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Zhukova A, Voznica J, Felipe MD, To TH, Pérez L, Martínez Y, Pintos Y, Méndez M, Gascuel O, Kouri V. Correction: Cuban history of CRF19 recombinant subtype of HIV-1. PLoS Pathog 2022; 18:e1010224. [PMID: 34990490 PMCID: PMC8736264 DOI: 10.1371/journal.ppat.1010224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Blassel L, Zhukova A, Villabona-Arenas CJ, Atkins KE, Hué S, Gascuel O. Drug resistance mutations in HIV: new bioinformatics approaches and challenges. Curr Opin Virol 2021; 51:56-64. [PMID: 34597873 DOI: 10.1016/j.coviro.2021.09.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/31/2021] [Accepted: 09/13/2021] [Indexed: 12/11/2022]
Abstract
Drug resistance mutations appear in HIV under treatment pressure. Resistant variants can be transmitted to treatment-naive individuals, which can lead to rapid virological failure and can limit treatment options. Consequently, quantifying the prevalence, emergence and transmission of drug resistance is critical to effectively treating patients and to shape health policies. We review recent bioinformatics developments and in particular describe: (1) the machine learning approaches intended to predict and explain the level of resistance of HIV variants from their sequence data; (2) the phylogenetic methods used to survey the emergence and dynamics of resistant HIV transmission clusters; (3) the impact of deep sequencing in studying within-host and between-host genetic diversity of HIV variants, notably regarding minority resistant variants.
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Affiliation(s)
- Luc Blassel
- Unité Bioinformatique Evolutive, Institut Pasteur, Paris, France; Sorbonne Université, Collège Doctoral, Paris, France
| | - Anna Zhukova
- Unité Bioinformatique Evolutive, Institut Pasteur, Paris, France; Hub de Bioinformatique et Biostatistique, Institut Pasteur, Paris, France
| | - Christian J Villabona-Arenas
- Centre for the Mathematical Modelling of Infectious Diseases (CMMID), London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Katherine E Atkins
- Centre for the Mathematical Modelling of Infectious Diseases (CMMID), London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK; Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Stéphane Hué
- Centre for the Mathematical Modelling of Infectious Diseases (CMMID), London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Olivier Gascuel
- Institut de Systématique, Evolution, Biodiversité (ISYEB, UMR 7205 - CNRS, Muséum National d'Histoire Naturelle, EPHE, SU, UA), Paris, France.
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