Objective  To analyze the characteristics of whole genome sequences of H3N2 influenza virus strains isolated in Guangzhou city for providing reference data to the prevention and control of H3N2 influenza.

  Methods  Whole-genome sequencing was performed for 13 strains of H3N2 influenza virus isolated in Guangzhou city in 2019 and the sequencing results were analyzed with bioinformatics software. Gene segments of H3N2 influenza vaccine strains recommended by World Health Organization for the northern hemisphere population over the years were extracted from the Global Initiative on Sharing Avian Influenza Data (GISAID) as the reference sequences.

  Results  For the 13 virus strains sequenced, the lowest nucleotide homology was 94% and the highest was 100%. Compared to the reference sequences, the gene with the greatest difference was NA (94% – 100%) and that with the least difference was PA (98.9% – 100%). The nucleotide variation rate of was the highest for NA gene (8.37%) and the lowest for PA gene (2.14%). All genes of the isolated strains, including both from out-patients under surveillance and from outbreak cases, belong to those of the same evolutionary branch of the vaccine strain (A/Hong Kong/2671/2019 H3N2). The HA, PB2, PB1, NP, M and NS genes of the strains could be further divided into three small branches (group 1 – 3) based on their epidemic time. Group 1, 2, and 3 were prevalent during periods of January – August, November – December, and January – August/November – December of 2019, respectively.

  Conclusion  The H3N2 influenza virus strains isolated in Guangzhou in 2019 were on the same evolutionary branch to the vaccine strain. The isolated strains had the same evolutionary origin but there were diversities in evolutionary characteristics, homologies and the variation rates of the whole genome among the strains.