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Initiated in 2009, the <jats:styled-content style=\"fixed-case\">USDA<\/jats:styled-content> passively surveils <jats:styled-content style=\"fixed-case\">IAV<\/jats:styled-content> in U.S. swine, with a focus on subtyping clinical respiratory submissions, sequencing the hemagglutinin (<jats:styled-content style=\"fixed-case\">HA<\/jats:styled-content>) and neuraminidase (<jats:styled-content style=\"fixed-case\">NA<\/jats:styled-content>) genes at a minimum, and sharing these data publicly.<\/jats:p><\/jats:sec><jats:sec><jats:title>Objectives<\/jats:title><jats:p>In this study, our goal was to quantify and describe regional and national patterns in the genetic diversity and evolution of <jats:styled-content style=\"fixed-case\">IAV<\/jats:styled-content> in U.S. swine from 2010 to 2016.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>A comprehensive phylogenetic and epidemiological analysis of publicly available <jats:styled-content style=\"fixed-case\">HA<\/jats:styled-content> and <jats:styled-content style=\"fixed-case\">NA<\/jats:styled-content> genes generated by the <jats:styled-content style=\"fixed-case\">USDA<\/jats:styled-content> surveillance system collected from January 2010 to December 2016 was conducted.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The dominant subtypes and genetic clades detected during the study period were H1N1 (H1\u2010\u03b3\/1A.3.3.3, N1\u2010classical, 29%), H1N2 (H1\u2010\u03b41\/1B.2.2, N2\u20102002, 27%), and H3N2 (H3\u2010<jats:styled-content style=\"fixed-case\">IV<\/jats:styled-content>\u2010A, N2\u20102002, 15%), but many other minor clades were also maintained. Year\u2010round circulation was observed, with a primary epidemic peak in October\u2010November and a secondary epidemic peak in March\u2010April. Partitioning these data into 5 spatial zones revealed that genetic diversity varied regionally and was not correlated with aggregated national patterns of <jats:styled-content style=\"fixed-case\">HA<\/jats:styled-content>\/<jats:styled-content style=\"fixed-case\">NA<\/jats:styled-content> diversity.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>These data suggest that vaccine composition and control efforts should consider <jats:styled-content style=\"fixed-case\">IAV<\/jats:styled-content> diversity within swine production regions in addition to aggregated national patterns.<\/jats:p><\/jats:sec>","DOI":"10.1111\/irv.12559","type":"journal-article","created":{"date-parts":[[2018,4,6]],"date-time":"2018-04-06T22:29:28Z","timestamp":1523053768000},"page":"262-273","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":84,"title":["Regional patterns of genetic diversity in swine influenza A viruses in the United States from 2010 to 2016"],"prefix":"10.1111","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7088-5535","authenticated-orcid":false,"given":"Rasna R.","family":"Walia","sequence":"first","affiliation":[{"name":"Virus and Prion Research Unit National Animal Disease Center USDA\u2010ARS  Ames IA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3138-5535","authenticated-orcid":false,"given":"Tavis K.","family":"Anderson","sequence":"additional","affiliation":[{"name":"Virus and Prion Research Unit National Animal Disease Center USDA\u2010ARS  Ames IA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4953-7285","authenticated-orcid":false,"given":"Amy L.","family":"Vincent","sequence":"additional","affiliation":[{"name":"Virus and Prion Research Unit National Animal Disease Center USDA\u2010ARS  Ames IA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2019,2,13]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1159\/000157337"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/0042-6822(85)90131-X"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/0042-6822(89)90353-X"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molimm.2013.02.008"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.3390\/vaccines3010022"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetmic.2016.11.026"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1863-2378.2008.01217.x"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/0042-6822(79)90540-3"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.40.3.1073-1079.2002"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.38.6.2453-2456.2000"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0065-3527(08)00403-X"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.73.10.8851-8856.1999"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11262-009-0386-6"},{"key":"e_1_2_7_15_1","doi-asserted-by":"publisher","DOI":"10.3201\/1709.110338"},{"key":"e_1_2_7_16_1","doi-asserted-by":"publisher","DOI":"10.3201\/eid1906.121637"},{"key":"e_1_2_7_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetmic.2012.02.014"},{"key":"e_1_2_7_18_1","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00459-15"},{"key":"e_1_2_7_19_1","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01675-15"},{"key":"e_1_2_7_20_1","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00275-16"},{"key":"e_1_2_7_21_1","unstructured":"BrodersenR.President's message: One million pigs on the road every day [Internet]. 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