Analyses of selection pressure on the Hemagglutinin gene of influenza A/H3N2 Viruses circulating in Kenya 2007-2011

Methods: Nasopharyngeal samples from patients meeting the WHO ILI case definition were collected between 2007 and 2010 from across Kenya. The detection of H3N2 virus was carried out using real-time RT-PCR. Positive samples were then cultured in MDCK cells and confirmed using the HAI assay. 156 isolates from this period were selected for amplification of the HA1 portion of the HA gene and the resulting amplicons sequenced. Global estimates, ω, of dN and dS, averaged over the entire alignment, were compared to calculate the overall strength of selection using the HyPhy 2.0 software package implemented in datamonkey.