ArticleScientific reports2016
HIV coreceptor tropism determination and mutational pattern identification.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Article
- HIV-1 exploits LBPA-dependent intraepithelial trafficking for productive infection of human intestinal mucosa.PLoS pathogens · 2024Article
- Distinct genetic clusters in HIV-1 CRF01_AE-infected patients induced variable degrees of CD4mBio · 2024Article
- SHIV-C109p5 NHP induces rapid disease progression in elderly macaques with extensive GI viral replication.Journal of virology · 2024Article
- Phylogenetic signatures reveal multilevel selection and fitness costs in SARS-CoV-2.Wellcome open research · 2024Article
- The Effect of Treatment-Associated Mutations on HIV Replication and Transmission Cycles.Viruses · 2022Review
- Review
- Differential recognition of HIV-stimulated IL-1β and IL-18 secretion through NLR and NAIP signalling in monocyte-derived macrophages.PLoS pathogens · 2021Article
- Targeting CCR5 as a Component of an HIV-1 Therapeutic Strategy.Frontiers in immunology · 2021Review
- Existence of Replication-Competent Minor Variants with Different Coreceptor Usage in Plasma from HIV-1-Infected Individuals.Journal of virology · 2020Article
- Sensing of HIV-1 by TLR8 activates human T cells and reverses latency.Nature communications · 2020Article
- HIV-1 tropism prediction by the XGboost and HMM methods.Scientific reports · 2019Article
- Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model.PLoS biology · 2017Article
- Performance comparison of next-generation sequencing platforms for determining HIV-1 coreceptor use.Scientific reports · 2017Article
- Identification of apolipoprotein using feature selection technique.Scientific reports · 2016Article
- HIV-1 Nef promotes migration and chemokine synthesis of human basophils and mast cells through the interaction with CXCR4.Clinical and molecular allergy : CMA · 2016Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In the early stages of infection, Human Immunodeficiency Virus Type 1 (HIV-1) generally selects CCR5 as the primary coreceptor for entering the host cell. As infection progresses, the virus evolves and may exhibit a coreceptor-switch to CXCR4. Accurate determination coreceptor usage and identification key mutational patterns associated tropism switch are essential for selection of appropriate therapies and understanding mechanism of coreceptor change. We developed a classifier composed of two coreceptor-specific weight matrices (CMs) based on a full-scale dataset. For this classifier, we found an AUC of 0.97, an accuracy of 95.21% and an MCC of 0.885 (sensitivity 92.92%; specificity 95.54%) in a ten-fold cross-validation, outperforming all other methods on an independent dataset (13% higher MCC value than geno2pheno and 15% higher MCC value than PSSM). A web server (http://spg.med.tsinghua.edu.cn/CM.html) based on our classifier was provided. Patterns of genetic mutations that occur along with coreceptor transitions were further identified based on the score of each sequence. Six pairs of one-AA mutational patterns and three pairs of two-AA mutational patterns were identified to associate with increasing propensity for X4 tropism. These mutational patterns offered new insights into the mechanism of coreceptor switch and aided in monitoring coreceptor switch.
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