ArticleNature communications2022
Influenza A virus undergoes compartmentalized replication in vivo dominated by stochastic bottlenecks.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed, 65 citations in OpenAlex.
- Exposure route, not dose, is the primary driver of infection patterns for a respiratory virus.Science advances · 2026Article
- Evolutionary constraints limit additional mammalian adaptation of bovine-derived H5N1 influenza viruses in ferrets.bioRxiv : the preprint server for biology · 2026Article
- Direct estimation of genotype fitness from time series.bioRxiv : the preprint server for biology · 2026Article
- Weak selection and stochastic processes limit the emergence of antigenic variants during household transmission of influenza A viruses.PLoS pathogens · 2026Article
- Viral lineage and mode of exposure modulate within-host spatial dynamics of influenza A viruses in a guinea pig model.Journal of virology · 2026Article
- Divergent Fates of Kidney-Resident Polyomaviruses: Stable Shedding Versus Near-Silent Persistence.Viruses · 2026Article
- Exposure route drives SARS-CoV-2 infection patterns in non-human primates.bioRxiv : the preprint server for biology · 2026Article
- Tandem split-GFP influenza A viruses for sensitive and accurate replication analyses.Microbiology spectrum · 2026Article
- Genetic drift acts strongly on influenza virus populations within acute human infections but is obscured by other factors within acutely infected swine.Virus evolution · 2026Article
- Quantifying host-microbe interactions with bacterial lineage tracing.Science (New York, N.Y.) · 2026Review
- Stochastic intracellular replication dynamics shape population-level evolution in Influenza A Virus.Virus evolution · 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
- Viral lineage and mode of exposure modulate within host spatial dynamics of influenza A viruses.bioRxiv : the preprint server for biology · 2025Article
- Viral expansion after transfer is a primary driver of influenza A virus transmission bottlenecks.PLoS biology · 2025Article
- Identification of the Matrix Protein as a Conserved and Central Determinant of Superinfection Exclusion in Plant Rhabdoviruses.Molecular plant pathology · 2025Article
- Article
- Viral expansion after transfer is a primary driver of influenza A virus transmission bottlenecks.bioRxiv : the preprint server for biology · 2025Article
- Predictive models of influenza A virus lethal disease yield insights from ferret respiratory tract and brain tissues.Scientific reports · 2025Article
- Shedding dynamics of a DNA virus population during acute and long-term persistent infection.PLoS pathogens · 2025Article
- Exploiting social traits for clinical applications in bacteria and viruses.npj antimicrobials and resistance · 2025Review
Corrections and comments
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Authors and funding
14 authors at 3 institutions in 1 country.
Funding
Abstract
Transmission of influenza A viruses (IAV) between hosts is subject to numerous physical and biological barriers that impose genetic bottlenecks, constraining viral diversity and adaptation. The bottlenecks within hosts and their potential impacts on evolutionary pathways taken during infection are poorly understood. To address this, we created highly diverse IAV libraries bearing molecular barcodes on two gene segments, enabling high-resolution tracking and quantification of unique virus lineages within hosts. Here we show that IAV infection in lungs is characterized by multiple within-host bottlenecks that result in "islands" of infection in lung lobes, each with genetically distinct populations. We perform site-specific inoculation of barcoded IAV in the upper respiratory tract of ferrets and track viral diversity as infection spreads to the trachea and lungs. We detect extensive compartmentalization of discrete populations within lung lobes. Bottleneck events and localized replication stochastically sample individual viruses from the upper respiratory tract or the trachea that become the dominant genotype in a particular lobe. These populations are shaped strongly by founder effects, with limited evidence for positive selection. The segregated sites of replication highlight the jackpot-style events that contribute to within-host influenza virus evolution and may account for low rates of intrahost adaptation.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.