ArticlePLoS computational biology2009
Identifying changes in selective constraints: host shifts in influenza.
Article in PLoS computational biology, 2009. 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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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.
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Who cites it
83 citing papers in PubMed, 141 citations in OpenAlex.
- The genetic foundations of convergent traits.Nature reviews. Genetics · 2026Review
- Detecting Convergence of Amino Acid Physicochemical Properties Underlying the Organismal Adaptive Convergent Evolution.Molecular ecology resources · 2025Article
- Multiple transitions to high l-DOPA 4,5-dioxygenase activity reveal molecular pathways to convergent betalain pigmentation in Caryophyllales.The New phytologist · 2025Article
- The evolution and epidemiology of H3N2 canine influenza virus after 20 years in dogs.Epidemiology and infection · 2025Article
- Complexin-1 enhances ultrasound neurotransmission in the mammalian auditory pathway.Nature genetics · 2024Article
- Accurate Detection of Convergent Mutations in Large Protein Alignments With ConDor.Genome biology and evolution · 2024Article
- Genomic characterization of equine influenza A subtype H3N8 viruses by long read sequencing and functional analyses of the PB1-F2 virulence factor of A/equine/Paris/1/2018.Veterinary research · 2024Article
- Changing selection on amino acid substitutions in Gag protein between major HIV-1 subtypes.Virus evolution · 2024Article
- Signatures of Extreme Longevity: A Perspective from Bivalve Molecular Evolution.Genome biology and evolution · 2023Article
- Genomic Signatures Associated with Transitions to Viviparity in Cyprinodontiformes.Molecular biology and evolution · 2023Article
- Interlocus Gene Conversion, Natural Selection, and Paralog Homogenization.Molecular biology and evolution · 2023Article
- Measuring the relative contribution to predictive power of modern nucleotide substitution modeling approaches.Bioinformatics advances · 2023Article
- Phylogenetic inference of changes in amino acid propensities with single-position resolution.PLoS computational biology · 2022Article
- Hunting alters viral transmission and evolution in a large carnivore.Nature ecology & evolution · 2022Article
- Whole-Genome Sequence Approach and Phylogenomic Stratification Improve the Association Analysis of Mutations With Patient Data in Influenza Surveillance.Frontiers in microbiology · 2022Article
- Characterizing Amino Acid Substitution with Complete Linkage of Sites on a Lineage.Genome biology and evolution · 2021Article
- Inferring the number and position of changes in selective regime in a non-equilibrium mutation-selection framework.BMC ecology and evolution · 2021Article
- Host-Adaptive Signatures of H3N2 Influenza Virus in Canine.Frontiers in veterinary science · 2021Article
- Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (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
23 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
The natural reservoir of Influenza A is waterfowl. Normally, waterfowl viruses are not adapted to infect and spread in the human population. Sometimes, through reassortment or through whole host shift events, genetic material from waterfowl viruses is introduced into the human population causing worldwide pandemics. Identifying which mutations allow viruses from avian origin to spread successfully in the human population is of great importance in predicting and controlling influenza pandemics. Here we describe a novel approach to identify such mutations. We use a sitewise non-homogeneous phylogenetic model that explicitly takes into account differences in the equilibrium frequencies of amino acids in different hosts and locations. We identify 172 amino acid sites with strong support and 518 sites with moderate support of different selection constraints in human and avian viruses. The sites that we identify provide an invaluable resource to experimental virologists studying adaptation of avian flu viruses to the human host. Identification of the sequence changes necessary for host shifts would help us predict the pandemic potential of various strains. The method is of broad applicability to investigating changes in selective constraints when the timing of the changes is known.
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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.