ArticleeLife2015
Population genomics of intrapatient HIV-1 evolution.
Article in eLife, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 149 papers.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
149 citing papers in PubMed.
- HIV RNA Rebound in Seminal Plasma after Antiretroviral Treatment Interruption.Journal of virology · 2020Trial
- Integrating haplotype-enhanced HIV surveillance with national databases improves the resolution of transmission networks, drug resistance, and risk assessment.Emerging microbes & infections · 2026Article
- Ultrasensitive single-genome sequencing reveals strong purifying selection in acute HIV-1 infection.bioRxiv : the preprint server for biology · 2026Article
- The genomic sequence of packaged viral ribonucleic acid predicts mucosal HIV-1 transmission fitness.iScience · 2026Article
- Identifying Conserved Regions in HIV-1 Proteins by Entropy Analysis of Sequence Variability.International journal of molecular sciences · 2026Article
- Recurrent mutations drive rapid HIV escape from two broadly neutralizing antibodies in vivo.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Atlas of HIV cis-regulatory elements reveals extensive transcriptional variation across clades, isolates, and within individuals.bioRxiv : the preprint server for biology · 2026Article
- Linkage-aware inference of fitness from short-read time-series genomic data.bioRxiv : the preprint server for biology · 2026Article
- Substantial deceleration of adaptation of HIV-1 within 1500 generations in an experimental evolution: a genomic perspective.Virus evolution · 2026Article
- Chronic infections can generate SARS-CoV-2-like bursts of viral evolution without epistasis.Virus evolution · 2026Article
- Linkage-aware inference of fitness from short-read time-series genomic data.Virus evolution · 2026Article
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- Ecological diversification in rapidly evolving populations.bioRxiv : the preprint server for biology · 2025Article
- Distinct modes of evolution drive HIV escape from two broadly neutralizing antibodies.bioRxiv : the preprint server for biology · 2025Article
- HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data.BMC bioinformatics · 2025Article
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- Inferring fitness seascapes from evolutionary histories.bioRxiv : the preprint server for biology · 2025Article
- Phylodynamics for Human Immunodeficiency Virus Prevention: A Miami-Dade County Case Study.The Journal of infectious diseases · 2025Article
- A binary trait model reveals the fitness effects of HIV-1 escape from T cell responses.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
89 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
Many microbial populations rapidly adapt to changing environments with multiple variants competing for survival. To quantify such complex evolutionary dynamics in vivo, time resolved and genome wide data including rare variants are essential. We performed whole-genome deep sequencing of HIV-1 populations in 9 untreated patients, with 6-12 longitudinal samples per patient spanning 5-8 years of infection. The data can be accessed and explored via an interactive web application. We show that patterns of minor diversity are reproducible between patients and mirror global HIV-1 diversity, suggesting a universal landscape of fitness costs that control diversity. Reversions towards the ancestral HIV-1 sequence are observed throughout infection and account for almost one third of all sequence changes. Reversion rates depend strongly on conservation. Frequent recombination limits linkage disequilibrium to about 100 bp in most of the genome, but strong hitch-hiking due to short range linkage limits diversity.
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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.