ArticleVirus evolution2017
The substitution rate of HIV-1 subtypes: a genomic approach.
Article in Virus evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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36 citing papers in PubMed, 42 citations in OpenAlex.
- Phylogenetic Evidence of Local HIV-1 Transmission and Antiretroviral Drug Resistance in the Middle East and North Africa.Viruses · 2026Article
- HIV Transmission Dynamics in Greater Mexico City are Shaped by Dense Spatial Mixing.Research square · 2026Article
- HIV Transmission Dynamics in Greater Mexico City are Shaped by Dense Spatial Mixing.medRxiv : the preprint server for health sciences · 2026Article
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- Robust phylodynamic inference and model specification for HIV transmission dynamics.Epidemics · 2025Article
- Topolow: a mapping algorithm for antigenic cross-reactivity and binding affinity assays.Bioinformatics (Oxford, England) · 2025Article
- Impact of Phylogenetic Method Choice on Indel Analyses in HIV-1 Subtype B.Genome biology and evolution · 2025Article
- Quantifying prevalence and risk factors of HIV multiple infection in Uganda from population-based deep-sequence data.PLoS pathogens · 2025Article
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- Phylodynamics analysis of HIV epidemic history in Belarus in 1987-2022.Frontiers in epidemiology · 2025Article
- Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model.Systematic biology · 2024Article
- Optimization of genetic distance threshold for inferring the CRF01_AE molecular network based on next-generation sequencing.Frontiers in cellular and infection microbiology · 2024Article
- Evolutionary implications of SARS-CoV-2 vaccination for the future design of vaccination strategies.Communications medicine · 2023Review
- Reconstructing the phylodynamic history and geographic spread of the CRF01_AE-predominant HIV-1 epidemic in the Philippines from PR/RT sequences sampled from 2008 to 2018.Virus evolution · 2023Article
- Article
- Phylodynamics of HIV in the Mexico City Metropolitan Region.Journal of virology · 2022Article
- Molecular epidemiology of HIV-1 in Oryol Oblast, Russia.Virus evolution · 2022Article
- Exploring the Evolutionary History and Phylodynamics of Human Immunodeficiency Virus Type 1 Outbreak From Unnao, India Using Phylogenetic Approach.Frontiers in microbiology · 2022Article
- Molecular Biology and Diversification of Human Retroviruses.Frontiers in virology (Lausanne, Switzerland) · 2022Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
HIV-1M causes most infections in the AIDS pandemic. Its genetic diversity is defined by nine pure subtypes and more than sixty recombinant forms. We have performed a comparative analysis of the evolutionary rate of five pure subtypes (A1, B, C, D, and G) and two circulating recombinant forms (CRF01_AE and CRF02 AG) using data obtained from nearly complete genome coding sequences. Times to the most recent common ancestor (tMRCA) and substitution rates of these HIV genomes, and their genomic partitions, were estimated by Bayesian coalescent analyses. Genomic substitution rate estimates were compared between the HIV-1 datasets analyzed by means of randomization tests. Significant differences in the rate of evolution were found between subtypes, with subtypes C and A1 and CRF01_AE displaying the highest rates. On the other hand, CRF02_AG and subtype D were the slowest evolving types. Using a different molecular clock model for each genomic partition led to more precise tMRCA estimates than when linking the same clock along the HIV genome. Overall, the earliest tMRCA corresponded to subtype A1 (median = 1941, 95% HPD = 1943-55), whereas the most recent tMRCA corresponded to subtype G and CRF01_AE subset 3 (median = 1971, 95% HPD = 1967-75 and median = 1972, 95% HPD = 1970-75, respectively). These results suggest that both biological and epidemiological differences among HIV-1M subtypes are reflected in their evolutionary dynamics. The estimates obtained for tMRCAs and substitution rates provide information that can be used as prior distributions in future Bayesian coalescent analyses of specific HIV-1 subtypes/CRFs and genes.
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