Characterisation, whole‐genome sequencing and phylogenetic analysis of three H3N2 avian influenza viruses isolated from domestic ducks at live poultry markets of Iran, 2017: First report

BACKGROUND: Avian influenza type A viruses (AIV) can infect a broad range of hosts including human and birds, making them an important viral pathogen with zoonotic potential. Ducks are a known reservoir for many avian viruses including the AIV. OBJECTIVES: To sequence the entire genome of duck‐derived H3N2 and ran comprehensive phylogenetic analysis on them to study their origin. METHODS: In this study, 962 cloacal swabs were collected from domestic ducks at several live poultry markets (LPMs) of Gilan, Mazandaran and Golestan provinces of Iran in the year 2017. RESULTS: Preliminary assays such as haemagglutination inhibition assay (HI), Neuraminidase Inhibition assay(NI) and RT‐qPCR suggested that 0.5% of the birds were infected by H3 low pathogenic influenza viruses (LPAI). Three isolates were selected for whole genome sequencing. The cleavage site of the HA genes showed a PEKQTR/GLF motif, an indicator of LPAI. Furthermore, BLAST and phylogenetic analyses of the HA gene showed high homology to the Eurasian lineage of H3N8 AIV (95.5%–97.1% to several European and East Asian isolates). However, the NA genes showed high homology (at most 96.5–96.9%) to those belonging to AIV N2 subtype. Furthermore, internal genes showed high homology (96%–98%) to a variety of duck‐origin subtypes and glycoprotein combinations, which were different for each segment. This showed a complex reassortment between different subtypes. DISCUSSION: This report is the first whole genome sequencing and complete characterisation of H3N2 AIV from Iran. CONCLUSION: Such surveillance should continue to study the evolution and possible emergence of viruses with pandemic potential.