Influenza A H3N2 human challenge study

Here, we analyze a unique viral dataset of next-generation sequencing (NGS) samples generated from a human influenza challenge study wherein 17 healthy subjects were inoculated with a strain of A/Wisconsin/67/2005 (H3N2) which had been passaged three times in avian primary chicken kidney cells, 4 times in embryonated chicken eggs, and twice in GMP Vero cells. Nasal wash samples collected from 7 of these subjects were successfully deep sequenced. From these, we characterized changes in the subjects' viral populations with a focus on the defective viral genomes present in each sample. A subset of these data were used to generate the assemblies in BioProject SRP091397.