ArticleGenetics2004
The molecular population genetics of HIV-1 group O.
Article in Genetics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Replicative fitness and pathogenicity of primate lentiviruses in lymphoid tissue, primary human and chimpanzee cells: relation to possible jumps to humans.EBioMedicine · 2024Article
- CGRWDL: alignment-free phylogeny reconstruction method for viruses based on chaos game representation weighted by dynamical language model.Frontiers in microbiology · 2024Article
- A snapshot on HIV-1 evolution through the identification of phylogenetic-specific properties of HIV-1 integrases M/O.PLoS pathogens · 2023Article
- Site-Specific Evolutionary Rate Shifts in HIV-1 and SIV.Viruses · 2020Article
- Phylogenetic Analysis of HIV-1 Genomes Based on the Position-Weighted K-mers Method.Entropy (Basel, Switzerland) · 2020Article
- Structural perspectives on HIV-1 Vif and APOBEC3 restriction factor interactions.Protein science : a publication of the Protein Society · 2020Review
- Article
- The Two-Phase Emergence of Non Pandemic HIV-1 Group O in Cameroon.PLoS pathogens · 2015Article
- Short Communication: HIV-1 Subtype B in the Dominican Republic: Evolution and Molecular Epidemiology.AIDS research and human retroviruses · 2015Article
- Eight challenges in phylodynamic inference.Epidemics · 2015Article
- Molecular epidemiology, phylogeny and evolution of the filarial nematode Wuchereria bancrofti.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2014Review
- Nef proteins of epidemic HIV-1 group O strains antagonize human tetherin.Cell host & microbe · 2014Article
- HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations.Science (New York, N.Y.) · 2014Article
- Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest?Journal of acquired immune deficiency syndromes (1999) · 2014Review
- Non-M variants of human immunodeficiency virus type 1.Clinical microbiology reviews · 2013Review
- Within-host and between-host evolutionary rates across the HIV-1 genome.Retrovirology · 2013Article
- Estimating the rate of intersubtype recombination in early HIV-1 group M strains.Journal of virology · 2013Article
- Viral phylodynamics.PLoS computational biology · 2013Review
- Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa.Nature genetics · 2012Article
- Article
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8 authors.
Funding
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Abstract
HIV-1 group O originated through cross-species transmission of SIV from chimpanzees to humans and has established a relatively low prevalence in Central Africa. Here, we infer the population genetics and epidemic history of HIV-1 group O from viral gene sequence data and evaluate the effect of variable evolutionary rates and recombination on our estimates. First, model selection tools were used to specify suitable evolutionary and coalescent models for HIV group O. Second, divergence times and population genetic parameters were estimated in a Bayesian framework using Markov chain Monte Carlo sampling, under both strict and relaxed molecular clock methods. Our results date the origin of the group O radiation to around 1920 (1890-1940), a time frame similar to that estimated for HIV-1 group M. However, group O infections, which remain almost wholly restricted to Cameroon, show a slower rate of exponential growth during the twentieth century, explaining their lower current prevalence. To explore the effect of recombination, the Bayesian framework is extended to incorporate multiple unlinked loci. Although recombination can bias estimates of the time to the most recent common ancestor, this effect does not appear to be important for HIV-1 group O. In addition, we show that evolutionary rate estimates for different HIV genes accurately reflect differential selective constraints along the HIV genome.
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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.