Influenza A Virus in Swine Surveillance

Fiscal Year 2019 Quarterly Report

Surveillance Summary for Third Quarter FY 2019: April 1 - June 30, 2019 

Report Summary1

 This report covers the third quarter (Q3) of FY 2019, from April 1 - June 30, 2019.

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

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

 In FY 2019 Q1-Q3, there were 3,227 samples submitted for influenza A virus (IAV) surveillance in 

swine from 2,128 accessions. 

 H1N1 continues to be the predominant subtype reported in USDA data.

 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 was also the most frequent subtype (see map in regional section).

 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 August 27, 2019, 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. Due to its voluntary nature, this surveillance system does not 

 

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

August 2019
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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 

National Animal Health Laboratory Network (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 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 the public sequence database GenBank®.

Program Updates

USDA’s website provides information on IAV-S and IAV-S surveillance. The IAV-S quarterly reports are 

also posted there. Please visit the webpage 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 viruses. The 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 in detail the 

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

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

influenza virus ecology; 
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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 FY 2010 through FY 2016, the total number of accessions and samples submitted increased.

Changes initiated in FY 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 FY 2019’s 

third quarter, 3,227 samples have been tested from 2,128 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, FY 2010 through FY 2019 Q3
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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 2019 Q3.

Figure 3 shows the number of subtype detections in fiscal year 2019 Q3. The total number of samples subtyped 

was 319, including H1N1 (n=123), H1N2 (n=107), H3N2 (N=83) and mixed (N=6). H3N1 was not isolated.

Figure 3. Number of influenza A subtype detections in swine fiscal year 2019 quarter 3

Figure 4 breaks down accessions by rRT-PCR subtype from FY 2010 Q1 to FY 2019 Q3. H1N1 was the 

predominant subtype detected in 2010, 2012, 2013, 2018 and 2019. H1N2 was detected most often in 

2011, 2015, 2016, and 2017 while detection of H3N2 subtype was the highest in 2014. 
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Figure 4. Number of subtypes, fiscal year 2010 through fiscal year 2019 Q3 to date

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 2015 to fiscal year 2019 Q3
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Laboratory accessions were evaluated by age-class for the third quarter. The most common subtype 

isolated among the nursery class was H1N2. Among suckling age class, H1N2 was also the predominant

isolated subtype. The grow/finish class had H1N1 as the predominant subtype. The sow/boar class had 

limited testing, with only one isolate of H1N1 and one isolate of H1N2. Among isolates for which the age 

class was unknown or not recorded, H1N1 was the predominant subtype (Table 1). Nasal specimens 

(swab or wipes) were the most successful at providing positive virus isolation and submission to 

GenBank (Table 2).

Table 1. Number of positive accessions tested for IAV in swine by age class and subtype fiscal year 2019, Q3

Age class No. of accessions with 

subtype reported

No. of 

H1N1

No. of 

H1N2

No. of 

H3N1

No. of 

H3N2

No. of 

Mixed

Suckling 66 21 28 0 15 2

Nursery 108 33 42 0 29 4

Sow/boar 2 1 1 0 0 0

Grow/finish 59 28 9 0 21 0

Unknown 37 8 19 0 8 2

Table 2. Number of positive accessions* tested for IAV in swine by specimen type** and subtype fiscal year 2019,

Q3

Specimen 

Type

No. of 

accessions 

with 

subtype 

reported

Percent of 

subtyped 

accessions with 

positive virus 

isolation

No. of 

H1N1

No. of 

H1N2

No. of 

H3N1

No. of 

H3N2

No. of 

Mixed

No. of 

samples 

sequenced 

and sent 

to 

GenBank

Lung 219 93% 86 63 0 64 5 201

Nasal 42 95% 5 28 0 7 2 39

Oral fluid 10 60% 0 7 0 2 1 7

Other 2 50% 0 2 0 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. 

** 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 current 

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 2-year window (fiscal year 2017

Q4 through fiscal year 2019, Q3)

Region Total number HA/NA subtype

1 271 Gamma H1/Classical N1

Delta2 H1/1998-N2

2010.1 H1/2002-N2

2 1,315 Gamma H1/Classical N1

2010.1 H3/2002-N2

Delta2 H1/1998-N2

3 181 Alpha H1/2002-N2

Gamma H1/Classical N1

2010.1 H3/2002-N2

4 189 Delta1b H1/2002-N2

IV-A H3/2002-N2

Gamma H1/Classical N1

5 30 Low participation

2010.1 H3/2002 N2

Pandemic H1/Pandemic N1

Delta 1a H1/1998-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 Q1 FY 2018

through Q3 FY 2019. 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 was also the most frequent subtype.

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 Q1 to fiscal year

2019 Q3

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 514 isolates with published sequences in GenBank was characterized by 

phylogenetic analysis for the Q3 FY 2019 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 IAV subtype by region for fiscal year 2017 Q4 to fiscal year 2019 Q3 

Figure 8 demonstrates the four subtypes H1N1, H1N2, H3N1, 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), there continued to be 

detections of alpha with two aa deletions. Delta 1a, delta 2, and gamma viruses are the predominant H1. 
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Figure 9. Temporal distribution of H1 phylogentic clades by region for fiscal year 2017 Q4 to fiscal year 2019 Q3

 

Figure 10. Temporal distribution of H3 phylogentic clades by region for fiscal year 2017 Q4 to fiscal year 2019 Q3

In Q3 FY 2019, there were 70 detections of H3s (Figure 10). 2010.2 H3 was detected in Arkansas, Iowa, 

Illinois, Indiana, and Oklahoma paired with human N2. Cluster I H3 was detected in Alabama, Iowa, 
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Illinois, Indiana, Minnesota, 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. 

Dominant patterns 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 (1.9% 2017-19), 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 

83.5 percent; and the 2002-lineage N2 represents 71 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 third quarter of FY 2019, the NVSL Diagnostic Virology Laboratory provided 29 isolates to three

government, 20 academic, four pharmaceutical, three government 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

2019 905

2018 994

2017 844

2016 1,046

2015 883

2014 765

TOTAL TO DATE 5,437

 

 
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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 1,891

H3N1 16

H1N1 2,533

H1N2 2,317

Mixed 302

TOTAL 7,059
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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 July 2016 to 

June 2018. 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 –271
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Region 1. Total HA & NA combinations –271
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Region 2. Total HA & NA combinations –1315
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Region 3. Total HA & NA combinations - 181
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Region 4. Total HA & NA combinations – 189
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Region 5. Total HA & NA combinations –30