ArticleAIDS research and therapy2010
HIV-1 V3 envelope deep sequencing for clinical plasma specimens failing in phenotypic tropism assays.
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 18 papers.
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Who cites it
18 citing papers in PubMed.
- Article
- Sanger and Next Generation Sequencing Approaches to Evaluate HIV-1 Virus in Blood Compartments.International journal of environmental research and public health · 2018Article
- Higher sequence diversity in the vaginal tract than in blood at early HIV-1 infection.PLoS pathogens · 2018Article
- Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing.Viruses · 2016Article
- Position-specific automated processing of V3 env ultra-deep pyrosequencing data for predicting HIV-1 tropism.Scientific reports · 2015Article
- Review
- 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
- Targeted deep sequencing of HIV-1 using the IonTorrentPGM platform.Journal of virological methods · 2014Article
- HIV migration between blood and cerebrospinal fluid or semen over time.The Journal of infectious diseases · 2014Article
- 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
- Quasispecies structure, cornerstone of hepatitis B virus infection: mass sequencing approach.World journal of gastroenterology · 2013Review
- Detection of cytomegalovirus drug resistance mutations by next-generation sequencing.Journal of clinical microbiology · 2013Article
- Study of genotypic and phenotypic HIV-1 dynamics of integrase mutations during raltegravir treatment: a refined analysis by ultra-deep 454 pyrosequencing.The Journal of infectious diseases · 2012Article
- Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data.Frontiers in microbiology · 2012Article
- Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism.PloS one · 2012Article
- Comparison of phenotypic and genotypic tropism determination in triple-class-experienced HIV patients eligible for maraviroc treatment.The Journal of antimicrobial chemotherapy · 2011Article
- Structure of HIV-1 quasi-species as early indicator for switches of co-receptor tropism.AIDS research and therapy · 2010Article
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Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHIV-1 infected patients for whom standard gp160 phenotypic tropism testing failed are currently excluded from co-receptor antagonist treatment. To provide patients with maximal treatment options, massively parallel sequencing of the envelope V3 domain, in combination with tropism prediction tools, was evaluated as an alternative tropism determination strategy. Plasma samples from twelve HIV-1 infected individuals with failing phenotyping results were available. The samples were submitted to massive parallel sequencing and to confirmatory recombinant phenotyping using a fraction of the gp120 domain.
resultsA cut-off for sequence reads interpretation of 5 to10 times the sequencing error rate (0.2%) was implemented. On average, each sample contained 7 different V3 haplotypes. V3 haplotypes were submitted to tropism prediction algorithms, and 4/14 samples returned with presence of a dual/mixed (D/M) tropic virus, respectively at 3%, 10%, 11%, and 95% of the viral quasispecies. V3 tropism prediction was confirmed by gp120 phenotyping, except for two out of 4 D/M predicted viruses (with 3 and 95%) which were phenotypically R5-tropic. In the first case, the result was discordant due to the limit of detection for the phenotyping technology, while in the latter case the prediction algorithms were not computing the viral tropism correctly.
conclusionsAlthough only demonstrated on a limited set of samples, the potential of the combined use of "deep sequencing + prediction algorithms" in cases where routine gp160 phenotype testing cannot be employed was illustrated. While good concordance was observed between gp120 phenotyping and prediction of R5-tropic virus, the results suggest that accurate prediction of X4-tropic virus would require further algorithm development.
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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.