title: Influenza A Virus in Backyard Pigs and Poultry in Rural Cambodia.
abstract: Surveillance of influenza virus in humans and livestock is critical, given the worldwide public health threats and livestock production losses. Livestock farming involving close proximity between humans, pigs and poultry is often practised by smallholders in low-income countries and is considered an important driver of influenza virus evolution. This study determined the prevalence and genetic characteristics of influenza A virus (IAV) in backyard pigs and poultry in Cambodia. A total of 751 animals were tested by matrix gene-based rRT-PCR, and influenza virus was detected in 1.5% of sampled pigs, 1.4% of chickens and 1.0% of ducks, but not in pigeons. Full-length genome sequencing confirmed triple reassortant H3N2 in all IAV-positive pigs and various low pathogenic avian influenza subtypes in poultry. Phylogenetic analysis of the swine influenza viruses revealed that these had haemagglutinin and neuraminidase genes originating from human H3N2 viruses previously isolated in South-East Asia. Phylogenetic analysis also revealed that several of the avian influenza subtypes detected were closely related to internal viral genes from highly pathogenic H5N1 and H9N2 formerly sequenced in the region. High sequence homology was likewise found with influenza A viruses circulating in pigs, poultry and wild birds in China and Vietnam, suggesting transboundary introduction and cocirculation of the various influenza subtypes. In conclusion, highly pathogenic subtypes of influenza virus seem rare in backyard poultry, but virus reassortment, involving potentially zoonotic and pandemic subtypes, appears to occur frequently in smallholder pigs and poultry. Increased targeted surveillance and monitoring of influenza circulation on smallholdings would further improve understanding of the transmission dynamics and evolution of influenza viruses in humans, pigs and poultry in the Mekong subregion and could contribute to limit the influenza burden.
authors.affiliation: Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
authors.forename: K
authors.initials: K
authors.lastname: Osbjer
authors.affiliation: Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
authors.forename: M
authors.initials: M
authors.lastname: Berg
authors.affiliation: Centre for Livestock and Agriculture Development, Phnom Penh, Cambodia.
authors.forename: S
authors.initials: S
authors.lastname: Sokerya
authors.affiliation: National Institute of Public Health, Phnom Penh, Cambodia.
authors.forename: K
authors.initials: K
authors.lastname: Chheng
authors.affiliation: National Veterinary Research Institute, Phnom Penh, Cambodia.
authors.forename: S
authors.initials: S
authors.lastname: San
authors.affiliation: National Veterinary Research Institute, Phnom Penh, Cambodia.
authors.forename: H
authors.initials: H
authors.lastname: Davun
authors.affiliation: Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
authors.forename: U
authors.initials: U
authors.lastname: Magnusson
authors.affiliation: Infectious Diseases, Zoonosis Science Center, Department of Medical Sciences and IMBIM, Uppsala University (UU), Uppsala, Sweden.
authors.forename: B
authors.initials: B
authors.lastname: Olsen
authors.affiliation: Department of Microbiology, National Veterinary Institute, Uppsala, Sweden.
authors.forename: S
authors.initials: S
authors.lastname: Zohari
mesh_terms: D000818:Animals; D002160:Cambodia / Q000453:epidemiology; D002645:Chickens; D004372:Ducks; D005814:Genes, Viral; D009980:Influenza A virus / Q000235:genetics* / Q000302:isolation & purification; D005585:Influenza in Birds / Q000453:epidemiology / Q000821:virology*; D009976:Orthomyxoviridae Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D010802:Phylogeny; D011201:Poultry Diseases / Q000453:epidemiology / Q000821:virology*; D016865:Reassortant Viruses / Q000235:genetics; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology / Q000821:virology*
keywords: low pathogenic; prevalence; reassortment; swine; transboundary zoonotic disease