ArticleJournal of virology2013
Quantifying selection against synonymous mutations in HIV-1 env evolution.
Article in Journal of virology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Analysis of temporal virus evolution and intra-host diversity in long-term non-progressors by bulk next-generation sequencing.Microbiology spectrum · 2026Article
- Profiling HIV1-host protein-protein interaction networks in patient-derived exosome proteins: impact on pathophysiology and innate immune pathways.Virology journal · 2025Article
- The Intersection of HIV and Pulmonary Vascular Health: From HIV Evolution to Vascular Cell Types to Disease Mechanisms.Journal of vascular diseases · 2024Article
- Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates.Virus evolution · 2023Article
- Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation.Virus evolution · 2023Article
- Innate immune pathways act synergistically to constrain RNA virus evolution in Drosophila melanogaster.Nature ecology & evolution · 2022Article
- Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution.Evolution, medicine, and public health · 2022Article
- MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution.Nucleic acids research · 2021Article
- Comprehensive analysis of genomic diversity of SARS-CoV-2 in different geographic regions of India: an endeavour to classify Indian SARS-CoV-2 strains on the basis of co-existing mutations.Archives of virology · 2021Article
- Inference of population genetic parameters from an irregular time series of seasonal influenza virus sequences.Genetics · 2021Article
- Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history.PLoS biology · 2020Article
- Assessing Genome-Wide Diversity in European Hantaviruses through Sequence Capture from Natural Host Samples.Viruses · 2020Article
- Coupling adaptive molecular evolution to phylodynamics using fitness-dependent birth-death models.eLife · 2019Article
- Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness.Cell host & microbe · 2019Article
- Evolution of HIV-1 within untreated individuals and at the population scale in Uganda.PLoS pathogens · 2018Article
- Neutral Theory and Rapidly Evolving Viral Pathogens.Molecular biology and evolution · 2018Article
- The Puzzle of HIV Neutral and Selective Evolution.Molecular biology and evolution · 2018Article
- Article
- New windows into retroviral RNA structures.Retrovirology · 2018Review
- Evaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts.Virus evolution · 2018Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Intrapatient evolution of human immunodeficiency virus type 1 (HIV-1) is driven by the adaptive immune system resulting in rapid change of HIV-1 proteins. When cytotoxic CD8(+) T cells or neutralizing antibodies target a new epitope, the virus often escapes via nonsynonymous mutations that impair recognition. Synonymous mutations do not affect this interplay and are often assumed to be neutral. We test this assumption by tracking synonymous mutations in longitudinal intrapatient data from the C2-V5 part of the env gene. We find that most synonymous variants are lost even though they often reach high frequencies in the viral population, suggesting a cost to the virus. Using published data from SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) assays, we find that synonymous mutations that disrupt base pairs in RNA stems flanking the variable loops of gp120 are more likely to be lost than other synonymous changes: these RNA hairpins might be important for HIV-1. Computational modeling indicates that, to be consistent with the data, a large fraction of synonymous mutations in this genomic region need to be deleterious with a cost on the order of 0.002 per day. This weak selection against synonymous substitutions does not result in a strong pattern of conservation in cross-sectional data but slows down the rate of evolution considerably. Our findings are consistent with the notion that large-scale patterns of RNA structure are functionally relevant, whereas the precise base pairing pattern is not.
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