Epidemiologic and Other Analyses of HPAI

Affected Poultry Flocks

July 2022 Interim Report 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

ii USDA APHIS VS

Suggested bibliographic citation for this report: 

USDA-APHIS (2022). Epidemiologic and other analyses of HPAI affected poultry flocks: July 1, 2022

Interim Report. USDA:APHIS:VS: Center for Epidemiology and Animal Health. Fort Collins, CO. 

July 2022. 74 pgs.

For more information, contact: 

Amy Delgado, MS DVM PhD

Director, Center for Epidemiology and Animal Health

USDA:APHIS:Veterinary Services

Center for Epidemiology and Animal Health

2150 Centre Avenue, Bldg. B-2E7, Fort Collins, CO, 80526-8117

Phone (970) 494-7302

Email: Amy.H.Delgado@usda.gov

Web: http://www.aphis.usda.gov/animal-health/ceah

Version Control

This document was first released in February 2023. The March 2023 update includes the following 

changes:

• Update to page numbers in the Table of Contents. 

• Update to page numbers in the List of Figures and Tables. 

• Footnote references revised on pages 15, 20, 23, and 44. 

• Revisions and additions to the Reference section.

• Revisions and clarifications to the Acknowledgments section.

The U.S. Department of Agriculture (USDA) prohibits 

discrimination in all its programs and activities on the basis 

of race, color, national origin, age, disability, and where 

applicable, sex, marital status, familial status, parental 

status, religion, sexual orientation, genetic information, 

political beliefs, reprisal, or because all or part of an 

individual's income is derived from any public assistance 

program. (Not all prohibited bases apply to all programs.) 

Persons with disabilities who require alternative means for 

communication of program information (Braille, large print, 

audiotape, etc.) should contact USDA's TARGET Center at 

(202) 720-2600 (voice and TDD). 

To file a complaint of discrimination, write USDA, Director, 

Office of Civil Rights, 1400 Independence Avenue, SW, 

Washington, DC 20250-9410 or call (800) 795-3272 or (202) 

720-6382 (TDD). USDA is an equal opportunity provider and 

employer.

Mention of companies or commercial products does not 

imply recommendation or endorsement by the U.S. 

Department of Agriculture over others not mentioned. USDA 

neither guarantees nor warrants the standard of any product 

mentioned. Product names are mentioned solely to report 

factually on available data and to provide specific 

information.

USDA–APHIS–VS-S&P–CEAH

NRRC Building B, M.S. 2W4

2150 Centre Avenue

Fort Collins, CO 80526-8117

(970) 494–7000

Email: vs.ceah@aphis.usda.gov

http://www.aphis.usda.gov/about_aphis/programs_

offices/veterinary_services/ceah.shtml

(July 2022)
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

1 USDA APHIS VS

Table of Contents

Executive Summary............................................................................................................................4

Introduction ......................................................................................................................................6

A. Description of Outbreak.......................................................................................................................... 7

B. Comparison of 2022 HPAI Outbreak to 2015 HPAI Outbreak ...............................................................15

Phylogenetic Analysis and Diagnostics..............................................................................................22

A. Phylogenetic Analyses...........................................................................................................................22

B. Public Health Aspects............................................................................................................................24

C. Diagnostics and Characterization..........................................................................................................24

Epidemiologic Study to Investigate the H5N1 Virus in Commercial and Backyard Poultry in 

the United States.......................................................................................................................25

A. Case Series.............................................................................................................................................25

Estimating Disease spread With the National HPAI Disease-Spread Model ........................................30

A. Highly Pathogenic Avian Influenza (HPAI) National Model Overview...................................................30

B. Applications for the HPAI National Model............................................................................................31

C. Configurations for the National HPAI Disease-Spread Model...............................................................31

D. Limitations on Estimating Disease Spread ............................................................................................36

Estimating the Time of H5N1 HPAI Introduction Into Commercial Poultry Flocks using 

Diagnostic Test Results and Production Data ..............................................................................38

A. Summary ...............................................................................................................................................38

B. Results...................................................................................................................................................38

C. Discussion..............................................................................................................................................43

Avian Influenza Surveillance in Wild Birds.........................................................................................44

Modeling Avian Influenza Transmission at the Interface of Wild Birds and Domestic Poultry .............50

A. Summary ...............................................................................................................................................50

B. Preliminary Results and Discussion.......................................................................................................50

Analysis of eBird and BirdCast Migration Data: Implications for Disease Introduction, 

Spread, and Prevention..............................................................................................................54

A. Potential Use of BirdCast Data for Awareness to Enhance Prevention Measures................................54

B. Space-time Cluster Analysis of eBird Observation Data .......................................................................56

References.......................................................................................................................................57

Acknowledgements..........................................................................................................................59

Appendix A: Initial Contact EPI Report Form .....................................................................................60

Appendix B: Time of Introduction Modeling Methods.......................................................................69
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

2 USDA APHIS VS

List of Figures and Tables

Figure 1. Counties with Highly Pathogenic Avian Influenza Detections in Poultry by Month and by 

Flyway ............................................................................................................................................................ 8

Figure 2. Bird Map of HPAI-Affected Counties by North American Flyway and Poultry Type or Wild 

Detection......................................................................................................................................................12

Figure 3. Weekly Highly Pathogenic Avian Influenza Detections by Species Type as of 31 May 2022...............15

Figure 4. Map Showing a Comparison of States Affected by the 2014–2015 Outbreak of HPAI and 

Those Affected by the 2022 Outbreak of HPAI as of 31 May 2022 .............................................................18

Figure 5. Comparison of Counties With Confirmed Detections of Highly Pathogenic Avian Influenza 

by Outbreak Year as of 31 May 2022...........................................................................................................18

Figure 6. Comparison of Weekly Confirmed Detections of Highly Pathogenic Avian Influenza and 

Total Birds Affected by Outbreak Year.........................................................................................................19

Figure 7. Example of State Level (New York) Egg Prices Delivered to Retailers 2014–2015 and 

2021–2022, US BLS/LMIC.............................................................................................................................21

Figure 8. HA/NA Network Analysis of Analysis of Viruses Isolated During the 2022 Outbreak of 

HPAI..............................................................................................................................................................23

Figure 9. Highly Pathogenic Avian Influenza National Model Overview ............................................................30

Figure 10. Geographic Areas With Greatest Potential for Disease Introductions in Preliminary 

Modeling Outcomes.....................................................................................................................................32

Figure 11. Geographic Projection of Areas with Highest Likelihood of Infected Premises in 

Minnesota Based on Modeling Results........................................................................................................34

Figure 12. Potential Geographic Spread of HPAI Associated With a Small Increase in Backyard Bird 

Placements...................................................................................................................................................36

Figure 13. Potential Geographic Spread of HPAI Associated With a Moderate Increase in Backyard 

Bird Placements. ..........................................................................................................................................36

Figure 14. Relative Timeline for Time of Introduction Analysis by Geographic Cluster, Premises, and 

Likely Source of Introduction. ......................................................................................................................40

Figure 15. Time from Estimated HPAI Introduction to Detection by Production Type and Likely 

Source of Introduction.................................................................................................................................41

Figure 16. Contact Rate by Production Type and Likely Source of Introduction, Estimated by Time 

of Introduction Analysis. ..............................................................................................................................42

Figure 17. Basic Reproduction Number (R0) by Production Type and Likely Source of Introduction, 

Estimated by Time of Introduction Analysis................................................................................................42

Figure 18. Map Depicting the Four Primary North American Waterfowl Flyways.............................................44

Figure 19. States With H5N1 Detections in Wild Bird Species as of 21 June 2022.............................................46

Figure 20. Weekly Relative Risk of Avian Influenza Spillover From Wild Birds to Domestic Poultry by 

County for Several Example Weeks.............................................................................................................51

Figure 21. Relative Risk of Avian Influenza Spillover From Wild Birds to Domestic Poultry for 

Several Example Weeks for the State of North Carolina. Counties With Initial Infected 

Premises Events Outlined in Red .................................................................................................................52

Figure 22. Validation of the Preliminary Interface Model Using Outbreak Data Through Spring 

2022, With Counties With a Spillover Event Shown in Red .........................................................................53

Figure 23. BirdCast’s Live Bird Migration Map for 1 February 2022 at 7:45 a.m. Eastern Time.........................54
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

3 USDA APHIS VS

Figure 24. Graph Showing BirdCast’s Highest Count of Millions of Birds in Flight by Day Overlayed 

With HPAI Detections in Wild Birds and on Non-Poultry and Poultry Premises..........................................55

Figure 25. Frequency Histogram Depicting Elapsed Number of Days Between Observed Highest 

Density of Wild Birds Within a 50km Radius and Detection Date for an HPAI-Positive Premise ................56

Table 1. Confirmed Detections of Highly Pathogenic Avian Influenza by State as of 31 May 2022...................13

Table 2. Confirmed Detections of Highly Pathogenic Avian Influenza by Production Type and World 

Organisation for Animal Health (WOAH) Reportable Species as of 31 May 2022.......................................14

Table 3. Numbers of Commercial and Backyard Farms Infected With H5N1 HPAI That Submitted 

Questionnaires for This Study by State Where the Farm is Located ...........................................................26

Table 4. Production Types of H5N1 Infected Farms That Submitted Questionnaires for This Study.................27

Table 5. Characteristics of H5N1 HPAI Infected Farms in the 21 Days Prior to Detection ................................. 27

Table 6. Variable Parameters Used in Preliminary Modeling Configurations ....................................................32

Table 7. Enhanced Parameters and Outcomes in Mid-Outbreak Modeling Configurations..............................33

Table 8. Modeling Outcomes Assuming Alternative Levels of Backyard Bird Placements................................. 35

Table 9. Number of Apparently Healthy and Sick/Dead Birds Sampled During the 2022 HPAI 

Outbreak. List Current as of 21 June 2022...................................................................................................46

Table 10. Number of Apparently Healthy and Sick/Dead Birds Sampled During the 2022 HPAI 

Outbreak. List Current as of 21 June 2022...................................................................................................47
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

4 USDA APHIS VS

EXECUTIVE SUMMARY

In January 2022, the clade 2.3.4.4b H5N1 highly pathogenic avian influenza (HPAI) was reported in a 

wild bird sample from Colleton County, South Carolina, and heralded what has become one of the 

largest avian influenza outbreaks in United States (U.S.) history, second only to the clade H5 2.3.4.4c 

outbreak in 2015. By 31 May 2022, HPAI had been confirmed in 35 States, including 130 turkey, 55 

chicken, 11 duck, 3 pheasant, 21 poultry, and 137 backyard (non-poultry/non-commercial poultry) 

premises. In comparison to the 2014–2015 outbreak, which shattered multiple records for outbreak 

size and cost, the 2022 HPAI outbreak has spread over a wider geographic area, creating a much 

larger demand for resources and personnel. As of 5 May 2022, over 500 USDA-APHIS personnel and 

contractors have been deployed in support of the response, with an additional 500 State personnel 

responding. Following the 2014–2015 outbreak, APHIS made numerous changes to response 

processes to improve efficiency in control activities, indemnity and virus elimination payments, and 

repopulation processes and timelines. Initial estimates from the 2022 outbreak suggest that 

significant improvements have been made in all these areas.

Phylogenetic analyses of viruses from this outbreak show one major introduction of the Eurasian H5 

clade 2.3.4.4b virus into the U.S. that has spread all the way to the Pacific Flyway. This H5 2.3.4.4b 

virus is more infectious for poultry species without the need for poultry adaptation, as compared to 

the earlier H5 clade 2.3.4.4c virus of 2015, and rapidly causes illness and death in chickens and 

turkeys, though some waterfowl may be infected and show no clinical signs. Additionally, when 

compared to the 2015 incursion, this virus lineage has caused significant wild bird mortalities. 

Reassortment of the H5 clade 2.3.4.4 virus with North American viruses were first identified in 

February 2022 from wild bird samples, and several genotypes have since been identified; 

reassortments account for at least 74 percent of wild bird viruses with several genotypes spilling 

over into poultry. At least 84 percent of analyzed U.S. detections in poultry are consistent with 

independent wild bird introductions. Unique to this outbreak, there have been several mammalian 

detections across all four flyways and as far south as Utah with at least nine species affected. To 

date, there have been only two reports of the H5N1 HPAI 2022 virus detected in humans—one in

the United Kingdom and one in the United States. 

In collaboration with State Animal Health Officials, USDA-APHIS conducted a case-series study of 

H5N1 HPAI infected commercial and backyard operations in the U.S. Risk factors examined include 

the movement of live and dead birds, transportation of manure, equipment sharing, and 

contaminated feed trucks, vehicles, water, and people. Visitors to the farm and employee 

connections with other farms were the most common risk factors identified among respondents. To 

better identify risk factors, USDA will be conducting case-control studies in layer and turkey 

operations with results expected in early 2023.

USDA-APHIS used the HPAI National Model to support budget and resource planning, as well as 

evaluate alternative control strategies and options. As the outbreak continued, disease spread and 

control modeling was used to help inform data-driven response strategies and resource allocation. 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

5 USDA APHIS VS

Other modeling approaches were also used to inform the response and improve our understanding 

of disease transmission. Time of introduction models use diagnostic testing, daily mortality, and 

water consumption data to predict the time of virus entry into a flock. Analysis of 26 commercial 

premises found that time to first positive sample varied by production type, introduction route, and 

reason for testing. The average adequate contact rate across all premises was 3.8 contacts per day, 

and overall mean R0 value was 13.3 (range 2–47), which would ensure rapid spread through a barn. 

This work highlighted the value of closely monitoring mortality, water consumption, and egg 

production to quickly identify disease issues in the flock, while recognizing that these factors may 

vary, so understanding the trends within each production setting is important. 

The U.S. National Surveillance Plan for Highly Pathogenic Avian Influenza in Wild Birds was 

developed to maximize our ability to detect IAV in wild waterfowl. Between 1 June 2021 and 1 June 

2022, over 22,000 wild waterfowl were sampled and tested by rRT-PCR for influenza A viruses. 

Overall, targeted surveillance and morbidity/mortality investigations of sick or dead birds has 

detected 1,611 H5N1 HPAI in wild birds from 42 States across all four U.S. flyways, with over 66 

different avian species affected. 

To better understand the risk of virus spillover from wild to domestic birds, USDA-APHIS 

collaborated with the University of Maryland, and the U.S. Geological Survey, Eastern Ecological 

Science Center to model spatio-temporal trends in transmission between wild waterfowl and 

domestic poultry. Model outputs were validated using the current outbreak, and counties with a 

spillover event had 12 times greater predicted risk, on average, than non-outbreak counties. Of the 

62 spillover counties, 54 were at above-average risk for a spillover event. There were almost no 

spillovers in counties designated as low risk by the interface model. Model results are now available 

online for poultry owners to use to understand their own risk context. 

Other valuable tools for understanding disease risk are eBird and BirdCast migration data. BirdCast 

migration maps show real-time intensities of nocturnal bird migration between local sunset to 

sunrise, as detected by the U.S. weather surveillance radar network. eBird is a database of speciesspecific, crowd-sourced observational data by scientists and birding enthusiasts. Intense periods of 

bird migration, as seen by BirdCast maps were correlated with outbreaks in domestic poultry, 

suggesting that this tool can be used to increase awareness of increased HPAI risk due to wild bird 

movements. Using eBird data, we estimated that HPAI-positive premises were more likely to be 

detected within the first seven days of heavy wild bird observation within a 50km spatial window.

Further information on the epidemiologic features of this outbreak and additional analyses will be 

provided in subsequent reports. 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

6 USDA APHIS VS

INTRODUCTION

In response to the H5N1 highly pathogenic avian influenza (HPAI) outbreaks in commercial and 

backyard poultry across a large portion of the United States, the United States Department of 

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

Wildlife Services, and the affected States have initiated epidemiologic, genetic, and wildlife 

investigations. Due to the unprecedented size of this outbreak, we have chosen to issue an interim 

report looking at data from the start of the outbreak, until 31 May 2022 in the case of epidemiologic 

investigations, and through 29 June 2022 for phylogenetic analyses. Updates to this report will be 

made in the future. These studies aim to provide a better understanding of factors associated with 

avian influenza virus transmission and its introduction into poultry flocks. 

These investigations include the following:

• Phylogenetic analyses of viral genomes; 

• A case series evaluating the data collected through site visits and interviews with farm 

personnel; 

• Application of the National HPAI Disease-Spread Model to inform the response; 

• Analysis of mortality records, diagnostics, and in some cases, water consumption and egg 

production to understand virus transmission in barns and time to detection; 

• Analysis of wild bird surveillance; 

• Analysis of avian influenza transmission risk at the wild bird domestic poultry interface; and

• Analysis of correlation between migratory wild bird numbers captured by open-source tools 

eBird and BirdCast on HPAI transmission risk and timing. 

This interim report includes the results from these investigations to provide producers, industry, and 

other stakeholders with current epidemiologic information. Infected domestic poultry premises 

were classified by species and production type. Species designations included chickens, turkeys, 

ducks, pheasants, and other poultry. In this report, backyard premises that met the World 

Organisation for Animal Health (WOAH, formerly known as OIE) reporting requirements for poultry 

are designated as “backyard/non-commercial” premises. Backyard premises that did not meet 

reporting requirements, because they only reared birds for household use and did not sell any 

animal products, are referred to as “backyard/non-poultry” premises.1 Production types included 

multiple commercial poultry premises types, backyard producers, a wild game farm, and an animal 

rescue. 

1 This terminology reflects premises designations used at the time of this report, which had a data cut-off of June 2022. Due to 

the evolving nature of terminology during an outbreak, the designations and numbers reported in this document may not 

match the data available online. For the most accurate case designations and numbers, see the APHIS HPAI website.
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

7 USDA APHIS VS

A. Description of Outbreak

USDA APHIS identified the Eurasian clade 2.3.4.4b H5N1 HPAI on 13 January 2022 in a wild bird in 

Colleton County, South Carolina.

2 This detection was the first Eurasian H5 HPAI detected in the 

United States since December 2016, and followed ongoing reports of clade 2.3.4.4b H5N1 HPAI in 

Europe3 (starting 27 October 2021 for the migration season; note that ancestors of clade 2.3.4.4b 

have been circulating along Eurasian flyways since 2017) and in Canada4 starting on 4 November 

2021. For Europe, Canada, and the United States, wild bird detections have preceded detections in 

domestic poultry. Figure 1 describes the temporospatial detections of clade 2.3.4.4b H5N1 HPAI 

virus in poultry in the U.S.; refer to the phylogenetics section for further details.

MISSISSIPPI FLYWAY February – March 2022 

The first poultry case in the U.S. was along the Mississippi Flyway in Indiana. On 7 February 

2022, a commercial meat bird turkey operation in Dubois County, Indiana, submitted 

diagnostic test samples to the Indiana Animal Disease Diagnostic Laboratory (a member of 

the National Animal Health Laboratory Network [NAHLN]) after observing signs of lethargy, 

increased mortality, and decreased water consumption in one tom turkey production house. 

The samples tested non-negative for H5 and were forwarded to the National Veterinary 

Services Laboratories (NVSL). On 8 February 2022, the NVSL received samples from the 

affected premises and confirmed clade 2.3.4.4b H5N1 HPAI. 

Continuing in the Mississippi Flyway, the next States affected were Kentucky and Virginia. 

On 11 February 2022, a commercial broiler production operation in Fulton County, 

Kentucky, submitted samples to the Murray State University Breathitt Veterinary Center 

laboratory (a member of the NAHLN network) after observing decreased water consumption 

and increasing mortality in one house. The NAHLN laboratory detected H5 and forwarded 

the samples; NVSL confirmed H5N1 HPAI on 12 February 2022. Also on 11 February 2022, 

oropharyngeal swabs from dead chickens and turkeys belonging to a mixed-species 

backyard flock in Fauquier County, Virginia, tested non-negative for H5 at the Virginia 

Department of Agriculture and Consumer Services Harrisonburg diagnostic laboratory (a 

member of the NAHLN network). The samples were transported to NVSL on 12 February 

2022, where H5 HPAI was confirmed. Subsequently, between 8 February 2022 and 2 March 

2022, H5N1 HPAI was confirmed in seven commercial meat bird turkey premises and one 

commercial broiler production premises in two counties in southern Indiana and two 

counties in western Kentucky (Figure 1). 

2 https://www.aphis.usda.gov/aphis/newsroom/stakeholder-info/sa_by_date/sa-2022/hpai-sc 3https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1070246/Highly_pathog

enic_avian_influenza__HPAI__in_the_UK_and_Europe__outbreak_update_23.pdf 4 https://wahis.woah.org/#/in-event/4191/dashboard 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

8 USDA APHIS VS

Figure 1. Counties with Highly Pathogenic Avian Influenza Detections in Poultry by Month and by

Flyway. 

ATLANTIC FLYWAY February – March 2022 

Moving to the Atlantic Flyway, on 18 February 2022, the NVSL confirmed clade 2.3.4.4b 

H5N1 HPAI in a non-poultry premises in Suffolk County, New York. This detection was the 

first of a series of detections among backyard premises in Atlantic Flyway States along the 

Northeastern Atlantic coastline (Figure 1); impacted States included Maine, Connecticut, 

and Massachusetts (Table 1). On 20 February 2022, a commercial laying hen facility in New 

Castle County, Delaware, observed increased mortality in a single house. Samples were 

collected and submitted from the affected house to the Allen Laboratory at the University of 

Delaware (a member of the NAHLN network) on 21 February 2022 and H5 was detected the 

same day. NVSL confirmed HPAI on 22 February 2022. On 3 March 2022, a table egg layer 

premises located in Cecil County, Maryland, and within the established New Castle Control 

Area, observed increased mortality. This premises was already conducting daily continuity of 

business testing for permitted movement. Diagnostic samples were submitted, and the 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

9 USDA APHIS VS

NAHLN Laboratory detected H5 the same day. The NVSL confirmed H5N1 HPAI the following 

day. Subsequently, six more premises on the Delmarva Peninsula were confirmed between 8 

March 2022 and 18 March 2022. Affected premises types included table egg layer, table egg 

processing, table egg pullet, and broiler production facilities. 

MISSISSPPI FLYWAY February – May 2022 

Back in the Mississippi Flyway, on 23 February 2022, the NVSL confirmed clade 2.3.4.4b 

H5N1 HPAI in a mixed species non-poultry flock in Kalamazoo County, Michigan. 

Subsequently, from 24 March 2022 to 10 May 2022, 12 additional premises in Michigan

were confirmed; these included 9 backyard/non-poultry, 2 non-commercial poultry chicken

flocks, and 1 commercial turkey meat bird premises. From 1 March 2022 to 18 May 2022, 

HPAI was confirmed in additional Midwest States located in the Mississippi Flyway, including 

Iowa, Missouri, Illinois, Wisconsin, Minnesota, and Ohio (Table 1; Figure 1). HPAI detections 

in Iowa and Missouri occurred predominately among commercial premises. In Iowa, 

affected premises included nine commercial turkey, six commercial table egg layers, and 

four non-poultry premises. In Missouri, detections included four commercial turkey, one 

commercial broiler, and three non-poultry premises. In Wisconsin, confirmed premises 

included 7 commercial turkey, 1 commercial table egg layer, 1 backyard/non-commercial, 

and 13 backyard/non-poultry premises. As of 31 May 2022, a total of 80 detections occurred 

in Minnesota, accounting for 22.4 percent of the total cases. Confirmed premises included 

57 commercial turkey, 1 commercial table egg layer, 1 commercial broiler, and 21 

backyard/non-poultry producers. Backyard premises in Minnesota included 19 non-poultry 

and 2 non-commercial poultry premises. HPAI detections in Illinois and Ohio were limited to 

backyard/non-poultry premises. From 8 April 2022 to 19 May 2022, additional confirmations

in Indiana were reported for three commercial duck premises and two backyard/nonpoultry premises.

CENTRAL FLYWAY March 2022 

The first of several poultry premises were affected in the Central Flyway, and on 5 March 

2022, the NVSL confirmed HPAI on a commercial meat-type turkey premises in Charles Mix 

County, South Dakota. From 12 March 2022 to 20 May 2022, additional detections in South 

Dakota were confirmed for 33 commercial turkey, 1 commercial table egg layer, 1 

commercial gamebird, 2 backyard/non-commercial chicken, and 2 backyard/non-poultry 

premises. Detections in South Dakota accounted for 11.2 percent of all detections in 

domestic poultry as of 31 May 2022, and predominately occurred in the eastern side of the 

State. Following initial detections in South Dakota, subsequent detections were confirmed in 

Kansas starting 11 March 2022, in Nebraska starting 15 March 2022, and in North Dakota 

starting 29 March 2022. Confirmed detections in Kansas included two backyard/non-poultry, 

two backyard/non-commercial poultry, one backyard/non-commercial chicken, and one 

commercial turkey premises. In Nebraska, the detections included four backyard/non-
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

10 USDA APHIS VS

poultry, two commercial broiler, and two commercial table egg layer premises. In North 

Dakota, HPAI affected predominately backyard premises but was also found in four 

commercial turkey premises.

ATLANTIC FLYWAY March – May 2022

While HPAI detections were increasing within the Mississippi and Central Flyways, reports 

were received from previously unaffected States along the east coast in the Atlantic Flyway. 

These States included North Carolina, Pennsylvania, Vermont, and New Jersey. On 29 March 

2022, the NVSL confirmed H5 HPAI in a commercial turkey premises in Johnston County, 

North Carolina. Active surveillance testing for the infection zone identified two additional 

commercial turkey premises. Between 1 April 2022 and 11 April 2022, HPAI was confirmed

in three commercial turkey and three commercial broiler bird premises in Wayne County, 

North Carolina. A few days later in Pennsylvania, on 15 April 2022, HPAI was confirmed in a 

commercial table egg layer premises in Lancaster County. The NVSL later confirmed HPAI in 

four additional table egg layer and two commercial broiler premises in Lancaster County. On 

29 April 2022, the NVSL confirmed HPAI infection in a commercial duck facility, which was 

the first detection in what would become a total of eight commercial duck premises in 

Lancaster and Berks Counties. Infections were also confirmed for two commercial table egg 

layer premises in Berks County. The confirmed detections in Vermont on 28 April 2022 and 

in New Jersey on 17 May 2022 occurred in backyard/non-poultry premises.

CENTRAL / PACIFIC FLYWAYS March – May 2022

Continuing in the Central Flyway and moving into the Pacific Flyway, on 28 March 2022, the 

NVSL confirmed the detection of H5N1 HPAI in a backyard/non-poultry premises in Johnson 

County, Wyoming. This detection represented movement of the outbreak into the Mountain 

West, which is split by the Central and Pacific Flyways (Figure 1). States with confirmed 

detections included Texas, Montana, Colorado, Idaho, Utah, and Oklahoma (Table 1). All

confirmations in Wyoming, Montana, and Idaho occurred among backyard premises. In 

Wyoming, all eight detections were backyard/non-poultry premises. In Montana, the 

detections were among seven non-poultry and two non-commercial poultry premises. The 

25 detections in Idaho included 15 backyard/non-poultry, 5 backyard/non-commercial 

chicken, 4 backyard/non-commercial poultry, and 1 backyard/non-commercial duck 

premises. NVSL-confirmed detections in Colorado and Utah included both backyard and 

commercial premises. In Colorado, one backyard/non-commercial chicken, one 

backyard/non-commercial poultry, one commercial broiler, one commercial table egg layer,

and one non-poultry premises were detected. The four detections in Utah included three 

backyard/non-poultry and one commercial table egg layer premises. Detection of HPAI in 

Texas and Oklahoma was limited to one commercial upland game bird and one commercial 

broiler breeder premises, respectively.
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

11 USDA APHIS VS

Moving to the west coast, on 29 April 2022, the NVSL confirmed the detection of H5N1 HPAI 

in a backyard/non-poultry premises in Matanuska Susitna, Alaska. This detection 

represented the first detection along the coastline of the Pacific Flyway. On 5 May 2022, 

HPAI was confirmed in a backyard/non-poultry premises in Linn County, Oregon, and a

backyard/non-commercial chicken premises in Pacific County, Washington. As of 31 May 

2022, additional detections occurred in one backyard/non-commercial poultry premises in 

Oregon.

As of 31 May 2022, HPAI was confirmed in 35 States (Table 1), including 130 turkey, 55 

chicken, 11 duck, 3 pheasant, 21 backyard/poultry, and 137 backyard/non-poultry premises

(Table 2). An additional three premises were identified as dangerous contacts and 

underwent depopulation, disposal, and virus elimination. Figure 2 shows a map of all HPAIaffected counties, including both poultry and wild bird detections by flyway as of May 31, 

2022. Figure 3 depicts the number of detections by week and species. Following all 

detections of HPAI, remaining birds on infected premises were depopulated, and active 

surveillance was conducted as outlined within the USDA HPAI Response Plan Red Book.5 For 

commercial premises detections and backyard/poultry detections, 10km Control Areas, 

consisting of a 3km Infected Zone and a 7km Buffer Zone, surrounded by a 10km 

Surveillance Zone were established; for detections within backyard/non-poultry flock 

premises, 10km Surveillance Zones were established. 

5 https://www.aphis.usda.gov/animal_health/emergency_management/downloads/hpai_response_plan.pdf 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

12 USDA APHIS VS

Figure 2. Bird Map of HPAI-Affected Counties by North American Flyway and Poultry Type or Wild 

Detection.
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

13 USDA APHIS VS

Table 1. Confirmed Detections of Highly Pathogenic Avian Influenza by State as of 31 May 2022.

State Total 

Detections

First 

Detection

Last Detection Chicken Turkey Duck Upland

Gamebird

Backyard 

Poultry

NPa

Indiana 11 2/8/2022 5/19/2022 6 3 2

Kentucky 2 2/12/2022 2/15/2022 1 1

Virginia 1 2/12/2022 2/12/2022 1

New York 8 2/18/2022 4/6/2022 1 1 2 4

Maine 12 2/19/2022 4/5/2022 1 11

Delaware 3 2/22/2022 3/17/2022 3

Michigan 13 2/23/2022 5/10/2022 2 1 10

Connecticut 1 3/1/2022 3/1/2022 1

Iowa 19 3/1/2022 5/4/2022 6 9 4

Maryland 4 3/4/2022 3/18/2022 4

Missouri 9 3/4/2022 4/6/2022 1 5 3

South Dakota 40 3/5/2022 5/19/2022 3 33 1 1 2

Illinois 4 3/11/2022 5/17/2022 4

Kansas 6 3/11/2022 4/27/2022 1 1 2 2

Wisconsin 22 3/14/2022 5/23/2022 1 7 1 13

Nebraska 8 3/15/2022 4/29/2022 4 4

New 1 3/16/2022 3/16/2022 1

Minnesota 80 3/26/2022 5/31/2022 2 57 2 19

Massachusetts 1 3/29/2022 3/29/2022 1

North Carolina 9 3/29/2022 4/12/2022 3 6

North Dakota 15 3/29/2022 5/17/2022 3 4 3 5

Ohio 1 3/29/2022 3/29/2022 1

Wyoming 8 3/29/2022 5/20/2022 8

Texas 1 4/3/2022 4/3/2022 1

Montana 9 4/7/2022 5/6/2022 2 7

Colorado 5 4/8/2022 5/19/2022 3 1 1

Idaho 25 4/14/2022 5/24/2022 5 1 4 15

Pennsylvania 16 4/15/2022 5/23/2022 9 7

Utah 4 4/15/2022 5/17/2022 1 3

Vermont 1 4/28/2022 4/28/2022 1

Alaska 1 4/29/2022 4/29/2022 1

Oklahoma 1 4/30/2022 4/30/2022 1

Oregon 2 5/5/2022 5/17/2022 1 1

Washington 13 5/5/2022 5/27/2022 1 12

New Jersey 1 5/17/2022 5/17/2022 1

Total 357 55 130 11 3 21 137

a Non-Poultry (NP) as defined by the World Organisation for Animal Health (WOAH)
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

14 USDA APHIS VS

Table 2. Confirmed Detections of Highly Pathogenic Avian Influenza by Production Type and World Organisation 

for Animal Health (WOAH) Reportable Species as of 31 May 2022. 

Production Type Chicken Turkey Duck Upland 

Gamebird

Backyard 

Poultry

NonPoultry

Commercial Broiler Production 11

Commercial Broiler Breeder Pullets 1

Commercial Broiler Breeder 2

Commercial Table Egg Layer 20

Commercial Table Egg Pullets 3

Commercial Table Egg Breeder 2

Commercial Turkey Meat Bird 118 1

Commercial Turkey Breeder Hens 8

Commercial Turkey Replacement Hens 2

Commercial Turkey Poult Supplier 1

Commercial Turkey Breeder Toms 1

Commercial Duck Meat Bird 4

Commercial Duck Breeder 6

Commercial Upland Gamebird Producer 3

Backyard Producer 16 1 20 135

Wild Game Farm 1

Animal Rescue / Rehabilitation 1

Total 55 130 11 3 21 137
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

15 USDA APHIS VS

Figure 3. Weekly Highly Pathogenic Avian Influenza Detections by Species Type as of 31 May 2022. 

B. Comparison of 2022 HPAI Outbreak to 2015 HPAI Outbreak

2014–2015 HPAI Outbreak Final Report Highlights6 

From December 2014 through June 2015, the U.S. endured what was at the time the largest 

animal health emergency in its history, with more than 200 cases of highly pathogenic avian 

influenza (HPAI) found in commercial and backyard poultry, as well as wild birds, across the 

country. In December 2014, HPAI was detected in the United States for the first time since 

2004. From 11 December 2014 to 16 January 2015, the USDA received a total of seven 

reports of HPAI H5N2 or H5N8 in captive wild birds and backyard flocks from the 

Northwestern United States. Additional detections occurred in wild birds. The first infected 

commercial flock was identified on 23 January 2015 in California. From January to March, 

the disease spread slowly to multiple States, including Minnesota, Missouri, Arkansas, and 

Kansas. A significant increase in HPAI H5N2 in turkey flocks occurred through early April in 

Minnesota, followed by a rapid increase in Iowa in late April and throughout May, where 

large numbers of chicken layer flocks were affected. The last case of HPAI was confirmed in 

a commercial flock on 16 June 2015. In total, during the 2014–2015 outbreak, there were 

211 detections on commercial operations and 21 detections on backyard premises 

6 https://www.aphis.usda.gov/animal_health/emergency_management/downloads/hpai/2015-hpai-final-report.pdf.
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

16 USDA APHIS VS

(including those premises designated as a Dangerous Contact Premises). HPAI was detected 

in commercial premises, backyard flocks, wild captive birds, and/or wild birds in 21 States 

(Arkansas, California, Iowa, Idaho, Indiana, Kansas, Kentucky, Michigan, Minnesota, 

Missouri, Montana, North Dakota, Nebraska, New Mexico, Nevada, Oregon, South Dakota, 

Utah, Washington, Wisconsin, and Wyoming). Approximately 7.4 million turkeys and 43 

million egg layers/pullet chickens, as well as a limited number of mixed poultry flocks, were 

affected by HPAI and died from the disease or were depopulated as part of the response. 

These birds accounted for about 12 percent of the U.S. table-egg laying population and 8 

percent of the estimated inventory of turkeys grown for meat. In response to this historic 

animal-disease event, many destination markets for U.S. poultry commodities levied trade 

restrictions on U.S. poultry exports, distorting markets and exacerbating economic losses.

Broiler export losses accounted for the overwhelming majority of lost poultry export 

income. In 2015, broiler exports were $1.1 billion lower than in 2014, a 26-percent 

decrease; egg export income declined $41 million, a loss of 13 percent; and turkey export 

income was $177 million lower, a 23-percent decline.

7

APHIS personnel deployed to the first HPAI cases in December 2014 and continued 

deploying throughout the response effort. The number of APHIS responders and contractors 

dedicated to the response continued to increase as the outbreak grew in scale. At the height 

of response operations, more than 3,400 personnel were deployed: approximately 250 

APHIS personnel, 180 State responders, and over 3,000 support contractors. Over the 

course of the outbreak, there were over 1,200 total deployments by APHIS personnel. 

Approximately 300 additional employees were deployed or worked at an APHIS 

headquarters location to support the outbreak as part of the Incident Coordination Group. 

While HPAI detections ended in mid-June 2015, many response operations—including virus 

elimination, environmental sampling, and restocking—continued throughout the fall. On 18 

November 2015, the United States sent a final report to the World Organisation for Animal 

Health (WOAH); at that time, the 2014–2015 outbreak in the United States was considered 

closed. For the 2014–2015 outbreak, nearly $850 million was obligated for response 

activities (including personnel support) and indemnity payments. Another $100 million was 

made available for further preparedness activities. At the time, it was the most expensive 

animal health incident recorded in U.S. history.

2022 Outbreak Comparison

The primary driver for the spatial extent of spread of the 2022 HPAI event has been

migratory wild bird movements. The first poultry detection was in the Mississippi Flyway, 

which followed earlier detections in wild birds along the Atlantic Flyway. The virus then

moved through the migration patterns in and out of Canada through the Atlantic, Central, 

7 U.S. Department of Agriculture, Foreign Agricultural Service (FAS). 2016. “Global Agricultural Trading System (GATS).”
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

17 USDA APHIS VS

and Pacific Flyways. In contrast, the 2015 HPAI event, while initially preceded by migratory 

movements, was more heavily influenced by spread through lateral transmission after 

introduction to the Midwest, with farm-to-farm spread potentially associated with

movement of people, equipment, and materials between farms. Figure 4 shows the overlap 

in affected States between the 2015 and 2022 outbreaks, while Figure 5 shows the same 

information at the county scale.

During the 2014–2015 outbreak, the virus was introduced into the Pacific Flyway and moved 

eastward as far as Indiana; there were no detections in the Atlantic Flyway. During 2022,

virus was initially introduced via the Atlantic Flyway, with that virus moving westward across 

all four flyways all the way to Alaska. Despite this expanded geographic range and reach of 

the virus in wild birds, at least 85 percent of the premises affected during the 2022 outbreak 

have been consistent with independent introductions of wild bird-origin virus, and shaping 

the spatial distribution of cases, as seen at the county level. Although more counties have 

been impacted in 2022, many of these counties represent a very small number of cases with 

no further spread. This shift may suggest that improvements in biosecurity on farms and 

increased messaging around the importance of proactive measures to reduce the spread 

between locations have had an impact on limiting lateral spread. 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

18 USDA APHIS VS

Figure 4. Map Showing a Comparison of States Affected by the 2014–2015 Outbreak of HPAI and 

Those Affected by the 2022 Outbreak of HPAI as of 31 May 2022. 

Figure 5. Comparison of Counties With Confirmed Detections of Highly Pathogenic Avian Influenza 

by Outbreak Year as of 31 May 2022. 

The greater geographic extent of this outbreak has had serious impacts on resource 

requirements for response. APHIS personnel began deploying to the first detection in 

February 2022 and have continued to deploy through the time of drafting this report. More 

than 500 USDA-APHIS personnel and contractors have been deployed in support of the 

response, with an additional 500 State personnel responding. 

The distribution of farm types impacted over the course of these outbreaks also differed. In 

comparison to the 2015 outbreak, which only had 21 backyard flocks impacted in total, the 

2022 outbreak has confirmed 172 backyard flocks as of 31 May 2022. This likely reflects the 

increased prevalence of the virus in wild birds across all flyways and requires appropriate 

messaging to promote the importance of reporting HPAI in backyard flocks by government 

and industry partners, increased social media information sharing, and an increased number 

of backyard birds overall. Additionally, during the 2020 COVID-19 event, the number of 

people engaged in backyard chickens being reared as a hobby and egg source increased 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

19 USDA APHIS VS

exponentially.8 To date, infections of backyard flocks help to alert the presence of virus 

among wild birds, but as with the outbreak in 2014–2015, there has been no evidence to 

support backyard flocks as a driver for virus spread to commercial poultry based on 

epidemiologic and phylogenetic analyses. Figure 6 shows a comparison of the epidemiologic 

curves and number of birds lost or depopulated due to disease between the two outbreaks. 

The larger number of cases but smaller number of birds seen during the 2022 outbreak is 

reflective of the increased detections of HPAI in backyard flocks seen during this outbreak. 

Figure 6. Comparison of Weekly Confirmed Detections of Highly Pathogenic Avian Influenza and 

Total Birds Affected by Outbreak Year. 

As the outbreak continues to evolve, additional comparisons and lessons learned between 

the two outbreaks are underway. Following the 2014–2015 outbreak, APHIS made 

numerous changes to response processes to improve efficiency in control activities, 

indemnity and virus elimination payments, and repopulation processes and timelines. Initial 

estimates from the 2022 outbreak suggest that significant improvements have been made in 

all these areas, and more detailed information will be provided in the final report for this 

outbreak. 

Trade impacts associated with the 2022 outbreak have been lower than those experienced 

during the 2014–2015 outbreak. As of 31 May 2022, the U.S.A. Poultry and Egg Export 

Council estimates that total losses associated with domestic drops in poultry value (broiler, 

turkey, egg) and export losses combined are over $800 million USD, significantly lower than 

the 2014–2015 outbreak losses. Supply impacts associated with the 2022 outbreak have 

8 5 ways 2020 changed the backyard chicken industry | The Poultry Site
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

20 USDA APHIS VS

also been lower.9 The realized effects of HPAI are the reduced number of layers on hand and 

the resulting effect on table and processed egg production. In the broiler industry, after 

cleaning, disinfection, and quarantine, replenishment can be addressed more rapidly than in 

the egg industry. The egg industry must wait for hatched eggs to reach sexual maturity 

before egg production begins (approximately 20 weeks); the broiler industry can start a new 

cycle after incubation (approximately 21 days). In response to increased demand for layers, 

the number of egg-type hatched eggs set increased early in 2022. In 2015, replenishment 

was delayed until near the end of the event through setbacks and general uncertainty. The 

lessons from that event led to a better understanding of replenishment in the face of a 

disease event and how to maintain business continuity during HPAI. For the 2022 event, the 

number of hatching eggs increased at the beginning of the event in preparation for 

restocking of layers. While pullets and layers were both affected, this forethought allowed 

for replenishment, reallocation of replacement stocks, and increased lay time to help 

support egg buyers and allied industry partners during the event. Forced molting in June 

2022 aimed to ease some of the logistic concerns of the replenishment process. Overall, the 

response from 2022 applied the recommendations identified during the 2015 outbreak’s 

areas for improvement.

Looking specifically at egg market impacts, the Bureau of Labor Statistics reports average 

retail prices (Figure 9), and the differences when prices spiked can be compared between 

the 2015 and 2022 events. Production supply will ultimately affect consumer prices for 

either table or processed eggs. These prices reflect the shortened supply and distributional 

challenges faced during HPAI. For the 2015 event, prices did not spike until May. This was 

related to the movement of eggs in the supply chain, the massive reduction in layer 

numbers, and from the previous section, the limited number of replacement layers on hand. 

These prices remained high for much of 2015 before easing into 2016. The impact of HPAI in 

2022 had a different timeline and was more geographically dispersed. This helps in 

replenishment efforts, where a farm can complete the entire response process in a timely 

manner without being placed in another control area due to additional detections in 

neighboring farms. The easing in prices from May 2022 to June 2022 may indicate the price 

changes will not be as long term as those seen in 2014–2015. 

This current outbreak is still on-going at the time of this report, and as the situation 

continues to evolve, comparisons with the 2014–2015 outbreak will evolve as well. To date, 

while the outbreaks share some similarities in terms of severity, there remain numerous 

differences in scale and complexity between the outbreaks. These differences suggest that 

the response costs and total economic impact of the two outbreaks may be influenced by 

different factors, ultimately yielding two very different outbreaks in terms of impact.

9 Economic analysis of supply impacts conducted and summarized by Dr. Jada Thompson, University of Arkansas, August 

12, 2022, personal communication; unreferenced.
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

21 USDA APHIS VS

Figure 7. Example of State Level (New York) Egg Prices Delivered to Retailers 2014–2015 and 2021–

2022, US BLS/LMIC. 

140

160

180

200

220

240

260

280

300

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Cents Per Dozen Eggs

State Level Retail Egg Prices Grade A Table Eggs

2014 2015 2021 2022
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

22 USDA APHIS VS

PHYLOGENETIC ANALYSIS AND DIAGNOSTICS

A. Phylogenetic Analyses

The overarching phylogenetic and biologic analysis has been conducted in collaboration with USDA 

Wildlife Services and the Southeast Poultry Research Laboratory. Phylogenetic analyses up to 31 

May 2022 show one major introduction of the Eurasian H5 clade 2.3.4.4b virus into the U.S. that has 

spread westward all the way to the Pacific Flyway. This H5 2.3.4.4b virus is more infectious for 

poultry species without the need for poultry adaptation, as compared to the earlier H5 clade 

2.3.4.4c virus of 2015, and rapidly causes illness and death in chickens and turkeys, though some 

waterfowl may be infected and show no clinical signs. Additionally, this lineage has caused 

significant wild bird mortalities as compared to the 2015 incursion. 

As shown in Figure 8, the initial introduction (Group 1) was followed by a second, smaller 

introduction (Group 2) identified in mid-February among a small number of wild birds and backyard 

flocks in the Northeastern U.S. (Connecticut, Maine, Massachusetts, New York, and North Carolina); 

a third introduction into the Pacific Flyway (Group 3) was identified from a wild bird in Alaska 

collected on 26 April 2022, with no detections in poultry as of 31 May 2022. Reassortment of the H5 

clade 2.3.4.4 virus with North American viruses were first identified in February 2022 from wild bird 

samples, and several genotypes have since been identified; reassortments account for at least 74 

percent of wild bird viruses (refer to the section on Avian Influenza Surveillance in Wild Birds for 

more details) with several genotypes spilling over into poultry. Unique to this outbreak, as 

compared to 2015, have been several mammalian detections across all four flyways with at least 

nine species affected. Mammals are typically dead-end hosts for this virus, but if predated or 

scavenged, could contribute to onward transmission. 

Based on analysis of more than 2,700 full genome sequences as of 31 May 2022 and in 

consideration of available epidemiologic data, at least 84 percent of U.S. detections in poultry 

premises and non-poultry flocks are consistent with independent introductions of wild bird-origin 

viruses. Representative poultry and mammal sequences have been uploaded to a public database.10

In-depth epidemiologic investigations have been launched where possible to investigate those with 

potential for common source exposure and/or lateral transmission. The National Veterinary Services 

Laboratories will continue to sequence all newly detected premises, analyze those results, and 

report them to appropriate officials.

10 https://gisaid.org/ 

NOTE: The outcomes of phylogenetic analysis should be interpreted in context of all 

available virus and epidemiologic information and should not be used directly to infer 

transmission.
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

23 USDA APHIS VS

Figure 8. HA/NA Network Analysis of Analysis of Viruses Isolated During the 2022 Outbreak of HPAI.

11 The 

initial introduction (G1) was followed by a second introduction (G2) identified in mid-February among a 

small number of wild birds and four backyard flocks in the Northeastern U.S. A third introduction (G3) 

into the Pacific Flyway has been found in wild bird mortalities and a wild fox in Alaska starting in April 

2022 but has not been detected in poultry to date. 

11 Information presented at the United States Animal Health Association (USAHA) October Conference by Dr. Sungsu Youk, 

USDA ARS Southeast Poultry Research Laboratory; unreferenced. 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

24 USDA APHIS VS

B. Public Health Aspects

The NVSL rapidly shares genetic and biological materials in collaboration with the Influenza Division 

of the Centers for Disease Control and Prevention, USDA-APHIS Wildlife Services, and USDA ARS

Southeast Poultry Research Laboratory, as well as other key partners. Whole genome sequence data 

is used to monitor the virus evolution and assess the risk to veterinary and public health based upon 

the presence/absence of specific amino acid substitutions or protein motifs. 

To date, there has only been one report of clade 2.3.4.4b H5N1 HPAI virus detection in humans in 

the U.S. and only two globally. The U.S. case was involved with bird depopulation at an affected site

in Colorado and tested positive by PCR only on the day of depopulation; all other testing was 

negative. No human-to-human transmission of this subclade has been identified. CDC will continue 

to watch this situation closely for signs that the risk to human health has changed. The health of 

response workers and on-farm personnel was monitored at the State level in cooperation with 

APHIS and CDC. 

C. Diagnostics and Characterization 

Avian influenza subtypes H5 and H7 are reportable worldwide because of their potential for 

mutation to high pathogenicity during replication in poultry. The presence of basic amino acids at 

the cleavage site contribute to the mutation from low to high pathogenicity. Mechanisms by which 

H5/H7 mutate from LPAI to HPAI include the gradual accumulation of basic amino acids (AA), 

insertion of repeated basic AA, and insertion of non-homologous genetic material (only reported for 

H7 viruses). 

Molecular diagnostic tests for influenza A virus (IAV) are used across the U.S. National Animal Health 

Laboratory Network (NAHLN). The most sensitive and specific tool for influenza A detection is the 

Type A-specific rRT-PCR, which targets at least the matrix gene (IAV-M); this is the primary

surveillance tool used and provides a semi-quantitative result. The NAHLN tests samples first by the 

IAV-M test and further by the NAHLN H5 and H7 tests where IAV is detected. Genetic data are also 

used to confirm that diagnostic assays are fit for purpose. In silico analysis confirmed high similarity 

between the H5N1 virus sequences and the relevant primers and probes used for the IAV and H5 

diagnostic rRT-PCR tests.

All poultry samples with a non-negative test result for IAV (serology or PCR) are forwarded to NVSL 

for confirmatory testing. The NVSL uses Sanger sequencing protocols to generate partial HA/NA 

gene sequence directly from the sample for subtype and pathotype determination, when sufficient 

viral RNA is present. Whole genome sequencing is conducted on all isolated viruses, and select 

viruses are further characterized by pathotype assay in specific pathogen-free chickens. 

NVSL confirms the virus HA and NA subtype through molecular sequencing and/or antibody 

subtyping, and the pathotype (LPAI vs HPAI). Where no virus can be recovered, nor sequence 

obtained directly from sample(s), the pathotype is determined by the clinical presentation of the 

flock compared to the USDA-APHIS HPAI case definition.
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

25 USDA APHIS VS

EPIDEMIOLOGIC STUDY TO INVESTIGATE THE H5N1 VIRUS IN COMMERCIAL AND 

BACKYARD POULTRY IN THE UNITED STATES

A. Case Series

In collaboration with State Animal Health Officials, USDA-APHIS conducted a case-series study of 

H5N1 HPAI infected commercial and backyard operations in the United States. A questionnaire was 

administered to the individual(s) on each farm most familiar with the farm’s management and 

operations. Questions focused on the three-week period prior to detection of HPAI (Appendix A). 

The purpose of the study was to generate hypotheses for potential risk factors for infection with 

HPAI based on descriptive information about farm characteristics and management practices. 

The outbreak was ongoing at the time of this study. A confirmed infection date of 5 April 2022 was 

used as a cutoff for inclusion. By that date, there were 146 farms confirmed infected with H5N1 

HPAI; 94 (64%) of those provided questionnaires in time to be included in this study. The 

questionnaires represented farms in 18 of the 24 States that had confirmed infections by 5 April 

2022 (Table 3). The largest number of questionnaires were from farms in South Dakota (n=30), 

followed by Iowa (n=15). Of the responding farms, 16 were backyard poultry operations, and the 

remaining 76 fell into 9 commercial poultry production types (Table 4). The most common

commercial production type was turkey meat bird (n=53), followed by table egg layer (n=9). 

Transmission of virus in previous outbreaks of avian influenza in the United States has been 

attributed to the movement of live and dead birds, transportation of manure, equipment sharing, 

and contaminated feed trucks, vehicles, water, and people (McQuiston et al., 2005, Halvorson, 2009, 

Garber et al., 2016). Results of the questionnaire, focusing on risk factors identified in previous 

outbreaks, are summarized below and in Table 5. 

• Movements of bird and bird products – 18 farms moved birds off site in the three weeks prior 

to detection and 21 farms introduced new birds. 17 farms moved eggs off site and 2 received 

eggs in the three weeks prior to detection.

• Dead-bird disposal method – Only 12 farms (13%) reported using rendering as a dead-bird 

disposal method. Most farms (59%) reported using composting. Of the farms that use 

rendering, 11 were commercial turkey meat bird operations and 1 was a table egg layer 

operation. Six of the farms that reported using rendering were located in North Carolina, four 

were in South Dakota, one was in Minnesota, and one was in Iowa.

• Employees – 20 farms reported that employees visited other premises with poultry in the 

three weeks prior to detection and 21 farms reported having employees in a community living 

situation where they interact with employees from other poultry premises. Fourteen farms 

reported having occasional workers on the farm during the three weeks prior to detection. 

• Visitors – 77 (82%) of the farms reported having visitors in the three weeks prior to detection. 

The most common categories of visitor were feed trucks (n=53), company service people 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

26 USDA APHIS VS

(n=29), crews (e.g., load-out crews or catch crews; n=24), garbage collectors (n=17), 

occasional workers (n=14), and private veterinarians (n=14).

• Shared equipment – Only 18 (19%) farms reported sharing equipment with other farms. The 

most common category of shared equipment was manure/litter handling equipment (n=7).

• Manure movement – Only eight premises reported moving manure off site and two farms 

reported receiving manure from another site in the three weeks prior to detection.

Results showed that some factors and management practices were shared across infected farms; 

however, the significance of these similarities is difficult to interpret given the study design and the 

lack of a non-infected farm group to use for comparison. When considered in conjunction with 

knowledge of practices and risk factors from previous outbreaks, this information may provide 

insights into trends of management practices over time and reveal opportunities to implement 

additional mitigations in the future.

Table 3. Numbers of Commercial and Backyard Farms Infected With H5N1 HPAI That Submitted Questionnaires 

for This Study by State Where the Farm is Located. 

State Total Number 

of Farms

Number of Commercial Farms Number of Backyard 

Farms

Delaware 3 3 0

Illinois 1 0 1

Indiana 6 6 0

Iowa 15 14 1

Kentucky 2 2 0

Maine 5 0 5

Maryland 4 4 0

Michigan 1 0 1

Minnesota 3 3 0

Missouri 8 5 3

Nebraska 1 1 0

New York 3 0 3

North Carolina 6 6 0

North Dakota 3 2 1

South Dakota 30 30 0

Texas 1 1 0

Virginia 1 0 1

Wisconsin 1 1 0
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

27 USDA APHIS VS

Table 4. Production Types of H5N1 Infected Farms That Submitted Questionnaires for This Study. 

Production Type Number of Farms

Backyard 16

Broiler production 5

Table egg breeder 1

Table egg layer 9

Table egg pullets 3

Turkey breeder hens 3

Turkey breeder replacement hens 2

Turkey meat bird 53

Turkey poult supplier 1

Upland game bird 1

Total 94

Table 5. Characteristics of H5N1 HPAI Infected Farms in the 21 Days Prior to Detection. 

Characteristic Level or Response Number/Responses

Movements of birds and bird products

Birds introduced Yes 21/88

Birds moved off site Yes 18/88

Eggs moved on site last 21 days Yes 2/87

Eggs moved off site Yes 17/86

Dead bird disposal method Compost 53/89

Burial 11/89

Incineration 11/89

Rendering 12/89

Landfill 3/86

Disposal offsite 16/89

Manure

Moved offsite Yes 8/87

Moved onsite Yes 3/86

Employees 

Visited other premises with poultry Yes 20/88
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

28 USDA APHIS VS

Shared living situation with employees 

from other poultry premises

Yes 21/86

Visitors 

Crews (e.g., catch-crew, load out) Yes 24/88

Federal/State animal health official Yes 9/87

University extension Yes 1/87

Private veterinarian Yes 14/87

Company service person Yes 29/86

Nutritionist/feed company consultant Yes 10/87

Inspector/auditor Yes 6/87

Feed delivery Yes 53/88

Egg truck Yes 9/87

Litter/bedding delivery Yes 6/87

Litter/bedding removal Yes 5/87

Renderer/dead bird pickup Yes 9/87

Pest control Yes 6/87

Manure truck Yes 5/87

Garbage collection Yes 17/87

Occasional worker Yes 14/87

Wholesaler/buyer Yes 1/87

Customer/private consumer Yes 4/87

Other Yes 19/87

Equipment shared with another premises

ATV/4-wheeler Yes 0/88

Tractor Yes 4/88

Gates Panels Yes 3/88

Skid steer loader Yes 4/84

Egg flats Yes 0/88

Egg racks Yes 2/89

Pallets Yes 1/89

Dead bird containers Yes 0/87
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

29 USDA APHIS VS

Manure/litter handling equipment Yes 7/88

Pressure sprayer/washer/foamer Yes 1/88

Other cleaning equipment Yes 1/88

Vaccination equipment Yes 0/88

Bird Catching equipment Yes 1/88

Live haul loader Yes 5/88

Other Yes 7/89
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

30 USDA APHIS VS

ESTIMATING DISEASE SPREAD WITH THE NATIONAL HPAI DISEASE-SPREAD MODEL

A. Highly Pathogenic Avian Influenza (HPAI) National Model Overview

A series of epidemiologic scenarios were developed in InterSpread Plus® v. 6.01.44 (Stevenson et al., 

2013) to model the introduction and spread of H5N1 HPAI from confirmed premises throughout the 

United States following the first detection. Chicken, turkey, and specialty bird (duck, geese, guinea 

fowl, and pheasant) flocks residing in commercial and backyard (less than 1,000 birds) farm units, 

hatcheries, and live bird markets were incorporated into the National HPAI Disease-Spread Model. 

The Model initiates disease spread and implements integrated control activities (Figure 9) across 28 

operation types to generate a series of outcomes that characterize the severity (number of infected, 

detected, and depopulated premises; estimated number of depopulated birds), duration, and 

geographic spread of simulated HPAI outbreaks.

Figure 9. Highly Pathogenic Avian Influenza National Model Overview. 12

The Farm Location and Animal Population Simulator (Burdett et al., 2015) was used to generate 

likely farm locations based on geospatial characteristics with backyard farm locations adapted from 

12 Note that restocking of farms is not explicitly included in the model, although this is a critical timestep in the actual 

response. 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

31 USDA APHIS VS

current and historic outbreak-related data. Model parameters were developed to reflect the impact 

of disease spread from wild migratory birds, variable levels of lateral spread, seasonal estimates of 

disease transmission, and alternative disease-response strategies.

B. Applications for the HPAI National Model

Applications for the HPAI National Model for this outbreak included: 

• Providing estimates of outbreak size for respective production classes to inform budget

estimates for outbreak response costs;

• Assessing the impact of alternative levels of lateral spread, relative species susceptibilities, 

and seasonal and geographic influences on outbreak size and duration;

• Evaluating the effect of alternative levels of biosecurity and disease reporting;

• Comparing the modeled effectiveness of alternative active surveillance strategies;

• Identifying geographic areas of highest risk for future infection;

• Forecasting county-level disease introductions and spread for State-based disease response 

teams; and

• Estimating the contribution of additional placements of backyard birds to disease 

introductions onto backyard poultry farms.

C. Configurations for the National HPAI Disease-Spread Model

To complete the listed modeling applications, several configurations of simulated HPAI outbreaks 

were developed to incorporate observed and evolving spread conditions and forecast outbreak size, 

duration, and geographic spread. Initially, parameters derived during previous HPAI outbreaks were 

used to generate preliminary outcomes. As the outbreak progressed, parameters specific to this 

outbreak, such as the potential for disease spread from wild birds, specific species susceptibilities, 

directionality of geographic spread, and alternative estimates for between-premises lateral spread, 

were added to subsequent disease-spread scenarios.

Disease-spread scenarios developed after the earliest detections in domestic poultry in the Atlantic 

and Mississippi Flyways suggested only a small likelihood of lateral spread between premises using 

baseline levels for seasonal influences on disease spread and baseline biosecurity. At this time, 

parameters describing disease introductions from exposure to wild birds and specific species 

susceptibilities were not included in the modeled scenarios.

After the potential impact of wild bird introductions was better understood, additional 100-iteration 

scenarios were developed to simulate the spread and control of HPAI. Expanding on configurations 

from the previous HPAI scenarios, these simulations integrated variable levels of disease 

introduction from exposure to wild birds, lateral spread from infectious premises to susceptible 

premises, and seasonal viral persistence (Table 6). 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

32 USDA APHIS VS

Table 6. Variable Parameters Used in Preliminary Modeling Configurations. 

Potential for Wild Bird 

Introductions

Potential for Lateral Spread Seasonal Viral Persistence

Static – High Moderate Moderate

Static – High Moderate Low

Static – High Low Moderate

Static – High Low Low

Progressive – High to Low Moderate Moderate

Progressive – High to Low Low Low

Outcomes from these modeled scenarios projected that greater numbers of commercial premises 

would be infected than backyard premises; turkey premises would be infected at higher rates than 

chicken premises; greater viral persistence led to longer outbreaks; and increased levels of lateral 

spread resulted in the largest simulated outbreaks. Additionally, four specific geographic regions 

experienced the greatest likelihood of future infections during the simulated outbreaks: central 

Minnesota, central North Carolina, Southeast Pennsylvania, and Northwest Arkansas/Southwest 

Missouri (Figure 10). In the period since these scenarios were completed, outbreaks among 

commercial premises were detected in areas forecasted by modeling in Minnesota, North Carolina, 

and Pennsylvania.

Figure 10. Geographic Areas With Greatest Potential for Disease Introductions in Preliminary Modeling 

Outcomes. 

A subsequent series of 100-iteration disease-spread scenarios incorporated additional parameters 

to simulate the evolving outbreak. Differing from previous HPAI scenarios, these simulations 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

33 USDA APHIS VS

integrated wild bird H5N1 introductions, alternative probabilities for lateral spread, estimated 

seasonal viral persistence, and estimated relative species’ susceptibilities to the H5N1 virus (Table 

7). Compatible with previous disease-spread scenarios, the largest outbreaks tended to be

associated with extended periods of lateral spread. Lowering the relative susceptibility for chicken 

and farm-raised specialty birds generated species-specific infection rates approximating the 

infection rates observed in the actual outbreak. Considering that very low to low levels of lateral 

spread had been estimated at this point in the outbreak, two scenarios with outcomes (highlighted 

in yellow) represented the best projection at that time for the potential severity of the outbreak. 

Outcomes associated with the number of infected premises, distribution of infected premises 

between commercial and backyard premises, and the estimated number of depopulated birds 

informed project cost estimates for outbreak response.

Table 7. Enhanced Parameters and Outcomes in Mid-Outbreak Modeling Configurations. 

Potential for 

Wild Bird 

Introductions

Potential 

for 

Lateral 

Spread

Seasonal 

Viral 

Persistence

Relative Avian Class 

Susceptibility to H5N1v

Number of 

Infected 

Premises

Birds 

Depopulated 

(millions)

Static – High Low Moderate

Chicken – high 

Specialty – moderate 

Turkey – very high

238 – 367 40 – 49

Static – High Low Moderate

Chicken – high to very high 

Specialty – moderate 

Turkey – very high

250 – 394 41 – 47

Static – High Moderate Moderate

Chicken – high 

Specialty – moderate 

Turkey – very high

300 – 674 43 – 69

Static – High Moderate Moderate

Chicken – high to very high 

Specialty – moderate 

Turkey – very high

406 – 1,089 41 – 76

In addition to offering national-level projections, disease-spread modeling was used to forecast the 

progression of H5N1 HPAI within high-risk States. After seeding the model with county-level 

approximations of known detections, simulated outbreaks introduced disease from exposure to 

infectious wild birds and lateral spread between infectious and susceptible premises. The scenario 

was configured to generate low levels of lateral spread, a low to moderate seasonal influence on 

disease spread, and a progressive geographic/seasonal-based reduction in exposure to migratory 

birds. Focusing on simulated spread occurring after the end of the known disease-history period, 

these new infections defined the future extent of spread within counties in Minnesota and 

contributed to total disease spread within Minnesota.
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

34 USDA APHIS VS

At the time of scenario development, modeled outcomes identified central Minnesota as the area 

with the greatest likelihood of future infections, especially premises in Kandiyohi, Morrison, Otter 

Tail, Stearns, and Todd Counties (Figure 11). Deriving outcomes from 100 simulated outbreaks, the 

total number of infected premises in Minnesota ranged from a minimum projection of 68 to a 

maximum of 116. Currently, 80 premises have been detected in Minnesota during the 2022 H5N1

HPAI outbreak.

Figure 11. Geographic Projection of Areas with Highest Likelihood of Infected Premises in Minnesota Based 

on Modeling Results. 

During the first three months of the outbreak in Minnesota and other States, disease was detected 

predominantly in commercial operations. Similarly, commercial operations represented 60 to 70 

percent of infected premises in simulated outbreaks. More recently, larger numbers of backyard 

operations have been detected with H5N1 HPAI. Consequently, disease-spread scenarios developed 

in the last month have been enhanced to reflect the observed change in detections.

To generate plausible revisions to existing parameters, an assumption that seasonal bird placements 

on backyard premises in northern latitudes contributed to increased exposure to wild migratory 

birds guided scenario development. Two new scenarios were developed in mid-May 2022: one 

depicting a small increase in exposure/susceptibility for backyard operations to represent a minimal 

expansion in seasonal bird placements, and one with a larger increase in exposure/susceptibility for 

backyard operations to represent a moderate expansion of seasonal bird placements.

Red to orange to yellow to white shading 

describes counties with the highest to lowest 

number of infected premises following the 

known disease-history period over 100 

simulated outbreaks.
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

35 USDA APHIS VS

The scope of additional assumptions affecting disease introduction and spread for these scenarios 

included:

• Low levels of lateral spread from movements of infected domestic birds; contaminated 

equipment, people, or vehicles; or local spread from nearby infected premises;

• Greater numbers of migratory wild birds in northern latitudes than in southern latitudes as 

birds progressively migrate from the United States to Canada;

• Consistent northwesterly movement of migratory wild birds throughout each iteration;

• Species-specific relative susceptibilities to the H5N1 virus (turkeys higher than chickens and 

specialty birds);

• Low to moderate seasonal impact on probabilities of disease transmission; and

• Higher rates of infections/detections in backyard operations than in commercial operations.

As could be expected, the assumption of placement of additional backyard bird flocks in northern 

latitudes of the conterminous United States resulted in greater levels of exposure, susceptibility, and 

subsequent disease transmission between wild or migratory birds and backyard flocks in simulated 

outbreaks. Compatible with the frequency of recent detections on backyard and commercial 

premises in the 2022 H5N1 HPAI outbreak, greater than 80 percent of new infections in modeled 

scenarios occurred in backyard premises. For these scenarios, as shown in Table 8, values for the 

median and maximum number of detected premises and outbreak duration are related to the 

magnitude of additional backyard bird placements. Commercial premises are still becoming infected 

in simulated outbreaks, albeit at a much lower rate than backyard operations. The potential for 

oversummering of the outbreak was observed in a small percentage of iterations and was associated 

with prolonged periods of disease introductions onto backyard premises.

Table 8. Modeling Outcomes Assuming Alternative Levels of Backyard Bird Placements. 

Scenario Description Number of 

Detected 

Premises 

[median]

Number of 

Detected 

Premises 

[maximum]

Outbreak Duration* 

(days) [median] 

[June 1 = day 113]

Outbreak Duration 

(days) [maximum] 

[June 1 = day 113]

Small increase in backyard 

bird placements 360 399 141 184

Moderate increase in 

backyard bird placements 378 438 154 213

*Outbreak duration is defined as the number of days from first detection to last detection for each iteration. Postoutbreak surveillance to regain disease-free status is not included in these values.

In terms of the spatial distribution of future infections, the majority of disease introductions in

simulated outbreaks occurred in States near the northern border of the United States. For outbreaks 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

36 USDA APHIS VS

assuming a small increase in backyard bird placements, Idaho, Minnesota, and Pennsylvania 

experienced the greatest number of new infections (Figure 12). As bird placements increased, New 

York, Oregon, Washington, and Wisconsin were added to the group of States with the highest 

likelihood of future infections (Figure 13). 

Figure 12. Potential Geographic Spread of HPAI Associated With a Small Increase in Backyard Bird 

Placements. 

Figure 13. Potential Geographic Spread of HPAI Associated With a Moderate Increase in Backyard Bird 

Placements. 

D. Limitations on Estimating Disease Spread

Any single disease-spread scenario offers only a snapshot view of an evolving outbreak. Although 

useful in estimating severity, duration, and geographic spread of an ongoing disease event and for 

comparing the effectiveness of alternative control strategies, modeling outcomes are sensitive to 

any biological, physical, or environmental change that impacts biosecurity, disease reporting, 

infectivity, environmental persistence, or other factors affecting disease transmission. 

Consequently, developing a series of scenarios throughout the outbreak and integrating data 

Red to orange to yellow to white shading 

describes States with the highest to 

lowest number of future infections. 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

37 USDA APHIS VS

generated from field and lab settings with scenario-specific assumptions evaluating alternative 

spread possibilities offers the greatest benefit to response planning.
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

38 USDA APHIS VS

ESTIMATING THE TIME OF H5N1 HPAI INTRODUCTION INTO COMMERCIAL 

POULTRY FLOCKS USING DIAGNOSTIC TEST RESULTS AND PRODUCTION DATA

A. Summary

Determining the time of HPAI virus introduction in a flock is an important part of outbreak 

investigations. By narrowing the time window of possible virus introduction, we can better identify 

the potential transmission routes and enhance our understanding of the pattern of disease spread. 

In this analysis, diagnostic testing, daily mortality, and water consumption data (where applicable) 

were used to estimate the time of introduction for 26 commercial poultry premises of interest. 

Premises included 13 commercial meat turkey flocks, 3 broiler chicken flocks, 7 table egg layer 

flocks, 1 table egg layer pullet flock, and 1 broiler breeder flock. Detailed modeling methodology can 

be found in Appendix B. 

B. Results

The analyzed premises were grouped into geographic clusters and results are presented by a clusterspecific, relative timeline (i.e., Day 1 for each cluster is a different calendar date than Day 1 for the 

other clusters, Figure 14). For each premises analyzed, a most likely day of introduction was 

estimated, as well as a 95 percent confidence interval, which represents a window of virus 

introduction for each premises. The day of presumptive diagnosis is also noted in Figure 14 to 

provide an indication of the period of likely infectiousness for each premises. The source of 

introduction, also indicated in Figure 14, is based on phylogenetic analysis (see Phylogenetic Analysis 

and Diagnostics) that is supportive of either independent wild bird introduction or common 

source/lateral spread. Phylogenetic evidence is valuable in identifying and supporting potential 

sources of introduction but cannot be considered definitive proof and must be evaluated in 

conjunction with available epidemiological data. Among the premises included in this analysis, the 

phylogenetic data supported independent, wild-bird introductions on 15 premises and common 

source of infection or lateral spread on 11 premises.

Each geographic cluster presents a unique pattern that in combination with phylogenetic evidence, 

can be suggestive of the timing and routes of introduction that can help narrow the focus of 

epidemiologic investigations.

Cluster A is comprised of four premises. The phylogenetic evidence supported three independent 

wild bird introductions and one common source or lateral spread introduction (premises A4). The 

window of introduction for A4 overlapped with periods of likely infectiousness for Premises A2 and 

A3. Also of note is that A2 was detected a day later than A3, but A2’s most likely day of introduction 

is earlier than A3’s, highlighting that the timing of detection may not always line up perfectly with 

the timing of infection.

Cluster B is comprised of six premises. The phylogenetic evidence supported only one independent 

wild bird introduction and five common source or lateral spread introductions. The suggestive wild 

bird introduction (premises B1) was the first premises detected in the cluster and its period of 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

39 USDA APHIS VS

infectiousness overlapped with only B2; however, B2 had a very long period of infectiousness which 

overlapped with the other four premises. B2 was also detected three days later than B3 but was 

estimated to have been infected much earlier than B3. This pattern suggested that a closer look at 

the timing of potential contacts between B2 and the other premises would be valuable, and this 

information was relayed to the local response. 

Cluster C includes only two premises, one with potential wild bird introduction and the other with a 

common source or lateral spread introduction. The windows of introduction for the two premises 

have tight overlap. Potential contacts between the two premises that occurred on days 3-8 were 

prioritized for epidemiologic investigation.

Cluster D is comprised of eight premises. The phylogenetic data supported independent wild bird 

introductions on five premises and common source or lateral spread on three premises. 

Interestingly, the windows of introduction for the three common source introduction premises 

occurred on or after the days of presumptive diagnosis for the five independent wild bird 

introductions, suggesting the possibility that another premises, not included in this analysis, may 

have served as an intermediary in the transmission chain.

Cluster E is comprised of six premises. The phylogenetic evidence suggests that the earliest infection 

was via an independent wild bird introduction, while the other five were common source or lateral 

spread introductions. The windows of introduction for the four earliest infections all closely overlap, 

while the two premises with later windows of infection (premises E5 & E6) overlap with the periods 

of infectivity for E2 and E4. Similar to premises A2 and A3, E2 had a later presumptive positive day 

than E3, but was estimated to have an earlier most likely introduction day. Assuming the order of 

infection matches the order of detection may lead to misinterpretation of contact tracing 

information. The infectious periods overlap for several premises in this cluster. The timing of

contacts before and after the detection of these premises should be evaluated to identify potential 

epidemiological links and directionality of disease spread. 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

40 USDA APHIS VS

Figure 14. Relative Timeline for Time of Introduction Analysis by Geographic Cluster, Premises, and Likely 

Source of Introduction. 

For this analysis, we defined time to first positive sample (TFPS) as the estimated time interval 

between flock exposure to when the first rRT-PCR positive samples were collected. We observed

differences among the production types in TFPS (Figure 15). Table egg layers or pullet premises had 

the shortest TFPS with a range of two to six days. Broiler production premises had the longest TFPS 

with a range of 8 to 17 days. Turkey meat bird premises were in between with a range of 6 to 11 

days. 

A potential explanation for the shorter time to first positive sample for table egg layers may be due 

to most of the table egg layer premises included in the analysis (seven out of eight) being under 

active surveillance as part of Control Area or Surveillance Zone protocols. When grouped by reason 

for testing, the estimated mean TFPS was 6.4 days for premises under ongoing surveillance testing; 

e.g., testing within a Surveillance Zone or Control Area or for movement permits, and 9.1 days when 

testing was requested based on observing HPAI clinical signs in the flock. When grouped by the likely 

source of introduction, the estimated median TFPS was seven days for common source or lateral 

spread introductions and eight days for independent or wild bird source introductions. However, 

TFPS for common source introductions is likely skewed due to broiler premises having delayed 

detections. Within table egg layer and turkey premises, TFPS was shorter for common source

introductions than for independent introductions.
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

41 USDA APHIS VS

Figure 15. Time from Estimated HPAI Introduction to Detection by Production Type and Likely Source of 

Introduction. 

The estimated adequate contact rate, or transmission parameter, is the number of contacts per day 

a bird has with other birds that would be sufficient to result in infection; it is the parameter that 

determines the rate of virus spread within the flock. The mean of the most likely value for the 

adequate contact rate from all premises was 3.8 contacts per day (range 0.5–9, Figure 16). Turkey 

and table egg layer/pullet premises had similar mean contact rates, while the mean contact rate for 

broiler production premises was lowest. For turkey premises, the mean contact rate was 4.2 (range 

0.5–9) contacts per day. For table egg layer and pullet premises, the mean was also 4.2 (range 1.1–

8.6) contacts per day. The mean contact rate in broiler production premises was 1.7 (range 0.6–2.7) 

contacts per day. The reason for the difference between broiler production premises and the other 

production types is unknown but may be a combination of factors related to species, housing, and 

other management practices. For example, turkey meat bird and broiler production premises are 

both floor-raised production types, where birds can interact with any other bird in the house; 

however, past studies have shown turkeys to be more susceptible to avian influenza viruses than 

chickens, which may result in a higher rate of spread in turkey houses (Pillai et al., 2010). The 

difference between broilers and table egg layers may be related to differences in housing type, 

ventilation, foot traffic, or other production practices that could increase the rate of spread in table 

egg layer houses compared to broilers. When grouped by the source of introduction, the estimated 

mean contact rate was 2.4 for common source or lateral spread introductions and 4.4 for 

independent wild bird introductions. 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

42 USDA APHIS VS

Figure 16. Contact Rate by Production Type and Likely Source of Introduction, Estimated by Time of 

Introduction Analysis. 

The following is a similar breakdown by production type for the estimated basic reproduction 

number (R0), the number of secondary infections that result when one infectious individual is 

introduced into a completely susceptible population (R0, Figure 17). The overall mean R0 value was 

13.3 (range 2–47). For turkeys, the mean R0 was 18.1 (range 3–47). For table egg layer and pullet 

premises, the mean R0 was 8.7 (range 2–22). For broilers, the mean R0 was 5.6 (range 2.4–-8). The 

basic reproduction number is a function of the rate of transmission and the duration of 

infectiousness; therefore, the difference in R0 between turkeys and table egg layers that wasn’t 

observed in their contact rates is due to differences in the duration of infectiousness. As mentioned 

previously in relation to TFPS, the difference in duration of infectiousness may be related to faster 

detection in table egg layers than turkeys because of a greater intensity of active surveillance and/or 

premovement testing applied to the table egg layers in this analysis. Grouped by source of 

introduction, the median basic reproduction number was 6 for common source introductions and 18 

for independent introductions, which may be indicative of a larger viral load initially introduced via 

independent wild bird introductions compared to common source or lateral spread introductions.

Figure 17. Basic Reproduction Number (R0) by Production Type and Likely Source of Introduction, Estimated 

by Time of Introduction Analysis. 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

43 USDA APHIS VS

C. Discussion

Estimating the time of HPAI virus introduction provides a valuable piece of information for 

epidemiologic investigations and outbreak response. In this analysis, we estimated the time window 

for HPAI introduction and transmission model parameters for 26 infected barns using diagnostic test 

results and production data. The analysis was used to narrow the time window of possible virus 

introduction to help identify routes of transmission.

We observed that broiler production premises had lower estimated mean contact rates and R0 than 

turkey meat bird and table egg layer/pullet production types. Turkey meat bird premises and table 

egg layer/pullet premises had similar adequate contact rates, but turkey meat bird premises had a 

higher mean estimated R0 than table egg layer/pullet premises, indicating a longer duration of 

infectiousness in turkey production types. We also observed that premises where the phylogenetic 

evidence supported independent wild bird introductions tended to have higher contact rates and 

R0, suggesting that a larger initial viral load may have been introduced via that route compared to 

common source or lateral spread.

This work is dependent on information on the progression of disease mortality and clinical signs 

from production records and regular laboratory diagnostic testing. Access to different categories of 

detailed, high quality production data such as daily mortality, egg production, and water 

consumption helps to provide more robust estimates of the time of introduction (TOI) and reduce 

the uncertainty. For example, the estimated TOI 95 percent confidence interval was narrower where 

both daily mortality and water consumption data were incorporated into the analysis. Conversely, 

the estimated intervals for time of introduction were wider for premises without elevated mortality 

and with fewer days of diagnostic testing. This work also highlights the value of closely monitoring 

mortality, water consumption, and egg production to quickly identify disease issues in the flock. 

These factors may vary across flocks and between barns, so understanding the trends within each 

production setting is important. 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

44 USDA APHIS VS

AVIAN INFLUENZA SURVEILLANCE IN WILD BIRDS 

Waterfowl are natural reservoir hosts for influenza A viruses (IAV; subtypes H1-H16), but not usually 

highly pathogenic avian influenza (HPAI). Influenza A viruses in wild birds tend to circulate seasonally 

within migratory flyways, and subtype prevalence can wax/wane in multiyear cycles. Areas where 

birds from different flyways congregate provide opportunities for viruses to mix across flyways. 

Waterfowl migration in North America generally consists of north-south seasonal movements 

between breeding grounds and wintering areas. There are four major flyways in North America 

(Figure 18). These flyways are broadly defined corridors where the migratory paths of many species 

of interest tend to converge and are associated with major topographical features in North America, 

which also tend to be aligned along a north-south axis. The four North American flyways have areas 

of overlap and convergence, particularly at the north and south ends. Flyway boundaries are defined 

administratively and are not biologically fixed or sharply defined.

Figure 18. Map Depicting the Four Primary North American Waterfowl Flyways.

13

North American flyways represent the predominant pathways of migratory bird movements within 

broad geographic areas. Many migratory bird species use specific flyways during spring and fall; 

13 North American Flyways 2016, https://www.multivu.com/players/English/7804651-ducks-unlimited-migration/
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

45 USDA APHIS VS

however, many species migrate across flyways. The first detection of Eurasian strain (EA) H5N1 HPAI 

in North America occurred in a great black-backed gull in December 2021in Newfoundland and 

Labrador, Canada. The bird was showing neurologic signs and was part of a large mortality event.

The first subsequent detection of H5N1 HPAI in the United States occurred in a dabbling duck in

January 2022 in South Carolina. The bird was exhibiting no neurologic signs and was an apparently

healthy bird collected during hunter harvest.

The U.S. National Surveillance Plan for Highly Pathogenic Avian Influenza in Wild Birds was

developed to maximize our ability to detect IAV in wild waterfowl. Surveillance helps to: 1)

understand how IAV is distributed in the United States, 2) detect the spread of IAV to new areas of 

concern, 3) monitor wild dabbling duck populations for introductions of novel viruses, and 4)

estimate the apparent prevalence of IAVs of concern (e.g., Eurasian lineage H5 and H7). The

surveillance plan targets areas with extensive mixing of wild bird populations and a history of IAV

detection.

Between 1 June 2021 and 1 June 2022, over 22,000 wild waterfowl were sampled and tested by rRTPCR for IAV. Table 9 and Table 10 break down sampling strategy by species and avian group,

respectively, for all HPAI detections. Overall, targeted surveillance and morbidity/mortality

investigations of sick or dead birds has resulted in the detection of 1,611 H5N1 HPAI lineage virus in

42 States (Figure 19) across all four Flyways: Atlantic – 557, Central – 422, Mississippi – 462, Pacific – 

117. The virus has been detected in a total of 66 different avian species (Table 10).
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

46 USDA APHIS VS

Figure 19. States With H5N1 Detections in Wild Bird Species as of 21 June 2022. 

Targeted surveillance focuses on sampling apparently healthy dabbling duck species. During 

morbidity and mortality events, sick or dead birds may be submitted for additional testing and cause 

of death determination, and a subset of birds may be sampled for avian influenza testing. 

The number of H5N1 lineage virus detections is based on viruses recovered at NVSL from H5N1 

presumptive samples forwarded by NAHLN laboratories.

• Wild bird surveillance testing follows the NAHLN testing algorithm: samples are first tested by 

a Type A-specific test (IAV-M) and further tested by the H5/H7 subtype tests in which viral 

RNA is detected. H5 and H7 samples are forwarded to NVSL, as genetic sequencing is the most 

reliable test for determining virus subtype(s) in wild birds. 

Table 9. Number of Apparently Healthy and Sick/Dead Birds Sampled During the 2022 HPAI Outbreak. List 

Current as of 21 June 2022. 

Avian Group # Apparently Healthy Birds 

Sampled

# Sick/Dead Birds Sampled 

(Morbidity/Mortality Events)

Blackbird 0 3

Crow/Jay 0 33

Duck 455 457

Game bird 0 18

Gull/Tern 0 38

Hawk/Falcon 0 418

Heron 0 9

Loon 0 3

Owl 0 105

Seabird 1 58

Shorebird 0 11

Sparrow 0 1

Thrush 0 1

Total 456 1155
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

47 USDA APHIS VS

Table 10. Number of Apparently Healthy and Sick/Dead Birds Sampled During the 2022 HPAI Outbreak. List 

Current as of 21 June 2022.

Species # Apparently Healthy Birds 

Sampled

# Sick/Dead Birds Sampled 

(Morbidity/Mortality Events)

American black duck 31 0

American crow 0 28

American green-winged teal 42 1

American kestrel 0 1

American robin 0 1

American white pelican 1 32

American wigeon 63 1

Bald eagle 0 164

Barred owl 0 7

Black vulture 0 114

Black-billed magpie 0 3

Blue-winged teal 11 0

Brant 0 1

Broad-winged hawk 0 1

Brown pelican 0 3

Canada goose 1 121

Caspian tern 0 9

Common goldeneye 0 2

Common grackle 0 1

Common loon 0 3

Common raven 0 2

Common tern 0 2

Cooper's hawk 0 6

Cormorant (not otherwise 

specified)

0 7

Dark-eyed junco 0 1

Double-crested cormorant 0 11

Duck (not otherwise 

specified)

0 2

Eared grebe 0 1

Fish crow 0 1

Gadwall 33 1
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

48 USDA APHIS VS

Goose (not otherwise 

specified)

0 2

Great blue heron 0 4

Great horned owl 0 84

Greater white-fronter goose 0 1

Gull (not otherwise 

specified)

0 1

Hawk (not otherwise 

specified)

0 1

Herring gull 0 20

Hooded merganser 1 19

Horned grebe 0 2

Laughing gull 0 1

Lesser scaup 3 22

Mallard 142 12

Merganser (not otherwise 

specified)

0 6

Muscovy duck 0 8

Mute swan 1 2

Neotropic cormorant 0 3

Northern harrier 0 2

Northern pintail 4 0

Northern shoveler 14 0

Owl (not otherwise 

specified)

0 4

Pelican (not otherwise 

specified)

0 2

Peregrine falcon 0 8

Pheasant (not otherwise 

specified)

0 3

Redhead duck 2 8

Red-shouldered hawk 0 2

Red-tailed hawk 0 76

Red-winged blackbird 0 1

Ring-billed gull 0 3

Ring-necked duck 0 5

Ross’s goose 14 49
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

49 USDA APHIS VS

Rough-legged hawk 0 4

Royal tern 0 2

Ruddy duck 0 2

Sanderling 0 11

Sandhill crane 0 4

Sharp-shinned hawk 0 3

Snow goose 77 150

Snowy egret 0 1

Snowy owl 0 10

Swainson’s hawk 0 1

Swan (not otherwise 

specified)

0 2

Trumpeter swan 0 6

Tundra swan 0 5

Turkey vulture 0 34

Vulture (not otherwise 

specified)

0 1

Wild turkey 0 15

Wood duck 16 26

Total 456 1155
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

50 USDA APHIS VS

MODELING AVIAN INFLUENZA TRANSMISSION AT THE INTERFACE OF WILD BIRDS 

AND DOMESTIC POULTRY

A. Summary

In collaboration with the University of Maryland, and the U.S. Geological Survey, Eastern Ecological 

Science Center, we have completed preliminary models that explore the spatio-temporal trends in 

avian influenza transmission from wild waterfowl to domestic poultry across the continental United 

States for the full annual cycle.

These models account for not only the number of waterfowl in an area but also species-specific 

prevalence rates to determine the effective waterfowl population or presented disease risk. When 

paired with information on the distribution of poultry farms, we can identify an area’s risk of 

spillover. Upon completion, these models should provide critical insight into how to best prepare for 

potential spillover events.

B. Preliminary Results and Discussion

Figure 20 shows sample results from our model at a county level by week for several example 

weeks, and Figure 21 looks more closely at model results from the State of North Carolina. For North 

Carolina, there is a general trend of the winter months (November through January) showing 

concentrated areas of risk in the East. As the year progresses, this risk becomes more evenly 

distributed throughout the State as the concentrated waterfowl populations along the East Coast 

disperse and migrate northward. 

Data from the current outbreak were used to evaluate model performance. Using data through 

spring 2022, we showed that the model performed well at predicting county-level avian influenza 

virus spillover risk (Figure 22). The model classified the average county that experienced a spillover 

event as being more at risk than random. Counties with a spillover event had 12 times greater 

predicted risk, on average, than non-outbreak counties, and 54 of the 62 spillover counties were at 

above-average risk for a spillover event. There were almost no spillovers in counties designated as 

low risk by the interface model.

These preliminary models have proven valuable in understanding spatial risk during the current 

outbreak. As more data from the current outbreak become available, we will update model 

parameters to further characterize and refine transmission at the wild bird domestic poultry 

interface across the continental United States. Model results and related information could be of 

use to mitigate on-farm risk, for response planning, and to support preparedness activities. The 

latest modeling results can be found online at: Visualizing Avian Influenza (usgs.gov). 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

51 USDA APHIS VS

Figure 20. Weekly Relative Risk of Avian Influenza Spillover From Wild Birds to Domestic Poultry by County 

for Several Example Weeks.
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

52 USDA APHIS VS

Figure 21. Relative Risk of Avian Influenza Spillover From Wild Birds to Domestic Poultry for Several Example 

Weeks for the State of North Carolina. Counties With Initial Infected Premises Events Outlined in Red.
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

53 USDA APHIS VS

Figure 22. Validation of the Preliminary Interface Model Using Outbreak Data Through Spring 2022, With 

Counties With a Spillover Event Shown in Red.
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

54 USDA APHIS VS

ANALYSIS OF EBIRD AND BIRDCAST MIGRATION DATA: IMPLICATIONS FOR DISEASE 

INTRODUCTION, SPREAD, AND PREVENTION

A. Potential Use of BirdCast Data for Awareness to Enhance Prevention Measures

The BirdCast live bird migration maps present real-time intensities of nocturnal bird migration as 

detected by the U.S. weather surveillance radar network, between local sunset to sunrise. All 

graphics are relative to the eastern time zone. When present, the red line moving east to west 

represents the timing of local sunset, with the yellow line representing the timing of local sunrise. 

Areas with lighter colors experienced more intense bird migration. Orange arrows show directions 

of bird movement. Green dots represent radar locations for which data are available, and red dots 

represent radar locations with no data available. Note that mountainous areas (e.g., the Rockies) 

have obstructions that restrict radar coverage, providing the appearance of no migration where 

migration may be occurring. Brighter colors indicate a higher migration traffic rate (MTR) expressed 

in units of birds/km/hour.

As another prevention tool following initial detections of HPAI in wild birds in the United States, 

BirdCast can be used to increase awareness of potential increased risk to poultry producers by 

noting areas of more intense bird migration. The following 1 February 2022 7:45 a.m. ET BirdCast 

live bird migration map depicts, with strong colors, areas of more intense bird migration over States, 

including Indiana and Kentucky, just five days prior to Indiana’s first HPAI detection on 6 February 

2022 on a commercial turkey farm, and eight to nine days prior to Kentucky’s first two HPAI 

detections on 9 February 2022 and 10 February 2022 on a commercial chicken farm and a 

commercial turkey farm, respectively (Figure 23). These early H5N1 HPAI detections were preceded 

by HPAI detections in wild birds, which began on 13 January 2022.

Figure 23. BirdCast’s Live Bird Migration Map for 1 February 2022 at 7:45 a.m. Eastern Time. 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

55 USDA APHIS VS

Figure 24 depicts data from the BirdCast maps, noting the daily highest number of birds in flight, in 

the millions (royal blue line), reported over 24-hour stretches, through BirdCast’s live bird migration 

maps. This line is drawn over stacked bars representing the 2022 United States HPAI H5 and H5N1 

detections in wild birds (turquoise stacked bar), and the H5N1 HPAI detections in domestic birds on 

WOAH non-poultry and WOAH poultry premises (dark orange and light orange stacked bars, 

respectively). 

The high migration numbers in October 2021 through December 2021 are a continued part of the 

fall migration season. Canada experienced their first HPAI detections in November 2021. The first 

wild bird detections in the United States were on 13 January 2022, followed by additional detections 

in wild birds in January and early February 2022. The increase in numbers of birds in flight, 

measured on the left axis, follows the initial increase in HPAI detections in domestic birds on WOAH

non-poultry and WOAH poultry premises, likely influencing the continued HPAI detections through 

May, and decreasing as the United States-reported HPAI detections have decreased over that same 

timeframe.

 

Figure 24. Graph Showing BirdCast’s Highest Count of Millions of Birds in Flight by Day Overlayed With HPAI 

Detections in Wild Birds and on Non-Poultry and Poultry Premises.
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

56 USDA APHIS VS

B. Space-time Cluster Analysis of eBird Observation Data

In the previous section, visual interpretation of BirdCast migration maps showed possible 

association of high densities of wild bird migration over areas where detections of HPAI occurred in 

commercial and backyard premises subsequently occurred. However, we did not have direct access 

to the spatial data layers behind BirdCast. To evaluate space-time associations between wild bird 

migration and HPAI-positive premises, we accessed eBird observational data. 

eBird is a database of species-specific, crowd-sourced observational data by scientists and birding 

enthusiasts. While the data does not capture birds in flight, we assumed that high numbers of bird 

observations correlate with heavy migration over the area.

Using the “reBird” R-package, we pulled eBird observations between 1 February 2022 and 15 April

2022. For each HPAI-positive premise during that timeframe, we pulled all eBird observations within 

a 50km window and up to 14 days prior to the date that premises was positive. We used a wide 

spatial window, assuming that the highly mobile nature of birds could result in an infectious bird 

exposing domestic birds within a potentially large area. Within each spatial window for each date of 

observation, we calculated the density of wild birds and retrieved the date of highest bird density 

observed around the premise within the 14-day window. We calculated the time difference in days 

between observations of highest wild bird densities with the date of onset for the premises (Figure 

25). HPAI-positive premises were more likely to be detected within the first seven days of heavy wild 

bird observation within a 50km spatial window.

Figure 25. Frequency Histogram Depicting Elapsed Number of Days Between Observed Highest Density of 

Wild Birds Within a 50km Radius and Detection Date for an HPAI-Positive Premise.
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

57 USDA APHIS VS

REFERENCES

Freath, L., Brown, I., Banyard, A., Byrne, A., Pacey, A., Gale, P., Perrin, L. 2022. Highly pathogenic 

avian influenza (HPAI) in the UK and Europe. United Kingdom: Assets Publishing Service. 

https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_

data/file/1070246/Highly_pathogenic_avian_influenza__HPAI__in_the_UK_and_Europe__o

utbreak_update_23.pdf.

Garber, L., Bjork, K., Patyk, K., Rawdon, T., Antognoli, M., Delgado, A., Ahola, S., McCluskey, B. 2016. 

Factors associated with highly pathogenic avian influenza H5N2 infection on table-egg layer 

farms in the Midwestern United States, 2015. Avian Diseases. 60:460–466.

Halvorson, D. 2009. Prevention and management of avian influenza outbreaks: experiences from the 

United States of America. Rev Sci Tech Off Int Epiz. 28:359–369.

Lesley, C. 2021. 5 ways 2020 changed the backyard chicken industry. The Poultry Site. 

https://www.thepoultrysite.com/articles/5-ways-2020-changed-the-backyard-chickenindustry.

McQuiston, J., Garber, L., Porter-Spalding, B., Hahn, J., Pierson, F., Wainwright, S., Senne, D., 

Brignole, T., Akey, B., Holt, T. 2005. Evaluation of risk factors for the spread of low 

pathogenicity H7N2 avian influenza virus among commercial poultry farms. JAVMA. 

225:767–772.

Newswire M-P. 2016. Flyways of North America [digital image]. Multivu. [accessed 2021 June 21]. 

http://www.multivu.com/players/English/7804651-ducks-unlimited-migration/.

Pillai, S., Pantin-Jackwood, M., Yassine, H., Saif, Y., Lee, C. 2010. The high susceptibility of turkeys to 

influenza viruses of different origins implies their importance as potential intermediate 

hosts. Avian Dis. 54(1 Suppl):522–526. doi:10.1637/8770-033109-Review.1.

U.S. Department of Agriculture, Animal and Plant Health Inspection Service (USDA APHIS). 2016. 

Final report for the 2014–2015 outbreak of highly pathogenic avian influenza (HPAI) in the 

United States. Fort Collins, CO: USDA–APHIS–VS–CEAH. 50 p. 

https://www.aphis.usda.gov/animal_health/emergency_management/downloads/hpai/201

5-hpai-final-report.pdf.

U.S. Department of Agriculture, Animal and Plant Health Inspection Service (USDA APHIS). 2017. The 

foreign animal disease preparedness and response plan (FAD PReP)—highly pathogenic 

avian influenza (HPAI) response plan: the red book. Riverdale, MD: USDA–APHIS–VS. 

https://www.aphis.usda.gov/animal_health/emergency_management/downloads/hpai_res

ponse_plan.pdf.
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

58 USDA APHIS VS

U.S. Department of Agriculture, Animal and Plant Health Inspection Service (USDA APHIS). 2022. 

USDA confirms highly pathogenic avian influenza in a wild bird in South Carolina. 

Washington, D.C.: USDA–APHIS. https://www.aphis.usda.gov/aphis/newsroom/stakeholderinfo/sa_by_date/sa-2022/hpai-sc. 

U.S. Department of Agriculture, Foreign Agricultural Service (USDA FAS). 2016. Global agricultural 

trading system (GATS). 

World Animal Health Information System (WAHIS). 2023. Canada - influenza A viruses of high 

pathogenicity (Inf. with) (non-poultry including wild birds) (2017-). World Organisation for 

Animal Health. https://wahis.woah.org/#/in-event/4191/dashboard.
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

59 USDA APHIS VS

ACKNOWLEDGEMENTS

We greatly appreciate the cooperation and support of the poultry industry, particularly the producers 

and farm owners for allowing access to their properties, providing biosecurity and production practice 

information, and their full cooperation with these investigations. 

We also appreciate the diligent efforts of state partners and APHIS–Veterinary Services responders to 

collect epidemiologic data and their partnership on the resulting analyses.

This report would not have been possible without the many researchers, epidemiologists, economists, 

laboratory staff, and data scientists who analyzed, drafted, and reviewed this report. We would like to 

extend our thanks to the National Veterinary Services Laboratories (NVSL), the Center for Informatics 

(CFI), Secure Poultry Supply (SPS; University of Minnesota), and State Veterinary Diagnostic 

Laboratories.

We’d like to convey our specific gratitude to the following individuals:

- Dr. Amos Ssematimba, Dr. Sasidhar Malladi, and Peter Bonney (SPS) 

- Dr. Mia Torchetti, Dr. Kris Lantz, Tod Stuber, Jessica Hicks, and Cameron Norris (NVSL)

- Dr. Philip Riggs, Dr. Jared Luxton, and Dr. Carolann Knutson (CFI)
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

60 USDA APHIS VS

APPENDIX A: INITIAL CONTACT EPI REPORT FORM

HPAI Response 

Initial Contact Epidemiological (Epi)

Report

June 27, 2016

I. PREMISES INFORMATION

Premises Identification Number: 

Name of Premises: 

Owner of Premises: 

Address of Premises: 

County of Premises: 

Premises Owner Phone: 

Premises Owner Email: 

Premises Entrance Latitude: 

Premises Entrance Longitude: 

II. OWNER INFORMATION

Owner of Animals: 

Address of Animal Owner: 

Animal Owner Phone: 

Animal Owner Email: 

III. INTERVIEW CONTACT INFORMATION

Name of person administering questionnaire: 

Name of person answering questionnaire: 

Phone: 

Position (e.g., owner, manager, veterinarian, etc.): 

Date of interview: 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

61 USDA APHIS VS

IV. FLOCK INFORMATION

Clinicalsigns

(brief description)

Baseline daily mortality rate: 

(insert rate from farm records)

Daily mortality rate

(# of dead birds/bird population on date 

of initial sampling)

Date first clinical signs were noted

Date initial samples were collected

Laboratory to which initialsamples were 

submitted

Results of any AI tests in past 21 days

Date premises quarantine or hold order 

was issued

House ID Type of 

Birds

Number 

of Birds

Age of 

Birds

House 

Dimensions

Ceiling 

Height

Ventilation 

Type

Date of 

Onset of 

Clinical

Signs

Do you have a veterinarian who regularly advises you on disease prevention? 

 Yes  No

If yes, name of veterinarian: 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

62 USDA APHIS VS

Do you have a pre-arranged depopulation plan for this flock?  Yes  No

If yes, briefly describe the pre-arranged depopulation method: 

Have you exercised or used this method previously?  Yes  No

V. TRACE-IN AND TRACE-OUT QUESTIONNAIRE

Name of person administering questionnaire: 

Name of person answering questionnaire: 

Phone: 

Position (e.g., owner, manager, veterinarian, etc.): 

1. How are dead birds (daily mortality) disposed of on this farm (please circle

one or more)? Also specify if disposal occurs on or off this premises.

a. Composting

b. Burial

c. Incineration

d. Rendering

e. Landfill

Other (specify): 

If disposal occurs at another premises:

Name and Location (company name) Transported by

2. List any locations that accept manure/litter from this premises during the last 21 days.

Name and location (company name) Date (mm/dd/yy) Intended use
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

63 USDA APHIS VS

3. Was manure or animal material from another premises brought onto this

premises during the last 21 days?

 Yes  No If yes:

Product Source Date (mm/dd/yy)

4. Have you or any of your employees (including any contractors or volunteers) visited

any other premises with poultry or any processors of eggs or poultry products during

the last 21 days (e.g., farm, slaughter, processing, market, residence with poultry)?

 Yes  No If yes:

Premises/processor name Person/title Date

(mm/dd/yy)

5. Is there a community living situation where farm workers from this premises interact

with workers from other poultry facilities?

 Yes  No

If Yes, describe: 

6. Did any crews (e.g., catch crews, load-out, vaccination, insemination) enter the

premises during the last 21 days?

 Yes  No If yes:
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

64 USDA APHIS VS

Date (mm/dd/yy) Crew type Name/company

7. Did any of the following visit the premises during the last 21 days? If Yes, 

give date and name or company information.

Visitor type Date(s) 

of visit Name/company

a. Federal/State veterinary or animal health 

worker

b. Extension agent or university veterinarian

c. Private or company veterinarian

d. Company service person

e. Nutritionist or feed company consultant

f. Inspector(e.g., FDA, NOP, biosecurity 

auditor, etc.)

g. Feed delivery

h. Egg truck

i. Litter/bedding delivery

j. Litter removal

k. Renderer/dead bird pick up

l. Pest/rodent control

m. Manure truck

n. Trash pick up

o. Occasional worker (e.g., family member, 

part-time help over holiday)

p. Wholesaler, buyer, or dealer
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

65 USDA APHIS VS

q. Customer/consumer(private individual)

r. Other
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

66 USDA APHIS VS

8. Specify if any equipment was shared with another premises during the last 21

days, whether you received or loaned the equipment, and the location and 

name of the companies or premises the equipment was shared with:

Vehicle Received/loaned Specify (name, company, location)

ATV/4-wheeler  Rec’d  Loaned

Tractor  Rec’d  Loaned

Gates/panels  Rec’d  Loaned

Skid-steer loaders  Rec’d  Loaned

Egg flats  Rec’d  Loaned

Egg racks  Rec’d  Loaned

Pallets  Rec’d  Loaned

Dead bird containers  Rec’d  Loaned

Manure/litter handling 

equipment

 Rec’d  Loaned

Pressure sprayers/ 

washers/foamers

 Rec’d  Loaned

Other cleaning 

equipment

 Rec’d  Loaned

Vaccination equipment  Rec’d  Loaned

Bird catching 

equipment

 Rec’d  Loaned

Live haul loader  Rec’d  Loaned

Other (specify: 

) 

 Rec’d  Loaned

9. Were any birds introduced onto the premises during the last 21 days?

 Yes  No If yes:

Date 

(mm/dd/yy)

Bird type (e.g., chicks, poults,

spiking roosters, layers, breeders, 

etc.)

Source Transported by
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

67 USDA APHIS VS

10. Have any birds moved off the premises during the last 21 days?

 Yes  No If yes:

Date 

(mm/dd/yy)

Bird type

(e.g., chicks, poults, spiking 

roosters, layers, breeders, etc.)

Destination Transported by

11. Were any birds moved within the premises during the last 21 days? (e.g., from one

barn to another on the same premises)

 Yes  No

If Yes,

a. Was a contract crew used?

 Yes  No

If Yes, specify company/crew name: 

b. Was farm specific equipment used?

 Yes  No

If No, describe: 

12. Were any eggs moved onto the premises during the last 21 days?

 Yes  No

If Yes,

a. List source (name and location) for eggs coming onto this premises during 

the last 21 days, the dates eggs were received, and whether the eggs were 

intended for hatching, or were processed or unprocessed from source.
Source name and location

(company name)

Date (mm/dd/yy) Intended

for hatching?

Processed?*

 Yes  No  Yes  No

 Yes  No  Yes  No

 Yes  No  Yes  No

 Yes  No  Yes  No

 Yes  No  Yes  No

*Method of processing: 

13. Were any eggs moved off the premises during the last 21 days?

 Yes  No

If Yes,

a. List source (name and location) for eggs moving off this premises during the

last 21 days, the dates eggs left, and whether the eggs were intended for

hatching, or were processed or unprocessed from source.

Source name and location

(company name)

Date (mm/dd/yy) Intended

for hatching?

Processed?*

 Yes  No  Yes  No

 Yes  No  Yes  No

 Yes  No  Yes  No

 Yes  No  Yes  No

 Yes  No  Yes  No

*Method of processing: 

14. Is there any additional or important information that we need to know at 

this time regarding the disease on your farm?

 Yes  No

If Yes, describe: 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

69 USDA APHIS VS

APPENDIX B: TIME OF INTRODUCTION MODELING METHODS

We used approximate Bayesian computation (ABC) to estimate the likely time of virus introduction and 

the key model parameters, such as the adequate contact rate (a parameter which regulates the rate of 

within-flock disease spread) from the available production and test data. 

A stochastic individual-based simulation model was first used to simulate the disease mortality, infection 

prevalence over time, and water consumption (where applicable) over a wide range of values for model 

parameters, such as the adequate contact rate, times of disease introduction, and bird-level latent and 

infectious period distributions (i.e., prior distributions). 

In the next step, the sum of the squared distance between the model-predicted daily mortality and 

water consumption (where applicable) and the observed data, and the difference between observed 

and simulated diagnostic test results was calculated as a measure of deviation between the model 

output and data (ψ). The parameters in model iterations where the metric ψ was sufficiently small, 

indicating a good fit to the data, were then accepted to estimate the distribution of the time of 

introduction and other model parameters. 

We used wide priors for input variables based on published literature and estimates from previous 

SEPRL challenge studies. Preliminary data from SEPRL challenge studies in turkeys and chickens with a 

current outbreak isolate (A/American Widgeon/SC/22-000345-001/2022 (H5N1) HPAIV) were made 

available in May 2022. We estimated the disease state durations from the challenge study data using 

MCMC algorithms. The estimated disease state durations were then used to update the prior 

distributions for the latent and infectious periods. The updated prior distributions used in the analysis 

for commercial meat turkey and table egg layer flocks based on SEPRL data and other published studies 

are summarized in Table B and table B2. We also performed a sensitivity analysis for the impact of the 

mean infectious period prior for selected premises given the uncertainty in this parameter.
Table B1. Input Prior Distribution Parameters Used in the ABC Approach to Estimate the Adequate Contact Rate 

and Time of Virus Introduction for Commercial Meat Turkey Flocks. 

Parameter 

Name

Description Distribution

Adequate 

Contact Rate

Daily average number of contacts a bird has with other 

birds that are sufficient to transmit infection

Uniform (min = 0.2, 

max = 7) per day

Latent Period 

Length 

Distribution

Length of the interval when a bird is latently infected 

and is not infectious

Gamma (shape = 

4.037, scale = 0.1809); 

mean = 0.64 days; 

variance = 0.67

Mean 

infectious 

period

Prior distribution for the mean infectious period Uniform (1.9–6.3 

days)

Shape 

parameter for 

infectious 

period

Prior distribution for shape parameter of gamma 

distributed infectious period

Uniform (1–20)

Table B2. Input Prior Distribution Parameters Used in the ABC Approach to Estimate the Adequate Contact Rate 

and Time of Virus Introduction for Table Egg Layer Flocks. 

Parameter 

Name

Description Distribution

Adequate 

Contact Rate

Daily average number of contacts a bird has with 

other birds that are sufficient to transmit infection

Uniform (min = 0.5, 

max = 9) per day

Latent Period 

Length 

Distribution

Length of the interval when a bird is latently infected 

and is not infectious

Gamma (shape = 2.54, 

scale = 0.33); mean = 

0.84 days

Mean 

infectious 

period

Prior distribution for the mean infectious period Uniform (0.74–4)

Shape 

parameter for 

infectious 

period

Prior distribution for shape parameter of gamma 

distributed infectious period

Uniform (1–20)
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks July 2022

71 USDA APHIS VS

Epidemiologic and Other Analyses of HPAI Affected 

Poultry Flocks

July 2022 Report

USDA  APHIS  VS

Center for Epidemiology and Animal Health

2150 Centre Avenue, Bldg. B, Fort Collins, CO, 80526-8117

Web: http://www.aphis.usda.gov/animal-health/ceah