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. Issue 4 (2nd June 2022)

• Record Type: Journal Article
• Authors: Abtin, Alireza; Shoushtari, Abdelhamid; Fallah Mehrabadi, Mohammad Hossein; Molouki, Aidin; Pourbakhsh, Seyed Ali; Pourtaghi, Hadi; Eshratabadi, Fatemeh
• Is Part Of: Veterinary medicine and science. Volume 8:Issue 4(2022)
• Page Start: 1594
• Page End: 1602
• Publication Date: 2022-06-02
• Subjects: avian influenza virus -- domestic ducks -- H3 subtype -- Iran -- live poultry market; Veterinary medicine -- Periodicals; Animal Diseases; Veterinary medicine; Periodicals; Periodicals; 636.08905
• DOI: 10.1002/vms3.819
• Languages: English
• ISSNs: 2053-1095

Abstract

Abstract: 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. Abstract :