Emergence and Temporal Variation of Hemagglutinin Mutations During Influenza Infection

Amplicons from individual patients infected with influenza A H1N1 or H3N2 were sequenced on an Illumina MiSeq and analyzed using the rare variant detection [RVD] method previously described in Cushing et al 2013. Sequences were chosen from multiple individuals, including longitudinal samples within a subset of patients, in order to understand variations in the HA gene within individual patients and how these variants change over the course of infection. Additionally, technical sample preparation replicates were generated and sequenced in order to measure the reproducibility of rare variant detection within viral samples.