Sequencing of influenza A/H1N1 virus from human challenge study and natural infections

Influenza A virus is an important respiratory virus with a significant public health impact. The most recent influenza pandemic is the 2009 H1N1 that caused several hundred thousand deaths worldwide. A great challenge of vaccine and therapeutic countermeasure development against influenza infection is its rapid, unpredictable evolution, resulting from immune evasion and escape from antiviral drugs. In the current study, nasal wash samples from 15 human volunteers challenged with GMP manufactured influenza A/California/04/2009(H1N1) and from 5 naturally infected influenza patients were deep sequenced. The evolution of a uniform 2009 pandemic influenza A viral inoculant was studied in 15 volunteer challenge participants and compared to that from naturally infected influenza patients. The significance of this research is that a uniform challenge virus was able to evolve and increase its diversity differently in individual human participants, providing a model for how an early stage influenza pandemic may evolve.