United States

Department of

Agriculture

Animal and Plant

Health Inspection

Service

Veterinary Services

Epidemiologic and Other Analyses of 

Avian Influenza Affected Poultry Flocks

May 25, 2018 Report
Epidemiologic and Other Analyses of LPAI Affected Poultry Flocks May 25, 2018

Suggested bibliographic citation for this report: 

USDA-APHIS (2018). Epidemiologic and other analyses of avian influenza affected poultry flocks: 

May 25, 2018 Report. United States Department of Agriculture: Animal and Plant Health 

Inspection Service: Veterinary Services: Science, Technology, and Analysis Services: Center 

for Epidemiology and Animal Health. Fort Collins, CO. May 2018. Doc #452.0518. 36 pgs.

For more information, contact: 

Amy Delgado, DVM PhD

Director, Monitoring and Modeling

USDA:APHIS:Veterinary Services

Science, Technology, and Analysis Services

Center for Epidemiology and Animal Health

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

Phone (970) 494-7256 | Mobile (970) 237-0857 | Fax (970) 494-7228

Email: Amy.H.Delgado@aphis.usda.gov

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

I. Contents..................................................................................................................................... i

II. List of Figures and Tables............................................................................................................ii

I. Executive Summary ....................................................................................................................1

II. Introduction ...............................................................................................................................1

Description of Outbreak .......................................................................................................................2

III. Epidemiologic Study to Investigate the H7N1 Virus in Commercial Poultry in Texas and Missouri .4

A. Case Series.......................................................................................................................................4

IV. Estimating the Time of H7N1 LPAI Infection for the Commercial Meat-type Turkey Flock in 

Missouri using Diagnostic Test Results and Flock Mortality Data..................................................6

Summary...............................................................................................................................................6

Methods Overview................................................................................................................................6

Summary of LPAI outbreak data ...........................................................................................................6

Overview of modeling approach...........................................................................................................8

Results...................................................................................................................................................9

Discussion............................................................................................................................................14

V. Phylogenetic Analysis and Diagnostics.......................................................................................14

Phylogenetic Analysis and Diagnostics...............................................................................................14

North American H7N1 LPAI from poultry (AM H7N1 2018) ...............................................................14

Comparison to Other Viruses/Lineages..............................................................................................16

Public Health Aspects..........................................................................................................................16

Diagnostics and Characterization for Influenza A Viruses..................................................................17

General Information ...........................................................................................................................17

VI. Waterfowl Surveillance.............................................................................................................17

VII. Acknowledgements..................................................................................................................21

Appendix A: Case Series Questionnaire.............................................................................................22

Appendix B: Estimation of Model Parameters for Within-Flock Spread of H7N1 LPAI Within a Turkey 

Barn.........................................................................................................................................30

Estimation of the latency and infectious period distributions ...........................................................30

Proportion of turkeys that seroconvert to LPAI .................................................................................31

References.......................................................................................................................................31
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List of Figures and Tables

Figure 1. Counties with confirmed findings of H7N1 LPAI since 1 March 2018 and administrative flyway 

designation of affected and surrounding states.....................................................................................................3

Figure 2. The estimated likelihood of LPAI introduction into Barn 2 on various days based on the results from 

each diagnostic test event (top) and the combined likelihood for all the test events (bottom). The diagnostic 

test events include all tests conducted on birds in Barn 2 (Table 3)....................................................................10

Figure 3. Daily mortality per 1000 birds in Barn 2. ..................................................................................................11

Figure 4. The approximate estimated likelihood of LPAI introduction into Barn 2 on various days based only on 

diagnostic test results (blue dashed line), and considering diagnostic tests as well as the timing of peak 

mortality (red solid line).......................................................................................................................................11

Figure 5. Daily mortality per 1000 birds in Barn 4. ..................................................................................................12

Figure 6. The estimated likelihood of LPAI introduction into Barn 4 on various days based on individual diagnostic 

test events (top) and the combined likelihood for all the test events (bottom). The diagnostic test events 

considered include all diagnostic tests conducted on birds in Barn 4 (Table 3)...................................................13

Figure 7. The approximate estimated likelihood LPAI introduction into Barn 4 on various days based only on 

diagnostic test results (blue dashed line), and considering diagnostic tests as well as the timing of peak 

mortality (red solid line). ......................................................................................................................................13

Figure 8. Phylogenetic analysis of viruses from these three events support independent introductions from a 

common source: a) indicates >99.9% probability that the introductions arose from wild birds in the 

Central/Mississippi flyway (abbreviations: TMRCA = estimated time to mean common ancestor; HPD=highest 

posterior density); b) network analysis of the HA gene. Courtesy of Interagency wild bird surveillance data, ML 

Killian NVSL, and DH Lee USDA ARS Southeast Poultry Research Laboratory......................................................16

Figure 9. The four primary North American waterfowl flyways ..............................................................................18

Figure 10. Timeline of virus detections in wild birds (upper panel) and locations of influenza A detections by IAVM PCR from wild bird Surveillance (lower panel).................................................................................................20

Table 1. Location, production type, and confirmation date of flocks infected by LPAI H7N1. ..................................4

Table 2. Characteristics of H7N1 LPAI infected commercial poultry farms. ..............................................................5

Table 3. Summary of surveillance protocols and test results from the epidemiological investigation of a LPAI 

outbreak in a commercial meat-type turkey flock in Missouri, date the sample was collected, purpose of the 

surveillance sample, sampling protocol, and qualitative interpretation of results................................................7

Table 4. Test results (Ct valuesa

) reported for various rRT-PCR tests conducted on samples from the 4 barns of 

the commercial meat-type turkey flock in Missouri. .............................................................................................7

Table 5. H7 hemagglutination inhibition (HI) assay titers from serum samples collected on 2 March 2018. HI titers 

for all Barns suggest that Barn 2 may have been the site of the original introduction, followed by Barns 1 and 

3, with Barn 4 affected last. Titers >=1:8 are suggestive of exposure....................................................................8

Table 6. Results for the estimated date of LPAI introduction for Barns 1, 2, and 3...................................................9

Table 7. Parameter estimates for the LPAI transmission model for turkey barns...................................................31
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I. Executive Summary

An outbreak of low pathogenic avian influenza (LPAI) was detected in early March, 2018. The 

outbreak was first detected through routine pre-movement testing of a commercial meat-type 

turkey farm in southern Missouri; H7N1 low pathogenicity avian influenza (LPAI) of North 

American wild bird lineage was confirmed via laboratory testing. Subsequently H7N1 LPAI was 

confirmed in a commercial broiler breeder farm in northeast Texas and a backyard chicken 

breeder farm in southern Missouri. Following response activities, a series of epidemiological and 

genetic investigations were initiated to better understand these findings across two states, 

three counties, and in apparently unrelated facilities. This is a report of the findings available todate, and these analyses are intended to assist in understanding disease introduction and 

transmission pathways. These studies were undertaken collaboratively with the poultry 

industry, state agricultural personnel, and the United States Department of Agriculture Animal 

and Plant Health Inspection Service (USDA-APHIS).

Genetic analysis determined that all H7N1 viruses detected from this event are of North 

American wild bird lineage and the viruses are 99% similar across all eight genes. Initial genetic 

and epidemiologic evidence suggest the possibility of three independent introductions. Analysis 

of mortality records and diagnostic test results suggest that H7N1 was most likely introduced 

into the first infected farm in early February. Based upon the previous and current yearly

Interagency Wild Bird Surveillance data in the U.S., H7 detections in wild birds tend to rise in 

early winter as the H5 detections decrease. Other wild bird lineage H7 outbreaks in poultry have 

been detected during the first three months of the year (January – March).

The two commercial H7N1 LPAI farms involved different production types and different 

integrated poultry companies suggesting unique sources of feed, birds, transport trucks and 

crews. The companies did not share epidemiologic links such as common conveyances, visitors, 

equipment, or disposal activities. Risk factors for virus introduction into barns from the 

environment that have been identified in past outbreaks such as the presence of rodents or 

other wild mammals and waterfowl near barns, the condition of the housing, and breaches in 

biosecurity protocols were likely. The fact that a backyard operation was among the impacted 

farms adds weight to the evidence that this outbreak was governed in large part by exposure to 

environmental sources of virus.

II. Introduction

In response to the H7N1 LPAI outbreaks in commercial and backyard poultry in MO and TX, 

USDA-APHIS and the affected states have initiated epidemiologic and genetic investigations. 

These investigations will help provide a better understanding of factors associated with avian 

influenza virus transmission and its introduction into poultry flocks.

These investigations include the following:
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• A field-based study of the commercial-case farms using data collected through site visits 

and interviews with farm personnel

• Analysis of barn-level mortality and diagnostic test data from the earliest affected 

commercial farm to estimate the date of introduction of LPAI

• Virus phylogenetic analysis

This report includes the results from those investigations, in an effort to provide producers, 

industry, and other stakeholders with current epidemiologic information.

Description of Outbreak

On 2 March 2018, the USDA-APHIS was notified that a pre-slaughter sample from a commercial 

meat-type turkey farm in Jasper County, MO tested positive by H7 PCR at the Missouri 

Department of Agriculture Veterinary Diagnostic Laboratory. The National Veterinary Services 

Laboratories (NVSL) confirmed H7 on 3 March 2018 and N1 was confirmed on 5 March 2018. A 

few days later in Texas, H7N1 LPAI was confirmed in commercial broiler breeders on 7 March

2018 in Hopkins County. Back in MO, a third case of H7N1 LPAI was confirmed in a backyard 

chicken breeder farm on 15 March 2018 in Webster County (Figure 1, Table 1). All three farms 

were detected through routine pre-movement testing of birds or eggs. Clinical signs were not 

apparent. Whole genome sequencing of virus isolated from all three of the farms by NVSL 

identified North American wild bird lineage H7N1 LPAI (AM H7N1 2018) that are >99% similar 

across the entire genome. Surveillance in the areas around the three farms to determine the 

status of other farms was immediately initiated. A total of 10 commercial and 55 backyard 

premises in TX and MO were tested through surveillance with no additional detected farms. 
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Figure 1. Counties with confirmed findings of H7N1 LPAI since 1 March 2018 and administrative flyway 

designation of affected and surrounding states.
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Table 1. Location, production type, and confirmation date of flocks infected by LPAI H7N1.

State County Production Type Confirmation Date

Missouri Jasper Commercial Turkey 3 March 2018

Texas Hopkins Commercial Broiler Breeder 7 March 2018

Missouri Webster Backyard Chicken Breeder 15 March 2018

III. Epidemiologic Study to Investigate the H7N1 Virus in Commercial 

Poultry in Texas and Missouri

A. Case Series

USDA-APHIS conducted a case-series study of the H7N1 affected commercial poultry operations. 

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

the H7N1 avian influenza virus. Additionally, the study respondents provided mortality and egg 

production data. Questions focused on the 3 weeks prior to the positive test result (Appendix A: 

Case Series Questionnaire). Results of the questionnaires are summarized in Table 2.

• Flocks appeared normal at testing. Retrospective records review revealed either minor 

respiratory symptoms or minor production losses at both farms prior to the positive AI 

test.

• Neither farm had water bodies within 350 yards of the houses; however, there was a 

stream approximately 500 yards from one and small ponds approximately 500 yards 

from the other.

• Workers did not visit other farms with poultry or live with workers from other poultry 

facilities.

• Feed truck deliveries were reported as the most frequent type of visitor at both farms, 

followed by company service personnel. Other visitors included propane delivery and a 

company veterinarian.

• The method of dead bird disposal was reported as composting on site for both, neither 

farm used renderers.

• Each farm is associated with a different parent company. No epidemiological links 

between the two farms were identified.

Results suggest that while the two farms exhibited some common practices and features, 

the significance is difficult to interpret with just two cases and in the absence of control 

farm data.
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Table 2. Characteristics of H7N1 LPAI infected commercial poultry farms.

Characteristic Level n Comments

Bird type Meat-type turkey

Broiler breeder

1

1

Clinical signs 2/2 Minor respiratory 

symptoms or production 

losses

Water body within 350 yards Pond

Stream

0/2

0/2

Stream approximately 

500 yards from 1 farm, 

surface water ponds 

approximately 500 yards 

from 1 farm 

Other Poultry no 2/2

Visitors Company service personnel

Feed delivery personnel

Egg truck personnel

2/2

2/2

1/1

Equipment shared with other 

farms

no 2/2

Vehicles enter the farm Feed Delivery

Company personnel

Egg truck

2/2

2/2

1/1

Dead bird disposal method Composting

Incineration

Rendering

2/2

Ventilation type Curtain

Tunnel

Ceiling/eaves

2/2

Fans located at end of barn 2/2

Birds introduced onto premises no 2/2

Manure from another premises 

brought onto premises

no 2/2

Workers visited other premises 

with poultry

no 2/2

Crews (e.g., catch or vaccination) 

visited premises

no 2/2
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IV. Estimating the Time of H7N1 LPAI Infection for the Commercial 

Meat-type Turkey Flock in Missouri using Diagnostic Test Results 

and Flock Mortality Data

Summary

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

investigations intended to identify the factors that likely contributed to virus introduction. By 

narrowing the time window of possible introduction, we can better isolate the potential routes 

of virus introduction and enhance our understanding of the pattern of disease spread. 

Consequently, we used the diagnostic test results and flock mortality data from each of the 4 

barns on the premises of the commercial meat-type turkey operation in Missouri to estimate 

the most likely time of introduction of H7N1 LPAI virus onto the farm, and the most likely barn 

first infected. Similar data were not available for the layer flock at the time of this analysis.

Using a disease transmission model, we simulated LPAI spread within a turkey barn and 

estimated the daily percentage of infectious and seropositive birds in the barn over time. Based 

on the results of this model, we estimated the time of LPAI introduction, given the observed 

diagnostic test results. 

Based on the results of our model and the observed diagnostic test results, the time of 

introduction of LPAI onto the premises in Barn 2 was estimated to be around 7 February, with a 

range of possible introduction dates extending from 31 January to 10 February. Barn 2 was likely 

to have been the first barn to become infected, considering the higher proportion of diagnostic 

samples with high hemagglutination inhibition (HI) titers. LPAI was estimated to have been 

introduced later into Barn 4, on 12 February, with a range of possible dates between 8 February 

and 14 February; and this barn continued to test positive via rRT-PCR even on later sampling 

dates. 

As with all analytic models, this analysis is subject to some data limitations. Information on the 

characteristics of disease spread of the specific LPAI virus from the recent outbreak were not 

available, so data from published studies of other H7N1 viruses were used in our disease 

transmission model. Strain variability and species susceptibility may impact virus transmission. 

Additional studies of the LPAI Missouri virus isolate will help improve future estimates of farm 

infection dates.

Methods Overview

Summary of LPAI outbreak data 

Outbreak data available for this analysis consisted of rRT-PCR, virus isolation (VI), and serological 

test results, including ELISA and hemagglutination inhibition (HI) tests. A summary of test results 

is provided in Table 3. Additional diagnostic test details including rRT-PCR Ct values and HI titers 

are provided in Table 4 and Table 5, respectively. Daily flock mortality data for each of the 4 

barns were also used in the analysis.
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Table 3. Summary of surveillance protocols and test results from the epidemiological investigation of a 

LPAI outbreak in a commercial meat-type turkey flock in Missouri, date the sample was collected, 

purpose of the surveillance sample, sampling protocol, and qualitative interpretation of results.

Date collected Purpose Sample Results

26 February National Poultry 

Improvement 

Program (NPIP)

1 pool of 6 swabsa rRT-PCR positive, VI negative

2 March Foreign Animal 

Disease (FAD)

investigation 

1 pool of 11 swabs 

per-Barnb

All Barns rRT-PCR positive, all 

VI negative 

10 serum samples 

per-Barn

All positive by ELISA and by HI

8 March Controlled marketing 3 pools of 11 swabs 

per-Barn

2 pools from Barn 4 rRT-PCR 

positive, remainder negative, 

1 of 2 VI positive 

14 March Controlled marketing 3 pools of 11 swabs 

per-Barn

2 pools from Barn 4 rRT-PCR 

positive, remainder negative, 

both VI negative

a NPIP pre-slaughter surveillance protocol b 4 Barns on the premises

Table 4. Test results (Ct valuesa) reported for various rRT-PCR tests conducted on samples from the 4 

barns of the commercial meat-type turkey flock in Missouri.

rRT-PCR test event Ct value

26 February NPIP - 1 pool tested at the 

NAHLN laboratory and at NVSL

Ct 34.8

2 March FAD investigation - 4 pooled 

samples tested at NVSL (sera collected at the 

same time reported in Table 5)

Barn 1 at Ct 37.8; Barn 2 at Ct 39.3; Barn 3 at Ct 38.8; 

Barn 4 at Ct 39.7

8 March Controlled marketing - 12 pooled 

samples tested at NVSL

Barn 4 sample 1 at Ct 36.4; Barn 4 sample 2 at Ct 39.7

14 March Controlled marketing - 12 pooled 

samples tested at NAHLN – 2 samples to 

NVSL for VI only

Barn 4 (front) Ct 39.2; Barn 4 (center) 39.3

a Ct (cycle threshold) values are inversely proportional to the amount of virus nucleic acid in the sample. 

So the lower the Ct value, the greater the amount of virus genetic material in the sample.
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Table 5. H7 hemagglutination inhibition (HI) assay titers from serum samples collected on 2 March

2018. HI titers for all Barns suggest that Barn 2 may have been the site of the original 

introduction, followed by Barns 1 and 3, with Barn 4 affected last. Titers >=1:8 are suggestive of 

exposure.

Barn 1 Barn 2 Barn 3 Barn 4

≥ 1:32 ≥ 1:32 ≥ 1:32 ≥ 1:32

≥ 1:32 ≥ 1:32 ≥ 1:32 1:16

≥ 1:32 ≥ 1:32 ≥ 1:32 1:16

≥ 1:32 ≥ 1:32 ≥ 1:32 1:16

≥ 1:32 ≥ 1:32 ≥ 1:32 1:16

≥ 1:32 ≥ 1:32 ≥ 1:32 1:8

1:16 ≥ 1:32 1:16 1:8

1:16 ≥ 1:32 1:16 1:8

1:16 1:16 1:8 1:8

1:8 1:16 1:8 1:8

Overview of modeling approach 

To estimate the possible dates of LPAI introduction into a barn, we used a disease transmission

model to predict the percentages of infectious and seropositive birds in a barn over time. 

Because data on the transmission characteristics for the recently isolated North American H7 

LPAI virus in turkeys were not available for this analysis, we estimated virus characteristics using 

data from a review of published literature. Specifically, we used studies describing the 

characteristics of the 1999 Italian H7N1 LPAI virus strain. 

The results of this model were used to estimate the time of LPAI introduction, based on the 

observed diagnostic test results. Specifically, the likelihood of observing each set of diagnostic 

test results was calculated for different possible dates of LPAI introduction (from 4 to 45 days 

prior to 2 March 2018). The average likelihood possible introduction dates given all test results 

was calculated by running the model 10,000 times. 

In some of the barns, there was an observed mild increase in mortality for only a few days 

within one month of the 2 March rRT-PCR positive test result. To improve our estimates of the 

day of introduction, we combined the results of our model using the diagnostic test results with 

the observed mortality data. When the observed timing of the peak in bird mortality, estimated 

by the disease transmission model, most closely matched the observed date of peak mortality, 

we considered the estimated date of introduction from the disease transmission model to be 

the most likely date.
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Results 

The pattern of diagnostic test results was the same for Barns 1, 2 and 3 (ELISA and rRT-PCR 

positive on 2 March, and rRT-PCR test negative on 8 March). As expected, the estimated date of 

LPAI introduction based on these results was also similar for these barns. LPAI may have been 

first introduced into Barn 2 given the greater proportion of samples with higher HI titers for this 

barn on 2 March (Table 5). The likelihood of observing the diagnostic test results from birds in

Barn 2 on each test date, and the combined likelihood of observing all three sets of test results

(ELISA on 2 March, rRT-PCR on 2 March and rRT-PCR on 8 March) are provided in Figure 2. The 

top graph in Figure 2 shows the likelihood of observing each set of diagnostic test results for a 

range of possible LPAI introduction dates. By taking into account:

a) available serology results which are impacted by the birds immune response, 

b) positive rRT-PCR results which are impacted by presence of the virus, and 

c) negative test results seen on 8 March (bottom graph of Figure 2), 

the likely time of introduction was estimated around 7 February with a range from 31 January to 

10 February.

Table 6. Results for the estimated date of LPAI introduction for Barns 1, 2, and 3.

Barn

Based only on observed diagnostic 

test results

Based on observed diagnostic test results and 

the timing of peak mortality

Mean (90% C.I.) Most likely Mean (90% C.I.) Most likely

Barn 2 6 February (31 Jan-10 Feb) 7 February 8 February (4 Feb-11 Feb) 8 February

Barn 3 6 February (31 Jan-10 Feb) 7 February 9 February (5 Feb-11 Feb) 9 February

Barn 1 6 February (1 Feb-11 Feb) 7 February NA NA
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Figure 2. The estimated likelihood of LPAI introduction into Barn 2 on various days based on the results 

from each diagnostic test event (top) and the combined likelihood for all the test events (bottom). 

The diagnostic test events include all tests conducted on birds in Barn 2 (Table 3).

As shown in Figure 3, observed peak mortality for Barn 2 occurred on 26 February when the mortality 

on the last day of growing was excluded (mortality on this day was likely related to culling before the 

flock was processed). When the timing of the peak mortality was taken into account, the estimated 

most likely introduction date shifted slightly (Figure 4) from 7 February to 8 February (range of dates 

between 4 February to 11 February). A similar approach was used for Barn 1, 2, and 3 and the most 

likely introduction dates are shown in Table 6.
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Figure 3. Daily mortality per 1000 birds in Barn 2.

Figure 4. The approximate estimated likelihood of LPAI introduction into Barn 2 on various days based 

only on diagnostic test results (blue dashed line), and considering diagnostic tests as well as the 

timing of peak mortality (red solid line)
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The diagnostic test results were different for Barn 4. In this case, LPAI was estimated to be 

introduced later relative to the other barns as shown in Figure 6, based on the observed positive 

rRT-PCR results on later sampling dates, as well as the lower HI titers from samples collected on 

2 March. The date of introduction estimated from test results alone was 12 February (range of 

dates between 8 February to 14 February), and 13 February (range of dates 10 February to 15 

February) when diagnostic test results and the observed peak mortality were considered 

together (Figure 7). Note that as shown in Figure 5, the peak mortality occurred a few days later 

(4 March) for this barn relative to Barn 2, potentially indicating a later time of introduction.

Figure 5. Daily mortality per 1000 birds in Barn 4.
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Figure 6. The estimated likelihood of LPAI introduction into Barn 4 on various days based on individual 

diagnostic test events (top) and the combined likelihood for all the test events (bottom). The 

diagnostic test events considered include all diagnostic tests conducted on birds in Barn 4 (Table 3).

Figure 7. The approximate estimated likelihood LPAI introduction into Barn 4 on various days based 

only on diagnostic test results (blue dashed line), and considering diagnostic tests as well as the 

timing of peak mortality (red solid line).
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Discussion 

Diagnostic test results and flock mortality data can be used to estimate the stage of infection of 

a LPAI infected flock, as well as the potential day of virus introduction. We estimated an 

approximate range for the time of LPAI introduction into barns on a commercial meat-type 

turkey operation in Missouri using a stochastic disease transmission model and other analytic 

methods. The most likely timing of LPAI introduction onto the premises was estimated to be 8 

February, with a 90% Confidence Interval between 31 January to 10 February. Barn 2 was also

likely to have been the first barn to become infected. LPAI was estimated to have been 

introduced later into Barn 4 in the interval from 8 February to 14 February (90% C.I.) consistent 

with the presence of viral RNA based upon rRT-PCR on later sampling dates. 

The estimated time of introduction based on our analyses is an approximation for a variety of 

reasons including that data from only one farm was available to develop the model, the 

characteristics of the LPAI virus infecting the farm were largely unknown, and the number and 

frequency of diagnostic tests were limited. The majority of experimental data used to estimate 

virus characteristics were based on the 1999 Italian H7N1 LPAI virus strain. Differences in 

disease transmission between the Italian H7N1 LPAI virus and the current Missouri H7N1 LPAI 

outbreak strain may have affected the accuracy of the predictions for the date of introduction. 

Similarly, most experimental studies estimating seroconversion in LPAI infected turkeys do not 

collect samples daily, making it a challenge to estimate the date of seroconversion following 

exposure to the virus. Therefore, we assumed that the time to seroconversion is similar to the 

time when birds are shedding virus. This assumption was based on similar work in broiler 

breeders where more data are available. 

Overall, the current analysis demonstrates that by evaluating the results of tests detecting virus 

(rRT-PCR) and tests detecting immune reaction in infected birds (ELISA and HI), as well as barnlevel bird mortality data, we can estimate the date of LPAI introduction into an infected flock. As 

more data become available, these types of analyses may improve our ability to determine 

routes of virus introduction to farms, better understand seasonal and environmental risk, and to 

characterize subsequent disease spread.

V. Phylogenetic Analysis and Diagnostics

Phylogenetic Analysis and Diagnostics

North American H7N1 LPAI from poultry (AM H7N1 2018) 

This section describes H7N1 LPAI from poultry confirmed by the National Veterinary Services 

Laboratories (NVSL) during February and March 2018. The first detection was from a routine 

pre-slaughter commercial turkey flock sample collected 26 February 2018 in Jasper County, 

Missouri (MO). Virus was recovered and characterized from Barn 4 as North American wild bird 

lineage H7N1 LPAI with an intravenous pathogenicity index (IVPI) of zero as defined by OIE. 

Shortly after the Missouri detection, samples from a broiler breeder flock in Texas (TX) collected 

2 March 2018 were confirmed by H7 and N1 antibody from sera, and H7 LPAI based upon direct 

sequence attempt from a swab sample. An H7N1 LPAI virus was characterized from these 

samples and found to have >99% identity with the MO H7N1 virus. The third detection was from 
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a backyard flock sample collected 14 March 2018 in MO; this virus also had >99% similarity to 

the other MO and TX H7N1 viruses across the entire genome. 

The current phylogenetic analysis of viruses from these three events support independent 

introductions from a common source, with a >99.9% probability that the introductions arose 

from wild birds in the Central/Mississippi flyway (Figure 8). The lack of epidemiologic links 

further supports this finding (refer to Section III.).

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.

a)
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Figure 8. Phylogenetic analysis of viruses from these three events support independent introductions 

from a common source: a) indicates >99.9% probability that the introductions arose from wild birds 

in the Central/Mississippi flyway (abbreviations: TMRCA = estimated time to mean common 

ancestor; HPD=highest posterior density); b) network analysis of the HA gene. Courtesy of 

Interagency wild bird surveillance data, ML Killian NVSL, and DH Lee USDA-ARS Southeast Poultry 

Research Laboratory. 

Comparison to Other Viruses/Lineages 

The H7N1 virus clusters with recent wild bird viruses and apart from other recent H7 poultry 

detections (H7N8 2016 and H7N9 2017) across the entire genome. The neuraminidase gene of 

the H7N1 was also compared to a recent H6N1 virus detected in Arkansas broiler breeders late 

February 2018. The neuraminidase sequences did not cluster together, but similarity was noted 

for one of the internal genes (PB1) between the H7N1 and H6N1 viruses. Although highly similar 

gene segments were identified from the recent Interagency wild bird surveillance, particularly 

from the Central/Mississippi flyway, no single wild bird virus ancestor was identified for the 

H7N1 identified in MO and TX poultry. This result suggests that reassortment event(s) occurred 

prior to introduction to poultry. 

Public Health Aspects 

To date, there have been no reports of H7N1 LPAI 2018 virus infection in humans. The health of 

response workers and on-farm personnel was monitored at the state level. The virus sequences 

have been shared with CDC for analysis which indicated that the viruses to date lack key amino 

b)
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acid substitutions associated with human-like receptor binding or substitutions in the polymerase 

or other internal genes associated with increased virulence and transmission in mammals; no 

known markers of neuraminidase inhibitor (Oseltamivir) resistance have been identified.

Diagnostics and Characterization for Influenza A Viruses 

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

Poultry Research Laboratory, the Influenza Division of the Centers for Disease Control and 

Prevention, USDA-APHIS Wildlife Services, as well as other key partners. Consensus data from 

whole genome sequencing are 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. Analysis of sequence data includes phylogeny of all eight 

segments and determination of amino acid substitutions across the HA1 protein. Genetic data 

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

high identity between the H7N1 virus sequences and the primers and probes used for the IAV 

and H7 diagnostic rRT-PCR tests.

General Information 

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. 

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.

VI. Waterfowl Surveillance

Waterfowl are natural reservoir hosts for influenza A viruses (IAV; subtypes H1-H16), but not 

usually HPAI. Influenza A viruses in wild birds tend to circulate seasonally within migratory 
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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 9). 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. 

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

implemented in 2015 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.

Since January 1, 2016, nearly 80,000 wild waterfowl have been sampled and tested by rRT-PCR 

for IAV, with H7 detected in over 550 samples across all four flyways. Of the H7 detections, 

nearly 250 were from the Central and Mississippi Flyways. H7 detections have occurred during 

Figure 9. The four primary North American waterfowl flyways
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summer, fall, and winter and throughout the Central and Mississippi Flyways (Figure 10). 

Annually, H7 detections in wild waterfowl tend to peak in early winter. This pattern may have 

contributed to the timing of the recent events in Missouri and Texas.

The graph for influenza A detections is based upon PCR testing at NAHLN laboratory by the Type 

A-specific (IAV-M) and H7 tests, regardless of the virus recovery status.

• 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 

where IAV 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. 

• Wild birds are often exposed to IAV and mount an antibody response that can kill the 

virus, leading to unsuccessful virus isolation in subsequent testing of samples.
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Figure 10. Timeline of virus detections in wild birds (upper panel) and locations of influenza A 

detections by IAV-M PCR from wild bird Surveillance (lower panel)
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VII. Acknowledgements

We greatly appreciate the cooperation and support of the poultry industry and farm owners for 

allowing us access to their properties, for providing information on their biosecurity and 

production practices, and for their full cooperation with this investigation. 

This report would not have been possible without a large group of researchers, epidemiologists, 

laboratory staff, and data scientists who participated in the various analyses, drafting, and

review of this report. We appreciate their dedication and professionalism in providing the best 

information possible to help producers reduce the risk of IAV introduction into their operations. 
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Appendix A: Case Series Questionnaire
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Appendix B: Estimation of Model Parameters for Within-Flock Spread 

of H7N1 LPAI Within a Turkey Barn

Estimation of the latency and infectious period distributions

In an experimental inoculation study, three groups of 10 turkeys were infected with H7N1 LPAI 

virus (Italy/1279) at nominal doses of 102

, 104, or 106 EID50, and the infection status of 

inoculated and contact turkeys was monitored at 24 hour intervals over 6 days using buccal and 

cloacal swabs tested for the presence of virus antigen by RRT-PCR (Iqbal et al., 2012). 

In a second study, three-week old broad-breasted turkeys were inoculated with 102

, 104, or 106

EID50 of LPAI H7N8 (turkey/IN/16-001571-6/2016) (Pantin-Jackwood et al., 2017). Infection 

status was monitored in directly inoculated turkeys at 12 hour intervals, and contact birds at 24 

hour intervals, using oropharyngeal and cloacal swabs tested for the presence of virus antigen 

by quantitative RRT-PCR (Pantin-Jackwood et al., 2017). Turkeys directly inoculated at 104 and 

106 EID50 and turkeys contact exposed to these turkeys became infected (Pantin-Jackwood et al., 

2017).

Saenz et al (2012), inoculated a three week old turkey with 106 EID50 H7N1 LPAI 

(A/chicken/Italy/1279/99, LP) virus and exposed 40 or 41 contact turkeys in two large scale 

transmission studies (Saenz et al., 2012). Buccal swabs were taken daily mostly) to monitor 

infection status (Saenz et al., 2012). 

Comin et al (2011), used data from a previously conducted vaccine study, where 18 twelve-week 

old turkeys had been inoculated with two LPAI strains (Comin et al., 2011). Nine birds were 

challenged with H5N2 LPAI virus (A/TK/IT/80) and 9 birds with H7N3 LPAI virus 

(A/TK/IT/8000/02) at an infective dose of 104 EID50 (Comin et al., 2011). Cloacal swabs were 

taken at day 3, 5, 7, 10, 12, 15 and 20 post inoculation and tested using a real-time RT-PCR assay 

and virus isolation in SPF fertile eggs (Comin et al., 2011). 

Three week old turkeys were inoculated with 107 EID50 H7N2 LPAI A/turkey/VA/SEP/67/2002, 

and oropharyngeal swabs were collected from all birds from 1 to 4 dpi, and at 6, 8, and 10 

(Costa-Hurtado et al., 2014). Results for 10 inoculated turkeys from Figure 1 of the publication 

were used in this analysis. 

To estimate the latent period distribution, we used buccal swab data from 10 turkeys inoculated 

with 103.8 EID50 (turkeys 81-90) from (Iqbal et al., 2012); and 10 turkeys inoculated with 105.2

EID50 (turkeys 21-30; Supplement Table S1) (Iqbal et al., 2012). We also used data from 

oropharyngeal swabs from 17 turkeys inoculated with 106 EID50 from (Pantin-Jackwood et al., 

2017). 

To estimate the infectious period distribution, we used data from 81 turkeys from two LPAI 

transmission studies from Saenz et al (2012), Table 5 and Table 6 from the published paper 

(Saenz et al., 2012). We also used data from 20 turkeys from Table 8 from (Iqbal et al., 2012), 

data from 8 turkeys (Table 3, K10 to K18), and data from (Comin et al., 2011). 

The gamma distribution parameters for the latent and infectious periods were estimated via 

maximum likelihood methods. Details are provided in Table 7.
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Table 7. Parameter estimates for the LPAI transmission model for turkey barns.

Parameter name Parameter description Distribution/Value

Contact rate (transmission 

parameter)

The number of direct or indirect 

contacts a bird has that are 

sufficient to transmit infection 

per unit time

Pert distribution (min 1.1, mode 

2.01, max 3.5 and lambda 4.0) based 

on estimates from Saenz et al., 2012.

Latent period distribution Length of the latent period Gamma distribution (shape 

2.4404741, scale 0.2607466; mean 

0.6363 days)

Infectious period 

distribution 

Length of the infectious period Gamma distribution (shape 

6.490312, scale 1.290292; mean 8.37 

days)

Time to seroconversion Time to seroconvert postinfectionGamma distribution (shape 

6.490312, scale 1.29029; mean 8.37 

days)

Proportion seroconverting Proportion of LPAI infected 

turkeys that seroconvert 

0.99

Proportion of turkeys that seroconvert to LPAI

In an experimental inoculation study comparing the pathogenesis of twelve H7 LPAI virus 

isolates from North America, nearly all (88/89 or 99%) surviving turkeys had detectable antibody 

by day 18 to 21 post inoculation (Spackman et al., 2010). For comparison, ~ 95 % (110/116) of 

surviving chickens seroconverted in the same study (Spackman et al., 2010). Based on this study, 

we estimated that 99% of turkeys would seroconvert following infection with LPAI virus. 

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