ArticleJournal of virology2014
Fifteen to twenty percent of HIV substitution mutations are associated with recombination.
Article in Journal of virology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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
25 citing papers in PubMed, 36 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
- Emergence of newly reported HIV-1 recombinants CRF120_0107 and CRF149_01B in Guangxi Zhuang Autonomous Region, China: Molecular evidence and public health challenges.Biosafety and health · 2026Article
- Review
- 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
- Molecular Biology and Diversification of Human Retroviruses.Frontiers in virology (Lausanne, Switzerland) · 2022Article
- Review
- Review
- Genetically barcoded SIV reveals the emergence of escape mutations in multiple viral lineages during immune escape.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Human T cell leukemia virus type 1 and Zika virus: tale of two reemerging viruses with neuropathological sequelae of public health concern.Journal of neurovirology · 2019Review
- G-quadruplexes may determine the landscape of recombination in HSV-1.BMC genomics · 2019Article
- Template-primer binding affinity and RNase H cleavage specificity contribute to the strand transfer efficiency of HIV-1 reverse transcriptase.The Journal of biological chemistry · 2018Article
- Retroviral RNA Dimerization: From Structure to Functions.Frontiers in microbiology · 2018Review
- Are RNA Viruses Candidate Agents for the Next Global Pandemic? A Review.ILAR journal · 2017Review
- Single-Strand Consensus Sequencing Reveals that HIV Type but not Subtype Significantly Impacts Viral Mutation Frequencies and Spectra.Journal of molecular biology · 2017Article
- On the importance of skewed offspring distributions and background selection in virus population genetics.Heredity · 2016Review
- Analysis of HIV-1 intersubtype recombination breakpoints suggests region with high pairing probability may be a more fundamental factor than sequence similarity affecting HIV-1 recombination.Virology journal · 2016Article
- Resolution of Specific Nucleotide Mismatches by Wild-Type and AZT-Resistant Reverse Transcriptases during HIV-1 Replication.Journal of molecular biology · 2016Article
- Article
- Central memory CD4+ T cells are preferential targets of double infection by HIV-1.Virology journal · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
HIV undergoes high rates of mutation and recombination during reverse transcription, but it is not known whether these events occur independently or are linked mechanistically. Here we used a system of silent marker mutations in HIV and a single round of infection in primary T lymphocytes combined with a high-throughput sequencing and mathematical modeling approach to directly estimate the viral recombination and mutation rates. From >7 million nucleotides (nt) of sequences from HIV infection, we observed 4,801 recombination events and 859 substitution mutations (≈1.51 and 0.12 events per 1,000 nt, respectively). We used experimental controls to account for PCR-induced and transfection-induced recombination and sequencing error. We found that the single-cycle virus-induced mutation rate is 4.6 × 10(-5) mutations per nt after correction. By sorting of our data into recombined and nonrecombined sequences, we found a significantly higher mutation rate in recombined regions (P = 0.003 by Fisher's exact test). We used a permutation approach to eliminate a number of potential confounding factors and confirm that mutation occurs around the site of recombination and is not simply colocated in the genome. By comparing mutation rates in recombined and nonrecombined regions, we found that recombination-associated mutations account for 15 to 20% of all mutations occurring during reverse transcription.
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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.