ArticleVirus evolution2016
Sequence amplification via cell passaging creates spurious signals of positive adaptation in influenza virus H3N2 hemagglutinin.
Article in Virus evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Intrahost HA polymorphisms and culture adaptation shape antigenic profiles of H3N2 influenza viruses.Journal of virology · 2026Article
- Epistasis mediates the evolution of the receptor binding mode in recent human H3N2 hemagglutinin.Nature communications · 2024Article
- Glyco-engineered MDCK cells display preferred receptors of H3N2 influenza absent in eggs used for vaccines.Nature communications · 2023Article
- Egg-adaptive mutations of human influenza H3N2 virus are contingent on natural evolution.PLoS pathogens · 2022Article
- MADE: A Computational Tool for Predicting Vaccine Effectiveness for the Influenza A(H3N2) Virus Adapted to Embryonated Eggs.Vaccines · 2022Article
- Within-Host Viral Diversity: A Window into Viral Evolution.Annual review of virology · 2020Review
- Cell culture propagation of foot-and-mouth disease virus: adaptive amino acid substitutions in structural proteins and their functional implications.Virus genes · 2020Review
- Linking influenza virus evolution within and between human hosts.Virus evolution · 2020Article
- Allele-specific nonstationarity in evolution of influenza A virus surface proteins.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season.Virus evolution · 2019Review
- Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility.Cell host & microbe · 2019Article
- Structures and functions linked to genome-wide adaptation of human influenza A viruses.Scientific reports · 2019Article
- Insights into the antigenic advancement of influenza A(H3N2) viruses, 2011-2018.Scientific reports · 2019Article
- Influenza passaging annotations: what they tell us and why we should listen.Virus evolution · 2019Article
- Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- The influenza virus hemagglutinin head evolves faster than the stalk domain.Scientific reports · 2018Article
- Hsp90 shapes protein and RNA evolution to balance trade-offs between protein stability and aggregation.Nature communications · 2018Article
- Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology.Trends in microbiology · 2018Review
- The evolution of seasonal influenza viruses.Nature reviews. Microbiology · 2018Review
- Integrating patient and whole-genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) viruses.Microbial genomics · 2018Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Clinical influenza A virus isolates are frequently not sequenced directly. Instead, a majority of these isolates (~70% in 2015) are first subjected to passaging for amplification, most commonly in non-human cell culture. Here, we find that this passaging leaves distinct signals of adaptation, which can confound evolutionary analyses of the viral sequences. We find distinct patterns of adaptation to Madin-Darby (MDCK) and monkey cell culture absent from unpassaged hemagglutinin sequences. These patterns also dominate pooled datasets not separated by passaging type, and they increase in proportion to the number of passages performed. By contrast, MDCK-SIAT1 passaged sequences seem mostly (but not entirely) free of passaging adaptations. Contrary to previous studies, we find that using only internal branches of influenza virus phylogenetic trees is insufficient to correct for passaging artifacts. These artifacts can only be safely avoided by excluding passaged sequences entirely from subsequent analysis. We conclude that future influenza virus evolutionary analyses should appropriately control for potentially confounding effects of passaging adaptations.
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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.