Genetic diversity and evolution of swine influenza viruses in Thailand during 2012-2015

Abstract

Influenza A viruses cause respiratory diseases in human and animals. In pigs, swine influenza virus (SIV) subtype H1N1, H1N2 and H3N2 can infect pigs worldwide. In avian, avian influenza virus (AIV) subtype H1-H16 and N1-N9 can infect several avian species. This dissertation entitled “Genetic diversity and evolution of swine influenza viruses in Thailand during 2012-2015” contains 3 parts. Part 1, a cross-sectional surveillance of swine influenza virus (SIV) was conducted during September 2011 to December 2015 in 46 commercial swine farms in 11 provinces, Thailand. The results showed that the occurrence of SIVs in Thailand was 3.81% (139/3,646). The SIV isolates in this study could be subtyped as H1N1 (n=77), H1N2 (n=13) and H3N2 (n=49). Subsequently, twelve SIVs (H1N1; n=5, H1N2; n=2, H3N2; n=5) were subjected to for whole genome sequencing and genetic characterization. Genetic analysis revealed that three SIV-H1N1 were endemic Thai SIVs circulating in Thai pig population. On the other hand, nine SIVs were reassotant viruses between pandemic H1N1 2009 and endemic Thai SIV. This results suggested that reassortant SIVs were predominant genotypes in Thai pig population. Part 2, mix-genotype of SIVs were investigated in four commercial swine farms. In total, 145 nasal swab samples were collected and 18 samples were successfully performed virus isolation. The samples were subsequently subjected to whole genome sequencing by next-generation sequencing, illumina Miseq. The results showed that mix-genotypes could be observed in this study. For example, swine farms A, B and D infected with mix-genotypes of SIVs (H1, H3, N1 and N2). Moreover, SIV-H3N1, an uncommon subtype in Thailand, was identified in this study. This results indicated that illumina sequencing is able to discriminate mix-genotypes of SIVs. Part 3, highly pathogenic avian influenza (HPAI) H5N2 in USA in 2015 was investigated. Forty-six samples from turkeys and their environment were collected during the outbreak and directly subjected to illumina sequencing. The viruses were then analyzed to identify origins and evolutionary changes. The results showed that the time to most recent common ancestor analysis suggest two likely possibilities of reassortant HPAI-H5N2 origins: either a reassortment in Alaska area or multiple reassortments with North American low pathogenic avian influenza strains. In summary, this dissertation provided useful information that swine influenza and avian influenza are fast evolving of the viruses especially after the introduction of new genetic pool of the viruses into population or interspecies transmission. Thus, influenza A virus surveillance should be continuously conducted to promote awareness and prevention and control of influenza A virus infection in human and animals in the future.