ArticlePLoS pathogens2016
Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality.
Article in PLoS pathogens, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 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.
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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.
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Who cites it
44 citing papers in PubMed.
- Longitudinal study reveals HIV-1-infected CD4+ T cell dynamics during long-term antiretroviral therapy.The Journal of clinical investigation · 2020Trial
- Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells.Cell systems · 2025Article
- Proviruses in CD4Science translational medicine · 2025Article
- Antiretroviral therapy reveals triphasic decay of intact SIV genomes and persistence of ancestral variants.Cell host & microbe · 2023Article
- bayroot: Bayesian sampling of HIV-1 integration dates by root-to-tip regression.Virus evolution · 2023Article
- Machine Learning Bolsters Evidence That D1, Nef, and Tat Influence HIV Reservoir Dynamics.Pathogens & immunity · 2023Article
- The Persistence of HIV Diversity, Transcription, and Nef Protein in Kaposi's Sarcoma Tumors during Antiretroviral Therapy.Viruses · 2022Article
- Discordance between HIV-1 Population in Plasma at Rebound after Structured Treatment Interruption and Archived Provirus Population in Peripheral Blood Mononuclear Cells.Microbiology spectrum · 2022Article
- Extensive characterization of HIV-1 reservoirs reveals links to plasma viremia before and during analytical treatment interruption.Cell reports · 2022Article
- Plasma-Derived HIV-1 Virions Contain Considerable Levels of Defective Genomes.Journal of virology · 2022Article
- Article
- Integration features of intact latent HIV-1 in CD4+ T cell clones contribute to viral persistence.The Journal of experimental medicine · 2021Article
- Similar Frequency and Inducibility of Intact Human Immunodeficiency Virus-1 Proviruses in Blood and Lymph Nodes.The Journal of infectious diseases · 2021Article
- Article
- In-depth single-cell analysis of translation-competent HIV-1 reservoirs identifies cellular sources of plasma viremia.Nature communications · 2021Article
- Proviral Turnover During Untreated HIV Infection Is Dynamic and Variable Between Hosts, Impacting Reservoir Composition on ART.Frontiers in microbiology · 2021Article
- Quantifying the clonality and dynamics of the within-host HIV-1 latent reservoir.Virus evolution · 2021Article
- Autologous IgG antibodies block outgrowth of a substantial but variable fraction of viruses in the latent reservoir for HIV-1.Proceedings of the National Academy of Sciences of the United States of America · 2020Observational
- Cells producing residual viremia during antiretroviral treatment appear to contribute to rebound viremia following interruption of treatment.PLoS pathogens · 2020Observational
- HIV persists throughout deep tissues with repopulation from multiple anatomical sources.The Journal of clinical investigation · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
In HIV-infected individuals receiving suppressive antiretroviral therapy, the virus persists indefinitely in a reservoir of latently infected cells. The proliferation of these cells may contribute to the stability of the reservoir and thus to the lifelong persistence of HIV-1 in infected individuals. Because the HIV-1 replication process is highly error-prone, the detection of identical viral genomes in distinct host cells provides evidence for the clonal expansion of infected cells. We evaluated alignments of unique, near-full-length HIV-1 sequences to determine the relationship between clonality in a short region and clonality in the full genome. Although it is common to amplify and sequence short, subgenomic regions of the viral genome for phylogenetic analysis, we show that sequence identity of these amplicons does not guarantee clonality across the full viral genome. We show that although longer amplicons capture more diversity, no subgenomic region can recapitulate the diversity of full viral genomes. Consequently, some identical subgenomic amplicons should be expected even from the analysis of completely unique viral genomes, and the presence of identical amplicons alone is not proof of clonally expanded HIV-1. We present a method for evaluating evidence of clonal expansion in the context of these findings.
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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.