H5N1 within-host diversity in humans and poultry in Cambodia

Avian influenza viruses (AIVs) periodically cross species barriers and infect humans. The likelihood that an AIV will evolve enhanced mammalian transmissibility depends on acquiring and selecting mutations during spillover. We analyze deep sequencing data from infected humans and poultry in Cambodia to examine H5N1 AIV evolution during natural spillover. Samples were collected from 8 infected humans and 5 infected domestic ducks in Cambodia between 2010 and 2014. DNA was sequenced on an Illumina MiSeq with human reads removed prior to upload.