ArticleVirology journal2016
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.
Article in Virology journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 17 citations in OpenAlex.
- Meiotic Recombination May Be Initiated by Copy Choice During DNA Synthesis Rather than Break/Join Mechanism.International journal of molecular sciences · 2025Review
- Genetic Evolution Between HIV-1 Groups M and O: HIV-1/MO Recombinant Forms.Journal of medical virology · 2025Review
- Estimates of HIV-1 within-host recombination rates across the whole genome.Virus evolution · 2025Article
- Editorial: The evolution, characterization, and role of human endogenous retroviruses in health and diseases.Frontiers in cellular and infection microbiology · 2024Article
- Article
- Comprehensive characterization of ERV-K (HML-8) in the chimpanzee genome revealed less genomic activity than humans.Frontiers in cellular and infection microbiology · 2024Article
- Identification of a New HIV-1 Circulating Recombinant Form CRF112_01B Strain in Baoding City, Hebei Province, China.Current HIV research · 2022Article
- Multiple CRF01_AE/CRF07_BC Recombinants Enhanced the HIV-1 Epidemic Complexity Among MSM in Shenyang City, Northeast China.Frontiers in microbiology · 2022Article
- First complete-genome documentation of HIV-1 intersubtype superinfection with transmissions of diverse recombinants over time to five recipients.PLoS pathogens · 2021Article
- Characterization of small genomic regions of the hepatitis B virus should be performed with more caution.Virology journal · 2018Article
- Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection.Nature communications · 2018Article
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWith increasing data on HIV-1, a more relevant molecular model describing mechanism details of HIV-1 genetic recombination usually requires upgrades. Currently an incomplete structural understanding of the copy choice mechanism along with several other issues in the field that lack elucidation led us to perform an analysis of the correlation between breakpoint distributions and (1) the probability of base pairing, and (2) intersubtype genetic similarity to further explore structural mechanisms.
methodsNear full length sequences of URFs from Asia, Europe, and Africa (one sequence/patient), and representative sequences of worldwide CRFs were retrieved from the Los Alamos HIV database. Their recombination patterns were analyzed by jpHMM in detail. Then the relationships between breakpoint distributions and (1) the probability of base pairing, and (2) intersubtype genetic similarities were investigated.
resultsPearson correlation test showed that all URF groups and the CRF group exhibit the same breakpoint distribution pattern. Additionally, the Wilcoxon two-sample test indicated a significant and inexplicable limitation of recombination in regions with high pairing probability. These regions have been found to be strongly conserved across distinct biological states (i.e., strong intersubtype similarity), and genetic similarity has been determined to be a very important factor promoting recombination. Thus, the results revealed an unexpected disagreement between intersubtype similarity and breakpoint distribution, which were further confirmed by genetic similarity analysis. Our analysis reveals a critical conflict between results from natural HIV-1 isolates and those from HIV-1-based assay vectors in which genetic similarity has been shown to be a very critical factor promoting recombination.
conclusionsThese results indicate the region with high-pairing probabilities may be a more fundamental factor affecting HIV-1 recombination than sequence similarity in natural HIV-1 infections. Our findings will be relevant in furthering the understanding of HIV-1 recombination mechanisms.
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