ArticlePLoS genetics2014
Influenza virus drug resistance: a time-sampled population genetics perspective.
Article in PLoS genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
- Evolution of virulence of a plant RNA virus in developmental stage-structured host populations.Molecular biology and evolution · 2026Article
- Assessing Ancient DNA Sampling Strategies for Natural Selection Inference in Humans Using Allele Frequency Time Series Data.Genome biology and evolution · 2026Article
- Selection Estimation from Genetic Time-Series Data: Effects of Limited Sampling and Genetic Drift.Molecular biology and evolution · 2025Article
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- A novel expectation-maximization approach to infer general diploid selection from time-series genetic data.PLoS genetics · 2025Article
- A novel expectation-maximization approach to infer general diploid selection from time-series genetic data.bioRxiv : the preprint server for biology · 2025Article
- Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients.Virus evolution · 2025Article
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- Influenza A virus within-host evolution and positive selection in a densely sampled household cohort over three seasons.bioRxiv : the preprint server for biology · 2024Article
- The distribution of fitness effects during adaptive walks using a simple genetic network.PLoS genetics · 2024Article
- Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples.PLoS pathogens · 2023Review
- Estimating Temporally Variable Selection Intensity from Ancient DNA Data.Molecular biology and evolution · 2023Article
- Bézier interpolation improves the inference of dynamical models from data.Physical review. E · 2023Article
- Unpredictable repeatability in molecular evolution.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Recommendations for improving statistical inference in population genomics.PLoS biology · 2022Article
- A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population.Molecular biology and evolution · 2022Article
- Inferring the distribution of fitness effects in patient-sampled and experimental virus populations: two case studies.Heredity · 2022Article
- Effects of Selection at Linked Sites on Patterns of Genetic Variability.Annual review of ecology, evolution, and systematics · 2021Article
23 more citing papers are in PubMed but not listed here.
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Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The challenge of distinguishing genetic drift from selection remains a central focus of population genetics. Time-sampled data may provide a powerful tool for distinguishing these processes, and we here propose approximate Bayesian, maximum likelihood, and analytical methods for the inference of demography and selection from time course data. Utilizing these novel statistical and computational tools, we evaluate whole-genome datasets of an influenza A H1N1 strain in the presence and absence of oseltamivir (an inhibitor of neuraminidase) collected at thirteen time points. Results reveal a striking consistency amongst the three estimation procedures developed, showing strongly increased selection pressure in the presence of drug treatment. Importantly, these approaches re-identify the known oseltamivir resistance site, successfully validating the approaches used. Enticingly, a number of previously unknown variants have also been identified as being positively selected. Results are interpreted in the light of Fisher's Geometric Model, allowing for a quantification of the increased distance to optimum exerted by the presence of drug, and theoretical predictions regarding the distribution of beneficial fitness effects of contending mutations are empirically tested. Further, given the fit to expectations of the Geometric Model, results suggest the ability to predict certain aspects of viral evolution in response to changing host environments and novel selective pressures.
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