Influenza A virus strain:A(H3N2) Genome sequencing

In total, 253 whole genomes of A(H3N2) viruses were obtained that were detected in mild, moderate and severe cases during the 2016-2017 influenza season in Belgium. Patient information, including age, gender, date of sampling, diseases severity, comorbidities and vaccine status, were integrated into the WGS data analysis. The WGS data were used to genetically characterize the different circulating strains, and to identify genetic drift variants, mutations and reassortments compared to the A/Hong Kong/4801/2014 vaccine strain. Integrating WGS data with patient vaccination history and disease outcome, will facilitate correlating (minor) genetic variants with vaccine effectiveness or disease severity. WGS data allowed to construct phylogenetic trees based on all segments in contrast to current methods based typically on only the HA segment. Therefore, it allows for more robust inference of reassortments and clusters of strains associated with diseases severity and/or vaccination history. Our study illustrates that WGS combined with clinical and epidemiological data is feasible to strengthen the laboratory surveillance of the influenza virus.