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Pimentel V, Pingarilho M, Sebastião CS, Miranda M, Gonçalves F, Cabanas J, Costa I, Diogo I, Fernandes S, Costa O, Corte-Real R, Martins MRO, Seabra SG, Abecasis AB, Gomes P. Applying Next-Generation Sequencing to Track HIV-1 Drug Resistance Mutations Circulating in Portugal. Viruses 2024; 16:622. [PMID: 38675962 PMCID: PMC11054263 DOI: 10.3390/v16040622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/02/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND The global scale-up of antiretroviral treatment (ART) offers significant health benefits by suppressing HIV-1 replication and increasing CD4 cell counts. However, incomplete viral suppression poses a potential threat for the emergence of drug resistance mutations (DRMs), limiting ART options, and increasing HIV transmission. OBJECTIVE We investigated the patterns of transmitted drug resistance (TDR) and acquired drug resistance (ADR) among HIV-1 patients in Portugal. METHODS Data were obtained from 1050 HIV-1 patient samples submitted for HIV drug resistance (HIVDR) testing from January 2022 to June 2023. Evaluation of DRM affecting viral susceptibility to nucleoside/tide reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), protease inhibitors (PIs), and integrase strand transfer inhibitors (INSTIs) was performed using an NGS technology, the Vela Diagnostics Sentosa SQ HIV-1 Genotyping Assay. RESULTS About 71% of patients were ART naïve and 29% were experienced. Overall, 20% presented with any DRM. The prevalence of TDR and ADR was 12.6% and 41.1%, respectively. M184V, T215S, and M41L mutations for NRTI, K103N for NNRTI, and M46I/L for PIs were frequent in naïve and treated patients. E138K and R263K mutations against INSTIs were more frequent in naïve than treated patients. TDR and ADR to INSTIs were 0.3% and 7%, respectively. Patients aged 50 or over (OR: 1.81, p = 0.015), originating from Portuguese-speaking African countries (PALOPs) (OR: 1.55, p = 0.050), HIV-1 subtype G (OR: 1.78, p = 0.010), and with CD4 < 200 cells/mm3 (OR: 1.70, p = 0.043) were more likely to present with DRMs, while the males (OR: 0.63, p = 0.003) with a viral load between 4.1 to 5.0 Log10 (OR: 0.55, p = 0.003) or greater than 5.0 Log10 (OR: 0.52, p < 0.001), had lower chances of presenting with DRMs. CONCLUSIONS We present the first evidence on TDR and ADR to INSTI regimens in followed up patients presenting for healthcare in Portugal. We observed low levels of TDR to INSTIs among ART-naïve and moderate levels in ART-exposed patients. Regimens containing PIs could be an alternative second line in patients with intermediate or high-level drug resistance, especially against second-generation INSTIs (dolutegravir, bictegravir, and cabotegravir).
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Affiliation(s)
- Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
| | - Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
| | - Cruz S. Sebastião
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
- Centro de Investigação em Saúde de Angola (CISA), Caxito, Angola
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Mafalda Miranda
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
| | - Fátima Gonçalves
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade Local de Saúde Lisboa Ocidental, Hospital Egas Moniz, 1349-019 Lisbon, Portugal; (F.G.); (J.C.); (I.C.); (I.D.); (S.F.); (P.G.)
| | - Joaquim Cabanas
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade Local de Saúde Lisboa Ocidental, Hospital Egas Moniz, 1349-019 Lisbon, Portugal; (F.G.); (J.C.); (I.C.); (I.D.); (S.F.); (P.G.)
| | - Inês Costa
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade Local de Saúde Lisboa Ocidental, Hospital Egas Moniz, 1349-019 Lisbon, Portugal; (F.G.); (J.C.); (I.C.); (I.D.); (S.F.); (P.G.)
| | - Isabel Diogo
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade Local de Saúde Lisboa Ocidental, Hospital Egas Moniz, 1349-019 Lisbon, Portugal; (F.G.); (J.C.); (I.C.); (I.D.); (S.F.); (P.G.)
| | - Sandra Fernandes
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade Local de Saúde Lisboa Ocidental, Hospital Egas Moniz, 1349-019 Lisbon, Portugal; (F.G.); (J.C.); (I.C.); (I.D.); (S.F.); (P.G.)
| | - Olga Costa
- Biologia Molecular, Serviço de Patologia Clínica, Centro Hospitalar de Lisboa Central, 1150-199 Lisbon, Portugal; (O.C.); (R.C.-R.)
| | - Rita Corte-Real
- Biologia Molecular, Serviço de Patologia Clínica, Centro Hospitalar de Lisboa Central, 1150-199 Lisbon, Portugal; (O.C.); (R.C.-R.)
| | - M. Rosário O. Martins
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
| | - Sofia G. Seabra
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
| | - Ana B. Abecasis
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
| | - Perpétua Gomes
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade Local de Saúde Lisboa Ocidental, Hospital Egas Moniz, 1349-019 Lisbon, Portugal; (F.G.); (J.C.); (I.C.); (I.D.); (S.F.); (P.G.)
- Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health & Science, Caparica, 2829-511 Almada, Portugal
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2
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Mbisa JL, Kirwan P, Tostevin A, Ledesma J, Bibby DF, Brown A, Myers R, Hassan AS, Murphy G, Asboe D, Pozniak A, Kirk S, Gill ON, Sabin C, Delpech V, Dunn DT. Determining the Origins of Human Immunodeficiency Virus Type 1 Drug-resistant Minority Variants in People Who Are Recently Infected Using Phylogenetic Reconstruction. Clin Infect Dis 2020; 69:1136-1143. [PMID: 30534981 PMCID: PMC6743824 DOI: 10.1093/cid/ciy1048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 12/06/2018] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Drug-resistant minority variants (DRMinVs) detected in patients who recently acquired human immunodeficiency virus type 1 (HIV-1) can be transmitted, generated de novo through virus replication, or technical errors. The first form is likely to persist and result in treatment failure, while the latter two could be stochastic and transient. METHODS Ultradeep sequencing of plasma samples from 835 individuals with recent HIV-1 infection in the United Kingdom was performed to detect DRMinVs at a mutation frequency between 2% and 20%. Sequence alignments including >110 000 HIV-1 partial pol consensus sequences from the UK HIV Drug Resistance Database (UK-HDRD), linked to epidemiological and clinical data from the HIV and AIDS Reporting System, were used for transmission cluster analysis. Transmission clusters were identified using Cluster Picker with a clade support of >90% and maximum genetic distances of 4.5% or 1.5%, the latter to limit detection to likely direct transmission events. RESULTS Drug-resistant majority variants (DRMajVs) were detected in 66 (7.9%) and DRMinVs in 84 (10.1%) of the recently infected individuals. High levels of clustering to sequences in UK-HDRD were observed for both DRMajV (n = 48; 72.7%) and DRMinV (n = 63; 75.0%) sequences. Of these, 43 (65.2%) with DRMajVs were in a transmission cluster with sequences that harbored the same DR mutation compared to only 3 (3.6%) sequences with DRMinVs (P < .00001, Fisher exact test). Evidence of likely direct transmission of DRMajVs was observed for 25/66 (37.9%), whereas none were observed for the DRMinVs (P < .00001). CONCLUSIONS Using a densely sampled HIV-infected population, we show no evidence of DRMinV transmission among recently infected individuals.
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Affiliation(s)
- Jean L Mbisa
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - Peter Kirwan
- National Infection Service, Public Health England, London, United Kingdom
| | - Anna Tostevin
- Institute for Global Health, University College London, London, United Kingdom
| | - Juan Ledesma
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - David F Bibby
- National Infection Service, Public Health England, London, United Kingdom
| | - Alison Brown
- National Infection Service, Public Health England, London, United Kingdom
| | - Richard Myers
- National Infection Service, Public Health England, London, United Kingdom
| | - Amin S Hassan
- HIV/STI Group, Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Programme, Kilifi, Kenya
| | - Gary Murphy
- National Infection Service, Public Health England, London, United Kingdom
| | - David Asboe
- Chelsea and Westminster Hospital, London, United Kingdom
| | - Anton Pozniak
- Chelsea and Westminster Hospital, London, United Kingdom
| | - Stuart Kirk
- University College London Hospital, London, United Kingdom
| | - O Noel Gill
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - Caroline Sabin
- National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom.,Institute for Global Health, University College London, London, United Kingdom
| | - Valerie Delpech
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - David T Dunn
- Institute for Global Health, University College London, London, United Kingdom
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3
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Machado LY, Blanco M, López LS, Díaz HM, Dubed M, Valdés N, Noa E, Martínez L, Pérez MT, Romay DM, Rivero CB, Joanes J, Cancio I, Lantero MI, Rodríguez M. National survey of pre-treatment HIV drug resistance in Cuban patients. PLoS One 2019; 14:e0221879. [PMID: 31479466 PMCID: PMC6719847 DOI: 10.1371/journal.pone.0221879] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/17/2019] [Indexed: 11/22/2022] Open
Abstract
Background The World Health Organization (WHO) recommends a method to estimate nationally representative pretreatment HIV drug resistance (PDR) in order to evaluate the effectiveness of first -line treatments. The objective of the present study was to determine the prevalence of PDR in Cuban adults infected with HIV-1. Materials and methods A cross-sectional study in Cuban adults infected with HIV-1 over 18 years was conducted. The probability proportional to size method for the selection of municipalities and patients without a prior history of antiretroviral treatment during the period from January 2017 to June 2017 was used. The plasma from 141 patients from 15 municipalities for the determination of viral subtype and HIV drug resistance was collected. Some clinical and epidemiological variables were evaluated. Results 80. 9% of the patients corresponded to the male sex and 76.3% were men who have sex with other men (MSM). The median CD4 count was 371 cells / mm3 and the median viral load was 68000 copies / mL. The predominant genetic variants were subtype B (26.9%), CRF19_cpx (24.1%), CRF 20, 23, 24_BG (23.4%) and CRF18_cpx (12%). Overall, the prevalence of PDR was 29.8% (95%, CI 22.3–38.1). The prevalence was 12.8% (95%, CI 6.07–16.9) for any nucleoside reverse transcriptase inhibitor (NRTI), 23.4% (95%, CI 16.7–31.3) for any non-reverse transcriptase inhibitor (NNRTI) and 1.4% (95%, CI 0.17–5.03) for any protease inhibitor (PI). The most frequent mutations detected were K103N (12.9%), G190A (6.4%) and Y181C (4.8%). Conclusions The NNRTI prevalence above 10% in our study indicates that the first-line antiretroviral therapy in Cuba may be less effective and supports the need to look for new treatment options that contribute to therapeutic success and help the country achieve the global goals 90-90-90 set forth by UNAIDS.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - José Joanes
- Department of STI/HIV/AIDS, Ministry of Public Health, Havana, Cuba
| | - Isis Cancio
- Department of STI/HIV/AIDS, Ministry of Public Health, Havana, Cuba
| | - María I. Lantero
- Department of STI/HIV/AIDS, Ministry of Public Health, Havana, Cuba
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4
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Truong HHM, Pipkin S, Grant RM, Liegler T, O'Keefe KJ, Scheer S. Increased uptake of early initiation of antiretroviral therapy and baseline drug resistance testing in San Francisco between 2001 and 2015. PLoS One 2019; 14:e0213167. [PMID: 30870438 PMCID: PMC6417784 DOI: 10.1371/journal.pone.0213167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 02/16/2019] [Indexed: 11/21/2022] Open
Abstract
Background Early initiation of antiretroviral therapy (eiART) can improve clinical outcomes for persons with HIV and reduce onward transmission risk. Baseline drug resistance testing (bDRT) can inform regimen selection upon subsequent treatment initiation. We examined the uptake of eiART and bDRT within 3 months and 30 days of HIV diagnosis. Methods We analyzed a population-based sample from the San Francisco Department of Public Health HIV/AIDS Case Registry of newly-diagnosed HIV/non-AIDS individuals between 2001 and 2015 who received care at publicly-funded facilities (N = 3,124). Results Uptake of eiART within 3 months of diagnosis increased significantly from 2001 to 2015 (p<0.001), peaking at 74% in 2015. bDRT uptake also increased significantly (p<0.001), peaking at 55% in 2012. eiART uptake was observed to be significantly associated with gender, age, race/ethnicity and transmission risk. There were no significant differences observed in demographic and risk characteristics of persons receiving bDRT in the more recent years. Of 990 persons diagnosed between 2010 and 2015, eiART uptake within 30 days of diagnosis increased from 13% to 38% (p<0.001); bDRT uptake increased from 35% to 39% but the change was not significant (p = 0.141). Conclusions Observed increases in eiART and bDRT uptake from 2010 to 2015 may reflect the adoption of treatment as prevention and a local public health policy statement in 2010 recommending treatment initiation at time of diagnosis irrespective of CD4 count. Concerns about stigma may underlie disparities in eiART, however such concerns would not bear as directly on a provider-initiated laboratory test like bDRT.
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Affiliation(s)
- Hong-Ha M Truong
- Department of Medicine, University of California, San Francisco, United States of America.,Gladstone Institute of Virology and Immunology, San Francisco, United States of America
| | - Sharon Pipkin
- Department of Public Health, San Francisco, United States of America
| | - Robert M Grant
- Department of Medicine, University of California, San Francisco, United States of America.,Gladstone Institute of Virology and Immunology, San Francisco, United States of America
| | - Teri Liegler
- Department of Medicine, University of California, San Francisco, United States of America
| | - Kara J O'Keefe
- Department of Public Health, San Francisco, United States of America
| | - Susan Scheer
- Department of Public Health, San Francisco, United States of America
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5
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Smoleń-Dzirba J, Rosińska M, Kruszyński P, Bratosiewicz-Wąsik J, Wojtyczka R, Janiec J, Szetela B, Beniowski M, Bociąga-Jasik M, Jabłonowska E, Wąsik TJ, The Cascade Collaboration In EuroCoord A. Prevalence of Transmitted Drug-Resistance Mutations and Polymorphisms in HIV-1 Reverse Transcriptase, Protease, and gp41 Sequences Among Recent Seroconverters in Southern Poland. Med Sci Monit 2017; 23:682-694. [PMID: 28167814 PMCID: PMC5310230 DOI: 10.12659/msm.898656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Monitoring of drug resistance-related mutations among patients with recent HIV-1 infection offers an opportunity to describe current patterns of transmitted drug resistance (TDR) mutations. Material/Methods Of 298 individuals newly diagnosed from March 2008 to February 2014 in southern Poland, 47 were deemed to have recent HIV-1 infection by the limiting antigen avidity immunoassay. Proviral DNA was amplified and sequenced in the reverse transcriptase, protease, and gp41 coding regions. Mutations were interpreted according to the Stanford Database algorithm and/or the International Antiviral Society USA guidelines. TDR mutations were defined according to the WHO surveillance list. Results Among 47 patients with recent HIV-1 infection only 1 (2%) had evidence of TDR mutation. No major resistance mutations were found, but the frequency of strains with ≥1 accessory resistance-associated mutations was high, at 98%. Accessory mutations were present in 11% of reverse transcriptase, 96% of protease, and 27% of gp41 sequences. Mean number of accessory resistance mutations in the reverse transcriptase and protease sequences was higher in viruses with no compensatory mutations in the gp41 HR2 domain than in strains with such mutations (p=0.031). Conclusions Despite the low prevalence of strains with TDR mutations, the frequency of accessory mutations was considerable, which may reflect the history of drug pressure among transmitters or natural viral genetic diversity, and may be relevant for future clinical outcomes. The accumulation of the accessory resistance mutations within the pol gene may restrict the occurrence of compensatory mutations related to enfuvirtide resistance or vice versa.
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Affiliation(s)
- Joanna Smoleń-Dzirba
- Department of Microbiology and Virology, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
| | - Magdalena Rosińska
- Department of Epidemiology, National Institute of Public Health - National Institute of Hygiene, Warsaw, Poland
| | - Piotr Kruszyński
- Department of Microbiology and Virology, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
| | - Jolanta Bratosiewicz-Wąsik
- Department of Biopharmacy, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
| | - Robert Wojtyczka
- Department of Microbiology and Virology, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
| | - Janusz Janiec
- Department of Epidemiology, National Institute of Public Health - National Institute of Hygiene, Warsaw, Poland
| | - Bartosz Szetela
- Department of Infectious Diseases, Hepatology, and Acquired Immune Deficiencies, Wrocław Medical University, Wrocław, Poland
| | - Marek Beniowski
- Outpatient Clinic for AIDS Diagnostics and Therapy, Specialistic Hospital in Chorzów, Chorzów, Poland
| | - Monika Bociąga-Jasik
- Department of Infectious Diseases, Jagiellonian University Medical College, Cracow, Poland
| | - Elżbieta Jabłonowska
- Department of Infectious Diseases and Hepatology, Medical University of Łódź, Łódź, Poland
| | - Tomasz J Wąsik
- Department of Microbiology and Virology, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
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6
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Cunningham E, Chan YT, Aghaizu A, Bibby DF, Murphy G, Tosswill J, Harris RJ, Myers R, Field N, Delpech V, Cane PA, Gill ON, Mbisa JL. Enhanced surveillance of HIV-1 drug resistance in recently infected MSM in the UK. J Antimicrob Chemother 2016; 72:227-234. [PMID: 27742812 DOI: 10.1093/jac/dkw404] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 08/19/2016] [Accepted: 08/26/2016] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To determine the prevalence of inferred low-frequency HIV-1 transmitted drug resistance (TDR) in MSM in the UK and its predicted effect on first-line therapy. METHODS The HIV-1 pol gene was amplified from 442 newly diagnosed MSM identified as likely recently infected by serological avidity testing in 2011-13. The PCR products were sequenced by next-generation sequencing with a mutation frequency threshold of >2% and TDR mutations defined according to the 2009 WHO surveillance drug resistance mutations list. RESULTS The majority (75.6%) were infected with subtype B and 6.6% with rare complex or unique recombinant forms. At a mutation frequency threshold of >20%, 7.2% (95% CI 5.0%-10.1%) of the sequences had TDR and this doubled to 15.8% (95% CI 12.6%-19.6%) at >2% mutation frequency (P < 0.0001). The majority (26/42, 62%) of low-frequency variants were against PIs. The most common mutations detected at >20% and 2%-20% mutation frequency differed for each drug class, these respectively being: L90M (n = 7) and M46IL (n = 10) for PIs; T215rev (n = 9) and D67GN (n = 4) for NRTIs; and K103N (n = 5) and G190E (n = 2) for NNRTIs. Combined TDR was more frequent in subtype B than non-B (OR = 0.38; 95% CI = 0.17-0.88; P = 0.024) and had minimal predicted effect on recommended first-line therapies. CONCLUSIONS The data suggest differences in the types of low-frequency compared with majority TDR variants that require a better understanding of the origins and clinical significance of low-frequency variants. This will better inform diagnostic and treatment strategies.
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Affiliation(s)
- Emma Cunningham
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Yuen-Ting Chan
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Adamma Aghaizu
- HIV and STI Department, National Infection Service, Public Health England, London, UK
| | - David F Bibby
- Virus Reference Department, National Infection Service, Public Health England, London, UK.,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
| | - Gary Murphy
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Jennifer Tosswill
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Ross J Harris
- Statistics, Modelling and Economics Department, National Infection Service, Public Health England, London, UK
| | - Richard Myers
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Nigel Field
- HIV and STI Department, National Infection Service, Public Health England, London, UK
| | - Valerie Delpech
- HIV and STI Department, National Infection Service, Public Health England, London, UK.,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
| | - Patricia A Cane
- Virus Reference Department, National Infection Service, Public Health England, London, UK.,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
| | - O Noel Gill
- HIV and STI Department, National Infection Service, Public Health England, London, UK.,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
| | - Jean L Mbisa
- Virus Reference Department, National Infection Service, Public Health England, London, UK .,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
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7
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HIV Drug Resistance in Antiretroviral Treatment-Naïve Individuals in the Largest Public Hospital in Nicaragua, 2011-2015. PLoS One 2016; 11:e0164156. [PMID: 27736898 PMCID: PMC5063387 DOI: 10.1371/journal.pone.0164156] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/20/2016] [Indexed: 11/19/2022] Open
Abstract
Background Increasing HIV pre-treatment drug resistance (PDR) levels have been observed in regions with increasing antiretroviral treatment (ART) coverage. However, data is lacking for several low/middle-income countries. We present the first PDR survey in Nicaragua since ART introduction in the country in 2003. Methods HIV-infected, ART-naïve Nicaraguan individuals were enrolled at Roberto Calderón Hospital, the largest national HIV referral center, from 2011 to 2015. HIV pol sequences were obtained at a WHO-accredited laboratory in Mexico by Sanger and next generation sequencing (NGS). PDR was assessed using the WHO surveillance drug resistance mutation (SDRM) list and the Stanford HIVdb tool. Results 283 individuals were enrolled in the study. The overall PDR prevalence based on the list of SDRMs was 13.4%. Using the Stanford HIVdb tool, overall PDR reached 19.4%; with both nucleoside and non-nucleoside reverse transcriptase inhibitor (NRTI and NNRTI) PDR levels independently reaching moderate levels (6.7% and 11.3% respectively). Protease inhibitor PDR was low (2.8%). Using NGS with 2% threshold to detect SDRMs, PDR increased to 25.3%. K103N and M41L were the most frequent SDRMs and were present mostly in proportions >20% in each individual. A significant temporal increase in NNRTI PDR was observed (p = 0.0422), with no apparent trends for other drug classes. Importantly, PDR to zidovudine + lamivudine + efavirenz and tenofovir + emtricitabine + efavirenz, the most widely used first-line regimens in Nicaragua, reached 14.6% and 10.4% respectively in 2015. Of note, a higher proportion of females was observed among individuals with PDR compared to individuals without PDR (OR 14.2; 95% CI: 7.1–28.4; p<0.0001). Conclusions Overall PDR in the Nicaraguan cohort was high (19.4%), with a clear increasing temporal trend in NNRTI PDR. Current HIVDR to the most frequently used first-line ART regimens in Nicaragua reached levels >10%. These observations are worrisome and need to be evidenced to strengthen the national HIV program. Also, our observations warrant further nationally representative HIVDR surveillance studies and encourage other countries to perform national surveys. Cost-effectiveness studies are suggested to analyze the feasibility of implementation of baseline HIV genotyping as well as to review the choice of first-line ART regimens in Nicaragua.
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HIV-1 drug resistance and resistance testing. INFECTION GENETICS AND EVOLUTION 2016; 46:292-307. [PMID: 27587334 DOI: 10.1016/j.meegid.2016.08.031] [Citation(s) in RCA: 200] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/24/2016] [Accepted: 08/27/2016] [Indexed: 12/23/2022]
Abstract
The global scale-up of antiretroviral (ARV) therapy (ART) has led to dramatic reductions in HIV-1 mortality and incidence. However, HIV drug resistance (HIVDR) poses a potential threat to the long-term success of ART and is emerging as a threat to the elimination of AIDS as a public health problem by 2030. In this review we describe the genetic mechanisms, epidemiology, and management of HIVDR at both individual and population levels across diverse economic and geographic settings. To describe the genetic mechanisms of HIVDR, we review the genetic barriers to resistance for the most commonly used ARVs and describe the extent of cross-resistance between them. To describe the epidemiology of HIVDR, we summarize the prevalence and patterns of transmitted drug resistance (TDR) and acquired drug resistance (ADR) in both high-income and low- and middle-income countries (LMICs). We also review to two categories of HIVDR with important public health relevance: (i) pre-treatment drug resistance (PDR), a World Health Organization-recommended HIVDR surveillance metric and (ii) and pre-exposure prophylaxis (PrEP)-related drug resistance, a type of ADR that can impact clinical outcomes if present at the time of treatment initiation. To summarize the implications of HIVDR for patient management, we review the role of genotypic resistance testing and treatment practices in both high-income and LMIC settings. In high-income countries where drug resistance testing is part of routine care, such an understanding can help clinicians prevent virological failure and accumulation of further HIVDR on an individual level by selecting the most efficacious regimens for their patients. Although there is reduced access to diagnostic testing and to many ARVs in LMIC, understanding the scientific basis and clinical implications of HIVDR is useful in all regions in order to shape appropriate surveillance, inform treatment algorithms, and manage difficult cases.
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Dimitrov DT, Boily MC, Hallett TB, Albert J, Boucher C, Mellors JW, Pillay D, van de Vijver DAMC. How Much Do We Know about Drug Resistance Due to PrEP Use? Analysis of Experts' Opinion and Its Influence on the Projected Public Health Impact. PLoS One 2016; 11:e0158620. [PMID: 27391094 PMCID: PMC4938235 DOI: 10.1371/journal.pone.0158620] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/20/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Randomized controlled trials reported that pre-exposure prophylaxis (PrEP) with tenofovir and emtricitabine rarely selects for drug resistance. However, drug resistance due to PrEP is not completely understood. In daily practice, PrEP will not be used under the well-controlled conditions available in the trials, suggesting that widespread use of PrEP can result in increased drug resistance. METHODS We surveyed expert virologists with questions about biological assumptions regarding drug resistance due to PrEP use. The influence of these assumptions on the prevalence of drug resistance and the fraction of HIV transmitted resistance was studied with a mathematical model. For comparability, 50% PrEP-coverage of and 90% per-act efficacy of PrEP in preventing HIV acquisition are assumed in all simulations. RESULTS Virologists disagreed on the following: the time until resistance emergence (range: 20-180 days) in infected PrEP users with breakthrough HIV infections; the efficacy of PrEP against drug-resistant HIV (25%-90%); and the likelihood of resistance acquisition upon transmission (10%-75%). These differences translate into projections of 0.6%- 1% and 3.5%-6% infected individuals with detectable resistance 10 years after introducing PrEP, assuming 100% and 50% adherence, respectively. The rate of resistance emergence following breakthrough HIV infection and the rate of resistance reversion after PrEP use is discontinued, were the factors identified as most influential on the expected resistance associated with PrEP. Importantly, 17-23% infected individuals could virologically fail treatment as a result of past PrEP use or transmitted resistance to PrEP with moderate adherence. CONCLUSIONS There is no broad consensus on quantification of key biological processes that underpin the emergence of PrEP-associated drug resistance. Despite this, the contribution of PrEP use to the prevalence of the detectable drug resistance is expected to be small. However, individuals who become infected despite the use of PrEP should be closely monitored due to higher risk of virological failure when initiating antiretroviral treatment in the future.
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Affiliation(s)
- Dobromir T. Dimitrov
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Applied Mathematics, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Marie-Claude Boily
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Timothy B. Hallett
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Charles Boucher
- Department of Virology, Erasmus Medical Centre, University Medical Centre Rotterdam, Rotterdam, Netherlands
| | - John W. Mellors
- Division of Infectious Diseases, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Deenan Pillay
- Research Department of Infection, University College Medical School, London, United Kingdom
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Prevalence of Transmitted HIV Drug Resistance Among Recently Infected Persons in San Diego, CA 1996-2013. J Acquir Immune Defic Syndr 2016; 71:228-36. [PMID: 26413846 DOI: 10.1097/qai.0000000000000831] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Transmitted drug resistance (TDR) remains an important concern when initiating antiretroviral therapy (ART). Here, we describe the prevalence and phylogenetic relationships of TDR among ART-naive, HIV-infected individuals in San Diego from 1996 to 2013. METHODS Data were analyzed from 496 participants of the San Diego Primary Infection Cohort who underwent genotypic resistance testing before initiating therapy. Mutations associated with drug resistance were identified according to the WHO-2009 surveillance list. Network and phylogenetic analyses of the HIV-1 pol sequences were used to evaluate the relationships of TDR within the context of the entire cohort. RESULTS The overall prevalence of TDR was 13.5% (67/496), with an increasing trend over the study period (P = 0.005). TDR was predominantly toward nonnucleoside reverse transcriptase inhibitors (NNRTIs) [8.5% (42/496)], also increasing over the study period (P = 0.005). By contrast, TDR to protease inhibitors and nucleos(t)ide reverse transcriptase inhibitors were 4.4% (22/496) and 3.8% (19/496), respectively, and did not vary with time. TDR prevalence did not differ by age, gender, race/ethnicity, or risk factors. Using phylogenetic analysis, we identified 52 transmission clusters, including 8 with at least 2 individuals sharing the same mutation, accounting for 23.8% (16/67) of the individuals with TDR. CONCLUSIONS Between 1996 and 2013, the prevalence of TDR significantly increased among recently infected ART-naive individuals in San Diego. Around one-fourth of TDR occurred within clusters of recently infected individuals. These findings highlight the importance of baseline resistance testing to guide selection of ART and for public health monitoring.
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Deep Sequencing of HIV-1 RNA and DNA in Newly Diagnosed Patients with Baseline Drug Resistance Showed No Indications for Hidden Resistance and Is Biased by Strong Interference of Hypermutation. J Clin Microbiol 2016; 54:1605-1615. [PMID: 27076656 DOI: 10.1128/jcm.00030-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/01/2016] [Indexed: 12/29/2022] Open
Abstract
Deep sequencing of plasma RNA or proviral DNA may be an interesting alternative to population sequencing for the detection of baseline transmitted HIV-1 drug resistance. Using a Roche 454 GS Junior HIV-1 prototype kit, we performed deep sequencing of the HIV-1 protease and reverse transcriptase genes on paired plasma and buffy coat samples from newly diagnosed HIV-1-positive individuals. Selection was based on the outcome of population sequencing and included 12 patients with either a revertant amino acid at codon 215 of the reverse transcriptase or a singleton resistance mutation, 4 patients with multiple resistance mutations, and 4 patients with wild-type virus. Deep sequencing of RNA and DNA detected 6 and 43 mutations, respectively, that were not identified by population sequencing. A subsequently performed hypermutation analysis, however, revealed hypermutation in 61.19% of 3,188 DNA reads with a resistance mutation. The removal of hypermutated reads dropped the number of additional mutations in DNA from 43 to 17. No hypermutation evidence was found in the RNA reads. Five of the 6 additional RNA mutations and all additional DNA mutations, after full exclusion of hypermutation bias, were observed in the 3 individuals with multiple resistance mutations detected by population sequencing. Despite focused selection of patients with T215 revertants or singleton mutations, deep sequencing failed to identify the resistant T215Y/F or M184V or any other resistance mutation, indicating that in most of these cases there is no hidden resistance and that the virus detected at diagnosis by population sequencing is the original infecting variant.
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12
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Ambrosioni J, Sued O, Nicolas D, Parera M, López-Diéguez M, Romero A, Agüero F, Marcos MÁ, Manzardo C, Zamora L, Gómez-Carrillo M, Gatell JM, Pumarola T, Miró JM. Trends in Transmission of Drug Resistance and Prevalence of Non-B Subtypes in Patients with Acute or Recent HIV-1 Infection in Barcelona in the Last 16 Years (1997-2012). PLoS One 2015; 10:e0125837. [PMID: 26039689 PMCID: PMC4454638 DOI: 10.1371/journal.pone.0125837] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 03/21/2015] [Indexed: 12/31/2022] Open
Abstract
Objectives To evaluate the prevalence of transmitted drug resistance (TDR) and non-B subtypes in patients with acute/recent HIV-1 infection in Barcelona during the period 1997-2012. Methods Patients from the “Hospital Clínic Primary HIV-1 Infection Cohort” with a genotyping test performed within 180 days of infection were included. The 2009 WHO List of Mutations for Surveillance of Transmitted HIV-1 Drug Resistance was used for estimating the prevalence of TDR and phylogenetic analysis for subtype determination. Results 189 patients with acute/recent HIV-1 infection were analyzed in 4 time periods (1997-2000, n=28; 2001-4, n=42; 2005-8, n=55 and 2009-12, n=64). The proportion of patients with acute/recent HIV-1 infection with respect to the total of newly HIV-diagnosed patients in our center increased over the time and was 2.18%, 3.82%, 4.15% and 4.55% for the 4 periods, respectively (p=0.005). The global prevalence of TDR was 9%, or 17.9%, 9.5%, 3.6% and 9.4% by study period (p=0.2). The increase in the last period was driven by protease-inhibitor and nucleoside-reverse-transcriptase-inhibitor resistance mutations while non-nucleoside-reverse-transcriptase inhibitor TDR and TDR of more than one family decreased. The overall prevalence of non-B subtypes was 11.1%, or 0%, 4.8%, 9.1% and 20.3 by study period (p=0.01). B/F recombinants, B/G recombinants and subtype F emerged in the last period. We also noticed an increase in the number of immigrant patients (p=0.052). The proportion of men-who-have-sex-with-men (MSM) among patients with acute/recent HIV-1 infection increased over the time (p=0.04). Conclusions The overall prevalence of TDR in patients with acute/recent HIV-1 infection in Barcelona was 9%, and it has stayed relatively stable in recent years. Non-B subtypes and immigrants proportions progressively increased.
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Affiliation(s)
- Juan Ambrosioni
- Hospital Clínic-Institut d’Investigacions Biomèdiques August Pi-Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Omar Sued
- Huésped Foundation, Buenos Aires, Argentina
| | - David Nicolas
- Hospital Clínic-Institut d’Investigacions Biomèdiques August Pi-Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Marta Parera
- Hospital Clínic-Institut d’Investigacions Biomèdiques August Pi-Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - María López-Diéguez
- Hospital Clínic-Institut d’Investigacions Biomèdiques August Pi-Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Anabel Romero
- Agency for Health Quality and Assessment of Catalonia (AQuAS), Barcelona, Spain
| | - Fernando Agüero
- Hospital Clínic-Institut d’Investigacions Biomèdiques August Pi-Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - María Ángeles Marcos
- Hospital Clínic-Institut d’Investigacions Biomèdiques August Pi-Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
- Department of Microbiology. Barcelona Centre for International Health Research (CRESIB) Hospital Clínic, Barcelona, Spain
| | - Christian Manzardo
- Hospital Clínic-Institut d’Investigacions Biomèdiques August Pi-Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Laura Zamora
- Hospital Clínic-Institut d’Investigacions Biomèdiques August Pi-Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | | | - José María Gatell
- Hospital Clínic-Institut d’Investigacions Biomèdiques August Pi-Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Tomás Pumarola
- Hospital Clínic-Institut d’Investigacions Biomèdiques August Pi-Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - José María Miró
- Hospital Clínic-Institut d’Investigacions Biomèdiques August Pi-Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
- * E-mail:
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Mbisa JL, Fearnhill E, Dunn DT, Pillay D, Asboe D, Cane PA. Evidence of Self-Sustaining Drug Resistant HIV-1 Lineages Among Untreated Patients in the United Kingdom. Clin Infect Dis 2015; 61:829-36. [PMID: 25991470 DOI: 10.1093/cid/civ393] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 04/05/2015] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND About 10% of new diagnoses of subtype B human immunodeficiency virus type 1 (HIV-1) in the United Kingdom are with viruses showing transmitted drug resistance (TDR). However, there is discordance between the mutation patterns observed in HIV-infected patients failing therapy and those seen in TDR. METHODS We extracted all subtype B HIV-1 pol gene sequences from treatment-naive patients within the United Kingdom HIV Drug Resistance Database sampled between 1997 and 2011 and carrying the most common protease inhibitors, nonnucleoside and nucleotide reverse transcriptase inhibitors TDR mutations, namely, L90M, K103N, and T215Y/F/rev, respectively (n = 1140). Transmission clusters (n ≥ 2 sequences) were identified by maximum-likelihood phylogeny using a genetic distance cutoff of ≤ 1.5%. The time of origin and the basic reproductive number (R0) of clusters were estimated by Bayesian methods. RESULTS T215rev was present alone in 47% of the sequences (n = 540), K103N in 31% (n = 359), and L90M in 10% (n = 109). The remaining sequences contained T215Y or combinations of L90M, K103N, and T215rev. Fifty-five percent (n = 624) of the sequences formed highly supported transmission clusters (n = 193) containing between 2 and 15 sequences. The time of origin of 10 large clusters (≥ 8 sequences) was estimated to be between 2000 (1999-2002; 95% highest posterior density [HPD]) and 2006 (2005-2007; 95% HPD). The oldest cluster had persisted for nearly 8 years. All 10 clusters had R0s ranging from 1.3 (0.4-2.5; 95% HPD) to 2.8 (0.6-6.5; 95% HPD). CONCLUSIONS A high proportion of the most common TDR in subtype B infections in the United Kingdom is derived by onward transmission from treatment-naive patients.
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Affiliation(s)
- Jean L Mbisa
- Antiviral Unit, Virus Reference Department, Public Health England
| | | | | | - Deenan Pillay
- Research Department of Infection, University College London
| | - David Asboe
- Chelsea and Westminster Hospital, London, United Kingdom
| | - Patricia A Cane
- Antiviral Unit, Virus Reference Department, Public Health England
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Yang WL, Kouyos R, Scherrer AU, Böni J, Shah C, Yerly S, Klimkait T, Aubert V, Furrer H, Battegay M, Cavassini M, Bernasconi E, Vernazza P, Held L, Ledergerber B, Günthard HF. Assessing the Paradox Between Transmitted and Acquired HIV Type 1 Drug Resistance Mutations in the Swiss HIV Cohort Study From 1998 to 2012. J Infect Dis 2015; 212:28-38. [PMID: 25576600 DOI: 10.1093/infdis/jiv012] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 11/28/2014] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Transmitted human immunodeficiency virus type 1 (HIV) drug resistance (TDR) mutations are transmitted from nonresponding patients (defined as patients with no initial response to treatment and those with an initial response for whom treatment later failed) or from patients who are naive to treatment. Although the prevalence of drug resistance in patients who are not responding to treatment has declined in developed countries, the prevalence of TDR mutations has not. Mechanisms causing this paradox are poorly explored. METHODS We included recently infected, treatment-naive patients with genotypic resistance tests performed ≤ 1 year after infection and before 2013. Potential risk factors for TDR mutations were analyzed using logistic regression. The association between the prevalence of TDR mutations and population viral load (PVL) among treated patients during 1997-2011 was estimated with Poisson regression for all TDR mutations and individually for the most frequent resistance mutations against each drug class (ie, M184V/L90M/K103N). RESULTS We included 2421 recently infected, treatment-naive patients and 5399 patients with no response to treatment. The prevalence of TDR mutations fluctuated considerably over time. Two opposing developments could explain these fluctuations: generally continuous increases in the prevalence of TDR mutations (odds ratio, 1.13; P = .010), punctuated by sharp decreases in the prevalence when new drug classes were introduced. Overall, the prevalence of TDR mutations increased with decreasing PVL (rate ratio [RR], 0.91 per 1000 decrease in PVL; P = .033). Additionally, we observed that the transmitted high-fitness-cost mutation M184V was positively associated with the PVL of nonresponding patients carrying M184V (RR, 1.50 per 100 increase in PVL; P < .001). Such association was absent for K103N (RR, 1.00 per 100 increase in PVL; P = .99) and negative for L90M (RR, 0.75 per 100 increase in PVL; P = .022). CONCLUSIONS Transmission of antiretroviral drug resistance is temporarily reduced by the introduction of new drug classes and driven by nonresponding and treatment-naive patients. These findings suggest a continuous need for new drugs, early detection/treatment of HIV-1 infection.
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Affiliation(s)
- Wan-Lin Yang
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
| | - Roger Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
| | - Alexandra U Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
| | - Jürg Böni
- Swiss National Center for Retroviruses, Institute of Medical Virology
| | - Cyril Shah
- Swiss National Center for Retroviruses, Institute of Medical Virology
| | - Sabine Yerly
- Laboratory of Virology, Division of Infectious Diseases, Geneva University Hospital
| | | | | | - Hansjakob Furrer
- Department of Infectious Diseases, Berne University Hospital and University of Berne
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel
| | | | | | - Pietro Vernazza
- Division of Infectious Diseases, Cantonal Hospital St. Gallen, Switzerland
| | - Leonhard Held
- Institute of Social and Preventive Medicine, University of Zurich
| | - Bruno Ledergerber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
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Pingen M, Wensing AMJ, Fransen K, De Bel A, de Jong D, Hoepelman AIM, Magiorkinis E, Paraskevis D, Lunar MM, Poljak M, Nijhuis M, Boucher CAB. Persistence of frequently transmitted drug-resistant HIV-1 variants can be explained by high viral replication capacity. Retrovirology 2014; 11:105. [PMID: 25575025 PMCID: PMC4263067 DOI: 10.1186/s12977-014-0105-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 11/05/2014] [Indexed: 11/10/2022] Open
Abstract
Background In approximately 10% of newly diagnosed individuals in Europe, HIV-1 variants harboring transmitted drug resistance mutations (TDRM) are detected. For some TDRM it has been shown that they revert to wild type while other mutations persist in the absence of therapy. To understand the mechanisms explaining persistence we investigated the in vivo evolution of frequently transmitted HIV-1 variants and their impact on in vitro replicative capacity. Results We selected 31 individuals infected with HIV-1 harboring frequently observed TDRM such as M41L or K103N in reverse transcriptase (RT) or M46L in protease. In all these samples, polymorphisms at non-TDRM positions were present at baseline (median protease: 5, RT: 6). Extensive analysis of viral evolution of protease and RT demonstrated that the majority of TDRM (51/55) persisted for at least a year and even up to eight years in the plasma. During follow-up only limited selection of additional polymorphisms was observed (median: 1). To investigate the impact of frequently observed TDRM on the replication capacity, mutant viruses were constructed with the most frequently encountered TDRM as site-directed mutants in the genetic background of the lab strain HXB2. In addition, viruses containing patient-derived protease or RT harboring similar TDRM were made. The replicative capacity of all viral variants was determined by infecting peripheral blood mononuclear cells and subsequently monitoring virus replication. The majority of site-directed mutations (M46I/M46L in protease and M41L, M41L + T215Y and K103N in RT) decreased viral replicative capacity; only protease mutation L90M did not hamper viral replication. Interestingly, most patient-derived viruses had a higher in vitro replicative capacity than the corresponding site-directed mutant viruses. Conclusions We demonstrate limited in vivo evolution of protease and RT harbouring frequently observed TDRM in the plasma. This is in line with the high in vitro replication capacity of patient-derived viruses harbouring TDRM compared to site-directed mutant viruses harbouring TDRM. As site-directed mutant viruses have a lower replication capacity than the patient-derived viruses with similar mutational patterns, we propose that (baseline) polymorphisms function as compensatory mutations improving viral replication capacity.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Charles A B Boucher
- Department of Virology, Viroscience Lab, Erasmus MC, Postbus 2040, Rotterdam, 3000 CA, the Netherlands.
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Lee GQ, Bangsberg DR, Muzoora C, Boum Y, Oyugi JH, Emenyonu N, Bennett J, Hunt PW, Knapp D, Brumme CJ, Harrigan PR, Martin JN. Prevalence and virologic consequences of transmitted HIV-1 drug resistance in Uganda. AIDS Res Hum Retroviruses 2014; 30:896-906. [PMID: 24960249 DOI: 10.1089/aid.2014.0043] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Few reports have examined the impact of HIV-1 transmitted drug resistance (TDR) in resource-limited settings where there are fewer regimen choices and limited pretherapy/posttherapy resistance testing. In this study, we examined TDR prevalence in Kampala and Mbarara, Uganda and assessed its virologic consequences after antiretroviral therapy initiation. We sequenced the HIV-1 protease/reverse transcriptase from n=81 and n=491 treatment-naive participants of the Uganda AIDS Rural Treatment Outcomes (UARTO) pilot study in Kampala (AMU 2002-2004) and main cohort in Mbarara (MBA 2005-2010). TDR-associated mutations were defined by the WHO 2009 surveillance mutation list. Posttreatment viral load data were available for both populations. Overall TDR prevalence was 7% (Kampala) and 3% (Mbarara) with no significant time trend. There was a slight but statistically nonsignificant trend indicating that the presence of TDR was associated with a worse treatment outcome. Virologic suppression (≤400 copies/ml within 6 months posttherapy initiation) was achieved in 87% and 96% of participants with wildtype viruses versus 67% and 83% of participants with TDR (AMU, MBA p=0.2 and 0.1); time to suppression (log-rank p=0.3 and p=0.05). Overall, 85% and 96% of study participants achieved suppression regardless of TDR status. Surprisingly, among the TDR cases, approximately half still achieved suppression; the presence of pretherapy K103N while on nevirapine and fewer active drugs in the first regimen were most often observed with failures. The majority of patients benefited from the local HIV care system even without resistance monitoring. Overall, TDR prevalence was relatively low and its presence did not always imply treatment failure.
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Affiliation(s)
| | - David R. Bangsberg
- Mbarara University of Science of Technology, Mbarara, Uganda
- Harvard Medical School, Boston, Massachusetts
- Harvard School of Public Health, Boston, Massachusetts
- Massachusetts General Hospital, Boston, Massachusetts
| | - Conrad Muzoora
- Mbarara University of Science of Technology, Mbarara, Uganda
| | - Yap Boum
- Mbarara University of Science of Technology, Mbarara, Uganda
| | - Jessica H. Oyugi
- University of California, San Francisco, California
- Independent consultant
| | - Nneka Emenyonu
- Mbarara University of Science of Technology, Mbarara, Uganda
| | - John Bennett
- University of California, San Francisco, California
| | | | - David Knapp
- B.C. Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
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Sey K, Ma Y, Lan YC, Song N, Hu YW, Ou Y, Frye D. Prevalence and circulation patterns of Variant, Atypical and Resistant HIV in Los Angeles County (2007-2009). J Med Virol 2014; 86:1639-47. [DOI: 10.1002/jmv.23989] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Kwa Sey
- Division of HIV and STD Programs; Los Angeles County Department of Public Health; Los Angeles California
| | - Yingbo Ma
- Division of HIV and STD Programs; Los Angeles County Department of Public Health; Los Angeles California
| | - Yu-Ching Lan
- Department of Health Risk Management; China Medical University; Taichung Taiwan
- Department of Community Health Sciences; School of Public Health; University of California at Los Angeles; Los Angeles California
| | - Nannie Song
- Division of HIV and STD Programs; Los Angeles County Department of Public Health; Los Angeles California
| | - Yunyin W. Hu
- Division of HIV and STD Programs; Los Angeles County Department of Public Health; Los Angeles California
| | - Ying Ou
- Division of HIV and STD Programs; Los Angeles County Department of Public Health; Los Angeles California
| | - Douglas Frye
- Division of HIV and STD Programs; Los Angeles County Department of Public Health; Los Angeles California
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Tupinambás U, Duani H, Martins AVC, Aleixo AW, Greco DB. Transmitted human immunodeficiency virus-1 drug resistance in a cohort of men who have sex with men in Belo Horizonte, Brazil--1996-2012. Mem Inst Oswaldo Cruz 2014; 108:470-5. [PMID: 23828000 DOI: 10.1590/s0074-0276108042013012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 04/09/2013] [Indexed: 11/22/2022] Open
Abstract
The presence of transmitted human immunodeficiency virus (HIV)-1 drug-resistance (TDR) at the time of antiretroviral therapy initiation is associated with failure to achieve viral load (VL) suppression. Here, we report TDR surveillance in a specific population of men who have sex with men (MSM) in Belo Horizonte, Brazil. In this study, the rate of TDR was evaluated in 64 HIV-infected individuals from a cohort of MSM between 1996-June 2012. Fifty-four percent had a documented recent HIV infection, with a seroconversion time of less than 12 months. The median CD4+T lymphocyte count and VL were 531 cells/mm3 and 17,746 copies/mL, respectively. Considering the surveillance drug resistance mutation criteria, nine (14.1%) patients presented TDR, of which three (4.7%), five (7.8%) and four (6.2%) had protease inhibitors, resistant against nucleos(t)ide transcriptase inhibitors and against non-nucleoside reverse-transcriptase inhibitors mutations, respectively. Two of the patients had multi-drug-resistant HIV-1. The most prevalent viral subtype was B (44, 68.8%), followed by subtype F (11, 17.2%). This study shows that TDR may vary according to the population studied and it may be higher in clusters of MSM.
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Affiliation(s)
- Unaí Tupinambás
- Departamento de Clínica Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil.
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Antiretroviral drug resistance in HIV-1 therapy-naive patients in Cuba. INFECTION GENETICS AND EVOLUTION 2013; 16:144-50. [PMID: 23416260 DOI: 10.1016/j.meegid.2013.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 01/31/2013] [Accepted: 02/03/2013] [Indexed: 11/23/2022]
Abstract
In Cuba, antiretroviral therapy rollout started in 2001 and antiretroviral therapy coverage has reached almost 40% since then. The objectives of this study were therefore to analyze subtype distribution, and level and patterns of drug resistance in therapy-naive HIV-1 patients. Four hundred and one plasma samples were collected from HIV-1 therapy-naive patients in 2003 and in 2007-2011. HIV-1 drug resistance genotyping was performed in the pol gene and drug resistance was interpreted according to the WHO surveillance drug-resistance mutations list, version 2009. Potential impact on first-line therapy response was estimated using genotypic drug resistance interpretation systems HIVdb version 6.2.0 and Rega version 8.0.2. Phylogenetic analysis was performed using Neighbor-Joining. The majority of patients were male (84.5%), men who have sex with men (78.1%) and from Havana City (73.6%). Subtype B was the most prevalent subtype (39.3%), followed by CRF20-23-24_BG (19.5%), CRF19_cpx (18.0%) and CRF18_cpx (10.3%). Overall, 29 patients (7.2%) had evidence of drug resistance, with 4.0% (CI 1.6%-4.8%) in 2003 versus 12.5% (CI 7.2%-14.5%) in 2007-2011. A significant increase in drug resistance was observed in recently HIV-1 diagnosed patients, i.e. 14.8% (CI 8.0%-17.0%) in 2007-2011 versus 3.8% (CI 0.9%-4.7%) in 2003 (OR 3.9, CI 1.5-17.0, p=0.02). The majority of drug resistance was restricted to a single drug class (75.8%), with 55.2% patients displaying nucleoside reverse transcriptase inhibitor (NRTI), 10.3% non-NRTI (NNRTI) and 10.3% protease inhibitor (PI) resistance mutations. Respectively, 20.7% and 3.4% patients carried viruses containing drug resistance mutations against NRTI+NNRTI and NRTI+NNRTI+PI. The first cases of resistance towards other drug classes than NRTI were only detected from 2008 onwards. The most frequent resistance mutations were T215Y/rev (44.8%), M41L (31.0%), M184V (17.2%) and K103N (13.8%). The median genotypic susceptibility score for the commonly prescribed first-line therapies was 2.5. This analysis emphasizes the need to perform additional surveillance studies to accurately assess the level of transmitted drug resistance in Cuba, as the extent of drug resistance might jeopardize effectiveness of first-line regimens prescribed in Cuba and might necessitate the implementation of baseline drug resistance testing.
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Hassan AS, Mwaringa SM, Obonyo CA, Nabwera HM, Sanders EJ, Rinke de Wit TF, Cane PA, Berkley JA. Low prevalence of transmitted HIV type 1 drug resistance among antiretroviral-naive adults in a rural HIV clinic in Kenya. AIDS Res Hum Retroviruses 2013; 29:129-35. [PMID: 22900472 DOI: 10.1089/aid.2012.0167] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Low levels of HIV-1 transmitted drug resistance (TDR) have previously been reported from many parts of sub-Saharan Africa (sSA). However, recent data, mostly from urban settings, suggest an increase in the prevalence of HIV-1 TDR. Our objective was to determine the prevalence of TDR mutations among HIV-1-infected, antiretroviral (ARV)-naive adults enrolling for care in a rural HIV clinic in Kenya. Two cross-sectional studies were carried out between July 2008 and June 2010. Plasma samples from ARV-naive adults (>15 years old) at the time of registering for care after HIV diagnosis and before starting ARVs were used. A portion of the pol subgenomic region of the virus containing the protease and part of the reverse transcriptase genes was amplified and sequenced. TDR mutations were identified and interpreted using the Stanford HIV drug resistance database and the WHO list for surveillance of drug resistance strains. Overall, samples from 182 ARV-naive adults [mean age (95% CI): 34.9 (33.3-36.4) years] were successfully amplified and sequenced. Two TDR mutations to nucleoside reverse transcriptase inhibitors [n=1 (T215D)] and protease inhibitors [n=1 (M46L)] were identified, giving an overall TDR prevalence of 1.1% (95% CI: 0.1-3.9). Despite reports of an increase in the prevalence of HIV-1 TDR in some urban settings in sSA, we report a prevalence of HIV-1 TDR of less than 5% at a rural HIV clinic in coastal Kenya. Continued broader surveillance is needed to monitor the extent of TDR in sSA.
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Affiliation(s)
| | | | | | | | - Eduard J. Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, United Kingdom
| | - Tobias F. Rinke de Wit
- PharmAccess Foundation, Amsterdam, The Netherlands
- Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | | | - James A. Berkley
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, United Kingdom
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Abstract
The efficacy of an antiretroviral (ARV) treatment regimen depends on the activity of the regimen's individual ARV drugs and the number of HIV-1 mutations required for the development of resistance to each ARV - the genetic barrier to resistance. ARV resistance impairs the response to therapy in patients with transmitted resistance, unsuccessful initial ARV therapy and multiple virological failures. Genotypic resistance testing is used to identify transmitted drug resistance, provide insight into the reasons for virological failure in treated patients, and help guide second-line and salvage therapies. In patients with transmitted drug resistance, the virological response to a regimen selected on the basis of standard genotypic testing approaches the responses observed in patients with wild-type viruses. However, because such patients are at a higher risk of harbouring minority drug-resistant variants, initial ARV therapy in this population should contain a boosted protease inhibitor (PI) - the drug class with the highest genetic barrier to resistance. In patients receiving an initial ARV regimen with a high genetic barrier to resistance, the most common reasons for virological failure are nonadherence and, potentially, pharmacokinetic factors or minority transmitted drug-resistant variants. Among patients in whom first-line ARVs have failed, the patterns of drug-resistance mutations and cross-resistance are often predictable. However, the extent of drug resistance correlates with the duration of uncontrolled virological replication. Second-line therapy should include the continued use of a dual nucleoside/nucleotide reverse transcriptase inhibitor (NRTI)-containing backbone, together with a change in the non-NRTI component, most often to an ARV belonging to a new drug class. The number of available fully active ARVs is often diminished with each successive treatment failure. Therefore, a salvage regimen is likely to be more complicated in that it may require multiple ARVs with partial residual activity and compromised genetic barriers of resistance to attain complete virological suppression. A thorough examination of the patient's ARV history and prior resistance tests should be performed because genotypic and/or phenotypic susceptibility testing is often not sufficient to identify drug-resistant variants that emerged during past therapies and may still pose a threat to a new regimen. Phenotypic testing is also often helpful in this subset of patients. ARVs used for salvage therapy can be placed into the following hierarchy: (i) ARVs belonging to a previously unused drug class; (ii) ARVs belonging to a previously used drug class that maintain significant residual antiviral activity; (iii) NRTI combinations, as these often appear to retain in vivo virological activity, even in the presence of reduced in vitro NRTI susceptibility; and rarely (iv) ARVs associated with previous virological failure and drug resistance that appear to have possibly regained their activity as a result of viral reversion to wild type. Understanding the basic principles of HIV drug resistance is helpful in guiding individual clinical decisions and the development of ARV treatment guidelines.
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Affiliation(s)
- Michele W Tang
- Stanford University, Division of Infectious Diseases, Stanford, CA 94305-5107, USA.
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Prevention of mother-to-child transmission, drug resistance, and implications for response to therapy. Curr Opin HIV AIDS 2012; 3:166-72. [PMID: 19372961 DOI: 10.1097/coh.0b013e3282f50bec] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW HIV-1 drug resistance can emerge in both maternal and infant virus after exposure to antiretroviral drugs for the prevention of mother-to-child transmission of HIV. The purpose of this review is to discuss the prevalence and clinical implications (for antiretroviral treatment outcomes) of this drug resistance, focusing on more recent information. RECENT FINDINGS New, highly sensitive laboratory assays have been developed that demonstrate even greater than previously known levels of drug resistance in minor HIV-1 variants after the use of single-dose nevirapine. At the same time, new data related to virological and immunological outcomes among women and infants after exposure to short-course prevention of mother-to-child transmission regimens suggest that although the response to nevirapine-based antiretroviral therapy after single-dose nevirapine may be compromised, this is less of a problem among women starting antiretroviral therapy more remotely from nevirapine exposure. SUMMARY Whereas single-dose nevirapine alone should be reserved for settings in which other combination antiretroviral interventions are not feasible for the prevention of mother-to-child transmission, recent data provide measured reassurance to women regarding their future response to nevirapine-containing antiretroviral therapy.
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23
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Buskin SE, Zhang S, Thibault CS. Prevalence of and viral outcomes associated with primary HIV-1 drug resistance. Open AIDS J 2012; 6:181-7. [PMID: 23049668 PMCID: PMC3462330 DOI: 10.2174/1874613601206010181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 08/18/2011] [Accepted: 09/19/2011] [Indexed: 11/26/2022] Open
Abstract
Primary, or transmitted, HIV antiretroviral resistance is an ongoing concern despite continuing development of
new antiretroviral therapies. We examined HIV surveillance data, including both patient demographic characteristics and
laboratory data, combined with HIV genotypic test results to evaluate the comprehensiveness of drug resistance
surveillance, prevalence of primary drug resistance, and impact, if any, of primary resistance on population-based
virological outcomes. The King County, WA Variant, Atypical, and Resistant HIV Surveillance (VARHS) system
increased coverage of eligible genotypic testing – within three months of an HIV diagnosis among antiretroviral naïve
individuals -- from – 15% in 2003 to 69% in 2010. VARHS under-represented females, Blacks, Native Americans, and
injection drug users. Primary drug resistance was more common among males, individuals aged 20 – 29 years, men who
had sex with men, and individuals with an initial CD4+ lymphocyte count of 200 cells/µL and higher. High level
resistance to two or three antiretroviral classes declined over time. Over 90% of sequences were HIV-1 subtype B. The
proportion of individuals with a most recent viral load (closest to April 2011) that was undetectable (<50 copies/mL) was
not statistically significantly associated with primary drug resistance. This was true for both number and type of
antiretroviral drug class; although small numbers of specimens with drug resistance may have limited our statistical
power. In summary, although we found disparities in testing coverage and prevalence of drug resistance, we were unable
to detect a significantly deleterious impact of primary drug resistance based on a most recent viral load.
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Affiliation(s)
- S E Buskin
- Public Health - Seattle & King County, Seattle, WA, USA ; University of Washington, Seattle, WA, USA
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Murillo W, Lorenzana de Rivera I, Albert J, Guardado ME, Nieto AI, Paz-Bailey G. Prevalence of transmitted HIV-1 drug resistance among female sex workers and men who have sex with men in El Salvador, Central America. J Med Virol 2012; 84:1514-21. [DOI: 10.1002/jmv.23381] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Thao VP, Le T, Török EM, Yen NTB, Chau TTH, Jurriaans S, van Doorn HR, de Jong MD, Farrar JJ, Dunstan SJ. Hiv-1 Drug Resistance in Antiretroviral-Naive Individuals with HIV-1-Associated Tuberculous Meningitis Initiating Antiretroviral Therapy in Vietnam. Antivir Ther 2012. [DOI: 10.3851/imp2098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Vu P Thao
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Thuy Le
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Hawaii Center for AIDS, University of Hawaii at Manoa, Honolulu, HI, USA
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Estee M Török
- University of Cambridge, Department of Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Nguyen TB Yen
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | - Tran TH Chau
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Suzanne Jurriaans
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - H Rogier van Doorn
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Menno D de Jong
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Jeremy J Farrar
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Sarah J Dunstan
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
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26
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Thao VP, Le T, Török EM, Yen NTB, Chau TTH, Jurriaans S, van Doorn HR, van Doorn RH, de Jong MD, Farrar JJ, Dunstan SJ. HIV-1 drug resistance in antiretroviral-naive individuals with HIV-1-associated tuberculous meningitis initiating antiretroviral therapy in Vietnam. Antivir Ther 2012; 17:905-13. [PMID: 22473024 DOI: 10.3851/imp2092] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2011] [Indexed: 10/28/2022]
Abstract
BACKGROUND Access to antiretroviral therapy (ART) for HIV-infected individuals in Vietnam is rapidly expanding, but there are limited data on HIV drug resistance (HIVDR) to guide ART strategies. METHODS We retrospectively conducted HIVDR testing in 220 ART-naive individuals recruited to a randomized controlled trial of immediate versus deferred ART in individuals with HIV-associated tuberculous meningitis in Ho Chi Minh City (HCMC) from 2005-2008. HIVDR mutations were identified by population sequencing of the HIV pol gene and were defined based on 2009 WHO surveillance drug resistance mutations (SDRMs). RESULTS We successfully sequenced 219/220 plasma samples of subjects prior to ART; 218 were subtype CRF01_AE and 1 was subtype B. SDRMs were identified in 14/219 (6.4%) subjects; 8/14 were resistant to nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs; T69D, L74V, V75M, M184V/I and K219R), 5/14 to non-nucleoside reverse transcriptase inhibitors (NNRTIs; K103N, V106M, Y181C, Y188C and G190A), 1/14 to both NRTIs and NNRTIs (D67N and Y181C) and none to protease inhibitors. After 6 months of ART, eight subjects developed protocol-defined virological failure. HIVDR mutations were identified in 5/8 subjects. All five had mutations with high-level resistance to NNRTIs and three had mutations with high-level resistance to NRTIs. Due to a high early mortality rate (58%), the effect of pre-existing HIVDR mutations on treatment outcome could not be accurately assessed. CONCLUSIONS The prevalence of WHO SDRMs in ART-naive individuals with HIV-associated tuberculous meningitis in HCMC from 2005-2008 is 6.4%. The SDRMs identified conferred resistance to NRTIs and/or NNRTIs, reflecting the standard first-line ART regimens in Vietnam.
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Affiliation(s)
- Vu P Thao
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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Parham L, de Rivera IL, Murillo W, Naver L, Largaespada N, Albert J, Karlsson AC. Short communication: high prevalence of drug resistance in HIV type 1-infected children born in Honduras and Belize 2001 to 2004. AIDS Res Hum Retroviruses 2011; 27:1055-9. [PMID: 21417948 DOI: 10.1089/aid.2010.0289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Antiretroviral therapy has had a great impact on the prevention of mother-to-child transmission (MTCT) of HIV-1. However, development of drug resistance, which could be subsequently transmitted to the child, is a major concern. In Honduras and Belize the prevalence of drug resistance among HIV-1-infected children remains unknown. A total of 95 dried blood spot samples was obtained from HIV-1-infected, untreated children in Honduras and Belize born during 2001 to 2004, when preventive antiretroviral therapy was often suboptimal and consisted of monotherapy with nevirapine or zidovudine. Partial HIV-1 pol gene sequences were successfully obtained from 66 children (Honduras n=55; Belize n=11). Mutations associated with drug resistance were detected in 13% of the Honduran and 27% of the Belizean children. Most of the mutations detected in Honduras (43%) and all mutations detected in Belize were associated with resistance to nonnucleoside reverse transcriptase inhibitors, which was expected from the wide use of nevirapine to prevent MTCT during the study period. In addition, although several mothers reported that they had not received antiretroviral therapy, mutations associated with resistance to nucleoside reverse transcriptase inhibitors and protease inhibitors were found in Honduras. This suggests prior and unreported use of these drugs, or that these women had been infected with resistant virus. The present study demonstrates, for the first time, the presence of drug resistance-associated mutations in HIV-1-infected Honduran and Belizean children.
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Affiliation(s)
- Leda Parham
- Department of Microbiology, National Autonomous University of Honduras, Tegucigalpa, Honduras
- Department of Virology, The Swedish Institute for Infectious Disease Control, Solna, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Wendy Murillo
- Department of Microbiology, National Autonomous University of Honduras, Tegucigalpa, Honduras
- Department of Virology, The Swedish Institute for Infectious Disease Control, Solna, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Lars Naver
- Department of Pediatrics, Karolinska University Hospital, Huddinge, Sweden
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | | | - Jan Albert
- Department of Virology, The Swedish Institute for Infectious Disease Control, Solna, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Annika C. Karlsson
- Department of Virology, The Swedish Institute for Infectious Disease Control, Solna, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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Kasang C, Kalluvya S, Majinge C, Stich A, Bodem J, Kongola G, Jacobs GB, Mlewa M, Mildner M, Hensel I, Horn A, Preiser W, van Zyl G, Klinker H, Koutsilieri E, Rethwilm A, Scheller C, Weissbrich B. HIV drug resistance (HIVDR) in antiretroviral therapy-naïve patients in Tanzania not eligible for WHO threshold HIVDR survey is dramatically high. PLoS One 2011; 6:e23091. [PMID: 21886779 PMCID: PMC3158766 DOI: 10.1371/journal.pone.0023091] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 07/05/2011] [Indexed: 11/18/2022] Open
Abstract
Background The World Health Organization (WHO) has recommended guidelines for a HIV drug resistance (HIVDR) survey for resource-limited countries. Eligibility criteria for patients include age below 25 years in order to focus on the prevalence of transmitted HIVDR (tHIVDR) in newly-infected individuals. Most of the participating sites across Africa have so far reported tHIVDR prevalences of below 5%. In this study we investigated whether the rate of HIVDR in patients <25 years is representative for HIVDR in the rest of the therapy-naïve population. Methods and Findings HIVDR was determined in 88 sequentially enrolled ART-naïve patients from Mwanza, Tanzania (mean age 35.4 years). Twenty patients were aged <25 years and 68 patients were aged 25–63 years. The frequency of HIVDR in the study population was 14.8% (95%; CI 0.072–0.223) and independent of NVP-resistance induced by prevention of mother-to-child transmission programs. Patients >25 years had a significantly higher HIVDR frequency than younger patients (19.1%; 95% CI 0.095–0.28) versus 0%, P = 0.0344). In 2 out of the 16 patients with HIVDR we found traces of antiretrovirals (ARVs) in plasma. Conclusions ART-naïve patients aged over 25 years exhibited significantly higher HIVDR than younger patients. Detection of traces of ARVs in individuals with HIVDR suggests that besides transmission, undisclosed misuse of ARVs may constitute a significant factor in the generation of the observed high HIVDR rate. The current WHO tHIVDR survey that is solely focused on the transmission of HIVDR and that excludes patients over 25 years of age may therefore result in substantial underestimation of the prevalence of HIVDR in the therapy-naïve population. Similar studies should be performed also in other areas to test whether the so far reported optimistic picture of low HIVDR prevalence in young individuals is really representative for the rest of the ART-naïve HIV-infected population.
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Affiliation(s)
- Christa Kasang
- Institute of Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Samuel Kalluvya
- Bugando Medical Centre, Mwanza, Tanzania
- BUCHS, Mwanza, Tanzania
| | | | | | - Jochen Bodem
- Institute of Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | | | - Graeme B. Jacobs
- Institute of Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | | | - Miriam Mildner
- Institute of Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Irina Hensel
- Institute of Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Anne Horn
- Institute of Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Wolfgang Preiser
- Division of Medical Virology, Department of Pathology, National Health Laboratory Service, University of Stellenbosch, Cape Town, South Africa
| | - Gert van Zyl
- Division of Medical Virology, Department of Pathology, National Health Laboratory Service, University of Stellenbosch, Cape Town, South Africa
| | - Hartwig Klinker
- Division of Infectious Diseases, Department of Internal Medicine, University of Würzburg, Würzburg, Germany
| | - Eleni Koutsilieri
- Institute of Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Axel Rethwilm
- Institute of Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Carsten Scheller
- Institute of Virology and Immunobiology, University of Würzburg, Würzburg, Germany
- * E-mail:
| | - Benedikt Weissbrich
- Institute of Virology and Immunobiology, University of Würzburg, Würzburg, Germany
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Dimitrov DT, Boily MC, Baggaley RF, Masse B. Modeling the gender-specific impact of vaginal microbicides on HIV transmission. J Theor Biol 2011; 288:9-20. [PMID: 21840324 DOI: 10.1016/j.jtbi.2011.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 06/16/2011] [Accepted: 08/02/2011] [Indexed: 01/05/2023]
Abstract
Vaginal microbicides (VMB) are currently among the few women-initiated biomedical interventions for preventing heterosexual transmission of HIV. In this paper we use a deterministic model of HIV transmission to assess the public-health benefits of a VMB intervention and evaluate its gender-specific impact over short (initial) and extended periods of time. We define two distinct quantitative benefit ratios (QBRs) based on infections prevented in men and women to create and study regions of male advantage in different parameter spaces. Our analysis exposes complicated temporal correlations between the QBRs and series of pre-intervention (e.g., HIV acquisition risks per act) and intervention parameters (e.g., VMB efficacy mechanisms, rates of resistance development and reversion) and indicates that different QBRs may often disagree on the gender distribution of the benefits from a VMB intervention. We also outline the strong influence of some modeling assumptions on the reported results and conclude that the assessment of VMB and other biomedical interventions must be based on more comprehensive analyses than calculations of infections prevented over a fixed period of time.
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Affiliation(s)
- Dobromir T Dimitrov
- Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA.
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Buckton AJ, Harris RJ, Pillay D, Cane PA. HIV type-1 drug resistance in treatment-naive patients monitored using minority species assays: a systematic review and meta-analysis. Antivir Ther 2011; 16:9-16. [PMID: 21311104 DOI: 10.3851/imp1687] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND The detection of mutations associated with drug resistance in HIV type-1 might be increased by applying minority species assays capable of identifying low frequency mutations in comparison with the use of population sequencing alone. Because minority species assays are mutation-specific, the benefit of this approach differs depending on the mutation being detected. METHODS We performed a systematic review of published data reporting detection of genotypic drug resistance using allele-specific (AS)-PCR minority assays and by standard DNA sequencing in drug-naive populations. We calculated the fold increase of mutation detection for each study and pooled these via meta-analysis, displaying results using Forest plots. RESULTS Our studies revealed an increase in detection of 1.9-fold (95% confidence interval [CI] 1.3-2.7; P < 0.0005) for K103N, 4.4-fold (95% CI 1.2-16.6; P = 0.026) for Y181C, 4.8-fold (95% CI 1.5-15.1; P = 0.008) for L90M and 8.7-fold (95% CI 4.0-18.6; P < 0.0005) for M184V. We found no relationship between AS-PCR assay sensitivity and frequency of additional mutation detection. CONCLUSIONS Additional detection of drug resistance mutations using AS-PCR minority mutation assays vary significantly depending on the mutation examined; however, the most marked increase in detection of resistance mutations was observed for M184V, a mutation seldom detected by standard techniques in drug-naive patients. We suggest that the presence of drug resistance mutations can be more accurately estimated using a combination of AS-PCR and standard genotyping.
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Poon AFY, Aldous JL, Mathews WC, Kitahata M, Kahn JS, Saag MS, Rodríguez B, Boswell SL, Frost SDW, Haubrich RH. Transmitted drug resistance in the CFAR network of integrated clinical systems cohort: prevalence and effects on pre-therapy CD4 and viral load. PLoS One 2011; 6:e21189. [PMID: 21701595 PMCID: PMC3118815 DOI: 10.1371/journal.pone.0021189] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 05/22/2011] [Indexed: 01/16/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) genomes often carry one or more mutations associated with drug resistance upon transmission into a therapy-naïve individual. We assessed the prevalence and clinical significance of transmitted drug resistance (TDR) in chronically-infected therapy-naïve patients enrolled in a multi-center cohort in North America. Pre-therapy clinical significance was quantified by plasma viral load (pVL) and CD4+ cell count (CD4) at baseline. Naïve bulk sequences of HIV-1 protease and reverse transcriptase (RT) were screened for resistance mutations as defined by the World Health Organization surveillance list. The overall prevalence of TDR was 14.2%. We used a Bayesian network to identify co-transmission of TDR mutations in clusters associated with specific drugs or drug classes. Aggregate effects of mutations by drug class were estimated by fitting linear models of pVL and CD4 on weighted sums over TDR mutations according to the Stanford HIV Database algorithm. Transmitted resistance to both classes of reverse transcriptase inhibitors was significantly associated with lower CD4, but had opposing effects on pVL. In contrast, position-specific analyses of TDR mutations revealed substantial effects on CD4 and pVL at several residue positions that were being masked in the aggregate analyses, and significant interaction effects as well. Residue positions in RT with predominant effects on CD4 or pVL (D67 and M184) were re-evaluated in causal models using an inverse probability-weighting scheme to address the problem of confounding by other mutations and demographic or risk factors. We found that causal effect estimates of mutations M184V/I (-1.7 log₁₀pVL) and D67N/G (-2.1[³√CD4] and 0.4 log₁₀pVL) were compensated by K103N/S and K219Q/E/N/R. As TDR becomes an increasing dilemma in this modern era of highly-active antiretroviral therapy, these results have immediate significance for the clinical management of HIV-1 infections and our understanding of the ongoing adaptation of HIV-1 to human populations.
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Affiliation(s)
- Art F. Y. Poon
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Jeannette L. Aldous
- Department of Medicine, University of California San Diego, San Diego, California, United States of America
| | - W. Christopher Mathews
- Department of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Mari Kitahata
- University of Washington, Seattle, Washington, United States of America
| | - James S. Kahn
- University of California San Francisco, San Francisco, California, United States of America
| | - Michael S. Saag
- University of Alabama Birmingham, Birmingham, Alabama, United States of America
| | - Benigno Rodríguez
- Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Stephen L. Boswell
- Fenway Community Health/Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Richard H. Haubrich
- Department of Medicine, University of California San Diego, San Diego, California, United States of America
- * E-mail:
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Jain V, Sucupira MC, Bacchetti P, Hartogensis W, Diaz RS, Kallas EG, Janini LM, Liegler T, Pilcher CD, Grant RM, Cortes R, Deeks SG, Hecht FM. Differential persistence of transmitted HIV-1 drug resistance mutation classes. J Infect Dis 2011; 203:1174-81. [PMID: 21451005 DOI: 10.1093/infdis/jiq167] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Transmitted human immunodeficiency virus type 1 (HIV-1) drug resistance (TDR) mutations can become replaced over time by emerging wild-type viral variants with improved fitness. The impact of class-specific mutations on this rate of mutation replacement is uncertain. METHODS We studied participants with acute and/or early HIV infection and TDR in 2 cohorts (San Francisco, California, and São Paulo, Brazil). We followed baseline mutations longitudinally and compared replacement rates between mutation classes with use of a parametric proportional hazards model. RESULTS Among 75 individuals with 195 TDR mutations, M184V/I became undetectable markedly faster than did nonnucleoside reverse-transcriptase inhibitor (NNRTI) mutations (hazard ratio, 77.5; 95% confidence interval [CI], 14.7-408.2; P<.0001), while protease inhibitor and NNRTI replacement rates were similar. Higher plasma HIV-1 RNA level predicted faster mutation replacement, but this was not statistically significant (hazard ratio, 1.71 log(10) copies/mL; 95% CI, .90-3.25 log(10) copies/mL; P=.11). We found substantial person-to-person variability in mutation replacement rates not accounted for by viral load or mutation class (P<.0001). CONCLUSIONS The rapid replacement of M184V/I mutations is consistent with known fitness costs. The long-term persistence of NNRTI and protease inhibitor mutations suggests a risk for person-to-person propagation. Host and/or viral factors not accounted for by viral load or mutation class are likely influencing mutation replacement and warrant further study.
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Affiliation(s)
- Vivek Jain
- HIV/AIDS Division, San Francisco General Hospital, University of California, San Francisco, San Francisco, CA 94143, USA
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Markovitz AR, Thibault CS, Brandauer PW, Buskin SE. Primary Antiretroviral Drug Resistance in Newly Human Immunodeficiency Virus-Diagnosed Individuals Testing Anonymously and Confidentially. Microb Drug Resist 2011; 17:283-9. [DOI: 10.1089/mdr.2010.0066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Amanda R. Markovitz
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan
- Blue Cross Blue Shield of Michigan, Southfield, Michigan
| | | | | | - Susan E. Buskin
- Public Health—Seattle and King County, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
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Pingen M, Nijhuis M, de Bruijn JA, Boucher CAB, Wensing AMJ. Evolutionary pathways of transmitted drug-resistant HIV-1. J Antimicrob Chemother 2011; 66:1467-80. [PMID: 21502281 DOI: 10.1093/jac/dkr157] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Several large studies in Europe and the USA revealed that approximately 10% of all newly diagnosed patients harbour HIV-1 variants with at least one major resistance-associated mutation. In this review we discuss the underlying mechanisms that drive the evolution of drug-resistant viruses after transmission to the new host. In a comprehensive literature search 12 papers describing the evolution of 58 cases of transmitted resistant HIV-1 variants were found. Based on observations in the literature we propose three pathways describing the evolution of resistant HIV-1 after transmission to a new host. Firstly, reversion of the resistance mutation towards wild-type may rapidly occur when drug resistance mutations severely impact replicative capacity. Alternatively, a second pathway involves replacement of transmitted drug resistance mutations by atypical amino acids that also improve viral replication capacity. In the third evolutionary pathway the resistance mutations persist either because they do not significantly affect viral replication capacity or evolution is constrained by fixation through compensatory mutations. In the near future ultra-sensitive resistance tests may provide more insight into the presence of archived and minority variants and their clinical relevance. Meanwhile, clinical guidelines advise population sequence analysis of the baseline plasma sample to identify transmission of resistance. Given the limited sensitivity of this technique for minority populations and the delay between the moment of infection and time of analysis, knowledge of the described evolutionary mechanisms of transmitted drug resistance patterns is essential for clinical management and public health strategies.
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Affiliation(s)
- Marieke Pingen
- Department of Virology, Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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Reuter S, Oette M, Sichtig N, Kaiser R, Balduin M, Jensen B, Häussinger D. Changes in the HIV-1 mutational profile before first-line HAART in the RESINA cohort. J Med Virol 2011; 83:187-95. [PMID: 21181911 DOI: 10.1002/jmv.21971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Sporadic observations have shown changing patterns of transmitted drug resistance mutations (TDRMs) in HIV infection even without selection pressure by antiretroviral treatment (ART). Repeated genotypic resistance analyses in treatment-naïve patients were performed, in order to analyze intraindividual variances of resistance patterns over time. Between the years 2001 and 2008 two genotypic resistance tests were performed at different time-points in 49 treatment-naïve HIV-positive patients aged >18 years. Wild-type virus was found at baseline and during follow-up in 31 patients (group A, median time between resistance tests 146 days), while resistance mutations were found either at baseline or during follow-up in 18 patients (group B, median time between resistance tests 297 days). In group B, the pattern of resistance changed in eight out of 18 patients over time, with three patients showing decreasing numbers and five patients showing increasing numbers of resistance mutations. The pattern of resistance mutations remained unchanged in 10 out of 18 patients. The mutational pattern in untreated HIV infection may change over time and a single resistance analysis may underestimate the true prevalence of preserved resistance mutations. If these findings can be confirmed in a larger number of patients, it would be prudent to perform genotypic resistance testing both at baseline and prior to the start of ART in order to capture a more complete picture of preserved mutations before initiating ART.
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Affiliation(s)
- Stefan Reuter
- Department of Gaastroenterology, Clinic for Gastroenterology, Hepatology and Infectious Diseases, University Hospital, Düsseldorf, Germany.
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36
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Jordan MR. Assessments of HIV Drug Resistance Mutations in Resource-Limited Settings. Clin Infect Dis 2011; 52:1058-60. [DOI: 10.1093/cid/cir093] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Michael R. Jordan
- Department of HIV/AIDS, World Health Organization, Geneva, Switzerland
- Division of Infectious Disease and Geographic Medicine
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, Massachusetts
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Transmitted Antiretroviral Drug Resistance in Individuals with Newly Diagnosed HIV Infection: South Carolina 2005–2009. South Med J 2011; 104:95-101. [DOI: 10.1097/smj.0b013e3181fcd75b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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38
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Buckton AJ, Prabhu D, Motamed C, Harris RJ, Hill C, Murphy G, Parry JV, Johnson JA, Lowndes CM, Gill N, Pillay D, Cane PA. Increased detection of the HIV-1 reverse transcriptase M184V mutation using mutation-specific minority assays in a UK surveillance study suggests evidence of unrecognized transmitted drug resistance. HIV Med 2010; 12:250-4. [PMID: 21371237 DOI: 10.1111/j.1468-1293.2010.00882.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVES The aim of the study was to estimate the levels of transmitted drug resistance (TDR) in HIV-1 using very sensitive assays to detect minority drug-resistant populations. METHODS We tested unlinked anonymous serum specimens from sexual health clinic attendees, who had not received an HIV diagnosis at the time of sampling, by both standard genotyping and using minority detection assays. RESULTS By standard genotyping, 21 of 165 specimens (12.7%) showed evidence of drug resistance, while, using a combination of standard genotyping and minority mutation assays targeting three commonly observed drug resistance mutations which cause high-level resistance to commonly prescribed first-line antiretroviral therapy (ART), this rose to 32 of 165 (19.4%). This increase of 45% in drug resistance levels [95% confidence interval (CI) 15.2-83.7%; P=0.002] was statistically significant. Almost all of this increase was accounted for by additional detections of the M184V mutation. CONCLUSIONS Future surveillance studies of TDR in the United Kingdom should consider combining standard genotyping and minority-specific assays to provide more accurate estimates, particularly when using specimens collected from chronic HIV infections in which TDR variants may have declined to low levels.
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Affiliation(s)
- A J Buckton
- Centre for Infections, Health Protection Agency, London, UK.
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Bartmeyer B, Kuecherer C, Houareau C, Werning J, Keeren K, Somogyi S, Kollan C, Jessen H, Dupke S, Hamouda O. Prevalence of transmitted drug resistance and impact of transmitted resistance on treatment success in the German HIV-1 Seroconverter Cohort. PLoS One 2010; 5:e12718. [PMID: 20949104 PMCID: PMC2951346 DOI: 10.1371/journal.pone.0012718] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Accepted: 08/10/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The aim of this study is to analyse the prevalence of transmitted drug resistance, TDR, and the impact of TDR on treatment success in the German HIV-1 Seroconverter Cohort. METHODS Genotypic resistance analysis was performed in treatment-naïve study patients whose sample was available 1,312/1,564 (83.9% October 2008). A genotypic resistance result was obtained for 1,276/1,312 (97.3%). The resistance associated mutations were identified according to the surveillance drug resistance mutations list recommended for drug-naïve patients. Treatment success was determined as viral suppression below 500 copies/ml. RESULTS Prevalence of TDR was stable at a high level between 1996 and 2007 in the German HIV-1 Seroconverter Cohort (N = 158/1,276; 12.4%; CI(wilson) 10.7-14.3; p(for trend) = 0.25). NRTI resistance was predominant (7.5%) but decreased significantly over time (CI(Wilson): 6.2-9.1, p(for trend) = 0.02). NNRTI resistance tended to increase over time (NNRTI: 3.5%; CI(Wilson): 2.6-4.6; p(for trend)= 0.07), whereas PI resistance remained stable (PI: 3.0%; CI(Wilson): 2.1-4.0; p(for trend) = 0.24). Resistance to all drug classes was frequently caused by singleton resistance mutations (NRTI 55.6%, PI 68.4%, NNRTI 99.1%). The majority of NRTI-resistant strains (79.8%) carried resistance-associated mutations selected by the thymidine analogues zidovudine and stavudine. Preferably 2NRTI/1PIr combinations were prescribed as first line regimen in patients with resistant HIV as well as in patients with susceptible strains (susceptible 45.3%; 173/382 vs. resistant 65.5%; 40/61). The majority of patients in both groups were treated successfully within the first year after ART-initiation (susceptible: 89.9%; 62/69; resistant: 7/9; 77.8%). CONCLUSION Overall prevalence of TDR remained stable at a high level but trends of resistance against drug classes differed over time. The significant decrease of NRTI-resistance in patients newly infected with HIV might be related to the introduction of novel antiretroviral drugs and a wider use of genotypic resistance analysis prior to treatment initiation.
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Affiliation(s)
- Barbara Bartmeyer
- HIV/AIDS, STD Unit, Department Infectious Disease Epidemiology, Robert Koch-Institute, Berlin, Germany
| | - Claudia Kuecherer
- Project HIV Variability and Molecular Epidemiology, Robert Koch-Institute, Berlin, Germany
| | - Claudia Houareau
- HIV/AIDS, STD Unit, Department Infectious Disease Epidemiology, Robert Koch-Institute, Berlin, Germany
| | - Johanna Werning
- HIV/AIDS, STD Unit, Department Infectious Disease Epidemiology, Robert Koch-Institute, Berlin, Germany
| | - Kathrin Keeren
- Project HIV Variability and Molecular Epidemiology, Robert Koch-Institute, Berlin, Germany
| | - Sybille Somogyi
- Project HIV Variability and Molecular Epidemiology, Robert Koch-Institute, Berlin, Germany
| | - Christian Kollan
- HIV/AIDS, STD Unit, Department Infectious Disease Epidemiology, Robert Koch-Institute, Berlin, Germany
| | - Heiko Jessen
- Gemeinschaftspraxis Jessen-Jessen-Stein, Berlin, Germany
| | - Stephan Dupke
- Gemeinschaftspraxis Dupke, Baumgarten, Carganico, Berlin, Germany
| | - Osamah Hamouda
- HIV/AIDS, STD Unit, Department Infectious Disease Epidemiology, Robert Koch-Institute, Berlin, Germany
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Micek MA, Blanco AJ, Beck IA, Dross S, Matunha L, Montoya P, Seidel K, Gantt S, Matediane E, Jamisse L, Gloyd S, Frenkel LM. Nevirapine resistance by timing of HIV type 1 infection in infants treated with single-dose nevirapine. Clin Infect Dis 2010; 50:1405-14. [PMID: 20384494 DOI: 10.1086/652151] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND In women, single-dose nevirapine for prophylaxis against mother-to-child transmission of human immunodeficiency virus type 1 (HIV-1) selects for nevirapine-resistant HIV-1, which subsequently decays rapidly. We hypothesized that the selection, acquisition, and decay of nevirapine-resistant HIV-1 differs in infants, varying by the timing of HIV-1 infection. METHODS We conducted a prospective, observational study of 740 Mozambican infants receiving single-dose nevirapine prophylaxis and determined the timing of infection and concentrations of nevirapine-resistant HIV-1 over time. RESULTS Infants with established in utero infection had a high rate (87.0%) of selection of nevirapine-resistant HIV-1 mutants, which rapidly decayed to undetectable levels. The few without nevirapine resistance received zidovudine with single-dose nevirapine and/or their mothers took alternative antiretroviral drugs. Infants with acute in utero infection had a lower rate of nevirapine-resistant HIV-1 (33.3%; P = .006, compared with established in utero infection), but mutants persisted over time. Infants with peripartum infection also had a lower rate of nevirapine-resistant HIV-1 (38.1%; P = .001, compared with established in utero infection) but often acquired 100% mutant virus that persisted over time (P = .017, compared with established in utero infection). CONCLUSIONS The detection and persistence of nevirapine-resistant HIV-1 in infants after single-dose nevirapine therapy vary by the timing of infection and the antiretroviral regimen. In infants with persistent high-level nevirapine-resistant HIV-1, nevirapine-based antiretroviral therapy is unlikely to ever be efficacious because of concentrations in long-lived viral reservoirs. However, the absence or decay of nevirapine-resistant HIV-1 in many infants suggests that nevirapine antiretroviral therapy may be effective if testing can identify these individuals.
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Affiliation(s)
- Mark A Micek
- Department of Global Health, University of Washington, Seattle, Washington, USA
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Supervie V, García-Lerma JG, Heneine W, Blower S. HIV, transmitted drug resistance, and the paradox of preexposure prophylaxis. Proc Natl Acad Sci U S A 2010; 107:12381-6. [PMID: 20616092 PMCID: PMC2901470 DOI: 10.1073/pnas.1006061107] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The administration of antiretrovirals before HIV exposure to prevent infection (i.e., preexposure prophylaxis; PrEP) is under evaluation in clinical trials. Because PrEP is based on antiretrovirals, there is considerable concern that it could substantially increase transmitted resistance, particularly in resource-rich countries. Here we use a mathematical model to predict the effect of PrEP interventions on the HIV epidemic in the men-who-have-sex-with-men community in San Francisco. The model is calibrated using Monte Carlo filtering and analyzed by constructing nonlinear response hypersurfaces. We predict PrEP interventions could substantially reduce transmission but significantly increase the proportion of new infections caused by resistant strains. Two mechanisms can cause this increase. If risk compensation occurs, the proportion increases due to increasing transmission of resistant strains and decreasing transmission of wild-type strains. If risk behavior remains stable, the increase occurs because of reduced transmission of resistant strains coupled with an even greater reduction in transmission of wild-type strains. We define this as the paradox of PrEP (i.e., resistance appears to be increasing, but is actually decreasing). We determine this paradox is likely to occur if the efficacy of PrEP regimens against wild-type strains is greater than 30% and the relative efficacy against resistant strains is greater than 0.2 but less than the efficacy against wild-type. Our modeling shows, if risk behavior increases, that it is a valid concern that PrEP could significantly increase transmitted resistance. However, if risk behavior remains stable, we find the concern is unfounded and PrEP interventions are likely to decrease transmitted resistance.
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Affiliation(s)
- Virginie Supervie
- Center for Biomedical Modeling, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA 90024; and
| | - J. Gerardo García-Lerma
- Laboratory Branch, Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329
| | - Walid Heneine
- Laboratory Branch, Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329
| | - Sally Blower
- Center for Biomedical Modeling, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA 90024; and
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Transmission of human immunodeficiency virus I drug resistance - a case report. What are the clinical implications? Eur J Med Res 2010; 15:225-30. [PMID: 20562063 PMCID: PMC3352013 DOI: 10.1186/2047-783x-15-5-225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The success of first-line antiretroviral therapy can be challenged by the acquisition of primary drug resistance. Here we report a case where baseline genotypic resistance testing detected resistance conferring nucleoside/nucleotide reverse transcriptase inhibitor (NRTI)-associated mutations, but no primary mutations for protease inhibitor (PI). Subsequent PI-based HAART with boosted saquinavir led to virological treatment success with persistently undetectable viral load. After treatment simplification from saquinavir to an atazanavir based PI-therapy and no change in backbone therapy rapid virological breakthrough occurred. Retrospective analysis displayed preexisting gag cleavage site mutations which may have reduced the genetic barrier in a clinical relevant manner in combination with the already existing NRTI resistance mutations. Alternatively, this effect could be explained with a different antiviral potency for the respective PIs used.
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Cellerai C, Little SJ, Loes SKD. Treatment of acute HIV-1 infection: are we getting there? Curr Opin HIV AIDS 2009; 3:67-74. [PMID: 19372946 DOI: 10.1097/coh.0b013e3282f31d4b] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
PURPOSE OF REVIEW Treatment of primary HIV-1 infection may alter the natural history of HIV-1 infection and delay the need for chronic antiretroviral therapy; it may also be a public health measure. We discuss the results of therapeutic trials and cohort studies, the occurrence of transmitted drug resistance, and recent findings in terms of immunopathogenesis and decay of viral reservoirs. RECENT FINDINGS Events at the time of primary HIV-1 infection are understood to set the scene for persistence of immunologic damage and chronic immune activation, with a rapid viral onslaught primarily on memory CD4 T cells at mucosal effector sites. The initiation of antiretroviral therapy at primary HIV-1 infection has been associated with a high degree of undetectable viremia in compliant patients and substantial decay of reservoirs in peripheral blood. The degree of immune reconstitution at the gut mucosal level, however, does not appear to be comparable to that in peripheral blood. SUMMARY Recent insights into the long-term consequences of the early burst of HIV-1 replication - together with transmitted drug resistance, onward transmission, and the possibility of decay of viral reservoirs - are important steps in helping to design future therapeutic strategies in primary HIV-1 infection in an era of intense drug and vaccine development.
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Affiliation(s)
- Cristina Cellerai
- Department of Immunology and Molecular Pathology, University College London, Royal Free Hospital Campus, London NW3 2QG, UK
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Abstract
PURPOSE OF REVIEW This review focuses on the evolution of protease inhibitor resistance and replication capacity in the presence and absence of protease inhibitor pressure. RECENT FINDINGS Classically, HIV escapes through mutations in the protease itself causing a decrease in affinity to the inhibitor, leading to resistance. These changes also affect the binding of the enzyme to the natural substrate, and as a consequence cause a decrease in replication capacity of the virus. Continuous replication of these viruses may result in the acquisition of compensatory changes, which will fixate the drug-resistant variant in the viral population. Furthermore, novel treatment strategies have been developed to combat the development of classic protease inhibitor resistance. Using these strategies, the development of resistance in the viral protease is blocked because single or double mutations do not confer significant resistance. Alternative protease inhibitor resistance pathways are described, which enable the virus to escape these novel strategies. SUMMARY Suboptimal protease inhibitor pressure clearly results in the selection of mutations conferring resistance and in the acquisition of mutations compensating the initial reduction in viral replicative capacity. The major implications of the selection of these compensatory changes on evolution in the absence of protease inhibitor pressure are discussed.
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Affiliation(s)
- Monique Nijhuis
- Eijkman-Winkler Center, Department of Virology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
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Marks AJ, Pillay D, McLean AR. The effect of intrinsic stochasticity on transmitted HIV drug resistance patterns. J Theor Biol 2009; 262:1-13. [PMID: 19766126 DOI: 10.1016/j.jtbi.2009.09.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Revised: 07/29/2009] [Accepted: 09/10/2009] [Indexed: 10/20/2022]
Abstract
Estimates of transmitted HIV drug-resistance prevalence vary widely among and within epidemiological surveys. Interpretation of trends from available survey data is therefore difficult. Because the emergence of drug-resistance involves small populations of infected drug-resistant individuals, the role of stochasticity (chance events) is likely to be important. The question addressed here is: how much variability in transmitted HIV drug-resistance prevalence patterns arises due to intrinsic stochasticity alone, i.e., if all starting conditions in the different epidemics surveyed were identical? This 'thought experiment' gives insight into the minimum expected variabilities within and among epidemics. A simple stochastic mathematical model was implemented. Our results show that stochasticity alone can generate a significant degree of variability and that this depends on the size and variation of the pool of new infections when drug treatment is first introduced. The variability in transmitted drug-resistance prevalence within an epidemic (i.e., the temporal variability) is large when the annual pool of all new infections is small (fewer than 200, typical of the HIV epidemics in Central European and Scandinavian countries) but diminishes rapidly as that pool grows. Epidemiological surveys involving hundreds of new infections annually are therefore needed to allow meaningful interpretation of temporal trends in transmitted drug-resistance prevalence within individual epidemics. The stochastic variability among epidemics shows a similar dependence on the pool of new infections if treatment is introduced after endemic equilibrium is established, but can persist even when there are more than 10,000 new infections annually if drug therapy is introduced earlier. Stochastic models may therefore have an important role to play in interpreting differences in transmitted drug-resistance prevalence trends among epidemiological surveys.
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Taylor S, Jayasuriya A, Smit E. Using HIV resistance tests in clinical practice. J Antimicrob Chemother 2009; 64:218-22. [DOI: 10.1093/jac/dkp205] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Lee CC, Sun YJ, Barkham T, Leo YS. Primary drug resistance and transmission analysis of HIV-1 in acute and recent drug-naïve seroconverters in Singapore. HIV Med 2009; 10:370-7. [PMID: 19490177 DOI: 10.1111/j.1468-1293.2009.00698.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
OBJECTIVES The aim of the study was to elucidate primary drug resistance and transmission of HIV-1 in acute and recent drug-naïve seroconverters in Singapore. METHODS Acute and recent HIV-1 seroconverters were enrolled in the study. The HIV-1 polymerase (pol) gene was sequenced and used for genotypic drug resistance analysis and phylogenetic analysis. HIV-1 transmission clusters were inferred from phylogenetic clustering analysis. RESULTS Of the 60 subjects analysed, 95% were men, and 73.3% were men who have sex with men (MSM). Six HIV-1 subtypes were identified, including CRF01_AE (46.7%), subtypes B (30%), B' (15%) and G (1.7%), CRF33_01B (1.7%) and CRF34_01B (5%). Primary genotypic resistance was detected in only one (1.7%) subtype B variant. Thirty-one patients (51.7%) were phylogenetically clustered, of whom 90% reported having local risk exposure, compared with 59% of the patients who were not phylogenetically clustered [odds ratio (OR) 6.35, 95% confidence interval (CI) 1.65-23.95]. MSM (OR 5.63, 95% CI 1.17-27.15), high viral load (OR 4.28, 95% CI 1.37-13.36) and young age (OR 0.92, 95% CI 0.85-0.99) were independently associated with clustered individuals. CONCLUSIONS In Singapore, HIV-1 primary resistance is insignificant; individuals with seroconversion account for about half of onward transmission among recently infected seroconverters. MSM, high viral load and young age are factors that facilitate transmission. Early detection of these individuals is of paramount importance for the prevention of HIV-1 transmission.
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Affiliation(s)
- C C Lee
- Department of Infectious Diseases, Tan Tock Seng Hospital, Tan Tock Seng 308433, Singapore
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Tossonian HK, Raffa JD, Grebely J, Viljoen M, Mead A, Khara M, McLean M, Krishnamurthy A, DeVlaming S, Conway B. Primary drug resistance in antiretroviral-naïve injection drug users. Int J Infect Dis 2008; 13:577-83. [PMID: 19111493 DOI: 10.1016/j.ijid.2008.08.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2008] [Revised: 08/02/2008] [Accepted: 08/31/2008] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES We evaluated the prevalence of primary HIV drug resistance in a population of 128 injection drug users (48 female) prior to initiating antiretroviral therapy. METHODS Genotypic and phenotypic profiles were obtained retrospectively for the period June 1996 to February 2007. Genotypic drug resistance was defined as the presence of a major mutation (IAS-USA table, 2007 revision), adding revertants at reverse transcriptase (RT) codon 215. Phenotypic drug resistance was defined as the fold change associated with >or=80% loss of the wild type virologic response due to viral resistance based on virtual phenotype analysis. RESULTS Genotypic drug resistance was uncommon, and was only identified in six (4.7%) cases, all in the RT gene (L100I, K103N, Y181C, M184V, Y188L, and T215D). There were no cases of multi-class or protease inhibitor (PI) resistance. However, polymorphisms in the protease and RT genes were extremely common. Phenotypic drug resistance was also identified in six (4.7%) patients, four in the RT gene (in patients with mutations K103N, Y181C, M184V and Y188L) and two the protease gene (in two patients with minor PI mutations). In addition, 25 (19.5%) of the patients had reduced susceptibility to PIs, defined as resistance>20% but <80% of the wild type virologic response, with no primary PI mutations detected in all these patients. CONCLUSION The prevalence of primary HIV drug resistance was low in this population of injection drug users.
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Affiliation(s)
- Harout K Tossonian
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, 2176 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
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Derache A, Maiga AI, Traore O, Akonde A, Cisse M, Jarrousse B, Koita V, Diarra B, Carcelain G, Barin F, Pizzocolo C, Pizarro L, Katlama C, Calvez V, Marcelin AG. Evolution of genetic diversity and drug resistance mutations in HIV-1 among untreated patients from Mali between 2005 and 2006. J Antimicrob Chemother 2008; 62:456-63. [PMID: 18556706 DOI: 10.1093/jac/dkn234] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To describe HIV-1 variants circulating in Mali and to estimate the rate of transmission of HIV-1 drug resistance in 2006. PATIENTS AND METHODS Viral reverse transcriptase (RT) and protease (PR) genes from 198 antiretroviral (ARV)-naive patients diagnosed HIV-1 positive in May 2006 in Bamako and Segou were sequenced. RESULTS Although CRF02_AG was always the predominant HIV-1 subtype observed (72%), a higher genetic diversity than that in 2005 was observed. The overall prevalence of primary resistance is 11.5% in Mali in 2006, according to the 2007 IAS-USA list of mutations [nucleoside RT inhibitor (NRTI): 1.5%, non-NRTI (NNRTI): 9% and PI: 1%], and 2.5% (NRTI: 1%, NNRTI: 1.5% and PI: 0%), according to the Stanford list of mutations. There was no significant difference between 2005 and 2006 in the overall primary resistance prevalence or in the prevalence of mutations in the different ARV classes. Resistance mutations found in RT and PR genes are in agreement with the highly active antiretroviral therapy regimen available in Mali, except for V90I, V106I and A98G mutations which are associated with etravirine resistance, but polymorphic in non-B subtypes. CONCLUSIONS HIV-1 genetic diversity seems increased in Mali, but the overall HIV-1 primary resistance prevalence remains low. This is consistent with the findings from other West African countries where prevalence rates are lower than 5%. However, considering the large scaling up of ARV use in this country, it is necessary to regularly monitor the development of primary resistance in Mali.
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Affiliation(s)
- Anne Derache
- UPMC Univ Paris 06, EA2387, 4 Place Jussieu, F-75005 Paris, France
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