The prevalence and genetic characteristics of avian influenza viruses subtype A/H5N6 in a number of northern border provinces in Vietnam

Abstract

The purpose of this study was to determine the prevalence and genetic characteristics of avian influenza viruses subtype A/H5N6 in five northern  border provinces. In the study, 15.248 swab samples and 2.830 internal organ samples of birds were collected at a number of markets in Quang Ninh, Lang Son, Lao Cai, Lai Chau, and Cao Bang. Using the Realtime RT-PCR method, samples positive for influenza A viruses were tested for H5 and N6 subtypes, then sequenced using the Beckman Coulter CEQ 8000, and followed by phylogenetic analysis of A/H5N6 influenza strains. The results showed that the A/H5N6 virus prevalence of swab samples was 5.79%, and that of internal organ samples was lower (2.05%). Ten strains of A/H5N6 viruses were sequenced, and the results of phylogenetic analysis showed that ten strains of H5 subtype belong to the clade 2.3.4.4 and belong to the branch of the A/H5N6 influenza viruses isolated in Laos in 2014 and in China from 2013 to 2014. Ten strains of N6 subtype were in the same Eurasian lineage. Of which, five strains were in the same A/H5N6 viruses isolated in Laos and China in 2014, and the five other strains were located in the same branch with A/H5N6 and H6N6 viruses isolated in Vietnam from 2011 to 2014. These results are important to predict the risk of avian influenza A/H5N6 viruses in the study areas.