ArticleAIDS (London, England)2017
Prevalence and clinical impacts of HIV-1 intersubtype recombinants in Uganda revealed by near-full-genome population and deep sequencing approaches.
Article in AIDS (London, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 34 citations in OpenAlex.
- Intact HIV-1 proviruses accumulate at distinct chromosomal positions during prolonged antiretroviral therapy.The Journal of clinical investigation · 2019Trial
- Analysis of HIV transmission characteristics and intervention effects in Guangxi based on molecular networks.AIDS (London, England) · 2025Article
- Subtypes A1 and D, and recombinant HIV-1 natural polymorphisms associated with lenacapavir drug resistance in Uganda.The Journal of antimicrobial chemotherapy · 2025Article
- HIV-1 subtype A1, D, and recombinant proviral genome landscapes during long-term suppressive therapy.Nature communications · 2024Article
- Increasing intra- and inter-subtype HIV diversity despite declining HIV incidence in Uganda.medRxiv : the preprint server for health sciences · 2024Article
- CD4+ T cells with latent HIV-1 have reduced proliferative responses to T cell receptor stimulation.The Journal of experimental medicine · 2024Article
- Rising role of 3D-printing in delivery of therapeutics for infectious disease.Journal of controlled release : official journal of the Controlled Release Society · 2024Review
- Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study.Virus evolution · 2024Article
- Lymph node dendritic cells harbor inducible replication-competent HIV despite years of suppressive ART.Cell host & microbe · 2023Article
- Infection with HIV-1 subtype D among acutely infected Ugandans is associated with higher median concentration of cytokines compared to subtype A.IJID regions · 2022Article
- Article
- Measuring Proviral HIV-1 DNA: Hurdles and Improvements to an Assay Monitoring Integration Events Utilising HumanLife (Basel, Switzerland) · 2021Article
- In-depth single-cell analysis of translation-competent HIV-1 reservoirs identifies cellular sources of plasma viremia.Nature communications · 2021Article
- Antigen-driven clonal selection shapes the persistence of HIV-1-infected CD4+ T cells in vivo.The Journal of clinical investigation · 2021Article
- Increased Frequency of Inter-Subtype HIV-1 Recombinants Identified by Near Full-Length Virus Sequencing in Rwandan Acute Transmission Cohorts.Frontiers in microbiology · 2021Article
- The Molecular Epidemiology and Transmission Dynamics of HIV Type 1 in a General Population Cohort in Uganda.Viruses · 2020Article
- Recombination Analysis of Near Full-Length HIV-1 Sequences and the Identification of a Potential New Circulating Recombinant Form from Rakai, Uganda.AIDS research and human retroviruses · 2020Observational
- Vaccines and Broadly Neutralizing Antibodies for HIV-1 Prevention.Annual review of immunology · 2020Review
- Pervasive and non-random recombination in near full-length HIV genomes from Uganda.Virus evolution · 2020Article
- Measurement error and variant-calling in deep Illumina sequencing of HIV.Bioinformatics (Oxford, England) · 2019Article
Corrections and comments
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Authors and funding
21 authors at 5 institutions in 3 countries.
Funding
Abstract
objectivesHIV-1 subtypes A1 and D cocirculate in a rural community in Mbarara, Uganda. This study examines HIV-1 intersubtype recombination in this community under a full-genome sequencing context. We aim to estimate prevalence, examine time trends, and test for clinical correlates and outcomes associated with intersubtype recombinants.
methodsNear-full-genome HIV-1 Sanger sequence data were collected from plasma samples of 504 treatment-naïve individuals, who then received protease inhibitor or nonnucleoside reverse transcriptase inhibitor-containing regimens and were monitored for up to 7.5 years. Subtypes were inferred by Los Alamos Recombinant Identification Program (RIP) 3.0 and compared with Sanger/REGA and MiSeq/RIP. 'Nonrecombinants' and 'recombinants' infections were compared in terms of pretherapy viral load, CD4 cell count, posttherapy time to virologic suppression, virologic rebound, first CD4 rise above baseline and sustained CD4 recovery.
resultsPrevalence of intersubtype recombinants varied depending on the genomic region examined: gag (15%), prrt (11%), int (8%), vif (10%), vpr (2%), vpu (9%), GP120 (8%), GP41 (18%), and nef (4%). Of the 200 patients with near-full-genome data, prevalence of intersubtype recombination was 46%; the most frequently observed recombinant was A1-D (25%). Sanger/REGA and MiSeq/RIP yielded generally consistent results. Phylogenetic tree revealed most recombinants did not share common ancestors. No temporal trend was observed (all P > 0.1). Subsequent subtype switches were detected in 27 of 143 (19%) study participants with follow-up sequences. Nonrecombinant versus recombinants infections were not significantly different in any pre nor posttherapy clinical correlates examined (all P > 0.2).
conclusionIntersubtype recombination was highly prevalent (46%) in Uganda if the entire HIV genome was considered, but was neither associated with clinical correlates nor therapy outcomes.
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