Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2020, Quarter 3

Influenza A Virus in Swine Surveillance

Fiscal Year 2020 Quarterly Report

Surveillance Summary for Third Quarter Fiscal Year 2020: April 1 to 

June 30, 2020

Report Summary1

• This report covers the third quarter (Q3) of fiscal year (FY) 2020 from April 1 to June 30, 2020.

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

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

• Through Q3 of FY2020, there were 2,270 samples submitted for influenza A virus (IAV)

surveillance in swine from 2,137 accessions. 

• H1N1was the predominant subtype reported in USDA data in the first 3 quarters of FY2020.

• Over the past 8 quarters, H1N2 was the main subtype in Regions 1, 3 and 5 while Region 2 and 

Region 4 most frequently isolated H1N1 and H3N2, respectively. For regions recorded as 

“unknown,” H1N2 and H3N2 were the most frequent subtypes.

• 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 August 19, 2020, 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 determine 

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

September 

2020
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2020, Quarter 3

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 2020, 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 FY2016 resulted in decreased laboratory accessions and samples, but a higher 

percentage of accessions resulting in a virus isolate that can be sequenced and analyzed. Through the 

end of Q3 FY2020, 2,270 samples have been tested from 2,137 accessions (Figure 1). 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 FY2011 through Q3 FY2020
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2020, 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, FY2011 through Q3 FY2020

Figure 3 shows the number of subtype detections in Q3 FY2020. The total number of samples subtyped 

was 257, including H1N1 (n=104), H1N2 (n=68), H3N2 (N=75), H3N1 (n=0), and mixed (N=10).

Figure 3. Number of IAV-S subtype detections in Q3 FY2020
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2020, Quarter 3

Figure 4 breaks down accessions by rRT-PCR subtype from FY2011 to Q3 FY2020. H1N1 was the 

predominant subtype detected in 2012, 2013, 2014, 2018, and so far in 2020. H1N2 was detected most 

often in 2011, 2015, 2016, 2017, and 2019. 

Figure 4. Breakdown of accessions by subtype rRT-PCR from FY2011 through Q3 FY2020

Figure 5 displays the number of times VI was conducted 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 FY2011 through Q3 

FY2020
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2020, Quarter 3

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

isolated among the suckling age class were H1N1 and H1N2 and among the nursery age class it was 

H1N2. Among the grow-finish age class, H1N1 was the predominant isolated subtype. The sow/boar

class had limited testing, with one isolate of H1N1 reported. Among isolates for which the age class was 

unknown or not recorded, H1N1 was the predominant subtype (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 FY2020

Table 2. Number of positive accessions* tested for IAV-S by specimen type** and by viral subtype, Q3 FY2020

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

in more than one specimen type category. 

** Other includes specimen types recorded as swab, mixed tissue, or unknown.
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2020, 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

Summary of Regional Data from ARS

Table 3. Summary of predominant subtypes by region in a 1-year window from July 2019- June 2020

Region Total number HA/NA subtype

1 128 Delta2 H1/1998-N2

Gamma H1/Classical N1 

Alpha H1/1998 N2

2 762 Most diversity of all regions

Gamma H1/Classical N1

Delta2 H1/1998-N2

Cluster IV-A H3/2002-N2

3 57 2010.1 H3/2002 N2

Alpha H1/2002-N2

Delta1a H1 / 2002-N2

Pandemic H1 / Pandemic N2

4 68 2010.1 H3/2002 N2 

Gamma H1/Classical N1 

Delta1b H1 / 2002 N2

Cluster IV-A H3 / 2002-N2

5 31 Low participation

Alpha H1/2002 N2

2010.1 H3/2002 N2

Delta1a H1/1998 N2

Most Predominant HA/NA phylotypes overall: 

H1N1 (Gamma H1/Classical N1) H3N2 (Cluster IV-A H3/2002-N2)

H1N2 (Delta2 H1/1998-N2) 

Figure 7 shows the distribution of rRT-PCR subtyped accessions among the five regions for Q3 FY2018 

through Q3 FY2020. Regions 1, 3 and 5 demonstrate H1N2 as the predominant subtype while Region 2 and 
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2020, Quarter 3

Region 4 isolated H1N1 and H3N2 most frequently, respectively. For regions recorded as “unknown,” H1N2

and H3N2 were equally the most frequent subtypes.

Figure 7. Distribution of rRT-PCR subtyped accessions among the five regions Q3 FY2018 through Q3 FY2020

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 237 isolates with published sequences in GenBank was characterized by 

phylogenetic analysis for the Q3 FY2020 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.

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 and H3 

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

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 2020, Quarter 3

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 FY2020, the H1 subtypes gamma viruses are the predominant H1, 

with a total of 72 detected, with delta2 and alpha also frequently being detected. Gamma2-beta-like LAIV 

paired with: MN99 continued to be detected at low levels with 23 detections, pdm had 2 detections, 2002 

had 4, and TX98 had 7 detections (Figure 9).

Figure 9. Temporal distribution of H1 phylogentic clades by region for Q4 FY2018 to Q3 FY2020

Figure 8. Temporal distribution of Influenza A virus subtype by region for Q4 FY2018 to Q3 FY2020
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2020, Quarter 3

In Q3 FY2020, there were 76 detections of H3s and Cluster IV-A was the predominant H3 with 40 detections

(Figure 10). Cluster I H3 LAIV paired with N2-2016 was detected once and paired with N2-TX98 had 22 

detections.

National phylogenetic NA gene information 

Whole genome patterns with HA/NA pairs with internal gene lineages were reported and the dominant 

patterns are in descending order below with most frequent pattern by HA/NA pair: 

• TTTPPT (n=67) - H1N2 (delta2/1998), H1N1 (gamma/classical), H3N2 (IV-A/2002)

• TTTTPT (n=62) - H3N2 (2010.1/2002), H1N1 (gamma/classical), H1N2 (delta1a/2002)

• TTPPPT (n=21) - H1N1 (gamma/classical), H1N2 (alpha/2002), H3N2 (IV-B2/2002)

Leading vaccine constellations are TVVTPT and VVVPPT, both being reported 4 times.

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 FY2020, the NVSL Diagnostic Virology Laboratory provided 11 isolates to one academic institution. 

NVSL received 329 isolates into the repository. Table 4 reports the total number of virus isolates received 

into the repository each year from FY2014 through Q3 of FY2020. Table 5 reports the total number of 

isolates available in the repository by subtype for sharing. 

Figure 10. Temporal distribution of H3 phylogentic clades by region for Q4 FY2018 to Q3 FY2020
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2020, Quarter 3

Table 4. Virus isolates received in repository 

Virus isolates in the repository

2020 929

2019 1,055

2018 994

2017 844

2016 1,046

2015 883

2014 765

TOTAL TO DATE 6,516

 

 

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

Subtyped isolates available through 

repository

H3N2 2,216

H3N1 18

H1N1 2,903

H1N2 2,699

Mixed 302

TOTAL 8,138
Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2020, 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 2019 through June 2020. 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. 
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Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2020, Quarter 3
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Influenza A Virus in Swine Surveillance Quarterly Report for Fiscal Year 2020, Quarter 3