Veterinary Services

Surveillance, Preparedness, and Response Services 

Animal and Plant Health Inspection Service 

Final Report for the 2017 Outbreak of Highly 

Pathogenic Avian Influenza (HPAI)/Low 

Pathogenicity Avian Influenza (LPAI) 

in the Southeastern United States

August 8, 2017

Public Version
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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Handling Instructions

1. The title of this document is USDA APHIS Final Report for the 2017 Outbreak of Highly

Pathogenic Avian Influenza (HPAI)/Low Pathogenicity Avian Influenza (LPAI) in the 

Southeastern United States, also referred to as “this document.”

2. Reproduction of this document, in whole or in part, without prior approval from Animal 

and Plant Health Inspection Service (APHIS) Veterinary Services (VS) National 

Preparedness and Incident Coordination is prohibited.

For more information, please consult the following point of contact:

Dr. Jon Zack

Director, National Preparedness and Incident Coordination

Surveillance, Preparedness, and Response Services

U.S. Department of Agriculture APHIS VS

4700 River Road, Unit 41

Riverdale, MD 20737

Jonathan.T.Zack@aphis.usda.gov

Acknowledgments

Many individuals and groups contributed to this outbreak’s successful response: affected poultry 

owners and growers responded quickly and effectively, as did State Animal Health Officials and 

their staffs. Numerous personnel effectively supported the response activities in Tennessee, Alabama, 

Kentucky, and Georgia—including, but not limited to—personnel from District 2 and District 3, 

Surveillance, Preparedness, and Response Services (SPRS), members of the VS National Incident 

Management Teams, the Center for Epidemiology and Animal Heath (CEAH), SPRS Logistics 

Center, APHIS Dispatch, National Poultry Improvement Plan (NPIP) staff, Avian Health 

Commodity Center, and Wildlife Services. A special thanks goes to the Emergency Management 

Response System 2.0 Specialists for information management activities throughout the incident, as 

well as the Avian Section at the National Veterinary Services Laboratories Diagnostic Virology 

Laboratory, Tennessee Alabama, Kentucky, and Georgia National Animal Health Laboratory 

Network (NAHLN) laboratories, and members of the National Incident Coordination Group who

contributed to this report. 
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Executive Summary

Incident Overview

After the 2014–2015 outbreak of highly pathogenic avian influenza (HPAI) in the United States, as 

well as the Indiana HPAI/low pathogenicity avian influenza (LPAI) outbreak in 2016, the U.S. 

Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) and 

poultry producers remained on high alert for HPAI in 2017. In early March, based on the appearance 

of clinical signs, a Tennessee commercial broiler breeder flock in Lincoln County was suspected to 

have HPAI. On March 3, 2017, samples from that farm were presumptive positive for the H7 

influenza subtype at a National Animal Health Laboratory Network (NAHLN) laboratory. At this 

time, HPAI response activities in Tennessee were initiated immediately, with State and Federal 

agreement, as the presumptive positive case definition for HPAI had been met. The next day, the 

National Veterinary Services Laboratories (NVSL) confirmed HPAI on the premises. The virus was 

subsequently identified as H7N9 of North American wild bird lineage (unrelated to Asian H7N9 

viruses). Surveillance in commercial and backyard premises began immediately. Four days later, on 

March 8, 2017, NVSL confirmed LPAI H7N9 in a neighboring Tennessee county, again in a 

commercial broiler breeder flock. In total, between March 4 and March 25, 2017, 14 premises were 

identified with confirmed H7 or confirmed H7N9 infection. In total, HPAI was confirmed on 2 

premises—the index case and a second commercial broiler breeder flock, both in Lincoln County. 

The remaining 12 premises had confirmed or presumptive LPAI: 6 commercial premises and 6 

backyard flocks.

There were no additional H7/H7N9 HPAI or LPAI detections in commercial or backyard flocks after 

March 25, 2017. Wild bird surveillance on and around the Infected Premises did not yield any 

positive H7 avian influenza (AI) results. The HPAI Infected Premises were depopulated rapidly, as 

were 9 of the 12 LPAI Infected Premises. One LPAI infected backyard premises conducted targeted 

euthanasia; additionally, two other LPAI infected backyard premises with no clinical signs did not 

depopulate. These three premises underwent intensified surveillance to be released from quarantine. 

In all, nearly 253,000 birds were depopulated as part of these HPAI and LPAI detections in the 

southeastern United States. 

This 2017 incident enabled yet another region in the United States to exercise their AI preparedness 

and response procedures; for APHIS, it offered a refresher of AI response and the ability to practice 

the improved processes and procedures that have been implemented since 2014–2015. This

successful HPAI/LPAI response in the southeast United States was largely based on the lessons 

learned by APHIS, States, and the poultry industry in the prior AI incidents.

Summary of Response Activities

In response to the HPAI detections, the State Animal Health Officials in Tennessee and Alabama,

alongside APHIS Veterinary Services (VS), took the lead in coordinating the response. A unified 

State-Federal Incident Command was established for Tennessee and Alabama, the region where the 

HPAI detections and HPAI Control Areas were located. For the LPAI detections in Kentucky and 

Georgia, these State Animal Health Officials led the LPAI response effort in their respective States.

Additional VS personnel supported activities—as requested by State Animal Health Officials—in

response to the LPAI detections.
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The response to the outbreak included the following activities at the national and/or field levels:

• Planning and conducting disease surveillance.

• Collecting samples and diagnostic testing.

• Planning and carrying out epidemiological investigations and tracing.

• Managing information from the field to the national level.

• Coordinating and communicating with State, local, and industry stakeholders.

• Providing guidance on personal protective equipment and responder health and safety and 

ensuring safety officers were in the field.

• Providing guidance and supervision on biosecurity measures.

• Conducting quarantine and movement control activities.

• Supporting continuity of business and issuing permits for the HPAI Control Area.

• Providing information and documentation for regionalization for international trade.

• Conducting and providing resources and guidance for mass depopulation and euthanasia.

• Safeguarding animal welfare during response operations. 

• Offering subject matter expertise for disposal.

• Providing guidance and options for cleaning and disinfection (virus elimination).

• Managing logistics through the National Veterinary Stockpile.

• Implementing revised financial procedures for appraisal and indemnity and providing support 

for compensating HPAI-infected poultry owners and contract growers.

• Providing overall incident management, support, and objectives.

APHIS contractors supported depopulation efforts, using foam, on both HPAI Infected Premises. On 

LPAI premises that depopulated, the company or producer typically led depopulation efforts with the 

assistance of State personnel, as required by the situation. A variety of methods were used for these

LPAI premises, including foam, KEDS, cervical dislocation, and CO2. Ventilation shutdown was not 

implemented during this outbreak. 

In terms of disposal, premises that depopulated birds used on-site burial (12 of 12). The 11 Infected 

Premises (9 LPAI; 2 HPAI) that depopulated in full also conducted cleaning and disinfection

activities (also known as virus elimination): 7 applied wet disinfectant, 2 conducted heat treatment, 1 

elected to fumigate, and 1 underwent an extended fallow period. The previously-infected HPAI 

premises were approved to restock on June 4, 2017: all premises were approved to conduct 

restocking by June 16, 2017.

Organizational Response

A unified Incident Command was established in Nashville on March 4, 2017, comprised primarily of 

personnel from Surveillance, Preparedness, and Response Services (SPRS) District 2 and the 

Tennessee Department of Agriculture. Because the HPAI Control Area boundary also included part 

of Madison County, Alabama, personnel from the State of Alabama also joined the unified Incident 

Command. Other APHIS personnel also supported SPRS District 2 responders in the unified Incident 

Command, both on-site and virtually, with activities like surveillance, finance/administration, and 

epidemiology for the HPAI Infected Premises and LPAI Infected Premises associated with the HPAI 

detections. SPRS District 2 personnel supported activities associated with the LPAI Infected 

Premises in Kentucky and Georgia; these States were not part of the unified Incident Command.
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The National Incident Coordination Group (ICG) was immediately ramped up when the presumptive 

positive case definition for HPAI was met; this group was prepared to support unified Incident 

Command operations. At the height of the response, the ICG consisted of approximately 20 people 

devoting significant time for the HPAI/LPAI outbreak in the southeastern United States. 

End of Outbreak and Cost

The HPAI Control Areas were released on April 11, 28 days after NVSL had confirmed the second 

HPAI infection. Response operations, including virus elimination, environmental sampling, and 

restocking approvals were completed throughout late spring. The final Infected Premises quarantine 

(an LPAI backyard premises) was released on June 16, 2017. For the 2017 H7N9 incident, the total 

commitments for indemnity on the HPAI premises, as well as obligations for overall response 

operations, was approximately $2.79 million. In 2017, indemnity funds were provided by APHIS for 

depopulated birds on HPAI Infected Premises; compensation was also provided to HPAI Infected 

Premises for virus elimination activities. In this incident, LPAI Infected Premises that made the 

decision to depopulate—in coordination with State officials—did not receive APHIS indemnity 

funds for depopulated birds or compensation for virus elimination activities.
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Contents

Handling Instructions................................................................................................................ iii

Acknowledgments..................................................................................................................... iii

Executive Summary ....................................................................................................................v

Section 1. Background ................................................................................................................1

Purpose....................................................................................................................................1

Nature of Disease ....................................................................................................................1

Prior Outbreaks in the United States........................................................................................1

The Foundation of Preparedness..............................................................................................2

Section 2. Characteristics of the 2017 H7 Southeastern Outbreak ................................................3

Scope of the Outbreak..............................................................................................................3

Disease Incidence ....................................................................................................................6

Subtyping and Pathotyping ......................................................................................................8

Viral Traits............................................................................................................................10

Introduction & Transmission .................................................................................................10

Section 3. Overview of Response Effort....................................................................................10

Regulatory Intervention .........................................................................................................10

Financial Resources...............................................................................................................11

Economic & Trade Impact.....................................................................................................11

Personnel...............................................................................................................................12

Section 4. Incident Management ...............................................................................................12

Overview...............................................................................................................................12

National Incident Coordination Group and APHIS Multiagency Coordination Group ............14

APHIS Multiagency Coordination Group...........................................................................14

National Incident Coordination Group ...............................................................................14

APHIS VS National Incident Management Teams & Deployments........................................17

APHIS Personnel Deployments..........................................................................................17

Contractors............................................................................................................................19

Section 5. Incident Coordination Group Response and Support Activities................................20

Overview...............................................................................................................................20

Reporting and Communicating Information...........................................................................20

Deployment/Personnel Management......................................................................................21

Policy and Guidance ..............................................................................................................21

Health and Safety ..................................................................................................................23

Section 6. Highlights of Response Activities.............................................................................23

Overview...............................................................................................................................23

Surveillance and Epidemiology..............................................................................................25
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Surveillance Around HPAI Infected Premises....................................................................25

Surveillance Around LPAI Infected Premises ....................................................................25

Incident Coordination Group and Unified Incident Command Activities............................25

Diagnostics............................................................................................................................29

Quarantine, Movement Control, and Continuity of Business..................................................29

State Quarantines and Unified Control Areas.....................................................................29

Movement Control and Continuity of Business..................................................................30

Depopulation .........................................................................................................................32

Disposal.................................................................................................................................33

Virus Elimination (Cleaning and Disinfection) ......................................................................35

Biosecurity ............................................................................................................................36

Health and Safety ..................................................................................................................37

Appraisal & Compensation....................................................................................................37

Indemnity for Birds Destroyed ...........................................................................................37

Compensation for Response Activities...............................................................................37

Logistics................................................................................................................................38

Restocking.............................................................................................................................38

Information Management & Reporting ..................................................................................39

Communications....................................................................................................................40

Section 7. Preparedness and Future Planning.............................................................................40

Section 8. Conclusion................................................................................................................41

Section 9. Abbreviations ...........................................................................................................44

Section 10. List of Appendices..................................................................................................46

Tables

Table 1. HPAI Outbreaks in the United States.............................................................................2

Table 2. List of Affected Premises ..............................................................................................9

Table 3. Premises Sampled and Number of Accessions as Surveillance for the 2017 HPAI 

Detections.................................................................................................................................26

Table 4. Premises Sampled and Number of Accessions as Surveillance for the 2017 LPAI 

Detections.................................................................................................................................28

Figures

Figure 1. Affected Counties in the 2017 H7 Outbreak ................................................................4

Figure 2. HPAI and LPAI H7/H7N9 Detections in the Southeastern United States, 

by Flock Type .............................................................................................................................4
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Figure 3. Approximate Number of Birds Affected in the Southeastern United States, by State and 

Production Type..........................................................................................................................5

Figure 4. Birds Affected in the Southeastern United States, by Production Type .........................5

Figure 5. All Detections by Flock Type and by NVSL Confirmation Date...................................7

Figure 6. Epidemiological Curve by Earliest Known Date of Infection........................................8

Figure 7. NVSL Confirmed Results for All Premises (Subtype & Pathotype) ..............................9

Figure 8. Overview of USDA APHIS Organizational Structure for Incident..............................13

Figure 9. Details of the USDA APHIS Organizational Structure for Incident.............................14

Figure 10. Total Number of APHIS Personnel Assigned to the National ICG at APHIS Hub or 

Home Location, by Organizational Unit ....................................................................................15

Figure 11. National Incident Coordination Group Structure During 2017 H7 Incident ...............16

Figure 12. Total Number of APHIS and State Personnel Deployed per Day ..............................17

Figure 13. Total Number of APHIS Personnel Deployed to the Field by Organizational Unit ...18

Figure 14. Total APHIS Deployments, by Appointment Type ...................................................18

Figure 15. Contractor Support for Response Operations for HPAI Infected Premises ................19

Figure 16. A Guide to Help You Understand the Response Process...........................................24

Figure 17. Number of Premises Sampled (First HPAI Control Area & Surveillance Zone)........27

Figure 18. Number of Premises Sampled (Second HPAI Control Area & Surveillance Zone)....27

Figure 19. Length of Quarantine on All Premises (Frequency Count)........................................30

Figure 20. Number of Permitted Movements During Incident by State of Destination (Control 

Area in Place; Three-Day Increments).......................................................................................31

Figure 21. Number of Permitted Movements by Item and Permit Class.....................................32

Figure 22. Time in Days to Depopulation from NVSL Confirmation (Frequency Count)...........33

Figure 23. Primary Disposal Method for Carcasses & Materials................................................34

Figure 24. Time in Days to Disposal Complete from NVSL Confirmation (Frequency Count) .34

Figure 25. Disinfection Method Used........................................................................................35

Figure 26. Time to Virus Elimination/C&D Complete (in Days) ...............................................36

Figure 27. Restock Approval Date for All Premises ..................................................................39

Figure 28. Time in Days to Restock Approval from NVSL Confirmation Date..........................39

Figure 29. 2017 AI Outbreak in Southeastern United States with Disease Status.......................41

Figure 30. 2017 Overall Timeline..............................................................................................42
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Section 1. Background

Purpose 

This document presents an overview of the 2017 high pathogenicity avian influenza (HPAI)/low 

pathogenicity avian influenza (LPAI) outbreak in the southeastern United States. It focuses on 

the characteristics of the outbreak, organizational structure employed in the response, activities 

of the Incident Coordination Group (ICG), and summary highlights of the field response 

measures. It is not an After Action Report, nor does it systemically identify corrective actions.

Please see the U.S. Department of Agriculture (USDA) Animal and Plant Health Inspection 

Service (APHIS) After Action Report for the 2017 Outbreak of HPAI/LPAI in the Southeastern 

United States for this information. The 2017 HPAI/LPAI incident response was largely based on 

the lessons learned in the 2014–2015 HPAI outbreak as well as the 2016 HPAI/LPAI outbreak in 

Indiana.

Nature of Disease

Avian influenza is an infectious disease of birds including poultry, such as chickens and turkeys. 

At times, it can be fatal. Influenza A viruses are broadly categorized based on a combination of 

two groups of proteins on the surface of the influenza A virus: hemagglutinin or “H” proteins, of 

which there are 16 (H1-H16), and neuraminidase or “N” proteins, of which there are 9 (N1-N9). 

Many different combinations of “H” and “N” proteins are possible. Waterfowl are natural 

reservoirs for avian influenza viruses, but most infections of wild birds are asymptomatic.

Common LPAI signs in poultry include decreased food and water consumption, coughing, 

sneezing, and decreased egg production. HPAI infections may also cause sudden death, lack of 

energy, the production of soft or deformed eggs, swelling (of head, eyelids, comb, wattles, and/or 

hocks), purple discoloration (of wattles and/or comb), nasal discharge, loss of coordination, 

and/or diarrhea. Transmission of HPAI typically occurs through direct contact with infectious 

respiratory secretions and feces. Viral spread via indirect contact with contaminated equipment 

and supplies (also known as fomites) is common. Avian influenza viruses can also infect other 

mammals such as pigs and cats, and rarely, humans.

In poultry, surveillance for avian influenza is conducted using a flock-based approach. Based on 

the severity of illness in chickens and the genetic features of the virus, the disease is classified as 

either HPAI or LPAI. Any HPAI and all H5 and H7 subtypes from poultry are reportable. This is 

because H5 and H7 subtypes have the potential to change from LPAI to HPAI during infections 

in domestic poultry, as seen during this outbreak.

Prior Outbreaks in the United States

While avian influenza (AI) is common in birds worldwide, some countries also have endemic

HPAI in their poultry. However, in the United States—and other countries considered to have

developed veterinary infrastructure and advanced animal agriculture industries—HPAI is not 

frequently detected in commercial poultry. A summary of HPAI outbreaks in the United States is 

provided in Table 1. Additionally, serious H7N2 and H5N2 LPAI outbreaks in the United States
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in 2002 and 2007 resulted in the destruction of 4 million and 25,600 commercial birds 

respectively.

Table 1. HPAI Outbreaks in the United States

Year(s) Strain Locations Impact

1924 H7 East Coast live bird markets Not available

1927 Unknown NJ Not available

1983–84 H5N2 Northeastern U.S. 17 million chickens, turkeys, and 

guinea fowl destroyed

2004 H5N2 TX Destruction of 1 flock

2014–15 H5N8, 

H5N1 

(wild bird 

only), 

H5N2

AR, CA, IA, ID, IN, KS, KY, 

MI, MN, MO, MT, ND, NE, 

NM, NV, OR, SD, UT, WA, 

WI, WY (includes wild bird 

detections)

50.5 million commercial birds affected

(including Dangerous Contacts)

2016 H7N8 IN (related LPAI cases were 

also detected in IN)

>400,000 commercial birds affected 

(including Dangerous Contacts)

2017 H7N9 TN (related LPAI cases were 

detected in AL, GA, and KY)

>249,000 commercial birds affected

The Foundation of Preparedness

APHIS continuously prepares for significant animal disease incidents. With the response to the

2014–2015 outbreak, the timely response in Indiana, and because USDA APHIS, States, and 

industry have been anticipating additional HPAI cases, all stakeholders were informed and ready 

for an immediate and effective response in 2017. 

In the wake of the 2014–2015 HPAI outbreak, Veterinary Services (VS) personnel worked to 

revise and update HPAI plans and procedures. When the Indiana outbreak occurred, work was 

continuing on corrective actions identified in the prior outbreak, applying lessons learned to 

improve policy and processes at both the APHIS VS National Incident Management Team 

(NIMT) and ICG levels. Additionally, the Foreign Animal Disease Preparedness and Response 

Plan (FAD PReP) Highly Pathogenic Avian Influenza Response Plan: The Red Book had been 

revised in 2015 (and was undergoing a revision as this outbreak occurred), and the HPAI 

Preparedness and Response Plan, first released in the fall of 2015, was updated in January 

2016.1

At the culmination of the 2014–2015 outbreak, one of the most important actions was to revise 

and streamline the existing, cumbersome indemnity and appraisal process. Revised appraisal and 

indemnity procedures were rolled out to relevant parties as the Indiana outbreak occurred, and 

publicly in February 2016. Highlights of these revisions included the following: only one form 

was required to be signed prior to depopulation, the method for all payments was simplified, 

producers received a flat-rate payment for virus elimination activities, and indemnity can be 

 1 An updated HPAI Response Plan: The Red Book was released in May 2017. It is available from 

www.aphis.usda.gov/fadprep. 
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split, as applicable, between the owner and the grower (via an interim rule in 9 Code of Federal 

Regulations [CFR] 53). 

Throughout 2016 and into early 2017, the HPAI National ICG remained active; VS NIMTs also 

met routinely—including conference calls by section (e.g., planning, operations)—to improve 

procedures, processes, and clarify roles and responsibilities. Both groups continued to work 

diligently on the corrective actions identified in the Corrective Action Plan Tracker and after 

action reports. For example, position descriptions were revised and distributed for the VS 

NIMTs; additional work was completed to ensure the contracting process is both efficient and 

transparent. The two previous HPAI outbreaks, which included the HPAI/LPAI incident in 

Indiana, left APHIS and stakeholders well prepared to manage the HPAI/LPAI outbreak in the 

southeastern United States successfully.2

Section 2. Characteristics of the 2017 H7 Southeastern Outbreak

Scope of the Outbreak 

The 2017 outbreak of the H7/H7N9 virus of North American lineage was limited to four States 

in the southeastern United States: Tennessee, Alabama, Kentucky, and Georgia. Lincoln County, 

Tennessee was the only location with HPAI detections (2 HPAI Infected Premises) (Figure 1). 

Both of the HPAI detections were in commercial broiler breeder flocks.

In total, as seen in Figure 2, there were 2 confirmed HPAI detections and 12 LPAI detections (8 

presumptive LPAI; 4 confirmed LPAI). 3 Of the 14 premises, 8 were commercial flocks and 6 

were backyard producers (Figure 2): all commercial premises affected were broiler breeder 

flocks. On the 14 affected premises, approximately 253,000 birds were depopulated, or 

succumbed to the virus in the case of the HPAI premises (Figure 3). Nearly 99 percent of these 

birds were in commercial broiler breeder flocks (Figure 4). There were no Dangerous Contact 

Premises identified in this outbreak.

 2 This incident is sometimes referred to as a “mixed HPAI/LPAI” incident. For both this incident (2017) and Indiana 

(2016), this “mixing” refers only to the response effort, which requires the management of both HPAI infected 

flocks (and premises) and LPAI infected flocks (and premises) as part of a single incident. Both the 2016 and 2017 

incidents were LPAI introductions into poultry followed by a single event of a mutation to HPAI. There were not 

“mixed” infections where HPAI and LPAI were found, simultaneously, in a flock.

3 In this outbreak, samples from some Infected Premises did not contain enough virus (specifically, viral RNA) to 

establish pathogenicity (e.g., LPAI or HPAI). As such, on some premises, the N-type and/or the pathotype (or 

pathogenicity) could not be determined. Where no virus or sequence could be recovered and the flock lacked clinical 

signs (e.g., did not meet the HPAI case definition), the flock status remained “presumptive LPAI.” All Infected 

Premises were confirmed at NVSL by either PCR, antibody testing, or sequence data. More information on the 

Infected Premises’ statuses can be found in Table 2.
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Figure 1. Affected Counties in the 2017 H7 Outbreak

Note: Map produced during the incident by the USDA APHIS VS Center for Epidemiology and Animal Health.

Figure 2. HPAI and LPAI H7/H7N9 Detections in the Southeastern United States, by 

Flock Type

6

2

6

0

2

4

6

8

10

12

14

HPAI LPAI (Presumptive or Confirmed)

Commercial

Backyard
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Figure 3. Approximate Number of Birds Affected in the Southeastern United States, by 

State and Production Type

Figure 4. Birds Affected in the Southeastern United States, by Production Type

20,580

145,500

65,630 18,000

2,700

71

455

2,700

71

455

Commercial Backyard

1.29%

98.70%

Backyard Producer

Commercial Broiler

Breeder
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Disease Incidence

In early March, based on the appearance of clinical signs, the index Tennessee flock in Lincoln 

County was suspected to have HPAI. The presumptive positive case definition for HPAI was met on 

March 3; HPAI was confirmed by APHIS National Veterinary Services Laboratories (NVSL) on 

March 4, 2017. The index flock consisted of 74,000 commercial broiler breeder birds. Surveillance 

sampling in the 10 kilometer Control Area (Infected Zone and Buffer Zone) began almost 

immediately when the HPAI presumptive positive case definition was met. This Control Area 

was primarily in Tennessee, but also overlapped into the State of Alabama. 

Four days later, in a neighboring county, NVSL confirmed an LPAI infection in another 

commercial broiler breeder flock. In total, between March 4, 2017 and March 15, 2017, there 

were 6 additional presumptive or confirmed LPAI detections in Alabama (3 detections) and 

Tennessee (3 detections). Additionally, on March 15, 2017, again in Lincoln County, Tennessee, 

a second premises was confirmed with HPAI. This premises was within the original HPAI 

Control Area (10 kilometers) of the first detection.4 Between March 16, 2017 and March 25, 

2017, there were additional presumptive and confirmed H7 LPAI detections—6 in total; of these, 

3 were additional H7 detections in Alabama, as well as 2 in Kentucky and a single detection in 

Georgia. Of the LPAI premises that were detected in Alabama (6 premises) and Tennessee (3 

premises), 3 of these detections were in backyard premises in the HPAI Control Area (2 in 

Tennessee and 1 in Alabama). 

There were no further HPAI findings. This timeline is illustrated in Figure 5 (HPAI cases are 

noted in parentheses). 

 4 Molecular and epidemiologic evidence suggests this site was infected due to lateral spread of the virus from the 

first HPAI Infected Premises.
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Figure 5. All Detections by Flock Type and by NVSL Confirmation Date5

The complete epidemiological curve for this incident is pictured in Figure 6, which shows 

detection by earliest known date of infection, as recorded in the Emergency Management 

Response System 2.0 (EMRS2). This may be the date clinical signs were observed, a suspect 

positive based on the Case Definition for H5/H7 Avian Influenza (AI), or first presumptive 

positive result date at a NAHLN laboratory. Further information is available in Appendix 7.

6

 5 NVSL confirmation date is the first date of a confirmatory test result from NVSL. As noted in Table 2, 

pathogenicity was not confirmed in some of the detections.

6 Please note that not all appendices noted in this document are publicly available. Publicly available appendices are 

posted at www.aphis.usda.gov/fadprep. March 1

March 15March 31

2017

Flock Type

Tennessee 3/4/2017 (HPAI)

Tennessee 3/8/2017 

Commercial

Backyard

Alabama 3/10/2017

Alabama 3/14/2017 

Alabama 3/15/2017

Tennessee 3/15/2017 (HPAI)

Tennessee 3/15/2017

Tennessee 3/15/2017

Alabama 3/16/2017 

Alabama 3/17/2017

Kentucky 3/17/2017 

Alabama 3/21/2017 

Kentucky 3/21/2017

Georgia 3/25/2017 
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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Figure 6. Epidemiological Curve by Earliest Known Date of Infection

Subtyping and Pathotyping

In this outbreak, samples from some Infected Premises did not contain enough virus 

(specifically, viral RNA) to conduct full subtype and pathotype (e.g., LPAI or HPAI) testing. As 

such, on some premises, the N-type and/or the pathotype (or pathogenicity) could not be 

determined. Where no virus or sequence could be recovered and the flock lacked clinical signs 

(e.g., did not meet the HPAI case definition), the flock status remained “presumptive LPAI.” All 

Infected Premises were confirmed at NVSL by either polymerase chain reaction (PCR), antibody 

testing, or sequence data. Table 2 provides a full list of the confirmatory test results from NVSL 

and associated dates for these results. 

Of the 12 presumptive or confirmed LPAI Infected Premises, NVSL was unable to confirm 

pathogenicity on 8 premises. As such, these flocks are considered “presumptive LPAI” based on 

the lack of clinical signs (which would indicate an HPAI infection). NVSL was able to sequence 

and confirm LPAI on 4 premises: 2 commercial premises in Alabama and Tennessee and 2 

backyard premises in Alabama.

To provide further clarity on the confirmatory results, Figure 7 illustrates the statuses for the 

Infected Premises in this 2017 outbreak. In terms of reporting, the date of the first confirmatory 

test result from NVSL is the “confirmed positive date”; other test results may become available 

after the first confirmatory test (e.g., a H5 or H7 PCR confirms infection; virus isolation results 

may be available at a later date).7

 7 Thanks to the NVSL Diagnostic Virology Laboratory, Avian Section, for assistance in collating the confirmatory 

tests on all premises throughout the outbreak.
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

9

Figure 7. NVSL Confirmed Results for All Premises (Subtype & Pathotype)

Table 2. List of Affected Premises

3

1

4 4

2

0

1

2

3

4

5

Confirmed H7N9

LPAI

Confirmed H7 LPAI Confirmed

H7N9/Presumptive

LPAI

Confirmed

H7/Presumptive

LPAI

Confirmed H7N9

HPAI

LPAI HPAI

State County

Approximate 

Flock Size Flock Type H-Type N-Type

Confirmatory 

Status

Date of First 

Confirmation

Pathotype 

Confirmation

Alabama Cullman 23,874

Commercial 

Broiler Breeder H7 N9

Confirmed 

Antibody + 

Sequence 3/21/17 Confirmed LPAI

Alabama Jackson 312

Backyard 

Producer H7 N9

Confirmed HA 

and NA 

Sequence 3/15/17 Confirmed LPAI

Alabama Lauderdale 16,931

Commercial 

Broiler Breeder H7 Unknown

Confirmed 

Antibody 3/14/17 Presumptive LPAI

Alabama Madison 77

Backyard 

Producer H7 Unknown

Confirmed 

PCR 3/10/17 Presumptive LPAI

Alabama Madison 66

Backyard 

Producer H7 Unknown

Confirmed HA 

Sequence 3/17/17 Confirmed LPAI

Alabama Pickens 24,825

Commercial 

Broiler Breeder H7 N9

Confirmed 

PCR + 

Antibody 3/16/17 Presumptive LPAI

Georgia Chattooga 18,000

Commercial 

Broiler Breeder H7 N9

Confirmed 

PCR + 

Antibody 3/25/17 Presumptive LPAI

Kentucky Christian 20,580

Commercial 

Broiler Breeder H7 N9

Confirmed 

PCR + 

Antibody 3/17/17 Presumptive LPAI

Kentucky Christian 2,700

Backyard 

Producer H7 N9

Confirmed 

Antibody 3/21/17 Presumptive LPAI

Tennessee Giles 16,500

Commercial 

Broiler Breeder H7 N9

Confirmed HA 

and NA 

Sequence 3/8/17 Confirmed LPAI

Tennessee Lincoln 15

Backyard 

Producer H7 Unknown

Confirmed 

PCR 3/15/17 Presumptive LPAI

Tennessee Lincoln 56

Backyard 

Producer H7 Unknown

Confirmed 

PCR 3/15/17 Presumptive LPAI

Tennessee Lincoln 55,000

Commercial 

Broiler 

Breeder H7 N9

Confirmed 

HA and NA 

Sequence 3/15/17 Confirmed HPAI

Tennessee Lincoln 74,000

Commercial 

Broiler 

Breeder H7 N9

Confirmed 

HA and NA 

Sequence 3/4/17 Confirmed HPAI
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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Viral Traits 

Partial and full genetic sequences of the HPAI and LPAI viruses recovered are highly similar, 

excluding the insertion at the cleavage site which was responsible for the mutation from H7N9 

LPAI to H7N9 HPAI. These H7N9 viruses are of North American wild bird lineage and not 

related to the H7N9 virus that is circulating throughout Asia. No cases of the North American 

lineage H7N9 virus have been reported in humans, including during this incident. Due to the 

zoonotic potential of influenza A viruses, personnel were monitored for influenza-like illness 

(ILI). H7N9 viruses of North American lineage have been previously detected in wild birds in 

the United States.

Introduction & Transmission

USDA APHIS, in collaboration with APHIS Wildlife Services (WS) and the affected States, 

collaborated to conduct epidemiologic, genetic, and wildlife investigations to evaluate the factors 

associated with the introduction and transmission of the H7N9 viruses during the 2017 outbreak. 

Based on molecular and epidemiological evidence, it appears that there was lateral spread 

between the first and second HPAI Infected Premises. In terms of LPAI, the information 

suggests that there were multiple, independent introductions of the H7N9 LPAI viruses.8

Unlike previous outbreaks, the movement of equipment and trucks on to and off the farm did not 

appear to be a significant risk for virus introduction. In 2017, risk factors included the presence 

of rodents or other wild mammals and waterfowl, condition of the poultry housing, and gaps in 

biosecurity protocols (specifically, allowing entry of the virus from the environment into barn 

structures). H7 influenza A viruses are known to circulate in low pathogenicity forms among 

wild waterfowl. Testing of more than 400 samples from wild birds and small mammals around 

the first HPAI Infected Premises did not detect the H7N9 virus. Notably, the introduction of the 

virus was likely several weeks prior to its detection, which may explain why the virus was not 

detected during these surveillance activities. However, other wild bird surveillance efforts 

recovered a highly similar virus (all eight gene segments) from a blue-winged teal from 

Wyoming in September 2016. This detection allowed for further genetic analysis, informing the 

timing of the introduction of the virus into poultry.

9

Section 3. Overview of Response Effort

Regulatory Intervention

Under the Animal Health Protection Act and Code of Federal Regulations 9 CFR 53, USDA 

APHIS has the authority to respond to and eradicate foreign animal diseases (FADs) in the 

United States. Accordingly, USDA APHIS responded to the case of HPAI, working in close 

 8 USDA APHIS. 2017. Epidemiological and Other Analyses of HPAI/LPAI Affected Poultry Flocks: June 26, 2017 

Report. USDA APHIS STAS Center for Epidemiology and Animal Health.

https://www.aphis.usda.gov/animal_health/animal_dis_spec/poultry/downloads/epi-ai.pdf. 

9 USDA APHIS. 2017. Epidemiological and Other Analyses of HPAI/LPAI Affected Poultry Flocks: June 26, 2017 

Report. USDA APHIS STAS Center for Epidemiology and Animal Health.

https://www.aphis.usda.gov/animal_health/animal_dis_spec/poultry/downloads/epi-ai.pdf. 
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

11

coordination with Tennessee to eradicate the disease. Because the HPAI Control Area extended 

beyond Tennessee boundaries, the State of Alabama joined with USDA APHIS and Tennessee as 

part of the unified State-Federal Incident Command (IC) to respond to the HPAI detections, as 

well as to the LPAI detections in Tennessee and Alabama that were related to the initial HPAI 

findings. A unified Incident Command Post (ICP) was established in Nashville, Tennessee. 

Additional APHIS personnel supported Surveillance, Preparedness, and Response (SPRS) District 

2 responders in the unified Incident Command, both on-site and virtually, with activities like 

surveillance, finance/administration, and epidemiology. Full VS NIMTs were not mobilized during 

this incident.

Kentucky and Georgia managed their LPAI Infected Premises with support from USDA APHIS 

VS SPRS District 2 and District 3 personnel, as requested/needed. Per 9 CFR 56, LPAI 

response—including the disposition of Infected Premises—is under the jurisdiction and authority 

of the States; States request assistance from USDA APHIS as needed.

For policy guidance and resource coordination, the National ICG at APHIS headquarters was 

ramped up. Due to the size and scope of the incident, an APHIS Multiagency Coordination 

(MAC) Group was not stood-up but remained on-call for issues that required resolution. 

Additionally, the VS Executive Team (VSET) handled any issues that were elevated from the 

ICG.

Financial Resources

As of June 29, 2017, the commitments and obligations for this incident were nearly $2.79

million. This includes the amount paid to HPAI affected producers for depopulated birds 

(indemnity), as well as obligations for other response activities. HPAI Infected Premises received 

flat-rate payments for virus elimination; these payments are also included in this total. For HPAI 

depopulated birds, USDA APHIS paid approximately $1.18 million in indemnity payments to 

flock owners and growers for the 2017 southeastern United States outbreak.

USDA APHIS also reimbursed States through supplemental agreements for activities conducted 

in response to the LPAI detections, including surveillance, and where applicable, specific 

depopulation and disposal activities. LPAI premises that depopulated and conducted virus 

elimination did not receive APHIS compensation for these activities. The overall cost of this 

outbreak was significantly less than in the 2016 Indiana outbreak due to the type of birds 

affected, flock size, and outbreak characteristics.10

Economic & Trade Impact

In 2017, major chicken producing (broiler and egg) States were affected by LPAI. The rapid 

control and containment of the HPAI infection helped to minimize trade restrictions; many 

 10 USDA APHIS. 2016. Presentation: Final Report for the 2016 HPAI Outbreak in the United States. USDA APHIS 

National Preparedness and Incident Coordination.

https://www.aphis.usda.gov/animal_health/emergency_management/downloads/hpai/finaloutbreakreport_shortppt.p

df. 
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

12

countries chose a regionalization approach. Notably, some countries still are imposing 

restrictions from previous HPAI outbreaks in the United States. 

Approximately 11 countries did impose restrictions on poultry and/or poultry products from the 

entire United States. In addition, approximately 23 countries placed State-level restrictions; most 

trading partners—including Canada and Mexico—imposed restrictions at the county or Control 

Area level. Such regionalization decisions helped to significantly limit the economic impact of 

this incident. VS National Import Export Services continues to work with trading partners on the 

removal of trade restrictions implemented as a result of HPAI and LPAI infections in the United 

States.

Personnel

In this 2017 outbreak, the unified Incident Command was staffed with primarily VS SPRS 

District 2 personnel. Full VS NIMTs were not rotated in for the incident. The height of response 

operations came after the second HPAI detection, the week of March 15–21. During this week, 

on average, there were 75 personnel deployed on any given day. Again, on average, this included 

approximately 30 APHIS personnel, 23 State personnel, and approximately 22 contractors. 

Notably, as many as 46 contractors were deployed on a single day that week to conduct response 

activities on the second HPAI Infected Premises. An additional 5–20 personnel were assigned to 

work part- or full-time as part of the ICG either remotely or at APHIS hubs. All APHIS 

personnel were demobilized from the unified Incident Command by April 14, 2017.

Section 4 provides additional information on the organizational structure for both field 

responders and headquarters personnel.

Section 4. Incident Management

Overview

Effective incident management was critical to respond to and eradicate HPAI. Figure 8 illustrates 

the overview of the incident management structure from 2017 (this same structure was used in 

2016). This HPAI incident was managed through use of the National Incident Management 

System (NIMS), to include the Incident Command System (ICS), which enables a scalable and 

flexible approach throughout the response. 
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

13

Figure 8. Overview of USDA APHIS Organizational Structure for Incident

Note: NASAHO = National Assembly of State Animal Health Officials, NASDA = National Association of State 

Departments of Agriculture.

In the 2017 HPAI/LPAI outbreak in the southeastern United States, the Office of the Secretary 

was kept closely informed. The APHIS Administrator also received routine briefings. Because of 

the limited size and scope of this incident, the APHIS MAC Group was not fully activated, 

though members stood by to address any requests that were elevated from the VSET. The VSET 

was responsible for strategic policy and procedures and provided assistance as requested by the 

HPAI ICG. The HPAI ICG played the largest role in incident coordination and resource requests.

At appropriate levels and opportunities, these groups interfaced with industry associations, 

NASAHO and NASDA, public health agencies (including the U.S. Centers for Disease Control 

and Prevention [CDC] and State agencies), and other external partners. The U.S. Chief 

Veterinary Officer (CVO) (the VS Deputy Administrator), or designee, routinely briefed 

NASAHO on incident updates via teleconference. 

At the field or operational level, District 2 personnel filled the role of an IMT and deployed to 

the ICP in Nashville, TN. VS NIMTs remained on-call in the event that the response needed to 

be scaled up, but were not fully deployed in this incident. The IMT and unified Incident 

Command routed requests for policy guidance, coordination, and additional resources through 

the National ICG.
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

14

National Incident Coordination Group and APHIS Multiagency Coordination

Group

A core HPAI ICG remained active since the 2014–2015 HPAI outbreak through the 2016 (and 

now 2017) incidents. To support the HPAI/LPAI response efforts and the unified Incident 

Command, additional staff were activated to the HPAI ICG immediately at the first HPAI 

detections. Other personnel were standing by to provide support and address requests as required 

by the incident. The VS Deputy Administrator (the U.S. CVO) and VSET provided additional, 

higher-level policy, resource, and coordination support as required. These structures are shown 

in blue in Figure 9. 

Figure 9. Details of the USDA APHIS Organizational Structure for Incident

Note: SAHO = State Animal Health Official.

APHIS Multiagency Coordination Group

The APHIS HPAI MAC Group was created during the 2014–2015 HPAI outbreak to provide 

immediate leadership and authority for resolving issues during the incident and to develop 

needed policies and processes for the future. In 2017, the APHIS HPAI MAC Group—consisting 

of senior-level representatives and subject-matter experts from across the agency—was on-call to 

provide cross-unit leadership and direction. The small size and scope of the incident minimized 

the need for full MAC Group activation.

National Incident Coordination Group

Immediately scaled up with the first HPAI-detection, the ICG’s primary purpose was to support 

the APHIS VS NIMTs in acquiring resources and formulating policy options. The ICG included

APHIS employees at the Riverdale, Ft. Collins, Ames, and Raleigh hubs in addition to other 

virtual personnel. The ICG personnel came primarily from SPRS and Science, Technology, and 
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

15

Analysis Services (STAS) (Figure 10). Other units throughout APHIS also supported the 

response. Personnel typically were assigned for the duration of the entire HPAI/LPAI incident.

Figure 10. Total Number of APHIS Personnel Assigned to the National ICG

at APHIS Hub or Home Location, by Organizational Unit

Note: MRPBS = Marketing and Regulatory Programs Business Services, ODA = Office of VS Deputy 

Administrator, PSS = Program Support Services, NIES = National Import Export Services, AC = Animal Care.

These organizational affiliations were accurate at time of assignment to the National ICG.

The ICG supported requests from the unified Incident Command for policy clarification, 

coordinated epidemiological investigations and analyses, facilitated indemnity payment 

processing, harmonized information management activities, provided support for contracting, 

developed daily and weekly situation reports and maps, and informed stakeholders about the 

response efforts. ICG command and control was accomplished via regular meetings and 

completion of Coordination Plans (Appendix 10). Figure 11 illustrates the ICG structure for the 

2017 southeastern HPAI/LPAI outbreak; all ICG structures are flexible and scalable to the 

specific incident.

22

16

3 2 2 1 1 1 1

0

5

10

15

20

25

SPRS STAS MRPBS WS ODA PSS LPA NIES AC
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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Figure 11. National Incident Coordination Group Structure During 2017 H7 Incident

Note: DA = Deputy Administrator; GIS = geographic information system; 3D = depopulation, disposal, disinfection; OPS = operations; NAHERC = National Animal 

Health Response Corps; VERRC = Volunteer Emergency Ready Response Corps.
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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APHIS VS National Incident Management Teams & Deployments

Due to the size and scale of the incident, as well as the rapid availability of skilled personnel 

from SPRS District 2, a VS NIMT was not deployed to the incident, though one remained on call 

if required. As soon as possible after the presumptive positive case definition for HPAI had been 

met, a unified Incident Command was established with SPRS District 2 personnel and

individuals representing the Tennessee Department of Agriculture.11 When the HPAI Control 

Area was established and included part of Alabama, personnel from Alabama immediately 

joined the unified Incident Command structure. The organizational structure of the unified 

Incident Command was consistent with NIMS/ICS. This partial VS IMT worked alongside State 

responders to execute field activities, including depopulation, disposal, and virus elimination on 

the HPAI-infected premises. The unified ICP was staffed between approximately March 4, 2017 

and April 12, 2017.

Figure 12. Total Number of APHIS and State Personnel Deployed per Day

APHIS Personnel Deployments

APHIS personnel deployed in over 25 different positions; the most frequently deployed positions 

were Surveillance Group Members (9 deployments), followed by Epidemiologists (5 

deployments). In total, there were 51 APHIS deployments—45 on-site and 6 virtual 

deployments. There were 29 on-site deployments of personnel from the States of Tennessee (19 

deployments) and Alabama (10 deployments). The total number of deployments—broken out by 

 11 In addition, the State of Tennessee also deployed an individual from the Division of Forestry, which is also in the 

Tennessee Department of Agriculture. 

9

13 15 16 17 17 19 18 19

24 24 25 26 29 28

32 33 34 35 36

31 31 31 33 33 35 35 35 35 35 35 34 34 34

28 28 28 26 25 25

0 0 0 2

11

13

13

17 17 19

19 19 19

22 22 22 23

23 23

23 23

27 27 27

22 22 22

22 22

22 22 22 22 22 20 19 19 19

19 19 19

19 19 19

0

0 0

10

20

30

40

50

60

70

State

Agriculture

Department

(TN and AL)

USDA:APHIS
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

18

virtual and on-site—for APHIS organizational units is provided in Figure 13. These data apply 

only to staffing of the unified Incident Command to manage the mixed HPAI/LPAI incident in 

Tennessee in Alabama. These data do not include individuals working on LPAI in other States, 

including Kentucky or Georgia, where a unified Incident Command was not established. A final 

deployment report for this incident is provided in Appendix 8. 

Figure 13. Total Number of APHIS Personnel Deployed to the Field 

by Organizational Unit

As a result of the 2014–2015 outbreak, APHIS hired a significant number of term personnel to 

augment its preparedness and improve response capabilities. In 2017, term-hires again supported 

response operations for the HPAI/LPAI cases in Tennessee and Alabama. Figure 14 shows the 

split between term-hires and permanent APHIS employees in terms of deployments. 

Figure 14. Total APHIS Deployments, by Appointment Type
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

19

Of the 45 total VS deployments, 41 (91 percent) where from SPRS. Of these 41 SPRS 

deployments, 34 were District 2 personnel (83 percent); District 2 took the lead in responding 

through the unified Incident Command to control and contain the outbreak.

Contractors

Additional incident support to both the NIMT and ICG was provided by contractors. Part-time 

personnel supported the ICG; APHIS-hired contractors worked to support the unified Incident 

Command personnel in the field, providing services and materials relating to depopulation and

disposal of the HPAI-infected flocks (Figure 15).

12 Contractors were deployed to assist in field 

operations related to both the first and second HPAI premises in Lincoln County, Tennessee. 

LPAI premises that depopulated did so with their own resources (company or contracted); 

APHIS-hired contractors did not support these operations.

Figure 15. Contractor Support for Response Operations for HPAI Infected Premises

As in the 2016 Indiana HPAI/LPAI outbreak, and in the 2017 HPAI/LPAI outbreak, producers of 

the HPAI-Infected Premises received a flat-rate payment for virus elimination activities which 

again reduced the number of contracts executed by USDA for response efforts. This flat-rate 

payment is paid directly to the producer; the producers then decide how this work should be 

completed, typically by conducting the work themselves or directly contracting with a company 

to have these services provided. LPAI premises that conducted virus elimination did not receive 

compensation from APHIS.

 12 Figure 15 only includes contractors hired by the SPRS Logistics Center/National Veterinary Stockpile (NVS) for 

the HPAI Infected Premises.

0 0 0

30 30 28

3 3

0 0 0 0 0 0

8

44 46

17

8

19

13

0 0 0 0 0 0 0 0 0

0

5

10

15

20

25

30

35

40

45

50

1-Mar2-Mar3-Mar4-Mar5-Mar6-Mar7-Mar8-Mar9-Mar

10-Mar11-Mar12-Mar13-Mar14-Mar15-Mar16-Mar17-Mar18-Mar19-Mar20-Mar21-Mar22-Mar23-Mar24-Mar25-Mar26-Mar27-Mar28-Mar29-Mar30-Mar
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

20

Section 5. Incident Coordination Group Response 

and Support Activities

Overview

The ICG worked with Federal, State, local, academic, and industry partners during the outbreak 

to control and eradicate HPAI. The ICG supported and provided policy guidance to the APHIS 

personnel working in the field as part of the unified Incident Command. This list is not 

exhaustive, but provides an overview of the many tasks that the ICG completed during the 

incident:

• Planned disease surveillance.

• Facilitated communication regarding sampling requirements and diagnostic test flow.

• Planned and carried out epidemiological investigations and tracing.

• Managed information from the field to the national level.

• Coordinated and communicated with State, local, and industry stakeholders.

• Provided guidance on PPE and responder health and safety, and ensuring Safety Officers 

were in the field.

• Provided guidance on biosecurity measures.

• Supported continuity of business and issued permits for the HPAI Control Area.

• Provided information and documentation for regionalization for international trade.

• Safeguarded animal welfare during response operations. 

• Offered subject matter expertise for disposal.

• Provided guidance and options for C&D (virus elimination).

• Supported logistics, as required, through the NVS.

• Implemented revised financial procedures for appraisal and indemnity and provided

support for compensating poultry owners and contract growers.

• Delivered overall incident management, support for the unified Incident Command, and 

short- and medium-term response objectives.

Reporting and Communicating Information 

The APHIS MAC, ICG, and the unified Incident Command were in close communication from 

the outset of the event. ICG leaders stayed in close contact with State partners at the ICP, as well 

as representatives from the affected poultry companies, especially during the first few weeks. 

Many personnel involved in the response were responsible for data entry, analysis, and reporting. 

Communication of this information both internally and externally was critical for effective 

coordination and communication. 

At the ICG level, the following were conducted/completed at routine intervals:

• Conference calls between the ICG Deputy Incident Coordinator and the unified Incident 

Commanders (daily at first, then bi-weekly).

• Conference calls between the ICG, APHIS co-Incident Commander, and affected States 

(daily, moving to every other day and then weekly).

• ICG HPAI Status Reports to APHIS staff, Administrator, and to NASAHO (daily 

initially, then weekly).
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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• Stakeholder announcements and/or GovDelivery notices (as needed).

• Reports distributed widely to States and USDA (weekly and then as needed):13

‒ National Situation Report (example in Appendix 2a, last report in Appendix 2b)

‒ National Infected Premises List (final list in Appendix 3)

‒ Map for State and APHIS Officials of all H7 HPAI/LPAI (example in Appendix 4a, 

final map in Appendix 4b)

‒ National Incident Maps (final mapbook in Appendix 5)

‒ National Control and Containment Maps (final maps in Appendix 6)

‒ Epidemiological Curve (final curve in Appendix 7)

‒ Deployment Report (for APHIS Personnel) (final report in Appendix 8)

‒ Permit and Movement Report (final report in Appendix 9).

• Incident Action Plans (IAPs) and corrective action reports (weekly) (Appendix 10).

At the unified Incident Command level, the following were completed as specified:

• VS SitReps (daily at first, then as needed)14

• IAPs (daily)

• Other ICS specific forms, like incident logs (daily).

Deployment/Personnel Management

Personnel were requested and deployed using APHIS Dispatch. APHIS personnel at the unified 

ICP used EMRS2 to create a resource request that is submitted to APHIS Dispatch personnel for 

entry and fulfillment through the Emergency Qualifications System (EQS). APHIS Dispatch 

distributes a daily record, from EQS, showing personnel currently at the incident or ICG, those 

that have been demobilized, and those that are scheduled to mobilize in the future. Records are 

also kept in EMRS2, including for State personnel in the unified Incident Command structure. 

Reconciliation between the two systems was conducted daily, or as needed, as the response 

progressed. 

Policy and Guidance

The HPAI Response Plan: The Red Book provided overarching guidance for the response 

effort;

15 many more specific policy documents concerning specific activities and lessons learned

have been developed since 2015. These national-level policies were developed by the ICG and 

had been distributed widely to States and stakeholders. These policy guidance documents are 

posted publicly at www.aphis.usda.gov/fadprep. Response and policy documents available 

include the following (current as of June 2017): 

 13 Appendices are not publicly available unless posted at www.aphis.usda.gov/fadprep. 14 The unified Incident Command created their own Situation Report each day that was reviewed by VS Poultry 

Staff. This situation report provided operational details and information about response activities on all the 

HPAI/LPAI Infected Premises. These reports contained sensitive information that is not appropriate for wide 

distribution; a template of this report is available upon request. 15 The new HPAI Response Plan: The Red Book was released in May 2017, after the conclusion of most of the 2017 

response activities, to encompass any additional information learned in the 2017 outbreak.
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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• Avian Sample Collection for Influenza A and Newcastle Disease

• Cleaning and Disinfection Basics: Virus Elimination

• Contact Premises

• Control Area Release

• Example Restocking Form

• Financing the Response: State/Tribal Information

• General Resources and Information

• H5/H7 Avian Influenza Case Definition

• HPAI Response Goals

• Initial Contact Epi Report

• Landfill Disposal Guidance—Recommended Waste Acceptance Practices for Landfills

• Mortality Composting Protocol for AI Infected Flocks (and Job Aids)

• New State Checklist

• Overview of the HPAI Control Area Permitting Process

• Overview of the EMRS2 Customer Permit Gateway

• Personal Protective Equipment (PPE) Recommendations for HPAI Responders

• Post C&D Environmental Sampling Guide

• Stamping-Out and Depopulation Policy

• Surveillance of Backyard Flocks Around Infected Premises

• Surveillance Sampling for Commercial Premises in Control Area

• Testing Requirements for Movement from the Control Area

• Timeline, Eligibility, and Approval for Restocking

• Use of the Antigen Capture Immunoassay

• Using Heat Treatment for Virus Elimination

• Ventilation Shutdown Evidence and Policy.

New finance and administration policies were implemented during the 2016 Indiana outbreak

and used again in the 2017 southeastern United States outbreak. These guidance documents 

institutionalized the revised appraisal and indemnity procedures that had been streamlined and 

improved based on lessons learned. As in 2016, only one form was required from the HPAI 

Infected Premises prior to depopulation. Additionally, as specified in the Interim Rule published 

in February 2016,

16 APHIS split indemnity payments between owners and growers in the 2017

outbreak. 

Financial response and policy guidance available at www.aphis.usda.gov/fadprep includes the 

following documents:

• Finance and Administration Processes

‒ Overview of Finance and Administration Procedures

‒ Details for Bird and Egg Appraisal and Indemnity Procedures

‒ Details for Virus Elimination Financial Processes

‒ Details for Materials Destroyed Financial Processes

‒ Appraisal and Indemnity Request Forms

 16 Docket No. APHIS-2015-00061. 

https://www.aphis.usda.gov/newsroom/federal_register/hpai_indemnity_rule.pdf. 
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

23

 Poultry Owner

 Contract Grower

‒ Appraisal and Indemnity Request Procedures

 Contract Grower Worksheet for Meat Birds

 Contract Grower Worksheet for Layers

 DUNS and SAM.

Health and Safety

APHIS proactively supported personnel to mitigate health and safety issues through the 

establishment of Safety Officers embedded within the unified Incident Command; there was also 

a Health & Safety Unit in the ICG. This Unit, staffed by individuals from VS Safety, Health, and 

Environmental Protection (SHEP), finalized health and safety protocols, provided guidance to 

Safety Officers in the field, and assisted with communication to other agencies during the 

incident. VS SHEP coordinated closely and followed any applicable guidance laid out by the 

APHIS Emergency Management Safety and Security Division (EMSSD). During the response, 

the Health & Safety Unit were responsible for the following tasks:

• Reviewing procedures to create site-specific health and safety plans.

• Reviewing health and safety plans of Federal contractors.

• Working with the unified Incident Command, EMSSD, and One Health on appropriate 

communication and documentation for ILI monitoring for responders.

Section 6. Highlights of Response Activities

Overview

To effectively respond to and recover from the HPAI outbreak, APHIS staff, industry, academic 

partners, State officials, and contractors worked together to illustrate the following 10 steps per 

Infected Premises, as outlined in Figure 16.17 The next sections highlight the key points of 

critical response activities that were conducted during the outbreak.

 17 A higher resolution copy of this figure, suitable for printing, can be found here: 

https://www.aphis.usda.gov/publications/animal_health/2015/poster-hpai-guide-to-understanding-the-process.pdf. 
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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Figure 16. A Guide to Help You Understand the Response Process
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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Surveillance and Epidemiology

Surveillance Around HPAI Infected Premises

A 10 km Control Area was established around the HPAI Infected Premises where the index case 

was found. When the second HPAI case was detected, a second Control Area was established. 

The two HPAI Infected Premises were geographically in close proximity; as such, the two HPAI 

Control Areas were nearly matching—the overall area was marginally increased.

A Surveillance Zone—in the Free Area—was also established in a 20 km circle around each of 

the HPAI Infected Premises (10 km beyond the HPAI Control Area). Sampling of all 

commercial poultry premises in the Surveillance Zone and Control Area, starting with those 

premises in the Control Area, was undertaken as a top priority as soon as HPAI was detected. 

Surveillance was also conducted on backyard premises in both the HPAI Control Areas and 

Surveillance Zones. 

Surveillance Around LPAI Infected Premises

For LPAI Infected Premises, Control Areas were not established. Instead, a 10 km Surveillance 

Zone (in the Free Area) was established around commercial LPAI Infected Premises; a 3 km 

Surveillance Zone was established around backyard LPAI Infected Premises. Appendix 4 

provides a map showing the Surveillance Zones that were established during the outbreak. 

It is important to note that regular notifiable AI surveillance is carried out as part of the National 

Poultry Improvement Plan (NPIP) for participating producers, who can opt-in to the program. 

The NPIP H5/H7 Clean and Monitored programs qualify flocks with at least 11 or 30 birds that 

show negative serology tests at certain intervals (90 or 180 days, usually) and/or before 

movements off a premises can occur, including movements of birds to slaughter and disposal.

NPIP surveillance provided (and continuously provides) additional confidence that H5/H7 

viruses were not circulating in the area.

Incident Coordination Group and Unified Incident Command Activities

Surveillance and epidemiological activities were coordinated by the unified Incident Command

and ICG. At the ICG level, response activities focused on supporting requests for surveillance 

design guidance from the unified Incident Command as well as from States with only LPAI 

infections. Guidance for conducting surveillance activities around HPAI Infected Premises was 

provided in two documents developed by the ICG in previous HPAI outbreaks: Surveillance of 

Backyard Flocks Around Infected Premises and Surveillance Sampling for Commercial Premises 

in Control Area (both are available at www.aphis.usda.gov/fadprep). These documents served as 

a framework for conducting surveillance activities in the 2017 outbreak. ICG personnel also 

developed epidemiological questionnaires to understand outbreak characteristics, identify risk 

factors, and examine how the H7N9 virus was transmitted throughout the outbreak. A report 

summarizing these epidemiological analyses was posted on June 26, 2017.18

 18 USDA APHIS. 2017. Epidemiological and Other Analyses of HPAI/LPAI Affected Poultry Flocks: June 26, 2017 

Report. USDA APHIS STAS Center for Epidemiology and Animal Health.

https://www.aphis.usda.gov/animal_health/animal_dis_spec/poultry/downloads/epi-ai.pdf.
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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At the ICP, epidemiologists coordinated the survey and interview process in the field to gather 

information from each premises. As part of the epidemiological investigation, all movements 

onto and off of Infected Premises (known as trace-backs and trace-forwards) were identified and 

evaluated for the possibility of HPAI transmission. In terms of surveillance, unified Incident 

Command personnel conducted diagnostic sampling for disease detection. The ICG and unified 

Incident Command both incorporated personnel with expertise in wildlife to coordinate wild bird 

(and wild mammal) surveillance sampling and analyze the role of wild birds in the 

outbreak/transmission.

Surveillance Data19

Surveillance included active surveillance of both backyard and commercial premises, as well as 

pre-slaughter testing, pre-movement testing, voluntary surveillance by poultry production 

companies, and sick-bird calls. All diagnostic testing illustrated here was completed using the 

real-time reverse transcription polymerase chain reaction (rRT-PCR) test at an approved 

NAHLN laboratory unless otherwise specified.

20

For surveillance related to the HPAI incident, including all sources of surveillance mentioned 

above, Table 3 provides information on the number of backyard and commercial premises 

sampled and the number of accessions submitted to the laboratory. Most of these were captured 

in the Laboratory Messaging System (LMS), though a handful of tests early in the outbreak were 

entered manually in EMRS2.21 Table 3 includes surveillance in the HPAI Control Areas and 

HPAI Surveillance Zones as well as other surveillance that occurred outside of the zones per the 

reasons mentioned (e.g. pre-movement testing, sick bird calls, voluntary testing by companies).

Table 3. Premises Sampled and Number of Accessions as Surveillance for the 

2017 HPAI Detections22

Premises State Premises Accessions

Alabama 16 47

Tennessee 93 261

Total 109 308

Door-to-door interviews were conducted throughout the HPAI Control Areas to identify and 

sample potential backyard premises. In total, personnel sampled over 90 backyard premises with 

poultry for surveillance or as a result of a sick bird call (both inside and outside of the HPAI 

 19 These data were collected and recorded in EMRS2. 

20 On commercial premises, oropharyngeal swabs were collected from pools of 5 or 11 clinically ill or dead birds. In 

backyard flocks, oropharyngeal swabs were collected from 5 clinically ill or dead birds (if available) per each 

species on the premises.

21 Table 3 captures all accessions, including those electronically messaged via LMS from testing laboratories and 

those that were not messaged (but were manually entered into EMRS2).

22 Table 3 does not include diagnostic testing on any HPAI Infected Premises or LPAI Infected Premises in the 

HPAI Control Areas (which would also include environmental sampling). Accessions were used as a proxy for the 

number of sampling events that occurred at each premises; NVSL accessions for confirmatory testing are included 

(only 3 accessions in total).
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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4 1

59

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10

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0

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70

Backyard Producer Commercial (Broiler Flock or Breeder)

Infected Zone Buffer Zone Surveillance Zone

Control Area). Notably, because the two HPAI premises were located in close proximity, the 

second HPAI detection increased the total size of the Control Areas very marginally.

Figure 17 and Figure 18 show the number of premises that were sampled (had a laboratory 

accession) per zone for both HPAI Control Areas. All Infected Premises (HPAI and the 3 LPAIInfected Premises that were associated with the HPAI incident) have been excluded from these 

figures.23

Figure 17. Number of Premises Sampled 

(First HPAI Control Area & Surveillance Zone)

Figure 18. Number of Premises Sampled 

(Second HPAI Control Area & Surveillance Zone)

 23 For the first HPAI Control Area, three additional premises subsequently became infected within that Control Area 

(1 HPAI; 2 LPAI). These premises were located in the Infected Zone (1) and Buffer Zone (2).

3 1

59

6 9

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30

40

50

60

70

Backyard Producer Commercial (Broiler Flock or Breeder)

Infected Zone Buffer Zone Surveillance Zone
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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In the first HPAI Control Area and Surveillance Zone, 79 total premises were sampled: there 

were 71 backyard producers and 8 commercial broiler premises (7 production; 1 breeder) that 

were sampled (Figure 17). In the second HPAI Control Area and Surveillance Zone (which 

overlaps significantly with the first HPAI Control Area), there were 81 total premises from 

which samples were collected during the outbreak: 73 backyard producers and 8 commercial 

broiler premises (7 production; 1 breeder) (Figure 18). Obviously, most of these farms were the 

same (Figures 17 and 18 are not mutually exclusive). Between the 2 Control Areas for the HPAI 

Infected Premises, there were a total of 82 premises sampled (based on laboratory accessions) as 

a part of HPAI surveillance activities: 16 in Alabama (1 commercial, 15 backyard) and 66 in 

Tennessee (59 backyard, 7 commercial). 

Backyard premises in the Control Area were typically tested twice. While commercial flocks 

were typically tested at least three times and often more, the number of testing events varied 

significantly based on the location of the flock to the existing HPAI Infected Premises and 

discretion of the unified Incident Command on the need for repeated testing for specific flocks. 

Because the second HPAI detection was over a week after the first HPAI detection, some

premises, particularly commercial premises, experienced an extended sampling and testing 

regimen. 

On the LPAI side of the incident, for LPAI Infected Premises, surveillance was conducted in 

Tennessee, Alabama, Kentucky, and Georgia (shown below in alphabetical order). Table 4 

shows the summary of the number of premises sampled and number of laboratory accessions that 

were submitted as part of the LPAI surveillance activities. Again, this includes both the number 

of premises sampled and number of accessions from the Surveillance Zones surrounding the 

LPAI Infected Premises as well as other surveillance that occurred outside of the zones per the 

reasons mentioned (e.g. pre-movement testing, traces, sick bird calls, voluntary testing by 

company). Most of these results were also messaged via LMS.24

Table 4. Premises Sampled and Number of Accessions as Surveillance for the 

2017 LPAI Detections 25

Premises State Premises Accessions

Alabama 222 469

Georgia 10 30

Kentucky 54 136

Tennessee 149 324

Total 435 959

 24 Table 4 captures all accessions, including those electronically messaged via LMS from testing laboratories and 

those that were not messaged (but were manually entered into EMRS2). 

25 This does not include diagnostic testing on any LPAI Infected Premises (which would also include environmental 

sampling). It also does not include testing around the LPAI premises that were associated with the 2 HPAI Infected 

Premises in Lincoln County, Tennessee (these 3 backyard LPAI Infected Premises were in the HPAI Control Areas). 

Accessions were used as a proxy for the number of testing events that occurred at each premises; NVSL accessions 

for confirmatory testing are included (only 3 accessions in total).
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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Diagnostics

Laboratory services were a major component of the response effort, for both initial diagnostics 

and surveillance activities. The Stamping-Out and Depopulation Policy provides guidance for 

presumptive positive HPAI premises; in this outbreak, the HPAI-Infected Premises were 

depopulated as soon as the presumptive positive case definition criteria had been met. In 

accordance with the H5/H7 Avian Influenza Case Definition, State officials—in cooperation with 

APHIS—determined whether LPAI-Infected Premises were also depopulated (9 of 12 

depopulated completely; 1 premises conducted targeted euthanasia). 

Laboratory services in support of the incident were divided between the APHIS NVSL and State

operated, USDA APHIS approved and proficiency tested NAHLN laboratories. At NVSL, there 

are three elements addressed for confirmation of flock status: 1) the HA-subtype, which is 

‘presumptive’ based on the NAHLN lab result and ‘confirmed’ based upon the NVSL result; 2) 

the virus pathotype, which is ‘presumptive’ based upon the clinical presentation of the flock 

compared to the H5/H7 Avian Influenza Case Definition, and ‘confirmed’ based upon the HA 

cleavage site sequence at NVSL, and 3) the NA-subtype. As mentioned, in this 2017 outbreak, 

some Infected Premises did not contain enough virus (specifically, viral RNA) to establish the 

pathotype (e.g. LPAI or HPAI). 

NAHLN laboratories were utilized for the initial presumptive positive diagnosis, subsequent 

surveillance sampling, as well as initial environmental testing (NVSL performed confirmatory 

testing on all environmental samples that were PCR-positive). NAHLN laboratory capacity was 

critical in rapidly determining the status of premises and conducting surveillance activities. 

Quarantine, Movement Control, and Continuity of Business

State Quarantines and Unified Control Areas

State quarantines were rapidly placed on premises; some States quarantined premises as soon as 

a suspect case definition was met. In this outbreak, in specific situations, States also quarantined 

premises in addition to the Infected Premises—for example, premises that were located in 

proximity to an HPAI Infected Premises. The date the State quarantine was first placed on the 

Infected Premises was recorded in EMRS2: the average length of the premises quarantine was 50 

days. Quarantines were placed for more extended periods on the HPAI Infected Premises—94 

days, on average. For LPAI-Infected Premises, quarantine was released on average in 50 days. 

The last quarantine was released in Kentucky on June 16, 2017. Figure 19 illustrates the length 

of the quarantines placed on premises during the outbreak. 
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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Figure 19. Length of Quarantine on All Premises (Frequency Count)

Two regulatory Control Areas were established around the HPAI Infected Premises under the 

jurisdiction of the unified Incident Command. The regulatory Control Areas during the 2017 

HPAI/LPAI incident in the southeastern United States lasted 38 days for the first Infected 

Premises and 28 days for the second HPAI Infected Premises.26 Both Control Areas were 

released on April 11, 2017. The first Control Area was placed on March 4; the second on March 

14, 2017. Release of the Control Area requires specific criteria be met (spelled out in the policy 

document Control Area Release), including that all birds on Infected Premises in the Control 

Area are depopulated and disposal is completed (or compost piles set; composting was not used 

in the 2017 outbreak). Required surveillance must be completed; release can occur prior to the 

date in which restocking is approved. Due to the absence of new HPAI detections, these 

activities were rapidly conducted and enabled the Control Areas to be quickly released in 

Tennessee. 

Movement Control and Continuity of Business

In the regulatory Control Areas, established around the HPAI Infected Premises, permits were 

required for movements into, within, and out of the Control Areas. Items permitted during the 

outbreak included those for both continuity of business (e.g., products, based on the Secure Food 

Supply Plans) and for movement control (e.g., the movement of feed or manure) to prevent the 

spread of AI to non-infected premises.

In this outbreak, permits were issued using EMRS2 and the EMRS2 Customer Permit Gateway. 

There were not a significant number of permits issued due to the location of the HPAI Infected 

Premises and the needs of surrounding premises for permitted movement. There were 19 total 

permits issued, 17 from the State of Tennessee and 2 from the State of Alabama. The first permit 

 26 For reference, the HPAI Control Area in Indiana (2016) was also released after 38 days.

1 11 111 1

2

1 1 1 11

0

1

2

3

24 days26 days28 days30 days32 days34 days36 days38 days40 days42 days44 days46 days48 days50 days52 days54 days56 days58 days60 days62 days64 days66 days68 days70 days72 days74 days76 days78 days80 days82 days84 days86 days88 days90 days92 days94 days
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

31

was approved on March 5, 2017; the last permit was approved on April 6, 2017. There were no 

tracked conveyances during this outbreak.27 These 19 permits resulted in 103 distinct 

movements. The first movement occurred on March 6, 2017; the last movement occurred on 

April 10, 2017. 

Figure 20 illustrates the number of permitted movements during the course of the incident by the 

State of Destination. Figure 21 shows the number of permitted movements by item permitted by 

permit class.

Figure 20. Number of Permitted Movements During Incident by State of Destination 

(Control Area in Place; Three-Day Increments)

 27 In EMRS2, tracked conveyances—which are negligible-risk products moved from Food Safety Inspection Service 

facilities—are separately reported as the unified Incident Command may not require those movements to be 

permitted. 

12

6

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8 8

12

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10

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1 1

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14

TN AL
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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Figure 21. Number of Permitted Movements by Item and Permit Class

Of these movements, the most common reason for movement was to move an item directly to a 

farm (93 movements or 90 percent of movements). There were also movements direct to 

hatchery (2 movements), direct to slaughter (5 movements), and into commerce (3 movements). 

Most of the movements (101 movements or 98 percent) originated in Tennessee. 

Depopulation

Depopulation (also known as stamping-out) was an immediate priority during this outbreak to 

prevent the spread of disease. Depopulation measures were undertaken immediately on the HPAI 

Infected Premises and on 9 of 12 of the LPAI Infected Premises. Ventilation shutdown was not 

used in the 2017 HPAI/LPAI outbreak.28 The HPAI Infected Premises were depopulated using 

foam with the assistance of APHIS-hired contractors (coordinated by the SPRS Logistics 

Center/NVS). 

Due to the location and characteristics of specific LPAI-infected backyard premises, State 

officials elected not to depopulate these flocks and instead conducted repeated surveillance 

testing over the duration of their quarantines. On one premises, the entire flock was not 

depopulated, but specific birds were euthanized based on diagnostic testing and epidemiological 

evidence. Of the 12 total LPAI Infected Premises, 9 depopulated in full; 1 euthanized specific 

birds; 2 conducted no depopulation or euthanasia. A variety of methods were used on these LPAI 

premises, including foam, KEDS, cervical dislocation, and CO2. Of the commercial LPAI Infected 

 28 After the delays experienced in the 2014–2015 HPAI outbreak, APHIS had developed a new policy prior to the 

2016 HPAI/LPAI outbreak in Indiana entitled Ventilation Shutdown Evidence & Policy, which states that the use of 

ventilation shutdown may be considered as an alternative, on a premises by premises basis, with close coordination 

and collaboration by State and APHIS officials to meet the goal of depopulation within 24 hours (established in the 

document Stamping-Out and Depopulation Policy). These policies are available on www.aphis.usda.gov/fadprep. 

2

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Into Control Area Out of Control Area

Eggs Feed Groups of animals
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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Premises (6 of 12), companies completed their own depopulation activities on 5 premises; on 1 

premises State personnel also assisted with the depopulation efforts. 

Figure 22 illustrates the amount of time it took to depopulate the 12 premises that conducted 

depopulation activities. The average time from NVSL confirmation to depopulation for all 

premises was less than 24 hours (.83 days). This is a reduction in average time from the 2016 

Indiana outbreak. Please note that depopulation can be conducted when the presumptive 

positive case definition for HPAI has been met, based on State and Federal agreement.

Therefore, in some cases, depopulation may occur prior to NVSL confirmation. The first HPAI 

Infected Premises had completed depopulation within 1 day of NVSL confirmation, while the 

second HPAI Infected Premises completed depopulation approximately 2 days after NVSL 

confirmation. 

Figure 22. Time in Days to Depopulation from NVSL Confirmation (Frequency Count)

Note: NVSL confirmation date is when a “confirmed status” was placed on the premises in 

EMRS2, based on a positive diagnostic test result at NVSL. For this outbreak, this was the date of 

the first confirmatory result from NVSL. “Negative” times in this graph are a result of depopulation 

being conducted based on a presumptive diagnosis, based on State and Federal agreement.

Disposal

Effective disposal is a key component of a successful response to an FAD outbreak. As shown in

Figure 23, all premises—including the 2 HPAI Infected Premises—that conducted depopulation 

activities used burial as their method of disposal.

1 1 1 1

4

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3

4

5

 -4 Days -3 Days -2 Days -1 Day 0 Days 1 Day 2 Days 3 Days 4 Days 5 Days
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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Figure 23. Primary Disposal Method for Carcasses & Materials

Figure 24 illustrates the time, in days, it took premises to complete disposal from NVSL 

confirmation. In this outbreak, the time it took premises to complete disposal activities was 

shortened, in comparison to prior outbreaks, due to the selection of burial (rather than 

composting) as the disposal method. Please note, completion of disposal date indicates that all 

carcasses and other high-risk material was buried. Disposal of other materials, such as feed, may 

have taken additional time to complete.

Figure 24. Time in Days to Disposal Complete from NVSL Confirmation 

(Frequency Count)

Note: NVSL confirmation date is when a “confirmed status” was placed on the premises in 

EMRS2, based on a positive diagnostic test result at NVSL. For this outbreak, this was the date of 

the first confirmatory result from NVSL. “Negative” times in this graph are a result of depopulation 

being conducted based on a presumptive diagnosis, based on State and Federal agreement.

8

4

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14

Burial No Disposal Conducted

Commercial Backyard

1 1 1

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 -3 Days -2 Days -1 Day 0 Days 1 Day 2 Days 3 Days 4 Days 5 Days 6 Days
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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On average, it took premises only 1.8 days from NVSL confirmation to complete disposal. The 

HPAI Infected Premises averaged 3.4 days to completion; the LPAI Infected Premises averaged 

1.5 days. In part, the delay on one of the Infected Premises was due to severe weather which 

limited outdoor activities. The 8 commercial Infected Premises (HPAI and LPAI) completed 

disposal on average in 1.7 days; it took the backyard Infected Premises only marginally longer, 

on average, at 1.9 days. 

Virus Elimination (Cleaning and Disinfection)

The HPAI virus can survive for extended periods in organic material and under certain 

environmental conditions. As such, virus elimination activities were important for the response. 

As in Indiana 2016, the HPAI Infected Premises were provided with a flat-rate payment for virus 

elimination on the premises. The flat-rate payment is based on the number of birds and 

production type; the producers then elected to conduct virus elimination in whatever manner they 

felt was most effective (in terms of both eliminating the virus and cost). The policy guidance 

document Cleaning & Disinfection Basics (Virus Elimination) outlines the options—including 

heat treatment—for cleaning and disinfection to eliminate HPAI virus from a previously Infected 

Premises. It also prescribes guidance for fallowing premises. More information about flat-rate 

payments is available here. LPAI Infected Premises that conducted virus elimination did not 

receive flat-rate payments from APHIS.

In the 2017 outbreak, premises primarily opted to apply wet disinfectant to complete their virus 

elimination, as seen in Figure 25. Both HPAI Infected Premises used wet disinfectant. In the case 

of a single backyard premises, State officials determined that the premises did not need to 

conduct virus elimination (same premises that only conducted selective euthanasia). 

Figure 25. Disinfection Method Used 

5

2

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2

3

4

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7

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Wet Disinfectant Heat Treatment Fumigation No Virus

Elimination

Extended Fallow

Commercial Broiler Backyard Premises
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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It took the HPAI Infected Premises 65 days on average to complete virus elimination activities 

after NVSL confirmation of HPAI on the premises. On average, all premises completed virus 

elimination activities in 37 days of NVSL confirmation. This average was 38 days for 

commercial premises (range of 26 to 70 days) and 37 days for backyard premises (range of 4 to 

72 days).

After depopulation was complete, it took premises on average 36 days to finish virus elimination 

activities. After disposal was complete, it took premises on average 36 days to finish these 

activities. The similarity in these time frames is directly related to the fact that disposal was 

performed rapidly, by burial, after depopulation in this incident. The average number of days 

from depopulation to virus elimination and disposal to virus elimination is broken out by 

premises type (HPAI and LPAI; backyard and commercial) in Figure 26. 

Figure 26. Time to Virus Elimination/C&D Complete (in Days)

Biosecurity

Following concerns about a lack of stringent farm biosecurity measures being a contributing 

factor to the spread of HPAI during the 2014–2015 outbreak, many new biosecurity materials 

were developed for the poultry industry to support implementation of revised biosecurity 

recommendations, which are available from www.poultrybiosecurity.org. Site managers were 

assigned to premises specifically to monitor and audit biosecurity as response operations were 

underway. 

The release of the Interim Rule in February 2016 confirmed the USDA APHIS focus on 

biosecurity, requiring that all owners and contractors, unless specifically exempted, provide a 

statement that, at the time of detection of HPAI in their facilities, they had in place and were 

following a biosecurity plan aimed at keeping HPAI from spreading to commercial premises. 

63.3 61.5

34.5 34.6

28.4 27.3

0.0

10.0

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50.0

60.0

70.0

Time to C&D Complete from Depop

Complete

Time to C&D Complete from Disposal

Complete

HPAI Commercial LPAI Backyard LPAI Commercial
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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The 2017 HPAI/LPAI outbreak affected commercial broiler breeder flocks—a flock type that 

had not been affected in prior HPAI outbreaks. Unlike in 2014–2015 and 2016, lateral spread 

between farms did not appear to be a significant risk factor during the 2017 outbreak. However, 

other biosecurity issues, including breaches in protocol, did appear to be risk factors that could 

bring viruses inside poultry barns from the environment.

29

Health and Safety

In addition to the ICG activities already discussed, Safety Officers participated in the unified 

Incident Command structure to ensure the proper use of PPE and facilitate appropriate health and 

safety measures. USDA APHIS also coordinated with CDC on the One Health aspect of the 

event, which included ILI monitoring. While this North-American lineage H7N9 virus has never 

been reported in humans, response workers were closely monitored. CDC and APHIS have 

coordinated to develop occupational guidance and protocols for monitoring responders for 

influenza like illness during and after mobilization. USDA also shared virus sequencing results 

with CDC. 

Appraisal & Compensation

Indemnity for Birds Destroyed

As a result of the challenges during the 2014–2015 outbreak, new finance and administration 

processes were defined (and are available at www.aphis.usda.gov/fadprep). These new 

procedures, discussed in Section 5, are consistent with the 24-hour depopulation goal in that only 

one form must be completed before depopulation started on a premises; this Appraisal and 

Indemnity Request Form enabled the poultry owners and growers to agree to accept fair market 

value for depopulated birds. As in the 2016 HPAI/LPAI outbreak, these processes were again 

implemented in the 2017 outbreak.

During or after depopulation, owners/growers and case managers gathered information and 

original records to work on the Contract Grower worksheet (if applicable) and VS 1-23 Form so 

that payment for birds could be processed quickly. Then the Flock Plan and Financial Plan were

completed so that full reimbursement for all response activities could be processed. Indemnity 

payments for the 2 HPAI Infected Premises were rapidly distributed. Owners and growers of 

LPAI-infected flocks that made the decision to depopulate, in coordination with State officials, 

were not indemnified by APHIS in the 2017 outbreak.

Compensation for Response Activities

APHIS-hired contractors (through the SPRS Logistics Center/NVS) conducted disposal activities 

on the HPAI-Infected Premises. Flat-rate payments were distributed to HPAI-Infected Premises 

for virus elimination activities. Based on current LPAI regulations, LPAI Infected Premises that 

 29 USDA APHIS. 2017. Epidemiological and Other Analyses of HPAI/LPAI Affected Poultry Flocks: June 26, 2017 

Report. USDA APHIS STAS Center for Epidemiology and Animal Health.

https://www.aphis.usda.gov/animal_health/animal_dis_spec/poultry/downloads/epi-ai.pdf.
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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elected to depopulate and subsequently completed disposal and virus elimination activities were 

not compensated by APHIS for these activities.

Logistics

The SPRS Logistics Center and the NVS led logistics for the 2017 HPAI/LPAI outbreak at the 

ICG-level, and also deployed personnel to the ICP to support deployed equipment. NVS 

responded to support requests through the unified Incident Command, coordinating and 

documenting contractor support for depopulation and disposal. NVS also contracted access to

necessary supplies and equipment for response activities. 

As in previous outbreaks, the 2017 outbreak again demonstrated that foam depopulation units are 

fickle and prone to breaking down. As such, the NVS continues to work on and exercise 

solutions that enable the use of multiple, redundant approaches that may improve the timeliness 

of depopulation efforts. 

Restocking

For previously HPAI Infected Premises, approved to restock means that 

• the premises/flocks are 21 days post completion of C&D/virus elimination,

• environmental sampling has been completed with no signs of HPAI, 

• requirements have been met per the USDA Flock Plan and State Quarantine Notice/Hold 

Order, AND

• State and APHIS officials have approved the restock in writing (typically termed the 

restock approval letter). 

On previously LPAI Infected Premises, based on the States’ LPAI Response Plan, a restock 

approval letter may also be issued from the State indicating that the premises can restock. 

However, in this outbreak, for all of the LPAI-infected backyard premises, the State elected to 

use the quarantine release notice to both release quarantine and approve restocking on the 

premises.30 This was also the case for one commercial LPAI premises. 

The HPAI-Infected Premises were approved to restock on June 6, 2017. On average, this was 87 

days after NVSL confirmed HPAI on the premises. Figure 27 shows the restock approval date 

for all premises, both HPAI and LPAI. The first premises approved to restock was a previously 

LPAI-infected commercial premises on April 6, 2017. The last premises approved to restock was 

a previously LPAI-infected backyard premises, which was on June 16, 2017. The average time to 

restock approval from NVSL confirmation was 48 days, with a range from 23 to 92 days (Figure 

28). 

 30 In the case of the three LPAI backyard premises that either did not depopulate at all or conducted selective 

euthanasia, these premises were also prohibited from adding birds to their premises during their intensified 

surveillance activities. Quarantine release (which played a dual purpose as restock approval) allowed these premises 

to again add birds to their flocks.
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

39

Figure 27. Restock Approval Date for All Premises

Figure 28. Time in Days to Restock Approval from NVSL Confirmation Date

Information Management & Reporting

Data integrity, timeliness of entry, and accuracy continued to be a priority for both the ICG and 

deployed APHIS personnel. EMRS2 Specialists were immediately deployed virtually and inperson to support the data-entry and reporting requirements of the outbreak. Previously 

developed HPAI data standards were incredibly helpful for the HPAI-related data entry; these 

1

3

1 1 1 1 1 1 1 1

2

0

1

2

3

4

6-Apr8-Apr

10-Apr12-Apr14-Apr16-Apr18-Apr20-Apr22-Apr24-Apr26-Apr28-Apr30-Apr

2-May4-May6-May8-May

10-May12-May14-May16-May18-May20-May22-May24-May26-May28-May30-May

1-Jun3-Jun5-Jun7-Jun9-Jun

11-Jun13-Jun15-Jun

LPAI Backyard LPAI Commercial HPAI Commercial

5

0

2

0

2

1

0 0 0 0

1 1 1 1

0

1

2

3

4

5

6

23-27

days

28-32

days

33-37

days

38-42

days

43-47

days

48-52

days

53-57

days

58-62

days

63-67

days

68-72

days

73-77

days

78-82

days

83-87

days

88-92

days
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

40

also provided a framework for LPAI-related data entry, where such data were different from 

those required for the HPAI detections (primarily diagnostics). 

The 2017 outbreak continued to use the EMRS2 Tally Sheet that was developed during the 2016 

HPAI/LPAI outbreak in Indiana. It contained data to be entered in nearly real-time as the 

response was ongoing. Data entered into the Tally Sheet can be changed at any time and is 

intended to be the best preliminary information currently available. At routine intervals, the full 

EMRS2 database is checked against the EMRS2 Tally Sheet data, and all inconsistencies are 

resolved through processes defined by the ICG Situation Unit.

During the 2017 outbreak, all incident reporting, including the production of distributed maps, 

were directly created using data entered into EMRS2. This includes both the unified Incident 

Command Situation Reports, the Weekly Situation Reports (Appendix 2), and other incident 

related reports. 

Communications

Public information and outbreak communication was coordinated by APHIS Legislative and 

Public Affairs (LPA) and the affected States. A virtual Joint Information Center (JIC) was 

established between APHIS LPA and the State of Tennessee to manage communications 

regarding the HPAI detections. LPA personnel were integrated into the ICG and coordinated 

closely with the unified Incident Command to support consistent messaging from APHIS and the 

affected States. Stakeholders were kept informed during the response through stakeholder 

announcements, conference calls, and updates to the APHIS AI page. 

Section 7. Preparedness and Future Planning

The 2017 HPAI/LPAI outbreak in the southeastern United States affected different States and a 

new industry when compared with either the 2014–2015 HPAI or 2016 HPAI/LPAI outbreaks. 

Importantly, this enabled new States to practice and implement their response plans and offered 

another opportunity for APHIS to refine its processes for HPAI and mixed HPAI/LPAI response. 

Like in 2016, HPAI was quickly controlled, contained, and eradicated.

Due to ongoing HPAI transmission worldwide, the APHIS, States, and the entire poultry industry 

remains on guard for a reoccurrence of HPAI in late 2017 and early 2018. APHIS continues to 

review existing policy guidance to incorporate additional lessons learned; the documents 

available on www.aphis.usda.gov/fadprep continue to be updated and clarified as needed. In 

addition, work continues on EMRS2Go, a mobile application which will significantly streamline 

field activities, including surveillance, by reducing data entry requirements. Initiatives to ensure 

all NAHLN laboratories can message diagnostic results to EMRS2 continue. VS NIMTs meet 

routinely to discuss position descriptions, procedural improvements, and corrective actions that 

need to occur based on prior outbreaks. 

While preparedness for HPAI has significantly improved in the last three years, the threat of 

another HPAI outbreak means that APHIS, States, and stakeholders continue to work on critical 

issues for the future. Further information on APHIS activities based on lessons-learned can be 

found in the USDA APHIS After Action Report for this incident.
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

41

Section 8. Conclusion 

The 2017 HPAI/LPAI incident in the southeastern United States was restricted in size and scope. 

Only a single county, Lincoln County, Tennessee was affected by HPAI. In total, 9 counties 

were affected in 4 States. There were 14 Infected Premises (12 LPAI; 2 HPAI). Of the 12 LPAI 

Infected Premises, 4 were confirmed LPAI; 8 were presumptive LPAI. Figure 29 geographically 

illustrates the 2017 southeastern United States outbreak region which includes NVSL confirmed 

disease status.

Figure 29. 2017 AI Outbreak in Southeastern United States with Disease Status

In all, approximately 253,000 birds were affected or depopulated during the response effort. The 

limited spread of HPAI limited the economic impact of the outbreak. Figure 30 provides an 

overview of key events during the outbreak, from the first NVSL confirmation to the last 

premises to gain restock approval. All quarantines were released on June 16, 2017, the same day 

the final LPAI commercial premises was approved to restock.
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

42

Figure 30. 2017 Overall Timeline

Note: NVSL confirmation date is when a “confirmed status” was placed on the premises in EMRS2, based on a positive diagnostic test result at 

NVSL. For this outbreak, this was the date of the first confirmatory result from NVSL. March April May June

2017

Commercial

Flock Type

First HPAI Detection 3/4/2017 

Control Area Released 4/11/2017 (only HPAI had Control Area)

First Restock Approved Premises 4/6/2017 

First LPAI Detection 3/8/2017 

First Quarantine Released 4/6/2017

Backyard

Commercial 

& Backyard

Last/Second HPAI Detection 3/15/2017 

Last LPAI Detection 3/25/2017 

All Surveillance Zones Released 4/27/2017 

HPAI Quarantines Released 6/6/2017

Last Quarantine Released 6/16/2017

Last Restock Approved Premises 6/16/2017
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

43

The success of the 2017 response is largely due to the lessons learned in 2014–2015 and 

particularly in the mixed HPAI/LPAI 2016 incident. The response was effective at detecting 

HPAI Infected Premises, depopulating these premises rapidly, and conducting timely response 

activities. SPRS District 2 personnel were able to manage the incident without the deployment of 

a VS NIMT, and effectively coordinated and integrated with the States of Tennessee and 

Alabama in a unified Incident Command structure. At the ICG level, the continuation of an 

HPAI ICG throughout 2016 and into 2017 resulted in rapid collaboration and efficient support of 

the unified Incident Command. Information management processes continued to improve, and 

financial procedures were again implemented in a timely and efficient manner.

While this outbreak was small in scale, there were still unique challenges. Ongoing areas for 

improvement include the following: 

• Confirming sufficient numbers of personnel are medically cleared and fit-tested, and that 

this information is readily available. 

• Ensuring NAHLN laboratories can electronically message diagnostic test results to LMS 

to automatically integrate with other data in EMRS2. 

• Rapid deployment of personnel and functioning equipment.

• Streamlining epidemiological investigations.

• Clarifying procedures for LPAI detections in a mixed HPAI/LPAI incident.

USDA APHIS has identified strengths and areas for improvement during the response, which 

will be released in the USDA APHIS After Action Report for this incident. USDA APHIS 

continues to prepare for HPAI and other FADs.
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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Section 9. Abbreviations

Abbreviation Term

AC Animal Care

AI avian influenza

APHIS Animal and Plant Health Inspection Service

C&D cleaning and disinfection

CDC U.S. Centers for Disease Control and Prevention

CEAH Center for Epidemiology and Animal Health

CFR Code of Federal Regulations

3D depopulation, disposal, and disinfection 

DA Deputy Administrator

DC Dangerous Contact

EMRS2 Emergency Management Response System 2.0

EMSSD Emergency Management Safety and Security Division

FAD foreign animal disease

FAD PReP Foreign Animal Disease Preparedness and Response Plan

GIS geographic information system

HPAI high pathogenicity avian influenza

IAP Incident Action Plan

ICG Incident Coordination Group 

ICP Incident Command Post

ICS Incident Command System

ILI influenza-like illness

JIC Joint Information Center

LMS Laboratory Messaging System

LPA Legislative and Public Affairs

LPAI low pathogenicity avian influenza

MAC Multiagency Coordination

MRPBS Marketing and Regulatory Program Business Services

NAHLN National Animal Health Laboratory Network

NASAHO National Assembly of State Animal Health Officials

NASDA National Association of State Departments of Agriculture

NIES National Import Export Services

NIMS National Incident Management System

NIMT National Incident Management Team

NPIP National Poultry Improvement Plan

NVS National Veterinary Stockpile

NVSL National Veterinary Services Laboratories

ODA Office of the Deputy Administrator

OPS operations

PCR polymerase chain reaction
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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Abbreviation Term

PPE Personal Protective Equipment

PSS Program Support Services

rRT-PCR real-time reverse transcription-polymerase chain reaction

SAHO State Animal Health Official

SHEP Safety, Health, and Environmental Protection

SPRS Surveillance, Preparedness, and Response Services

STAS Science, Technology, and Analysis Services

USDA U.S. Department of Agriculture

VS Veterinary Services

VSET VS Executive Team

WS Wildlife Services
USDA APHIS HPAI Response Final Report, 2017 HPAI/LPAI Southeastern United States

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Section 10. List of Appendices 

This section contains a list of appendices; all of these appendices are not publicly available. 

Publicly available appendices are posted at www.aphis.usda.gov/fadprep. 

Appendix 1. Abbreviations for the Appendices

Appendix 2a. H7 Avian Influenza National Situation Report (March 31, 2017)

Appendix 2b. Last H7 Avian Influenza National Situation Report (May 11, 2017)

Appendix 3. Final List of Infected Premises from 2017 Outbreak (May 31, 2017)

Appendix 4a. HPAI and LPAI H7 2017 Map for State and APHIS Officials (March 26, 2017)

Appendix 4b. Final HPAI and LPAI H7 2017 Map for State and APHIS Officials (June 22, 

2017)

Appendix 5. Final Mapbook Weekly Report (May 1, 2017)

Appendix 6. Final National Control & Containment Map (June 4, 2017)

Appendix 7. Epidemiology Curve (March 30, 2017)

Appendix 8. Final Summary Deployment Report (May 4, 2017)

Appendix 9. Final Permitting and Movement Report (April 11, 2017)

Appendix 10. Incident Coordination Group Coordination Plan (April 7, 2017)