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Influenza A Virus in Swine Surveillance Information

Influenza A virus in swine (IAV-S) can result in respiratory disease in swine that can be caused by multiple subtypes of type A influenza virus. IAV-S is not a reportable or regulated animal disease in the United States. The virus is endemic in swine populations in North and South America, Asia, and Europe. The influenza virus genome consists of eight distinct gene segments and the subtypes of viruses are generally described by the characterization of two gene segments, the hemagglutinun (HA) gene and neuraminidase (NA) gene.

Classic IAV-S infection was caused by the H1N1 subtype and remained relatively unchanged while circulating in U.S. swine populations for over 75 years. Since 1998, IAV-S infections in the United States have evolved from a seasonal disease caused by a single, relatively stable H1N1 genotype to an endemic, year-round respiratory disease caused by multiple genetically unstable IAV-S subtypes (H1N1, H1N2, and H3N2). Advances in molecular diagnostic capabilities have allowed diagnosticians and researchers to establish that recently characterized IAV-S  strains have recombined from gene segments originating in multiple species (swine, humans, and avian), illustrating the shared nature of influenza virus lineages in poultry, swine, and humans.

The USDA, in cooperation with State and industry, conducts voluntary surveillance for IAV-S in the U.S. This surveillance is not conducted to define prevalence - the goal is to identify viruses that may be circulating in swine, and gain knowledge to contribute to improved animal health diagnostics and vaccines. The USDA has identified spillover events where human influenza viruses have been passed to pigs and also where influenza virus’s normally circulating in pigs have spilled over into humans. Influenza viruses that normally circulate in pigs are called “variant” viruses when they are found in people.

USDA's IAV-S Surveillance Program has tested over 120,000 samples from 33,000 swine diagnostic lab submissions collected from October 1, 2010 through December 31, 2016. Over that time period, over 10,000 case submissions have been identified as positive for Influenza A infection and over 5,000 virus isolates have been collected. Quarterly surveillance reports have been posted to the Swine Health Monitoring Surveillance website since fiscal year 2015. These reports provide a breakdown of current circulating viruses in swine found through the voluntary surveillance and a brief phylogenic analysis overview of USDA surveillance data provided by USDA’s Agriculture Research Service, National Animal Disease Center in Ames, IA. . The USDA IAV-S Surveillance Program continues to collect and test samples to monitor for the type and distribution of all influenza viruses in swine. Virus isolates collected through the program are made available upon request from the National Veterinary Services Laboratories.

Appendix A:
National Swine Influenza Virus Surveillance Plan

Appendix B: VS District Offices Points of Contact and the State Animal Health Official Directory

Appendix C: Testing Guidelines, Forms, Submission Instructions

Influenza A in Swine Testing Algorithm Instructions 

Appendix D: Participating NAHLN labs

Appendix E: Notification plan for novel influenza A virus in swine laboratory finding

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