Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 3

Influenza A Virus in Swine Surveillance

Fiscal Year 2021 Quarterly Report

Surveillance Summary for Third Quarter Fiscal Year 2021: April 1 to 

June 30, 2021

Report Summary1

• This report covers the third quarter (Q3) of fiscal year (FY) 2021 from April 1 through June 30, 

2021.

• Where relevant, the report also includes previous years’ data for historical perspective. 

• The report provides data from both national and regional levels.

• In Q3 of FY2021, there were 569 samples submitted for influenza A virus (IAV) surveillance in 

swine from 516 accessions. 

• H1N1was the predominant subtype reported in USDA data in Q3 FY2021.

• Over the past 8 quarters, H1N2 was the main subtype in Regions 1, 3 and 5, and H1N1 was 

isolated most frequently in Regions 2 and 4.

• Limited accessions from a region can skew data and lead to misinterpretation. Therefore, less 

inference can be applied to results from Regions 3, 4, and 5.

• All IAV-S submissions are voluntary and based on clinical case submissions to veterinary 

diagnostic labs. These data are not a statistically representative sampling of the U.S. swine 

population.

• Due to the voluntary nature of this surveillance, the information in this report cannot be used to 

determine regional and/or national incidence, prevalence, or other epidemiological measures, 

but it may help identify IAV-S trends. 

Introduction

This report, based on data received into the database as of September 30, 2021, provides a brief update 

on the status of national surveillance for IAV in swine for producers, swine practitioners, diagnosticians 

and the public. Summaries in this report may differ from those provided in past reports due to the 

regular addition of data from participating laboratories. Reporting months are based on the month the 

sample was collected. The IAV-S surveillance program is voluntary and, as a result, the accessions and 

samples submitted represent a subset of the swine population. Submitted samples should only be 

collected from animals displaying influenza-like illness. When the submitter does not report relevant 

information, data are recorded as “unknown.” Due to its voluntary nature, this surveillance system does

not entirely represent the total U.S. domestic swine population. Therefore, the data cannot be used to 

1 In November 2016, VS modernized the process that prepares and stages laboratory results data for reporting. Consequently, 

VS recognizes there is a small difference in previously reported summary numbers for IAV-S surveillance. The results in this 

report reflect updated and corrected numbers achieved with the modernized data process.

Animal and 

Plant Health 

Inspection 

Service

Veterinary 

Services

Sept 2021
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 3

determine IAV-S prevalence or other epidemiologic measures in the swine population. However, the 

data may help identify trends of influenza in swine. 

A laboratory accession generally represents a set of samples collected at a single premises on a single 

day and received at the laboratory. While a nasal swab or lung tissue sample represents a single animal 

within the herd, a single oral fluid sample may represent one to two pens of animals in a herd. A positive 

sample status is based on the screening real-time reverse transcriptase polymerase chain reaction (rRTPCR) on one or more samples within the accession. The subtype result is based on rRT-PCR-based 

subtyping assays. Virus isolation (VI) and sequencing in the NAHLN labs are only attempted on rRT-PCR 

positives meeting criteria with sequences deposited into GenBank, the public sequence database. On a 

monthly basis, USDA NVSL also performs whole genomic sequencing (WGS) on a selected subset of virus 

isolates received into the repository through the surveillance program and deposits those sequences

into Genbank. On a quarterly basis, a phylogenetic analysis is performed by ARS influenza researchers; 

phylogenetic analyses are based on all successful USDA surveillance sequencing results deposited into 

GenBank, the public sequence database. 

Program Updates

Information on IAV-S and the IAV-S surveillance program, as well as previous IAV-S quarterly reports, are 

found at:

https://www.aphis.usda.gov/aphis/ourfocus/animalhealth/animal-disease-information/swine-diseaseinformation/influenza-a-virus

The focus of IAV-S surveillance remains on acquiring and analyzing contemporary viruses from sick swine 

for ongoing genetic studies. The National Animal Health Laboratory Network (NAHLN) has several 

submission options to ensure that unusual viruses identified by methods other than standardized

NAHLN testing processes can be submitted into the program. An updated version of the IAV-S NAHLN 

testing guidelines and instruction sheet can be found at:

• Algorithm: 

https://www.aphis.usda.gov/animal_health/animal_dis_spec/swine/downloads/appendix_c_tes

ting_guidelines.pdf

• Instructions: 

https://www-author.aphis.usda.gov/animal_health/animal_dis_spec/swine/downloads/iav-salgorithm-instructions.pdf

IAV-S Surveillance Objectives

USDA’s National Surveillance Plan for Swine Influenza Virus in Pigs (July 2010) describes the current 

surveillance system for IAV in swine in detail. The surveillance objectives are to: 

1. Monitor genetic evolution of endemic IAV in swine to better understand endemic and emerging 

influenza virus ecology; 

2. Make influenza isolates from swine available for research and establish a data management system to 

facilitate genetic analysis of these isolates and related information; and 

3. Select proper isolates for the development of relevant diagnostic reagents, updated diagnostic assays, 

and vaccine seed stock products. 
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 3

Objective 1. Monitoring Genetic Evolution of Endemic IAV in Swine to Better 

Understand Endemic and Emerging Influenza Virus Ecology

Objective 1 is met through the submission of diagnostic laboratory samples to the surveillance system, 

collection of the viruses that are isolated from the samples, and analysis of the hemagglutinin (HA) and 

neuraminidase (NA) sequences that are generated at the NAHLN laboratories. Each month, selected

viruses undergo whole genomic sequencing by the National Veterinary Services Laboratories (NVSL). 

Phylogenic analysis of the genetic sequences submitted through the surveillance program is provided 

through an interagency agreement with the USDA’s Agricultural Research Service (ARS) National Animal 

Disease Center (NADC). 

National Surveillance Data Summary

From FY2010 through FY2015, the total number of accessions and samples submitted increased.

Changes initiated in the program in FY2016 resulted in decreased laboratory accessions and samples

however yielded higher percentage of accessions resulting in a virus isolate that could be sequenced and 

analyzed. Based on historical data for successful virus isolation, cycle threshold (Ct) maximum values for 

different sample types were established to try to improve the efficiency of the surveillance program 

while reducing the required resources. If lung/nasal samples have a Ct value of 25 or less and oral fluid 

samples have a Ct value of 20 or less, virus isolation and sequencing will be attempted. If there is 

something unique related to the virus, like causing high mortality, but the samples have higher than the 

established maximum Ct values, they will still enter the surveillance stream. In FY 2021, through the end 

of Q3, a total of 1,669 samples have been tested from 1,522 accessions (Figure 1), with 569 samples 

being tested from 516 accessions in Q3. Figure 2 shows the overall trends in total accessions, rRT-PCR

and VI positive accessions, and subtyped accessions.

 Figure 1. Number of IAV laboratory accessions and samples tested in swine FY2017 through Q3 FY2021
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 3

Figure 2. Accessions submitted, subtyped accessions, rRT-PCR positive accessions, and virus isolation positive accessions over 

time with trend lines for IAV-S, FY2017 through Q3 FY2021

Figure 3 shows the number of subtype detections in Q3 FY2021. The total number of samples subtyped 

was 291, including H1N1 (n=124), H1N2 (n=74), H3N2 (n=84), H3N1 (n=2), and mixed (n=7).

Figure 3. Number of IAV-S subtype detections in Q3 FY2021

Figure 4 breaks down accessions by rRT-PCR subtype from FY2017 through Q3 FY2021. H1N1 was the 

predominant subtype detected in 2018, 2020 and through Q3 FY2021. H1N2 was detected most often in 

2017 and 2019. 
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 3

Figure 4. Breakdown of accessions by subtype rRT-PCR from FY2017 through Q3 FY2021

Figure 5 displays the number of times virus isolation (VI) was attempted in blue, the number of times VI 

was conducted and was positive in purple, and the number of viral isolates submitted to GenBank in 

green. Since the implementation of the June 2016 modifications to the program, almost all VIs 

attempted now yield a virus and the sequences are submitted to Genbank for analysis.

Figure 5. Number of virus isolations attempted, positive virus isolations, and GenBank submissions from FY2017 through Q3

FY2021
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 3

Laboratory accessions were evaluated by age-class for the third quarter. The most common subtype 

isolated among the nursery class was H1N1. Among the suckling age class, H1N1 and H1N2 were the 

predominant isolated subtypes. The sow/boar class had limited testing, with one isolate of H3N2

reported and two H1N1 subtypes reported. Among isolates for which the age class was unknown or not 

recorded, H1N1 was the predominant subtype. The grow/finish class had H1N1 isolated the most. (Table 

1). Excluding specimen types with less than 10 percent of total submissions, lung samples were the most 

successful at providing positive virus isolation and submission to GenBank (Table 2). 

Table 1. Number of positive accessions tested for IAV-S by age class and viral subtype, Q3 FY2021 

Age Class (group)

Number 

of H1N1

Number 

of H1N2

Number of 

H3N1

Number 

of H3N2

Number 

of Mixed

Suckling 25 24 1 20 0

Nursery 45 26 0 34 4

Sow/Boar 2 0 0 1 0

Not Recorded/Unknown 16 9 1 14 1

Grow/Finish 36 15 0 15 2

Table 2. Number of positive accessions* tested for IAV-S by specimen type and by viral subtype, Q3 FY2021 

Specimen 

Type 

(group)

Number of 

accessions 

with 

subtype 

reported

Percent of 

subtyped 

accessions 

with 

positive 

virus 

isolation

Number 

of H1N1

Number 

of H1N2

Number 

of H3N1

Number 

of H3N2

Number 

of 

Mixed

Number of 

samples 

sequenced 

and sent to 

GenBank

Lung 271 73% 119 72 1 73 6 231

Nasal or 

Nasal Swab 15 97.5% 3 1 0 10 1 13

Oral Fluids 2 100% 1 0 0 1 0 2

Other 

Specimens 3 66% 1 1 1 0 0 2

*Accessions may include samples with multiple specimen types. In these cases, individual accessions are counted 

in more than one specimen type category. 
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 3

Regional surveillance data

In this section, we present data in five different regions (Figure 6). These regions are based on former USDA 

administrative districts only and do not represent specific industry distribution. Submissions are voluntary, 

as is any identifying information accompanying the submission (except the State of animal origin), and 

therefore no sampling strategies can be applied to the regions.

Figure 6. A map of the regions for national IAV-S surveillance

Table 3. Summary of predominant HA/NA* phylo-types by region in a 1 year window from July 2020

through June 2021.

Region Total number HA/NA subtype

1 121 H3N2 (H3-Cluster IV-A / N2-2002B) (n=50)

H1N2 (H1-Delta2 / N2-1998B) (n=33)

H1N1 (H1-Gamma / N1-Classical) (n=17))

2 724 Most diversity of all regions

H1N1 (H1-Gamma / N1-Classical) (n=225)

H1N2 (H1-Delta2 / N2-1998B) (n=141)

H3N2 (H3-Cluster IV-A / N2-2002B) (n=116)

3 76 H1N1 (H1-Pandemic / N1-Pandemic) (n=18)

H1N2 (H1-Delta1b / N2-2002A) (n=10)

H3N2 (H3-2010.1 / N2-2002A) (n=9)

H3N2 (H3-2010.1 / N2-2002B) (n=8)

4 64 H1N1 (H1-Gamma / N1-Classical) (n=17)

H3N2 (H3-2010.1 / N2-2002B) (n=10)

H1N1 (H1-Pandemic / N1-Pandemic) (n=7)

H3N2 (H3-2010.1 / N2-2002A) (n=7

5 14 Low participation

H1N2 (H1-Alpha / N2-2002B) (n=3)

H1N1 (H1-Pandemic / N1-Pandemic) (n=3)

H3N2 (H3-2010.1 / N2-2002B) (n=3)

Most Predominant HA/NA phylo-types overall: 

H1N1 (H1-Gamma / N1-Classical) (n=264)

H1N2 (H1-Delta2 / N2-1998B) (n=183)
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 3

Summary of Regional Data from ARS

Figure 7 shows the distribution of rRT-PCR subtyped accessions among the five regions for Q3 FY2019

through Q3 FY2021. Regions 1, 3 and 5 demonstrate H1N2 as the predominant subtype, Regions 2 and 4 

demonstrate H1N1 as the most predominant. Table 3 displays the three to four most predominant HA/NA 

phylo-type pairs by region and displays the total number of HA/NA phylo-type pairs identified in each 

region from July 2020-June 2021.

Figure 7. Distribution of rRT-PCR subtyped accessions among the five regions Q3 FY2019 through Q3 FY2021

Regional phylogenetic analysis

Phylogenetic analysis of sequences from the IAV-S surveillance system

Phylogenetic analysis of gene sequences of IAV in swine is conducted to further examine the genetic 

changes that occur in HA, NA, and Matrix (M) genes of this rapidly changing virus. Through collaboration 

with ARS, a dataset2,3 of 252 isolates with published sequences in GenBank was characterized by 

phylogenetic analysis for the Q3 FY2021 report. This analysis provides information on the genetic diversity 

and evolution patterns of influenza in swine and allows for inferences about population and/or vaccine 

immunity.

2 Participating NAHLN labs included M gene sequencing in their testing until July 2016 because the 2009 H1N1 M gene was the 

predominant circulating gene. 3 The ARS dataset is comprised of IAV-S surveillance isolate sequences that were posted in Genbank. This represents only a subset 

of the complete IAV-S surveillance dataset that includes PCR diagnostic test-based results as well as sequencing results. Therefore, 

ARS dataset results, such as subtype percentages, differ from the complete IAV-S dataset results provided in other sections of this 

report.

H3N2 (H3-Cluster IV-A / N2-2002B) (n=177)

*HA/NA pairs included if they compromise over 10% from a region
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 3

The following series of bar charts parse the data into an approximately 2-year window by quarters and 

subtypes for each region, followed by charts further describing the phylogenetic clades of H1, H3, N1 and 

N2 subtypes. Regional charts depicting the various combinations of HA and NA are in Appendix 1.

Figure 8 demonstrates the four subtypes H1N1, H1N2, H3N1 and H3N2 across the five regions. Regions 1 

and 2 reported the most submissions, with a mixture of mostly H1N1, H1N2, and H3N2. Limited accessions 

from a region can skew data and lead to misinterpretation and therefore, less inference can be applied to 

results from Regions 3, 4, and 5. 

National phylogenetic HA gene information 

HA genes from H1 subtype viruses are classified as alpha, beta, gamma, delta-1, delta-2, or pandemic H1N1 

2009 (H1N1pdm09) phylogenetic clades based on a previously published nomenclature system. Similarly, 

H3 subtype viruses are classified as Cluster IV, Cluster IV-A, Cluster IV-B, Cluster IV-C, Cluster IV-D, Cluster 

IV-E, Cluster IV-F, or human-like. In Q3 FY2021: H1-Gamma remained the predominant H1 H1-Delta2/N2-

1998B and H1-Pandemic/N1-Classical are the next most common (Figure 9).

Figure 9. Temporal distribution of H1 phylogenetic clades by region for Q4 FY2019 to Q3 FY2021

Figure 8. Temporal distribution of Influenza A virus subtype by region for Q4 FY2019 to Q3 FY2021
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 3

National phylogenetic NA gene information

Figure 11. Temporal distribution of N1 phylogenetic clades by region for Q4 FY2019 to Q3 FY2021

In Q3 FY2021: N1-Classical (n=73) was the most predominant N1 (Figure 11) and paired with H1-gamma 

(n=72), H1-pandemic (n=1); N1-Pandemic (n=21) paired with H1-Pandemic (n=21) was the next most 

common.

In Q3 FY2021: The most predominant N2 is N2-2002B with N2-2002A + N2-2002B represent (20 + 81) / 156

of N2 collections and N2-1998B is the next most common and represents 49 / 156 of N2 collections (Figure 

12).

Figure 10. Temporal distribution of H3 phylogenetic clades by region for Q4 FY2019 to Q3 FY2021
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 3

Figure12. Temporal distribution of N2 phylogenetic clades by region for Q4 FY2019 to Q3 FY2021

The most dominant whole genome patterns with HA/NA pairs and internal gene lineages over FY 2021 Q1 

and Q2 (Q3 whole genome sequencing were still pending at the time this report was created and Q1 and 

Q2 were previously pending but have since been completed and the results are displayed below):

Internal gene constellations (Q1 and Q2, n=185)

• TTTPPT is dominant in H3-Cluster IV-A, H1-Gamma, H1-Delta2, and common in H1-Alpha

• TTTTPT is dominant in H3-2010.1 and H1-Delta1A and common in H1-Alpha

• TTPPPT is common in H1-Gamma

• TTPTPT is dominant in H1-Delta1B

• H1-Pandemic has highly variable internal genes

Objective 2. Make Influenza Isolates from Swine Available for Research and 

Establish a Data Management System to Facilitate Genetic Analysis of these 

Isolates and Related Information

A primary goal of IAV swine surveillance is to share selected virus isolates obtained through the surveillance 

system with public health, animal health, and academic researchers to facilitate genetic analysis and 

research on viruses of interest. The NVSL Diagnostic Virology Laboratory maintains a repository of the 

viruses submitted into the surveillance system and provides these viruses upon request. 

In Q3 FY2021, the NVSL Diagnostic Virology Laboratory provided 20 isolates to one academic institution, 

and two pharmaceutical requestors. NVSL received 167 isolates into the repository in Q3 FY2021. Table 4

reports the total number of virus isolates received into the repository each year from FY2014 through Q3 of 

FY2021. Table 5 reports the total number of isolates available in the repository by subtype for sharing. 
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 3

Table 4. Virus isolates received in repository 

Virus isolates in the repository

FY2021 784

FY2020 1,074

FY2019 1,055

FY2018 994

FY2017 844

FY2016 1,046

FY2015 883

FY2014 765

TOTAL TO DATE 7,445

 

 

Objective 3. Select Proper Isolates for Development of Relevant Diagnostic 

Reagents, Updating Diagnostic Assays, and Vaccine Seed Stock Products

USDA makes IAV-S isolates available in the public domain for further research. ARS-NADC conducts 

research on isolates obtained from the repository and sequences generated from the surveillance system. 

Genetic sequencing from the USDA program that is reported to GenBank is available for private 

corporations, government entities, academia, and other scientific community partners for research and 

vaccine strain selection and efficacy testing. NVSL and ARS staff are consulted as subject matter experts 

when necessary. 

Conclusion

The IAV voluntary surveillance system in swine continues to provide insight into the genetic makeup of 

circulating influenza A virus in limited populations of commercial pigs. Genetic information and virus 

isolates are made publicly available for further research and possible vaccine strain selection and efficacy 

testing. Influenza A virus in swine remains a dynamic virus with high levels of genetic variability in the

hemagglutinin and neuraminidase genes. 

Table 5. Total number of subtyped 

isolates available through repository from 

2009-Present

Subtyped isolates available through 

repository

H3N2 2,515

H3N1 22

H1N1 3,232

H1N2 2,996

Mixed 302

TOTAL 9,067
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 3

Appendix 1. Regional Charts of HA and NA Combinations by Percentage

The following charts present the percentages of combinations of HA and NA on the national and regional scales based on ARS-NADC phylogenetic 

analyses. The results are reported from July 2020 through June 2021. These “heat maps” represent the percentage of combinations by using a 

color gradient where a deeper gradient color represents a greater percentage occurrence for a particular HA-NA combination. HA clusters are 

listed on the left vertical axis of the chart and NA clusters are listed on the bottom horizontal axis. Line up the HA cluster with the corresponding 

NA cluster to determine the occurrence of that particular combination. 
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 3
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 3
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 3
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 3
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 3