ArticleAIDS research and therapy2010
Structure of HIV-1 quasi-species as early indicator for switches of co-receptor tropism.
Article in AIDS research and therapy, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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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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Who cites it
14 citing papers in PubMed, 18 citations in OpenAlex.
- Multiple third-generation recombinants formed by CRF55_01B and CRF07_BC in newly diagnosed HIV-1 infected patients in Shenzhen city, China.Virology journal · 2024Article
- Compartmentalization and Clonal Amplification of HIV-1 in the Male Genital Tract Characterized Using Next-Generation Sequencing.Journal of virology · 2020Article
- Comparative analyses of error handling strategies for next-generation sequencing in precision medicine.Scientific reports · 2020Article
- Laboratory Methods in Molecular Epidemiology: Viral Infections.Microbiology spectrum · 2018Review
- Molecular Antiretroviral Resistance Markers of Human Immunodeficiency Virus-1 of CRF01_AE Subtype in Bali, Indonesia.Current HIV research · 2018Observational
- EFS: an ensemble feature selection tool implemented as R-package and web-application.BioData mining · 2017Article
- SHIVA - a web application for drug resistance and tropism testing in HIV.BMC bioinformatics · 2016Article
- Deep Sequencing of the HIV-1 env Gene Reveals Discrete X4 Lineages and Linkage Disequilibrium between X4 and R5 Viruses in the V1/V2 and V3 Variable Regions.Journal of virology · 2016Article
- Genotypic Prediction of Co-receptor Tropism of HIV-1 Subtypes A and C.Scientific reports · 2016Article
- Exploiting HIV-1 protease and reverse transcriptase cross-resistance information for improved drug resistance prediction by means of multi-label classification.BioData mining · 2016Article
- Position-specific automated processing of V3 env ultra-deep pyrosequencing data for predicting HIV-1 tropism.Scientific reports · 2015Article
- Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study.Journal of clinical microbiology · 2014Article
- A simple structure-based model for the prediction of HIV-1 co-receptor tropism.BioData mining · 2014Article
- Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Deep sequencing is able to generate a complete picture of the retroviral quasi-species in a patient. We demonstrate that the unprecedented power of deep sequencing in conjunction with computational data analysis has great potential for clinical diagnostics and basic research. Specifically, we analyzed longitudinal deep sequencing data from patients in a study with Vicriviroc, a drug that blocks the HIV-1 co-receptor CCR5. Sequences covered the V3-loop of gp120, known to be the main determinant of co-receptor tropism. First, we evaluated this data with a computational model for the interpretation of V3-sequences with respect to tropism, and we found complete agreement with results from phenotypic assays. Thus, the method could be applied in cases where phenotypic assays fail. Second, computational analysis led to the discovery of a characteristic pattern in the quasi-species that foreshadows switches of co-receptor tropism. This analysis could help to unravel the mechanism of tropism switches, and to predict these switches weeks to months before they can be detected by a phenotypic assay.
Identifiers
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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.