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Mulato A, Acosta R, Chang S, Martin R, Yant SR, Cihlar T, White K. Simulating HIV Breakthrough and Resistance Development During Variable Adherence to Antiretroviral Treatment. J Acquir Immune Defic Syndr 2021; 86:369-377. [PMID: 33196554 DOI: 10.1097/qai.0000000000002562] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/26/2020] [Indexed: 01/04/2023]
Abstract
BACKGROUND Barriers to lifelong HIV-1 suppression by antiretrovirals include poor adherence and drug resistance; regimens with higher tolerance to missed doses (forgiveness) would be beneficial to patients. To model short-term nonadherence, in vitro experiments monitoring viral breakthrough (VB) and resistance development were conducted. METHODS HIV breakthrough experiments simulated drug exposures at full adherence or suboptimal adherence to bictegravir+emtricitabine+tenofovir alafenamide (BIC+FTC+TAF) or dolutegravir + lamivudine (DTG+3TC). MT-2 cells were infected with wild-type or low frequency M184V HIV-1, exposed to drug combinations, monitored for VB, and rebound virus was deep sequenced. Drug concentrations were determined using human plasma-free adjusted clinical trough concentrations (Cmin), at simulated Cmin after missing 1 to 3 consecutive doses (Cmin - 1 or Cmin - 2, and Cmin - 3) based on drug or active metabolite half-lives. RESULTS Cultures infected with wild-type or low frequency M184V HIV-1 showed no VB with BIC+FTC+TAF at drug concentrations corresponding to Cmin, Cmin - 1, or Cmin - 2 but breakthrough did occur in 26 of 36 cultures at Cmin - 3, where the M184V variant emerged in one culture. Experiments using DTG + 3TC prevented most breakthrough at Cmin concentrations (9/60 had breakthrough) but showed more breakthroughs as drug concentrations decreased (up to 36/36) and variants associated with resistance to both drugs emerged in some cases. CONCLUSIONS These in vitro VB results suggest that the high potency, long half-lives, and antiviral synergy provided by the BIC/FTC/TAF triple therapy regimen may protect from viral rebound and resistance development after short-term lapses in drug adherence.
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Mbunkah HA, Bertagnolio S, Hamers RL, Hunt G, Inzaule S, Rinke De Wit TF, Paredes R, Parkin NT, Jordan MR, Metzner KJ. Low-Abundance Drug-Resistant HIV-1 Variants in Antiretroviral Drug-Naive Individuals: A Systematic Review of Detection Methods, Prevalence, and Clinical Impact. J Infect Dis 2021; 221:1584-1597. [PMID: 31809534 DOI: 10.1093/infdis/jiz650] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/04/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The presence of high-abundance drug-resistant HIV-1 jeopardizes success of antiretroviral therapy (ART). Despite numerous investigations, the clinical impact of low-abundance drug-resistant HIV-1 variants (LA-DRVs) at levels <15%-25% of the virus population in antiretroviral (ARV) drug-naive individuals remains controversial. METHODS We systematically reviewed 103 studies assessing prevalence, detection methods, technical and clinical detection cutoffs, and clinical significance of LA-DRVs in antiretroviral drug-naive adults. RESULTS In total, 14 919 ARV drug-naive individuals were included. Prevalence of LA-DRVs (ie, proportion of individuals harboring LA-DRVs) was 0%-100%. Technical detection cutoffs showed a 4 log range (0.001%-10%); 42/103 (40.8%) studies investigating the impact of LA-DRVs on ART; 25 studies included only individuals on first-line nonnucleoside reverse transcriptase inhibitor-based ART regimens. Eleven of those 25 studies (44.0%) reported a significantly association between preexisting LA-DRVs and risk of virological failure whereas 14/25 (56.0%) did not. CONCLUSIONS Comparability of the 103 studies is hampered by high heterogeneity of the studies' designs and use of different methods to detect LA-DRVs. Thus, evaluating clinical impact of LA-DRVs on first-line ART remains challenging. We, the WHO HIVResNet working group, defined central areas of future investigations to guide further efforts to implement ultrasensitive resistance testing in routine settings.
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Affiliation(s)
- Herbert A Mbunkah
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zürich, Switzerland.,Institute of Medical Virology, University of Zurich, Zürich, Switzerland.,Paul-Ehrlich-Institut, Langen, Germany
| | | | - Raph L Hamers
- Amsterdam Institute for Global Health and Development, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Eijkman-Oxford Clinical Research Unit, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gillian Hunt
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Seth Inzaule
- Amsterdam Institute for Global Health and Development, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Tobias F Rinke De Wit
- Amsterdam Institute for Global Health and Development, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Roger Paredes
- Infectious Diseases Service and IrsiCaixa AIDS Research Institute for AIDS Research, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | | | - Michael R Jordan
- Division of Geographic Medicine and Infectious Disease, Tufts University School of Medicine, Tufts Medical Center, Boston, Massachusetts, USA
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zürich, Switzerland.,Institute of Medical Virology, University of Zurich, Zürich, Switzerland
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Silver N, Paynter M, McAllister G, Atchley M, Sayir C, Short J, Winner D, Alouani DJ, Sharkey FH, Bergefall K, Templeton K, Carrington D, Quiñones-Mateu ME. Characterization of minority HIV-1 drug resistant variants in the United Kingdom following the verification of a deep sequencing-based HIV-1 genotyping and tropism assay. AIDS Res Ther 2018; 15:18. [PMID: 30409215 PMCID: PMC6223033 DOI: 10.1186/s12981-018-0206-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/30/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The widespread global access to antiretroviral drugs has led to considerable reductions in morbidity and mortality but, unfortunately, the risk of virologic failure increases with the emergence, and potential transmission, of drug resistant viruses. Detecting and quantifying HIV-1 drug resistance has therefore become the standard of care when designing new antiretroviral regimens. The sensitivity of Sanger sequencing-based HIV-1 genotypic assays is limited by its inability to identify minority members of the quasispecies, i.e., it only detects variants present above ~ 20% of the viral population, thus, failing to detect minority variants below this threshold. It is clear that deep sequencing-based HIV-1 genotyping assays are an important step change towards accurately monitoring HIV-infected individuals. METHODS We implemented and verified a clinically validated HIV-1 genotyping assay based on deep sequencing (DEEPGEN™) in two clinical laboratories in the United Kingdom: St. George's University Hospitals Healthcare NHS Foundation Trust (London) and at NHS Lothian (Edinburgh), to characterize minority HIV-1 variants in 109 plasma samples from ART-naïve or -experienced individuals. RESULTS Although subtype B HIV-1 strains were highly prevalent (44%, 48/109), most individuals were infected with non-B subtype viruses (i.e., A1, A2, C, D, F1, G, CRF02_AG, and CRF01_AE). DEEPGEN™ was able to accurately detect drug resistance-associated mutations not identified using standard Sanger sequencing-based tests, which correlated significantly with patient's antiretroviral treatment histories. A higher proportion of minority PI-, NRTI-, and NNRTI-resistance mutations was detected in NHS Lothian patients compared to individuals from St. George's, mainly M46I/L and I50 V (associated with PIs), D67 N, K65R, L74I, M184 V/I, and K219Q (NRTIs), and L100I (NNRTIs). Interestingly, we observed an inverse correlation between intra-patient HIV-1 diversity and CD4+ T cell counts in the NHS Lothian patients. CONCLUSIONS This is the first study evaluating the transition, training, and implementation of DEEPGEN™ between three clinical laboratories in two different countries. More importantly, we were able to characterize the HIV-1 drug resistance profile (including minority variants), coreceptor tropism, subtyping, and intra-patient viral diversity in patients from the United Kingdom, providing a rigorous foundation for basing clinical decisions on highly sensitive and cost-effective deep sequencing-based HIV-1 genotyping assays in the country.
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Moscona R, Ram D, Wax M, Bucris E, Levy I, Mendelson E, Mor O. Comparison between next-generation and Sanger-based sequencing for the detection of transmitted drug-resistance mutations among recently infected HIV-1 patients in Israel, 2000-2014. J Int AIDS Soc 2017; 20:21846. [PMID: 28799325 PMCID: PMC5577736 DOI: 10.7448/ias.20.1.21846] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 07/22/2017] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION Transmitted drug-resistance mutations (TDRM) may hamper successful anti-HIV-1 therapy and impact future control of the HIV-1 epidemic. Recently infected, therapy-naïve individuals are best suited for surveillance of such TDRM. In this study, TDRM, detected by next-generation sequencing (NGS) were compared to those identified by Sanger-based population sequencing (SBS) in recently infected HIV-1 patients. METHODS Historical samples from 80 recently infected HIV-1 patients, diagnosed between 2000 and 2014, were analysed by MiSeq (NGS) and ABI (SBS). DeepChek-HIV (ABL) was used for interpretation of the results. RESULTS Most patients were males (80%); Men who have sex with men (MSM) was the major transmission group (58.8%). Overall, TDRM were detected in 31.3% of patients by NGS and 8.8% by SBS, with SBS TDRM restricted to persons infected with subtype B. All SBS-detected TDRM were identified by NGS. The prevalence of TDRM impacting protease inhibitors (PI), nucleoside reverse transcriptase inhibitors (NRTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI) was 11.3, 26.2 7.5%, respectively, in NGS analyses and 0, 3.8 and 5%, respectively, in SBS analyses. More patients with NGS and SBS TDRM were identified in 2008-2014 (37.2% or 13.9%, respectively) compared to 2000-2007 (24.3% or 2.7%, respectively), and a significantly greater number of these patients had multiple NGS TDRM. The most abundant, albeit, minor-frequency RT TDRM, were the K65R and D67N, while K103N, M184V and T215S were high-frequency mutations. Minor TDRM did not become a major variant in later samples and did not hinder successful treatment. CONCLUSIONS NGS can replace SBS for mutation detection and allows for the detection of low-frequency TDRM not identified by SBS. Although rates of TDRM in Israel continued to increase from 2000 to 2014, minor TDRM did not become major species. The need for ongoing surveillance of low-frequency TDRM should be revisited in a larger study.
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Affiliation(s)
- Roy Moscona
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Daniela Ram
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Marina Wax
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Itzchak Levy
- Infectious Disease Unit, Sheba Medical Center, Ramat-Gan, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
- School of Public Health, Tel Aviv University, Ramat-Aviv, Israel
| | - Orna Mor
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
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Response to Therapy in Antiretroviral Therapy-Naive Patients With Isolated Nonnucleoside Reverse Transcriptase Inhibitor-Associated Transmitted Drug Resistance. J Acquir Immune Defic Syndr 2017; 72:171-6. [PMID: 26855248 PMCID: PMC4866916 DOI: 10.1097/qai.0000000000000942] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Nonnucleoside reverse transcriptase inhibitor (NNRTI)-associated transmitted drug resistance (TDR) is the most common type of TDR. Few data guide the selection of antiretroviral therapy (ART) for patients with such resistance. METHODS We reviewed treatment outcomes in a cohort of HIV-1-infected patients with isolated NNRTI TDR who initiated ART between April 2002 and May 2014. In an as-treated analysis, virological failure (VF) was defined as not reaching undetectable virus levels within 24 weeks, virological rebound, or switching regimens during viremia. In an intention-to-treat analysis, failure was defined more broadly as VF, loss to follow-up, and switching during virological suppression. RESULTS Of 3245 patients, 131 (4.0%) had isolated NNRTI TDR; 122 received a standard regimen comprising 2 NRTIs plus a boosted protease inhibitor (bPI; n = 54), an integrase strand transfer inhibitor (INSTI; n = 52), or an NNRTI (n = 16). The median follow-up was 100 weeks. In the as-treated analysis, VF occurred in 15% (n = 8), 2% (n = 1), and 25% (n = 4) of patients in the bPI, INSTI, and NNRTI groups, respectively. In multivariate regression, there was a trend toward a lower risk of VF with INSTIs than with bPIs (hazard ratio: 0.14; 95% confidence interval: 0.02 to 1.1; P = 0.07). In intention-to-treat multivariate regression, INSTIs had a lower risk of failure than bPIs (hazard ratio: 0.38; 95% confidence interval: 0.18 to 0.82; P = 0.01). CONCLUSIONS Patients with isolated NNRTI TDR experienced low VF rates with INSTIs and bPIs. INSTIs were noninferior to bPIs in an analysis of VF but superior to bPIs when frequency of switching and loss to follow-up were also considered.
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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: 19] [Impact Index Per Article: 2.4] [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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Pham QD, Wilson DP, Nguyen TV, Do NT, Truong LX, Nguyen LT, Zhang L. Projecting the epidemiological effect, cost-effectiveness and transmission of HIV drug resistance in Vietnam associated with viral load monitoring strategies. J Antimicrob Chemother 2016; 71:1367-79. [PMID: 26869689 DOI: 10.1093/jac/dkv473] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/09/2015] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The objective of this study was to investigate the potential epidemiological impact of viral load (VL) monitoring and its cost-effectiveness in Vietnam, where transmitted HIV drug resistance (TDR) prevalence has increased from <5% to 5%-15% in the past decade. METHODS Using a population-based mathematical model driven by data from Vietnam, we simulated scenarios of various combinations of VL testing coverage, VL thresholds for second-line ART initiation and availability of HIV drug-resistance tests. We assessed the cost per disability-adjusted life year (DALY) averted for each scenario. RESULTS Projecting expected ART scale-up levels, to approximately double the number of people on ART by 2030, will lead to an estimated 18 510 cases (95% CI: 9120-34 600 cases) of TDR and 55 180 cases (95% CI: 40 540-65 900 cases) of acquired drug resistance (ADR) in the absence of VL monitoring. This projection corresponds to a TDR prevalence of 16% (95% CI: 11%-24%) and ADR of 18% (95% CI: 15%-20%). Annual or biennial VL monitoring with 30% coverage is expected to relieve 12%-31% of TDR (2260-5860 cases), 25%-59% of ADR (9620-22 650 cases), 2%-6% of HIV-related deaths (360-880 cases) and 19 270-51 400 DALYs during 2015-30. The 30% coverage of VL monitoring is estimated to cost US$4848-5154 per DALY averted. The projected additional cost for implementing this strategy is US$105-268 million over 2015-30. CONCLUSIONS Our study suggests that a programmatically achievable 30% coverage of VL monitoring can have considerable benefits for individuals and leads to population health benefits by reducing the overall national burden of HIV drug resistance. It is marginally cost-effective according to common willingness-to-pay thresholds.
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Affiliation(s)
- Quang Duy Pham
- Disease Modelling and Financing Program, Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia Department for Disease Control and Prevention, Pasteur Institute, Ho Chi Minh City, Vietnam
| | - David P Wilson
- Disease Modelling and Financing Program, Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Thuong Vu Nguyen
- Department for Disease Control and Prevention, Pasteur Institute, Ho Chi Minh City, Vietnam
| | - Nhan Thi Do
- Department of HIV Care and Treatment, Vietnam Administration of HIV/AIDS Control, Hanoi, Vietnam
| | - Lien Xuan Truong
- Department of Laboratory Analysis, Pasteur Institute, Ho Chi Minh City, Vietnam
| | | | - Lei Zhang
- Disease Modelling and Financing Program, Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia Research Center for Public Health, School of Medicine, Tsinghua University, China Melbourne Sexual Health Centre, Alfred Health, Melbourne, Australia Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
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Katzenstein DA. HIV RNA and genotype in resource-limited settings: can we do better? Clin Infect Dis 2013; 58:110-2. [PMID: 24076967 DOI: 10.1093/cid/cit634] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Abstract
Technologic advances in human immunodeficiency virus type 1 (HIV-1) sequencing have revolutionized the study of antiretroviral drug resistance and are increasingly moving from the laboratory to clinical practice. These techniques are able to detect HIV-1 drug resistance mutations present at low frequencies not detectable by current HIV-1 genotyping assays. For a number of commonly used antiretroviral medications, such as nonnucleoside reverse transcriptase inhibitors, the detection of these drug-resistant minority variants significantly increases the risk of treatment failure. The level of evidence, however, is insufficient to determine the impact of HIV-1 minority variants for several other classes of antiretroviral medications. Clinicians should be aware of the novel technologies that are moving into routine clinical use and the clinical implications of HIV-1 minority variants. Additional studies are needed to determine the optimal platform for clinical application of these new technologies and to provide guidance to clinicians on the type and frequency of clinically important HIV-1 minority variants.
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Affiliation(s)
- Jonathan Z Li
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
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MacVeigh MS, Kosmetatos MK, McDonald JE, Reeder JL, Parrish DA, Young TP. Prevalence of drug-resistant HIV type 1 at the time of initiation of antiretroviral therapy in Portland, Oregon. AIDS Res Hum Retroviruses 2013; 29:337-42. [PMID: 22697610 DOI: 10.1089/aid.2011.0386] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The presence of transmitted drug-resistant HIV-1 (TDR) at the time of antiretroviral therapy (ART) initiation is associated with failure to achieve viral load suppression. Rates of TDR in ART-naive patients have been reported from various parts of the world through ongoing national, regional, and global evaluations; however, surveillance of TDR in Portland, Oregon has not been previously described. We describe the prevalence of TDR in patients in the Portland area who have recently entered care. Genotypic data were obtained from plasma specimens collected between 2003 and 2009 from 165 recently identified HIV-1-positive, ART-naive adults in care at the Multnomah County Health Department. Median time from diagnosis to first genotype was 2.7 months. Mutations associated with TDR were observed in 33 (20.0%) patients. Mutations associated with resistance to nucleoside reverse transcriptase (RT) inhibitors (NRTI), nonnucleoside RT inhibitors (NNRTI), and protease inhibitors (PI) were found in 15 (9.1%), 17 (10.3%), and 5 (3.0%) patients, respectively (p=0.013 for NNRTI vs. PI, and 0.035 for NRTI vs. PI, Fisher exact test). Dual class resistance was observed in four (2.4%) patients. Predominant RT mutations included M41L, T215C or S, and K103N. The prevalence of HIV-1 with NRTI resistance-associated mutations increased from 2006 to 2008-2009 (p=0.004) based on date of diagnosis. These data indicate relatively high rates of drug resistance present prior to ART initiation among patients in the Portland area, and support continued surveillance of local trends of TDR to inform optimal individual treatment strategies and public health decisions.
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Affiliation(s)
| | | | | | - Joan L. Reeder
- Department of Health, Multnomah County, Portland, Oregon
| | | | - Thomas P. Young
- University of California San Francisco, San Francisco, California
- Abbott Molecular, Des Plaines, Illinois
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Stadeli KM, Richman DD. Rates of emergence of HIV drug resistance in resource-limited settings: a systematic review. Antivir Ther 2012; 18:115-23. [PMID: 23052978 PMCID: PMC4295493 DOI: 10.3851/imp2437] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2012] [Indexed: 10/27/2022]
Abstract
BACKGROUND The increasing availability of antiretroviral therapy (ART) has improved survival and quality of life for many infected with HIV, but can also engender drug resistance. This review summarizes the available information on drug resistance in adults in resource-limited settings. METHODS The online databases PubMed and Google Scholar, pertinent conference abstracts and references from relevant articles were searched for publications available before November 2011. Data collected after ART rollout were reviewed. RESULTS A total of 7 studies fulfilled the criteria for the analysis of acquired drug resistance and 22 fulfilled the criteria for the analysis of transmitted drug resistance (TDR). Acquired resistance was detected in 7.2% of patients on ART for 6-11 months, 11.1% at 12-23 months, 15.0% at 24-35 months, and 20.7% at ≥ 36 months. Multi-class drug resistance increased steadily with time on ART. The overall rate of TDR in all resource-limited countries studied was 6.6% (469/7,063). Patients in countries in which ART had been available for ≥ 5 years were 1.7 × more likely to have TDR than those living in a country where ART had been available for <5 years (P<0.001). The reported prevalence of TDR was 5.7% (233/4,069) in Africa, 7.6% (160/2,094) in Asia and 8.4% (76/900) in Brazil. CONCLUSIONS The emergence of drug resistance following access to ART in resource-limited settings resembles what was seen in resource-rich countries and highlights the need for virological monitoring for drug failure, drug resistance testing and alternative drug regimens that have proven beneficial in these resource-rich settings.
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Affiliation(s)
| | - Douglas D Richman
- Center of AIDS Research, VA San Diego Healthcare System, University of California, San Diego, San Diego, CA, USA
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12
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Subunit-selective mutational analysis and tissue culture evaluations of the interactions of the E138K and M184I mutations in HIV-1 reverse transcriptase. J Virol 2012; 86:8422-31. [PMID: 22623801 DOI: 10.1128/jvi.00271-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The emergence of HIV-1 drug resistance remains a major obstacle in antiviral therapy. M184I/V and E138K are signature mutations of clinical relevance in HIV-1 reverse transcriptase (RT) for the nucleoside reverse transcriptase inhibitors (NRTIs) lamivudine (3TC) and emtricitabine (FTC) and the second-generation (new) nonnucleoside reverse transcriptase inhibitor (NNRTI) rilpivirine (RPV), respectively, and the E138K mutation has also been shown to be selected by etravirine in cell culture. The E138K mutation was recently shown to compensate for the low enzyme processivity and viral fitness associated with the M184I/V mutations through enhanced deoxynucleoside triphosphate (dNTP) usage, while the M184I/V mutations compensated for defects in polymerization rates associated with the E138K mutations under conditions of high dNTP concentrations. The M184I mutation was also shown to enhance resistance to RPV and ETR when present together with the E138K mutation. These mutual compensatory effects might also enhance transmission rates of viruses containing these two mutations. Therefore, we performed tissue culture studies to investigate the evolutionary dynamics of these viruses. Through experiments in which E138K-containing viruses were selected with 3TC-FTC and in which M184I/V viruses were selected with ETR, we demonstrated that ETR was able to select for the E138K mutation in viruses containing the M184I/V mutations and that the M184I/V mutations consistently emerged when E138K viruses were selected with 3TC-FTC. We also performed biochemical subunit-selective mutational analyses to investigate the impact of the E138K mutation on RT function and interactions with the M184I mutation. We now show that the E138K mutation decreased rates of polymerization, impaired RNase H activity, and conferred ETR resistance through the p51 subunit of RT, while an enhancement of dNTP usage as a result of the simultaneous presence of both mutations E138K and M184I occurred via both subunits.
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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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Wainberg MA, Moisi D, Oliveira M, Toni TD, Brenner BG. Transmission dynamics of the M184V drug resistance mutation in primary HIV infection. J Antimicrob Chemother 2011; 66:2346-9. [PMID: 21750100 DOI: 10.1093/jac/dkr291] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES M184V in HIV-1 reverse transcriptase is among the most common mutations in patients failing antiretroviral therapy but is found only rarely in cases of transmitted drug resistance. METHODS To investigate this apparent paradox, we developed an allele-specific real-time PCR (AS-PCR) assay to determine the transmission of M184V in newly infected individuals. RESULTS M184V transmission may occur to a greater extent than previously thought. Persistence of M184V may commonly involve linkage to other drug resistance mutations. The presence of M184V as a single substitution in newly infected individuals was shown to wane over time, as a likely consequence of reversion and overgrowth by more fit wild-type viruses. CONCLUSIONS The M184V mutation can be documented in newly infected individuals, and the alternative hypothesis that this substitution might impact on the ability of HIV to be transmitted is unfounded.
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Affiliation(s)
- Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada.
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