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USDA Comments on Recent H3N2 Reassortant in Pennsylvania

All state public health laboratories have the capacity to test respiratory specimens for influenza viruses with sensitive and specific assays that can detect human and non-human influenza A viruses. They also have the capacity to subtype currently circulating human influenza A H1, H3, and avian H5 (Asian lineage) viruses (http://www.cdc.gov/osels/ph_surveillance/nndss/casedef/novel_influenzaA.htm). If the virus is an un-subtypable influenza A or inconclusive using those tests, it is forwarded to CDC for testing/confirmation.

CDC laboratory confirmation of these sporadic human infections with novel influenza A viruses, including swine-origin influenza virus infections, results in prompt CDC and United States Department of Agriculture (USDA) staff notifications per established algorithms. This is followed by discussions and close joint investigation collaboration between CDC, USDA, and state and local public and animal health officials to ascertain whether these viruses are transmitted among humans and to limit further exposure of humans to infected animals, if infected animals are identified.

In this case, upon isolation and sequencing, the virus was found to be a "swine origin" H3N2 virus with the M gene from reassortment with pH1N1. This led epidemiologists to ask questions about swine contact among the children, which in turn led back to county fair in PA where swine were present - thus the Pennsylvania Department of Agriculture became involved. The USDA coordinates a national swine influenza virus (SIV) surveillance program (described at http://www.aphis.usda.gov/animal_health/animal_dis_spec/swine/siv_surv_manual.shtml ) to develop a better understanding of the epidemiology and ecology of SIV in the US swine population. The voluntary surveillance system samples swine from any of these 3 categories:

  1. Case-compatible swine accessions submitted to veterinary diagnostic laboratories. This surveillance will cover on-farm swine populations exhibiting ILI;
  2. Surveillance of groups of swine exhibiting ILI at first points of concentration or commingling events such as auctions, markets, fairs, or other swine exhibition events; and
  3. Surveillance of swine populations epidemiologically linked to a confirmed isolation of SIV in a human. This stream covers swine that are linked with a human SIV infection and that is where the swine surveillance program began with these PA findings.

As noted in the MMWR, analysis of data submitted to GenBank via the USDA SIV Surveillance Program subsequent to this case identified two additional influenza A (H3N2) isolates from swine containing the M gene from the 2009 influenza A (H1N1) virus.