Running Title: Deep Sequencing-based HIV-1 Genotyping and Coreceptor Tropism Assay
نویسندگان
چکیده
Running Title: Deep Sequencing-based HIV-1 Genotyping and Coreceptor Tropism Assay 5 6 7 Richard M. GIBSON , Ashley M. MEYER , Dane WINNER , John ARCHER , Felix FEYERTAG , 8 Ezequiel RUIZ-MATEOS , Manuel LEAL , David L. ROBERTSON , Christine L. SCHMOTZER , and 9 Miguel E. QUIÑONES-MATEU 1,4,* 10 11 1 University Hospital Translational Laboratory, University Hospitals Case Medical Center, Cleveland, Ohio, USA; 12 2 Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, United 13 Kingdom; 3 Laboratory of Immunovirology, Biomedicine Institute of Seville, Service of Infectious Diseases, Virgen 14 del Rocio University Hospital, Seville, Spain; and 4 Department of Pathology, Case Western Reserve University, 15
منابع مشابه
Sensitive Deep Sequencing-based HIV-1 Genotyping Assay to Simultaneously
Running Title: Deep Sequencing-based HIV-1 Genotyping and Coreceptor Tropism Assay 5 6 7 Richard M. GIBSON , Ashley M. MEYER , Dane WINNER , John ARCHER , Felix FEYERTAG , 8 Ezequiel RUIZ-MATEOS , Manuel LEAL , David L. ROBERTSON , Christine L. SCHMOTZER , and 9 Miguel E. QUIÑONES-MATEU 1,4,* 10 11 1 University Hospital Translational Laboratory, University Hospitals Case Medical Center, Clevela...
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The role of HIV-1 minority variants on transmission, pathogenesis, and virologic failure to antiretroviral regimens has been explored; however, most studies of low-level HIV-1 drug-resistant variants have focused in single target regions. Here we used a novel HIV-1 genotypic assay based on deep sequencing, DEEPGEN (Gibson et al 2014 Antimicrob Agents Chemother 58∶2167) to simultaneously analyze...
متن کاملComparison of population and 454 "deep" sequence analysis for HIV type 1 tropism versus the original trofile assay in non-B subtypes.
HIV-1 tropism can be predicted using V3 genotypic algorithms. The performance of these prediction algorithms for non-B subtypes is poorly characterized. Here, we use these genotypic algorithms to predict viral tropism of HIV-1 subtype A, B, C, and D to find apparent sensitivity, specificity, and concordance against a recombinant phenotypic assay, the original Trofile assay. This is a substudy o...
متن کاملPossible involvement of distinct phylogenetic clusters of HIV-1 variants in the discrepancies between coreceptor tropism predictions based on viral RNA and proviral DNA
BACKGROUND The coreceptor tropism testing should be conducted prior to commencing a regimen containing a CCR5 antagonist for treatment of HIV-1 infection. For aviremic patients on long antiretroviral therapy, proviral DNA is often used instead of viral RNA in genotypic tropism testing. However, the tropism predictions from RNA and DNA are sometimes different. We examined the cause of the discre...
متن کاملHIV-1 Tropism Dynamics and Phylogenetic Analysis from Longitudinal Ultra-Deep Sequencing Data of CCR5- and CXCR4-Using Variants
OBJECTIVE Coreceptor switch from CCR5 to CXCR4 is associated with HIV disease progression. The molecular and evolutionary mechanisms underlying the CCR5 to CXCR4 switch are the focus of intense recent research. We studied the HIV-1 tropism dynamics in relation to coreceptor usage, the nature of quasispecies from ultra deep sequencing (UDPS) data and their phylogenetic relationships. METHODS H...
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