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Title:   Author  item
                                            RAJAO, DANIELA - Non ARS Employeeitem
                                            WALIA, RASNA - Orise Fellowitem
                                            Campbell, Brianitem
                                            GAUGER, PHILLIP - Iowa State Universityitem
                                            JANAS-MARTINDALE, ALICIA - Animal And Plant Health Inspection Service (APHIS)item
                                            KILLIAN, MARY LEA - Animal And Plant Health Inspection Service (APHIS)item
                                            Baker, Amy
  Submitted to: International Pig Veterinary Society (IPVS)
                                    Publication Type: Abstract Only
                                    Publication Acceptance Date: 3/1/2016
                                    Publication  Date: N/A
                                    Citation: N/AInterpretive Summary:
                                Technical Abstract: Introduction
Influenza A virus (IAV) is a significant pathogen to the swine industry. Since its introduction in 2009, the H1N1 pandemic virus (H1N1pdm09) has been repeatedly transmitted from humans to swine, but onward transmission in U.S. swine was mostly restricted to its internal genes. Reassortment between the H1N1pdm09 and endemic swine viruses resulted in substantial evolution of IAV and led to the circulation of different genomic constellations in pigs. We conducted phylogenetic analyses of IAV circulating in swine from 2009 to 2014 in the U.S. and compared the pathogenesis and transmission of six representative genotypes in pigs.

Materials and Methods
Whole genome phylogenetic analyses were performed on 496 H3N2 IAV isolated from U.S. swine from 2009 to 2014. Isolates were classified into genotypes when the eight gene segments phylogenies resulted in a unique genome constellation.
Six swine H3N2 genotypes were selected to be tested in vivo: two with HA of cluster IV-A, two IV-B, and two IV-F with varied internal gene constellations. Pigs were challenged with each assigned virus and indirect contact pigs were placed at 2 days post infection (dpi) to evaluate transmission. Nasal swabs were collected from primary and indirect contact pigs. At 5 dpi, macroscopic and microscopic lung lesions were evaluated in challenged pigs, and bronchoalveolar lavage fluid was collected.

Results
At least 54 different swine H3N2 genotypes were identified in the U.S., with the most common genotype (32.2%) containing a cluster IV-A HA gene, 2002-lineage NA gene, H1N1pdm09 M gene, and remaining genes of triple reassortant internal gene (TRIG) origin. After 2011, there was a rapid increase in predominance of the H1N1pdm09 M gene in all genome constellations. More than 65% of the isolates had at least 1 H1N1pdm09 internal gene.
Although the six genotypes tested efficiently infected pigs with similar lung viral titers, they resulted in different degrees of pathology (mild to moderate lung lesions). Nasal viral shedding also differed among viruses, but all were transmitted to indirect contacts. Differences in pathology, lung replication and viral shedding did not seem to correlate with individual genes.

Conclusion
These results highlight the great diversity of H3N2 genotypes circulating in U.S. swine after 2009, and 6 common genotypes were shown to be fully virulent and transmissible in swine. This continued evolution could have important implications to the control of this disease by the swine industry and to the risk of zoonotic infection in humans due to incorporation of the H1N1pdm09 genes.


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