ArticleGenetics2004
Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infection.
Article in Genetics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 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
31 citing papers in PubMed, 75 citations in OpenAlex.
- Comparative Evaluation of Open-Source Bioinformatics Pipelines for Full-Length Viral Genome Assembly.Viruses · 2024Article
- Predator-Prey Dynamics of Intra-Host Simian Immunodeficiency Virus Evolution Within the Untreated Host.Frontiers in immunology · 2021Article
- Molecular evolution of HIV-1 integrase during the 20 years prior to the first approval of integrase inhibitors.Virology journal · 2017Article
- New insights into HCV replication in original cells from Aedes mosquitoes.Virology journal · 2017Article
- Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model.PLoS biology · 2017Article
- Human Immunodeficiency Virus Immune Cell Receptors, Coreceptors, and Cofactors: Implications for Prevention and Treatment.AIDS patient care and STDs · 2016Review
- Genetic Consequences of Antiviral Therapy on HIV-1.Computational and mathematical methods in medicine · 2015Review
- Intra-host evolutionary rates in HIV-1C env and gag during primary infection.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2013Article
- HIV populations are large and accumulate high genetic diversity in a nonlinear fashion.Journal of virology · 2013Article
- The intra-host evolutionary and population dynamics of human immunodeficiency virus type 1: a phylogenetic perspective.Infectious disease reports · 2013Review
- The dynamics of HIV-1 adaptation in early infection.Genetics · 2012Article
- Stochastic simulations suggest that HIV-1 survives close to its error threshold.PLoS computational biology · 2012Article
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- Estimating frequencies of minority nevirapine-resistant strains in chronically HIV-1-infected individuals naive to nevirapine by using stochastic simulations and a mathematical model.Journal of virology · 2010Article
- Fitness epistasis and constraints on adaptation in a human immunodeficiency virus type 1 protein region.Genetics · 2010Article
- Recombination rate and selection strength in HIV intra-patient evolution.PLoS computational biology · 2010Article
- Genetic drift of HIV populations in culture.PLoS genetics · 2009Article
- Selection dramatically reduces effective population size in HIV-1 infection.BMC evolutionary biology · 2008Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Human immunodeficiency virus type 1 (HIV-1) has high replication and mutation rates that generate large census populations and high levels of genetic variation. We examined the roles of natural selection, population growth, random genetic drift, and recombination in shaping the variation in 1509 C2-V5 env sequences derived from nine men with chronic HIV-1 infection. These sequences were obtained from clinical visits that reflect the first 6-13.7 years of infection. Pairwise comparisons of nonsynonymous and synonymous distances, Tajima's D test, Fu and Li's D* test, and a test of recurrent mutation revealed evidence for episodes of nonneutral evolution in a total of 22 out of 145 blood samples, representing six of the nine individuals. Using three coalescent-based maximum-likelihood estimators, we found viral effective population sizes in all nine individuals to be approximately 10(3). We also show that a previous estimate of the effective population size of approximately 10(5) based on rare haplotype frequencies decreases to approximately 10(3) upon correcting a biased sampling procedure. We conclude that the genetic variation in these data sets can be explained by a predominance of random genetic drift of neutral mutations with brief episodes of natural selection that were frequently masked by recombination.
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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.