ArticleMolecular biology and evolution2015
Fitness Inference from Short-Read Data: Within-Host Evolution of a Reassortant H5N1 Influenza Virus.
Article in Molecular biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 41 citations in OpenAlex.
- Direct estimation of genotype fitness from time series.bioRxiv : the preprint server for biology · 2026Article
- Linkage-aware inference of fitness from short-read time-series genomic data.bioRxiv : the preprint server for biology · 2026Article
- Linkage-aware inference of fitness from short-read time-series genomic data.Virus evolution · 2026Article
- Article
- Variable rates of SARS-CoV-2 evolution in chronic infections.PLoS pathogens · 2025Article
- Efficient epistasis inference via higher-order covariance matrix factorization.bioRxiv : the preprint server for biology · 2024Article
- Divergent Pathogenesis and Transmission of Highly Pathogenic Avian Influenza A(H5N1) in Swine.Emerging infectious diseases · 2024Article
- Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection.Virus evolution · 2024Article
- Viruses of a key coral symbiont exhibit temperature-driven productivity across a reefscape.ISME communications · 2023Article
- Inferring Epistasis from Genetic Time-series Data.Molecular biology and evolution · 2022Article
- Herpesviruses and their genetic diversity in the blood virome of healthy individuals: effect of aging.Immunity & ageing : I & A · 2022Article
- Reconstruction of evolving gene variants and fitness from short sequencing reads.Nature chemical biology · 2021Article
- Article
- Within-Host Viral Diversity: A Window into Viral Evolution.Annual review of virology · 2020Review
- Evolutionary dynamics of Tomato spotted wilt virus within and between alternate plant hosts and thrips.Scientific reports · 2020Article
- A large effective population size for established within-host influenza virus infection.eLife · 2020Article
- Inferring Transmission Bottleneck Size from Viral Sequence Data Using a Novel Haplotype Reconstruction Method.Journal of virology · 2020Article
- A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection.PLoS pathogens · 2020Article
- Symbiont evolution during the free-living phase can improve host colonization.Microbiology (Reading, England) · 2019Article
- Host and viral determinants of influenza A virus species specificity.Nature reviews. Microbiology · 2019Review
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1 author at 1 institution in 1 country.
Funding
Abstract
We present a method to infer the role of selection acting during the within-host evolution of the influenza virus from short-read genome sequence data. Linkage disequilibrium between loci is accounted for by treating short-read sequences as noisy multilocus emissions from an underlying model of haplotype evolution. A hierarchical model-selection procedure is used to infer the underlying fitness landscape of the virus insofar as that landscape is explored by the viral population. In a first application of our method, we analyze data from an evolutionary experiment describing the growth of a reassortant H5N1 virus in ferrets. Across two sets of replica experiments we infer multiple alleles to be under selection, including variants associated with receptor binding specificity, glycosylation, and with the increased transmissibility of the virus. We identify epistasis as an important component of the within-host fitness landscape, and show that adaptation can proceed through multiple genetic pathways.
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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.