title: Influenza A Viruses of Swine (IAV-S) in Vietnam from 2010 to 2015: Multiple Introductions of A(H1N1)pdm09 Viruses into the Pig Population and Diversifying Genetic Constellations of Enzootic IAV-S.
abstract: Active surveillance of influenza A viruses of swine (IAV-S) involving 262 farms and 10 slaughterhouses in seven provinces in northern and southern Vietnam from 2010 to 2015 yielded 388 isolates from 32 farms; these viruses were classified into H1N1, H1N2, and H3N2 subtypes. Whole-genome sequencing followed by phylogenetic analysis revealed that the isolates represented 15 genotypes, according to the genetic constellation of the eight segments. All of the H1N1 viruses were entirely A(H1N1)pdm09 viruses, whereas all of the H1N2 and H3N2 viruses were reassortants among 5 distinct ancestral viruses: H1 and H3 triple-reassortant (TR) IAV-S that originated from North American pre-2009 human seasonal H1, human seasonal H3N2, and A(H1N1)pdm09 viruses. Notably, 93% of the reassortant IAV-S retained M genes that were derived from A(H1N1)pdm09, suggesting some advantage in terms of their host adaptation. Bayesian Markov chain Monte Carlo analysis revealed that multiple introductions of A(H1N1)pdm09 and TR IAV-S into the Vietnamese pig population have driven the genetic diversity of currently circulating Vietnamese IAV-S. In addition, our results indicate that a reassortant IAV-S with human-like H3 and N2 genes and an A(H1N1)pdm09 origin M gene likely caused a human case in Ho Chi Minh City in 2010. Our current findings indicate that human-to-pig transmission as well as cocirculation of different IAV-S have contributed to diversifying the gene constellations of IAV-S in Vietnam.
  
  
  OBJECTIVE
  This comprehensive genetic characterization of 388 influenza A viruses of swine (IAV-S) isolated through active surveillance of Vietnamese pig farms from 2010 through 2015 provides molecular epidemiological insight into the genetic diversification of IAV-S in Vietnam after the emergence of A(H1N1)pdm09 viruses. Multiple reassortments among A(H1N1)pdm09 viruses and enzootic IAV-S yielded 14 genotypes, 9 of which carried novel gene combinations. The reassortants that carried M genes derived from A(H1N1)pdm09 viruses became predominant, replacing those of the IAV-S that had been endemic in Vietnam since 2011. Notably, one of the novel reassortants likely caused a human case in Vietnam. Given that Vietnam is the second-largest pig-producing country in Asia, continued monitoring of IAV-S is highly important from the viewpoints of both the swine industry and human public health.
authors: Division of Transboundary Animal Disease, National Institute of Animal Health, NARO, Tsukuba, Japan.|Thailand-Japan Zoonotic Diseases Collaboration Center, Bangkok, Thailand.
authors: Nobuhiro
authors: N
authors: Takemae
authors: Division of Transboundary Animal Disease, National Institute of Animal Health, NARO, Tsukuba, Japan.
authors: Michiyo
authors: M
authors: Harada
authors: Regional Animal Health Office No. 6, Department of Animal Health, Ho Chi Minh City, Vietnam.
authors: Phuong Thanh
authors: PT
authors: Nguyen
authors: Epidemiology Division, Department of Animal Health, Hanoi, Vietnam.
authors: Tung
authors: T
authors: Nguyen
authors: Epidemiology Division, Department of Animal Health, Hanoi, Vietnam.
authors: Tien Ngoc
authors: TN
authors: Nguyen
authors: National Centre for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam.
authors: Thanh Long
authors: TL
authors: To
authors: National Centre for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam.
authors: Tho Dang
authors: TD
authors: Nguyen
authors: Regional Animal Health Office No. 6, Department of Animal Health, Ho Chi Minh City, Vietnam.
authors: Vu Phong
authors: VP
authors: Pham
authors: Regional Animal Health Office No. 6, Department of Animal Health, Ho Chi Minh City, Vietnam.
authors: Vu Tri
authors: VT
authors: Le
authors: National Centre for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam.
authors: Hoa Thi
authors: HT
authors: Do
authors: Regional Animal Health Office No. 6, Department of Animal Health, Ho Chi Minh City, Vietnam.
authors: Hung Van
authors: HV
authors: Vo
authors: Regional Animal Health Office No. 6, Department of Animal Health, Ho Chi Minh City, Vietnam.
authors: Quang Vinh Tin
authors: QVT
authors: Le
authors: Regional Animal Health Office No. 6, Department of Animal Health, Ho Chi Minh City, Vietnam.
authors: Tan Minh
authors: TM
authors: Tran
authors: Regional Animal Health Office No. 6, Department of Animal Health, Ho Chi Minh City, Vietnam.
authors: Thanh Duy
authors: TD
authors: Nguyen
authors: Regional Animal Health Office No. 6, Department of Animal Health, Ho Chi Minh City, Vietnam.
authors: Phuong Duy
authors: PD
authors: Thai
authors: National Centre for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam.
authors: Dang Hoang
authors: DH
authors: Nguyen
authors: Regional Animal Health Office No. 6, Department of Animal Health, Ho Chi Minh City, Vietnam.
authors: Anh Quynh Thi
authors: AQT
authors: Le
authors: Epidemiology Division, Department of Animal Health, Hanoi, Vietnam.
authors: Diep Thi
authors: DT
authors: Nguyen
authors: Division of Transboundary Animal Disease, National Institute of Animal Health, NARO, Tsukuba, Japan.|Thailand-Japan Zoonotic Diseases Collaboration Center, Bangkok, Thailand.
authors: Yuko
authors: Y
authors: Uchida
authors: Division of Transboundary Animal Disease, National Institute of Animal Health, NARO, Tsukuba, Japan taksaito@affrc.go.jp.|Thailand-Japan Zoonotic Diseases Collaboration Center, Bangkok, Thailand.|United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan.
authors: Takehiko
authors: T
authors: Saito
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D062665:Epidemiological Monitoring; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000145:classification / Q000235:genetics*; D057221:Influenza A Virus, H1N2 Subtype / Q000145:classification / Q000235:genetics*; D053122:Influenza A Virus, H3N2 Subtype / Q000145:classification / Q000235:genetics*; D008390:Markov Chains; D009010:Monte Carlo Method; D009976:Orthomyxoviridae Infections / Q000453:epidemiology / Q000635:transmission / Q000662:veterinary* / Q000821:virology; D010802:Phylogeny; D016865:Reassortant Viruses / Q000235:genetics; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology* / Q000635:transmission / Q000821:virology; D014744:Vietnam / Q000453:epidemiology
keywords: Vietnam; influenza; phylogeny; pig; reassortment