Deep sequencing of 2009 influenza A/H1N1 virus isolated from volunteer human challenge study participants and natural infections.

Nasal wash samples from 15 human volunteers challenged with GMP manufactured influenza A/California/04/2009(H1N1) and from 5 naturally infected influenza patients of the 2009 pandemic were deep sequenced using viral targeted hybridization enrichment. Ten single nucleotide polymorphism (SNP) positions were found in the challenge virus. Some of the nonsynonymous changes in the inoculant virus were maintained in some challenge participants, but not in others, indicating that virus is evolving away from the Vero cell adapted inoculant, for example SNPs in the neuraminidase. Many SNP sites in challenge patients and naturally infected patients were found, many not identified previously. The SNPs identified, and phylogenetic analyses, showed that intrahost evolution of the virus are different in challenge participants and naturally infected patients. This study, using hybridization enrichment without PCR, provided an accurate and unbiased assessment of differential intrahost viral evolution from a uniform influenza inoculant in humans and comparison to naturally infected patients. Published by Elsevier Inc.