ArticleJournal of virology2010
RNA structures facilitate recombination-mediated gene swapping in HIV-1.
Article in Journal of virology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
38 citing papers in PubMed, 65 citations in OpenAlex.
- Pervasive HIV recombination limits the utility of circulating recombinant form nomenclature.PLoS pathogens · 2026Article
- Enhanced strand transfer and mismatch extension by HIV-1C reverse transcriptase promote sequence motif duplication.Journal of virology · 2026Article
- Conserved recombination patterns across hepatitis B genotypes: a retrospective study.Virology journal · 2025Article
- Estimates of HIV-1 within-host recombination rates across the whole genome.Virus evolution · 2025Article
- Chikungunya Virus RNA Secondary Structures Impact Defective Viral Genome Production.Microorganisms · 2024Article
- Characterization of Variant RNAs Encapsidated during Bromovirus Infection by High-Throughput Sequencing.Pathogens (Basel, Switzerland) · 2024Article
- Deciphering the evolutionary landscape of severe fever with thrombocytopenia syndrome virus across East Asia.Virus evolution · 2024Article
- Is the Intergenic Region ofViruses · 2022Article
- Recombination in Positive-Strand RNA Viruses.Frontiers in microbiology · 2022Review
- Conserved recombination patterns across coronavirus subgenera.Virus evolution · 2022Article
- Molecular Biology and Diversification of Human Retroviruses.Frontiers in virology (Lausanne, Switzerland) · 2022Article
- Phylodynamic study of the conserved RNA structure encompassing the hemagglutinin cleavage site encoding region of H5 and H7 low pathogenic avian influenza viruses.Virus evolution · 2021Article
- Global Patterns of Recombination across Human Viruses.Molecular biology and evolution · 2021Article
- HIV-1-Specific Immunodominant T-Cell Responses Drive the Dynamics of HIV-1 Recombination Following Superinfection.Frontiers in immunology · 2021Article
- Pervasive and non-random recombination in near full-length HIV genomes from Uganda.Virus evolution · 2020Article
- Review
- Patterns of genomic site inheritance in HIV-1M inter-subtype recombinants delineate the most likely genomic sites of subtype-specific adaptation.Virus evolution · 2018Article
- RNA Structure-A Neglected Puppet Master for the Evolution of Virus and Host Immunity.Frontiers in immunology · 2018Review
- Increasing the CpG dinucleotide abundance in the HIV-1 genomic RNA inhibits viral replication.Retrovirology · 2017Article
- Pausing kinetics dominates strand-displacement polymerization by reverse transcriptase.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
4 authors at 4 institutions in 3 countries.
Funding
Abstract
Many viruses, including retroviruses, undergo frequent recombination, a process which can increase their rate of adaptive evolution. In the case of HIV, recombination has been responsible for the generation of numerous intersubtype recombinant variants with epidemiological importance in the AIDS pandemic. Although it is known that fragments of genetic material do not combine randomly during the generation of recombinant viruses, the mechanisms that lead to preferential recombination at specific sites are not fully understood. Here we reanalyze recent independent data defining (i) the structure of a complete HIV-1 RNA genome and (ii) favorable sites for recombination. We show that in the absence of selection acting on recombinant genomes, regions harboring RNA structures in the NL4-3 model strain are strongly predictive of recombination breakpoints in the HIV-1 env genes of primary isolates. In addition, we found that breakpoints within recombinant HIV-1 genomes sampled from human populations, which have been acted upon extensively by natural selection, also colocalize with RNA structures. Critically, junctions between genes are enriched in structured RNA elements and are also preferred sites for generating functional recombinant forms. These data suggest that RNA structure-mediated recombination allows the virus to exchange intact genes rather than arbitrary subgene fragments, which is likely to increase the overall viability and replication success of the recombinant HIV progeny.
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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.