Influenza A Virus in Swine Surveillance

Fiscal Year 2020 Quarterly Report

Surveillance Summary for First Quarter Fiscal Year 2020: October 1 to 

December 31, 2019

Report Summary1

 This report covers the first quarter (Q1) of fiscal year 2020 from October 1 to December 31, 

2019.

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

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

 In fiscal year 2020 Q1, there were 896 samples submitted for influenza A virus (IAV) surveillance 

in swine from 942 accessions. 

 H1N2 was the predominant subtype reported in USDA data in Q1 FY2020.

 Over the past 7 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 as of July 15, 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 

 

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

February 2020
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submitted represent a subset of the swine population. Submitted samples should only be collected from 

animals displaying influenza-like illness. 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 IAV-S prevalence or other epidemiologic measures in the swine population. However, the 

data may help identify trends of influenza in swine. 

When the submitter does not report relevant information, data are recorded as “unknown.” Summaries 

in this report may differ from those provided in past reports due to the ongoing addition of data from 

participating labs. Reporting months are based on the month when the sample was collected. 

A laboratory accession is generally a set of samples collected at a single premises on a single day and 

received at the laboratory. A maximum of 10 samples of any kind is allowed per accession for 

reimbursement under the USDA IAV-S system. However, no more than five of the 10 samples may be 

oral fluid for any given accession. This does not prevent additional samples from being tested at the 

owner’s expense. 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 (rRT-PCR). The 

subtype result is based on the 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 also performs whole genomic 

sequencing (WGS) on a selected subset of virus isolates received through surveillance and deposits 

those sequences into Genbank. On a quarterly basis, a phylogenetic analysis is performed; phylogenetic 

analyses are based on all successful USDA surveillance sequencing results, with sequences deposited 

into GenBank®, the public sequence database.

Program Updates

There have been recent changes to the USDA’s webpages that provide information on IAV-S and IAV-S 

surveillance. Please visit the new webpage and navigate around to find the information you may be 

seeking as well as the IAV-S quarterly reports. The new web address is:

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 viruses. The National Animal Health Laboratory 

Network (NAHLN) has several submission options to ensure unusual viruses identified by methods other 

than those approved for NAHLN testing can be submitted into the program. An updated version of the 

IAV-S NAHLN testing guidelines and instruction sheet can be found at:

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

_guidelines.pdf

and 

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: 
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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. 

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 fiscal year 2010 through fiscal year 2016, the total number of accessions and samples submitted 

increased. Changes initiated in fiscal year 2016 resulted in decreased laboratory accessions and samples,

but a higher percentage of accessions resulting in a virus isolate that can be sequenced and analyzed. In

fiscal year 2020, 942 samples have been tested from 896 accessions (Figure 1). Figure 2 shows the 

overall increasing trends in total accessions, rRT-PCR and VI positive accessions, and subtyped 

accessions.

Figure 1. Number of IAV-S laboratory accessions and samples tested in swine, fiscal year 2012 through fiscal 

year 2020 Q1.
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Figure 2. Accessions submitted, subtyped accessions, rRT-PCR positive accessions, and virus isolation positive 

accessions over time with trend lines for influenza A virus in swine, fiscal year 2011 to fiscal year 2020 Q1.

Figure 3 shows the number of subtype detections in fiscal year 2020 Q1. The total number of samples

subtyped was 380, including H1N1 (n=130), H1N2 (n=135), H3N2 (N=106) and mixed (N=17). H3N1 was 

not isolated.

Figure 3. Number of influenza A subtype detections in swine fiscal year 2020 Q1.

Figure 4 breaks down accessions by rRT-PCR subtype from fiscal year 2011 Q1 to fiscal year 2020 Q1. 

H1N1 was the predominant subtype detected in 2012, 2013, 2014 and 2018. H1N2 was detected most 

often in 2011, 2015, 2016, 2017, 2019 and 2020.
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Figure 4. Number of subtypes, fiscal year 2012 through fiscal year 2020 Q1.

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. Due to an unresolvable data processing 

coding error, samples sequenced and sent to Genbank during FY2019 Q1 appear greatly reduced in 

Figure 5. As with other fiscal years, the samples sent during that timeframe closely follow the number of 

attempted virus isolations as well as the number of positive virus isolation samples.

Figure 5. Number of influenza A virus isolations attempted, number of virus isolations that were positive, and 

the number of viruses submitted to GenBank from fiscal year 2011 to fiscal year 2020 Q1.

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

isolated among grow/finish age class was H1N1. Among nursery and suckling age classes, H1N2 was the 

predominant isolated subtype. The sow/boar class had limited testing, with four isolates of H1N2 and 
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two isolates of H3N2. Among isolates for which the age class was unknown or not recorded, both H1N1 

and H1N2 were the predominant subtype with 15 isolates each (Table 1). Excluding specimen types with 

less than 10 percent of total submissions, samples collected from lung and nasal specimens (swabs or 

wipes) were the most successful at providing a virus isolate which enables sequence submission to 

GenBank (Table 2).

Table 1. Number of positive accessions tested for influenza A virus in swine by age class and subtype fiscal year

2020, Q1.

Age class Number of accessions with 

subtype reported

Number 

of H1N1

Number 

of H1N2

Number 

of H3N1

Number 

of H3N2

Number 

of Mixed

Suckling 62 13 27 0 19 3

Nursery 160 54 63 0 37 7

Sow/Boar 6 0 4 0 2 0

Grow/finish 113 51 25 0 34 4

Unknown 42 15 15 0 13 3

Table 2. Number of positive accessions* tested for influenza A virus in swine by specimen type** and subtype fiscal 

year 2020 Q1.

Specimen 

Type

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 327 88% 122 110 0 88 8 287

Nasal 33 88% 4 16 0 8 5 26

Oral Fluid 15 80% 1 5 0 5 4 9

Other 2 100% 0 1 0 1 0 2

*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.

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

Summary of Regional Data from ARS

Table 3. Summary of predominant subtypes in each region in a 2 year window (fiscal year 2018

Q1 through fiscal year 2020 Q1).

Region Total number HA/NA subtype

1 264 Gamma H1/Classical N1

Delta2 H1/1998-N2

2010.1 H1/2002-N2

2 1,275 Gamma H1/Classical N1

2010.1 H3/2002-N2

Delta2 H1/1998-N2

3 159 Alpha H1/2002-N2

Gamma H1/Classical N1

2010.1 H3/2002-N2

4 172 2010.1 H3/2002-N2

IV-A H3/2002-N2

Gamma H1/Classical N1

5 38 Low participation

2010.1 H3/2002 N2

Pandemic H1/Pandemic N1

Alpha H1/2002-N2

Most Predominant HA/NA phylo-types overall: H1N1 (Gamma H1/Classical N1), H3N2 (2010.1 H3/2002-

N2) and H1N2 (Delta2 H1/1998-N2) 

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

2018 through Q1 fiscal year 2020. Regions 1, 3 and 5 demonstrate H1N2 as the predominant subtype 

while Region 2 and Region 4 isolated H1N1 and H3N2 most frequently, respectively. For regions 

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

Region 5 Region 3 Region 1
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Figure 7. Percentage of influenza A subtyped accessions for swine by region for fiscal year 2018 Q3 to fiscal year 

2020 Q1.

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 376 isolates with published sequences in GenBank was characterized by 

phylogenetic analysis for the Q1 fiscal year 2020 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.
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Figure 8. Temporal distribution of Influenza A virus subtype by region for Q2 fiscal year 2018 to Q1 fiscal year 

2020

Figure 8 demonstrates the four subtypes H1N1, H1N2, H3N2 and mixed subtypes 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 the H1 subtypes (Figure 9), gamma viruses are the 

predominant H1 with delta2 and alpha frequently detected.
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Figure 9. Temporal distribution of H1 phylogentic clades by region for fiscal year 2018 Q2 to fiscal year 2020 Q1.

 

Figure 10. Temporal distribution of H3 phylogentic clades by region for fiscal year 2018 Q2 to fiscal year 2020 Q1.

In Q1 fiscal year 2020, there were 45 detections of H3s (Figure 10). 2010.2 H3 was detected in Arkansas,

Iowa, Illinois, Indiana and Oklahoma paired with human N2 with on Iowa paired with 2002 N2. Cluster I 
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H3 was detected in Alabama, Iowa, Illinois, Indiana, Kansas, Minnesota, Missouri, Nebraska, South 

Dakota and Tennessee. Human-like_2010.1 H3 was the predominant H3.

National phylogenetic NA gene information 

Whole genome patterns with HA/NA pairs were reported and the dominant patterns are in descending 

order below with most frequent pattern by HA/NA pair: 

 TTTTPT: H3.2010.1/N2-02, H1.gamma/cN1, H1.delta1a/N2-02,

 TTTPPT: H1.delta2/N2-98, H1.gamma/cN1, H1.delta1b/N2-02, 

 TTPPPT: H1.gamma/cN1, H1.alpha/N2-02, H1.delta1a/N2-02. 

Leading vaccine constellation is TVVTPT, with other patterns detected. Both the N1 and N2 subtypes are 

found in circulating swine viruses. Classical N1 continued to be the dominant cluster at 82.5 percent; 

and the 2002-lineage N2 represents 65 percent of N2 collections. 

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 the first quarter of fiscal year 2020, the NVSL Diagnostic Virology Laboratory provided 33 isolates to 

two government, two academic, two pharmaceutical, and two international institutions. NVSL received

328 isolates into the repository (Table 4). Table 5 reports the total number of isolates available in the 

repository by subtype for sharing. 

Table 4. Virus isolates received in repository. 

Virus isolates in the repository

2020 277

2019 1,055

2018 994

2017 844

2016 1,046

2015 883

2014 765

TOTAL TO DATE 5,864

 

 
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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 1,932

H3N1 16

H1N1 2,563

H1N2 2,396

Mixed 302

TOTAL 7,209
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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 January 2018 to December 2019. 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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Region 1. Total HA & NA combinations –264
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Region 2. Total HA & NA combinations –1,278
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Region 3. Total HA & NA combinations - 159
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Region 4. Total HA & NA combinations – 172
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Region 5. Total HA & NA combinations – 38