ArticleJournal of virology2020
Inferring Transmission Bottleneck Size from Viral Sequence Data Using a Novel Haplotype Reconstruction Method.
Article in Journal of virology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Evolutionary constraints limit additional mammalian adaptation of bovine-derived H5N1 influenza viruses in ferrets.bioRxiv : the preprint server for biology · 2026Article
- The impact of viral and host factors on the influenza A virus transmission bottleneck.PLoS pathogens · 2026Article
- Barcoded SARS-CoV-2 viruses define the impact of duration and route of exposure on the transmission bottleneck in a hamster model.Science advances · 2025Article
- Changes in intra-host mycovirus population diversity after vertical and horizontal transmission.Virus evolution · 2025Article
- ViralBottleneck: an R package for estimating viral transmission bottlenecks from deep sequencing data using multiple methods.Virus evolution · 2025Article
- Host obesity impacts genetic variation in influenza A viral populations.Journal of virology · 2024Article
- Barcoded SARS-CoV-2 viruses define the impact of time and route of transmission on the transmission bottleneck in a Syrian hamster model.bioRxiv : the preprint server for biology · 2024Article
- The airborne transmission of viruses causes tight transmission bottlenecks.Nature communications · 2024Article
- Transmission Bottleneck Size Estimation from De Novo Viral Genetic Variation.Molecular biology and evolution · 2024Article
- Inference of Infectious Disease Transmission through a Relaxed Bottleneck Using Multiple Genomes Per Host.Molecular biology and evolution · 2024Article
- Co-evolution of immunity and seasonal influenza viruses.Nature reviews. Microbiology · 2023Review
- Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data.Nature communications · 2023Article
- The evolution of SARS-CoV-2.Nature reviews. Microbiology · 2023Review
- The Origin of Internal Genes Contributes to the Replication and Transmission Fitness of H7N9 Avian Influenza Virus.Journal of virology · 2022Article
- Influenza A virus undergoes compartmentalized replication in vivo dominated by stochastic bottlenecks.Nature communications · 2022Article
- Within-host evolutionary dynamics of seasonal and pandemic human influenza A viruses in young children.eLife · 2021Article
- SARS-CoV-2 within-host diversity and transmission.Science (New York, N.Y.) · 2021Article
- VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples.Patterns (New York, N.Y.) · 2021Article
- Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa.Virus evolution · 2021Article
- Asynchrony between virus diversity and antibody selection limits influenza virus evolution.eLife · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The transmission bottleneck is defined as the number of viral particles that transmit from one host to establish an infection in another. Genome sequence data have been used to evaluate the size of the transmission bottleneck between humans infected with the influenza virus; however, the methods used to make these estimates have some limitations. Specifically, viral allele frequencies, which form the basis of many calculations, may not fully capture a process which involves the transmission of entire viral genomes. Here, we set out a novel approach for inferring viral transmission bottlenecks; our method combines an algorithm for haplotype reconstruction with maximum likelihood methods for bottleneck inference. This approach allows for rapid calculation and performs well when applied to data from simulated transmission events; errors in the haplotype reconstruction step did not adversely affect inferences of the population bottleneck. Applied to data from a previous household transmission study of influenza A infection, we confirm the result that the majority of transmission events involve a small number of viruses, albeit with slightly looser bottlenecks being inferred, with between 1 and 13 particles transmitted in the majority of cases. While influenza A transmission involves a tight population bottleneck, the bottleneck is not so tight as to universally prevent the transmission of within-host viral diversity.
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Registered trials
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.