ReviewJournal of theoretical biology2009
Modeling sequence evolution in acute HIV-1 infection.
Review in Journal of theoretical biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 115 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
115 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards.Scientific reports · 2017Pooled it
- Designing a genome-based HIV incidence assay with high sensitivity and specificity.AIDS (London, England) · 2011Pooled it
- Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand.PLoS pathogens · 2020Trial
- HIV-1 genetic diversity to estimate time of infection and infer adherence to preexposure prophylaxis.AIDS (London, England) · 2019Trial
- Different pattern of stool and plasma gastrointestinal damage biomarkers during primary and chronic HIV infection.PloS one · 2019Trial
- Quantifying the diversification of hepatitis C virus (HCV) during primary infection: estimates of the in vivo mutation rate.PLoS pathogens · 2012Trial
- Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing.PLoS pathogens · 2012Trial
- Ultrasensitive single-genome sequencing reveals strong purifying selection in acute HIV-1 infection.bioRxiv : the preprint server for biology · 2026Article
- Viral Simulation Reveals Overestimation Bias in Within-Host Phylodynamic Migration Rate Estimates Under Selection.Molecular biology and evolution · 2026Article
- A Darwinian model for the evolution of drug resistance to long-acting PrEP during an early HIV infection.PloS one · 2026Article
- Review
- Article
- The Performance of the Current Algorithm of HIV Diagnosis.Iranian journal of public health · 2024Article
- Modeling resistance to the broadly neutralizing antibody PGT121 in people living with HIV-1.PLoS computational biology · 2024Article
- Leveraging Donor Populations to Study the Epidemiology and Pathogenesis of Transfusion-Transmitted and Emerging Infectious Diseases.Transfusion medicine reviews · 2023Article
- Article
- Propensity of selecting mutant parasites for the antimalarial drug cabamiquine.Nature communications · 2023Article
- Article
- Article
- Evolution during primary HIV infection does not require adaptive immune selection.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
55 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
17 authors.
Funding
Abstract
We describe a mathematical model and Monte Carlo (MC) simulation of viral evolution during acute infection. We consider both synchronous and asynchronous processes of viral infection of new target cells. The model enables an assessment of the expected sequence diversity in new HIV-1 infections originating from a single transmitted viral strain, estimation of the most recent common ancestor (MRCA) of the transmitted viral lineage, and estimation of the time to coalesce back to the MRCA. We also calculate the probability of the MRCA being the transmitted virus or an evolved variant. Excluding insertions and deletions, we assume HIV-1 evolves by base substitution without selection pressure during the earliest phase of HIV-1 infection prior to the immune response. Unlike phylogenetic methods that follow a lineage backwards to coalescence, we compare the observed data to a model of the diversification of a viral population forward in time. To illustrate the application of these methods, we provide detailed comparisons of the model and simulations results to 306 envelope sequences obtained from eight newly infected subjects at a single time point. The data from 68 patients were in good agreement with model predictions, and hence compatible with a single-strain infection evolving under no selection pressure. The diversity of the samples from the other two patients was too great to be explained by the model, suggesting multiple HIV-1-strains were transmitted. The model can also be applied to longitudinal patient data to estimate within-host viral evolutionary parameters.
Indexed as
Identifiers
What OpenQuestion holds
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.