ArticleRetrovirology2013
Within-host and between-host evolutionary rates across the HIV-1 genome.
Article in Retrovirology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed.
- Preservation of tetherin and CD4 counter-activities in circulating Vpu alleles despite extensive sequence variation within HIV-1 infected individuals.PLoS pathogens · 2014Trial
- Divalent HIV-1 gp120 Immunogen Exhibits Selective Avidity for Broadly Neutralizing Antibody VRC01 Precursors.Vaccines · 2026Article
- Phylogenetics and molecular evolution to understand and curb the HIV pandemic.Nature reviews. Microbiology · 2026Review
- Bayesian mixture models for phylogenetic source attribution from consensus sequences and time since infection estimates.Statistical methods in medical research · 2025Article
- Spillover: Mechanisms, Genetic Barriers, and the Role of Reservoirs in Emerging Pathogens.Microorganisms · 2024Review
- Impact of Variable Sampling on Estimates of HIV-1 Reservoir Formation Dates.The Journal of infectious diseases · 2024Article
- Increasing intra- and inter-subtype HIV diversity despite declining HIV incidence in Uganda.medRxiv : the preprint server for health sciences · 2024Article
- Characterization of an imported HIV-1 A1/A7/G recombinant in China.Virology journal · 2024Article
- Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study.Virus evolution · 2024Article
- Evolutionary dynamics of dengue virus in India.PLoS pathogens · 2023Article
- Recombinant characteristics of three novel HIV-1 second-generation recombinant forms composed of CRF01_AE and CRF07_BC isolated in Hebei province, China.Archives of virology · 2023Article
- bayroot: Bayesian sampling of HIV-1 integration dates by root-to-tip regression.Virus evolution · 2023Article
- Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates.Virus evolution · 2023Article
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- Factors influencing estimates of HIV-1 infection timing using BEAST.PLoS computational biology · 2021Article
- Predator-Prey Dynamics of Intra-Host Simian Immunodeficiency Virus Evolution Within the Untreated Host.Frontiers in immunology · 2021Article
- Cross-scale dynamics and the evolutionary emergence of infectious diseases.Virus evolution · 2021Article
- Persistence of HIV transmission clusters among people who inject drugs.AIDS (London, England) · 2020Article
- PIQMEE: Bayesian Phylodynamic Method for Analysis of Large Data Sets with Duplicate Sequences.Molecular biology and evolution · 2020Article
22 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
Abstract
backgroundHIV evolves rapidly at the epidemiological level but also at the within-host level. The virus' within-host evolutionary rates have been argued to be much higher than its between-host evolutionary rates. However, this conclusion relies on analyses of a short portion of the virus envelope gene. Here, we study in detail these evolutionary rates across the HIV genome.
resultsWe build phylogenies using a relaxed molecular clock assumption to estimate evolutionary rates in different regions of the HIV genome. We find that these rates vary strongly across the genome, with higher rates in the envelope gene (env). Within-host evolutionary rates are consistently higher than between-host rates throughout the HIV genome. This difference is significantly more pronounced in env. Finally, we find weak differences between overlapping and non-overlapping regions.
conclusionsWe provide a genome-wide overview of the differences in the HIV rates of molecular evolution at the within- and between-host levels. Contrary to hepatitis C virus, where differences are only located in the envelope gene, within-host evolutionary rates are higher than between-host evolutionary rates across the whole HIV genome. This supports the hypothesis that HIV strains that are less adapted to the host have an advantage during transmission. The most likely mechanism for this is storage and then preferential transmission of viruses in latent T-cells. These results shed a new light on the role of the transmission bottleneck in the evolutionary dynamics of HIV.
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