1. THETA
- Author
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Nicolas Jeanne, Caroline Lefebvre, Pierre Delobel, Romain Carcenac, Florence Nicot, Chloé Dimeglio, Stéphanie Raymond, Christelle Reynes, Michelle Cazabat, Jacques Izopet, Laboratoire de Virologie [Toulouse], CHU Toulouse [Toulouse], Centre de Physiopathologie Toulouse Purpan (CPTP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Service des maladies infectieuses et tropicales [Toulouse], and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Hôpital Purpan [Toulouse]
- Subjects
Statistics and Probability ,Receptors, CXCR4 ,Silver ,Genotype ,Receptors, CCR5 ,MESH: HIV-1 ,viruses ,Human immunodeficiency virus (HIV) ,HIV Infections ,Computational biology ,MESH: HIV Infections ,MESH: Receptors, CCR5 ,HIV Envelope Protein gp120 ,Biology ,Gp41 ,medicine.disease_cause ,Biochemistry ,MESH: Receptors, CXCR4 ,MESH: Genotype ,MESH: HIV Envelope Protein gp120 ,03 medical and health sciences ,Data sequences ,[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases ,MESH: Silver ,medicine ,Molecular Biology ,Tropism ,030304 developmental biology ,0303 health sciences ,030306 microbiology ,virus diseases ,3. Good health ,Computer Science Applications ,Europe ,Viral Tropism ,Computational Mathematics ,Computational Theory and Mathematics ,GenBank ,HIV-1 ,Tissue tropism ,MESH: Europe ,MESH: Viral Tropism ,Selection operator - 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.
- Published
- 2019
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