Quantifying within-host evolution of H5N1 influenza in humans and poultry in Cambodia

Avian influenza viruses (AIVs) periodically cross species barriers and infect humans. The likelihood that an AIV will evolve mammalian transmissibility depends on acquiring and selecting mutations during spillover. We analyze deep sequencing data from infected humans and ducks in Cambodia to examine H5N1 evolution during spillover. Viral populations in both species are predominated by low-frequency (