ArticleMolecular biology and evolution2012
Detecting patches of protein sites of influenza A viruses under positive selection.
Article in Molecular biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed, 30 citations in OpenAlex.
- Integrated Genomic Analysis Uncovers the Evolutionary Landscape and Global Dissemination of Senecavirus A.Veterinary sciences · 2026Article
- Genetic Characterization and Pathogenicity of a Triple-Reassortant H1N1 Swine Influenza Virus Isolated in Guangdong.Transboundary and emerging diseases · 2026Article
- Two genotypes of H3N2 swine influenza viruses identified in pigs from Shandong Province, China.Frontiers in cellular and infection microbiology · 2024Article
- 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
- Relative Evolutionary Rates in Proteins Are Largely Insensitive to the Substitution Model.Molecular biology and evolution · 2018Article
- The influenza virus hemagglutinin head evolves faster than the stalk domain.Scientific reports · 2018Article
- EDEN: evolutionary dynamics within environments.Bioinformatics (Oxford, England) · 2017Article
- Article
- Sequence amplification via cell passaging creates spurious signals of positive adaptation in influenza virus H3N2 hemagglutinin.Virus evolution · 2016Article
- Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi.Nature communications · 2016Article
- mutation3D: Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome.Human mutation · 2016Article
- Causes of evolutionary rate variation among protein sites.Nature reviews. Genetics · 2016Review
- Determination of antigenicity-altering patches on the major surface protein of human influenza A/H3N2 viruses.Virus evolution · 2016Article
- Structure and receptor binding preferences of recombinant human A(H3N2) virus hemagglutinins.Virology · 2015Article
- Genetic and epidemiological insights into the emergence of peste des petits ruminants virus (PPRV) across Asia and Africa.Scientific reports · 2014Article
- The genetics of host-virus coevolution in invertebrates.Current opinion in virology · 2014Review
- Computational prediction of vaccine strains for human influenza A (H3N2) viruses.Journal of virology · 2014Article
- Phylogenetic Gaussian process model for the inference of functionally important regions in protein tertiary structures.PLoS computational biology · 2014Article
- Monitoring the antigenic evolution of human influenza A viruses to understand how and when viruses escape from existing immunity.BMC research notes · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Influenza A viruses are single-stranded RNA viruses capable of evolving rapidly to adapt to environmental conditions. Examples include the establishment of a virus in a novel host or an adaptation to increasing immunity within the host population due to prior infection or vaccination against a circulating strain. Knowledge of the viral protein regions under positive selection is therefore crucial for surveillance. We have developed a method for detecting positively selected patches of sites on the surface of viral proteins, which we assume to be relevant for adaptive evolution. We measure positive selection based on dN/dS ratios of genetic changes inferred by considering the phylogenetic structure of the data and suggest a graph-cut algorithm to identify such regions. Our algorithm searches for dense and spatially distinct clusters of sites under positive selection on the protein surface. For the hemagglutinin protein of human influenza A viruses of the subtypes H3N2 and H1N1, our predicted sites significantly overlap with known antigenic and receptor-binding sites. From the structure and sequence data of the 2009 swine-origin influenza A/H1N1 hemagglutinin and PB2 protein, we identified regions that provide evidence of evolution under positive selection since introduction of the virus into the human population. The changes in PB2 overlap with sites reported to be associated with mammalian adaptation of the influenza A virus. Application of our technique to the protein structures of viruses of yet unknown adaptive behavior could identify further candidate regions that are important for host-virus interaction.
Indexed as
Identifiers
What OpenQuestion holds
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.