ArticlePLoS computational biology2010
Accurately measuring recombination between closely related HIV-1 genomes.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 68 citations in OpenAlex.
- Pool-packaged AAV libraries exhibit extensive length-dependent and homology-dependent chimerism.Nature biotechnology · 2026Article
- HIV-1 Genetic Diversity and Drug Resistance Mutations Among Patients on Antiretroviral Therapy in Nairobi County, Kenya.Advances in virology · 2026Article
- Aberrant strand transfer events across multiple stages of reverse transcription shape the heterogeneous landscape of the HIV-1 reservoir.Communications biology · 2025Article
- CROPseq-multi: a universal solution for multiplexed perturbation in high-content pooled CRISPR screens.bioRxiv : the preprint server for biology · 2025Article
- The Confluence of HIV-1 and HIV-2: Implications for Disease Progression and Insights for Therapy.International journal of microbiology · 2025Review
- Estimates of HIV-1 within-host recombination rates across the whole genome.Virus evolution · 2025Article
- A binary trait model reveals the fitness effects of HIV-1 escape from T cell responses.bioRxiv : the preprint server for biology · 2024Article
- Deep mutational scanning reveals functional constraints and antibody-escape potential of Lassa virus glycoprotein complex.Immunity · 2024Article
- Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex.bioRxiv : the preprint server for biology · 2024Article
- Elevated HIV Viral Load is Associated with Higher Recombination Rate In Vivo.Molecular biology and evolution · 2024Article
- Elevated HIV viral load is associated with higher recombination ratebioRxiv : the preprint server for biology · 2023Article
- Mapping the neutralizing specificity of human anti-HIV serum by deep mutational scanning.Cell host & microbe · 2023Article
- Massively parallel evaluation and computational prediction of the activities and specificities of 17 small Cas9s.Nature methods · 2023Article
- Mapping the neutralizing specificity of human anti-HIV serum by deep mutational scanning.bioRxiv : the preprint server for biology · 2023Article
- Article
- A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike.bioRxiv : the preprint server for biology · 2022Article
- Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City.Nature communications · 2022Article
- Review
- Predicting the efficiency of prime editing guide RNAs in human cells.Nature biotechnology · 2021Article
- Prediction of the sequence-specific cleavage activity of Cas9 variants.Nature biotechnology · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Retroviral recombination is thought to play an important role in the generation of immune escape and multiple drug resistance by shuffling pre-existing mutations in the viral population. Current estimates of HIV-1 recombination rates are derived from measurements within reporter gene sequences or genetically divergent HIV sequences. These measurements do not mimic the recombination occurring in vivo, between closely related genomes. Additionally, the methods used to measure recombination make a variety of assumptions about the underlying process, and often fail to account adequately for issues such as co-infection of cells or the possibility of multiple template switches between recombination sites. We have developed a HIV-1 marker system by making a small number of codon modifications in gag which allow recombination to be measured over various lengths between closely related viral genomes. We have developed statistical tools to measure recombination rates that can compensate for the possibility of multiple template switches. Our results show that when multiple template switches are ignored the error is substantial, particularly when recombination rates are high, or the genomic distance is large. We demonstrate that this system is applicable to other studies to accurately measure the recombination rate and show that recombination does not occur randomly within the HIV genome.
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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.