tested. 

5) Any animals that die at over 14 months of age or that have lambed will be 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 84 

necropsied and tested. 

6) A negative live animal test before sale of any genetically susceptible female 

animal born in the same or subsequent lambing season that the high-risk 

animal lambed unless sent direct to slaughter. The test must be conducted 

after the animal is over 14 months of age. 

7) High-risk ewes will only be bred to rams that are RR at codon 171. 

b. These flocks will remain an exposed flock until the PEMMP is completed. 

c. The PEMMP will remain in force until all high-risk animals have been tested for 

scrapie on brain and lymph node. 

d. PEMMP formats are available on the Scrapie SharePoint site. 

e. Failure to test as required will result in the flock being designated noncompliant 

with all genetically susceptible female animals restricted to movement to 

slaughter under permit only. 

10. If high-risk female24 animals that may have lambed in the flock (“may have lambed” 

refers to any ewe/doe old enough to lamb, unless it can be documented that she did 

not lamb) are no longer available (sold, died, cannot be positively identified, etc.): 

a. Their progeny and any birth cohorts of their progeny remaining in the flock, and 

when appropriate, subsequent lambing cohorts, will be genotyped if they are 

sheep. In cases where there are insufficient lambing cohorts to test, the SGHSE 

may approve testing of ewes or does present during the lambing seasons in which 

the missing ewes or does lambed. In cases where the high-risk animal is believed 

to be present but could be one of several animals, the SGHSE may approve 

genotype testing of these sheep, or if goats live animal testing or necropsy. 

b. All goats and the QQ sheep in these groups, and, when appropriate, other 

susceptible animals over 14 months of age, will be tested by a live animal test or 

by necropsy testing of obex and lymph node. Additionally, all animals that are 

live animal tested must be identified with two official identification devices or 

methods to decrease the risk of their identity being lost over time. After reviewing 

the results of the initial test, the DSE will determine whether additional testing is 

required and the type of PEMMP that will be used. The decision will be based on 

the number and percent of valid tests, the infection rate and genotype distribution 

in the source flock, the genotype of the positive sheep, if known, and the number 

of high-risk animals missing. The flock will remain in Flock Under Investigation 

program status until all animals required for testing have been tested (see Figure 

1). Once testing is completed, the Flock Under Investigation program will be 

closed. 

Note: Necropsy testing with indemnity must be approved by the SGHSE; see 14

for approval criteria. 

c. All animals required for testing will be restricted until testing is completed. 

 

24 If based on an epidemiological investigation the risk is determined to be very low, and with the concurrence of the 

SGHSE, AD, and the SAHO, the DSE may determine that a flock with a missing high-risk ewe does not require 

further flock testing. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 85 

Figure 1—Trace High-Risk Female Animals 

Animal is in the flock and ID is 

adequate to document*

No—Indemnify and 

necropsy 

Can you verify that the animal 

did not lamb? 

Does the owner want to retain 

the animal? 

Yes—ID and for sheep 

genotype 

Positive 

Live animal test 

Genetically lesssusceptible exposed 

ewe 

If necropsy declined 

1ive animal test when 

>14 months 

Retained Animal PEMMP—required, see part 

VII.F.9 for PEMMP requirements 

All high-risk animals 

tested at necropsy 

No Yes 

Negative 

Positive 

Close Flock Under 

Investigation program 

(No PEMMP) 

Infected flock 

Positive 

Negative 

Release exposed flock status and 

PEMMP 

Genetically susceptible 

exposed animal** (strongly 

recommend indemnity and 

necropsy) 

Negative (if insufficient 

retest) 

* If ID is not adequate, use animal 

missing flowchart. 

** Apply official yellow metal tag 

Genetically resistant 

exposed ewe 

Close Flock Under 

Investigation program 

(PEMMP only if animal 

restricted) 

Can you verify that 

the animal did not 

lamb in and was not 

born in flock? 

Yes No 

Close Flock Under 

Investigation program (No 

PEMMP) 

Close Flock Under 

Investigation 

program (if animal is 

positive, identify all 

the low-risk exposed 

animals and 

complete a basic 

PEMMP) 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 86 

 

High-risk female is 

missing 

Can you verify through 

records that the animal did 

not lamb? 

Close Flock Under 

Investigation program 

No 

Officially ID with 2 eartags animals born in the 

flock in the same or subsequent lambing 

season(s) that the missing high-risk animal 

lambed* and for sheep genotype. (Note: if the 

animal already has an ID that is unique in the 

flock, one official tag may be used.)

Test at slaughter or submit all QQ 

for necropsy. Note: See Part 

VII.F.12 for limitations on 

indemnity. 

Negative 

Live animal test all such QQ sheep and goats when 

they reach 14 months 

Yes 

Close Flock Under 

Investigation program 

(Basic PEMMP) 

Positive 

Infected flock 

Negative or 

insufficient 

Basic PEMMP-including a list of 

animals required for testing. For all QQ 

ewes and goats identified for testing, 

live animal test at 14 months of age, 

negative live animal test before sale, 

and require necropsy test of all animals 

required for testing that are culled or 

found dead at over 14 months or after 

they have lambed. 

Retest or submit animals with 

insufficient follicles for necropsy. 

Hold all too young to test for 

testing or send to slaughter 

Negative 

All tests negative for 5 

years 

All QQs identified 

for test are negative 

Close PEMMP and Close Flock 

Under Investigation program 

Close Flock Under 

Investigation program. 

(Basic PEMMP) 

DSE: Need more 

testing? 

Yes 

No 

Close Flock Under 

Investigation program 

(Basic PEMMP) 

*These sheep/goats may be limited to 

contemporary lambing groups, if large enough (at 

least 30 susceptible animals), and to animals under 

60 months. If no contemporary or subsequent 

groups are available, ewes or does present when 

the high-risk animal lambed may be tested with the 

SGHSE’s approval. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 87 

11. If testing is done, a test submission will be created in VSLS. Individual records will 

be made in the NSD for each tested, genotyped, exposed, and high-risk animal. The 

exposed and high-risk animals and any other animals required for testing must be 

restricted until the testing is completed and the flock and individual animal statuses 

are determined. All animals determined to be high-risk or exposed must be 

maintained on the premises unless redesignated or moved in accordance with 

9 CFR part 79. 

12. The following animals, which are required to be tested for scrapie, may be 

indemnified and tested at necropsy when funds are available and with the concurrence 

of the owner and the SGHSE: 

a. Sheep with insufficient follicles to test (Note: in the case of high-value sheep, two 

attempts should be made to collect biopsies.). 

b. Sheep designated for testing in cases in which the sheep are under 1 year of age 

(too young to test by live animal test) and the owner does not want to retain the 

sheep until they are old enough to test. Tissues collected on these animals must 

include Peyer’s patches in addition to the standard tissue set. 

c. Sheep when it is cost effective due to their low value. 

d. All genetically susceptible female animals in a highly exposed flock when 

recommended by the DSE and approved by the AVIC, the SGHSE or National 

Scrapie Program Coordinator, and the SAHO; 

e. Any suspect animal; and 

f. Goats. 

Note: Indemnity is not available for animals subsequently required to be tested 

because the owner elected to retain a genetically susceptible exposed animal. 

13. Owners of flocks under investigation or exposed flocks who do not make animals 

available for testing or do not comply with a PEMMP will have their flocks 

designated as noncompliant flocks. 

14. The DSE must provide a monthly report to the SGHSE detailing the status of, and 

final disposition of, all high-risk animals traced to the State as part of the monthly 

Epidemiology and Compliance Report. The SGHSE will make these reports available 

to the national program scrapie staff through the Scrapie SharePoint site. 

Note: All NSD flock program and status information should be entered within 1 week 

and individual animal information within 3 weeks of the DSE’s designation. 

G. Testing a Flock Pending Designation as a Source or Infected Flock to Determine 

Whether the Flock is Infected 

1. Flocks are typically designated as source or infected flocks based on meeting the 

applicable definitions. In cases where the DSE, with the concurrence of the SGHSE 

for the States involved and the National Scrapie Program Coordinator, determines 

there is significant doubt as to whether a flock that is pending designation as a source 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 88 

or infected flock is currently infected, the flock may be tested to determine whether 

the flock should be designated as a source or infected flock. Such flocks not 

designated source or infected flocks will be placed on PEMMPs. 

2. When the potential exposure to a flock was the result of a purchased positive female 

animal possibly lambing in the flock, genetically susceptible animals born after the 

positive animal might have lambed and female animals present during the lambing 

seasons in which the positive female animal resided on the premises will be tested 

first. Such female animals must be tested at least 18 months after the last possible 

lambing of the infected animal and at over 14 months of age. 

3. To detect disease at 1 percent prevalence with 95 percent confidence by IHC of the 

third eyelid or rectal mucosa or by necropsy, it is necessary to test, at a minimum, 

specific numbers of genetically susceptible animals depending on overall flock size. 

Table 2 provides the number of animals to test for various flock sizes. Sheep that are 

not of the QQ genotype may be tested only by necropsy. The number of valid 

diagnostic samples required is the same as the number of necropsies required when 

necropsy is used instead of live animal testing. Due to a 10 percent average nontestable rate when conducting the live-animal test, 10 percent more animals have been 

added to each sample size. Use rectal biopsy unless multiple samples did not yield a 

valid result.
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 89 

Table 2—Determining the Number of Animals to Test 

Number of goats* and QQ 

sheep greater than 14 

months in the flock

Number of valid results 

required** 

Estimated number of animals 

to sample using rectal biopsy 

to achieve the required 

number of valid results 

<215 All*** All 

215-300 217 237 

301-400 239 263 

401-500 256 282 

501-1,000 293 322 

* Goats may be tested by necropsy or rectal biopsy; if rectal biopsy is used, all goats should be 

tested due to lower apparent sensitivity of the test in goats. 

**If needed to achieve the required number of valid tests, retest using a live test, test additional 

animals not previously tested, or necropsy animals that have invalid live animal test results. 

*** Sensitivity = 87 percent for sheep and specificity = 100 percent are assumed for sheep. The 

confidence level in small flocks (fewer than 300) will be less than 95 percent. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 90 

Part VIII: Flock Cleanup Plans and PEMMPs 

A. Movement Restrictions on Animals in Flocks on a Flock Plan or PEMMP 

 

See part II.N of these standards and the standard APHIS flock plan formats. 

B. Requirements for Flock Plans and Post Exposure Management and Monitoring 

Plans (PEMMPs) 

1. The VMO will prepare a flock plan and PEMMP using the standard plan formats 

posted on the Scrapie SharePoint site. The species and genotype of the positive 

animal and the epidemiology of the flock will determine the types of flock plan the 

VMO may offer the producer. The PEMMP selected will be determined based on 

whether the owner retains any high-risk animals. If no high-risk animals are retained, 

use a basic PEMMP. If genetically susceptible exposed female animals are retained, 

use a retained susceptible animal Flock Plan and PEMMP. If a flock does not retain 

genetically susceptible exposed female animals but does retain other animals required 

for testing or genetically susceptible exposed male animals, use a basic PEMMP with 

an attachment listing all animals required for testing and the type of tests required. 

The attachment should also list when the test is required and contain a separate list of 

the genetically susceptible exposed restricted male animals. The list must include the 

official ID, age, sex, and breed or face color. For flocks with animals exposed only to 

Nor98-like scrapie, a flock plan is not required and the PEMMP will be limited to 

officially identifying all sexually intact animals before change of ownership or 

movement off the premises, reporting of suspect animals, and submission of mature 

animals found dead. 

2. When a flock plan requires an animal to be destroyed, the SGHSE must approve the 

indemnity and determine if the animal is needed for research or developmental 

projects. 

3. Types of flock plans: Genetics-based flock plans and whole flock depopulation flock 

plans: 

a. Genetics-Based Flock Plans – General guidelines. (See step-by-step instructions 

in 3.b for standard genetic plan.) 

1) A genetic plan is preferred for most flocks. When using a genetics-based flock 

cleanup plan, in most cases owners can retain or sell RR sheep, QR rams, and 

most QR ewes without restriction. Indemnity, if available, will be provided for 

animals removed as part of a flock plan. 

2) Genetics-based plans require removing all of the following animals: 

a) All genetically susceptible exposed female animals25; 

 

25 There is evidence that genetic resistance to scrapie may exist in goats similar to sheep, with a similar level of 

certainty as genetic resistance in sheep when it was first piloted by APHIS for flock cleanup in sheep. APHIS may 

pilot the use of genetic resistance in goats to determine the designation of scrapie-exposed goats as part of a herd 

cleanup plan.
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 91 

b) All test positive and suspect animals; and 

c) All female offspring of positive female animals (regardless of genotype, 

unless the genotype proves it could not be the offspring of the positive 

animal). 

3) Owners should be advised that exposed QQ rams and bucks are unlikely to 

transmit scrapie and exposed QR sheep are unlikely to either contract or 

transmit scrapie. However, retaining QQ rams for breeding will increase the 

risk of scrapie recurrence by increasing the genetic susceptibility of their 

offspring to any residual environmental contamination. 

4) APHIS encourages removing exposed QQ rams and bucks and strongly 

encourages removing AVQQ and VVQQ rams, due to their increased 

susceptibility, but does not require it. These animals may be removed at the 

owner’s request. Exposed QQ rams and buck goats not removed may only 

move for destruction on a permit. 

5) Animals not designated genetically susceptible exposed animals may also be 

removed when requested by the SGHSE and when agreed to by the owner to 

provide animals or tissues for study. 

6) Any animals removed may qualify for indemnity. These animals must be 

euthanized or moved to a quarantine facility for research. Slaughter may not 

be used to dispose of indemnified animals and the carcass may not be used for 

human or animal food. 

7) Confirmed genetically resistant and genetically less susceptible exposed sheep 

and low-risk exposed animals may be retained or sold without restriction after 

they have been officially identified as described in 10, and entered in the 

NSD. 

8) Flocks whose owners complete a flock plan where all genetically susceptible 

exposed female animals are removed will not be considered exposed flocks. 

9) In unusual cases where producers need to keep genetically susceptible 

exposed ewes, a genetics-based flock plan that includes live animal testing 

and genetic selection will be used. 

10) Exposed animals will be identified with an official tamper-evident/resistant 

eartag, and if a suitable secondary ID is not already in place another official 

identification device will be added to prevent loss of identity while the flock 

plan is being completed. 

a) The eartag number and the genotype will be recorded in the NSD. 

b) High-risk animals and sexually intact genetically susceptible exposed male 

animals that are not removed will also be identified with electronic 

implants, official tattoos, or another form of permanent official ID and a 

yellow metal restricted animal tag to ensure that the animal can be 

accounted for until submitted for necropsy testing. 

11) Flocks where all genetically susceptible exposed female animals are not 

removed will be designated as exposed flocks. Accordingly, until the PEMMP 

is completed, these flocks will have movement restrictions placed on these 

animals and all other genetically susceptible female animals (and in some 

cases less susceptible female animals) residing in the flock, including such 

animals born or brought into the flock. During the annual PEMMP inspection 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 92 

these animals must be accounted for and live animal tested for scrapie and the 

genotype of the rams verified by reconciliation of their official ID and the test 

charts. Flocks not in compliance with the requirements of a retained 

susceptible animal PEMMP will be placed in infected flock program with the 

appropriate status until all high-risk animals have been removed and tested. 

Note: Flocks that retain test positive, suspect animals, or genetically 

susceptible exposed female animals that do not have a “not detected” result on 

a live animal test will remain infected or source flocks until these animals are 

removed. 

12) Steps for completing a standard genetic based flock plan for source and 

infected flocks that retain only QR, HR, KR, and RR ewes and male sheep and 

male goats: 

a) Complete the flock plan and PEMMP agreements labeled “For Source and 

Infected Flocks that Retain Only QR, HR, and RR Ewes and Male Sheep 

and Male Goats” posted on the Scrapie SharePoint site. Have the 

completed form reviewed by the DSE and then have the owner sign both 

forms.

b) Request authorization to submit blood for genotyping. (See instructions in 

part II.O and on the Scrapie SharePoint site.)

c) Bleed all sexually intact sheep for genotyping and send blood to the 

authorized APHIS contract genotyping laboratory. Request codon 171 

testing on all sheep unless instructed otherwise. Do not genotype goats. 

All genotype submissions must be entered in VSLS.

d) Designate all animals in the flock as suspects, genetically susceptible 

exposed animals, genetically less susceptible exposed animals, genetically 

resistant exposed sheep, high-risk animals (high-risk includes female 

genetically susceptible exposed animals, female offspring of positive 

female animals, and suspect animals), or low-risk exposed animals. Some 

animals will have multiple designations.

e) Have the DSE review and approve the designations.

f) Provide an estimate of indemnity and disposal costs through the AVIC to 

the SGHSE for the State involved in the format provided.

g) Work with the DSE and AVIC to develop a necropsy (see necropsy 

instructions on the Scrapie SharePoint site) and disposal plan.

h) Complete an indemnity request that includes the following:

 All suspect and high-risk animals;

 When agreed to by the owner, male genetically susceptible animals; 

and

 Any other animals required to be removed by the flock plan.

Have the AVIC review and approve the request and forward it to the 

SGHSE and copy Scrapie@USDA.gov, along with a preliminary 

epidemiological investigation report as described in part X providing 

whatever information is known as of the request date.

i) Complete an indemnity form (VS Form 1–23) that includes:

 All suspect and high-risk animals; 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 93 

 Male genetically susceptible exposed animals, when agreed to by the 

owner; and

 Any other animals required to be removed by the flock plan.

The owner must complete the form and he or she, or a legal 

representative, must sign it before depopulating the animals. Animals 

moved for destruction must move on a VS Form 1-27 or State 

equivalent. 

Depopulate and necropsy indemnified animals. In most cases, all 

animals over 14 months of age should be sampled for scrapie testing as 

described in the necropsy protocol posted on the Scrapie SharePoint

site. When a large number of animals is involved and it is not practical 

to sample them all, with concurrence of the SGHSE an appropriate 

statistical sample may be taken. In addition, all test positive and 

suspect animals of any age, any high-risk QR or RR animals, female 

offspring of positive female animals, and any animals that may 

implicate another flock that are destroyed at over 14 months of age as 

evidenced by eruption of the first incisor must be sampled. The AVIC 

must review and approve VS Form 1-23, and must forward a copy to 

the SGHSE and copy Scrapie@USDA.gov. 

j) Request authorization to submit blood from the remaining sexually 

intact sheep at another contract laboratory to confirm the result at 

codon 171 and, when indicated, codon 136. Note: If female genetically 

susceptible exposed animals are retained, the retained susceptible 

animal Flock Plan and PEMMP must be used (which has additional 

requirements). High-risk animals and sexually intact genetically 

susceptible exposed male animals not removed are identified with 

EIDs, or another form of permanent official ID such as an official 

tattoo, and a yellow restricted animal metal tag. In most cases, this 

should be done at the same time the second bleeding is done.

k) Owners should be encouraged to include the use of RR rams as part of 

the PEMMP. As long as funds are available APHIS will provide 

genotyping for sire rams when this provision is a part of a PEMMP. 

PEMMPs for flocks where infection has recurred in animals born on 

the premises after a previous flock plan was completed will include the 

requirement to use only RR rams unless the breed of sheep involved 

makes this impractical.

l) Observe and document cleaning and disinfection of premises.

m) If the owner has signed the PEMMP and the previous steps have been 

completed, release infected or source flock program with an 

appropriate status.

b. Whole-Flock Depopulation Flock Plan: Whole-flock depopulation (removal of all 

sexually intact animals) may be used when recommended by the DSE and with 

the concurrence of the owner, AVIC, SAHO, and the SGHSE or National Scrapie 

Program Coordinator. Such concurrence will be based on the availability of funds 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 94 

and whether a particular depopulation will enhance scrapie eradication. The DSE 

should recommend whole-flock depopulation for further consideration for: 

1) Flocks for which the cost of depopulation is less than the cost of conducting 

another type of flock plan and PEMMP; 

2) Any flock in which an RR sheep is determined to be infected with classical 

scrapie; 

3) Goat herds; 

4) Flocks where infection has recurred in animals born on the premises after a 

flock plan was completed and where the owner agrees not to restock with 

sheep or goats on the premises for at least 5 years; and 

5) When requested by the owner, when the owner agrees not to restock with 

sheep or goats on the premises for at least 5 years. 

4. The DSE must review and approve the flock plan and the PEMMP. 

a. The PEMMP may include enrollment in the SFCP with the subsequent 

requirements for exposed flocks. The flock plan, the PEMMP and, when it is a 

part of the PEMMP, the SFCP application, must be signed by the flock owner and 

a State representative and/or an APHIS official (this depends on the delegation of 

duties within the State). 

b. A flock plan program and status will be entered in the NSD. Being in a flock plan 

program means that a flock plan and PEMMP have been signed and the owner is 

in compliance with the plans. 

c. All high-risk, exposed, suspect animals, and all animals under a plan will also be 

entered in the NSD animal inventory, including the genotype of all exposed sheep 

and any other testing. 

d. If the infected animal was not born in and did not lamb in the flock, cleaning and 

disinfection can be waived. 

5. Before releasing the flock’s plan and infected or source programs26 in SCS SCR, a 

VMO must verify completion of the flock plan requirements through an inspection, 

inventory, and records review, and the PEMMP must be signed. In general the 

PEMMP should be signed at the same time as the flock plan so that the owner knows 

what he or she is agreeing to up front. On verification, some or all of the movement 

restrictions may be removed and the flock’s plan and infected or source programs in 

SCS SCR will be closed. Any remaining movement restrictions must be documented 

in the PEMMP and in SCS SCR. Restrictions are removed from animals in SCS SCR 

that are not high-risk animals, animals required for test, or genetically susceptible 

exposed intact male animals. Restrictions will remain on any high-risk animals and 

any retained sexually intact genetically susceptible male animals throughout their 

lives and on animals required for test until testing is completed. A PEMMP program 

and status will be entered. 

6. Actions required during a PEMMP inspection. 

a. Animal inspection and inventory 

1) Inspection. 

 

26 Programs in SCS SCR are equivalent to the former Animal Health and Surveillance Management statuses. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 95 

a) Inspect all animals currently in the flock for signs of scrapie. 

b) Confirm with the owner that all animals exhibiting signs of scrapie or 

found dead at over 14 months of age were reported in a timely manner to 

the State or VS Area Office (if any such animals were not reported, notify 

the DSE immediately). 

2) Inventory. 

a) Perform a head count of the mature and immature animals present in the 

flock or herd, and reconcile the count with the numbers from the previous 

year. If the head counts do not reconcile with the records of animals 

disposed of and acquired, or there is any other reason the inspector 

believes that the flock records are not being accurately maintained or that 

dead animals are not being recorded, or animals that require official ID are 

not officially identified, the inspector will do an individual animal 

inventory and ensure that the animals that require official ID are 

identified. If the inventory indicates noncompliance notify the DSE 

immediately. The inspector will attach the complete inventory to the 

inspection report noting any discrepancies with the flock or tagging 

records, animals identified during the inspection, and any evidence that 

found dead animals were not sampled. 

b) If the flock is on a PEMMP that allowed the owner to retain high risk 

animals, confirm the status of each retained high-risk animal. If any are 

missing or cannot be accounted for (e.g., died, sold, or missing without 

scrapie testing), notify the DSE immediately. 

b. Records review (see VS Form 5-19C, Scrapie PEMMP Inspection Report, for the 

information to be reviewed). 

c. Confirm that the producer has additional identification devices available for 

additions to the flock or herd. If none are available, assist the producer with 

obtaining them to ensure additions are properly identified. 

d. Complete VS Form 5-19C, Scrapie PEMMP Inspection Report, or equivalent 

State form, have the owner sign the form, and turn in the signed form to the DSE 

within 30 days of the inspection. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 96 

Part IX: Diagnostic Laboratory Approval Procedures and Test 

Interpretation 

Laboratories and diagnostic tests will be approved in accordance with 9 CFR 54.11 and 

applicable appendices of these standards.27

NVSL will do confirmatory testing on all tissues with suspect (presumptive positive) or repeat 

(inconclusive) results generated by other laboratories on regulatory and surveillance samples. 

Part X: Reports 

Reports will be made in accordance with the following:

A. Epidemiological Investigation Report 

1. Purpose of the Report: The VMO or DSE prepares the epidemiological report and the 

DSE uses it to determine which animals are designated high-risk or exposed, which 

animals will be redesignated, and which other flocks may be exposed, infected, or 

source flocks.

2. Data Source: The information required for the epidemiological report may be 

gathered using VS Forms 5-19D, 5-20, and 5-18, or the equivalent information may 

be submitted in Microsoft Word or Excel. 

3. Protocol: The report will include the information listed below.

a. Information about the owners: 

1) Name; and 

2) Address (mailing and physical address, including county, and, where 

applicable township, section, and/or GPS coordinates). 

b. Information about the positive animals, including: 

1) Date and place of birth or approximate age if date of birth is unknown; 

2) Sex, species, and breed or cross (if breed or cross is unknown, for sheep the 

face color and for goats the use ([dairy, meat or fiber)); 

3) Official identification, any other identification, and any distinguishing marks 

or features; 

4) Date of death; 

5) Genotype at codons 112, 136, 141, 154, and 171; 

6) All flocks in which the animal has resided, the dates during which the animal 

resided on each premises, and whether the animal lambed or may have lambed 

on any of the premises and the date of each lambing; and 

 

27 See Appendix A: Approval of Laboratories to Conduct Official Genotype Tests in Sheep, Appendix B: Approval 

of Laboratories to Conduct Official Diagnostic Tests for Scrapie in Sheep and Goats, and Appendix C: Program 

Approval of Diagnostic Tests for Scrapie in Sheep and Goats. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 97 

7) Results of all scrapie tests conducted and the information listed above for any 

additional positive animals. 

c. Information about the flock, including: 

1) Address (mailing and physical address, including county, and, where 

applicable township, section, and/or GPS coordinates); 

2) An inventory of sheep and goats owned at the time of the first visit and any 

animals added before completion of the flock plan (inventory will include all 

identification numbers and marks; sex; breed; flock of origin if different; date 

of acquisition; date of birth or approximate age; genotype; if done, live animal 

test results; the designation of each animal; whether the animal will be 

indemnified, otherwise disposed of, or retained; any restrictions on animals 

not to be indemnified; and whether the animal was a part of any distinct group 

that would affect its exposure risk, such as offspring of a female positive 

animal, twin of a positive, and maintained in a separate group); 

3) An inventory of animals that have left the premises since the date of 

introduction of infection to the premises as determined by the DSE, or a date 

2 years before the birth of the oldest scrapie-positive animal born in the flock 

will be used. If the actual birth date is unknown, the date of birth will be 

estimated based on examination of the teeth and any available records. If an 

age estimate cannot be made, the animal will be assumed to have been 4 years 

of age on the date samples were collected for scrapie diagnosis. The inventory 

will include all information required in 2) and the date the animal left the 

premises; the name and address of the person who acquired the animal or a 

statement that the animal died on the premises and any other information that 

would allow the animal to be traced; and whether the animal is an exposed or 

high-risk animal.; 

4) Movements of animals into the flock, including the date acquired; name and 

address of the previous owner; all ID numbers and marks; sex, breed, and 

flock of origin if different; date of acquisition; date of birth or approximate 

age; genotype and live animal test results if available; and whether the flock 

of origin has any record of scrapie infection or exposure; 

5) The animals required to be removed and the test results at necropsy will be 

added to the report when available; 

6) Whether any QR animals will be required to be removed or restricted 

specifying which ones and why; 

7) The management and health history of the flock; and 

8) A copy of the proposed flock plan and PEMMP. 

d. The epidemiological report will be provided to the DSE for review. The DSE will 

determine the status of the flock and review and approve the designation of the 

animals in the flock. 

e. The DSE will send interim summary reports to the SGHSE, including the request 

for indemnity and a monthly update provided by the 15th of the following month, 

until the complete report is provided. 

f. A summary of the epidemiological report, a copy of the full epidemiological 

report, and a copy of the completed VS Form 1-23 will be provided to the SGHSE 

by the DSE within 14 days of completing the flock plan (see the Scrapie 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 98 

SharePoint site for the summary report format). The SGHSE will make these 

reports available to the NSEP staff through the Scrapie SharePoint site. 

B. Monthly Epidemiology and Compliance Report 

1. Purpose: The monthly epidemiology and compliance report provides a summary of 

epidemiological and compliance information.

2. Data source: VS and State reports and the NSD.

3. Protocol: The DSE will use the epidemiology and compliance report template 

available on the Scrapie SharePoint site. The report will be electronically submitted 

monthly or quarterly, within 30 days of the end of the month or quarter, as instructed 

by the SGHSE based on the level of activity in the State. The SGHSE will then 

electronically submit the report to the National Scrapie Program Coordinator. The 

report must summarize the following information for the current fiscal year to date:

a. Sheep investigations;

b. Goat investigations;

c. Infected and source flock data;

d. Positive animals data;

e. Out of State traces; and

f. ID compliance at slaughter establishments, markets, and other sheep and goat 

concentration points.

C. End-of-Year Epidemiology and Compliance Report 

1. Purpose: The end-of-year epidemiology and compliance report accompanies the 

annual VS Form 5-24 (see section D). It provides summary epidemiological and 

compliance information.

2. Data source: VS and State reports and the NSD.

3. Protocol: The DSE will use the epidemiology and compliance report template 

available on the Scrapie SharePoint site. The report must summarize the following 

information for the fiscal year covered in the accompanying VS Form 5-24:

a. Sheep investigations;

b. Goat investigations;

c. Infected and source flock data;

d. Positive animals data;

e. Out of State traces; and

f. ID compliance at slaughter establishments, markets, and other sheep and goat 

concentration points.
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 99 

D. VS Form 5-24, Application for Scrapie Classification, Classification Renewal, or 

Reclassification of a State 

1. Purpose: VS Form 5-24 is the application for annual classification, classification 

renewal, or reclassification of a State for national scrapie status recognition as a 

Consistent State. 

2. Data source: VS and State reports and the NSD. 

3. Protocol: 

a. VS Area Office. The VS Area Office must file a completed VS Form 5-24 

application and a complete epidemiology and compliance summary for the fiscal 

year using the spreadsheet template provided on the Scrapie SharePoint site or 

equivalent for each State annually. Any State not meeting surveillance or 

identification compliance minimums must also submit an action plan and timeline 

for correcting the deficiency. The completed VS Form 5-24 and report must be 

submitted to the SGHSE by January 15 for the preceding fiscal year. The 

application must be signed by both the SAHO and AVIC. (Refer to the Scrapie 

SharePoint site for instructions.) 

b. National. The SGHSE will review the VS Form 5-24 applications, the 

epidemiology and compliance spreadsheet, and when required an action plan from 

the States in his or her area of responsibility for completeness to determine if the 

State or States meet the requirements in both 9 CFR 79.6 and these standards, and 

forward them with a recommendation for approval, provisional approval, or 

disapproval to the National Scrapie Program Coordinator within 30 days of 

receipt. The National Scrapie Program Coordinator will approve, provisionally 

approve, or disapprove all VS Form 5-24 applications based on the 

recommendations of the SGHSE and the submitted application package within 30 

days of receipt. The National Scrapie Program Coordinator will inform the SAHO 

of any proposed change in status by letter with copies to the District Director, 

SGHSE, and AVIC. In cases where a change in status is proposed, the National 

Scrapie Program Coordinator will provide a copy of the application and proposed 

action to the Scrapie Committee of the United States Animal Health Association 

for information and comment. APHIS will publish notice of changes and provide 

opportunity for public comment through the Federal Register. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 100 

Appendix A: Approval of Laboratories to Conduct Official 

Genotype Tests

A. Background 

Genotype testing for susceptibility to scrapie is a key element of the NSEP. Resources to 

conduct large-scale genotype testing to fulfill the needs of this program are not available 

at NVSL. The regulations at 9 CFR 54.11 provide guidelines for approving laboratories 

to conduct official genotype testing for program purposes. This appendix describes the 

requirements for laboratories requesting such approval and the procedures for APHIS 

units to follow when responding to such requests. 

B. Laboratory Responsibilities 

1. All initial requests for a laboratory approval should be made in writing to the NVSL 

Director. A laboratory may request approval to conduct one or more types of 

genotype tests on one or more types of tissue. 

2. Application package: Once an initial request for approval is submitted to the NVSL 

Director, NVSL will send a copy of this appendix to the laboratory. A laboratory 

must send the NVSL Director an application package electronically in pdf format (or 

other format acceptable to NVSL) containing the information listed below. 

a. Name and address of the laboratory; 

b. Name of the legally responsible official and, if different, the director of the 

laboratory; 

c. A description of the laboratory facilities and equipment that will be used in 

performing genotype tests; 

d. A list of the types of samples that will be tested; 

e. The SOP for each test to be used, including methods, materials, equipment, and 

other relevant information; 

f. A list of the names of individuals performing specific tests and a detailed 

statement of each individual’s qualifications; 

g. A detailed description of the procedures used to satisfy the recordkeeping 

requirements of the NSEP. (Note: To satisfy these requirements, the approved 

laboratory must retain records of all tests performed and all DNA samples for 5 

years.); 

h. A description of the specific procedures used for reporting test results. (Note: The 

results must be reported to the person submitting the sample, as well as to persons 

designated by NVSL, within 2 working days of completing the test.); 

i. The laboratory quality assurance manual; and 

j. A statement authorizing APHIS to inspect the laboratory, without prior notice, 

during normal business hours. The inspection may include, but is not limited to, 

reviewing and copying records, observing tests, and interviewing personnel. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 101 

C. NVSL and National Scrapie Program Coordinator Responsibilities 

1. On receiving a request for laboratory approval, the NVSL Director will inform the 

National Scrapie Program Coordinator, the District Director, and the AVIC. 

2. The NVSL Director will provide the requesting laboratory a copy of this appendix 

and discuss the requirements for laboratory approval with the laboratory director or 

other appropriate individuals. 

3. On receiving an application package (see B.2), authorized NVSL personnel will 

review the package to ensure satisfactory completion. If the application package is 

determined to be deficient, it will be returned to the laboratory with a statement 

giving the reasons for denying approval, and inviting the laboratory to remedy the 

deficiencies and resubmit the package. 

4. After receiving a satisfactory application package (see B.2), authorized NVSL 

personnel will schedule and conduct a site visit. An authorized NVSL employee will 

inform the District Director and the AVIC of the site visit. During the site visit, 

authorized NVSL personnel will again review the requirements for laboratory 

approval, review the test procedures the laboratory intends to use, and confirm the 

information in the application package is correct. 

5. If the application process is satisfactory, the National Scrapie Program Coordinator 

(or designee) will notify the director of the laboratory requesting approval that the 

laboratory will be approved to conduct the specific tests listed in the package, 

provided the laboratory: 

a. Satisfactorily completes laboratory proficiency testing; and 

b. Demonstrates the ability to electronically receive a submission and transmit a 

sample set of results in the prescribed format as specified by APHIS, and to enter 

data and results into the VSLS system from hard copy forms. 

1) APHIS contract laboratories may be required to demonstrate receipt of 

electronic test charts, entry of results in the appropriate fields of the 

submission files, and transmittal of the resulting file to VSLS. APHIS contract 

laboratories would also need to receive and process Web submissions and 

hard copy forms and transmit the results to or enter the results in VSLS. 

2) Approved laboratories that are not contract laboratories will have the option of 

entering the results through a Web page rather than using electronic 

messaging. 

Note: Nearly all Federal and State funded program specimens will be submitted in 

VSLS. Privately funded official program-approved testing specimens will, for the 

most part, continue to be submitted using hard copies of VS Form 5-29. This will 

require the genotyping laboratory to enter all the information supplied on the 

submitted VS 5-29 into VSLS. This reporting system is not used for unofficial 

privately funded testing. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 102 

6. If the laboratory proficiency testing is unsatisfactory, the NVSL Director will indicate 

the deficiencies in writing and send this information to the laboratory director 

requesting approval and to the National Scrapie Program Coordinator. The laboratory 

must submit a report detailing the cause of the error and the steps implemented to 

prevent a recurrence to reapply for approval. Those steps must be incorporated into 

the relevant documents that make up the application package. A corrected application 

package in pdf format (or other format acceptable to NVSL), must be submitted 

electronically to the NVSL Director, and a copy forwarded to the National Scrapie 

Program Coordinator. If the report and the corrected package are satisfactory, the 

laboratory may repeat the proficiency testing.

D. Changes to Laboratory Approval 

1. A laboratory must notify NVSL of any changes in the information contained in the 

application package (see B.2). Amendments to the package must be submitted to 

NVSL electronically in pdf format (or other format acceptable to NVSL)). 

2. The amendments will be reviewed for approval as in section B of this appendix. 

3. NVSL may elect to forgo conducting a new site visit or requiring additional 

proficiency testing. 

E. Maintaining Laboratory Approval 

1. Laboratory proficiency tests. To maintain approval, laboratories are required annually 

to demonstrate satisfactory completion of proficiency tests (or as deemed necessary 

by NVSL). Proficiency test results will be forwarded to the National Scrapie Program 

Coordinator by NVSL.

2. Annual inspections. To maintain approval, laboratories will undergo inspections by 

NVSL or a designee annually or as deemed necessary by NVSL. Among other items, 

the inspector will review:

a. Records;

b. Maintaining of archival samples;

c. Compliance with standard operating procedures; and

d. Compliance with 9 CFR and this appendix.

F. Removal of Laboratory Approval 

1. The NVSL Director may withdraw or suspend approval of a laboratory for any of the 

reasons listed below.

a. Failure to meet any of the conditions stated in this appendix (9 CFR 54.11).

b. One or more criteria for approval or for maintaining approval are no longer being 

met.

c. Submission by the approved laboratory of a request for withdrawing approval.
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 103 

d. Unsatisfactory performance on required proficiency tests or on regular samples 

submitted for testing.

e. Unsatisfactory conditions or procedures at the laboratory.

f. Failure to accurately input test data and report results electronically as required.

2. The NVSL Director will give written notice of a suspension or a proposed withdrawal 

to the director of the laboratory and will give the director an opportunity to respond. 

Any conflicts concerning the reasons for withdrawal will be resolved by holding a 

hearing.

G. List of Approved Laboratories 

The National Scrapie Program Coordinator will maintain a list of laboratories approved 

to conduct official genotype tests for scrapie. The list is publicly available here.

28

 

28 https://www.aphis.usda.gov/animal_health/nahln/downloads/scrapie_lab_list.pdf. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 104 

Appendix B: Approval of Laboratories to Conduct Official 

Program-Approved Diagnostic Tests for Scrapie in Sheep and Goats

A. Purpose 

Following are the procedures for approval of laboratories to conduct diagnostic tests for 

scrapie in accordance with 9 CFR 54.11. 

B. Definitions 

1. Official test: 

A program-approved test for the diagnosis of scrapie conducted at a laboratory 

approved by VS to conduct the test, NVSL, or another laboratory to which NVSL has 

referred a case for confirmatory testing. 

2. Program-approved test: 

A test kit or test method for the diagnosis of scrapie in a live or dead animal approved 

for use in the NSEP or the SFCP or both in accordance with 9 CFR 54.10, or that was 

approved by APHIS for the diagnosis of scrapie before September 20, 2001.

3. Confirmatory test: 

A test for the diagnosis of scrapie in a live or dead animal; conducted by NVSL or a 

laboratory to which NVSL has referred a case for such testing. Confirmatory testing 

may include any of the following methods, used alone or in combination: 

immunohistochemistry (IHC); Western Blot; histopathology; enzyme 

immunoassay/enzyme-linked immunosorbent assay (EIA/ELISA) test, if different 

from the EIA/ELISA test originally performed on the sample and the results are in 

agreement; or animal inoculation studies (i.e., bioassay). The results of a 

confirmatory test may be used to designate an animal in accordance with 9 CFR 79.4.

C. General 

1. Only State, Federal, and university laboratories (as required in 9 CFR 54.11) that are 

also members of the National Animal Health Laboratory Network (NAHLN) will be 

approved to conduct official scrapie diagnostic testing.

2. Only program-approved tests conducted in approved laboratories, at NVSL, or at 

another laboratory to which NVSL has referred a case for confirmatory testing, are 

considered to be official diagnostic tests for scrapie.

3. The approved laboratory must submit all specimens with an initial positive, suspect, 

repeat, or inconclusive test result, and all specimens from clinically suspect animals 

to NVSL for confirmation within 5 business days.
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 105 

4. Repeat or additional testing is the preferred method for confirming an initial positive 

or inconclusive test result. NVSL may, however, confirm an initial positive or 

inconclusive test result based on the review of slides from an IHC test or a developed 

Western blot if appropriate tissues or tissue blocks are not available or are not suitable 

for repeat or additional testing.

D. Laboratory Approval 

1. General:

a. Requests for laboratory approval should be made in writing to the NAHLN 

program office at NAHLN@aphis.usda.gov. After the NAHLN program office 

receives an initial request for approval, staff will provide a copy of the NAHLN 

Laboratory Qualification Checklist for Membership of a Veterinary Diagnostic 

Laboratory. 

b. Participation is contingent on approval from the NAHLN Coordinator, National 

Scrapie Program Coordinator, and NVSL Reference Laboratory, as well as 

successfully completing the associated proficiency test. Approval will be based 

on the need for additional testing capacity and technical ability. 

c. Approval requires reporting of results for tests supported by VSLS through the 

VSLS Web page or by using an electronic message in the VS-specified format. 

Other test results will be reported via spreadsheets or other formats provided by 

the NVSL Reference Laboratory. Results for IHC testing will be reported within 

10 business days of sample receipt. Results for ELISA testing and other assays 

will be reported as specified in an NVSL Reference Laboratory SOP. Further, all 

positive, suspect, repeat, and inconclusive results must also be reported by email 

to the NVSL Reference Laboratory within 1 business day after testing is 

completed. 

d. Approval requires that slides, blocks, and other specimens for all submissions are 

retained for at least 1 year, except when NVSL has authorized shorter retention 

times for formalin-fixed tissues not in blocks or for fresh or frozen tissue from 

accessions where no specimens are either pending confirmatory testing or were 

confirmed positive. All materials for cases with positive, repeat, suspect, and 

inconclusive test results and materials from clinically suspect animals must be 

forwarded to NVSL by overnight shipping within 1 business day after testing is 

completed.

2. Application package: The laboratory must submit the information listed below to the 

NAHLN program office at NAHLN@aphis.usda.gov.

a. The NAHLN Laboratory Qualification Checklist.

b. A copy of the laboratory’s APHIS VS permit (as required for receipt of 

proficiency panels and positive controls).

c. A description of the specific procedures to be used to report test results. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 106 

d. A description of recordkeeping procedures. Approval requires that records from 

all specimens be retained for at least 1 year, and records pertaining to cases with 

positive, suspect, repeat, or inconclusive test results be retained for at least 5 

years.

e. A description of sample/tissue holding and retention procedures. 

E. NAHLN Responsibilities 

1. On receiving a request for laboratory approval, the NAHLN Coordinator will inform 

the NVSL Director, NVSL Reference Laboratory, and the National Scrapie Program 

Coordinator as well as the appropriate APHIS District Director and AVIC, based on 

the location of the laboratory. The NAHLN Coordinator will consult with the NVSL 

Reference Laboratory and National Scrapie Program Coordinator to determine if 

additional testing capacity is needed.

2. The NAHLN Coordinator or designee will give the requesting laboratory a copy of 

this document and discuss requirements for laboratory approval with the laboratory 

director or other appropriate individuals. The NAHLN Coordinator, after consultation 

with the NVSL Reference Laboratory and National Scrapie Program Coordinator, 

will advise the requesting laboratory whether capacity is needed at that time.

3. On receiving an application package as described in D.2, appropriate NAHLN 

program and NVSL Reference Laboratory personnel will review the submitted 

materials.

F. Recommendation for Approval 

1. If the laboratory meets all requirements, the NAHLN Coordinator will notify the 

NVSL Director, the NVSL Reference Laboratory, the National Scrapie Program 

Coordinator, and the laboratory director regarding the laboratory’s ability to conduct 

the specific tests on the specified tissues (as listed in the NAHLN Checklist). 

Approval will be granted if the laboratory: 

 

a. Completes proficiency testing for the specific test, as directed by NVSL. 

Satisfactory performance requires that the laboratory correctly identify the scrapie 

status of 100 percent of samples in the test panel.

1) If discrepant results are obtained, NVSL, the participating laboratory, and 

others as required will investigate the cause.

2) If the apparent cause of discrepant results is determined and rectified to 

NVSL’s satisfaction, no additional corrective actions may be needed.

3) At NVSL’s discretion, the laboratory may need to train additional personnel 

or may need additional proficiency testing. NVSL can deny laboratory 

approval for the specific test after a second proficiency test failure.

4) The NVSL reference laboratory will forward proficiency test results to the 

National Scrapie Program Coordinator and the NAHLN program office.

 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 107 

b. Demonstrates the ability to receive submission information and transmit test 

results by the following methods:

1) Access submission information entered previously by field 

collectors/submitters and enter submission information for other specimens 

not submitted electronically on the appropriate VSLS Web site; and

2) Enter test results on the appropriate VSLS Web site or submit test results via 

electronic messaging to the VS database, as directed; and

3) Supply submission information and test results using a spreadsheet or other 

NVSL-provided format for tests not supported by VSLS.

2. If the results of a laboratory’s proficiency testing are unsatisfactory or the laboratory 

cannot sufficiently demonstrate its ability to electronically receive and transmit test 

results, the NVSL reference laboratory will document the deficiencies in writing and 

send this information to the laboratory director, the NAHLN program office, and the 

National Scrapie Program Coordinator.

a. Laboratories may reapply for approval by contacting the NAHLN program office 

and the NVSL reference laboratory to discuss retraining and retaking the 

proficiency test and/or re-evaluation of the laboratory’s ability to receive and 

transmit data electronically. The NVSL reference laboratory may require the lab 

to submit a satisfactory report detailing the cause of the error or errors and the 

steps implemented to prevent recurrence before allowing the lab to retake the 

proficiency test.

b. Failure of the subsequent proficiency test or electronic data transmission test will 

be ground to deny laboratory approval.

1) A laboratory denied approval as a result of failed proficiency testing as 

described in 1 may be required to wait until the next scheduled round of 

proficiency testing to complete the testing and submit a new application 

package.

2) A laboratory denied approval as a result of a failed electronic data 

transmission test may be approved, within 12 months of a successful 

diagnostic proficiency panel, after a successful electronic data transmission 

test. Laboratories failing to demonstrate electronic data transmission 

proficiency within 12 months must submit a new application package.

3) The new application package must detail the factors associated with the denial 

of the previous application and the actions implemented to prevent 

recurrences.

G. Changes to Laboratory Approval 

1. A laboratory must notify the NVSL Director and the NAHLN program office of any 

changes in the information contained in the application package within 30 days of the 

effective date of the change. Changes in procedures or equipment must be approved 

in advance. Changes in personnel requiring notification include individuals serving as 

the responsible laboratory official, laboratory director, and the responsible individual 

for technical issues regarding scrapie testing or their contact information. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 108 

2. The amendments will be reviewed for approval as described in section E of this 

appendix. The NAHLN program may conduct a new site visit or may require 

additional proficiency testing before approving the amendment, depending on the 

nature and scope of the requested change.

a. If the amended application is approved, the NAHLN Coordinator will notify the 

NVSL Director and the National Scrapie Program Coordinator.

b. If the amended application is not approved, the NAHLN Coordinator will give the 

laboratory director, NVSL Director, and the National Scrapie Program 

Coordinator a statement giving the reasons for denying approval. The laboratory 

can address the deficiencies and resubmit the amendment.

H. Maintaining Laboratory Approval 

1. Approved laboratories are required to submit a NAHLN Qualification Checklist 

annually for re-approval. Continued participation is contingent on approval from the 

NAHLN Coordinator, National Scrapie Program Coordinator, and NVSL Reference 

Laboratory. 

2. To maintain approval, laboratories must satisfactorily complete proficiency tests 

annually or as NVSL deems necessary. A final score of 100 percent correctly 

identified samples is considered a satisfactory score. The procedure described in F.1

will be used if discrepant results are obtained.

3. As stated in the NAHLN Qualification Checklist, approved laboratories may be 

required to undergo inspections or audits, or both, as designated by the NAHLN 

program. 

I. Removal of Laboratory Approval 

1. The NVSL Director, acting on behalf of the Administrator, may withdraw or suspend 

approval of a laboratory for any of the following reasons:

a. Failure to meet any of the conditions stated in this appendix or in 9 CFR 54.11.

b. One or more criteria for obtaining or maintaining approval are no longer being 

met.

c. Submission by the approved laboratory of a request for withdrawal of approval.

d. Unsatisfactory performance on regular samples submitted for testing or required 

proficiency tests as defined in section H.1 of this appendix.

e. A finding of unsatisfactory conditions or procedures at the laboratory.

f. Failure to accurately input test data and report results in the manner and within the 

time frames specified in this appendix, the SOP provided by NVSL, in a contract, 

blanket purchase agreement, or other binding agreement. 

g. Loss of NAHLN approval. 

2. The NVSL Director, acting on behalf of the Administrator, may withdraw or suspend 

a laboratory’s approval to conduct a specific test kit or method on any or all tissues 

approved to be tested using the kit or method based on proficiency test failures on any 

tissue using the kit or method. For example, a laboratory that fails a second 

proficiency test for approval to conduct the IHC test on the obex may also have its 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 109 

approval to conduct the IHC test on additional tissue types withdrawn.

3. The NVSL Director, acting on behalf of the Administrator, will provide written notice 

of a proposed withdrawal to the laboratory director and include an opportunity for the 

laboratory’s response. Any conflicts concerning the reason or reasons for withdrawal 

will be resolved by holding a hearing. A hearing will include the NVSL Director, the 

requesting laboratory’s director, the National Scrapie Program Coordinator, and their 

respective subject matter experts.

J. List of Approved Laboratories 

The NAHLN program office will maintain a list of approved laboratories conducting 

official diagnostic tests for scrapie. The list is publicly available here.

29

 

29 https://www.aphis.usda.gov/animal_health/nahln/downloads/scrapie_lab_list.pdf 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 110 

Appendix C: Program Approval of Diagnostic Tests for Scrapie in 

Sheep and Goats 

A. Purpose 

Following are the procedures for approving new test kits or test methods for diagnosing 

scrapie in the NSEP or the SFCP, or both. This appendix also provides guidance for 

implementing the regulations in 9 CFR 54.10). 

B. Definitions

1. Official test:

A program-approved test for the diagnosis of scrapie conducted at a laboratory VS 

approves to conduct the test, NVSL, or another laboratory to which NVSL has 

referred a case for confirmatory testing. 

2. Program-approved test:

A test kit or test method for diagnosing scrapie in a live or dead animal approved for 

use in the Scrapie Eradication Program or the SFCP, or both in accordance with 9 

CFR 54.10, or approved by APHIS for diagnosing scrapie before September 20, 

2001. 

3. Confirmatory test:

A test for diagnosing scrapie in a live or dead animal conducted by NVSL or a 

laboratory to which NVSL has referred a case for such testing. Confirmatory testing 

may include any of the following methods, used alone or in combination: 

immunohistochemistry (IHC); Western Blot; histopathology; enzyme 

immunoassay/enzyme-linked immunosorbent assay (EIA/ELISA) test, if different 

from the EIA/ELISA test originally performed on the sample and the results are in 

agreement; or animal inoculation studies (i.e., bioassay). The results of a 

confirmatory test may be used to designate an animal in accordance with 9 CFR 79.4.

C. General

1. Routine laboratory diagnosis of scrapie is accomplished by detecting the proteaseresistant form of the prion protein, PrPres, in CNS or lymphoid tissue, or both. 

2. As new test kits or test methods are developed for diagnosing scrapie, APHIS must 

evaluate their characteristics and intended uses to determine if they are suitable for 

use in the Scrapie Eradication Program or the SFCP. 

3. Only program-approved tests performed in approved laboratories, at NVSL, or at 

another laboratory to which NVSL has referred a case for confirmatory testing, are 

considered official diagnostic tests for scrapie. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 111 

D. Request for Program Approval of Tests

1. Initial requests for program approval of a test kit or test method should be made in 

writing to the NVSL Director (or his or her designee). Once an initial request for 

approval is submitted, a copy of this appendix will be sent to the requestor. 

2. Program evaluation of tests may also be initiated by the NVSL. 

3. Application package: The requestor must submit the following information 

(electronically in pdf or other format acceptable to NVSL) to the NVSL Director. 

This information will be referred to as the application package. 

a. A standardized test protocol that includes a description of the test, a description of 

the reagents, materials, and equipment used for the test, the specific tissue or 

tissues on which the test is to be performed, the test methodology, and any control 

or quality assurance procedures. 

b. A description of the intended use of the test including if it will be used to test 

sheep, goats, or both; or live or dead animals or both (i.e., 

antemortem/postmortem test) for scrapie. 

c. Data to support repeatability (i.e., the ability to reproduce the same result 

repeatedly on a given sample). 

d. Data to support reproducibility (i.e., data to show that similar results can be 

produced when the test is run at other laboratories). 

e. Data to support the diagnostic sensitivity and specificity of the test and data to 

support the analytical sensitivity and specificity for assays, as appropriate. 

f. A summary of the advantages offered by the new test kit or test method relative to 

the methods currently approved for a similar use. 

g. The NVSL Director may request additional data or information at any time during 

the review process to determine the suitability of the test for program use. This 

may include but is not limited to past performance, cost of test materials and 

equipment, ease of test performance, generation of waste, and potential use of 

existing equipment. 

h. APHIS-licensed test kit manufacturers may use the data submitted to obtain 

licensure to support their applications for program approval. 

E. NVSL and National Scrapie Program Coordinator Responsibilities

1. On receiving a request for program approval, the NVSL Director will inform the 

National Scrapie Program Coordinator. 

2. The NVSL Director, or designee, will provide the requestor a copy of this appendix 

and discuss the requirements for program approval of a test with the requestor or 

other appropriate individuals. 

3. If the application package is complete and the test kit or test method warrants further 

consideration, authorized NVSL personnel will coordinate a review of the submitted 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 112 

materials with the National Scrapie Program Coordinator and, if appropriate, other 

scientists. 

4. The NVSL Director may decline to evaluate any test kit for program approval that has 

not been licensed for the intended use. The Director may also decline to evaluate any 

test kit or test method unless the requestor demonstrates the new method offers a 

statistically significant advantage over currently approved methods, or is likely to 

provide a savings that will offset the cost of evaluation. If the Director declines 

further evaluation of the test, the application package will be returned to the requestor 

with a written statement providing the reason or reasons for the denial. The requestor 

may address the deficiencies identified and resubmit the application package. 

F. Evaluation Criteria for Program Approval of Tests

1. The approval or disapproval of a test for use in the Scrapie Eradication Program or 

the SFCP will be based on APHIS’ evaluation of the submitted application package 

and testing at NVSL. APHIS may use outside scientists during the evaluation process, 

as appropriate. APHIS will use the following evaluation criteria: 

a. The test must be able to be readily and successfully performed at NVSL. 

b. The test must have a reliable, timely, and cost-effective method of proficiency 

testing. 

c. A test, or combination of tests, may be approved for the identification of suspect 

animals, for the identification of scrapie-positive animals, or for other purposes, 

such as flock certification. 

1) Test approval for the identification of scrapie-positive animals requires that 

the test demonstrate a diagnostic specificity comparable to or greater than that 

of current program-approved tests. 

2) Test approval for the removal of high-risk, exposed, or suspect animal 

designations requires that the test demonstrates a sensitivity comparable to or 

greater than that of current program-approved tests used for the stated 

purpose. 

3) Test approval for a live animal screening test to identify suspect animals 

requires that the test be reliable but need not be definitive for diagnosing 

scrapie. 

d. Test kits that are not USDA-licensed will be approved only if they offer an 

advantage over other test methods as determined by NVSL or have a limited use 

(i.e. such as Western Blot test kits used for discriminatory or confirmatory 

testing). 

e. Test procedures must be consistent with established scientific principles and 

practices for diagnostic testing for scrapie. 

2. The NVSL Director may request additional data or information at any time during the 

review process to facilitate the evaluation of the test’s suitability for program 

approval. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 113 

3. VS may provisionally approve a test method or test kit to allow additional evaluation 

of its performance during field use. 

4. After determining that the test kit or test method meets the criteria for program 

approval or provisional approval, the National Scrapie Program Coordinator will draft 

VS Guidance for approval of the test. 

5. Specific guidelines for the use of program-approved tests within the Scrapie 

Eradication Program or the SFCP will be published in the VS Guidance approving the 

test and may subsequently be incorporated in the NSEPS. These guidelines will be 

developed according to the characteristics of the test, including specificity, 

sensitivity, and predictive value in defined groups of animals. 

6. If the test kit or test method does not meet the criteria for program approval, the 

application package will be returned to the requestor with a statement giving the 

reasons for denying approval. The requestor may address the deficiencies and 

resubmit the application package. 

G. Changes to Test Methodology

1. The requestor must notify the NVSL Director of any changes or modifications to the 

test protocol from that contained in the application package. Amendments to the 

package must be submitted in writing (electronically in pdf or other format acceptable 

to NVSL) to the NVSL Director. 

2. The amendments will be reviewed by NVSL to determine if the proposed changes are 

approved, disapproved, require additional information or testing before approval, or 

require a full evaluation for program approval as a new test. 

a. If the amended protocol does not require full evaluation, the NVSL Director will 

notify the requestor and the National Scrapie Program Coordinator regarding 

approval of the modification, additional information needed, or testing required 

before approval. 

b. If the amended protocol requires full evaluation, the NVSL Director will notify 

the requestor and the National Scrapie Program Coordinator that a reapplication is 

necessary for approval. 

H. Removal of Program Approval for a Test

1. The NVSL Director, acting on behalf of the Administrator, may withdraw or suspend 

approval of any test kit or test method for the following reasons: 

a. Failure to meet any of the conditions stated in this document or in 

9 CFR 54.10. 

b. The test kit or test method does not perform as expected following program 

approval. 

c. A more effective test kit or test method is subsequently approved. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 114 

2. The NVSL Director, acting on behalf of the Administrator, will give written notice of 

the proposed withdrawal to the director of the laboratories using the test or method, or 

in the case of test kits, to the manufacturer, and will give the director or manufacturer 

an opportunity to respond. A hearing will be held to resolve conflicts regarding any 

material fact concerning the reason for withdrawal. 

3. The NVSL Director, acting on behalf of the Administrator, may suspend approval by 

notifying the laboratory or the kit manufacturer. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 115 

I. List of Program-Approved Diagnostic Tests for Scrapie

Listed in the table below are the following: 

 The diagnostic tests approved for diagnosing scrapie in sheep and goats in the United 

States; 

 The tissues on which those tests can be run as official scrapie tests; 

 The laboratories authorized to run preliminary (screening) scrapie tests; and 

 The laboratories authorized to run confirmatory scrapie tests. 

Diagnostic Test Tissue Authorized Laboratory: 

Preliminary Testing 

Authorized 

Laboratory: 

Confirmation 

Testing30

Immunohistochemistry 

(IHC) 

Brain, 

brainstem (obex) 

1. Approved Scrapie NAHLN 

Laboratories31

2. NVSL 

NVSL 

IHC Lymph Node 

(LN)32

1. Approved Scrapie NAHLN 

Laboratories 

2. NVSL 

NVSL 

IHC Tonsil 1. Approved Scrapie NAHLN 

Laboratories 

2. NVSL 

NVSL 

IHC Rectal lymph 

tissue 

(RAMALT)33

1. RAMALT Approved Scrapie 

NAHLN Laboratories 

2. NVSL 

NVSL 

IHC Third eyelid 

biopsy33, other 

lymphoid tissue 

NVSL NVSL 

Western Blot34 Brain, obex, LN, 

tonsil, other 

lymphoid tissue 

NVSL NVSL 

Bioassay35 Any tissue NVSL 

ELISA36

 

30 Routinely only NVSL conducts confirmatory tests for scrapie in the United States; however, NVSL may refer a 

sample for confirmatory testing at another laboratory. 

31 For a list of NAHLN laboratories approved for scrapie diagnostic testing, please visit 

https://www.aphis.usda.gov/animal_health/nahln/downloads/scrapie_lab_list.pdf . NVSL is included on this list. 

32 The most commonly tested lymph tissue is the retropharyngeal lymph node (RLN). 

33 The RAMALT and third eyelid lymph tissues can be tested on either live or dead animals. The RAMALT test is 

the preferred live-animal test due to increased sensitivity, reliability, repeatability, and animal comfort. While NVSL 

may authorize NAHLN labs to run RAMALT tests, they are currently conducted only at NVSL. 

34 Western blot is generally reserved for scrapie-exposed animals, scrapie suspect, and test-positive animals. 

35 Bioassay, while rarely used, may be used by NVSL for confirmatory testing. 

36 Although other countries use ELISA for scrapie testing and it is used for bovine spongiform encephalopathy 

testing in the United States, APHIS has not currently approved an ELISA test for use in the NSEP. NVSL may use 

ELISA as a supplemental test. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 116 

This page left intentionally blank. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 117 

Appendix D: Scrapie Surveillance

A. General 

The national performance goal for scrapie surveillance is to collect samples from at least 

40,000 mature targeted sheep or goats each year. Mature animals are those with at least 

one completely erupted first permanent incisor. The AVIC and SAHO are responsible for 

ensuring that surveillance minimums for their State or area of responsibility are met and 

that targeted sheep and goats slaughtered in their area are sampled. The National Scrapie 

Surveillance Plan published in 2010 is currently being revised. When it is finalized it will 

supersede sections B-D below and will replace the 2010 National Scrapie Surveillance 

Plan. 

B. Animals Targeted for Surveillance Sampling 

1. All mature blackfaced sheep and clinical suspects should be sampled regardless of 

traceability, including those from flocks on the “Do Not Collect” list. 

2. Mature sheep that are not blackfaced and mature goats should only be sampled if they 

are traceable, are not from a flock on the “Do Not Collect” list, and meet at least one 

of the additional criteria listed below. 

a. The animal is a Southdown or Montadale sheep.37

b. The animal is dead before slaughter or condemned on antemortem inspection for 

any reason. 

c. The animal is nonambulatory: 

1) Down and unable to rise, or able to rise but only for brief periods. 

2) Nonambulatory animals can include those with broken appendages, severed 

tendons or ligaments, nerve paralysis, fractured vertebral columns, or 

metabolic conditions. 

d. The animal exhibits signs of CNS disease, including any of the following: 

1) Weakness of any kind, including stumbling, falling down or having difficulty 

rising (not including those with visible traumatic injuries, which should be 

recorded as nonambulatory animals). 

2) Behavioral abnormalities. 

3) Increased sensitivity to noise and sudden movement. 

4) Tremors. 

5) Star gazing. 

6) Head pressing. 

7) Bilateral gait abnormalities, including incoordination, ataxia, high stepping 

gait of forelimbs, bunny-hop movement of rear legs, or swaying of back end, 

but not including abnormalities involving only one leg or one front and one 

 

37 Southdowns have wool-covered gray to mouse-brown faces. Montadales cannot be readily identified by 

observation of the head, so these can only be selected if advised by the plant. The Montadale is typically bright 

white with a clean head and black nose, similar to the Cheviot. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 118 

back leg. 

8) Other CNS signs. 

e. The animal shows signs of intense rubbing, abrasions, or rough, thickened, and/or 

hyperpigmented skin: 

1) Repeated intense rubbing with bare areas in similar locations on both sides of 

the animal’s body or, if on the head, both sides of the poll; and/or 

2) Abraded, rough, thickened, or hyperpigmented areas of skin in areas of wool 

or hair loss in similar locations on both sides of the animal’s body or, if on the 

head, both sides of the poll. 

f. The animals are scrapie-exposed animals not in source or infected flocks (i.e., 

those identified with a yellow “Exposed” eartag or received on a VS 1-27 permit). 

g. Any goat or sheep, including hair sheep, that is 2, 3, 4, or 5 years of age as 

evidenced by examination of the teeth. 

h. Condemned postmortem for emaciation. 

i. Animals of higher risk than the general population or needed to achieve State 

sampling minimums as determined by the SGHSE. 

j. Sheep or goats identified with an SFCP tag. 

3. Note:

a. Below is the list of options for age in VSLS: 

AGE DESCRIPTION 

12 to < 18 months First permanent incisor erupted, but lower than remaining 

deciduous teeth 

18 to < 24 months First permanent incisor level with or extends above 

remaining deciduous teeth; second permanent incisor erupted 

2 years Second permanent incisor erupted and level with first 

permanent incisor; third permanent incisor not erupted 

3 years Third permanent incisor erupted; fourth permanent incisor 

not erupted 

4 years Fourth permanent incisor erupted; no dental wear on fourth 

incisor 

Full mouth – min. Animal has full mouth, all incisors fully erupted, with 

minimal dental wear 

Full mouth – mod. Animal has full mouth; all incisors fully erupted, with 

moderate dental wear. No broken, missing or markedly 

splayed teeth 

Full mouth – sev. Animal has full mouth; all incisors fully erupted, with severe 

dental wear. Teeth may be broken, missing, or markedly 

splayed 

b. In plants where the collector does not see the live sheep or goat, arrangements 

should be made with the FSIS inspector in charge to identify the heads from 

animals meeting the clinical signs criteria. 

c. The targeted groups may be revised based on ongoing analysis of RSSS data. 

d. Reminder: Unlike other sheep and goats, all mature sheep that have a black face 

should be sampled regardless of traceability and “Do Not Collect” list status so 

that the NSEP can accurately measure program effectiveness. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 119 

C. Surveillance Minimums 

1. To ensure that the last remaining classical scrapie cases in the United States are 

detected, each State must test a minimum number of sheep and goats for scrapie 

annually. Both sheep and goat sampling minimums are calculated based on each 

State’s breeding ewe and breeding doe populations, as reported by NASS annually in 

its Sheep and Goat report (usually released the last week of January each year). 

2. For sheep, the minimum annual sample numbers required by a State are the lesser of 

the following: 

a. Twenty percent of the number of samples needed to detect classical scrapie at a 

prevalence of 0.1 percent with 95 percent confidence; or 

b. 1 percent of the breeding sheep population in the State based on NASS data. 

3. For goats, the minimum annual sample numbers are determined based on the 

occurrence of classical scrapie in a goat since 2001. 

a. For States that have had at least 1 case of classical scrapie in a goat since 2001, 

the sampling minimum is calculated the same as it is for sheep, using the breeding 

doe population, and is the lesser of: 

1) Twenty percent of the number of samples needed to detect classical scrapie at 

a prevalence of 0.1 percent with 95 percent confidence; or 

2) 1 percent of the breeding goat population in the State based on NASS data. 

b. For States that have not had a case of classical scrapie in a goat since 2001 or that 

have met the 5-year sampling minimum since their last case, the sampling 

minimum is the State’s prorated share of the national goal of 3,000 goats based on 

NASS data. 

4. Annual Sampling Minimum 

a. NSEP staff determines the annual sampling minimums for the upcoming fiscal 

year based on the most recent NASS data available on March 1, and the 

minimums are distributed to the VS Area Offices by April 1. 

5. For further information about the NSEP surveillance strategy, please refer to the 

National Scrapie Surveillance Plan38. 

 

D. Surveillance at Sources Other Than Slaughter

1. State-of-origin minimums may be fulfilled by submitting surveillance specimens 

from mature dead, disabled, or suspect animals from non-slaughter sources. Such 

sources include, but are not limited to, the following: 

a. Veterinary diagnostic laboratories (even if another diagnosis was achieved). 

b. Public health laboratories (rabies-negative submissions). 

c. Renderers. 

d. Dead-stock haulers. 

 

38 http://www.aphis.usda.gov/animal_health/animal_diseases/scrapie/downloads/national_scrapie_surv_plan.pdf
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 120 

e. Markets. 

f. Cull ewe feedlots. 

g. Research facilities. 

h. Farms (including home slaughter of targeted animals, up to 30 per flock of 

origin). 

i. Other sites. 

2. In addition, surveillance specimens may include approved live-animal tests on codon 

171 QQ sheep or goats over 14 months of age that are: 

a. Black-faced; 

b. Southdowns; 

c. Montadales; or 

d. Reside in flocks that contain or contained female animals of these types or that are 

at higher risk than the average population or as needed to meet surveillance 

objectives, as identified by the DSE. 

Note: Contact the SGHSE for guidance on live animal testing for surveillance. 

E. Sampling Procedures and Forms 

1. Specimens must be collected using the sampling procedure provided in the National 

Scrapie Reference Library, which is available to State and Federal animal health 

employees on the APHIS-NSEP Scrapie SharePoint site (see E.6). 

2. Sampling supplies to collect scrapie samples are available from NVSL by e-mailing 

NVSLshipping@aphis.usda.gov. Boxes for shipment of whole heads are available by 

e-mailing Remington.Locker@aphis.usda.gov. 

3. All on-farm necropsy and live animal submissions must be made electronically 

through the VSLS on-farm module. Guidance for entering submissions in VSLS is 

available in the National Scrapie Reference Library, which is available to State and 

Federal animal health employees on the APHIS-NSEP site (see E.6). 

4. All specimens collected at slaughter plants or other concentration points, where the 

owner information is not known at the time of collection, must be submitted 

electronically through the VSLS RSSS module. 

5. Whole head submissions shipped to the Remington Locker in Indiana must include a 

completed RSSS or On-Farm Submission Worksheet as appropriate. The worksheet is 

used by collection personnel to enter the submission in VSLS. Refer to the Whole 

Head Collection Manual for a copy of the worksheet and for additional information. 

A copy of the Manual is available in the National Scrapie Reference Library (see 

E.6). 

6. The Scrapie SharePoint site is available to State and Federal animal health employees 

at https://share.aphis.usda.gov/sites/vs-sgh/. Information from this site is also 

available on CD or hard copy for Federal and State employees who cannot access the 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 121 

Scrapie SharePoint site, and can be obtained by contacting the Scrapie Program 

Specialist by email at scrapie@aphis.usda.gov. 

7. The AD for the collecting State is responsible for initiating traces for positive animals 

in accordance with part VII of these Program Standards. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 122 

This page left intentionally blank. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 123 

Appendix E: Scrapie Cleaning and Disinfection Guidelines 

The following procedures do not guarantee total and complete disinfection and inactivation of 

the infectious agent. Nonetheless, current information regarding the efficacy of following these 

disinfection procedures under laboratory conditions suggests these procedures will reduce 

infectivity in the environment. Until more specific information is available, good sanitary 

practices are recommended following each lambing. The following methods below should be 

applied to lambing areas where infected or exposed animals have lambed. 

Pastures 

1. If practical, till soil under or do not use area to graze susceptible animals. 

2. If this is impractical, do not use the pasture until the animal waste has decomposed and 

the weather has had an opportunity to dilute any infectivity. 

Drylots 

1. Remove the manure and bedding and, when practical, the top 1 to 2 inches of soil to 

reduce contamination. 

2. Bury or till under the removed material; or compost the removed material in areas not 

accessed by domestic or wild ruminants until it can be buried or tilled under. 

Earth Surfaces Inside Structures or Used for Confined Lambing Pens 

1. Remove the organic material and, when practical, the top 1 to 2 inches of soil to reduce 

contamination. 

2. Bury or till under the removed material; or, compost the removed material in areas not 

accessed by domestic or wild ruminants until it can be buried or tilled under. 

Non-Earth Surfaces 

(These include cement, wood, metal, tools, equipment, instruments, feed, hay, bedding, and other 

materials.) 

1. Remove all organic material. Bury, incinerate, or compost the removed material in areas 

not accessed by domestic or wild ruminants and then till under, bury, or incinerate. 

2. When practical for other items bury or incinerate by high-temperature incineration 

methods. 

3. Clean and wash surfaces and remaining items using hot water and detergent. Allow all 

surfaces, tools, and equipment to dry completely before disinfecting and sanitizing using 

one of the following methods: 

a. Autoclave instruments, small tools, and other items at 277 F for 1 hour. This method 

is more effective when preceded by the treatment described in b or c. 
Scrapie Program Standards Volume 1 March 2019 

For General Distribution 124 

b. To clean dry surfaces, apply a 2 percent available chlorine solution39 (equivalent to 

about 20,000 p/m; available chlorine: 50 ounces or 6-1/4 cups of normal strength 

(5.25 percent) bleach) to enough water (78 ounces. or 9 3⁄4 cups) to give 1 gallon of 

solution) at room temperature (at least 65 F) for 1 hour. 

Note: Bleach is caustic and can be hazardous if swallowed, gets in the eyes, is 

breathed in, or is left on the skin. Further, care must be taken to prevent 

contamination of water from runoff and to comply with any environmental 

regulations for use of this product. Read the material safety data sheet before use and 

use appropriate personal protective equipment or hire trained personnel to do the 

work. 

c. To clean dry surfaces, apply a 1-molar solution of sodium hydroxide39 (approximately 

4-percent solution (5 ounces sodium hydroxide dissolved in l gallon water)) at room 

temperature (at least 65 F) for at least 1 hour. Synonyms for sodium hydroxide are 

caustic soda, soda lye, and sodium hydrate. 

Note: Sodium hydroxide is caustic and can be hazardous if swallowed, gets in the 

eyes, is breathed in, or is left on the skin. Further, care must be taken to prevent 

contamination of water from runoff and to comply with any environmental 

regulations for use of this product. Read the material safety data sheet before use and 

use appropriate personal protective equipment or hire trained personnel to do the 

work. 

Use of chlorine and sodium hydroxide must be reported to scrapie@aphis.usda.gov or directly to 

the designated individual for compilation into a report for submission to EPA.

 

39 40 CFR part 152 declares prions a pest under the Federal Insecticide, Fungicide and Rodenticide Act (FIFRA). 

Accordingly, only products registered with the EPA specifically for the reduction of prion infectivity can be used to 

disinfect these sites. Currently there are no EPA-registered products available; EPA has therefore granted APHIS an 

exemption for the use of chlorine and sodium hydroxide for use in its prion control and eradication programs. These 

instructions conform to those provided in the exemption labels.