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Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis

dc.rights.licenseopenen_US
hal.structure.identifierStanford University
dc.contributor.authorRHEE, Soo-Yon
hal.structure.identifierClinic Barcelona Hospital Universitari
dc.contributor.authorBLANCO, Jose Luis
hal.structure.identifierTufts University School of Medicine [Boston]
dc.contributor.authorJORDAN, Michael
hal.structure.identifierUniversity of Aberdeen
dc.contributor.authorTAYLOR, Jonathan
hal.structure.identifierRega Institute for Medical Research [Leuven]
dc.contributor.authorLEMEY, Philippe
hal.structure.identifierStanford University
dc.contributor.authorVARGHESE, Vici
hal.structure.identifierUniversiteit van Amsterdam = University of Amsterdam [UvA]
dc.contributor.authorHAMERS, Raph
hal.structure.identifierWHO-TDR Suisse
dc.contributor.authorBERTAGNOLIO, Silvia
hal.structure.identifierUniversiteit van Amsterdam = University of Amsterdam [UvA]
dc.contributor.authorRINKE DE WIT, Tobias
hal.structure.identifierInstitut de Recherches Médicales et d'Etudes des Plantes Médicinales [IMPM]
dc.contributor.authorAGHOKENG, Avelin
hal.structure.identifierKarolinska Institutet = Karolinska Institute [Stockholm]
dc.contributor.authorALBERT, Jan
hal.structure.identifierTartu Ülikool = University of Tartu [Estonie]
dc.contributor.authorAVI, Radko
dc.contributor.authorAVILA-RIOS, Santiago
hal.structure.identifierUniversity of Venda [Thohoyandou, South Africa] [UNIVEN]
dc.contributor.authorBESSONG, Pascal
dc.contributor.authorBROOKS, James
hal.structure.identifierErasmus University Medical Center [Rotterdam] [Erasmus MC]
dc.contributor.authorBOUCHER, Charles
hal.structure.identifierSimon Fraser University = Université Simon Fraser [SFU.ca]
hal.structure.identifierBritish Columbia Centre for Excellence in HIV/AIDS [Vancouver]
dc.contributor.authorBRUMME, Zabrina
hal.structure.identifierUniversity of California [San Francisco] [UC San Francisco]
dc.contributor.authorBUSCH, Michael
hal.structure.identifierBotswana Harvard AIDS Institute Partnership
dc.contributor.authorBUSSMANN, Hermann
hal.structure.identifierGénétique et Ecologie des Virus, Génétique des Virus et Pathogénèse des Maladies Virales
hal.structure.identifierLaboratoire de Virologie [CHU Saint-Louis]
dc.contributor.authorCHAIX, Marie Laure
dc.contributor.authorCHIN, Bum Sik
hal.structure.identifierCENTRE INTÉGRÉ DE RECHERCHES BIOCLINIQUES D'ABIDJAN (CIRBA) [CIRBA]
dc.contributor.authorD'AQUIN, Toni
hal.structure.identifierUniversity College Dublin [Dublin] [UCD]
dc.contributor.authorDE GASCUN, Cillian
hal.structure.identifierCHU Pitié-Salpêtrière [AP-HP]
dc.contributor.authorDERACHE, Anne
hal.structure.identifierAP-HP - Hôpital Bichat - Claude Bernard [Paris]
hal.structure.identifierInfection, Anti-microbiens, Modélisation, Evolution [IAME (UMR_S_1137 / U1137)]
dc.contributor.authorDESCAMPS, Diane
dc.contributor.authorDESHPANDE, Alaka
dc.contributor.authorDJOKO, Cyrille
hal.structure.identifierJohns Hopkins University School of Medicine [Baltimore]
dc.contributor.authorESHLEMAN, Susan
hal.structure.identifierCentre Hospitalier Universitaire de Bordeaux [CHU Bordeaux]
hal.structure.identifierMicrobiologie Fondamentale et Pathogénicité [MFP]
dc.contributor.authorFLEURY, Herve
hal.structure.identifierHôpital Necker - Enfants Malades [AP-HP]
dc.contributor.authorFRANGE, Pierre
hal.structure.identifierNational Institute of Infectious Diseases [Tokyo]
dc.contributor.authorFUJISAKI, Seiichiro
hal.structure.identifierUniversity of British Columbia [Canada] [UBC]
dc.contributor.authorHARRIGAN, P Richard
dc.contributor.authorHATTORI, Junko
hal.structure.identifierHospital Universitario Ramón y Cajal [Madrid]
dc.contributor.authorHOLGUIN, Africa
hal.structure.identifierNational Institute for Communicable Diseases [Johannesburg] [NICD]
dc.contributor.authorHUNT, Gillian
hal.structure.identifierKanazawa University [KU]
dc.contributor.authorICHIMURA, Hiroshi
hal.structure.identifierMRC/UVRI & LSHTM Uganda Research Unit
dc.contributor.authorKALEEBU, Pontiano
hal.structure.identifierStanford University
dc.contributor.authorKATZENSTEIN, David
hal.structure.identifierMahidol University [Bangkok]
dc.contributor.authorKIERTIBURANAKUL, Sasisopin
hal.structure.identifierWalter Reed Army Institute of Research
dc.contributor.authorKIM, Jerome
dc.contributor.authorKIM, Sung Soon
hal.structure.identifierChinese Academy of Sciences [Wuhan Branch]
dc.contributor.authorLI, Yanpeng
hal.structure.identifierTartu Ülikool = University of Tartu [Estonie]
dc.contributor.authorLUTSAR, Irja
hal.structure.identifierNational Institute for Communicable Diseases [Johannesburg] [NICD]
dc.contributor.authorMORRIS, Lynn
dc.contributor.authorNDEMBI, Nicaise
hal.structure.identifierFaculty of Medicine, University of Malaya [Kuala Lumpur, Malaisie]
dc.contributor.authorNG, Kee Peng
hal.structure.identifierIndian Council of Medical Research [New Dehli] [ICMR]
dc.contributor.authorPARANJAPE, Ramesh
hal.structure.identifierRecherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes [TransVIHMI]
dc.contributor.authorPEETERS, Martine
hal.structure.identifierUniversity of Ljubljana
dc.contributor.authorPOLJAK, Mario
hal.structure.identifierUniversity of California [UC]
dc.contributor.authorPRICE, Matt
hal.structure.identifierThe University of Edinburgh
dc.contributor.authorRAGONNET-CRONIN, Manon
dc.contributor.authorREYES-TERÁN, Gustavo
hal.structure.identifierWalter Reed Army Institute of Research
dc.contributor.authorROLLAND, Morgane
hal.structure.identifierChulalongkorn University [Bangkok]
dc.contributor.authorSIRIVICHAYAKUL, Sunee
hal.structure.identifierUniversity of California [San Diego] [UC San Diego]
dc.contributor.authorSMITH, Davey
hal.structure.identifierUniversidade Federal do Estado do Rio de Janeiro [UNIRIO]
dc.contributor.authorSOARES, Marcelo
hal.structure.identifierHospital Universitario La Paz-Carlos III [Madrid]
dc.contributor.authorSORIANO, Vincent
hal.structure.identifierMRC/UVRI & LSHTM Uganda Research Unit
dc.contributor.authorSSEMWANGA, Deogratius
hal.structure.identifierUniversity of Belgrade [Belgrade]
dc.contributor.authorSTANOJEVIC, Maja
hal.structure.identifierFederal University of Goiás [UFG]
dc.contributor.authorSTEFANI, Mariane
dc.contributor.authorSUGIURA, Wataru
hal.structure.identifierMahidol University [Bangkok]
dc.contributor.authorSUNGKANUPARPH, Somnuek
hal.structure.identifierUniversidade Federal do Estado do Rio de Janeiro [UNIRIO]
dc.contributor.authorTANURI, Amilcar
hal.structure.identifierFaculty of Medicine, University of Malaya [Kuala Lumpur, Malaisie]
dc.contributor.authorTEE, Kok Keng
hal.structure.identifierUniversity of California [UC]
dc.contributor.authorTRUONG, Hong-Ha
hal.structure.identifierErasmus University Medical Center [Rotterdam] [Erasmus MC]
dc.contributor.authorVAN DE VIJVER, David
hal.structure.identifierInstitut de Recherche pour le Développement [IRD [Occitanie]]
dc.contributor.authorVIDAL, Nicole
hal.structure.identifierCenters for Disease Control and Prevention [Atlanta] [CDC]
dc.contributor.authorYANG, Chunfu
hal.structure.identifierChinese Academy of Sciences [Wuhan Branch]
dc.contributor.authorYANG, Rongge
hal.structure.identifierInstituto Ramon y Cajal de Investigacion Sanitaria [Madrid, Spain] [IRYCIS]
dc.contributor.authorYEBRA, Gonzalo
hal.structure.identifierStanford University
dc.contributor.authorIOANNIDIS, John
hal.structure.identifierCatholic University of Leuven = Katholieke Universiteit Leuven [KU Leuven]
dc.contributor.authorVANDAMME, Anne-Mieke
hal.structure.identifierStanford University
dc.contributor.authorSHAFER, Robert
dc.date.accessioned2025-03-18T14:25:00Z
dc.date.available2025-03-18T14:25:00Z
dc.date.issued2015
dc.identifier.issn1549-1277en_US
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/205533
dc.description.abstractEnBackground: Regional and subtype-specific mutational patterns of HIV-1 transmitted drug resistance (TDR) are essential for informing first-line antiretroviral (ARV) therapy guidelines and designing diagnostic assays for use in regions where standard genotypic resistance testing is not affordable. We sought to understand the molecular epidemiology of TDR and to identify the HIV-1 drug-resistance mutations responsible for TDR in different regions and virus subtypes.Methods and findings: We reviewed all GenBank submissions of HIV-1 reverse transcriptase sequences with or without protease and identified 287 studies published between March 1, 2000, and December 31, 2013, with more than 25 recently or chronically infected ARV-naïve individuals. These studies comprised 50,870 individuals from 111 countries. Each set of study sequences was analyzed for phylogenetic clustering and the presence of 93 surveillance drug-resistance mutations (SDRMs). The median overall TDR prevalence in sub-Saharan Africa (SSA), south/southeast Asia (SSEA), upper-income Asian countries, Latin America/Caribbean, Europe, and North America was 2.8%, 2.9%, 5.6%, 7.6%, 9.4%, and 11.5%, respectively. In SSA, there was a yearly 1.09-fold (95% CI: 1.05-1.14) increase in odds of TDR since national ARV scale-up attributable to an increase in non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance. The odds of NNRTI-associated TDR also increased in Latin America/Caribbean (odds ratio [OR] = 1.16; 95% CI: 1.06-1.25), North America (OR = 1.19; 95% CI: 1.12-1.26), Europe (OR = 1.07; 95% CI: 1.01-1.13), and upper-income Asian countries (OR = 1.33; 95% CI: 1.12-1.55). In SSEA, there was no significant change in the odds of TDR since national ARV scale-up (OR = 0.97; 95% CI: 0.92-1.02). An analysis limited to sequences with mixtures at less than 0.5% of their nucleotide positions—a proxy for recent infection—yielded trends comparable to those obtained using the complete dataset. Four NNRTI SDRMs—K101E, K103N, Y181C, and G190A—accounted for >80% of NNRTI-associated TDR in all regions and subtypes. Sixteen nucleoside reverse transcriptase inhibitor (NRTI) SDRMs accounted for >69% of NRTI-associated TDR in all regions and subtypes. In SSA and SSEA, 89% of NNRTI SDRMs were associated with high-level resistance to nevirapine or efavirenz, whereas only 27% of NRTI SDRMs were associated with high-level resistance to zidovudine, lamivudine, tenofovir, or abacavir. Of 763 viruses with TDR in SSA and SSEA, 725 (95%) were genetically dissimilar; 38 (5%) formed 19 sequence pairs. Inherent limitations of this study are that some cohorts may not represent the broader regional population and that studies were heterogeneous with respect to duration of infection prior to sampling.Conclusions: Most TDR strains in SSA and SSEA arose independently, suggesting that ARV regimens with a high genetic barrier to resistance combined with improved patient adherence may mitigate TDR increases by reducing the generation of new ARV-resistant strains. A small number of NNRTI-resistance mutations were responsible for most cases of high-level resistance, suggesting that inexpensive point-mutation assays to detect these mutations may be useful for pre-therapy screening in regions with high levels of TDR. In the context of a public health approach to ARV therapy, a reliable point-of-care genotypic resistance test could identify which patients should receive standard first-line therapy and which should receive a protease-inhibitor-containing regimen.
dc.language.isoENen_US
dc.rightsAttribution 3.0 United States*
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/us/*
dc.subject.meshAfrica
dc.subject.meshAmericas
dc.subject.meshEurope
dc.subject.meshHIV Infections
dc.subject.meshHIV Reverse Transcriptase
dc.subject.meshHIV-1
dc.subject.meshHumans
dc.subject.meshMolecular Epidemiology
dc.subject.meshMutation
dc.subject.meshPhylogeny
dc.subject.meshAnti-HIV Agents
dc.subject.meshAsia
dc.subject.meshBase Sequence
dc.subject.meshDrug Resistance, Viral
dc.title.enGeographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis
dc.typeArticle de revueen_US
dc.identifier.doi10.1371/journal.pmed.1001810en_US
dc.subject.halSciences du Vivant [q-bio]/Santé publique et épidémiologieen_US
dc.subject.halSciences du Vivant [q-bio]/Génétique/Génétique des populations [q-bio.PE]en_US
dc.subject.halSciences du Vivant [q-bio]/Médecine humaine et pathologie/Maladies infectieusesen_US
dc.subject.halSciences du Vivant [q-bio]/Microbiologie et Parasitologie/Virologieen_US
dc.identifier.pubmed25849352en_US
bordeaux.journalPLoS Medicineen_US
bordeaux.pagee1001810en_US
bordeaux.volume12en_US
bordeaux.hal.laboratoriesMFP (Laboratoire Microbiologie Fondamentale et Pathogénicité) - UMR 5234en_US
bordeaux.issue4en_US
bordeaux.institutionCNRSen_US
bordeaux.peerReviewedouien_US
bordeaux.inpressnonen_US
bordeaux.import.sourcehal
hal.identifierhal-04987612
hal.version1
hal.popularnonen_US
hal.audienceInternationaleen_US
hal.exportfalse
workflow.import.sourcehal
dc.rights.ccPas de Licence CCen_US
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=PLoS%20Medicine&rft.date=2015&rft.volume=12&rft.issue=4&rft.spage=e1001810&rft.epage=e1001810&rft.eissn=1549-1277&rft.issn=1549-1277&rft.au=RHEE,%20Soo-Yon&BLANCO,%20Jose%20Luis&JORDAN,%20Michael&TAYLOR,%20Jonathan&LEMEY,%20Philippe&rft.genre=article


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