We found a match
Your institution may have rights to this item. Sign in to continue.
- Title
THETA: a new genotypic approach for predicting HIV-1 CRF02-AG coreceptor usage.
- Authors
Dimeglio, Chloé; Raymond, Stéphanie; Jeanne, Nicolas; Reynes, Christelle; Carcenac, Romain; Lefebvre, Caroline; Cazabat, Michelle; Nicot, Florence; Delobel, Pierre; Izopet, Jacques
- Abstract
Motivation The circulating recombinant form of HIV-1 CRF02-AG is the most frequent non-B subtype in Europe. Anti-HIV therapy and pathophysiological studies on the impact of HIV-1 tropism require genotypic determination of HIV-1 tropism for non-B subtypes. But genotypic approaches based on analysis of the V3 envelope region perform poorly when used to determine the tropism of CRF02-AG. We, therefore, designed an algorithm based on information from the gp120 and gp41 ectodomain that better predicts the tropism of HIV-1 subtype CRF02-AG. Results We used a bio-statistical method to identify the genotypic determinants of CRF02-AG coreceptor use. Toulouse HIV Extended Tropism Algorithm (THETA), based on a Least Absolute Shrinkage and Selection Operator method, uses HIV envelope sequence from phenotypically characterized clones. Prediction of R5X4/X4 viruses was 86% sensitive and that of R5 viruses was 89% specific with our model. The overall accuracy of THETA was 88%, making it sufficiently reliable for predicting the tropism of subtype CRF02-AG sequences. Availability and implementation Binaries are freely available for download at https://github.com/viro-tls/THETA. It was implemented in Matlab and supported on MS Windows platform. The sequence data used in this work are available from GenBank under the accession numbers MK618182-MK618417.
- Subjects
EUROPE; TROPISMS; HIV; VIRUS cloning; GENETIC techniques
- Publication
Bioinformatics, 2020, Vol 36, Issue 2, p416
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btz585