{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,21]],"date-time":"2024-07-21T09:10:07Z","timestamp":1721553007787},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2019,7,26]],"date-time":"2019-07-26T00:00:00Z","timestamp":1564099200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Agence Nationale de Recherches sur le SIDA et les h\u00e9patites virales"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>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.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz585","type":"journal-article","created":{"date-parts":[[2019,7,24]],"date-time":"2019-07-24T11:27:00Z","timestamp":1563967620000},"page":"416-421","source":"Crossref","is-referenced-by-count":4,"title":["THETA: a new genotypic approach for predicting HIV-1 CRF02-AG coreceptor usage"],"prefix":"10.1093","volume":"36","author":[{"given":"Chlo\u00e9","family":"Dimeglio","sequence":"first","affiliation":[{"name":"CHU de Toulouse, H\u00f4pital Purpan , Laboratoire de Virologie"}]},{"given":"St\u00e9phanie","family":"Raymond","sequence":"additional","affiliation":[{"name":"CHU de Toulouse, H\u00f4pital Purpan , Laboratoire de Virologie"},{"name":"INSERM U1043\u2014CNRS UMR 5282\u2014Toulouse University Paul Sabatier , CPTP, Toulouse F-31300, France"}]},{"given":"Nicolas","family":"Jeanne","sequence":"additional","affiliation":[{"name":"CHU de Toulouse, H\u00f4pital Purpan , Laboratoire de Virologie"}]},{"given":"Christelle","family":"Reynes","sequence":"additional","affiliation":[{"name":"Institut de G\u00e9nomique Fonctionnelle , 34090 Montpellier, France"},{"name":"UM-Universit\u00e9 de Montpellier , 34090 Montpellier, France"},{"name":"Facult\u00e9 de Pharmacie , 34090 Montpellier, France"}]},{"given":"Romain","family":"Carcenac","sequence":"additional","affiliation":[{"name":"CHU de Toulouse, H\u00f4pital Purpan , Laboratoire de Virologie"}]},{"given":"Caroline","family":"Lefebvre","sequence":"additional","affiliation":[{"name":"CHU de Toulouse, H\u00f4pital Purpan , Laboratoire de Virologie"}]},{"given":"Michelle","family":"Cazabat","sequence":"additional","affiliation":[{"name":"CHU de Toulouse, H\u00f4pital Purpan , Laboratoire de Virologie"}]},{"given":"Florence","family":"Nicot","sequence":"additional","affiliation":[{"name":"CHU de Toulouse, H\u00f4pital Purpan , Laboratoire de Virologie"}]},{"given":"Pierre","family":"Delobel","sequence":"additional","affiliation":[{"name":"CHU de Toulouse, Service de Maladies Infectieuses et Tropicales , 31059 Toulouse, France"}]},{"given":"Jacques","family":"Izopet","sequence":"additional","affiliation":[{"name":"CHU de Toulouse, H\u00f4pital Purpan , Laboratoire de Virologie"},{"name":"INSERM U1043\u2014CNRS UMR 5282\u2014Toulouse University Paul Sabatier , CPTP, Toulouse F-31300, France"}]}],"member":"286","published-online":{"date-parts":[[2019,7,26]]},"reference":[{"key":"2023013112062004400_btz585-B1","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevitch","year":"2012","journal-title":"J. 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