within-host diversity in H5N1-infected humans and poultry in Cambodia

H5N1 within-host diversity in humans and poultry in Cambodia

Louise H. Moncla1, Trevor Bedford1,2, Philippe Dussart3, Philippe Buchy4, Huachen Zhu5,6, Thomas C. Friedrich7,8, Paul F. Horwood9,10

1Fred Hutchinson Cancer Research Center, Seattle, Washington, United States, 2University of Washington, Seattle, Washington, United States, 3Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia, 4GlaxoSmithKline, Vaccines R&D, Singapore, Singapore,5Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, People's Republic of China,6State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, SAR, People's Republic of China,7Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI, United States,8Wisconsin National Primate Research Center, Madison, WI, United States,9Papua New Guinea Institute of Medical Research, Goroka, Paula New Guinea,10Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia.


H5N1 viruses periodically cross species barriers and cause disease in humans. The likelihood that an avian influenza virus will acquire mammalian-adapting mutations and evolve enhanced mammalian transmissibility depends on its ability to acquire and select mutations within hosts during spillover. We use deep sequence data from infected humans and poultry in Cambodia to examine how H5N1 viruses evolve during natural spillover infection. We find that viral populations in both species are characterized by predominantly low-frequency (<10%) variation shaped by a combination of purifying selection and genetic drift. Human samples had a greater number of within-host polymorphisms on average, although the distribution of single nucleotide polymorphism (SNP) frequencies and overall mean SNP frequency was similar in both host species. We detect a handful of mutations in humans at sites explicitly linked to H5N1 mammalian adaptation (PB2 627 Lys, HA 150 Val, and HA 238 Leu), although these mutations were present at low frequencies, despite ≥8 days of infection. Finally, we show that mutations detected within-host are not enriched among viruses that have caused spillover infections in the past. By comparing signatures of diversity among humans and poultry, we show that H5N1 viruses are capable of generating known markers of human adaptation during natural spillover infection. However, a short duration of infection, randomness and purifying selection together severely limit the evolutionary capacity of H5N1 viruses to evolve extensively within human hosts.