Genetic characteristics of avian influenza A (H9N9) virus in Poyang Lake area, 2014–2019

Objective  To understand the molecular characteristics of avian influenza A (H9N9) virus isolated in Poyang Lake area in Jiangxi province between 2014 and 2019. Methods  A total of 31854 poultry related environmental samples were collected in Poyang Lake area between 2014 and 2019. The samples were transported to Chinese National Influenza Center (CNIC) at low temperatures for virus isolation. All allantoic fluids were tested by influenza A virus fast diagnostic kits and influenza A virus positive allantoic fluids were harvested, then, the isolates were deeply sequenced. Software CLC, CD-HIT, MAFFT 7.475, MEGA 6.06, FastTree and FigTree v1.4.4 were used for the sequence analysis. Results  Between 2014 and 2019, a total of 18 influenza A (H9N9) virus strains were isolated in Poyang Lake area. Phylogenetic analysis of their full genome showed that they were reassortant of H9N2 virus and H7N9 virus. The NA segments of the H9N9 virus isolated in Jiangxi and the H9N9 virus isolated from Eastern China were in different sub-clade. Amino acid sites analysis of these H9 subtype viruses showed that they belonged to low pathogenic avian influenza virus, but some crucial amino acids substitution had been found, such as Q226L in HA protein, 550L in PA protein, N30D, T215A in M1 protein and P189D, F103L and M106I in NS1 genes. Conclusion  The influenza A (H9N9) virus strains isolated in our study during 2014–2019 were the reassortant of H9N2 and H7N9 viruses, which might be highly associated with the high incidences of H9N2 virus and H7N9 virus infections during 2013–2017. Although, there were no reported about human infection with influenza A (H9N9) virus, the genetic characteristic analysis results has shown it has potential to infect human. It is necessary to strengthen the continuous surveillance and research on reassortant of avian influenza viruses.