Molecular characterisation of novel reassortment of the G57 genotype of low pathogenic avian influenza H9N2 virus isolated from poultry farms in Malaysia

Abstract

AbstractIn late 2017, Malaysia reported repeated low pathogenic avian influenza virus (LPAI) H9N2 in commercial poultry flocks. However, the complete genome characterisation of the H9N2 viruses has not been studied. Two H9N2 viruses, A/chicken/Malaysia/Negeri Sembilan/UPM994/2018 and A/chicken/Malaysia/Johore/ UPM2033/2019 that were isolated from breeder and layer flocks in Peninsular Malaysia are characterised in this study. A phylogenetic analysis reveals that both viruses are multiple genotype reassortant strains with genes originating from Y280-like (HA gene), F/98-like (NS, NP and PA), G1-like (M and PB2) and Korean-like (PB1) lineages, indicating the viruses belong to a novel genotype divergent from the G57 lineage of Chinese origin. A deduced amino acid analysis reveals a dibasic cleavage site at position 333-PSRSSR-GLF-341 of HA gene cleavage locations. In conclusion, the characterised Malaysian H9N2 is a Y280-like virus resembling H9N2 isolated from Indonesia, Taiwan, Japan and Cambodia. However, the virus is of G57 lineage with a novel genotype of the PB1 gene originating from the Korean lineage H9N2 virus, which has not been detected before in the region.