ArticleScientific reports2018
Sweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed.
- In silico genomic surveillance by CoVerage predicts and characterizes SARS-CoV-2 variants of interest.Nature communications · 2025Article
- Characterization of Conserved Evolution in H7N9 Avian Influenza Virus Prior Mass Vaccination.Virulence · 2024Article
- Evolution of the North American Lineage H7 Avian Influenza Viruses in Association with H7 Virus's Introduction to Poultry.Journal of virology · 2022Article
- Genetic and Antigenic Characterization of an Expanding H3 Influenza A Virus Clade in U.S. Swine Visualized by Nextstrain.mSphere · 2022Article
- Antigenic characterization of influenza and SARS-CoV-2 viruses.Analytical and bioanalytical chemistry · 2022Review
- Limited Predictability of Amino Acid Substitutions in Seasonal Influenza Viruses.Molecular biology and evolution · 2021Article
- Article
- Spatial and temporal coevolution of N2 neuraminidase and H1 and H3 hemagglutinin genes of influenza A virus in US swine.Virus evolution · 2021Article
- Low 2018/19 vaccine effectiveness against influenza A(H3N2) among 15-64-year-olds in Europe: exploration by birth cohort.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2019Article
- Review
- Structures and functions linked to genome-wide adaptation of human influenza A viruses.Scientific reports · 2019Article
- Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.Viruses · 2018Article
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8 authors.
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Abstract
Monitoring changes in influenza A virus genomes is crucial to understand its rapid evolution and adaptation to changing conditions e.g. establishment within novel host species. Selective sweeps represent a rapid mode of adaptation and are typically observed in human influenza A viruses. We describe Sweep Dynamics (SD) plots, a computational method combining phylogenetic algorithms with statistical techniques to characterize the molecular adaptation of rapidly evolving viruses from longitudinal sequence data. SD plots facilitate the identification of selective sweeps, the time periods in which these occurred and associated changes providing a selective advantage to the virus. We studied the past genome-wide adaptation of the 2009 pandemic H1N1 influenza A (pH1N1) and seasonal H3N2 influenza A (sH3N2) viruses. The pH1N1 influenza virus showed simultaneous amino acid changes in various proteins, particularly in seasons of high pH1N1 activity. Partially, these changes resulted in functional alterations facilitating sustained human-to-human transmission. In the evolution of sH3N2 influenza viruses, we detected changes characterizing vaccine strains, which were occasionally revealed in selective sweeps one season prior to the WHO recommendation. Taken together, SD plots allow monitoring and characterizing the adaptive evolution of influenza A viruses by identifying selective sweeps and their associated signatures.
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