Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 4

Influenza A Virus in Swine Surveillance

Fiscal Year 2021 Quarterly Report 

Surveillance Summary for Fourth Quarter Fiscal Year 2021: July 1 to 

September 30, 2021 

Report Summary1

• This report covers the fourth quarter (Q4) of fiscal year (FY) 2021 from July 1 through September 

30, 2021. 

• In Q4 of FY2021, there were 409 samples submitted for influenza A virus (IAV) surveillance in 

swine from 376 accessions. 

• H1N1was the predominant subtype reported in USDA data in Q4 FY2021. 

• Over the past 8 quarters, H1N2 was the predominant subtype in region 1. In regions 2, 4, and 5 

H1N1 was the most predominant. H3N2 was the predominant subtype for region 3.

• The Agricultural Research Service (ARS) characterized 201 isolates with published sequences in 

GenBank by phylogenetic analysis for the Q4 FY2021 report

• In Q4 FY2021, the NVSL Diagnostic Virology Laboratory provided 69 isolates to five academic 

institutions, three government entities, and three pharmaceutical requestors. NVSL received 

324 isolates into the repository in Q4 FY2021.

Key Points

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

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

• 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 January 20, 2022, provides a brief update on 

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

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 

Feb 2022
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 4

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 is not representative of

the total U.S. domestic swine population. Therefore, the data cannot be used to determine IAV-S 

prevalence or other epidemiologic measures in the swine population. However, the data may help 

identify influenza trends 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 
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 4

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

and vaccine seed stock products. 

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 genome 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 Q4, a total of 2,078 samples were tested from 1,898 accessions (Figure 1), with 409 samples tested 

from 376 accessions in Q4. Figure 2 shows the overall trends in rRT-PCR and VI positive accessions and 

subtyped accessions. 

 Figure 1. Number of IAV laboratory accessions and samples tested in swine FY2018 through Q4 FY2021
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 4

Figure 2. Subtyped accessions, rRT-PCR positive accessions, and virus isolation positive accessions over time with trend lines 

for IAV-S, FY2017 through Q4 FY2021

Figure 3 shows the number and distirbution of subtype detections in Q4 FY2021. A total of 208 samples 

were subtyped, including H1N1 (n=80), H1N2 (n=71), H3N2 (n=52), H3N1 (n=2), and mixed (n=3). 

Figure 3. Number of IAV-S subtype detections in Q4 FY2021 

Figure 4 breaks down accessions by rRT-PCR subtype for FY2017 through Q4 FY2021. H1N1 was the 

predominant subtype detected in 2018, 2020 and through Q4 FY2021. H1N2 was detected most often in 

2017 and 2019. It is important to note that there is wide genetic diversity within each subtype.
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 4

Figure 4. Breakdown of accessions by subtype rRT-PCR from FY2017 through Q4 FY2021

Figure 5 displays the number of times VI was attempted in blue, the number of successful VI attempts in 

purple, and the number of sequenced viral isolates submitted to GenBank in green. Since the 

implementation of the June 2016 program modifications, almost all VIs attempted now yield a virus with

the sequences submitted to Genbank for analysis. 

Figure 5. Number of virus isolations attempted, positive virus isolations, and GenBank submissions from FY2017 through Q4 

FY2021 
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 4

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

isolated among the nursery and grow/finish classes was H1N1. Among the suckling age class, H3N2 was

the predominant isolated subtype. The sow/boar class had limited testing, with one isolate of H1N2

reported. Among isolates for which the age class was unknown or not recorded, H1N1, H1N2, and H3N2 

were all equally subtyped (Table 1). After excluding specimen types that comprised less than 10 percent 

of total sample submissions, samples taken from lung tissue 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, Q4 FY2021 

Age Class (group)

Number 

of H1N1

Number 

of H1N2

Number of 

H3N1

Number 

of H3N2

Number 

of Mixed

Suckling 14 14 1 16 1

Nursery 31 27 1 12 0

Grow/Finish 29 23 0 18 2

Sow/Boar 0 1 0 0 0

Not Recorded/Unknown 6 6 0 6 0

Table 2. Number of positive accessions* tested for IAV-S by specimen type and by viral subtype, Q4 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 199 94% 119 72 1 73 6 187

Nasal or 

Nasal Swab 9 100% 3 2 0 3 0 7

Oral Fluids 0 NA 0 0 0 0 0 0

Other 

Specimens 1 0% 0 0 0 1 0 0

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

in more than one specimen type category. 

Regional surveillance data

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

former USDA administrative districts only and do not represent specific industry distributions. 

Submissions are voluntary, as is providing any identifying information beyond State of animal origin with

the submission. Therefore, regional and/or national incidence, prevalence, or other epidemiological 

measures cannot be determined from this data.
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 4

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 October 

2020 through September 2021.

Region Total number Predominant HA/NA subtypes

1 117 H3N2 (H3-Cluster IV-A / N2-2002B) (n=48)

H1N2 (H1-Delta2 / N2-1998B) (n=32)

H1N1 (H1-Gamma / N1-Classical) (n=20)

2+ 773 H1N1 (H1-Gamma / N1-Classical) (n=241)

H1N2 (H1-Delta2 / N2-1998B) (n=155)

H3N2 (H3-Cluster IV-A / N2-2002B) (n=115)

3 70 H1N1 (H1-Pandemic / N1-Pandemic) (n=16)

H3N2 (H3-2010.1 / N2-2002A) (n=11)

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

H1N1(H1-Delta1B / N2-2002A) (n=7)

4 70 H1N1 (H1-Gamma / N1-Classical) (n=18)

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

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

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

5++

All

13

1043

H1N1 (H1-Pandemic / N1-Pandemic) (n=4)

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

H1N2 (H1-Delta1A / N2-1998A) (n=2)

H1N2 (H1-Delta2 / N2-1998B) (n=2)

H3N2 (H3-2010.1 / N2-2002B) (n=2)

H1N1 (H1-Gamma / N1-Classical) (n=283)

H1N2 (H1-Delta2 / N2-1998B) (n=195)

H3N2 (H3-Cluster IV-A / N2-2002B) (n=170)

*HA/NA pairs included if they compromise over 10% from a region

+ Most diversity of all regions ++ Low participation
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 4

Summary of Regional Data from ARS

Table 3 lists the most predominant HA/NA phylo-type pairs by region from October 2020-September 2021, 

with predominant being defined as comprising at least 10% of a region’s HA/NA pairs. The total number 

column displays the number of isolates that were phylo-typed for each region from October 2020-

September 2021.

Figure 7 shows the distribution of rRT-PCR subtyped accessions across the five regions for Q4 FY2019 

through Q4 FY2021. Over the last 8 quarters, H1N2 was the predominant subtype in region 1. In regions 2, 

4, and 5 H1N1 was the most predominant. H3N2 was the predominant subtype for region 3. 

Figure 7. Distribution of rRT-PCR subtyped accessions across the five regions for Q4 FY2019 through Q4 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 201 isolates with published sequences in GenBank was characterized by 

phylogenetic analysis for the Q4 FY2021 report. This analysis provides information on the genetic diversity 

and evolutionary 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.
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 4

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

region, describing virus subtypes (Figure 8) and phylogenetic clades of H1, H3, N1 and N2 subtypes (Figures 

9-12). Regional charts depicting the various combinations of HA and NA are available 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, 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. Similarly, H3 subtype viruses are classified as Cluster IV, Cluster IVA, Cluster IV-B, Cluster IV-C, Cluster IV-D, Cluster IV-E, Cluster IV-F, or human-like. From Q1 FY2020 through

Q4 FY2021, H1-Gamma remained the predominant H1 HA gene (Figure 9) and H3-Cluster IV-A remained the 

predominant H3 HA gene (Figure 10). 

Figure 9. Temporal distribution of H1 phylogenetic clades by region for Q1 FY2020 to Q4 FY2021

Figure 8. Temporal distribution of Influenza A virus subtype by region for Q1 FY2020 to Q4 FY2021
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 4

 

National phylogenetic NA gene information

In Q4 FY2021, N1-Classical (n=55) was the most predominant N1 phylogenetic-clade (Figure 11) and was

most commonly paired with H1-gamma (n=51), H1-pandemic (n=2, and H1-Alpha (n=2). N1-Pandemic 

(n=20) was the next most common N1 clade, paired with H1-Pandemic (n=15), H3-2010.1 (n=2), H1-Alpha 

(n=1), H1-Gamma (n=1), and H1-Delta2 (n=1). The final most common N1 phylogenetic-clade was N1-LAIV 

(n=4), paired with H1-LAIV (n=3) and H1-Delta1B (n=1).

In Q4 FY2021, the most predominant N2 phylogenetic-clade was N2-2002 (n=75) followed by N2-1998 

(n=42), thenN2-LAIV (n=3) (Figure 12).

Gene constellations information

The most dominant internal gene constellations for FY2021 were TTTPPT (56%), TTTTPT (21%) and TTPPPT 

(8%). From October 2019 to July 2021, out of 583 strains with completed whole genomic sequencing that 

were analyzed, 35% were H1N1, 32% were H1N2, and 32% were H3N2, with 25 unique gene constellations 

and 49 unique HA/NA pairs. 

Figure 10. Temporal distribution of H3 phylogenetic clades by region for Q1 FY2020 to Q4 FY2021
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 4

Figure 11. Temporal distribution of N1 phylogenetic clades by region for Q1 FY2020 to Q4 FY2021

Figure12. Temporal distribution of N2 phylogenetic clades by region for Q1 FY2020 to Q4 FY2021 

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 the IAV swine surveillance program 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 Q4 FY2021, the NVSL Diagnostic Virology Laboratory provided 69 isolates to five academic institutions, 

three government entities, and three pharmaceutical requestors. NVSL received 324 isolates into the 

repository in Q4 FY2021. Table 4 reports the total number of virus isolates received into the repository 

each year from FY2014 through Q4 of FY2021. Table 5 reports the total number of isolates by subtype 

available in the repository for sharing. 
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 4

Table 4. Virus isolates received in NVSL

repository by year 

 Fiscal Year Number of isolates

FY2021 1,108

FY2020 1,074

FY2019 1,055

FY2018 994

FY2017 844

FY2016 1,046

FY2015 883

FY2014 765

 

 

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 collected from 2009-present and 

available through the NVSL repository

Subtyped isolates available 

H3N2 2,617

H3N1 24

H1N1 3,351

H1N2 3,097

Mixed 302

TOTAL 9,391
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 4

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

The following charts present the percentages of combinations of HA and NA by region based on ARS-NADC phylogenetic analyses. The results are 

reported from October 2020 through September 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 4
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 4
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 4
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 4
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2021, Quarter 4