Whole genome analysis of human H3N2 influenza virus outbreak in a poultry farm

Objective To understand the epidemiological characteristics of outbreaks and analyze the genetic characteristics of the whole genome of influenza H3N2 virus among avian-human-swine, and to elaborate the source of influenza virus. Methods The epidemic information was collected using the case investigation, the pharyngeal swab samples from influenza-like-illness cases were detected by real-time PCR and virus isolation. The phylogeny and molecular features of whole-genome were analyzed with EditSeq and MEGA 5.05 software. Results The prevalence rate of this outbreak was 34.88%, 15 samples of throat swabs were collected, the positive rate of nucleic acid detection was 73.33%, 5 strains of seasonal influenza A (H3N2) influenza viruses were isolated. The phylogenetic analysis showed the eight gene segments of the isolated influenza viruses belonged to the same cluster with 2015-2016 influenza vaccine strain A/Switzerland/9715293/2013(H3N2), and no recombination was found. Compared with vaccine strain, 14 variant amino acids of protein of HA were identified, and 8 of them were located in antigenic sites. All strains were sensitive to neuraminidase inhibitors while they showed resistance to blockers of M2 ion channel. The glycosylation sites analysis showed that two new glycosylation sites NRT151-153 and NAT245-247were added. Conclusions The outbreak was caused by seasonal influenza A (H3N2) virus which had an antigenic drift and no genetic avian-human-swine recombination was found. Key words: Influenza A; Outbreak; Gene sequence; Antigenic analysis