Full-genome analysis of avian influenza virus H9N2 from Bangladesh reveals internal gene reassortments with two distinct highly pathogenic avian influenza viruses

Abstract

Low-pathogenic avian influenza viruses (LPAIVs) of subtype H9N2 have become widespread in poultry in many Asian countries with relevance to respiratory diseases of multifactorial origin. In Bangladesh, LPAIVs of subtype H9N2 co-circulate simultaneously with highly pathogenic avian influenza viruses (HPAIVs) of subtype H5N1 in commercial and backyard poultry. The aim of this study was to characterize LPAIVs of subtype H9N2 currently circulating in Bangladesh. The selected isolate A/Chicken/Bangladesh/VP01/2006 (H9N2) was propagated in chicken embryos. All eight gene segments were amplified by RT-PCR, cloned, and subjected to full-length sequencing. The sequence data obtained were compared with reference strains available in GenBank. Phylogenetic analysis of LPAIV H9N2 from Bangladesh revealed a close relationship to Indian, Pakistani and Middle Eastern isolates and identified an ancestor relationship to LPAIV H9N2 Quail/HK/G1/1997. The internal genes M and NP belong to lineage G1, whereas NS, PA, PB1 and PB2 belong to the prototype virus A/Chicken/Korea/38349-p96323/96. The internal genes showed high sequence homology to an HPAIV of subtype H7N3 from Pakistan, whereas the PB1 gene showed similarly high nucleotide homologies to recently circulating HPAIV H5N1 from Bangladesh, revealing two independent reassortment events. Examination of the hemagglutinin cleavage site of LPAIV H9N2 confirmed its low pathogenicity. The receptor-binding sites indicated a binding preference for human-type receptors. Several mutations in internal proteins are associated with increased virulence and altered host range, while other amino acids were found to be highly conserved among LPAIV H9N2 isolates.

Biosecurity Strategies for Backyard Poultry: A Controlled Way for Safe Food Production

“…In Bangladesh (Asia), H9N2 subtype of LPAI is frequently detected in commercial poultry and backyard flocks that are phylogenetically related to South Asian and Middle East isolates (Parvin et al, 2014). Moreover, H9N2 isolates of Bangladesh also possessed the evidence of reassortment between H7N3 and H5N1 subtypes like their counterparts in Pakistan (Parvin et al, 2014). A low proportion (7%) of backyard birds in Bangladesh die every day due to HPAI infection.…”

Serological and virological surveillance of avian influenza virus in domestic ducks of the north-east region of Bangladesh

“…As of 19 July 2016, 8 human cases of H5N1 AI virus with one case fatality have been reported from Bangladesh [13]. In addition to H5N1 HPAI, low pathogenic H9N2 influenza virus also has been circulating in poultry [14–16]. …”

The Continuing Evolution of H5N1 and H9N2 Influenza Viruses in Bangladesh Between 2013 and 2014

“…Influenza viruses of the H9N2 subtype were circulating widely in Bangladesh at the same time, having been first reported in 2006 (15). The H9N2 viruses currently circulating in Bangladesh are a novel variant that originated in China from the G1 lineage but has evolved tremendously via continuing genetic shift and by inter-subtype reassortment with HPAI H7N3 viruses (17).…”