ArticlePLoS pathogens2007
Adaptation to human populations is revealed by within-host polymorphisms in HIV-1 and hepatitis C virus.
Article in PLoS pathogens, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 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
42 citing papers in PubMed, 58 citations in OpenAlex.
- Selection profiles in RNA viruses reflect the characteristics of viruses more than individual proteins.PLoS pathogens · 2026Article
- Balancing under constraint: Structural insights into norovirus evolution and antigenic innovation.PLoS pathogens · 2026Article
- Evolution of tandem repeats in putative circumsporozoite protein to enhance its function: A recent and exclusive event inCurrent research in microbial sciences · 2025Article
- Optimization of genetic distance threshold for inferring the CRF01_AE molecular network based on next-generation sequencing.Frontiers in cellular and infection microbiology · 2024Article
- Highly Ambiguous HIV-1 Pol Positions Encoding Multiple Amino Acids Usually Result from Antiviral or Immune Selection Pressure.AIDS research and human retroviruses · 2023Article
- Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification.PLoS computational biology · 2022Article
- The source of individual heterogeneity shapes infectious disease outbreaks.Proceedings. Biological sciences · 2022Article
- The Puzzle of HIV Neutral and Selective Evolution.Molecular biology and evolution · 2018Article
- Neutral Theory and Rapidly Evolving Viral Pathogens.Molecular biology and evolution · 2018Article
- Article
- High resolution sequencing of hepatitis C virus reveals limited intra-hepatic compartmentalization in end-stage liver disease.Journal of hepatology · 2017Article
- More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1.eLife · 2016Article
- Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV Variants.Viruses · 2015Observational
- Global Database-Driven Assessment of HIV-1 Adaptation to the Immune Repertoires of Human Populations.Journal of virology · 2015Article
- Genetic Consequences of Antiviral Therapy on HIV-1.Computational and mathematical methods in medicine · 2015Review
- Pathogen evolution and the immunological niche.Annals of the New York Academy of Sciences · 2014Article
- Comparison of viral Env proteins from acute and chronic infections with subtype C human immunodeficiency virus type 1 identifies differences in glycosylation and CCR5 utilization and suggests a new strategy for immunogen design.Journal of virology · 2013Article
- How effectively can HIV phylogenies be used to measure heritability?Evolution, medicine, and public health · 2013Article
- Higher HIV-1 genetic diversity is associated with AIDS and neuropsychological impairment.Virology · 2012Article
- Characterizing HIV transmission networks across the United States.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2012Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
CD8(+) cytotoxic T-lymphocytes (CTLs) perform a critical role in the immune control of viral infections, including those caused by human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV). As a result, genetic variation at CTL epitopes is strongly influenced by host-specific selection for either escape from the immune response, or reversion due to the replicative costs of escape mutations in the absence of CTL recognition. Under strong CTL-mediated selection, codon positions within epitopes may immediately "toggle" in response to each host, such that genetic variation in the circulating virus population is shaped by rapid adaptation to immune variation in the host population. However, this hypothesis neglects the substantial genetic variation that accumulates in virus populations within hosts. Here, we evaluate this quantity for a large number of HIV-1- (n > or = 3,000) and HCV-infected patients (n > or = 2,600) by screening bulk RT-PCR sequences for sequencing "mixtures" (i.e., ambiguous nucleotides), which act as site-specific markers of genetic variation within each host. We find that nonsynonymous mixtures are abundant and significantly associated with codon positions under host-specific CTL selection, which should deplete within-host variation by driving the fixation of the favored variant. Using a simple model, we demonstrate that this apparently contradictory outcome can be explained by the transmission of unfavorable variants to new hosts before they are removed by selection, which occurs more frequently when selection and transmission occur on similar time scales. Consequently, the circulating virus population is shaped by the transmission rate and the disparity in selection intensities for escape or reversion as much as it is shaped by the immune diversity of the host population, with potentially serious implications for vaccine design.
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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.