Show simple item record

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
dc.contributor.authorRHEE, Soo-Yon
dc.contributor.authorBLANCO, Jose Luis
dc.contributor.authorJORDAN, Michael R
dc.contributor.authorTAYLOR, Jonathan
dc.contributor.authorLEMEY, Philippe
dc.contributor.authorVARGHESE, Vici
dc.contributor.authorHAMERS, Raph L
dc.contributor.authorBERTAGNOLIO, Silvia
dc.contributor.authorRINKE DE WIT, Tobias F
dc.contributor.authorAGHOKENG, Avelin F
dc.contributor.authorALBERT, Jan
dc.contributor.authorAVI, Radko
dc.contributor.authorAVILA-RIOS, Santiago
dc.contributor.authorBESSONG, Pascal O
dc.contributor.authorBROOKS, James I
dc.contributor.authorBOUCHER, Charles A B
dc.contributor.authorBRUMME, Zabrina L
dc.contributor.authorBUSCH, Michael P
dc.contributor.authorBUSSMANN, Hermann
dc.contributor.authorCHAIX, Marie-Laure
dc.contributor.authorCHIN, Bum Sik
dc.contributor.authorD'AQUIN, Toni T
dc.contributor.authorDE GASCUN, Cillian F
dc.contributor.authorDERACHE, Anne
dc.contributor.authorDESCAMPS, Diane
dc.contributor.authorDESHPANDE, Alaka K
dc.contributor.authorDJOKO, Cyrille F
dc.contributor.authorESHLEMAN, Susan H
hal.structure.identifierMicrobiologie Fondamentale et Pathogénicité [MFP]
dc.contributor.authorFLEURY, Herve
dc.contributor.authorFRANGE, Pierre
dc.contributor.authorFUJISAKI, Seiichiro
dc.contributor.authorHARRIGAN, P Richard
dc.contributor.authorHATTORI, Junko
dc.contributor.authorHOLGUIN, Africa
dc.contributor.authorHUNT, Gillian M
dc.contributor.authorICHIMURA, Hiroshi
dc.contributor.authorKALEEBU, Pontiano
dc.contributor.authorKATZENSTEIN, David
dc.contributor.authorKIERTIBURANAKUL, Sasisopin
dc.contributor.authorKIM, Jerome H
dc.contributor.authorKIM, Sung Soon
dc.contributor.authorLI, Yanpeng
dc.contributor.authorLUTSAR, Irja
dc.contributor.authorMORRIS, Lynn
dc.contributor.authorNDEMBI, Nicaise
dc.contributor.authorNG, Kee Peng
dc.contributor.authorPARANJAPE, Ramesh S
dc.contributor.authorPEETERS, Martine
dc.contributor.authorPOLJAK, Mario
dc.contributor.authorPRICE, Matt A
dc.contributor.authorRAGONNET-CRONIN, Manon L
dc.contributor.authorREYES-TERÁN, Gustavo
dc.contributor.authorROLLAND, Morgane
dc.contributor.authorSIRIVICHAYAKUL, Sunee
dc.contributor.authorSMITH, Davey M
dc.contributor.authorSOARES, Marcelo A
dc.contributor.authorSORIANO, Vincent V
dc.contributor.authorSSEMWANGA, Deogratius
dc.contributor.authorSTANOJEVIC, Maja
dc.contributor.authorSTEFANI, Mariane A
dc.contributor.authorSUGIURA, Wataru
dc.contributor.authorSUNGKANUPARPH, Somnuek
dc.contributor.authorTANURI, Amilcar
dc.contributor.authorTEE, Kok Keng
dc.contributor.authorTRUONG, Hong-Ha M
dc.contributor.authorVAN DE VIJVER, David A M C
dc.contributor.authorVIDAL, Nicole
dc.contributor.authorYANG, Chunfu
dc.contributor.authorYANG, Rongge
dc.contributor.authorYEBRA, Gonzalo
dc.contributor.authorIOANNIDIS, John P A
dc.contributor.authorVANDAMME, Anne-Mieke
dc.contributor.authorSHAFER, Robert W
dc.date.accessioned2025-03-14T08:27:56Z
dc.date.available2025-03-14T08:27:56Z
dc.date.issued2015-04-01
dc.identifier.issn1549-1676en_US
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/205502
dc.description.abstractEnRegional 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. 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. 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.enAfrica
dc.subject.enAmericas
dc.subject.enAnti-HIV Agents
dc.subject.enAsia
dc.subject.enBase Sequence
dc.subject.enDrug Resistance
dc.subject.enViral
dc.subject.enEurope
dc.subject.enHIV Infections
dc.subject.enHIV Reverse Transcriptase
dc.subject.enHIV-1
dc.subject.enHumans
dc.subject.enMolecular Epidemiology
dc.subject.enMutation
dc.subject.enPhylogeny
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.title.alternativePLoS Meden_US
dc.typeArticle de revueen_US
dc.identifier.doi10.1371/journal.pmed.1001810en_US
dc.subject.halSciences du Vivant [q-bio]/Médecine humaine et pathologieen_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.sourcepubmed
hal.popularnonen_US
hal.audienceInternationaleen_US
hal.exportfalse
workflow.import.sourcepubmed
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=2015-04-01&rft.volume=12&rft.issue=4&rft.spage=e1001810&rft.epage=e1001810&rft.eissn=1549-1676&rft.issn=1549-1676&rft.au=RHEE,%20Soo-Yon&BLANCO,%20Jose%20Luis&JORDAN,%20Michael%20R&TAYLOR,%20Jonathan&LEMEY,%20Philippe&rft.genre=article


Files in this item

Thumbnail
Name:
MFP_PlosMed_2015_Rhee.pdf
Size:
1.928Mb
Format:
PDF
View/Open
Thumbnail
Name:
license_rdf
Size:
914bytes
Format:
application/rdf+xml
View/Open

This item appears in the following Collection(s)

Show simple item record