ArticlePLoS pathogens2020
Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia.
Article in PLoS pathogens, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 34 citations in OpenAlex.
- Zoonotic neglected tropical diseases at the animal-human interface in the Greater Mekong Subregion: Two decades of surveillance in Laos and Cambodia.PLoS neglected tropical diseases · 2026Review
- Weak selection and stochastic processes limit the emergence of antigenic variants during household transmission of influenza A viruses.PLoS pathogens · 2026Article
- Weak selection and stochastic processes limit the emergence of antigenic variants during household transmission of influenza A viruses.bioRxiv : the preprint server for biology · 2025Article
- An emerging PB2-627 polymorphism increases the zoonotic risk of avian influenza virus by overcoming ANP32 host restriction in mammalian and avian hosts.Journal of virology · 2025Article
- Genetic diversity of H9N2 avian influenza viruses in poultry across China and implications for zoonotic transmission.Nature microbiology · 2025Article
- Prevention and control of avian influenza virus: Recent advances in diagnostic technologies and surveillance strategies.Nature communications · 2025Article
- A rapid review of the avian influenza PB2 E627K mutation in human infection studies.Canada communicable disease report = Releve des maladies transmissibles au Canada · 2025Article
- Quantifying the impact of vaccination on transmission and diversity of influenza A variants in pigs.Journal of virology · 2024Article
- Divergent Pathogenesis and Transmission of Highly Pathogenic Avian Influenza A(H5N1) in Swine.Emerging infectious diseases · 2024Article
- SARS-CoV-2 shedding and evolution in patients who were immunocompromised during the omicron period: a multicentre, prospective analysis.The Lancet. Microbe · 2024Article
- Within-host influenza viral diversity in the pediatric population as a function of age, vaccine, and health status.Virus evolution · 2024Article
- Cross-species infection potential of avian influenza H13 viruses isolated from wild aquatic birds to poultry and mammals.Emerging microbes & infections · 2023Article
- SARS-CoV-2 shedding and evolution in immunocompromised hosts during the Omicron period: a multicenter prospective analysis.medRxiv : the preprint server for health sciences · 2023Article
- Avian H7N9 influenza viruses are evolutionarily constrained by stochastic processes during replication and transmission in mammals.Virus evolution · 2023Article
- A road map for in vivo evolution experiments with blood-borne parasitic microbes.Molecular ecology resources · 2022Review
- Vaccination decreases the risk of influenza A virus reassortment but not genetic variation in pigs.eLife · 2022Article
- Influenza A virus undergoes compartmentalized replication in vivo dominated by stochastic bottlenecks.Nature communications · 2022Article
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- Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck.PLoS pathogens · 2021Article
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Authors and funding
13 authors at 5 institutions in 5 countries.
Funding
Abstract
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, but data from natural infection is limited. We analyze deep sequencing data from infected humans and domestic ducks in Cambodia to examine how H5N1 viruses evolve during spillover. Overall, viral populations in both species are predominated by low-frequency (<10%) variation shaped by purifying selection and genetic drift, and half of the variants detected within-host are never detected on the H5N1 virus phylogeny. However, we do detect a subset of mutations linked to human receptor binding and replication (PB2 E627K, HA A150V, and HA Q238L) that arose in multiple, independent humans. PB2 E627K and HA A150V were also enriched along phylogenetic branches leading to human infections, suggesting that they are likely human-adaptive. Our data show that H5N1 viruses generate putative human-adapting mutations during natural spillover infection, many of which are detected at >5% frequency within-host. However, short infection times, genetic drift, and purifying selection likely restrict their ability to evolve extensively during a single infection. Applying evolutionary methods to sequence data, we reveal a detailed view of H5N1 virus adaptive potential, and develop a foundation for studying host-adaptation in other zoonotic viruses.
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