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Cozzi-Lepri A, Dunn D, Tostevin A, Marvig RL, Bennedbaek M, Sharma S, Kozal MJ, Gompels M, Pinto AN, Lundgren J, Baxter JD. Rate of response to initial antiretroviral therapy according to level of pre-existing HIV-1 drug resistance detected by next-generation sequencing in the strategic timing of antiretroviral treatment (START) study. HIV Med 2024; 25:212-222. [PMID: 37775947 PMCID: PMC10872720 DOI: 10.1111/hiv.13556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/12/2023] [Indexed: 10/01/2023]
Abstract
OBJECTIVES The main objective of this analysis was to evaluate the impact of pre-existing drug resistance by next-generation sequencing (NGS) on the risk of treatment failure (TF) of first-line regimens in participants enrolled in the START study. METHODS Stored plasma from participants with entry HIV RNA >1000 copies/mL were analysed using NGS (llumina MiSeq). Pre-existing drug resistance was defined using the mutations considered by the Stanford HIV Drug Resistance Database (HIVDB v8.6) to calculate the genotypic susceptibility score (GSS, estimating the number of active drugs) for the first-line regimen at the detection threshold windows of >20%, >5%, and >2% of the viral population. Survival analysis was conducted to evaluate the association between the GSS and risk of TF (viral load >200 copies/mL plus treatment change). RESULTS Baseline NGS data were available for 1380 antiretroviral therapy (ART)-naïve participants enrolled over 2009-2013. First-line ART included a non-nucleoside reverse transcriptase inhibitor (NNRTI) in 976 (71%), a boosted protease inhibitor in 297 (22%), or an integrase strand transfer inhibitor in 107 (8%). The proportions of participants with GSS <3 were 7% for >20%, 10% for >5%, and 17% for the >2% thresholds, respectively. The adjusted hazard ratio of TF associated with a GSS of 0-2.75 versus 3 in the subset of participants with mutations detected at the >2% threshold was 1.66 (95% confidence interval 1.01-2.74; p = 0.05) and 2.32 (95% confidence interval 1.32-4.09; p = 0.003) after restricting the analysis to participants who started an NNRTI-based regimen. CONCLUSIONS Up to 17% of participants initiated ART with a GSS <3 on the basis of NGS data. Minority variants were predictive of TF, especially for participants starting NNRTI-based regimens.
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Affiliation(s)
| | - David Dunn
- Institute for Global Health, UCL, London, UK
| | | | - Rasmus L Marvig
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marc Bennedbaek
- Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institute, Copenhagen, Denmark
| | - Shweta Sharma
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
| | | | | | - Angie N Pinto
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Jens Lundgren
- Copenhagen HIV Programme, Rigs Hospitalet, University of Copenhagen, Copenhagen, Denmark
| | - John D Baxter
- Cooper Medical School of Rowan University and Cooper University Health Care, Camden, New Jersey, USA
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Bandyopadhyay A, Palepu S, Saini B, Chaurasia RC, Yadav RK. Tenofovir-based first-line regimen in newly diagnosed HIV-patients: An experience from a Tertiary Care Hospital in India. Indian J Sex Transm Dis AIDS 2023; 44:143-146. [PMID: 38223158 PMCID: PMC10785115 DOI: 10.4103/ijstd.ijstd_90_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 06/29/2022] [Accepted: 09/11/2022] [Indexed: 01/16/2024] Open
Abstract
Introduction India has a huge burden of HIV/AIDS infection. Tenofovir-based first-line therapy is the preferred treatment for newly diagnosed cases of HIV infection. Materials and Methods The present prospective study was done among newly diagnosed cases of HIV infection. The patients were followed up for 6 months from the day of enrollment. Sociodemographic parameters, CD4 counts, and adverse drug reactions (ADRs) were analyzed at baseline and after 6 months. Bivariate and multivariate logistic regression was performed with the occurrence of ADRs as outcome variable. Results In this study, 67 patients were enrolled with a mean age of 32.75 (±14.39) years. Mean CD4 count at the start of treatment was 241.5/mm3. The mean difference in CD4 count was 383.05/mm3 (standard deviation = 274.9). Dizziness, tingling, numbness of extremities, and muscle cramps were the most common adverse effects. On multivariate logistic regression, the occurrence of ADRs was seen to be significantly higher only in illiterate patients. Conclusion The present study highlights the importance of long-term follow-up of the patients on antiretroviral therapy. Adequate monitoring of the treatment parameters is of utmost importance.
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Affiliation(s)
- Arkapal Bandyopadhyay
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Sarika Palepu
- Department of Community Medicine, VCSGGMS & RI, Srinagar, Uttarakhand, India
| | - Bhawna Saini
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | | | - Rakesh Kumar Yadav
- Department of Internal Medicine, Moti Lal Nehru Medical College, Allahabad, Uttar Pradesh, India
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3
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El Bouzidi K, Datir RP, Kwaghe V, Roy S, Frampton D, Breuer J, Ogbanufe O, Murtala-Ibrahim F, Charurat M, Dakum P, Sabin CA, Ndembi N, Gupta RK. Deep sequencing of HIV-1 reveals extensive subtype variation and drug resistance after failure of first-line antiretroviral regimens in Nigeria. J Antimicrob Chemother 2021; 77:474-482. [PMID: 34741609 PMCID: PMC8809188 DOI: 10.1093/jac/dkab385] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/28/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Deep sequencing could improve understanding of HIV treatment failure and viral population dynamics. However, this tool is often inaccessible in low- and middle-income countries. OBJECTIVES To determine the genetic patterns of resistance emerging in West African HIV-1 subtypes during first-line virological failure, and the implications for future antiretroviral options. PATIENTS AND METHODS Participants were selected from a Nigerian cohort of people living with HIV who had failed first-line ART and subsequently switched to second-line therapy. Whole HIV-1 genome sequences were generated from first-line virological failure samples with Illumina MiSeq. Mutations detected at ≥2% frequency were analysed and compared by subtype. RESULTS HIV-1 sequences were obtained from 101 participants (65% female, median age 30 years, median 32.9 months of nevirapine- or efavirenz-based ART). Thymidine analogue mutations (TAMs) were detected in 61%, other core NRTI mutations in 92% and NNRTI mutations in 99%. Minority variants (<20% frequency) comprised 18% of all mutations. K65R was more prevalent in CRF02_AG than G subtypes (33% versus 7%; P = 0.002), and ≥3 TAMs were more common in G than CRF02_AG (52% versus 24%; P = 0.004). Subtype G viruses also contained more RT cleavage site mutations. Cross-resistance to at least one of the newer NNRTIs, doravirine, etravirine or rilpivirine, was predicted in 81% of participants. CONCLUSIONS Extensive drug resistance had accumulated in people with West African HIV-1 subtypes, prior to second-line ART. Deep sequencing significantly increased the detection of resistance-associated mutations. Caution should be used if considering newer-generation NNRTI agents in this setting.
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Affiliation(s)
- Kate El Bouzidi
- Division of Infection & Immunity, University College London, London, UK.,Institute for Global Health, University College London, London, UK
| | - Rawlings P Datir
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Vivian Kwaghe
- University of Abuja Teaching Hospital, Abuja, Nigeria
| | - Sunando Roy
- Division of Infection & Immunity, University College London, London, UK
| | - Dan Frampton
- Division of Infection & Immunity, University College London, London, UK.,Farr Institute of Health Informatics Research, University College London, London, UK
| | - Judith Breuer
- Division of Infection & Immunity, University College London, London, UK
| | - Obinna Ogbanufe
- U.S. Centers for Disease Control and Prevention, U.S. Embassy, Abuja, Nigeria
| | | | - Man Charurat
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | | | - Caroline A Sabin
- Institute for Global Health, University College London, London, UK
| | - Nicaise Ndembi
- Institute of Human Virology Nigeria, Abuja, Nigeria.,Africa Centres for Disease Control and Prevention, African Union Commission, Addis Ababa, Ethiopia
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK.,Africa Health Research Institute, Durban, South Africa
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Abstract
HIV-1 is genetically heterogeneous, having different subtypes and circulating recombinant forms (CRFs). HIV-1 genotyping is used to determine drug resistance profiles and is based on the use of a mixture of consensus and degenerate primers targeting the pol gene. However, the use of this type of primers is associated with either PCR bias or PCR failure. Consensus-degenerate hybrid oligonucleotide primers (CODEHOPs) can detect and identify unknown and distantly related gene sequences by PCR. CODEHOPs designed using different HIV-1 subtypes and CRFs were evaluated for HIV-1 genotyping by Sanger and MinION sequencing. A total of 321 plasma samples were used for the validation of CODEHOP-mediated HIV-1 genotyping. CODEHOP-mediated PCR showed 100% sensitivity and specificity, with limits of detection and genotyping below 200 copies/ml. The head-to-head evaluation of CODEHOP-mediated PCR and standard PCR showed 97 to 98% and 82 to 84% PCR success rates, respectively. There was 100% agreement between the CODEHOP and the reference method in the drug resistance profiles determined by Sanger-based sequencing. Using MinION sequencing, the CODEHOP-mediated PCR scheme resulted in better depth of genome coverage and detection of more drug resistance variants in the protease and reverse transcriptase genes than the standard amplification scheme. The overall prevalences of drug resistance mutations were 17.1% in treatment-experienced patients and 1.2% in treatment-naive patients. They were mainly associated with resistance to reverse transcriptase inhibitors and were linked to virological failure and the patient’s treatment history. Findings from this study suggest that the performance of HIV-1 genotyping is improved by using CODEHOP-mediated PCR. IMPORTANCE HIV-1 drug resistance is the main cause of treatment failure. Regular surveillance of resistance-associated mutations in HIV-1 genomes is essential for the optimal management of HIV-1 infections. Due to HIV-1’s genetic diversity, different HIV-1 genotypes are circulating worldwide. Standard primers used in the amplification of HIV-1 RNA have not been designed to cover all HIV-1 genotypes and are the main cause of amplification and drug resistance test failure. In this study, new sets of PCR primers targeting the protease, reverse transcriptase, and integrase genes were designed using the CODEHOP approach. They were compared to primers recommended in part by WHO for drug resistance testing using in-house PCR. Unsuccessful HIV-1 RNA amplification was less likely to occur with CODEHOP primers, leading to fewer test failures and lower cost. Furthermore, CODEHOP primers were more effective than standard primers for the detection of minority resistant variants by MinION sequencing.
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Application of next generation sequencing in HIV drug resistance studies in Africa, 2005–2019: A systematic review. SCIENTIFIC AFRICAN 2021. [DOI: 10.1016/j.sciaf.2021.e00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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6
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Transmitted HIV drug resistance among individuals with newly diagnosed HIV infection: a multicenter observational study. AIDS 2020; 34:609-619. [PMID: 31895143 DOI: 10.1097/qad.0000000000002468] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
OBJECTIVES Fifteen years after the roll-out of antiretroviral treatment (ART) in China, there is limited information available on transmitted HIV drug resistance (TDR). This study aimed to characterize the epidemiology of TDR in China. DESIGN We conducted a prospective cross-sectional observational study. METHODS We analyzed the demographic, clinical, and virological data of individuals with newly diagnosed HIV infection using data from the Beijing HIV laboratory network collected between 2001 and 2017. We did population-based sequencing of the pol gene on plasma specimens and identified TDR mutations using the WHO list for surveillance of TDR mutations. RESULTS Data on TDR were available for 91% of the 10 115 individuals with newly diagnosed HIV infection tested, of whom 19.2% were from rural areas. The overall prevalence of TDR was 4.1% [95% confidence interval (CI): 3.7-4.5%], with a declining trend over the period 2001-2017. In the multivariable analysis, the risk of TDR differed significantly according to sex [odds ratio (OR) for women vs. men: 0.41, 95% CI: 0.22-0.69, P = 0.002]; infection type (OR for CRF07_BC vs. CRF01_AE: 0.24, 95% CI: 0.16-0.36, P < 0.001); and sampling period (OR for 2009-2012 vs. 2001-2008: 0.57, 95% CI: 0.41-0.79; P = 0.01), and was significantly higher among individuals from Hebei province than in those from Beijing (OR: 1.43, 95% CI: 1.05-1.96; P = 0.02). CONCLUSION In China, the prevalence of TDR among individuals with newly diagnosed HIV infection is relatively low. Trends in TDR should be assessed in other countries with a high TDR burden.
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Inzaule SC, Hamers RL, Noguera-Julian M, Casadellà M, Parera M, Kityo C, Steegen K, Naniche D, Clotet B, Rinke de Wit TF, Paredes R. Clinically relevant thresholds for ultrasensitive HIV drug resistance testing: a multi-country nested case-control study. Lancet HIV 2018; 5:e638-e646. [PMID: 30282603 DOI: 10.1016/s2352-3018(18)30177-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/04/2018] [Accepted: 07/13/2018] [Indexed: 11/30/2022]
Abstract
BACKGROUND Implementation of ultrasensitive HIV drug resistance tests for routine clinical use is hampered by uncertainty about the clinical relevance of drug-resistant minority variants. We assessed different detection thresholds for pretreatment drug resistance to predict an increased risk of virological failure. METHODS We did a case-control study nested within a prospective multicountry cohort. Our study included patients from 12 clinical sites in Kenya, Nigeria, South Africa, Uganda, and Zambia. We defined cases as patients with virological failure (ie, those who had either viral load ≥400 copies per mL at 12 months or had switched to second-line antiretroviral therapy [ART] as a result of virological failure before 12 months) and controls as those with viral suppression (viral load <400 copies per mL at 12 months) on first-line non-nucleoside reverse transcriptase inhibitor-based antiretroviral therapy. We assessed pretreatment drug resistance with Illumina MiSeq next-generation sequencing, using the International Antiviral Society (IAS)-USA mutation list or the Stanford HIV Drug Resistance Database (HIVDB) genotypic sensitivity score. We calculated diagnostic accuracy measures and assessed the odds of virological failure using conditional logistic regression for 1%, 5%, and 10% pretreatment drug resistance detection thresholds, compared with the conventional 20% or more used in Sanger-based sequencing. FINDINGS Paired viral load results before ART and at month 12 of follow-up were available from 1896 participants. We identified 178 patients with virological failure and selected 338 matched controls. We excluded 117 patients from pretreatment drug resistance analysis; therefore, 152 cases of virological failure and 247 controls were included in the final analysis. With the IAS-USA mutation list, at a detection threshold of 20% or more in patients with pretreatment drug resistance, the adjusted odds ratio (OR) for virological failure was 9·2 (95% CI 4·2-20·1) compared with those without pretreatment drug resistance. Lowering the threshold resulted in adjusted ORs of virological failure of 6·8 (95% CI 3·3-13·9) at the 10% threshold, 7·6 (3·4-17·1) at the 5% threshold, and 4·5 (2·0-10·2) at the 1% threshold. Lowering the detection threshold from 20% improved the sensitivity (ie, ability to identify cases) from 12% (n=18) to 13% (n=19) at detection threshold 10%, to 15% (n=23) at detection threshold 5%, and to 17% (n=26) at detection threshold 1%, but caused a slight reduction in specificity (ie, ability to identify controls) from 98% (n=241) to 96% (n=238) at the 10% threshold, 96% (n=236) at the 5% threshold, and a larger reduction to 92% (n=227) at the 1% threshold. Diagnostic ORs were 5·4 (95% CI 2·1-13·9) at the 20% threshold, 3·8 (1·7-8·6) at the 10% threshold, 3·8 (1·8-8·1) at the 5% threshold, and 2·3 (1·2-4·2) at the 1% threshold. Use of the Stanford HIVDB genotypic sensitivity scores yielded similar ORs for virological failure, sensitivities, specificities, and diagnostic ORs. INTERPRETATION Ultrasensitive resistance testing for pretreatment drug resistance improved identification of people at risk of virological failure; however, this came with a reduction in our ability to identify people with viral suppression, especially at very low thresholds. Further modelling is needed to estimate the optimal trade-off for the 5% and 20% thresholds, balancing improved case finding against unnecessary regimen switching. FUNDING The Netherlands Ministry of Foreign Affairs, IrsiCaixa, and European Union.
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Affiliation(s)
- Seth C Inzaule
- Department of Global Health, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Raph L Hamers
- Department of Global Health, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Department of Internal Medicine, Division of Infectious Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands; Eijkman-Oxford Clinical Research Unit, Eijkman Institute for Molecular Biology, and Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Marc Noguera-Julian
- Infectious Diseases Service & IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain; Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
| | - Maria Casadellà
- Infectious Diseases Service & IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Mariona Parera
- Infectious Diseases Service & IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Cissy Kityo
- Joint Clinical Research Centre, Kampala, Uganda
| | - Kim Steegen
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa; National Health Laboratory Service, Johannesburg, South Africa
| | - Denise Naniche
- ISGlobal, Barcelona Institute for Global Health Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Bonaventura Clotet
- Infectious Diseases Service & IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain; Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
| | - Tobias F Rinke de Wit
- Department of Global Health, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Roger Paredes
- Infectious Diseases Service & IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain; Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
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8
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Nicot F, Jeanne N, Raymond S, Delfour O, Carcenac R, Lefebvre C, Sauné K, Delobel P, Izopet J. Performance comparison of deep sequencing platforms for detecting HIV-1 variants in the pol gene. J Med Virol 2018; 90:1486-1492. [PMID: 29750364 DOI: 10.1002/jmv.25224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/01/2018] [Indexed: 01/08/2023]
Abstract
The present study compares the performances of an in-house sequencing protocol developed on MiSeq, the Sanger method, and the 454 GS-FLX for detecting and quantifying drug-resistant mutations (DRMs) in the human immunodeficiency virus polymerase gene (reverse transcriptase [RT] and protease [PR]). MiSeq sequencing identified all the resistance mutations detected by bulk sequencing (n = 84). Both the MiSeq and 454 GS-FLX platforms identified 67 DRMs in the RT and PR regions, but a further 25 DRMs were identified by only one or other of them. Pearson's analysis showed good concordance between the percentage of drug-resistant variants determined by MiSeq and 454 GS-FLX sequencing (ρ = .77, P < .0001). The MiSeq platform is as accurate as the 454 GS-FLX Roche system for determining RT and PR DRMs and could be used for monitoring human immunodeficiency virus type 1 drug resistance.
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Affiliation(s)
- Florence Nicot
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Nicolas Jeanne
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Stéphanie Raymond
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France.,INSERM, U1043, Toulouse, France.,Faculté de Médecine Toulouse-Purpan, Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Olivier Delfour
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Romain Carcenac
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Caroline Lefebvre
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Karine Sauné
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France.,INSERM, U1043, Toulouse, France.,Faculté de Médecine Toulouse-Purpan, Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Pierre Delobel
- INSERM, U1043, Toulouse, France.,Faculté de Médecine Toulouse-Purpan, Université Toulouse III Paul-Sabatier, Toulouse, France.,CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse, France
| | - Jacques Izopet
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France.,INSERM, U1043, Toulouse, France.,Faculté de Médecine Toulouse-Purpan, Université Toulouse III Paul-Sabatier, Toulouse, France
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9
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Rupérez M, Noguera-Julian M, González R, Maculuve S, Bellido R, Vala A, Rodríguez C, Sevene E, Paredes R, Menéndez C. HIV drug resistance patterns in pregnant women using next generation sequence in Mozambique. PLoS One 2018; 13:e0196451. [PMID: 29742132 PMCID: PMC5942837 DOI: 10.1371/journal.pone.0196451] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/13/2018] [Indexed: 11/30/2022] Open
Abstract
Background Few data on HIV resistance in pregnancy are available from Mozambique, one of the countries with the highest HIV toll worldwide. Understanding the patterns of HIV drug resistance in pregnant women might help in tailoring optimal regimens for prevention of mother to child transmission of HIV (pMTCT) and antenatal care. Objectives To describe the frequency and characteristics of HIV drug resistance mutations (HIVDRM) in pregnant women with virological failure at delivery, despite pMTCT or antiretroviral therapy (ART). Methods Samples from HIV-infected pregnant women from a rural area in southern Mozambique were analysed. Only women with HIV-1 RNA >400c/mL at delivery were included in the analysis. HIVDRM were determined using MiSeq® (detection threshold 1%) at the first antenatal care (ANC) visit and at the time of delivery. Results Ninety and 60 samples were available at the first ANC visit and delivery, respectively. At first ANC, 97% of the women had HIV-1 RNA>400c/mL, 39% had CD4+ counts <350 c/mm3 and 30% were previously not on ART. Thirteen women (14%) had at least one HIVDRM of whom 70% were not on previous ART. Eight women (13%) had at least one HIVDRM at delivery. Out of 37 women with data available from the two time points, 8 (21%) developed at least one new HIVDRM during pMTCT or ART. Twenty seven per cent (53/191), 32% (44/138) and 100% (5/5) of the mutations that were present at enrolment, delivery and that emerged during pregnancy, respectively, were minority mutations (frequency <20%). Conclusions Even with ultrasensitive HIV-1 genotyping, less than 20% of women with detectable viremia at delivery had HIVDRM before initiating pMTCT or ART. This suggests that factors other than pre-existing resistance, such as lack of adherence or interruptions of the ANC chain, are also relevant to explain lack of virological suppression at the time of delivery in women receiving antiretrovirals drugs during pregnancy.
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Affiliation(s)
- María Rupérez
- Manhiça Health Research Center (CISM), Manhiça, Maputo, Mozambique
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic—Universitat de Barcelona, Barcelona, Spain
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- * E-mail:
| | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic, Catalonia, Spain
| | - Raquel González
- Manhiça Health Research Center (CISM), Manhiça, Maputo, Mozambique
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic—Universitat de Barcelona, Barcelona, Spain
| | - Sonia Maculuve
- Manhiça Health Research Center (CISM), Manhiça, Maputo, Mozambique
| | - Rocío Bellido
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain
| | - Anifa Vala
- Manhiça Health Research Center (CISM), Manhiça, Maputo, Mozambique
| | | | - Esperança Sevene
- Manhiça Health Research Center (CISM), Manhiça, Maputo, Mozambique
- Faculdade de Medicina, Universidade Eduardo Mondlane (UEM), Maputo, Mozambique
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic, Catalonia, Spain
- Lluita Contra la Sida Foundation, HIV Unit, Hosp Univ Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Clara Menéndez
- Manhiça Health Research Center (CISM), Manhiça, Maputo, Mozambique
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic—Universitat de Barcelona, Barcelona, Spain
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
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10
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Stella-Ascariz N, Arribas JR, Paredes R, Li JZ. The Role of HIV-1 Drug-Resistant Minority Variants in Treatment Failure. J Infect Dis 2017; 216:S847-S850. [PMID: 29207001 DOI: 10.1093/infdis/jix430] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) drug resistance genotyping is recommended to help in the selection of antiretroviral therapy and to prevent virologic failure. There are several ultrasensitive assays able to detect HIV-1 drug-resistance minority variants (DRMVs) not detectable by standard population sequencing-based HIV genotyping assays. Presence of these DRMVs has been shown to be clinically relevant, but its impact does not appear to be uniform across drug classes. In this review, we summarize key evidence for the clinical impact of DRMVs across drug classes for both antiretroviral treatment-naive and antiretroviral treatment-experienced patients, and highlight areas where more supporting evidence is needed.
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Affiliation(s)
| | - José Ramón Arribas
- HIV Unit, Internal Medicine Service, Hospital Universitario La Paz-IdiPAZ
| | - Roger Paredes
- HIV Unit and irsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona and Universitat de Vic-UCC, Spain
| | - Jonathan Z Li
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School
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Noguera-Julian M, Edgil D, Harrigan PR, Sandstrom P, Godfrey C, Paredes R. Next-Generation Human Immunodeficiency Virus Sequencing for Patient Management and Drug Resistance Surveillance. J Infect Dis 2017; 216:S829-S833. [PMID: 28968834 PMCID: PMC5853595 DOI: 10.1093/infdis/jix397] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
High-quality, simplified, and low-cost human immunodeficiency virus (HIV) drug resistance tests that are able to provide timely actionable HIV resistance data at individual, population, and programmatic levels are needed to confront the emerging drug-resistant HIV epidemic. Next-generation sequencing technologies embedded in automated cloud-computing analysis environments are ideally suited for such endeavor. Whereas NGS can reduce costs over Sanger sequencing, automated analysis pipelines make NGS accessible to molecular laboratories regardless of the available bioinformatic skills. They can also produce highly structured, high-quality data that could be examined by healthcare officials and program managers on a real-time basis to allow timely public health action. Here we discuss the opportunities and challenges of such an approach.
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Affiliation(s)
- Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute
- Universitat Autònoma de Barcelona
- Universitat de Vic-Universitat Central de Catalunya, Spain
| | - Dianna Edgil
- United States Agency for International Development
| | - P Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, University of British Columbia
| | - Paul Sandstrom
- National HIV and Retrovirology Laboratory, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Canada
| | - Catherine Godfrey
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute
- Universitat Autònoma de Barcelona
- Universitat de Vic-Universitat Central de Catalunya, Spain
- Infectious Diseases Unit, Hospital Universitari Germans Trias i Pujol, Spain
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HIV Drug Resistance Mutations in Non-B Subtypes After Prolonged Virological Failure on NNRTI-Based First-Line Regimens in Sub-Saharan Africa. J Acquir Immune Defic Syndr 2017; 75:e45-e54. [PMID: 28129253 PMCID: PMC5427983 DOI: 10.1097/qai.0000000000001285] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
OBJECTIVE To determine drug resistance mutation (DRM) patterns in a large cohort of patients failing nonnucleoside reverse transcriptase inhibitor (NNRTI)-based first-line antiretroviral therapy regimens in programs without routine viral load (VL) monitoring and to examine intersubtype differences in DRMs. DESIGN Sequences from 787 adults/adolescents who failed an NNRTI-based first-line regimen in 13 clinics in Uganda, Kenya, Zimbabwe, and Malawi were analyzed. Multivariable logistic regression was used to determine the association between specific DRMs and Stanford intermediate-/high-level resistance and factors including REGA subtype, first-line antiretroviral therapy drugs, CD4, and VL at failure. RESULTS The median first-line treatment duration was 4 years (interquartile range 30-43 months); 42% of participants had VL ≥100,000 copies/mL and 63% participants had CD4 <100 cells/mm. Viral subtype distribution was A1 (40%; Uganda and Kenya), C (31%; Zimbabwe and Malawi), and D (25%; Uganda and Kenya), and recombinant/unclassified (5%). In general, DRMs were more common in subtype-C than in subtype-A and/or subtype-D (nucleoside reverse transcriptase inhibitor mutations K65R and Q151M; NNRTI mutations E138A, V106M, Y181C, K101E, and H221Y). The presence of tenofovir resistance was similar between subtypes [P (adjusted) = 0.32], but resistance to zidovudine, abacavir, etravirine, or rilpivirine was more common in subtype-C than in subtype-D/subtype-A [P (adjusted) < 0.02]. CONCLUSIONS Non-B subtypes differ in DRMs at first-line failure, which impacts on residual nucleoside reverse transcriptase inhibitor and NNRTI susceptibility. In particular, higher rates of etravirine and rilpivirine resistance in subtype-C may limit their potential utility in salvage regimens.
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Collier D, Iwuji C, Derache A, de Oliveira T, Okesola N, Calmy A, Dabis F, Pillay D, Gupta RK. Virological Outcomes of Second-line Protease Inhibitor-Based Treatment for Human Immunodeficiency Virus Type 1 in a High-Prevalence Rural South African Setting: A Competing-Risks Prospective Cohort Analysis. Clin Infect Dis 2017; 64:1006-1016. [PMID: 28329393 PMCID: PMC5439490 DOI: 10.1093/cid/cix015] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/12/2017] [Indexed: 11/20/2022] Open
Abstract
Background Second-line antiretroviral therapy (ART) based on ritonavir-boosted protease inhibitors (bPIs) represents the only available option after first-line failure for the majority of individuals living with human immunodeficiency virus (HIV) worldwide. Maximizing their effectiveness is imperative. Methods This cohort study was nested within the French National Agency for AIDS and Viral Hepatitis Research (ANRS) 12249 Treatment as Prevention (TasP) cluster-randomized trial in rural KwaZulu-Natal, South Africa. We prospectively investigated risk factors for virological failure (VF) of bPI-based ART in the combined study arms. VF was defined by a plasma viral load >1000 copies/mL ≥6 months after initiating bPI-based ART. Cumulative incidence of VF was estimated and competing risk regression was used to derive the subdistribution hazard ratio (SHR) of the associations between VF and patient clinical and demographic factors, taking into account death and loss to follow-up. Results One hundred one participants contributed 178.7 person-years of follow-up. Sixty-five percent were female; the median age was 37.4 years. Second-line ART regimens were based on ritonavir-boosted lopinavir, combined with zidovudine or tenofovir plus lamivudine or emtricitabine. The incidence of VF on second-line ART was 12.9 per 100 person-years (n = 23), and prevalence of VF at censoring was 17.8%. Thirteen of these 23 (56.5%) virologic failures resuppressed after a median of 8.0 months (interquartile range, 2.8-16.8 months) in this setting where viral load monitoring was available. Tuberculosis treatment was associated with VF (SHR, 11.50 [95% confidence interval, 3.92-33.74]; P < .001). Conclusions Second-line VF was frequent in this setting. Resuppression occurred in more than half of failures, highlighting the value of viral load monitoring of second-line ART. Tuberculosis was associated with VF; therefore, novel approaches to optimize the effectiveness of PI-based ART in high-tuberculosis-burden settings are needed. Clinical Trials Registration NCT01509508.
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Affiliation(s)
- Dami Collier
- Department of Infection and Immunity, University College London, United Kingdom
| | - Collins Iwuji
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
- Research Department of Infection and Population Health, University College London, United Kingdom
| | - Anne Derache
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
- Sorbonne Universités, University Pierre and Marie Curie Université Paris 06, Inserm, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
| | - Tulio de Oliveira
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
- University of KwaZulu-Natal, Durban, South Africa
| | | | - Alexandra Calmy
- Geneva University Hospital, HIV Unit, Department of Internal Medicine, Switzerland
| | - Francois Dabis
- INSERM U1219-Centre Inserm Bordeaux Population Health, Université de Bordeaux, France
- Université de Bordeaux, ISPED, Centre INSERM U1219-Bordeaux Population Health, France
| | - Deenan Pillay
- Department of Infection and Immunity, University College London, United Kingdom
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
| | - Ravindra K Gupta
- Department of Infection and Immunity, University College London, United Kingdom
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
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14
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Gregson J, Kaleebu P, Marconi VC, van Vuuren C, Ndembi N, Hamers RL, Kanki P, Hoffmann CJ, Lockman S, Pillay D, de Oliveira T, Clumeck N, Hunt G, Kerschberger B, Shafer RW, Yang C, Raizes E, Kantor R, Gupta RK. Occult HIV-1 drug resistance to thymidine analogues following failure of first-line tenofovir combined with a cytosine analogue and nevirapine or efavirenz in sub Saharan Africa: a retrospective multi-centre cohort study. THE LANCET. INFECTIOUS DISEASES 2016; 17:296-304. [PMID: 27914856 PMCID: PMC5421555 DOI: 10.1016/s1473-3099(16)30469-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/06/2016] [Accepted: 10/14/2016] [Indexed: 01/08/2023]
Abstract
Background HIV-1 drug resistance to older thymidine analogue nucleoside reverse transcriptase inhibitor drugs has been identified in sub-Saharan Africa in patients with virological failure of first-line combination antiretroviral therapy (ART) containing the modern nucleoside reverse transcriptase inhibitor tenofovir. We aimed to investigate the prevalence and correlates of thymidine analogue mutations (TAM) in patients with virological failure of first-line tenofovir-containing ART. Methods We retrospectively analysed patients from 20 studies within the TenoRes collaboration who had locally defined viral failure on first-line therapy with tenofovir plus a cytosine analogue (lamivudine or emtricitabine) plus a non-nucleoside reverse transcriptase inhibitor (NNRTI; nevirapine or efavirenz) in sub-Saharan Africa. Baseline visits in these studies occurred between 2005 and 2013. To assess between-study and within-study associations, we used meta-regression and meta-analyses to compare patients with and without TAMs for the presence of resistance to tenofovir, cytosine analogue, or NNRTIs. Findings Of 712 individuals with failure of first-line tenofovir-containing regimens, 115 (16%) had at least one TAM. In crude comparisons, patients with TAMs had lower CD4 counts at treatment initiation than did patients without TAMs (60·5 cells per μL [IQR 21·0–128·0] in patients with TAMS vs 95·0 cells per μL [37·0–177·0] in patients without TAMs; p=0·007) and were more likely to have tenofovir resistance (93 [81%] of 115 patients with TAMs vs 352 [59%] of 597 patients without TAMs; p<0·0001), NNRTI resistance (107 [93%] vs 462 [77%]; p<0·0001), and cytosine analogue resistance (100 [87%] vs 378 [63%]; p=0·0002). We detected associations between TAMs and drug resistance mutations both between and within studies; the correlation between the study-level proportion of patients with tenofovir resistance and TAMs was 0·64 (p<0·0001), and the odds ratio for tenofovir resistance comparing patients with and without TAMs was 1·29 (1·13–1·47; p<0·0001) Interpretation TAMs are common in patients who have failure of first-line tenofovir-containing regimens in sub-Saharan Africa, and are associated with multidrug resistant HIV-1. Effective viral load monitoring and point-of-care resistance tests could help to mitigate the emergence and spread of such strains.
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Affiliation(s)
- John Gregson
- Department of Statistics, London School of Hygiene & Tropical Medicine, London, UK
| | - Pontiano Kaleebu
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda; Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Vincent C Marconi
- Department of Global Health, Emory University Rollins School of Public Health, Emory University, Atlanta, GA, USA; Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA, USA
| | - Cloete van Vuuren
- Division of Infectious Diseases, University of the Free State, and 3 Military Hospital, Bloemfontein, South Africa
| | | | - Raph L Hamers
- Amsterdam Institute for Global Health and Development, Department of Global Health, Academic Medical Center, University of Amsterdam, Netherlands
| | - Phyllis Kanki
- Department of Immunology and Infectious Disease, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Christopher J Hoffmann
- Aurum Institute, Johannesburg South Africa; Johns Hopkins University, Baltimore, MD, USA
| | | | - Deenan Pillay
- Department of Infection, University College London, London, UK; Africa Health Research Institute, KwaZulu Natal, South Africa
| | - Tulio de Oliveira
- Nelson R Mandela School of Medicine, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu Natal, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Nathan Clumeck
- Saint-Pierre University Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Gillian Hunt
- National Institute for Communicable Diseases, Sandringham, South Africa
| | | | - Robert W Shafer
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Chunfu Yang
- International Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Elliot Raizes
- Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rami Kantor
- Division of Infectious Diseases, Alpert Medical School, Brown University, Providence, RI, USA
| | - Ravindra K Gupta
- Department of Infection, University College London, London, UK; Africa Health Research Institute, KwaZulu Natal, South Africa.
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Casadellà M, Paredes R. Deep sequencing for HIV-1 clinical management. Virus Res 2016; 239:69-81. [PMID: 27818211 DOI: 10.1016/j.virusres.2016.10.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 10/10/2016] [Accepted: 10/18/2016] [Indexed: 02/05/2023]
Abstract
The emerging HIV-1 resistance epidemic is threatening the impressive global advances in HIV-1 infection treatment and prevention achieved in the last decade. Next-generation sequencing is improving our ability to understand, diagnose and prevent HIV-1 resistance, being increasingly cost-effective and more accessible. However, NGS still faces a number of limitations that need to be addressed to enable its widespread use. Here, we will review the main NGS platforms available for HIV-1 diagnosis, the factors affecting the clinical utility of NGS testing and the evidence supporting -or not- ultrasensitive genotyping over Sanger sequencing for routine HIV-1 diagnosis. Now that global HIV-1 eradication might be within our reach, making NGS accessible also to LMICs has become a priority. Reductions in sequencing costs, particularly in library preparation, and accessibility to low-cost, robust but simplified automated bioinformatic analyses of NGS data will remain essential to end the HIV-1 pandemic.
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Affiliation(s)
- Maria Casadellà
- IrsiCaixa AIDS Research Institute, Badalona, Spain; Universitat Autònoma de Barcelona, Catalonia, Spain.
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Badalona, Spain; Universitat Autònoma de Barcelona, Catalonia, Spain; Universitat de Vic - Central de Catalunya, Vic, Catalonia, Spain; HIV-1 Unit, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
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White E, Smit E, Churchill D, Collins S, Booth C, Tostevin A, Sabin C, Pillay D, Dunn DT. No Evidence That HIV-1 Subtype C Infection Compromises the Efficacy of Tenofovir-Containing Regimens: Cohort Study in the United Kingdom. J Infect Dis 2016; 214:1302-1308. [PMID: 27732929 PMCID: PMC5079361 DOI: 10.1093/infdis/jiw213] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/14/2016] [Indexed: 11/26/2022] Open
Abstract
Concern has been expressed that tenofovir-containing regimens may have reduced effectiveness in the treatment of human immunodeficiency virus type 1 (HIV-1) subtype C infections because of a propensity for these viruses to develop a key tenofovir-associated resistance mutation. We evaluated whether subtype influenced rates of virological failure in a cohort of 8746 patients from the United Kingdom who received a standard tenofovir-containing first-line regimen and were followed for a median of 3.3 years. In unadjusted analyses, the rate of failure was approximately 2-fold higher among patients infected with subtype C virus as compared to those with subtype B virus (hazard ratio [HR], 1.86; 95% confidence interval [CI], 1.50–2.31; P < .001). However, the increased risk was greatly attenuated in analyses adjusting for demographic and clinical factors (adjusted HR, 1.14; 95% CI, .83–1.58; P = .41). There were no differences between subtypes C and subtypes non-B and non-C in either univariate or multivariate analysis. These observations imply there is no intrinsic effect of viral subtype on the efficacy of tenofovir-containing regimens.
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Affiliation(s)
| | - Erasmus Smit
- Public Health England, Birmingham Heartlands Hospital
| | | | | | - Clare Booth
- Health Service Laboratories, Royal Free Hospital, London
| | | | | | - Deenan Pillay
- Division of Infection and Immunity, University College London.,Africa Centre for Population Health, University of KwaZulu-Natal, Durban, South Africa
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