United States

Department of

Agriculture

Animal and

Plant Health

Inspection

Service

Veterinary

Services

National

Animal Health

Monitoring

System

January 2004

SOSS

Phase II: Scrapie: Ovine Slaughter Surveillance

Study 2002-2003
Mention of companies or commercial products does

not imply recommendation or endorsement by the

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.

USDA:APHIS:VS:CEAH

NRRC Building B, M.S. 2E7

2150 Centre Avenue

Fort Collins, CO 80526-8117

970.494.7000

E-mail: NAHMSweb@aphis.usda.gov

www.aphis.usda.gov/vs/ceah/cahm

#N419.0104

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, 1400 Independence Avenue, SW,

Washington, DC 20250-9410 or call (202) 720-5964

(voice and TDD). USDA is an equal opportunity

provider and employer.
USDA APHIS VS / i

Acknowledgments

Phase II of the Scrapie: Ovine Slaughter Surveillance study (SOSS) was

prepared from material received and analyzed by the U.S. Department of

Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS),

Veterinary Services (VS) during a study to estimate the regional and national

prevalence of scrapie in mature cull sheep in the United States.

VS is grateful to the American Sheep Industry Association (ASI), which

provided invaluable assistance in the design of the SOSS study, helped

coordinate efforts among industry and participating States, and made a

substantial monetary contribution. Recognition also goes to the Food Safety

Inspection Service (FSIS), and the contract laboratories that worked in

cooperation with the National Veterinary Services Laboratory (NVSL).

We want to thank the State and Federal veterinary medical officers (VMOs) and

animal health technicians (AHTs) who visited the plants and collected the data

and samples. Their hard work and dedication to SOSS were invaluable.

All participants are to be commended, particularly the slaughter plants, whose

voluntary efforts made the SOSS study possible.

Thomas E. Walton

Director

Centers for Epidemiology and Animal Health
ii / SOSS 2003

Suggested bibliographic citation for this report:

USDA. 2003. Phase II: Scrapie: Ovine Slaughter Surveillance Study 2002-2003

USDA:APHIS:VS,CEAH, National Animal Health Monitoring System, Fort Collins, CO

#N419.0104

Contacts for further information:

Questions or comments on the Scrapie: Ovine Slaughter Surveillance Study

2002-2003: Dr. Randy Pritchard or Dr. Katherine Marshall: 970.494.7000

Information on reprints or other NAHMS reports: Mr. Brad Doty: 970.494.7000

E-mail: NAHMSweb@aphis.usda.gov
USDA APHIS VS / iii

Table of Contents

Introduction 1

Terms Used in this Report 2

Section I: Prevalence Estimates 5

A. Weighted Test Results 5

1. Overall prevalence 5

2. Prevalence by tissue type 7

3. Prevalence by face color 8

4. Prevalence by age 9

5. Logistic regression model 10

B. Unweighted Genetic Results 11

1. Distribution of sampling 11

Section II: Methodology 16

A. Background 16

1. Mature sheep slaughter and marketing 16

2. Mature sheep marketed to Mexico 18

3. Projected number of sheep culled 19

B. Sampling 21

1. Total sample size 21

2. Plant selection and sampling allocation 21

3. Animal selection 22

4. Laboratory allocations 22

5. Genetic testing 22

C. Region of Origin 23

D. Population Inferences 23

E. Data Validation and Analysis 23

Appendix I: Sample Profile 24

Appendix II: U.S. Sheep Inventory and Operations 26

Appendix III: Scrapie: Ovine Slaughter Surveillance – Phase I

Information Sheet 27

Appendix IV: Laboratory Selection and Results 29

Appendix V: Age Determination by Teeth Examination 30
Introduction

USDA APHIS VS / 1

Introduction

The purpose of the SOSS study was to estimate the regional and national

prevalence of scrapie in mature cull sheep in the United States.

Phase I of SOSS was conducted from February 2001 through March 2002 and

included refinement of the study design and sample collection training. The

purpose of Phase I was to develop and modify the sample collection and

testing processes, without emphasizing statistical results (see appendix III).

SOSS Phase II is similar to Phase I in that similar sample collection procedures

and testing were used, along with a representative sample allocation.

Beginning April 1, 2002, and continuing through March 31, 2003, Phase II

included the collection of tissue samples from 12,508 sheep from 22 slaughter

plants and 1 large livestock market.

Prior to the SOSS study, the estimated prevalence of scrapie in the United

States was 0.07 percent (based on unpublished data from the NAHMS Sheep

’96 study). However, the Sheep ’96 estimate was based on a mail-in survey of

producers who reported the presence of suspected or confirmed cases of

scrapie in their flock over a period of 5 years, including lambs and mature

sheep. The flock estimate was then expanded based on flock size to generate

the animal-level prevalence estimate. The results of the SOSS study cannot be

directly compared to the Sheep ‘96 prevalence estimate because of differences

in study design, reference population, and data collection methods.
Introduction

2 / SOSS 2003

Terms Used in

this Report

Age: Determined by examining the teeth (number of permanent incisors) in

carcass heads presented for sampling (see appendix V).

Face color: A phenotypic characteristic of sheep associated with breed.

White: Wool and/or hair on face are primarily white in color (e.g.,

Rambouillet and Dorset breeds).

Black: Wool and/or hair on face are primarily black in color (e.g., Suffolk

and Hampshire breeds).

Mottled: Some wool and/or hair on the face is darker and form spots,

freckles, or blotches that create a mottled appearance (usually associated

with crossbreds or composites).

Fiscal year, 2002 (FY02): Time period from October 1, 2001, through

September 30, 2002.

Genotypes: A codon is defined as a set of three nucleotides that encode for a

specific amino acid. Three codons that encode for amino acids at postions 136,

154, and 171 in the PrP protein have been associated with scrapie

susceptibility in sheep in the United States. However, codon 171 is thought to

be the major determinant of scrapie susceptibility in the United States.

PrP genotypes are reported as the diploid PrP genotype at codons, 136, 154,

and 171, such as QQ at codon 171. Amino acid single-letter abbreviations are

shown below:

A: alanine

H: histidine

K: lysine

Q: glutamine

R: arginine

V: valine

Mature sheep: a sheep 1 year of age or older.

No test: Samples could not be genotyped because of insufficient DNA or other

reasons.
Introduction

USDA APHIS VS / 3

Obex: A specific anatomical location in the brainstem between the cerebellum

and the medulla oblongata where a v-shaped portion of the fourth ventricle of

the brain is formed. This location is a critical area for sampling because of the

accumulation of the scrapie prion protein in this region.

Prevalence estimates: Estimates in this report were statistically weighted to

reflect the population from which the sample was selected and are provided

with a measure of precision called the standard error. A 95-percent confidence

interval can be created with bounds equal to the estimate, plus or minus two

standard errors. If the only error is sampling error, the confidence intervals

created in this manner will contain the true population mean 95 out of 100

times. For example, an estimate of 7.5 with a standard error of 1.0 results in

limits of 5.5 to 9.5 (two-times the standard error above and below the estimate).

The second estimate of 3.4 shows a standard error of 0.3 and results in limits

of 2.8 and 4.0. Alternatively, the 90-percent confidence interval would be

created by multiplying the standard error by 1.65 instead of 2. In general, when

comparing point estimates between categories, estimates with confidence

levels that overlap are not considered different. Most estimates in this report

are rounded to the nearest hundreth. If rounded to 0, the standard error was

reported. If there were no reports of the event, no standard error was reported.

Regions/States:

West: California, Oregon, and Washington

Mountain: Arizona, Colorado, Idaho, Montana, Nevada, New Mexico,

Oklahoma, Texas, Utah, Wyoming

Central: Iowa, Kansas, Minnesota, Missouri, Nebraska, North Dakota,

South Dakota

East: Alabama, Arkansas, Connecticut, Delaware, Florida, Georgia,

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

Michigan, Mississippi, New Hampshire, New Jersey, New York, North

Carolina, Ohio, Pennsylvania, Rhode Island, South Carolina, Tennessee,

Vermont, Virginia, West Virginia, Wisconsin

Multiregion: Unable to trace animals to a specific region (e.g., a group of

animals gathered from numerous States in different regions and sold at a

livestock market).

National: All regions combined, including multiregion.

Examples of a 

95% Confidence Interval

(1.0) (0.3)

Standard Errors

0

2

4

6

8

10

95% 

Confidence

Intervals
Section I: Prevalence Estimates

4 / SOSS 2003

Sample profile: Information that describes characteristics of the sample from

which SOSS data were collected (see appendix I).

Weighted estimates: Sample estimates expanded to statistically represent the

population being considered (see Section II: Methodology, D. Population

Inferences).

States/Regions
Section I: Prevalence Estimates

USDA APHIS VS / 5

Section I: Prevalence Estimates

A. Weighted Test

Results

1. Overall prevalence

Of the 12,508 mature sheep sampled, valid (at least one testable tissue) test

results were obtained from 12,491 (99.9 percent). A positive result was

recorded for any animal that tested positive by immunohistochemistry (IHC) on

one or more of the tissues sampled. The overall weighted national

prevalence of scrapie in mature sheep is 0.20 percent. Estimates could not be

made in the West region due to the low number of samples obtained. However,

national estimates include samples collected in the West region.

a. Percentage of sheep that tested positive for scrapie, by region*:

Percent Sheep 

Region 

Mountain Central East Multiregion National 

Pct. 

Std. 

Error Pct. 

Std. 

Error Pct. 

Std. 

Error Pct. 

Std. 

Error Pct. 

Std. 

Error 

0.14 (0.06) 0.21 (0.10) 0.52 (0.15) 0.13 (0.07) 0.20 (0.04) 

*Because of the low number of samples obtained in the West region, results for the 

West region are included in the National estimates but are not listed individually. 
Section I: Prevalence Estimates

6 / SOSS 2003

0.0

0.2

0.4

0.6

0.8

0.14

0.21

0.52

0.13

0.20

Mountain Central East Multiregion National

Region

Percent

Percent of Sheep that Tested Positive for Scrapie, by Region*

*Because of the low number of samples obtained in the West region, results for the 

West region are included in the National estimates but are not listed individually.
Section I: Prevalence Estimates

USDA APHIS VS / 7

2. Prevalence by tissue type

Three tissue types (obex, tonsil, and retropharyngeal lymph node) were

collected from each sheep head for IHC testing. As expected, each tissue type

differed slightly in the number tested as well as the number of positive results;

however, the prevalence was similar for the three tissue types.

a. Percentage of sheep that tested positive for scrapie, by tissue type:

Tissue Type Percent Standard Error 

Obex 0.18 (0.04) 

Tonsil 0.19 (0.04) 

Retropharyngeal 

lymph node 0.20 (0.04) 

0.0

0.2

0.4

0.6

0.18 0.19 0.20

Obex Tonsil Retropharyngeal lymph node

Tissue Type

Percent

Percent of Sheep That Tested Positive for Scrapie, by Tissue Type
Section I: Prevalence Estimates

8 / SOSS 2003

3. Prevalence by face color

Scrapie prevalence (one or more tissue samples tested positive) was highest in

black-faced sheep (0.84 percent). White-faced sheep were far less likely to test

positive for scrapie (less than 0.01 percent). Some animals were presented for

sample collection with the skin removed. Therefore, face color could not be

determined on these animals and they were not included in these estimates.

a. Percentage of sheep that tested positive for scrapie, by face color.

Face Color Percent Sheep Standard Error 

White 0.00 (0.00) 

Black 0.84 (0.19) 

Mottled 0.12 (0.07) 

0.0

0.2

0.4

0.6

0.8

1.0

0.84

0.12

White Black Mottled

Face Color

Percent

Percent of Sheep that Tested Positive for Scrapie, by Face Color

0.00
Section I: Prevalence Estimates

USDA APHIS VS / 9

4. Prevalence by age

Age was determined based on the number of visible permanent incisors (see

appendix V). Four-year-old sheep tested positive (one or more tissue samples

tested positive) most frequently (0.49 percent of sheep tested). Scrapie

prevalence increased with age until the animals reached 4 years old, then

decreased.

a. Percentage of sheep that tested positive for scrapie (national and blackfaced sheep), by age:

 Percent Sheep 

 National Black-faced 

Age Percent Standard Error Percent Standard Error 

1 and 2 years 0.11 (0.07) 0.00 (--) 

3 years 0.21 (0.11) 0.54 (0.32) 

4 years 0.49 (0.16) 1.77 (0.60) 

5 years or 

more 0.13 (0.04) 0.69 (0.24) 

0.0

0.5

1.0

1.5

2.0

Black-faced sheep

National

0.11

0.00

0.21

0.54 0.49

1.77

0.13

0.69

1 and 2 years 3 years 4 years 5 years or more

Age

Percent

Percent of Sheep that Tested Positive for Scrapie (National and 

Black-faced Sheep), by Age
Section I: Prevalence Estimates

10 / SOSS 2003

5. Logistic regression model

Black-faced sheep were significantly more likely to test positive for scrapie than

white- or mottled-faced sheep (OR = 38, p < 0.001), even when adjusting for

age and region. Age was marginally significant in association with scrapie (p =

0.06), with 4-year-old sheep more likely to test positive for scrapie than sheep

younger or older than 4 years. Although the East region had the highest scrapie

prevalence, the difference was not significant after adjusting for face color and

age.

a. Association of face color, age, and region with scrapie:

Factor Odds Ratio 

95-Percent 

Confidence 

Interval P-value 

Black Face: 

Yes 

 No 

38.4 

1.0 

10.5–139.9 Less 

than 0.001 

Age: 

Less than 4 years 

4 years 

More than 4 years 

0.6 

2.1 

1.0 

 0.2–1.7 

 0.7–6.0 0.06 

East Region: 

Yes 

No 

1.6 

1.0 

 0.6–4.3 0.36 

Note: The odds (OR) ratio is a measure of the risk of an outcome (e.g., scrapie)

for one group (e.g., blackface) compared to a reference group (e.g., white or

mottled face). The 95-percent confidence interval indicates the precision of the

OR estimate (e.g., the OR for face color could be anywhere from 10.5 to

139.9). The p-value measures the likelihood that the association is due to

chance (e.g., face color vs. scrapie; there is less than a 0.1 percent probability

this association is due to chance alone).
Section I: Prevalence Estimates

USDA APHIS VS / 11

B. Unweighted

Genetic Results

Two laboratories were sent cerebellum samples for genetic testing. The first

laboratory reported results for codon 171 only; the second laboratory reported

results for codons 136, 154, and 171. In addition, the second laboratory tested

for the K and H alleles at codon 171. The significance of these alleles to

scrapie susceptibility is still being researched.

1. Distribution of sampling

The first laboratory conducted genetic testing on 1,245 randomly selected

cerebellum samples. The RR genotype accounted for 15.74 percent of sheep

tested at the first laboratory. In addition, all sheep that tested positive for

scrapie were submitted for genetic testing.

a. Genotype distribution for tested cerebellum samples (first laboratory), by

genotype at codon 171:

Genotype 

(Codon 171) 

Number 

Cerebellum Samples Percent 

QQ 506 40.64 

QR 543 43.62 

RR 196 15.74 

Total 1,245 100.00 
Section I: Prevalence Estimates

12 / SOSS 2003

b. Genotype distribution for all tested cerebellum samples (first and second

laboratories), by genotype at codon 171:

The second laboratory tested 1,784 cerebellum samples, including 79 “no test”

samples from the first laboratory. Also, as a quality control measure, 124

samples from the first laboratory were randomly selected and tested at the

second laboratory. In addition, all positive samples were retested at the second

laboratory, if tissues were available (see table c, next page).

Genotype 

(Codon 171) 

Number 

Cerebellum Samples Percent 

QQ 1,138 39.31 

QR 1,291 44.60 

RR 454 15.68 

H* 9 0.31 

K** 3 0.10 

Total 2,895*** 100.00 

*Includes: HH, QH, RH (second lab) 

** Includes: KQ, KR (second lab) 

*** Adding the total samples tested at the first laboratory (table a) to the total 

samples tested at the second laboratory (table c) does not equal the total in 

table b. This discrepancy is due to duplicate testing and “no test” results. 
Section I: Prevalence Estimates

USDA APHIS VS / 13

c. Genotype distribution for tested cerebellum samples (second laboratory), by

genotype at codons 136, 154, and 171:

Genotype 

(Codons 136, 154, 171) 

Number 

Cerebellum Samples Percent 

**/RR/QQ 1 0.06 

AA/**/QQ 4 0.22 

AA/**/QR 10 0.56 

AA/**/RR 2 0.11 

AA/HH/QQ 5 0.28 

AA/HR/QQ 55 3.08 

AA/HR/QR 30 1.68 

AA/HR/RR 2 0.11 

AA/RR/** 2 0.11 

AA/RR/HH 1 0.06 

AA/RR/KQ 2 0.11 

AA/RR/KR 1 0.06 

AA/RR/QH 4 0.22 

AA/RR/QQ 531 29.77 

AA/RR/RH 4 0.22 

AA/RR/QR 695 38.96 

AA/RR/RR 265 14.86 

VA/**/QQ 1 0.06 

VA/**/QR 2 0.11 

VA/HH/QQ 1 0.06 

VA/HR/QQ 9 0.50 

VA/RR/QQ 86 4.82 

VA/RR/QR 63 3.53 

VV/RR/QQ 8 0.45 

Total 1,784 100.00 

**No test 
Section I: Prevalence Estimates

14 / SOSS 2003

d. Genotype distribution for tested cerebellum samples (second laboratory), by

genotype at codon 136:

e. Genotype distribution for tested cerebellum samples (second laboratory), by

genotype at codons 136 and 171:

Genotype 

(Codon 136) 

Number 

Cerebellum Samples Percent 

AA 1,613 90.47 

VA 162 9.08 

VV 8 0.45 

Total 1,783 100.00 

Genotype 

(Codons 136, 171) 

Number 

Cerebellum Samples Percent 

AA/HH 1 0.06 

AA/KQ 2 0.11 

AA/KR 1 0.06 

AA/QH 4 0.22 

AA/QQ 595 33.35 

AA/QR 735 41.20 

AA/RH 4 0.22 

AA/RR 269 15.08 

VA/QQ 97 5.44 

VA/QR 65 3.64 

VV/QQ 8 0.45 

AA/** 2 0.11 

**/QQ 1 0.06 

Total 1,784 100.00 

**No test 
Section I: Prevalence Estimates

USDA APHIS VS / 15

Tissue samples from the 33 sheep that tested positive for scrapie were

submitted for genetic testing. All 33 samples were of the QQ genotype at codon

171. This genotype has been characterized as the least resistant to scrapie.

f. Genotype distribution for postive cerebellum samples (second laboratory), by

genotype at codons 136, 154, and 171:

Genotype (Codons 

136, 154, 171) 

Number 

Cerebellum Samples Percent 

AA/RR/QQ 30 90.91 

**/RR/QQ 1 3.03 

VA/RR/QQ 2 6.06 

Total 33 100.00 

**No test 
Section II: Methodology

16 / SOSS 2003

Section II: Methodology

A. Background 1. Mature sheep slaughter and marketing

Federally-inspected slaughter for 2002 accounted for 94.1 percent of the total

commercial slaughter. There were 148,000 mature sheep slaughtered in

Federally-inspected plants in 2002. Slaughter numbers for tables a and b were

taken from the Livestock Slaughter Annual Summary published by NASS.

a. Sheep and lamb slaughter in the United States (1,000 head):

Sheep and Lamb Slaughter1

 (1,000 Head) 

Commercial Slaughter

Federally Inspected Other3

Farm 

Slaughter

Total 

Slaughter2

Year 

Mature 

Sheep Lambs Total 

Sheep 

and 

Lambs

Sheep and 

Lambs

Sheep and 

Lambs

1999 188 3,368 3,556 145 65 3,766 

2000 167 3,141 3,308 152 67 3,527 

2001 144 2,921 3,065 157 68 3,290 

2002 148 2,944 3,092 194 65 3,351 

1

NASS Livestock Slaughter Annual Summary 

2

Total commercial slaughter plus farm slaughter 

3

State and other nonfederally inspected commercial slaughter
Section II: Methodology

USDA APHIS VS / 17

The number of mature sheep slaughtered varies only slightly from month to

month. For 2002, mature sheep slaughter ranged from a low of 10,000 head in

January to a high of 14,000 head in May and October.

b. Monthly distribution of Federally-inspected mature sheep slaughter in the

United States (1,000 head):

Mature Sheep Slaughter1

 (1,000 Head) 

Year 1999 2000 2001 2002 

January 13 13 12 10 

February 13 13 10 11 

March 17 15 13 11 

April 17 13 12 12 

May 15 16 13 14 

June 17 15 12 12 

July 15 13 12 13 

August 16 15 12 12 

September 17 14 10 13 

October 15 14 13 14 

November 16 13 12 13 

December 17 13 13 13 

Total 188 167 144 148 

1

Nass Livestock Slaughter Annual Summary 
Section II: Methodology

18 / SOSS 2003

2. Mature sheep marketed to Mexico

The San Angelo, Texas market sold approximately 244,000 mature sheep in

2002 (estimated based on a summary of weekly auction reports), of which

approximately 201,000 (82.5 percent) were exported to Mexico. This market

was selected for the SOSS study because large numbers of mature sheep are

shipped to Mexico through this market and thus are not represented in U.S.

slaughter plants. The following table shows: a recent history of the number of

sheep and lambs exported to Mexico (Foreign Agricultural Service (FAS)); the

Texas live-market volume; the estimated number of mature sheep sold through

the market (60 to 65 percent of the market volume); and that a high percentage

(80 to 85 percent) of the mature sheep sold through the market go to Mexico

(USDA-Texas Department of Agriculture Market News estimate).

a. Annual sheep exports to Mexico (FAS) and sheep sold at the Texas live

market (USDA-Texas Department of Agriculture Market News estimate):

Texas Live Market2 Live Sheep 

Exported to 

Mexico1 Total Sheep 

and Lambs 

Mature 

Sheep 

Mature Sheep 

to Mexico 

Year 

No. 

(1,000 Head) 

No. 

(1,000 Head) 

No. 

(1,000 Head) 

Est. 

Pct. of 

Total 

No. 

(1,000 Head) 

Est. 

Pct. of 

Mature 

1999 435 404 253 62.6 209 82.5 

2000 378 448 269 60.0 222 82.5 

2001 383 337 211 62.5 174 82.5 

2002 403 390 244 62.5 201 82.5 

1

Foreign Agricultural Service (FAS) 

2

USDA—Texas Department of Agriculture Market News
Section II: Methodology

USDA APHIS VS / 19

3. Projected number of sheep culled

a. In the United States, the number of mature sheep culled in a single year

varies and is difficult to measure directly. Four different methods were used to

project or estimate the number of head culled in 2002:

Methods 1 and 2 use similar calculations but different slaughter components.

Method 1 uses FY02 data and sums the mature sheep slaughter in Federallyinspected plants (144,201 head) and the number of live sheep exported to

Mexico (403,000 head) for a total of 547,201 head culled. Method 2 uses NASS

annual slaughter data for mature sheep and yields a total of 551,000 head

culled. The results from these two slaughter indicators are similar. The results

assume that: most culled sheep that remain in the United States are

slaughtered in Federally-inspected facilities; most live sheep exported to

Mexico are cull sheep; and that there is not a substantial number of cull sheep

exported to other countries.

Method 

Projected Number 

of Sheep Culled in 2002 

1. FSIS FY02 mature sheep slaughter 

+Export of live animals to Mexico 

=Cull indicator or total culled 

 144,201 

403,000 

547,201 

2. NASS annual mature slaughter 

+Export of live animals to Mexico 

=Cull indicator or total culled 

 148,000 

403,000 

551,000 

3. Ewes* (Jan. 1 end-of-year NASS inventory) 

 Rams* (Jan. 1 end-of-year NASS inventory) 

 Ewe cull rate @ 18.3 percent (NAHMS) 

+ Ram cull rate @ 23.8 percent (NAHMS) 

 =Ewes and rams culled 

x Mature culled @ 90 percent (estimate) 

 3,789,000 

191,500 

693,387 

45,577 

738,964 

665,068 

4. Replacement lambs (Jan. 1 end-of-year NASS

 inventory) 

- Sheep deaths (NASS) 

=Cull indicator or total culled 

701,500 

 (263,900) 

437,600 

*Ewes/Rams 1 year or older 
Section II: Methodology

20 / SOSS 2003

The third method applies the overall culling rate. Data from the NAHMS Sheep

2001 study indicated that 18.3 percent of ewes and 23.8 percent of rams were

culled. Further, it is roughly estimated that 90 percent of culled sheep are

mature sheep, resulting in an estimate for 2002 of 665,068 head. However, the

2002 estimate may be high since sheep culled from one producer could have

ended up in another producer’s inventory and been counted twice.

The fourth method uses the NASS end-of-year estimate for the number of

replacement lambs. NASS estimated the number of replacement lambs for

January 1, 2003, to be 701,500 head. These lambs not only replaced the cull

breeding stock but also replaced any mature sheep death loss that occurred

during the year. NASS provides separate estimates of death loss for sheep and

for lambs. The resulting indicator for number culled in 2002 is 437,600 head.

For all four methods, these approaches yield estimates for number of sheep

culled in 2002 at 547,201, 551,000, 665,068, and 437,600 head, respectively.

The two slaughter approaches yield similar results. The two inventory

approaches vary widely on each side of the slaughter approaches. For SOSS

purposes, a rounded “average” of 550,000 head was chosen to represent the

cull sheep population.

If the U.S. slaughter is estimated at 148,000 (NASS), then the remaining

403,000 are exported (primarily to Mexico). In 2002 an estimated 244,000 cull

sheep moved through the market at San Angelo, Texas (USDA-Texas

Department of Agriculture Market News). Of these 244,000 animals,

approximately 80 to 85 percent (201,000) went to Mexico and the rest

remained in the United States. Thus, the San Angelo market represents about

50 percent (201,000/403,000) of the mature sheep export to Mexico.
Section II: Methodology

USDA APHIS VS / 21

B. Sampling 1. Total sample size

A minimum sample size requirement of 11,000 was calculated based on the

previous prevalence estimate of 0.07 percent (+/- .05 percent, with 95-percent

confidence). The actual sampling plan exceeded this estimate in order to

ensure an adequate sample size.

A total of 12,508 animals were sampled between April 1, 2002, and March 31,

2003. Obex, tonsil, and lymph-node tissues from each sheep were tested using

the immunohistochemistry (IHC) technique at NVSL and its approved

laboratories (see appendix IV). A positive case was defined as having a

positive test result on any tissue. Approximately one-fourth of the cerebellum

samples were submitted for genetic testing. In addition, all sheep that tested

positive for scrapie were submitted for genetic testing.

2. Plant selection and sampling allocation

Slaughter plants were selected based on historical slaughter of mature sheep

at Federally-inspected slaughter facilities (FSIS FY2001 data). The 21 highest

volume FSIS-inspected plants were selected. In addition, a high-volume Stateinspected plant was selected. Plants were grouped into strata based on

volume. Each stratum was allocated samples based on historic volume for the

stratum. Each plant stratum was then allocated a weekly sampling goal for a

total of 15,050 samples allocated for the 50-week collection period. Collections

from smaller plants were often taken biweekly or monthly due to the

fluctuations in mature sheep slaughter times at these facilities.

a. Number of samples allocated:

Samples Per Week 50-Week Total

Stratum 

No. 

Plants 

Per 

Stratum 

Per 

Plant 

Per 

Stratum 

Per 

Plant 

Total 

Samples 

Collected

1 (mkt.) 1 150 150 7,500 7,500 6,969 

2 5 75 15 3,750 750 3,052 

3 5 40 8 2,000 400 1,319 

4 12 36 3 1,800 150 1,168 

Total 23 301 15,050 12,508 
Section II: Methodology

22 / SOSS 2003

3. Animal selection

Sample collectors were instructed to collect samples using systematic

sampling. Sheep were selected based on the number of animals needed to

meet the weekly plant allocation.

4. Laboratory allocations

Samples were submitted to NVSL for testing or for distribution to approved

laboratories. Laboratory distribution was dependent on the number of

laboratories with available testing capacity. Efforts were made to evenly

distribute samples from each plant to all participating laboratories.

For quality control, all positive samples and one-eighth of all negative samples

were retested by NVSL to confirm the results.

5. Genetic testing

One in four cerebellum samples was randomly selected for genetic testing

using a random numbers table. In addition, all positive cerebellum samples

were submitted for genetic testing. One laboratory provided codon 171 results.

A second laboratory provided results at codons 136, 154, and 171.
Section II: Methodology

USDA APHIS VS / 23

C. Region of

Origin

Sheep were traced to State of origin based on ear tags and/or other information

obtained by the collector at the plant or market. For analysis purposes, samples

identified to individual States were assigned to one of four defined regions.

Sometimes only a listing of multiple States could be obtained for a group of

sheep (e.g., market animals accumulated across numerous states). These

samples were assigned to the Multiregion category if the States they came from

were not all in the same region. In cases where a trace State was not identified

by the collector (n = 2,020), a region was assigned based on their official

identification information. The 2001 NAHMS Sheep study showed that at least

95 percent of cull sheep movement was within the region of origin.

D. Population

Inferences

The study included 22 major mature sheep slaughter plants throughout the

United States (21 FSIS inspected, 1 State plant), and one large livestock

market in Texas. Inferences cover the population of mature sheep from these

sources. The 21 FSIS plants represented approximately two-thirds of the total

FSIS mature sheep slaughtered during the study period. The livestock market

represented approximately one-half of the live sheep exported to Mexico. All

sample data were statistically weighted to reflect the population from which the

sample was selected. The number of samples collected from each plant on a

specific day was statistically weighted to represent the volume of mature sheep

slaughtered (sold) through each plant (market) that specific day. This weight

was adjusted for the total volume of mature sheep through the plant (market)

from April 2002 through March 2003. Results of genotype testing were

unweighted because of the small sample size. Overall, the samples collected

from the 22 plants and the livestock market represented 299,000 sheep (54

percent of the cull sheep population, estimated at 550,000 head).

E. Data

Validation and

Analysis

Data were double-entered into SAS data sets. Data were validated using

double entry comparison (SAS Proc Compare). Additional data validation was

performed by APHIS/VS/CEAH staff after all data were entered. Final analysis

was accomplished using SUDAAN software.
Appendix I: Sample Profile

24 / SOSS 2003

Appendix I: Sample Profile

a. Number of samples submitted, by face color and by region:

b. Number of samples submitted, by age and by region:

 Samples Submited 

 Region 

Face Color West Mountain Central East Multiregion Total 

Black 100 535 680 1,023 453 2,791 

White 493 2,997 1,993 1,283 1,472 8,238 

Mottled 71 305 413 404 194 1,387 

Unknown 6 32 4 42 8 92 

Total 670 3,869 3,090 2,752 2,127 12,508 

 Samples Submited 

 Region 

Age West Mountain Central East Multiregion Total 

1-2 years 28 161 178 413 109 889 

3 years 41 163 181 414 100 899 

4 years 100 410 430 1,053 178 2,171 

5+ years 492 3,107 2,293 832 1,723 8,447 

Unknown 9 28 8 40 17 102 

Total 670 3,869 3,090 2,752 2,127 12,508 
Appendix I: Sample Profile

USDA APHIS VS / 25

c. Number of samples submitted, by month:

Month Samples Submitted 

April 2002 809 

May 2002 1,492 

June 2002 1,234 

July 2002 990 

August 2002 1,158 

September 2002 1,179 

October 2002 1,325 

November 2002 926 

December 2002 828 

January 2003 825 

February 2003 832 

March 2003 910 

Total 12,508 
Appendix II: U.S. Sheep Inventory and Operations (NASS)

26 / SOSS 2003

Appendix II: U.S. Sheep Inventory and Operations

 NASS1

 

Breeding Sheep 

1-year and older 

January 1, 2003 

 Ewes Rams Total 

Number of 

Operations with 

Sheep 2002 

Region State 

Head 

(1,000) 

Head 

(1,000) 

Head 

(1,000) Pct.

Number 

(1,000) Pct.

West California 295.0 10.0 305.0 2,800 

 Oregon 125.0 7.0 132.0 3,100 

 Washington 34.0 2.0 36.0 1,200 

 Total 454.0 19.0 473.0 11.9 7,100 11.1

Mountain Arizona 56.0 3.0 59.0 270 

 Colorado 155.0 6.0 161.0 1,900 

 Idaho 184.0 5.0 189.0 1,000 

 Montana 213.0 8.0 221.0 1,700 

 Nevada 65.0 2.0 67.0 300 

 New Mexico 140.0 9.0 149.0 800 

 Oklahoma 41.0 3.0 44.0 1,500 

 Texas 680.0 40.0 720.0 6,800 

 Utah 250.0 9.0 259.0 1,400 

 Wyoming 295.0 10.0 305.0 800 

 Total 2,079.0 95.0 2,174.0 54.6 16,470 25.7

Central Iowa 135.0 7.0 142.0 4,600 

 Kansas 47.0 2.5 49.5 1,400 

 Minnesota 85.0 5.0 90.0 2,300 

 Missouri 48.0 3.0 51.0 1,600 

 Nebraska 56.0 3.0 59.0 1,500 

 North Dakota 77.0 3.0 80.0 1,000 

 South Dakota 265.0 10.0 275.0 2,300 

 Total 713.0 33.5 746.5 18.8 14,700 22.9

East Illinois 42.0 3.0 45.0 2,200 

 Indiana 34.0 2.5 36.5 2,000 

 Michigan 41.0 2.0 43.0 1,900 

 New England* 32.0 3.0 35.0 2,000 

 New York 40.0 3.0 43.0 1,500 

 Ohio 97.0 6.0 103.0 3,500 

 Pennsylvania 55.0 5.0 60.0 2,600 

 Virginia 38.0 3.5 41.5 1,500 

 West Virginia 23.0 1.0 24.0 1,100 

 Wisconsin 52.0 3.0 55.0 2,300 

 Other States** 89.0 12.0 101.0 5,300 

 Total 543.0 44.0 587.0 14.7 25,900 40.3

U.S. 3,789.0 191.5 3,980.5 100.0 64,170 100.0

1Source: National Agricultural Statistics Service (NASS), USDA; NASS Sheep and Goats, January 31, 2003 

*New England includes CT, ME, MA, NH, RI, and VT 

**Other States not published individually include AL, AK, AR, DE, FL, GA, HI, KY, LA, MD, MS, NJ, NC, SC, and 

TN. Note that AK and HI cannot be removed individually from this grouping. 
 Appendix III: Scrapie: Ovine Slaughter Surveillance – Phase I Information Sheet

USDA APHIS VS / 27

Appendix III: Scrapie: Ovine Slaughter Surveillance –

Phase I Information Sheet

Veterinary Services 

Centers for Epidemiology and Animal Health March 2003 

_______________________________________________________________________________________________________________________________________ 

Scrapie: Ovine Slaughter 

Surveillance — Phase I 

Overview 

The overall objective of the Scrapie: Ovine 

Slaughter Surveillance (SOSS) study is to estimate 

the national and regional prevalence of scrapie in 

mature cull sheep entering slaughter channels. The 

study was initiated at the request of members of the 

sheep industry, who wanted to accelerate 

eradication of the disease. 

Beginning in February 2001 and ending in 

March 2002, Phase I included the study design, 

methods development, and sample-collection 

training. The objective of Phase I was to develop 

and modify the sample collection and testing 

processes, without emphasizing statistical results. 

Phase II, which is the actual prevalence study, 

started April 1, 2002, and will continue for 

approximately 1 year. The number of samples to be 

collected from each participating plant on a weekly 

or bi-weekly basis was determined based on the 

number of cull ewes killed at the plant in 2001. 

Phase III will evaluate and analyze data received 

during Phase II. Phase III results will be published 

in fall 2003. 

Phase I Methods 

The slaughter plants selected to participate in 

SOSS Phase I were identified based on historical 

slaughter data obtained through the Food Safety 

and Inspection Service and the National 

Agricultural Statistics Service. Since the currently 

accepted diagnostics are for adult animals, plants 

that slaughtered large numbers of mature cull ewes 

were targeted for the SOSS study. 

Coordinators and sample collectors were 

selected for each State with a participating plant. 

Coordinators served as primary contacts in their 

States and were responsible for ensuring that the 

correct number of quality samples were submitted, 

supplies were ordered and provided to collection 

personnel, and information was disseminated as 

needed. Sample collectors were responsible for the 

actual collection of tissues at the slaughter plants. 

Training the sample collectors was a critical 

component of SOSS Phase I and was 

accomplished via hands-on instruction and a 

Procedures Manual that identified the specific 

anatomical locations of the needed tissues. As the 

study progressed, regular field reports were 

produced to inform collectors of the quality of their 

submitted samples. 

Established goals for submitting proper tissue in 

desirable condition were defined and met prior to 

Phase II of the study. 

Diagnostic laboratories were contracted by the 

National Veterinary Services Laboratory (NVSL). 

Three contract labs were used for Phase I. Before 

SOSS tissues were submitted, laboratory personnel 

were trained and the labs were approved by NVSL. 

To remain consistent with Phase I objectives, 

convenience sampling, which is sampling at will 

and without regard to randomness, was used for all 

samples taken during Phase I. 

A standard kit was used that included tools and 

materials to collect, package, and ship the needed 

tissues to NVSL. 

Samples were collected from the brainstem 

(obex), cerebellum, both tonsils, both 

retropharyngeal lymph nodes, and the lymphoid 

tissue of the third eyelid. 

At the time of tissue collection, data regarding 

each head were recorded on a submission form. 

These data included a unique sample number, 

animal identification, face color, and age of the 

animal based on the number and condition of 

permanent teeth. Ear tags and plant or market 

records (when available), and the Veterinary 

Services generic data base were used to determine 

the region of animal origin. 

Phase I Findings 

SOSS Phase I was a “pilot” project. Samples 

were not collected with the intention of performing 

rigorous statistical analysis. Therefore, results 

shown below do not reflect the U.S. cull ewe 

population. 
Appendix III: Scrapie: Ovine Slaughter Surveillance – Phase I Information Sheet

28 / SOSS 2003

__________________________________________________ 

Tissue samples were collected from 1,159 cull 

ewes in 23 slaughter plants from 13 States. 

__________________________________________________

Sheep Face 

Color Number Percent 

White 648 55.9 

Black 318 27.4 

Mottled 143 12.4 

Not recorded 50 4.3 

 Total 1,159 100.0 

Age of Sheep Number Percent 

1 year 54 4.7 

2 years 127 10.9 

3 years 201 17.3 

4 years 407 35.1 

5 years or older 338 29.2 

Not recorded 32 2.8 

 Total 1,159 100.0 

__________________________________________________ 

Tissues were tested using the 

immunohistochemistry technique (IHC). 

__________________________________________________ 

Tissue Test 

Result (IHC) Obex Tonsil 

Lymph 

Node 

Negative 1,079 939 1,139 

Positive 2 2 2 

Untestable 78 218 18 

 Total 1,159 1,159 1,159 

_____________________ 

For more information, contact: 

USDA:APHIS:VS:CEAH 

NRRC Building B., M.S. 2E7 

2150 Centre Avenue 

Fort Collins, CO 80526-8117 

970.494.7000 

E-mail: NAHMSweb@aphis.usda.gov 

www.aphis.usda.gov/vs/ceah/cahm

#N390.0303 

________________________________________________

Genotype results were obtained for 611 of the 

1,159 samples. 

 _________________________________________________ 

Genotype Results Number Percent

QQ 237 20.4 

QR 279 24.1 

RR 95 8.2 

XX (not testable) 44 3.8 

Not tested 504 43.5 

Total 1,159 100.0 

Two animals out of the 1,159 tested were 

positive for scrapie. In these animals, all three 

tissues (obex, tonsil, and lymph node) tested 

positive. Both were 4-year-old ewes and were QQ 

genotypes. One was white -faced, the other blackfaced. Neither sample could be identified back to 

the region of origin. 

Lessons Learned 

Phase I allowed for the development of plant 

relations, modification of forms, and the fine-tuning 

of tissue collection protocols before the 

implementation of the full study in April of 2002. 

Since approximately two-thirds of all mature cull 

ewes are exported to Mexico annually, a livestock 

market sampling protocol was developed for Phase 

II that calls for the sampling of sheep that are 

typically exported to Mexico and not sent to 

domestic slaughter plants. 

An instructional CD-ROM containing video 

clips, color pictures, and the SOSS instruction 

manual was developed and distributed for Phase II. 

By the time Phase II began, proficiency (percent 

testable tissues) for each tissue type was at least 

80 percent. 

Collecting third eyelid tissue from dead animals 

was extremely difficult and was stopped a few 

months into Phase I. 

Additional diagnostic laboratories were 

contracted by NVSL to assist with the increased 

workload during Phase II. 

________________________________________________________

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 status 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, 1400 

Independence Avenue, SW, Washington, DC 20250-9410 or call (202) 720-5964 

(voice and TDD). USDA is an equal opportunity provider and employer.
 Appendix IV: Laboratory Selection and Results

USDA APHIS VS / 29

Appendix IV: Laboratory Selection and Results

a. Participating laboratories

Immunohistochemistry:

University of California – Davis (CAHFS)

Colorado State Universtiy Diagnostic Lab

Cornell University Animal Health Diagnostic Laboratory

Kansas State University

Michigan State University

National Veterinary Services Laboratory (NVSL)

University of Nebraska Veterinary Diagnostic Center

Ohio Department of Agriculture Animal Disease Diagnostic Laboratory

Texas Veterinary Medical Diagnostic Laboratory

Wyoming State Veterinary Laboratory

Genetics:

USDA Agricultural Research Service – Pullman, Washington

University of California – Davis

GeneSeek

Qiagen

b. Sample distribution and positive results:

Samples 

Laboratory 

Number 

Heads 

Tested 

Percent 

of Total 

Tested 

Number 

Positive 

Percent 

of Total 

Positives 

University of 

California – Davis 2,377 19.0 6 18.2 

Colorado State University 

Diagnostic Lab 1,799 14.4 8 24.3 

Cornell University Animal 

Health Diagnostic Laboratory 241 1.9 2 6.1 

Kansas State University 284 2.3 1 3.0 

Michigan State University 968 7.7 3 9.1 

National Veterinary Services 

Laboratory 1,064 8.5 1 3.0 

University of Nebraska 

Veterinary Diagnostic Center 370 3.0 1 3.0 

Ohio Department of 

Agriculture Animal Disease 

Diagnostic Laboratory

 572 4.6 1 3.0 

Texas Veterinary Medical 

Diagnostic Laboratory1 2,232 17.9 4 12.1 

Texas Veterinary Medical 

Diagnostic Laboratory2 1,256 10.1 2 6.1 

Wyoming State 

Veterinary Laboratory 1,328 10.6 4 12.1 

Total 12,491 100.0 33 100.0 

1

Amarillo location; 2Texas-College Station location 
Appendix V:Age Determination

30 / SOSS 2003

Appendix V: Age Determination by Teeth Examination

 Observe size of first incisors. Observe size of first incisors.

Observe first incisors and eruption Observe eruption of third incisors.

of second incisors.

 Adult sheep with full mouth. Broken mouth (sheep 5 years and

 older, incisors erupted).