ArticleProceedings of the National Academy of Sciences of the United States of America2007
Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 128 papers.
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128 citing papers in PubMed, 248 citations in OpenAlex.
- VirPLM: antigenic prediction of influenza A/H3N2 viruses with a fine-tuned protein language model.Bioinformatics (Oxford, England) · 2026Article
- Marked Antigenic Divergence and Evolutionary Analysis of H5 AIVs from Wild Birds in East China, 2013-2022.Animals : an open access journal from MDPI · 2026Article
- Predicting the antigenic evolution of seasonal influenza viruses using phylogenetic convergence.bioRxiv : the preprint server for biology · 2026Article
- Genomic surveillance of H1N1, H3N2 and influenza B Victoria lineage viruses in Qingyang (2020-2023): phylogenetic and molecular characteristics analysis of HA/NA genes.BMC infectious diseases · 2026Article
- CAPYBARA: A generalizable framework for predicting serological measurements across human cohorts.PLoS computational biology · 2026Article
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- High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains.bioRxiv : the preprint server for biology · 2025Article
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- Epitope-Specific Antibody Immunodominance Driving Antibody and Influenza Viral Evolution During 2010- 2024.Open forum infectious diseases · 2025Article
- Evolving Dynamics of Whole-Genome Influenza A/H3N2 Viruses Isolated in Cameroon.Advances in virology · 2025Article
- Concepts and Methods for Predicting Viral Evolution.Methods in molecular biology (Clifton, N.J.) · 2025Article
- The Development History, Structural Composition, and Functions of Influenza Viruses and the Progress of Influenza Virus Inhibitors in Clinics and Clinical Trials.Mini reviews in medicinal chemistry · 2025Review
- Progress of Influenza Viruses and Inhibitors.Current medicinal chemistry · 2025Review
- Concepts and methods for predicting viral evolution.bioRxiv : the preprint server for biology · 2024Article
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- Evolutionary Insights from Association Rule Mining of Co-Occurring Mutations in Influenza Hemagglutinin and Neuraminidase.Viruses · 2024Article
- Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States.eLife · 2024Article
- Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States.medRxiv : the preprint server for health sciences · 2024Article
- Seasonal antigenic prediction of influenza A H3N2 using machine learning.Nature communications · 2024Article
- Predictive evolutionary modelling for influenza virus by site-based dynamics of mutations.Nature communications · 2024Article
68 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The HA1 domain of HA, the major antigenic protein of influenza A viruses, contains all of the antigenic sites of HA and is under continual immune-driven selection. To resolve controversies on whether only a few or many residue sites of HA1 have undergone positive selection, whether positive selection at HA1 is continual or punctuated, and whether antigenic change is punctuated, we introduce an approach to analyze 2,248 HA1 sequences collected from 1968 to 2005. We identify 95 substitutions at 63 sites from 1968 to 2005 and show that each substitution occurred very rapidly. The rapid substitution and the fact that 57 of the 63 sites are antigenic sites indicate that hitchhiking plays a minor role and that most of these sites, many more than previously found, have undergone positive selection. Strikingly, 88 of the 95 substitutions occurred in groups, and multiple mutations at antigenic sites sped up the fixation process. Our results suggest that positive selection has been ongoing most of the time, not sporadic, and that multiple mutations at antigenic sites cumulatively enhance antigenic drift, indicating that antigenic change is less punctuated than recently proposed.
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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.