ArticleAntimicrobial agents and chemotherapy2011
Concordance between two phenotypic assays and ultradeep pyrosequencing for determining HIV-1 tropism.
Article in Antimicrobial agents and chemotherapy, 2011. 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.
- Genotypic and phenotypic characteristics of CXCR4-using transmitted/founder HIV-1 envelope glycoproteins.Journal of virology · 2026Article
- A highly sensitive method for the detection of recombinant PERV-A/C env RNA using next generation sequencing technologies.Scientific reports · 2020Article
- Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses.Viruses · 2020Article
- Higher sequence diversity in the vaginal tract than in blood at early HIV-1 infection.PLoS pathogens · 2018Article
- Performance comparison of next-generation sequencing platforms for determining HIV-1 coreceptor use.Scientific reports · 2017Article
- Emergence of CXCR4-tropic HIV-1 variants followed by rapid disease progression in hemophiliac slow progressors.PloS one · 2017Article
- Frequent detection of CXCR4-using viruses among Brazilian blood donors with HIV-1 long-standing infection and unknown clinical stage: Analysis of massive parallel sequencing data.Data in brief · 2016Article
- Position-specific automated processing of V3 env ultra-deep pyrosequencing data for predicting HIV-1 tropism.Scientific reports · 2015Article
- A diagnostic HIV-1 tropism system based on sequence relatedness.Journal of clinical microbiology · 2015Article
- HIV-1 Coreceptor Usage Assessment by Ultra-Deep Pyrosequencing and Response to Maraviroc.PloS one · 2015Article
- Deep sequencing: becoming a critical tool in clinical virology.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2014Review
- Next-Generation Sequencing to Help Monitor Patients Infected with HIV: Ready for Clinical Use?Current infectious disease reports · 2014Article
- Sensitive deep-sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism.Antimicrobial agents and chemotherapy · 2014Article
- Algorithm-based prediction of HIV-1 subtype D coreceptor use.Journal of clinical microbiology · 2013Article
- Sensitive cell-based assay for determination of human immunodeficiency virus type 1 coreceptor tropism.Journal of clinical microbiology · 2013Article
- HIV-1 dynamics and coreceptor usage in Maraviroc-treated patients with ongoing replication.Antimicrobial agents and chemotherapy · 2013Article
- Article
- Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism.PloS one · 2012Article
- Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data.Frontiers in microbiology · 2012Article
- Routine use of microbial whole genome sequencing in diagnostic and public health microbiology.PLoS pathogens · 2012Review
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
There have been few studies on the concordance between phenotypic assays for predicting human immunodeficiency virus type 1 (HIV-1) coreceptor usage. The sensitivity of ultradeep pyrosequencing combined with genotyping tools is similar to that of phenotypic assays for detecting minor CXCR4-using variants. We evaluated the agreement between two phenotypic assays, the Toulouse tropism test (TTT) and the Trofile assay, and ultradeep pyrosequencing for determining the tropism of HIV-1 quasispecies. The concordance between the TTT and Trofile assays was assessed for 181 samples successfully phenotyped by both assays. The TTT was 86% concordant with the standard Trofile assay and 91.7% with its enhanced-sensitivity version. The concordance between phenotypic characterization of HIV-1 tropism and ultradeep pyrosequencing genotypic prediction was further studied in selected samples. The HIV-1 tropism inferred from ultradeep pyrosequencing of 11 samples phenotyped as X4 and dualtropic and 12 phenotyped as R5-tropic agreed closely with the results of phenotyping. However, ultradeep pyrosequencing detected minor CXCR4-using variants in 3 of 12 samples phenotyped as R5-tropic. Ultradeep pyrosequencing also detected minor CXCR4-using variants that had been missed by direct sequencing in 6 of 9 samples phenotyped as X4-tropic but genotyped as R5-tropic by direct sequencing. Ultradeep pyrosequencing was 87% concordant with the Trofile and TTT phenotypic assays and was in the same range of sensitivity (0.4%) than these two phenotypic assays (0.3 to 0.5%) for detecting minor CXCR4-using variants. Ultradeep pyrosequencing provides a new way to improve the performance of genotypic prediction of HIV-1 tropism to match that of the phenotypic assays.
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