Genetic characterization of avian influenza A(H5N6) virus from two patients in Yunnan province

Objective To analyze the genetic features for two human avian influenza A(H5N6) virus strains from patients in Yunnan province, and to provide the scientific basis for the prevent and control of avian influenza virus A(H5N6) in the future. Methods Throat swab samples from two patients with pneumonia and samples from livestock near the patients’ houses in Yunnan province were collected to detect avian influenza A(H5N6) virus. Whole genome sequences of the strains were obtained from the positive samples with high throughput sequencing. Sequence alignment with MEGA software was used to analyze mutations in functional loci, and the phylogenetic tree of hemaglutinin (HA) gene was constructed. Results Whole genome analysis showed that the similarities of the 8 RNA fragments in the two virus stains from Yunnan province were 98.5%-100.0%. Comparing to the strains from Sichuan and Guangzhou, differences in functional loci were found in all seven fragments of Yunnan strains except for NP fragment. The changes led to changes in receptor specificity, enhanced viral power and changes in resistance to amantadine ammonia. Phylogenetic tree analysis of HA genes showed that the strains from Yunnan, Sichuan and Guangzhou belonged to sub-branch 2.3.4.4 of H5 clade 2.3.4. Six strains of avian influenza virus A(H5N6) isolated from environmental samples and the two strains from patients in Yunnan province related to the strains from Guangzhou. All strains belonged to the same clade. The two strains from Yunnan showed a certain genetic distance from Sichuan and Guangzhou strains. Conclusions The genetic diversity and complexity of avian influenza A(H5N6) virus in Yunnan province are observed. The variation in functional loci of the virus may be one of the cross-species transmission mechanisms of of avian influenza virus. Dynamically monitoring the distribution and genetic variations of avian influenza viruses in live poultry markets should be used to provide research data for the study of cross-species transmission of avian influenza viruses and to provide scientific basis for the prevention and control of avian influenza viruses in Yunnan province. Key words: H5N6; Avian influenza virus; Functional loci; Phylogenetic analysis