Objective To sequence the whole genome of a human-infected H9N2 avian influenza virus strain in Kunming city, so as to analyze the genetic evolution of the virus and variation in sites of amino acids.

Methods Real-time RT-PCR method was used for influenza virus typing, and MDCK cell was used for virus isolation. The whole genome of the virus strain was sequenced by Illumina Miseq high-throughput sequencer. The data from the machine were used for assembly, using CLC Genomicsworkbench 8.0 software. Sequences were aligned and phylogenetic tree were constructed using Mega7.0 software.

Results The throat swab samples of the patient were positive for the influenza A virus subtype H9N2. The H9N2 strain was obtained by virus culture. The whole genome was sequenced and the complete genome sequence of the strain was obtained. The sources of sequences with the highest similarity to the 8 genes of the strain was inconsistent. Phylogenetic analysis showed that the HA, NA and PB2 genes belonged to G9-like branch, the M gene belonged to G1-like branch, and NS1, PB1, PA, NP belonged to F/98-like branch. The receptor binding site in HA gene showed mutations of I155T, H183N and Q226L. The M1 gene showed mutations of N30D, T215A and V15I. The mutations of L55F, P42S and L13P were in M2, NS1 and PB1 gene, respectively. The PA gene showed mutations of K356R and S409N.

Conclusions The origin of the eight gene fragments of isolated strain in Kunming city was inconsistent, and the receptor binding characteristics tended to preferentially bind to human receptors, indicating a trend of enhanced pathogenicity. More frequent active surveillances should be conducted in the future to detect timely the changes in virus distribution and mutations.