Influenza A Virus in Swine Surveillance

Fiscal Year 2018 Quarterly Report

Surveillance Summary for Second Quarter: Jan. 1 – Mar. 31, 2018

Report Summary1

 This report covers the second quarter (Q2) of FY 2018, from Jan. 1 – Mar. 31, 2018.

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

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

 In FY 2018 Q1-Q2, a total of 7,284 samples were submitted for influenza A virus in swine (IAV-S)

surveillance from 2,448 accessions. 

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

 Over the past 8 quarters, H1N2 predominated in Regions 1, 3, 4 and 5. H1N1 predominated in 

Region 2. When regions are recorded as “unknown,” there was an even mix between H1N2 and 

H1N1.

 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 2, 2018, 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 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 

USDA-APHIS website provides general information about the IAV-S surveillance program

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

 

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

July 2018
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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 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 in influenza in swine. 

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

in this report may differ from those 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 considered 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 matrix real-time reverse transcriptase polymerase chain 

reaction (rRT-PCR). The subtype is based on the rRT-PCR- subtyping assays and sequencing if the sample 

is sequenced. Virus isolation (VI) and sequencing are only attempted on rRT-PCR positives meeting 

criteria listed in the testing algorithm posted on the web. 

On a monthly basis, USDA performs whole genomic sequencing on a selected subset of isolates received

through surveillance. 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.

IAV-S Surveillance Objectives

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

surveillance system for IAV-S 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. 
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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 HA and NA sequences 

that are generated at the NAHLN laboratories and posted into GenBank®. Each month selected viruses

undergo whole genomic sequencing by NVSL. Phylogenic analysis of the genetic sequences is provided 

through an interagency agreement with the USDA-ARS National Animal Disease Center (NADC). 

National Surveillance Data Summary

From FY 2011 through FY 2016, the total number of accessions and samples submitted rose over time.

Changes initiated in FY 2016 have resulted in decreased laboratory accessions and samples, but a higher 

percentage of accessions that yield a virus that can be sequenced and analyzed. For FY 2018’s second

quarter, 7,284 samples have been tested from 2,448 accessions (Figure 1). Figure 2 shows the overall 

trends in total accessions, PCR-positive accessions, subtyped accessions, and VI positive accessions. 

Figure 1. Number of IAV-S laboratory accessions and samples tested in swine, FY 2011 through FY 2018 Q2
Figure 2. Accessions submitted, subtyped accessions, positive accessions, and VI positive accessions over time with trend lines, FY 2011 through FY 2018 Q2
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Figure 3 shows the number of subtype detections in FY 2018 Q2. The total number of samples subtyped was 253, including 110 H1N1, 73 H1N2, 53 

H3N2, 1 H3N1, and 16 mixed.

Figure 3. Number of subtype detections in FY 2018 Q2
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Figure 4 breaks down accessions by rRT-PCR subtype from FY 2011 to FY 2018 Q2. H1N1 remains the major subtype over the course of the 

surveillance; however, H1N2 and H3N2 detections have increased substantially since 2012 and H1N1 was the most predominant subtype in FY 

2018 (to date, July 2, 2018). 

Figure 4. Number of subtypes, FY 2011 through FY 2018 Q2
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Figure 5 displays the number of VIs attempted in blue, the number of those attempts that were positive in red, and the number of positive VIs that 

are 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 FY 2014 through FY 2018 Q2

0

100

200

300

400

500

600

Number of virus isolations attempted

Number of virus isolation positive samples

Number of samples sequenced and sent to GenBank
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When accessions were evaluated by age-class for the second quarter, the following observations were noted. H1N2 was the most common 

subtype among suckling pigs. H1N1 was the most common subtype among nursery and grower/ finisher pigs. Sow/boar had limited testing, with 

only four accessions of which one was H1N1, one was H1N2, and two were H3N2. Among accessions 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-S by age class and by viral subtype, Q2 FY 2018

Table 2. Number of positive accessions tested for IAV-S by specimen type and by viral subtype, Q2 FY 2018.

*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.
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Regional surveillance data

In this section, we present data in five different regions (Figure 6) to parse the analysis across regions. 

These regions are based on current USDA administrative districts for simplicity; these divisions 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 4. Summary of predominant subtypes in each region for FY 2016 Q3 through FY 2018 Q2

Most Predominant HA/NA phylo-types overall:

H1N1 (Gamma H1/Classical N1) 

H1N2 (Delta1a H1/2002-N2) 

H3N2 (hu-like_2010.1 H3/2002-N2) 

Region 1 (Total HA/NA: 274)

Gamma H1/Classical N1

Delta2 H1/1998-N2

Alpha H1/2002-N2

Region 2 (Total HA/NA: 1,146)

Most diversity of all regions

Gamma H1/Classical N1

Delta1a H1/2002-N2

Hu-like_2010.1 H3/2002-N2

Region 3 (Total HA/NA: 137)

Delta1a H1/2002-N2

Gamma H1/Classical N1

Hu-like_2010.1 H3/2002-N2

Region 4 (Total HA/NA: 159)

Delta1b H1/2002-N2

IV-A H3/2002-N2

Gamma H1/Classical N1

Region 5 (Total HA/NA: 11)

Delta 1b H1/2002-N2

Hu-like_2010.1 H3/2002 N1

Delta1a H1/1998-N2

Figure 7 shows the distribution of rRT-PCR subtyped accessions among the five regions for Q2 FY 2016

through Q2 FY 2018. Regions 1, 3, 4, and 5 demonstrate H1N2 as the predominant subtype. Region 2 

demonstrates H1N1 as the predominant subtype. For regions recorded as “unknown,” there was an 

even mix between H1N2 and H1N1.

Region 1

Region 2

Region 3

Region 5

Region 5 Region 3

Region 4
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Figure 7. Percentage of subtyped accessions by region for FY 2016 Q2 through FY2018 Q2

Regional phylogenetic analysis

Phylogenetic analysis of sequences from the IAV-S surveillance system

Phylogenetic analysis is conducted on gene sequences of the influenza A virus in swine to further 

examine the genetic changes that occur in HA, NA, and M genes, when available, of this rapidly changing 

virus. Through collaboration with ARS, a dataset2 of 473 isolates with published sequences in GenBank®

was characterized by phylogenetic analysis for the Q2 FY 2018 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 bar charts parse the data into an approximate 2-year window by quarters and subtypes 

for each region, followed by charts further parsing the H1 and H3 subtypes into phylogenetic clades.

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

 

2

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. Virus type by region 2-year summary Q3 FY 2016 to Q2 FY 2018

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 (see Figure 9), there continued to be 

detections of alpha with two aa deletions (n=10). Delta 1a, delta 2, and gamma viruses are the 

predominant H1. 
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Figure 9. H1 phylo-cluster by region – 2-year summary Q3 FY 2016 to Q2 FY 2018

 
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Figure 10. H3 phylo-cluster by region, 2-year summary Q3 FY 2016 to Q2 FY 2018

In Q2 FY 2018, there were 60 H3s. Human-like_2010.2 H3 was detected in Illinois (North Carolina, 

Oklahoma, Indiana, and Illinois). Cluster I H3 was detected in Iowa, paired with 1998N2. Humanlike_2010.1 H3 is the predominant H3.

National phylogenetic NA gene information 

Both the N1 and N2 subtypes are found in circulating swine viruses. Classical N1 continued to be the 

dominant cluster. The 2002-lineage N2 represents 82 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-S 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. 
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The USDA’s National Veterinary Services Laboratories (NVSL) in Ames, IA, receives virus isolates acquired 

through USDA’s IAV-S surveillance and deposits the isolates into the IAV-S virus repository. NAHLN 

testing labs post the genomic sequences from the isolates into GenBank®, a publically accessible 

database maintained by the National Institutes for Health. USDA swine surveillance influenza A virus 

isolates can be identified in GenBank® by their eight-digit barcode designations in the virus name, e.g. 

A/swine/NY/A01104005/2011(H3N2). The information in GenBank® will usually list “USDA Swine 

Surveillance” or similar in the Consortium field. The majority of available isolates will have H and N 

sequenced, but some will also have full genome sequencing completed, including the M gene. The 

repository contains over 3,000 viruses. NVSL makes these viruses available to the public upon request. 

Instructions for repository IAV-S isolate requests can be downloaded from here: 

https://www.aphis.usda.gov/animal_health/lab_info_services/downloads/OrderingIAVSRepositoryIsolates.pdf

In the second quarter of FY 2018, the NVSL Diagnostic Virology Laboratory provided 64 isolates to five

institutions: one governmental, two pharmaceutical, and two international (government). NVSL

received 274 isolates into the repository in Q2 for a total of 554 in FY 2018 YTD (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

2018 554

2017 844

2016 1,046

2015 883

2014 765

TOTAL TO DATE 3,818

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 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. 

Table 5. Total number of subtyped 

isolates available through repository

Subtyped isolates available through 

repository

H3N2 1,545

H3N1 16

H1N1 2,027

H1N2 1,828

Mixed 298

TOTAL 5,714
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Conclusion

The IAV-S voluntary surveillance system continues to provide insight into the genetic makeup of 

circulating influenza 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. 
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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 April 2016 to 

March 2018. These “heat maps” represent the percentage of combinations by using a color gradient; a 

deeper gradient 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 percentage 

of occurrence of that particular combination. 

Total HA & NA combinations – 1,721
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Region 1. Total HA & NA combinations – 276
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Region 2. Total HA & NA combinations – 1,136
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Region 3. Total HA & NA combinations – 138
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Region 4. Total HA & NA combinations – 154
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Region 5. Total HA & NA combinations – 11