title: Co-infection of influenza A viruses of swine contributes to effective shuffling of gene segments in a naturally reared pig.
abstract: Following the 2009 H1N1 pandemic, surveillance activities have been accelerated globally to monitor the emergence of novel reassortant viruses. However, the mechanism by which influenza A viruses of swine (IAV-S) acquire novel gene constellations through reassortment events in natural settings remains poorly understood. To explore the mechanism, we collected 785 nasal swabs from pigs in a farm in Thailand from 2011 to 2014. H3N2, H3N1, H1N1 and H1N2 IAVs-S were isolated from a single co-infected sample by plaque purification and showed a high degree of diversity of the genome. In particular, the H1N1 isolates, possessing a novel gene constellation previously unreported in Thailand, exhibited greater variation in internal genes than H3N2 IAVs-S. A pair of isolates, designated H3N2-B and H1N1-D, was determined to have been initially introduced to the farm. These results demonstrate that numerous IAVs-S with various gene constellations can be created in a single co-infected pig via reassortment.
authors.affiliation: Influenza and Prion Disease Research Center, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0856, Ibaraki, Japan; Thailand-Japan Zoonotic Diseases Collaboration Center (ZDCC), Kasetklang, Chatuchak, Bangkok 10900, Thailand.
authors.forename: Haruka
authors.initials: H
authors.lastname: Abe
authors.affiliation: Influenza and Prion Disease Research Center, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0856, Ibaraki, Japan; Thailand-Japan Zoonotic Diseases Collaboration Center (ZDCC), Kasetklang, Chatuchak, Bangkok 10900, Thailand.
authors.forename: Junki
authors.initials: J
authors.lastname: Mine
authors.affiliation: National Institute of Animal Health, Kasetklang, Chatuchak, Bangkok 10900, Thailand.
authors.forename: Sujira
authors.initials: S
authors.lastname: Parchariyanon
authors.affiliation: Influenza and Prion Disease Research Center, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0856, Ibaraki, Japan; Thailand-Japan Zoonotic Diseases Collaboration Center (ZDCC), Kasetklang, Chatuchak, Bangkok 10900, Thailand.
authors.forename: Nobuhiro
authors.initials: N
authors.lastname: Takemae
authors.affiliation: National Institute of Animal Health, Kasetklang, Chatuchak, Bangkok 10900, Thailand.
authors.forename: Prakit
authors.initials: P
authors.lastname: Boonpornprasert
authors.affiliation: National Institute of Animal Health, Kasetklang, Chatuchak, Bangkok 10900, Thailand.
authors.forename: Namfon
authors.initials: N
authors.lastname: Ubonyaem
authors.affiliation: National Institute of Animal Health, Kasetklang, Chatuchak, Bangkok 10900, Thailand.
authors.forename: Phornnachat
authors.initials: P
authors.lastname: Patcharasinghawut
authors.affiliation: National Institute of Animal Health, Kasetklang, Chatuchak, Bangkok 10900, Thailand.
authors.forename: Bandit
authors.initials: B
authors.lastname: Nuansrichay
authors.affiliation: Influenza and Prion Disease Research Center, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0856, Ibaraki, Japan; Thailand-Japan Zoonotic Diseases Collaboration Center (ZDCC), Kasetklang, Chatuchak, Bangkok 10900, Thailand.
authors.forename: Taichiro
authors.initials: T
authors.lastname: Tanikawa
authors.affiliation: Influenza and Prion Disease Research Center, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0856, Ibaraki, Japan; Thailand-Japan Zoonotic Diseases Collaboration Center (ZDCC), Kasetklang, Chatuchak, Bangkok 10900, Thailand.
authors.forename: Ryota
authors.initials: R
authors.lastname: Tsunekuni
authors.affiliation: Influenza and Prion Disease Research Center, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0856, Ibaraki, Japan; Thailand-Japan Zoonotic Diseases Collaboration Center (ZDCC), Kasetklang, Chatuchak, Bangkok 10900, Thailand. Electronic address: taksaito@affrc.go.jp.
authors.forename: Takehiko
authors.initials: T
authors.lastname: Saito
mesh_terms: D000818:Animals; D060085:Coinfection / Q000662:veterinary* / Q000821:virology; D009980:Influenza A virus / Q000235:genetics* / Q000254:growth & development*; D009297:Nasal Mucosa / Q000821:virology; D009976:Orthomyxoviridae Infections / Q000662:veterinary* / Q000821:virology; D016865:Reassortant Viruses / Q000302:isolation & purification*; D011995:Recombination, Genetic; D013552:Swine; D013785:Thailand
keywords: Bayesian MCMC; Co-infection; IAV-S; Surveillance; Swine influenza virus; Thailand