A reassortant highly pathogenic avian influenza H5N6 virus originating from the wildbird-origin H5N6 and the poultry H9N2/H7N9 viruses in Xinjiang, China

The asian lineage of H5, H7, and H9 avian influenza viruses (AIVs) is the most prevalent in the world, and the co-existence of H5, H7, and H9 viruses provide an opportunity to generate some novel reassortants. Herein we report our isolation of two H5N6 virus strains (named XJ-H5N6) from domestic geese in live poultry markets (LPMs) in Urumqi during the winter of 2016-2017, and analysis of the viral genetic mutations, pathogenicity, reassortant, and origin. BLAST analysis revealed that the HA, NA, MP, NP, and NS of XJ-H5N6 had the highest sequence identity (98.5-99.5%) with those 5 genes from H5N6 highly pathogenic avian influenza virus (HPAIV) isolated from wild birds in Ningxia (NX-WB-H5N6); the viral PA and PB1 had the highest sequence identity (98.6% and 98.9%) with those 2 genes from HPAIV strain A/Environment/Chongqing/45373/2015 (H5N6) (CQ-EN-H5N6); while the viral PB2 had the highest sequence identity (99.0%) with this gene from low pathogenic avian influenza virus (LPAIV) strain A/environment/Jiangsu/01.20 TCCX004/2015 (H9N2). Except for the PB2, phylogenetic analysis showed that the other 7 viral genes were clustered together with NX-WB-H5N6 and CQ-EN-H5N6, while the viral PB2 was clustered together with the poultry H9N2/H7N9 viruses. The viral HA protein contained multiple basic amino acid residues (RRRKR/GL) at the cleavage site which represents HPAIV. Additionally, the viral multiple mutations could enhance the viral virulence and the capacity of cross-species transmission. Our data indicate that XJ-H5N6 has been generated by the reassortant of H5N6 HPAIV from wild birds in Ningxia and H9N2/H7N9 LPAIV in poultry. The results of this study may help us understand the viral adaptation and transmission patterns from wild birds to poultry.