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Neufeld B, Munyuza C, Reimer A, Capiña R, Lee ER, Becker M, Sandstrom P, Ji H, Cholette F. A validated in-house assay for HIV drug resistance mutation surveillance from dried blood spot specimens. J Virol Methods 2024; 327:114939. [PMID: 38604585 DOI: 10.1016/j.jviromet.2024.114939] [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: 08/10/2023] [Revised: 03/28/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024]
Abstract
Despite increasing scale-up of antiretroviral therapy (ART) coverage, challenges related to adherence and HIV drug resistance (HIVDR) remain. The high cost of HIVDR surveillance is a persistent challenge with implementation in resource-constrained settings. Dried blood spot (DBS) specimens have been demonstrated to be a feasible alternative to plasma or serum for HIVDR genotyping and are more suitable for lower resource settings. There is a need for affordable HIVDR genotyping assays which can amplify HIV-1 sequences from DBS specimens, particularly those with low viral loads, at a low cost. Here, we present an in-house assay capable of reliably amplifying HIV-1 protease and partial reverse transcriptase genes from DBS specimens, which covers the complete World Health Organization 2009 list of drug resistance mutations under surveillance. DBS specimens were prepared using whole blood spiked with HIV-1 at concentrations of 10,000, 5000, 1000, and 500 copies/mL (n=30 for each concentration). Specimens were tested in triplicate. A two-step approach was used consisting of cDNA synthesis followed by nested PCR. The limit of detection of the assay was calculated to be approximately 5000 (95% CI: 3200-10,700) copies/mL for the protease gene and 3600 (95% CI: 2200-10,000) copies/mL for reverse transcriptase. The assay was observed to be most sensitive with higher viral load specimens (97.8% [95% CI: 92.2-99.7]) for both protease and reverse transcriptase at 10,000 copies/mL with performance decreasing with the use of specimens with lower viral loads (46.7% [36.1-57.5] and 60.0% [49.1-70.2] at 500 copies/mL for protease and reverse transcriptase, respectively). Ultimately, this assay presents a promising opportunity for use in resource-constrained settings. Future work should involve validation under field conditions including sub-optimal storage conditions and preparation of DBS with fingerprick blood in order to accurately reflect real-world collection scenarios.
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Affiliation(s)
- Bronwyn Neufeld
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada.
| | - Chantal Munyuza
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Alexandria Reimer
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Rupert Capiña
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Emma R Lee
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Marissa Becker
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada; Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Paul Sandstrom
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Hezhao Ji
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - François Cholette
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
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Steytler J, van der Ryst E, Craig C, Van Baelen B, Nuttall J, van Niekerk N, Mellors J, Parikh U, Wallis C. Clinical Presentation, Treatment Response, and Virology Outcomes of Women Who Seroconverted in the Dapivirine Vaginal Ring Trials-The Ring Study and DREAM. Clin Infect Dis 2023; 76:389-397. [PMID: 36189636 PMCID: PMC10169386 DOI: 10.1093/cid/ciac804] [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: 07/19/2022] [Revised: 09/20/2022] [Accepted: 09/29/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Participants with human immunodeficiency virus (HIV) seroconversion in The Ring Study, a phase 3 trial of dapivirine vaginal ring (DVR), or in the open-label extension trial dapivirine ring extended access and monitoring (DREAM) were offered enrollment in an observational cohort study (IPM 007) to assess clinical presentation and response to antiretroviral therapy (ART). METHODS Participants' HIV infection was managed at local treatment clinics according to national treatment guidelines. IPM 007 study visits occurred 3 and 6 months after enrollment and every 6 months thereafter. Assessments included plasma HIV-1 RNA, CD4+ T-cell counts, and recording of HIV/AIDS-associated events and antiretroviral use. Post hoc virology analyses were performed for participants identified with virologic failure. RESULTS One hundred fifty-one of 179 eligible participants (84.4%) enrolled into IPM 007; 103 had previously received the DVR in the Ring or DREAM studies, and 48 had received placebo in The Ring Study. HIV-1 RNA and CD4+ T-cell counts after 12 months' follow-up were similar for participants who used the DVR in The Ring Study and DREAM, compared to those who received placebo. Of the 78 participants with a study visit approximately 6 months after ART initiation, 59 (75.6%) had HIV-1 RNA <40 copies/mL (The Ring Study: placebo: 13/23 [56.5%]; DVR: 32/39 [82.1%]; DREAM [DVR]: 14/16 [87.5%]). Post hoc virology analysis indicated that genotypic patterns observed at virologic failure were as expected of a nonnucleoside reverse transcriptase inhibitor (NNRTI)-based regimen. CONCLUSIONS Seroconversion during DVR use did not negatively affect clinical presentation or treatment outcome. Mutation patterns at virologic failure were in line with individuals failing an NNRTI-based regimen. CLINICAL TRIALS REGISTRATION NCT01618058.
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Affiliation(s)
- John Steytler
- International Partnership for Microbicides South Africa NPC, Johannesburg, South Africa
| | | | - Charles Craig
- Research Virology Consulting Ltd, Cambridgeshire, United Kingdom
| | | | - Jeremy Nuttall
- International Partnership for Microbicides, Silver Spring, Maryland, USA
| | - Neliëtte van Niekerk
- International Partnership for Microbicides South Africa NPC, Johannesburg, South Africa
| | - John Mellors
- Microbicide Trials Network Virology Core Laboratory, University of Pittsburgh, Pennsylvania, USA
| | - Urvi Parikh
- Microbicide Trials Network Virology Core Laboratory, University of Pittsburgh, Pennsylvania, USA
| | - Carole Wallis
- Bio-Analytical Research Corporation Laboratory, Johannesburg, South Africa
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Beesham I, Parikh UM, Mellors JW, Joseph Davey DL, Heffron R, Palanee-Phillips T, Bosman SL, Beksinska M, Smit J, Ahmed K, Makkan H, Selepe P, Louw C, Kotze P, Hofmeyr GJ, Singata‐Madliki M, Rees H, Baeten JM, Wallis C. High Levels of Pretreatment HIV-1 Drug Resistance Mutations Among South African Women Who Acquired HIV During a Prospective Study. J Acquir Immune Defic Syndr 2022; 91:130-137. [PMID: 36094478 PMCID: PMC9651927 DOI: 10.1097/qai.0000000000003027] [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: 10/21/2021] [Accepted: 04/07/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Pretreatment HIV drug resistance (PDR) undermines individual treatment success and threatens the achievement of UNAIDS 95-95-95 targets. In many African countries, limited data are available on PDR as detection of recent HIV infection is uncommon and access to resistance testing is limited. We describe the prevalence of PDR among South African women with recent HIV infection from the Evidence for Contraceptive Options and HIV Outcomes (ECHO) Trial. METHODS HIV-uninfected, sexually active women, aged 18-35 years, and seeking contraception were enrolled in the ECHO Trial at sites in South Africa, from 2015 to 2018. HIV testing was done at trial entry and repeated quarterly. We tested stored plasma samples collected at HIV diagnosis from women who seroconverted during follow-up and had a viral load >1000 copies/mL for antiretroviral resistant mutations using a validated laboratory-developed population genotyping assay, which sequences the full protease and reverse transcriptase regions. Mutation profiles were determined using the Stanford Drug Resistance Database. RESULTS We sequenced 275 samples. The median age was 23 years, and majority (98.9%, n = 272) were infected with HIV-1 subtype C. The prevalence of surveillance drug resistance mutations (SDRMs) was 13.5% (n = 37). Nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations were found in 12.4% of women (n = 34). Few women had NRTI (1.8%, n = 5) and protease inhibitor (1.1%, n = 3) mutations. Five women had multiple NRTI and NNRTI SDRMs. CONCLUSIONS The high levels of PDR, particularly to NNRTIs, strongly support the recent change to the South African national HIV treatment guidelines to transition to a first-line drug regimen that excludes NNRTIs.
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Affiliation(s)
- Ivana Beesham
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | - Urvi M. Parikh
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - John W. Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Dvora L. Joseph Davey
- Division of Epidemiology and Biostatistics, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
- Department of Epidemiology, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA
| | - Renee Heffron
- Department of Global Health and Department of Epidemiology, University of Washington, Seattle, WA
| | - Thesla Palanee-Phillips
- Wits Reproductive Health and HIV Institute (Wits RHI), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shannon L. Bosman
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | - Mags Beksinska
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | - Jennifer Smit
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | - Khatija Ahmed
- Setshaba Research Centre, Soshanguve, South Africa
- Faculty of Health Sciences, Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Heeran Makkan
- The Aurum Institute, Klerksdorp, South Africa
- Department of Interdisciplinary Social Science, Public Health, Utrecht University, Utrecht, The Netherlands
| | | | - Cheryl Louw
- Madibeng Centre for Research, Brits, South Africa
- Department of Family Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Philip Kotze
- Qhakaza Mbokodo Research Clinic, Ladysmith, South Africa
| | - G. Justus Hofmeyr
- Effective Care Research Unit, Universities of the Witwatersrand, Walter Sisulu and Fort Hare and Eastern Cape Department of Health, East London, South Africa
- Department of Obstetrics and Gynaecology, University of Botswana, Gaborone, Botswana
| | - Mandisa Singata‐Madliki
- Effective Care Research Unit, Universities of the Witwatersrand, Walter Sisulu and Fort Hare and Eastern Cape Department of Health, East London, South Africa
- Effective Care Research Unit, Universities of the Witwatersrand and Fort Hare and Eastern Cape Department of Health, East London, South Africa
| | - Helen Rees
- Wits Reproductive Health and HIV Institute (Wits RHI), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jared M. Baeten
- Department of Global Health, Department of Epidemiology, Department of Medicine, University of Washington, Seattle, WA
- Currently, Gilead Sciences, Foster City, CA; and
| | - Carole Wallis
- BARC-SA and Lancet Laboratories, Johannesburg, South Africa
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Hermans LE, Umunnakwe CN, Lalla-Edward ST, Hebel SK, Tempelman HA, Nijhuis M, Venter WDF, Wensing AMJ. Point-of-Care Tenofovir Urine Testing for the Prediction of Treatment Failure and Drug Resistance During Initial Treatment for Human Immunodeficiency Virus Type 1 (HIV-1) Infection. Clin Infect Dis 2022; 76:e553-e560. [PMID: 36136811 PMCID: PMC9907515 DOI: 10.1093/cid/ciac755] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Viral rebound during antiretroviral treatment (ART) is most often driven by suboptimal adherence in the absence of drug resistance. We assessed the diagnostic performance of point-of-care (POC) tenofovir (TFV) detection in urine for the prediction of viral rebound and drug resistance during ART. METHODS We performed a nested case-control study within the ADVANCE randomized clinical trial (NCT03122262) in Johannesburg, South Africa. Adults with human immunodeficiency virus (HIV) and newly initiating ART were randomized to receive either dolutegravir or efavirenz, tenofovir disoproxil fumarate or alafenamide, and emtricitabine. All participants with rebound ≥200 copies/mL between 24 and 96 weeks of follow-up were selected as cases and matched to controls with virological suppression <50 copies/mL. Rapid POC urine-TFV detection was performed retrospectively. RESULTS We included 281 samples from 198 participants. Urine-TFV was detectable in 30.7% (70/228) of cases and in 100% (53/53) of controls. Undetectable urine-TFV predicted rebound with a sensitivity of 69% [95% confidence interval {CI}: 63-75] and specificity of 100% [93-100]. In cases with virological failure and sequencing data (n = 42), NRTI drug resistance was detected in 50% (10/20) of cases with detectable urine-TFV versus in 8.3% (2/24) of cases with undetectable urine-TFV. Detectable urine-TFV predicted NRTI resistance (odds ratio [OR] 10.4 [1.8-114.4] P = .005) with a sensitivity of 83% [52-98] and specificity of 69% [50-84]. CONCLUSIONS POC objective adherence testing using a urine-TFV test predicted viral rebound with high specificity. In participants with rebound, urine-TFV testing predicted the selection of drug resistance. Objective adherence testing may be used to rapidly provide insight into adherence, suppression, and drug resistance during ART.
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Affiliation(s)
- Lucas E Hermans
- Correspondence: L. E. Hermans, ward G26, Groote Schuur Hospital, Anzio Rd, Observatory, 7925, Cape Town, South Africa ()
| | | | - Samanta T Lalla-Edward
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shane K Hebel
- OraSure Technologies Inc., Bethlehem, Pennsylvania, USA
| | | | - Monique Nijhuis
- Department of Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands,HIV Pathogenesis Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Willem D F Venter
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Castillo‐Mancilla JR, Edwards JA, Brijkumar J, Moosa M, Zhao Y, Ofotokun I, Johnson BA, Lee MH, Pillay S, Pillay M, Moodley P, Kuritzkes DR, Sunpath H, Bushman LR, Ellison L, Anderson PL, Marconi VC. Tenofovir diphosphate levels in dried blood spots are associated with virologic failure and resistance to first-line therapy in South Africa: a case-control cohort study. J Int AIDS Soc 2021; 24:e25849. [PMID: 34910844 PMCID: PMC8673924 DOI: 10.1002/jia2.25849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 11/02/2021] [Indexed: 01/04/2023] Open
Abstract
INTRODUCTION Tenofovir diphosphate (TFV-DP) in dried blood spots (DBS), a measure of cumulative antiretroviral therapy (ART) adherence, is associated with viral suppression and predicts future viremia in persons with HIV (PWH). However, its utility to identify those at risk for virologic failure (VF) and drug resistance is unknown. To address this, we aimed to establish the association between this adherence biomarker and VF with drug resistance in a cohort of PWH initiating first-line ART in KwaZulu-Natal, South Africa. METHODS PWH initiating TFV disoproxil fumarate (TDF)-based ART within a parent prospective cohort were evaluated. Using a nested design, DBS for TFV-DP were collected from cases who developed VF (HIV-1 RNA ≥1000 copies/ml) after ≥5 months on ART versus controls, matched 1:2 by site, age, gender, race and ART duration. Cases were categorized as having VF with or without resistance using genotyping. One-way analysis of variance (ANOVA) was used to compare TFV-DP for controls, cases with VF and resistance, and cases with VF without resistance. Data are presented as mean (standard deviation, SD) or geometric mean [95% confidence interval, 95% CI]. RESULTS AND DISCUSSION One thousand participants were enrolled in the parent study between 2014 and 2016, of which 288 (29%) had DBS available. Of these, 94 (33%) were cases and 194 (67%) were controls; 59% were women. Mean age of our population was 33 (SD 8) years. Genotyping was available in 50 (53%) of the 94 cases. Geometric mean TFV-DP in DBS from controls was 708 [95% CI; 647-773] fmol/punch, which was higher compared to participants having VF with resistance (n = 36), 386 [95% CI; 241-617] fmol/punch and VF without resistance (n = 14), 61 [95% CI; 22-164] fmol/punch; p<0.001. Genotype could not be obtained in 44 (47%) cases. CONCLUSIONS TFV-DP in DBS showed a stepwise association with VF and drug resistance in South African PWH. Participants having VF with resistance had mid-range concentrations of TFV-DP, which were higher than those for PWH without resistance. Future research on the clinical utility of TFV-DP concentrations in DBS to predict and prevent the development of VF and drug resistance is needed.
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Affiliation(s)
- Jose R. Castillo‐Mancilla
- Division of Infectious DiseasesDepartment of MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Johnathan A. Edwards
- Division of Infectious DiseasesDepartment of MedicineEmory University School of MedicineAtlantaGeorgiaUSA
- School of Health and Social CareUniversity of LincolnLincolnUK
| | | | | | - Yuan Zhao
- Division of Infectious DiseasesDepartment of MedicineEmory University School of MedicineAtlantaGeorgiaUSA
| | - Igho Ofotokun
- Division of Infectious DiseasesDepartment of MedicineEmory University School of MedicineAtlantaGeorgiaUSA
| | - Brent A. Johnson
- Department of Biostatistics and Computational BiologyUniversity of RochesterRochesterNew YorkUSA
| | - Mitchell H. Lee
- Division of Infectious DiseasesDepartment of MedicineEmory University School of MedicineAtlantaGeorgiaUSA
| | - Selvan Pillay
- National Health Laboratory ServiceDurbanSouth Africa
| | | | - Pravi Moodley
- National Health Laboratory ServiceDurbanSouth Africa
- University of KwaZulu‐NatalDurbanSouth Africa
| | - Daniel R. Kuritzkes
- Divison of Infectious DiseasesBrigham and Women's HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | - Henry Sunpath
- National Health Laboratory ServiceDurbanSouth Africa
| | - Lane R. Bushman
- Division of Infectious DiseasesDepartment of MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Lucas Ellison
- Division of Infectious DiseasesDepartment of MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Peter L. Anderson
- Division of Infectious DiseasesDepartment of MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Vincent C. Marconi
- Division of Infectious DiseasesDepartment of MedicineEmory University School of MedicineAtlantaGeorgiaUSA
- Rollins School of Public HealthEmory UniversityAtlantaGeorgiaUSA
- Emory Vaccine CenterEmory UniversityAtlantaGeorgiaUSA
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Manyana S, Gounder L, Pillay M, Manasa J, Naidoo K, Chimukangara B. HIV-1 Drug Resistance Genotyping in Resource Limited Settings: Current and Future Perspectives in Sequencing Technologies. Viruses 2021; 13:1125. [PMID: 34208165 PMCID: PMC8230827 DOI: 10.3390/v13061125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 12/14/2022] Open
Abstract
Affordable, sensitive, and scalable technologies are needed for monitoring antiretroviral treatment (ART) success with the goal of eradicating HIV-1 infection. This review discusses use of Sanger sequencing and next generation sequencing (NGS) methods for HIV-1 drug resistance (HIVDR) genotyping, focusing on their use in resource limited settings (RLS). Sanger sequencing remains the gold-standard method for detecting HIVDR mutations of clinical relevance but is mainly limited by high sequencing costs and low-throughput. NGS is becoming a more common sequencing method, with the ability to detect low-abundance drug-resistant variants and reduce per sample costs through sample pooling and massive parallel sequencing. However, use of NGS in RLS is mainly limited by infrastructure costs. Given these shortcomings, our review discusses sequencing technologies for HIVDR genotyping, focusing on common in-house and commercial assays, challenges with Sanger sequencing in keeping up with changes in HIV-1 treatment programs, as well as challenges with NGS that limit its implementation in RLS and in clinical diagnostics. We further discuss knowledge gaps and offer recommendations on how to overcome existing barriers for implementing HIVDR genotyping in RLS, to make informed clinical decisions that improve quality of life for people living with HIV.
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Affiliation(s)
- Sontaga Manyana
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Lilishia Gounder
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Melendhran Pillay
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Justen Manasa
- Department of Laboratory Medicine and Investigative Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe;
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa;
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban 4013, South Africa
| | - Benjamin Chimukangara
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa;
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Ondoa P, Kim AA, Boender TS, Zhang G, Kroeze S, Wiener J, Botes M, Botes E, Akanmu AS, Akanmu S, Wellington M, Siwale M, Mandaliya K, Kityo C, Labib EE, Adeyemo TA, Rinke de Wit T, Nkengasong J. Access to HIV Viral Load Testing and Antiretroviral Therapy Switch Practices: A Multicountry Prospective Cohort Study in Sub-Saharan Africa. AIDS Res Hum Retroviruses 2020; 36:918-926. [PMID: 32722958 DOI: 10.1089/aid.2020.0049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Poor access to HIV viral load (VL) testing prevents the timely monitoring of HIV treatment adherence and efficacy. Factors enabling clinical benefits of VL testing when added to local standards of care, can inform the development of more cost-effective routine VL scale-up plans. We compared antiretroviral therapy (ART) switch practices in 13 clinics across 6 countries, with full (N = 8), phasing-in (N = 3) or no onsite access (N = 2) to VL. The analysis used data from the Pan-African Studies to Evaluate Resistance (PASER), observing virological and drug resistance outcomes among adults receiving first- or second-line ART between 2008 and 2015. Study plasma viral load (sVL) determined at baseline, every 12 months thereafter and at the time of switch served for retrospectively validating switch decisions, categorized into "necessary," "unnecessary," and "missed." Virological failure was defined as two consecutive sVL ≥1,000 HIV-RNA copies/mL. One thousand nine hundred ninety-five of the 2,420 (82.4%) study participants had continuous virological suppression during the median 30 months of follow-up. Among the 266 virological failures (11.0%), the proportion of necessary switches were similar in clinics with full (37%), phasing-in (25%), or no access (39%) to local VL testing. Documented utilization of local VL results for the switch decision was associated with higher percentage of necessary switch (87.6% vs. 67.9%). Shorter time to necessary switch was associated with higher rates of long-term virological suppression, regardless of access to local viral load. Availability of HIV VL testing capacity does not systematically result in adequate switch practices or better virological outcomes. Systems supporting sufficient test demand execution, and actual utilization of results for patient management need strengthening.
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Affiliation(s)
- Pascale Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
- Amsterdam Institute for Global Health and Development, Academic Medical Center, Department of Global Health, University of Amsterdam, the Netherlands
| | - Andrea A. Kim
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Los Angeles County Public Health Department, Los Angeles, California, USA
| | - T. Sonia Boender
- Amsterdam Institute for Global Health and Development, Academic Medical Center, Department of Global Health, University of Amsterdam, the Netherlands
| | - Guoqing Zhang
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Stefanie Kroeze
- Amsterdam Institute for Global Health and Development, Academic Medical Center, Department of Global Health, University of Amsterdam, the Netherlands
| | - Jeffrey Wiener
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | | | | | | | | | | | | | | | | | | | - Tobias Rinke de Wit
- Amsterdam Institute for Global Health and Development, Academic Medical Center, Department of Global Health, University of Amsterdam, the Netherlands
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Ogbenna AA, Meloni S, Inzaule S, Hamers RL, Sigaloff K, Osibogun A, Adeyemo TA, Okonkwo P, Samuels JO, Kanki PJ, Rinke de Wit TF, Akanmu AS. The impact of HIV-1 subtypes on virologic and immunologic treatment outcomes at the Lagos University Teaching Hospital: A longitudinal evaluation. PLoS One 2020; 15:e0238027. [PMID: 32841264 PMCID: PMC7447033 DOI: 10.1371/journal.pone.0238027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 08/10/2020] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION HIV is a highly diverse virus with significant genetic variability which may confer biologic differences that could impact on treatment outcomes. MATERIALS AND METHODS We studied the association between HIV subtypes and immunologic and virologic outcomes in a longitudinal cohort of 169 patients on combination antiretroviral therapy. Participants were followed up for 5 years. Demographic data, CD4 cell count and viral loads (VL) were extracted from medical records. Whole protease gene and codon 1-300 of the reverse transcriptase gene were sequenced and analysed. RESULTS Sixty-four percent of participants were females with a median age of 35 years. Twelve different subtypes were observed, the commonest being CRF 02_AG (55.0%) and subtypes G (23.1%). All subtypes showed steady rise in CD4 count and there was no difference in proportion who achieved CD4+ cell count rise of ≥100 cells/μL from baseline within 12 months' post-initiation of ART, or ≥350 cells/μL at 60 months' post-initiation. Median time to attaining a rise of ≥350 cells/μL was 24 months (6-48 months). The proportion that achieved undetectable VL at month 6 and 12 post-initiation of ART were comparable across subtypes. At end of 5th year, there was no statistical difference in proportion with virologic failure. CONCLUSION No association between HIV subtypes and immunologic or virologic response to therapy was observed, suggesting that current first-line ART may have similar efficacy across subtype predominating in South-West Nigeria.
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Affiliation(s)
- Ann Abiola Ogbenna
- Department of Haematology and Blood Transfusion, Faculty of Clinical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Seema Meloni
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Seth Inzaule
- Department of Global Health, Amsterdam UMC, Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, Netherlands
| | - Raph L. Hamers
- Department of Global Health, Amsterdam UMC, Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, Netherlands
- Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Kim Sigaloff
- Department of Global Health, Amsterdam UMC, Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, Netherlands
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam UMC, Amsterdam, Netherlands
| | - Akin Osibogun
- Department of Community Health and Primary Care, College of Medicine, Faculty of Clinical Sciences, University of Lagos, Lagos, Nigeria
| | - Titilope Adenike Adeyemo
- Department of Haematology and Blood Transfusion, Faculty of Clinical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
| | | | | | - Phyllis J. Kanki
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Tobias F. Rinke de Wit
- Department of Global Health, Amsterdam UMC, Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, Netherlands
| | - Alani Sulaimon Akanmu
- Department of Haematology and Blood Transfusion, Faculty of Clinical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
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9
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Discordance between Etravirine Phenotype and Genotype-Based Predicted Phenotype for Subtype C HIV-1 from First-Line Antiretroviral Therapy Failures in South Africa. Antimicrob Agents Chemother 2020; 64:AAC.02101-19. [PMID: 32071061 DOI: 10.1128/aac.02101-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/12/2020] [Indexed: 12/25/2022] Open
Abstract
Etravirine (ETR) is a nonnucleoside reverse transcriptase inhibitor (NNRTI) used in treatment-experienced individuals. Genotypic resistance test-interpretation systems can predict ETR resistance; however, genotype-based algorithms are derived primarily from HIV-1 subtype B and may not accurately predict resistance in non-B subtypes. The frequency of ETR resistance among recombinant subtype C HIV-1 and the accuracy of genotypic interpretation systems were investigated. HIV-1LAI containing full-length RT from HIV-1 subtype C-positive individuals experiencing virologic failure (>10,000 copies/ml and >1 NNRTI resistance-associated mutation) were phenotyped for ETR susceptibility. Fold change (FC) was calculated against a composite 50% effective concentration (EC50) from treatment-naive individuals and three classifications were assigned: (i) <2.9-FC, susceptible; (ii) ≥2.9- to 10-FC, partially resistant; and (iii) >10-FC, fully resistant. The Stanford HIVdb-v8.4 was used for genotype predictions merging the susceptible/potential low-level and low-level/intermediate groups for 3 × 3 comparison. Fifty-four of a hundred samples had reduced ETR susceptibility (≥2.9-FC). The FC correlated with HIVdb-v8.4 (Spearman's rho = 0.62; P < 0.0001); however, 44% of samples were partially (1 resistance classification difference) and 4% completely discordant (2 resistance classification differences). Of the 34 samples with an FC of >10, 26 were HIVdb-v8.4 classified as low-intermediate resistant. Mutations L100I, Y181C, or M230L were present in 27/34 (79%) of samples with an FC of >10 but only in 2/46 (4%) of samples with an FC of <2.9. No other mutations were associated with ETR resistance. Viruses containing the mutation K65R were associated with reduced ETR susceptibility, but 65R reversions did not increase ETR susceptibility. Therefore, genotypic interpretation systems were found to misclassify ETR susceptibility in HIV-1 subtype C samples. Modifications to genotypic algorithms are needed to improve the prediction of ETR resistance for the HIV-1 subtype C.
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10
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Chrysostomou AC, Topcu C, Stylianou DC, Hezka J, Kostrikis LG. Development of a new comprehensive HIV-1 genotypic drug resistance assay for all commercially available reverse transcriptase, protease and integrase inhibitors in patients infected with group M HIV-1 strains. INFECTION GENETICS AND EVOLUTION 2020; 81:104243. [PMID: 32061896 DOI: 10.1016/j.meegid.2020.104243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 12/28/2022]
Abstract
Comprehensive PCR assays for the genotypic drug resistance analysis of all HIV-1 antiretroviral agents (reverse transcriptase, protease and integrase inhibitors) are increasingly in demand due to introduction of integrase inhibitors in the first line regimens and the increasing presence of non-B HIV-1 clades around the world. This study focused on the development and evaluation of a new PCR-based assay for the amplification and sequencing of the entire HIV-1 pol region of major circulating group M HIV-1 strains in Europe for genotypic drug resistance analysis. The comprehensive touchdown PCR assay developed in this study utilized HIV-1 RNA extracted from the plasma of blood samples of consenting HIV-1 infected patients in Cyprus, collected from 2017 to 2019. The HIV-1 pol region was amplified by touchdown PCR for both the primary RT-PCR and the secondary PCR steps. Successful PCR amplicons were determined by population DNA sequencing, using the Sanger method and the genotypic drug resistance analysis was performed with the Stanford University HIV Drug Resistance Database Program. The newly developed assay successfully amplified the entire HIV-1 pol region (2844 nucleotides long) of 141 out of 144 samples of group M HIV-1 subtypes and recombinant strains of the Cyprus HIV-1 Transmission Cohort Study (CHICS) isolated from 2017 to 2019 and genotypic analyses were conducted for all currently available HIV-1 reverse transcriptase, protease and integrase inhibitors. The drug resistance, epidemiological and demographic data of these study subjects will be expanded upon in the CHICS (L.G. Kostrikis et al., manuscript in preparation for publication). The newly developed HIV-1 genotypic drug resistance assay would benefit clinical settings, and research focusing on the world-wide spread of HIV-1 drug-resistant strains, especially in geographic regions characterized by polyphyletic HIV-1 infections.
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Affiliation(s)
- Andreas C Chrysostomou
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus
| | - Cicek Topcu
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus
| | - Dora C Stylianou
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus
| | - Johana Hezka
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus
| | - Leondios G Kostrikis
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus.
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11
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Seatla KK, Choga WT, Mogwele M, Diphoko T, Maruapula D, Mupfumi L, Musonda RM, Rowley CF, Avalos A, Kasvosve I, Moyo S, Gaseitsiwe S. Comparison of an in-house 'home-brew' and commercial ViroSeq integrase genotyping assays on HIV-1 subtype C samples. PLoS One 2019; 14:e0224292. [PMID: 31751353 PMCID: PMC6871785 DOI: 10.1371/journal.pone.0224292] [Citation(s) in RCA: 6] [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: 06/03/2019] [Accepted: 10/09/2019] [Indexed: 12/22/2022] Open
Abstract
Background Roll-out of Integrase Strand Transfer Inhibitors (INSTIs) such as dolutegravir for HIV combination antiretroviral therapy (cART) in sub-Saharan Africa necessitates the development of affordable HIV drug resistance (HIVDR) assays targeting the Integrase gene. We optimised and evaluated an in-house integrase HIV-1 drug resistance assay (IH-Int) and compared it to a commercially available assay, ViroSeq™ Integrase Genotyping kit (VS-Int) amongst HIV-1 clade C infected individuals. Methods We used 54 plasma samples from treatment naïve participants and one plasma sample from a patient failing INSTI based cART. Specimens were genotyped using both the VS-Int and IH-Int assays. Stanford HIV drug resistance database were used for integrase resistance interpretation. We compared the major and minor resistance mutations, pairwise nucleotide and amino-acid identity, costs and assay time. Results Among 55 specimens tested with IH-Int, 53 (96.4%) successfully amplified compared to 45/55 (81.8%) for the VS-Int assay. The mean nucleotide and amino acid similarity from 33 paired sequences was 99.8% (SD ± 0.30) and 99.8% (SD ± 0.39) for the IH-Int and VS-Int assay respectively. The reagent cost/sample were 32 USD and 147 USD for IH-Int and VS-Int assay, respectively. All sequenced samples were confirmed as HIV-1 subtype C. Conclusions The IH-Int assay had a high amplification success rate and high concordance with the commercial assay. It is significantly cheaper compared to the commercial assay. Our assay has the needed specifications for routine monitoring of participants on Dolutegravir based regimens in Botswana.
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Affiliation(s)
- Kaelo K. Seatla
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana
| | - Wonderful T. Choga
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mompati Mogwele
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana
| | - Thabo Diphoko
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana
| | - Lucy Mupfumi
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana
| | - Rosemary M. Musonda
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Christopher F. Rowley
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Ava Avalos
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Careena Centre for Health, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
| | - Ishmael Kasvosve
- Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
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12
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Penrose KJ, Brumme CJ, Scoulos-Hanson M, Hamanishi K, Gordon K, Viana RV, Wallis CL, Harrigan PR, Mellors JW, Parikh UM. Frequent cross-resistance to rilpivirine among subtype C HIV-1 from first-line antiretroviral therapy failures in South Africa. Antivir Chem Chemother 2019; 26:2040206618762985. [PMID: 29566538 PMCID: PMC5890541 DOI: 10.1177/2040206618762985] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background Rilpivirine (TMC278LA) is a promising drug for pre-exposure prophylaxis of HIV-1 because of its sub-nanomolar potency and long-acting formulation; however, increasing transmission of non-nucleoside reverse transcriptase inhibitor-resistant HIV-1 with potential cross-resistance to rilpivirine could reduce its preventive efficacy. This study investigated rilpivirine cross-resistance among recombinant subtype C HIV-1 derived from 100 individuals failing on first-line non-nucleoside reverse transcriptase inhibitor-containing antiretroviral therapy in South Africa whose samples were sent for routine HIV-1 drug resistance testing to Lancet Laboratories (Johannesburg, South Africa). Methods Plasma samples were selected from individuals with HIV-1 RNA > 10,000 copies/ml and ≥1 non-nucleoside reverse transcriptase inhibitor-resistance mutation in reverse transcriptase. Recombinant HIV-1LAI-containing bulk-cloned full-length reverse transcriptase sequences from plasma were assayed for susceptibility to nevirapine (NVP), efavirenz (EFV) and rilpivirine in TZM-bl cells. Fold-change (FC) decreases in drug susceptibility were calculated against a mean IC50 from 12 subtype C HIV-1 samples from treatment-naïve individuals in South Africa. Cross-resistance was evaluated based on biological cutoffs established for rilpivirine (2.5-FC) and the effect of mutation combinations on rilpivirine phenotype. Results Of the 100 samples from individuals on failing antiretroviral therapy, 69 had 2.5- to 75-fold decreased susceptibility to rilpivirine and 11 had >75-fold resistance. Rilpivirine resistance was strongly associated with K103N especially in combination with other rilpivirine-associated mutations. Conclusion The frequently observed cross-resistance of HIV-1 suggests that the preventive efficacy of TMC278LA pre-exposure prophylaxis could be compromised by transmission of HIV-1 from individuals with failure of first-line non-nucleoside reverse transcriptase inhibitor-containing antiretroviral therapy.
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Affiliation(s)
- Kerri J Penrose
- 1 Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Chanson J Brumme
- 2 Laboratory Program, 198129 British Columbia Centre for Excellence in HIV/AIDS , Vancouver, British Columbia, Canada
| | - Maritsa Scoulos-Hanson
- 1 Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kristen Hamanishi
- 1 Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kelley Gordon
- 1 Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Raquel V Viana
- 3 Specialty Molecular Division, BARC-SA and Lancet Laboratories, Johannesburg, South Africa
| | - Carole L Wallis
- 3 Specialty Molecular Division, BARC-SA and Lancet Laboratories, Johannesburg, South Africa
| | - P Richard Harrigan
- 2 Laboratory Program, 198129 British Columbia Centre for Excellence in HIV/AIDS , Vancouver, British Columbia, Canada
| | - John W Mellors
- 1 Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Urvi M Parikh
- 1 Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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13
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Praparattanapan J, Tragoolpua Y, Wongtrakul J, Kotarathitithum W, Chaiwarith R, Nuntachit N, Sirisanthana T, Supparatpinyo K. Comparison of in-house HIV-1 genotypic drug resistant test with commercial HIV-1 genotypic test kit. ASIAN BIOMED 2017. [DOI: 10.5372/1905-7415.0502.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Abstract
Background: The use of combination antiretroviral therapy (cART) has become a standard of care in the treatment of HIV infection. However, antiretroviral drug resistance occurs in a substantial number of patients. In resource-limited settings, genotypic resistance assay using a commercial kit is costly.
Objective: Focus on the validation of an in-house HIV-1 specific genotypic drug resistance assay in Thai patients failing cART.
Materials and methods: Results of HIV-1 genotypic drug resistance assay was evaluated by comparing an inhouse method to a commercial test. The TRUGENE HIV-1 genotyping kit was used in 79 plasma specimens (49 from HIV patients failing cART therapy and 30 from proficiency testing panels).
Results: The results from the in-house assay were comparable to those obtained from the TRUGENE HIV-1 genotyping kit with >99.0% codon-to-codon agreement. The lower limit of detection by the in-house assay was approximately 100 copies/mL of HIV-1 RNA. In addition, this in-house assay would allow testing of samples from patients infected with HIV-1 subtype other than B.
Conclusion: The in-house HIV-1 genotypic drug resistance assay may be used as an alternative to commercial kits, particularly in resource limited settings.
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Affiliation(s)
- Jutarat Praparattanapan
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand Thailand
- Department of Medicine, Faculty of Medicine; Chiang Mai University, Chiang Mai 50200, Thailand
| | - Yingmanee Tragoolpua
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jeerang Wongtrakul
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Wilai Kotarathitithum
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Romanee Chaiwarith
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nontakan Nuntachit
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thira Sirisanthana
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Khuanchai Supparatpinyo
- Correspondence to: Department of Medicine, Faculty of Medicine Chiang Mai University, Chiang Mai 50200, Thailand Thailand
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
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14
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Frequent Cross-Resistance to Dapivirine in HIV-1 Subtype C-Infected Individuals after First-Line Antiretroviral Therapy Failure in South Africa. Antimicrob Agents Chemother 2017; 61:AAC.01805-16. [PMID: 27895013 DOI: 10.1128/aac.01805-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/04/2016] [Indexed: 12/18/2022] Open
Abstract
A vaginal ring containing dapivirine (DPV) has shown moderate protective efficacy against HIV-1 acquisition, but the activity of DPV against efavirenz (EFV)- and nevirapine (NVP)-resistant viruses that could be transmitted is not well defined. We investigated DPV cross-resistance of subtype C HIV-1 from individuals on failing NVP- or EFV-containing antiretroviral therapy (ART) in South Africa. Plasma samples were obtained from individuals with >10,000 copies of HIV RNA/ml and with HIV-1 containing at least one non-nucleoside reverse transcriptase (NNRTI) mutation. Susceptibility to NVP, EFV, and DPV in TZM-bl cells was determined for recombinant HIV-1LAI containing bulk-amplified, plasma-derived, full-length reverse transcriptase sequences. Fold change (FC) values were calculated compared with a composite 50% inhibitory concentration (IC50) from 12 recombinant subtype C HIV-1LAI plasma-derived viruses from treatment-naive individuals in South Africa. A total of 25/100 (25%) samples showed >500-FCs to DPV compared to treatment-naive samples with IC50s exceeding the maximum DPV concentration tested (132 ng/ml). A total of 66/100 (66%) samples displayed 3- to 306-FCs, with a median IC50 of 17.6 ng/ml. Only 9/100 (9%) samples were susceptible to DPV (FC < 3). Mutations L100I and K103N were significantly more frequent in samples with >500-fold resistance to DPV compared to samples with a ≤500-fold resistance. A total of 91% of samples with NNRTI-resistant HIV-1 from individuals on failing first-line ART in South Africa exhibited ≥3-fold cross-resistance to DPV. This level of resistance exceeds expected plasma concentrations, but very high genital tract DPV concentrations from DPV ring use could block viral replication. It is critically important to assess the frequency of transmitted and selected DPV resistance in individuals using the DPV ring.
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15
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Boender TS, Hamers RL, Ondoa P, Wellington M, Chimbetete C, Siwale M, Labib Maksimos EEF, Balinda SN, Kityo CM, Adeyemo TA, Akanmu AS, Mandaliya K, Botes ME, Stevens W, Rinke de Wit TF, Sigaloff KCE. Protease Inhibitor Resistance in the First 3 Years of Second-Line Antiretroviral Therapy for HIV-1 in Sub-Saharan Africa. J Infect Dis 2016; 214:873-83. [PMID: 27402780 DOI: 10.1093/infdis/jiw219] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/19/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND As antiretroviral therapy (ART) programs in sub-Saharan Africa mature, increasing numbers of persons with human immunodeficiency virus (HIV) infection will experience treatment failure, and require second- or third-line ART. Data on second-line failure and development of protease inhibitor (PI) resistance in sub-Saharan Africa are scarce. METHODS HIV-1-infected adults were included if they received >180 days of PI-based second-line ART. We assessed risk factors for having a detectable viral load (VL, ≥400 cps/mL) using Cox models. If VL was ≥1000 cps/mL, genotyping was performed. RESULTS Of 227 included participants, 14.6%, 15.2% and 11.1% had VLs ≥400 cps/mL at 12, 24, and 36 months, respectively. Risk factors for a detectable VL were as follows: exposure to nonstandard nonnucleoside reverse-transcriptase inhibitor (NNRTI)-based (hazard ratio, 7.10; 95% confidence interval, 3.40-14.83; P < .001) or PI-based (7.59; 3.02-19.07; P = .001) first-line regimen compared with zidovudine/lamivudine/NNRTI, PI resistance at switch (6.69; 2.49-17.98; P < .001), and suboptimal adherence (3.05; 1.71-5.42; P = .025). Among participants with VLs ≥1000 cps/mL, 22 of 32 (69%) harbored drug resistance mutation(s), and 7 of 32 (22%) harbored PI resistance. CONCLUSIONS Although VL suppression rates were high, PI resistance was detected in 22% of participants with VLs ≥1000 cps/mL. To ensure long-term ART success, intensified support for adherence, VL and drug resistance testing, and third-line drugs will be necessary.
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Affiliation(s)
- T Sonia Boender
- Amsterdam Institute for Global Health and Development, Department of Global Health
| | - Raph L Hamers
- Amsterdam Institute for Global Health and Development, Department of Global Health Department of Internal Medicine, Division of Infectious Diseases, Academic Medical Center, University of Amsterdam, The Netherlands
| | - Pascale Ondoa
- Amsterdam Institute for Global Health and Development, Department of Global Health
| | | | | | | | | | | | | | - Titilope A Adeyemo
- Department of Haematology & Blood transfusion, College of Medicine of the University of Lagos, Nigeria
| | - Alani Sulaimon Akanmu
- Department of Haematology & Blood transfusion, College of Medicine of the University of Lagos, Nigeria
| | | | | | - Wendy Stevens
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, and the National Health Laboratory Service, Johannesburg, South Africa
| | | | - Kim C E Sigaloff
- Amsterdam Institute for Global Health and Development, Department of Global Health Department of Internal Medicine, Division of Infectious Diseases, Academic Medical Center, University of Amsterdam, The Netherlands
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16
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Fox MP, Berhanu R, Steegen K, Firnhaber C, Ive P, Spencer D, Mashamaite S, Sheik S, Jonker I, Howell P, Long L, Evans D. Intensive adherence counselling for HIV-infected individuals failing second-line antiretroviral therapy in Johannesburg, South Africa. Trop Med Int Health 2016; 21:1131-7. [PMID: 27383454 DOI: 10.1111/tmi.12741] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OBJECTIVE In resource-limited settings, where genotypic drug resistance testing is rarely performed and poor adherence is the most common reason for treatment failure, programmatic approaches to handling treatment failure are essential. This study was performed to describe one such approach to adherence optimisation. METHODS This was a single-arm study of patients on second-line protease inhibitor (PI)-based antiretroviral therapy (ART) with a HIV-1 RNA ≥400 copies/ml in Johannesburg, South Africa, between 1 March 2012 and 1 December 2013. Patients underwent enhanced adherence counselling. Those with improved adherence and a repeat viral load of >1000 copies/ml underwent HIV-1 drug resistance testing. We describe results using simple proportions and 95% confidence intervals. RESULTS Of the 400 patients who underwent targeted adherence counselling after an elevated viral load on second-line ART, 388 (97%) underwent repeat viral load testing. Most of these (n = 249; 64%, 95% CI 59-69) resuppressed (<400 copies/ml) on second line. By the end of follow-up (1 March 2014), among the 139 (36%, 95% CI: 31-41%), who did not initially resuppress after being targeted, 106 had a viral load >400 copies/ml, 11 switched to third line, 5 were awaiting third line, 4 had died and 13 were lost to follow-up. Among the unsuppressed, 48 successfully underwent resistance testing with some resistance detected in most (41/48). CONCLUSIONS Most (64%) second-line treatment failure in this clinic is related to adherence and can be overcome with careful adherence support. Controlled interventions are needed to determine what the optimal approach is to improving second-line outcomes and reducing the need for third-line ART.
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Affiliation(s)
- Matthew P Fox
- Health Economics and Epidemiology Research Office, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Global Health, Boston University School of Public Health, Boston, MA, USA.,Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Rebecca Berhanu
- Health Economics and Epidemiology Research Office, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Right to Care, Johannesburg, South Africa
| | - Kim Steegen
- Department of Haematology and Molecular Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cindy Firnhaber
- Right to Care, Johannesburg, South Africa.,Clinical HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Prudence Ive
- Clinical HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | | | - Ingrid Jonker
- Witkoppen Health and Welfare Center, Johannesburg, South Africa
| | - Pauline Howell
- Department of Haematology and Molecular Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lawrence Long
- Health Economics and Epidemiology Research Office, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Denise Evans
- Health Economics and Epidemiology Research Office, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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17
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Boender TS, Kityo CM, Boerma RS, Hamers RL, Ondoa P, Wellington M, Siwale M, Nankya I, Kaudha E, Akanmu AS, Botes ME, Steegen K, Calis JCJ, Rinke de Wit TF, Sigaloff KCE. Accumulation of HIV-1 drug resistance after continued virological failure on first-line ART in adults and children in sub-Saharan Africa. J Antimicrob Chemother 2016; 71:2918-27. [PMID: 27342546 DOI: 10.1093/jac/dkw218] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/09/2016] [Indexed: 01/17/2023] Open
Abstract
OBJECTIVES Limited availability of viral load (VL) monitoring in HIV treatment programmes in sub-Saharan Africa can delay switching to second-line ART, leading to the accumulation of drug resistance mutations (DRMs). The objective of this study was to evaluate the accumulation of resistance to reverse transcriptase inhibitors after continued virological failure on first-line ART, among adults and children in sub-Saharan Africa. METHODS HIV-1-positive adults and children on an NNRTI-based first-line ART were included. Retrospective VL and, if VL ≥1000 copies/mL, pol genotypic testing was performed. Among participants with continued virological failure (≥2 VL ≥1000 copies/mL), drug resistance was evaluated. RESULTS At first virological failure, DRM(s) were detected in 87% of participants: K103N (38.7%), G190A (21.8%), Y181C (20.2%), V106M (8.4%), K101E (8.4%), any E138 (7.6%) and V108I (7.6%) associated with NNRTIs, and M184V (69.7%), any thymidine analogue mutation (9.2%), K65R (5.9%) and K70R (5.0%) associated with NRTIs. New DRMs accumulated with an average rate of 1.45 (SD 2.07) DRM per year; 0.62 (SD 1.11) NNRTI DRMs and 0.84 (SD 1.38) NRTI DRMs per year, respectively. The predicted susceptibility declined significantly after continued virological failure for all reverse transcriptase inhibitors (all P < 0.001). Acquired drug resistance patterns were similar in adults and children. CONCLUSIONS Patterns of drug resistance after virological failure on first-line ART are similar in adults and children in sub-Saharan Africa. Improved VL monitoring to prevent accumulation of mutations, and new drug classes to construct fully active regimens, are required.
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Affiliation(s)
- T Sonia Boender
- Amsterdam Institute for Global Health and Development, Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands Global Child Health Group, Emma Children's Hospital/Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | | | - Ragna S Boerma
- Amsterdam Institute for Global Health and Development, Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands Global Child Health Group, Emma Children's Hospital/Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Raph L Hamers
- Amsterdam Institute for Global Health and Development, Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands Department of Internal Medicine, Division of Infectious Diseases, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Pascale Ondoa
- Amsterdam Institute for Global Health and Development, Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | | | | | | | | | - Alani Sulaimon Akanmu
- Department of Haematology and Blood Transfusion, College of Medicine of the University of Lagos, Lagos, Nigeria
| | | | - Kim Steegen
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Job C J Calis
- Global Child Health Group, Emma Children's Hospital/Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands Department of Pediatric Intensive Care, Emma Children's Hospital/Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Tobias F Rinke de Wit
- Amsterdam Institute for Global Health and Development, Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Kim C E Sigaloff
- Amsterdam Institute for Global Health and Development, Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands Department of Internal Medicine, Division of Infectious Diseases, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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Mungati M, Mhangara M, Gonese E, Mugurungi O, Dzangare J, Ngwende S, Musasa P, Wellington M, Shambira G, Apollo T, Yang C, DeVos J, Sabatier J, Kilmarx P, Chakanyuka-Musanhu C, Tshimanga M. Pre-treatment drug resistance among patients initiating antiretroviral therapy (ART) in Zimbabwe: 2008-2010. BMC Res Notes 2016; 9:302. [PMID: 27287672 PMCID: PMC4902981 DOI: 10.1186/s13104-016-2101-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 05/25/2016] [Indexed: 11/16/2022] Open
Abstract
Background Zimbabwe set up 12 sentinel sites to monitor HIV drug resistance (HIVDR) following the international standards for prevention of HIVDR from 2008 to 2010. Methods Participants were consecutively enrolled. Blood was collected and used for CD4 count, viral load (VL) and pre-treatment DR (PDR) tests besides routine baseline tests. We analyzed the characteristics of participants enrolled into the survey and estimated the point prevalence of PDR and its associated factors among ART initiators in a cross-sectional analysis using the baseline data collected from a prospective cohort in 12 purposefully selected sentinel sites. Results A total of 1728 participants (96 % response rate) were enrolled and 1610 had complete data. Of the 1610 there were more females (68.7 %) than males (31.3 %). The median CD4 count was 168 cells/mm3 with males having lower values (P = 0.003). Ninety-six percent of participants had a VL ≥ 1000 copies/ml and the median VL was 128,000. Previous exposure to antiretroviral drugs (ARVs) was mainly through PMTCT (5 % of the participants). Overall, PDR mutations were detected in 6.3 % (95 % CI 5.2–7.7) of the 1480 successfully genotyped participants. However, the prevalence of PDR mutations was double for those with previous exposure (12.1 %) to ARVs compared with those without previous exposure (5.7 %, P = 0.002). Conclusions The results show a moderate level of PDR prevalence among ART initiators. To maintain the efficacy of the current first-line regimens, there is need to strengthen all HIVDR prevention efforts and to conduct further studies to investigate optimal strategies that can prolong the efficacy of first-line ARV regimens in the country.
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Affiliation(s)
- More Mungati
- Ministry of Health and Child Care, Harare, Zimbabwe. .,Department of Community Medicine, University of Zimbabwe, Harare, Zimbabwe.
| | | | | | | | | | - Stella Ngwende
- National Microbiology Reference Laboratory (NMRL), Harare, Zimbabwe
| | - Patience Musasa
- National Microbiology Reference Laboratory (NMRL), Harare, Zimbabwe
| | | | - Gerald Shambira
- Department of Community Medicine, University of Zimbabwe, Harare, Zimbabwe
| | | | - Chunfu Yang
- Center for Disease Control and Prevention, Atlanta, GA, USA
| | - Joshua DeVos
- Center for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Peter Kilmarx
- Centers for Disease Control and Prevention, Harare, Zimbabwe
| | | | - Mufuta Tshimanga
- Department of Community Medicine, University of Zimbabwe, Harare, Zimbabwe
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Rowley CF, MacLeod IJ, Maruapula D, Lekoko B, Gaseitsiwe S, Mine M, Essex M. Sharp increase in rates of HIV transmitted drug resistance at antenatal clinics in Botswana demonstrates the need for routine surveillance. J Antimicrob Chemother 2016; 71:1361-6. [PMID: 26929269 DOI: 10.1093/jac/dkv500] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/26/2015] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The aim of the study was to evaluate for the presence of drug resistance to HIV medications in treatment-naive individuals in Botswana. METHODS Two different populations were evaluated for evidence of HIV drug resistance at three different geographical locations in Botswana. In the first study population, consisting of pregnant females diagnosed with HIV during pregnancy, participants were enrolled at the time of their HIV diagnosis. The second population included pre-ART enrollees at Infectious Diseases Care Clinics (IDCCs) who had a CD4 T cell count >350 cells/μL. RESULTS A total of 422 genotypes were determined: 234 for samples from antenatal clinic (ANC) participants and 188 for samples from IDCC participants. Between 2012 and 2014, 6 of 172 (3.5%) genotypes from ANC participants exhibited transmitted drug resistance (TDR), with 3 (1.7%) showing resistance to first-line ART. In a subset of samples from Gaborone, Botswana's capital and largest city, the TDR rate was 3 in 105 (2.9%), but only 1 in 105 (1.0%) showed first-line ART resistance. Between December 2014 and April 2015, the rate of resistance to any ART in Gaborone was 6 in 62 (9.7%), with 5 (8.1%) exhibiting first-line ART resistance. CONCLUSIONS These data demonstrate that TDR rates for HIV differ geographically and temporally in Botswana, with significant increases in TDR observed at ANCs in Gaborone between 2012 and 2015. These findings stress the importance of continued testing for TDR, particularly as access to HIV treatment increases and guidelines recommend treatment at the time of HIV diagnosis.
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Affiliation(s)
- C F Rowley
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA Harvard School of Public Health, Boston, MA, USA
| | - I J MacLeod
- Harvard School of Public Health, Boston, MA, USA
| | - D Maruapula
- Botswana Harvard AIDS Institute, Gaborone, Botswana
| | - B Lekoko
- Botswana Harvard AIDS Institute, Gaborone, Botswana
| | - S Gaseitsiwe
- Botswana Harvard AIDS Institute, Gaborone, Botswana
| | - M Mine
- Botswana Ministry of Health, Gaborone, Botswana
| | - M Essex
- Harvard School of Public Health, Boston, MA, USA Botswana Harvard AIDS Institute, Gaborone, Botswana
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Aitken SC, Wallis CL, Stevens W, de Wit TR, Schuurman R. Stability of HIV-1 Nucleic Acids in Dried Blood Spot Samples for HIV-1 Drug Resistance Genotyping. PLoS One 2015; 10:e0131541. [PMID: 26147689 PMCID: PMC4493047 DOI: 10.1371/journal.pone.0131541] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 06/03/2015] [Indexed: 11/19/2022] Open
Abstract
Dried blood spots (DBS) are an easy to collect sample-type that can stabilize biological material at ambient temperature for transport and storage, making them ideal for use in resource-limited settings (RLS). We investigated the effect of storage temperature and duration on ability to detect mixed HIV-1 viral RNA populations, and subsequently viral RNA populations in a background of proviral DNA. Part one of the study used DBS samples of whole blood spiked with specific quantities of HIV-1 subtype-B and -C RNA to study mixed virus population detection. Part two used DBS comprising of HIV-1 subtype-B proviral DNA containing U1 cells combined with HIV-1 subtype-C RNA to mimic HIV-1 infected clinical samples as a model system to study the relative stability of HIV-1 RNA and DNA in DBS. Prepared DBS were stored at -20 °C and +30 °C for periods of one day, one, two, and four weeks. Samples were genotyped to determine changes in the detection of mixtures in the sample over time. From two weeks onwards, storage at +30 °C resulted in gradual, time-related reduction in the detection of mixed virus population at log10 VL 4.0 but not at log10 5.0. Proviral DNA and viral RNA were both stable for at least 52 weeks when stored at -20 °C, compared to progressive RNA decay over time at +30 °C. DBS storage conditions and duration had a significant effect on HIV-1 RNA amplification. Our results demonstrate that DBS storage at ambient temperature (+30 °C) should not exceed two weeks, with long-term storage at -20 °C or lower.
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Affiliation(s)
- Susan C. Aitken
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | - Wendy Stevens
- Department of Molecular Medicine and Hematology, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
| | - Tobias Rinke de Wit
- PharmAccess International, Amsterdam, The Netherlands
- Global Health Department, Amsterdam Institute for Global Health and Development (AIGHD), Academic Medical Center, Amsterdam, the Netherlands
| | - Rob Schuurman
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
- * E-mail:
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Long-Range HIV Genotyping Using Viral RNA and Proviral DNA for Analysis of HIV Drug Resistance and HIV Clustering. J Clin Microbiol 2015; 53:2581-92. [PMID: 26041893 DOI: 10.1128/jcm.00756-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/26/2015] [Indexed: 12/15/2022] Open
Abstract
The goal of the study was to improve the methodology of HIV genotyping for analysis of HIV drug resistance and HIV clustering. Using the protocol of Gall et al. (A. Gall, B. Ferns, C. Morris, S. Watson, M. Cotten, M. Robinson, N. Berry, D. Pillay, and P. Kellam, J Clin Microbiol 50:3838-3844, 2012, doi:10.1128/JCM.01516-12), we developed a robust methodology for amplification of two large fragments of viral genome covering about 80% of the unique HIV-1 genome sequence. Importantly, this method can be applied to both viral RNA and proviral DNA amplification templates, allowing genotyping in HIV-infected subjects with suppressed viral loads (e.g., subjects on antiretroviral therapy [ART]). The two amplicons cover critical regions across the HIV-1 genome (including pol and env), allowing analysis of mutations associated with resistance to protease inhibitors, reverse transcriptase inhibitors (nucleoside reverse transcriptase inhibitors [NRTIs] and nonnucleoside reverse transcriptase inhibitors [NNRTIs]), integrase strand transfer inhibitors, and virus entry inhibitors. The two amplicons generated span 7,124 bp, providing substantial sequence length and numbers of informative sites for comprehensive phylogenic analysis and greater refinement of viral linkage analyses in HIV prevention studies. The long-range HIV genotyping from proviral DNA was successful in about 90% of 212 targeted blood specimens collected in a cohort where the majority of patients had suppressed viral loads, including 65% of patients with undetectable levels of HIV-1 RNA loads. The generated amplicons could be sequenced by different methods, such as population Sanger sequencing, single-genome sequencing, or next-generation ultradeep sequencing. The developed method is cost-effective-the cost of the long-range HIV genotyping is under $140 per subject (by Sanger sequencing)-and has the potential to enable the scale up of public health HIV prevention interventions.
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Seu L, Mulenga LB, Siwingwa M, Sikazwe I, Lambwe N, Guffey MB, Chi BH. Characterization of HIV drug resistance mutations among patients failing first-line antiretroviral therapy from a tertiary referral center in Lusaka, Zambia. J Med Virol 2015; 87:1149-57. [PMID: 25754408 DOI: 10.1002/jmv.24162] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2015] [Indexed: 11/10/2022]
Abstract
In settings of resource constraint, an understanding of HIV drug resistance can guide antiretroviral therapy (ART) at switch to second-line therapy. To determine the prevalence of such HIV drug resistance mutations (HIV DRM), we used an in-house sequencing assay in the pol gene (protease and partial reverse transcriptase) in a cohort of patients suspected of failing a first-line regimen, which in Zambia comprises two nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) and one non-nucleoside reverse transcriptase inhibitor (NNRTI). Our analysis cohort (n = 68) was referred to the University Teaching Hospital in Lusaka from November 2009 to October 2012. Median duration on first-line ART to suspected treatment failure was 3.2 years (IQR 1.7-4.7 years). The majority of patients (95%) harbored HIV-1 subtype C virus. Analysis of reverse transcriptase revealed M184V (88%), K103N/S (32%), and Y181C/I/V (41%) DRMs, with the latter conferring reduced susceptibility to the salvage therapy candidates etravirine and rilpivirine. Three patients (5%) had major protease inhibitor (PI) resistance mutations: all three had the V82A mutation, and one patient (Clade J virus) had a concurrent M46I, Q58E, and L76V DRM. HIV-1 genotyping revealed major and minor DRMs as well as high levels of polymorphisms in subtype C isolates from patients failing first-line antiretroviral therapy. Closer monitoring of DRM mutations at first-line failure can inform clinicians about future options for salvage therapy.
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Affiliation(s)
- Lillian Seu
- School of Medicine, University of Alabama at Birmingham, Alabama; Centre for Infectious Disease Research Zambia, Lusaka, Zambia
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Alemán Y, Vinken L, Kourí V, Pérez L, Álvarez A, Abrahantes Y, Fonseca C, Pérez J, Correa C, Soto Y, Schrooten Y, Vandamme AM, Van Laethem K. Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba. PLoS One 2015; 10:e0117176. [PMID: 25671421 PMCID: PMC4324769 DOI: 10.1371/journal.pone.0117176] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 12/19/2014] [Indexed: 11/20/2022] Open
Abstract
As commercial human immunodeficiency virus type 1 drug resistance assays are expensive, they are not commonly used in resource-limited settings. Hence, a more affordable in-house procedure was set up taking into account the specific epidemiological and economic circumstances of Cuba. The performance characteristics of the in-house assay were evaluated using clinical samples with various subtypes and resistance patterns. The lower limit of amplification was determined on dilutions series of 20 clinical isolates and ranged from 84 to 529 RNA copies/mL. For the assessment of trueness, 14 clinical samples were analyzed and the ViroSeq HIV-1 Genotyping System v2.0 was used as the reference standard. The mean nucleotide sequence identity between the two assays was 98.7% ± 1.0. Additionally, 99.0% of the amino acids at drug resistance positions were identical. The sensitivity and specificity in detecting drug resistance mutations was respectively 94.1% and 99.5%. Only few discordances in drug resistance interpretation patterns were observed. The repeatability and reproducibility were evaluated using 10 clinical samples with 3 replicates per sample. The in-house test was very precise as nucleotide sequence identity among paired nucleotide sequences ranged from 98.7% to 99.9%. The acceptance criteria were met by the in-house test for all performance characteristics, demonstrating a high degree of accuracy. Subsequently, the applicability in routine clinical practice was evaluated on 380 plasma samples. The amplification success rate was 91% and good quality consensus sequences encoding the entire protease and the first 335 codons in reverse transcriptase could be obtained for 99% of the successful amplicons. The reagent cost per sample using the in-house procedure was around € 80 per genotyping attempt. Overall, the in-house assay provided good results, was feasible with equipment and reagents available in Cuba and was half as expensive as commercial assays.
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Affiliation(s)
- Yoan Alemán
- Virology Department, Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Lore Vinken
- Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Vivian Kourí
- Virology Department, Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Lissette Pérez
- Virology Department, Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Alina Álvarez
- Virology Department, Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Yeissel Abrahantes
- Hospital at Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Carlos Fonseca
- Hospital at Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Jorge Pérez
- Hospital at Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Consuelo Correa
- Virology Department, Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Yudira Soto
- Virology Department, Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Yoeri Schrooten
- Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Anne-Mieke Vandamme
- Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- Centro de Malária e outras Doenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universida de Nova de Lisboa, Lisboa, Portugal
| | - Kristel Van Laethem
- Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- * E-mail:
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Skhosana L, Steegen K, Bronze M, Lukhwareni A, Letsoalo E, Papathanasopoulos MA, Carmona SC, Stevens WS. High prevalence of the K65R mutation in HIV-1 subtype C infected patients failing tenofovir-based first-line regimens in South Africa. PLoS One 2015; 10:e0118145. [PMID: 25659108 PMCID: PMC4320083 DOI: 10.1371/journal.pone.0118145] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 01/05/2015] [Indexed: 12/04/2022] Open
Abstract
Background Tenofovir (TDF) has replaced stavudine (d4T) as the preferred nucleoside reverse transcriptase inhibitor (NRTI) in first-line regimens in South Africa, but limited information is available on the resistance patterns that develop after the introduction of TDF. This study investigated the antiretroviral drug resistance patterns in South African HIV-1 subtype C-infected patients failing stavudine- (d4T) and tenofovir- (TDF) based first-line regimens and assess the suitability of TDF as the preferred first-line nucleotide reverse transcriptase inhibitor (NRTI). Methods Resistance patterns of HIV-1 from 160 adult patients virologically failing TDF- (n = 80) and d4T- (n = 80) based first-line regimens were retrospectively analyzed. The pol gene was sequenced using an in-house protocol and mutations were analysed using the IAS-USA 2014 Drug Resistance Mutation list. Results Compared to d4T-exposed patients (n = 7), patients failing on a TDF-containing regimen (n = 43) were almost 5 times more likely to present with a K65R mutation (aRR 4.86 95% CI 2.29 – 10.34). Y115F was absent in the d4T group, and detected in 13.8% (n = 11) of TDF-exposed patients, p = 0.0007. Virus from 9 of the 11 patients (82.0%) who developed the Y115F mutation also developed K65R. Intermediate or high-level resistance to most NRTIs was common in the TDF-treatment group, but these patients twice more likely to remain susceptible to AZT as compared to those exposed to d4T (aRR 2.09 95% CI 1.13 – 3.90). Conclusion The frequency of the TDF induced K65R mutation was higher in our setting compared to non-subtype C dominated countries. However, despite the higher frequency of cross-resistance to NRTIs, most patients remained susceptible to AZT, which is reflected in the South African treatment guidelines that recommend AZT as an essential component of second-line regimens.
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Affiliation(s)
- Lindiwe Skhosana
- Department of Haematology and Molecular Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kim Steegen
- Department of Haematology and Molecular Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
| | - Michelle Bronze
- Department of Haematology and Molecular Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Azwidowi Lukhwareni
- National Health Laboratory Services, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Esrom Letsoalo
- Department of Haematology and Molecular Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maria A. Papathanasopoulos
- Department of Haematology and Molecular Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sergio C. Carmona
- Department of Haematology and Molecular Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Wendy S. Stevens
- Department of Haematology and Molecular Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
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25
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Dudley DM, Bailey AL, Mehta SH, Hughes AL, Kirk GD, Westergaard RP, O'Connor DH. Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq. Retrovirology 2014; 11:122. [PMID: 25533166 PMCID: PMC4302432 DOI: 10.1186/s12977-014-0122-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 12/03/2014] [Indexed: 11/30/2022] Open
Abstract
Background Viral resistance to antiretroviral therapy threatens our best methods to control and prevent HIV infection. Current drug resistance genotyping methods are costly, optimized for subtype B virus, and primarily detect resistance mutations to protease and reverse transcriptase inhibitors. With the increasing use of integrase inhibitors in first-line therapies, monitoring for integrase inhibitor drug resistance mutations is a priority. We designed a universal primer pair to PCR amplify all major group M HIV-1 viruses for genotyping using Illumina MiSeq to simultaneously detect drug resistance mutations associated with protease, nucleoside reverse transcriptase, non-nucleoside reverse transcriptase, and integrase inhibitors. Results A universal primer pair targeting the HIV pol gene was used to successfully PCR amplify HIV isolates representing subtypes A, B, C, D, CRF01_AE and CRF02_AG. The universal primers were then tested on 62 samples from a US cohort of injection drug users failing treatment after release from prison. 94% of the samples were successfully genotyped for known drug resistance mutations in the protease, reverse transcriptase and integrase gene products. Control experiments demonstrate that mutations present at ≥ 2% frequency are reliably detected and above the threshold of error for this method. New drug resistance mutations not found in the baseline sample were identified in 54% of the patient samples after treatment failure. 86% of patients with major drug resistance mutations had 1 or more mutations associated with drug resistance to the treatment regimen at the time point of treatment failure. 59% of the emerging mutations were found at frequencies between 2% and 20% of the total sequences generated, below the estimated limit of detection of current FDA-approved genotyping techniques. Primary plasma samples with viral loads as low as 799 copies/ml were successfully genotyped using this method. Conclusions Here we present an Illumina MiSeq-based HIV drug resistance genotyping assay. Our data suggests that this universal assay works across all major group M HIV-1 subtypes and identifies all drug resistance mutations in the pol gene known to confer resistance to protease, reverse transcriptase and integrase inhibitors. This high-throughput and sensitive assay could significantly improve access to drug resistance genotyping worldwide. Electronic supplementary material The online version of this article (doi:10.1186/s12977-014-0122-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dawn M Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Adam L Bailey
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Shruti H Mehta
- Department of Epidemiology, Epidemiology and Oncology, Johns Hopkins University, Baltimore, MD, USA.
| | - Austin L Hughes
- Department of Biology, University of South Carolina, Columbia, South Carolina, USA.
| | - Gregory D Kirk
- Departments of Medicine, Epidemiology and Oncology, Johns Hopkins University, Baltimore, MD, USA.
| | - Ryan P Westergaard
- Department of Medicine, Division of Infectious Disease, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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Acharya A, Vaniawala S, Shah P, Misra RN, Wani M, Mukhopadhyaya PN. Development, validation and clinical evaluation of a low cost in-house HIV-1 drug resistance genotyping assay for Indian patients. PLoS One 2014; 9:e105790. [PMID: 25157501 PMCID: PMC4144911 DOI: 10.1371/journal.pone.0105790] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/24/2014] [Indexed: 01/08/2023] Open
Abstract
Human Immunodeficiency Virus-1 (HIV-1) drug resistance genotyping assay is a part of clinical management of HIV-1 positive individuals under treatment with highly active antiretroviral therapy (HAART). Routine monitoring of drug resistance mutations in resource limited settings like India is not possible due to high cost of commercial drug resistance assays. In this study we developed an in-house, cost effective HIV-1 drug resistance genotyping assay for Indian patients and validated it against the US-FDA-approved ViroSeq HIV-1 drug resistance testing system. A reference panel of 20 clinical samples was used to develop and validate the assay against ViroSeq HIV-1 drug resistance testing system which was subsequently used to genotype a clinical panel of 225 samples. The Stanford HIV database was used to identify drug resistant mutations. The analytical sensitivity of the assay was 1000 HIV-1 RNA copies/ml of plasma sample while precision and reproducibility was 99.68±0.16% and 99.76±0.18% respectively. One hundred and one drug resistant mutations were detected by the in-house assay compared to 104 by ViroSeq system in the reference panel. The assay had 91.55% success rate in genotyping the clinical panel samples and was able to detect drug resistant mutations related to nucleoside reverse transcriptase inhibitor (NRTI), non-nucleoside reverse-transcriptase inhibitor (NNRTI) as well as protease inhibitor (PI) classes of antiretroviral drugs. It was found to be around 71.9% more cost effective compared to ViroSeq genotyping system. This evaluation of the assay on the clinical panel demonstrates its potential for monitoring clinical HIV-1 drug resistance mutations and population-based surveillance in resource limited settings like India.
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Affiliation(s)
- Arpan Acharya
- Department of Molecular Biology, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Salil Vaniawala
- Department of Molecular Diagnostics, SN Genelab, Surat, Gujarat, India
| | - Parth Shah
- Department of Molecular Diagnostics, Supratech Micropath Laboratory & Research Institute, Ahmedabad, Gujarat, India
| | - Rabindra Nath Misra
- Department of Microbiology, Padmashree Dr. D. Y. Patil Medical College & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Minal Wani
- Department of Molecular Biology, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Pratap N. Mukhopadhyaya
- Department of Microbiology, Interdisciplinary Science, Technology and Research Academy, AISC, Pune, Maharashtra, India
- * E-mail:
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Seu L, Mwape I, Guffey MB. Single genome amplification of proviral HIV-1 DNA from dried blood spot specimens collected during early infant screening programs in Lusaka, Zambia. J Virol Methods 2014; 203:97-101. [PMID: 24667303 PMCID: PMC4024391 DOI: 10.1016/j.jviromet.2014.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 02/28/2014] [Accepted: 03/04/2014] [Indexed: 01/28/2023]
Abstract
The ability to evaluate individual HIV-1 virions from the quasispecies of vertically infected infants was evaluated in a field setting at the Centre for Infectious Disease Research in Zambia. Infant heel-prick blood specimens were spotted onto dried blood spot (DBS) filter paper cards at government health clinics. Nucleic acid was extracted and used as a template for HIV-1 proviral DNA detection by a commercial Amplicor HIV-1 PCR test (Roche, version 1.5). On samples that tested positive by commercial diagnostic assay, amplification of DNA was performed using an in-house assay of the 5' and 3' region of the HIV-1 genome. Additionally, fragments covering 1200 nucleotides within pol (full length protease and partial reverse transcriptase) and 1400 nucleotides within env (variable 1-variable 5 region) were further analyzed by single genome amplification (SGA). In summary, we have demonstrated an in-house assay for amplifying the 5' and 3' proviral HIV-1 DNA as well as pol and env proviral DNA fragments from DBS cards collected and analyzed entirely in Zambia. In conclusion, this study shows the feasibility of utilizing DBS cards to amplify the whole proviral HIV-1 genome as well as perform SGA on key HIV-1 genes.
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Affiliation(s)
- Lillian Seu
- Centre for Infectious Disease Research Zambia, 5032 Great North Road, P.O. Box 34681, Lusaka, Zambia; University of Alabama at Birmingham, Division of Infectious Diseases, 1900 University Boulevard, THT 215E, Birmingham, AL 35294, United States.
| | - Innocent Mwape
- University of Alabama at Birmingham, Division of Infectious Diseases, 1900 University Boulevard, THT 215E, Birmingham, AL 35294, United States.
| | - M Bradford Guffey
- Centre for Infectious Disease Research Zambia, 5032 Great North Road, P.O. Box 34681, Lusaka, Zambia; University of Alabama at Birmingham, Division of Infectious Diseases, 1900 University Boulevard, THT 215E, Birmingham, AL 35294, United States.
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Steegen K, Levin L, Ketseoglou I, Bronze M, Papathanasopoulos MA, Carmona S, Stevens W. High-level cross-resistance to didanosine observed in South African children failing an abacavir- or stavudine-based 1st-line regimen. PLoS One 2014; 9:e97067. [PMID: 24816790 PMCID: PMC4016228 DOI: 10.1371/journal.pone.0097067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 04/14/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The knowledge-base of emerging drug resistance profiles in children exposed to abacavir-based antiretroviral regimens in South Africa is very limited. This study investigated the suitability of didanosine-based 2nd-line regimens for children in the context of antiretroviral drug resistance patterns emerging after 1st-line virologic failure. METHODS A retrospective dataset of 354 antiretroviral drug resistant genotypes from children failing either abacavir (n = 81) or stavudine (n = 273) based 1st-line regimens, was analysed. Samples were sent to the HIV genotyping laboratory at Charlotte Maxeke Johannesburg Academic Hospital, for routine testing. Pol sequences were submitted to the Stanford HIV drug resistance database for genotypic predictions. RESULTS Children were exposed to abacavir or stavudine-based 1st-line regimens for an average of 21 and 36 months, respectively. The frequency of reduced susceptibility to didanosine was substantial in the abacavir-exposed group (69.1%).This reduced susceptibility was commonly attributed to L74V/I (n = 44) and to a lesser extent K65R (n = 10) mutations. Didanosine resistance was observed in 43.2% of patients exposed to stavudine-based regimens. In contrast, most children remained susceptible to stavudine regardless of exposure to abacavir (77.8%) or stavudine (74.7%). At least 80% of children remained susceptible to zidovudine irrespective of stavudine or abacavir-exposure. The presence of the K65R mutation was more common after abacavir pressure (12.3% vs 1.8%). CONCLUSION Analysis revealed that didanosine-based 2nd-line regimens have limitations for South African children, given the high frequency of mutations that confer cross-resistance to didanosine; especially after abacavir-exposure. This data has influenced South African paediatric treatment guidelines, which now recommend zidovudine-based 2nd-line regimens.
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Affiliation(s)
- Kim Steegen
- Department of Haematology and Molecular Medicine, University of Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
- * E-mail:
| | - Leon Levin
- Right to Care, Johannesburg, South Africa
| | - Irene Ketseoglou
- Department of Haematology and Molecular Medicine, University of Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
| | - Michelle Bronze
- Department of Haematology and Molecular Medicine, University of Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
| | - Maria A. Papathanasopoulos
- Department of Haematology and Molecular Medicine, University of Witwatersrand, Johannesburg, South Africa
| | - Sergio Carmona
- Department of Haematology and Molecular Medicine, University of Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
| | - Wendy Stevens
- Department of Haematology and Molecular Medicine, University of Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
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Wallis CL, Aga E, Ribaudo H, Saravanan S, Norton M, Stevens W, Kumarasamy N, Bartlett J, Katzenstein D. Drug susceptibility and resistance mutations after first-line failure in resource limited settings. Clin Infect Dis 2014; 59:706-15. [PMID: 24795328 DOI: 10.1093/cid/ciu314] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The development of drug resistance to nucleoside reverse transcriptase inhibitors (NRTIs) and nonnucleoside reverse transcriptase inhibitors (NNRTIs) has been associated with baseline human immunodeficiency virus (HIV)-1 RNA level (VL), CD4 cell counts (CD4), subtype, and treatment failure duration. This study describes drug resistance and levels of susceptibility after first-line virologic failure in individuals from Thailand, South Africa, India, Malawi, Tanzania. METHODS CD4 and VL were captured at AIDs Clinical Trial Group (ACTG) A5230 study entry, a study of lopinavir/ritonavir (LPV/r) monotherapy after first-line virologic failure on an NNRTI regimen. HIV drug-resistance mutation associations with subtype, site, study entry VL, and CD4 were evaluated using Fisher exact and Kruskall-Wallis tests. RESULTS Of the 207 individuals who were screened for A5230, sequence data were available for 148 individuals. Subtypes observed: subtype C (n = 97, 66%) AE (n = 27, 18%), A1 (n = 12, 8%), and D (n = 10, 7%). Of the 148 individuals, 93% (n = 138) and 96% (n = 142) had at least 1 reverse transcriptase (RT) mutation associated with NRTI and NNRTI resistance, respectively. The number of NRTI mutations was significantly associated with a higher study screening VL and lower study screening CD4 (P < .001). Differences in drug-resistance patterns in both NRTI and NNRTI were observed by site. CONCLUSIONS The degree of NNRTI and NRTI resistance after first-line virologic failure was associated with higher VL at study entry. Thirty-two percent of individuals remained fully susceptible to etravirine and rilpivirine, protease inhibitor resistance was rare. Some level of susceptibility to NRTI remained; however, VL monitoring and earlier virologic failure detection may result in lower NRTI resistance.
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Affiliation(s)
| | - Evgenia Aga
- Statistical Data Analysis Center, Harvard School of Public Health, Boston, Massachusetts
| | - Heather Ribaudo
- Statistical Data Analysis Center, Harvard School of Public Health, Boston, Massachusetts
| | | | - Michael Norton
- Medical Affairs Therapeutic Area, Virology and Nanotechnology, Global Pharmaceutical Research and Development, AbbVie, Chicago, Illinois
| | - Wendy Stevens
- University of Witwatersrand, Johannesburg, South Africa
| | | | - John Bartlett
- Duke Global Health Institute, Duke University, Durham, North Carolina Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - David Katzenstein
- Division of Infectious Diseases, Stanford University, Palo Alto, California
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Chaturbhuj DN, Nirmalkar AP, Paranjape RS, Tripathy SP. Evaluation of a cost effective in-house method for HIV-1 drug resistance genotyping using plasma samples. PLoS One 2014; 9:e87441. [PMID: 24533056 PMCID: PMC3922725 DOI: 10.1371/journal.pone.0087441] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 12/25/2013] [Indexed: 11/18/2022] Open
Abstract
Objectives Validation of a cost effective in-house method for HIV-1 drug resistance genotyping using plasma samples. Design The validation includes the establishment of analytical performance characteristics such as accuracy, reproducibility, precision and sensitivity. Methods The accuracy was assessed by comparing 26 paired Virological Quality Assessment (VQA) proficiency testing panel sequences generated by in-house and ViroSeq Genotyping System 2.0 (Celera Diagnostics, US) as a gold standard. The reproducibility and precision were carried out on five samples with five replicates representing multiple HIV-1 subtypes (A, B, C) and resistance patterns. The amplification sensitivity was evaluated on HIV-1 positive plasma samples (n = 88) with known viral loads ranges from 1000–1.8 million RNA copies/ml. Results Comparison of the nucleotide sequences generated by ViroSeq and in-house method showed 99.41±0.46 and 99.68±0.35% mean nucleotide and amino acid identity respectively. Out of 135 Stanford HIVdb listed HIV-1 drug resistance mutations, partial discordance was observed at 15 positions and complete discordance was absent. The reproducibility and precision study showed high nucleotide sequence identities i.e. 99.88±0.10 and 99.82±0.20 respectively. The in-house method showed 100% analytical sensitivity on the samples with HIV-1 viral load >1000 RNA copies/ml. The cost of running the in-house method is only 50% of that for ViroSeq method (112$ vs 300$), thus making it cost effective. Conclusions The validated cost effective in-house method may be used to collect surveillance data on the emergence and transmission of HIV-1 drug resistance in resource limited countries. Moreover, the wide applications of a cost effective and validated in-house method for HIV-1 drug resistance testing will facilitate the decision making for the appropriate management of HIV infected patients.
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Affiliation(s)
- Devidas N. Chaturbhuj
- Drug Resistance Lab, National AIDS Research Institute, Indian Council of Medical Research, Bhosari, Pune, India
| | - Amit P. Nirmalkar
- Department of Epidemiology & Biostatistics, National AIDS Research Institute, Indian Council of Medical Research, Bhosari, Pune, India
| | - Ramesh S. Paranjape
- National AIDS Research Institute, Indian Council of Medical Research, Bhosari, Pune, India
| | - Srikanth P. Tripathy
- National JALMA Institute Of Leprosy And Other Mycobacterial Diseases, Indian Council of Medical Research, Bhosari, Agra, India
- * E-mail:
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No clinically significant drug-resistance mutations in HIV-1 subtype C-infected women after discontinuation of NRTI-based or PI-based HAART for PMTCT in Botswana. J Acquir Immune Defic Syndr 2013; 63:572-7. [PMID: 23542639 DOI: 10.1097/qai.0b013e31829308f8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Risk of developing drug resistance after stopping antiretroviral regimens to prevent mother-to-child HIV-1 transmission is unknown. The Mma Bana Study randomized treatment-naive pregnant women with CD4 ≥200 cells per cubic millimeter to receive either abacavir/zidovudine/lamivudine [triple nucleoside reverse transcriptase inhibitor (NRTI) arm] or lopinavir/ritonavir/zidovudine/lamivudine [protease inhibitor (PI) arm]. Drugs were discontinued after 6 months of breastfeeding. One month after discontinuation, 29 NRTI arm samples and 25 PI arm samples were successfully genotyped. No clinically significant antiretroviral resistance mutations were detected. Eight minor resistance mutations were found among 11 (20%) women (3 from NRTI arm and 8 from PI arm), occurring at similar frequencies to those reported in HIV-1 subtype C treatment-naive cohorts.
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Lessells RJ, Avalos A, de Oliveira T. Implementing HIV-1 genotypic resistance testing in antiretroviral therapy programs in Africa: needs, opportunities, and challenges. AIDS Rev 2013; 15:221-9. [PMID: 24322382 PMCID: PMC3951902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Tremendous progress has been made with the scale-up of antiretroviral therapy in Africa, with an estimated seven million people now receiving antiretroviral therapy in the region. The long-term success of antiretroviral therapy programs depends on appropriate strategies to deal with potential threats, one of which is the emergence and spread of antiretroviral drug resistance. Whilst public health surveillance forms the mainstay of the World Health Organization approach to antiretroviral drug resistance, there is likely to be increasing demand for access to drug resistance testing as programs mature and as HIV clinical management becomes more complex. African-owned research initiatives have helped to develop affordable resistance testing appropriate for use in the region, and have developed delivery models for resistance testing at different levels of the public health system. Some upper-middle-income countries such as Botswana and South Africa have introduced drug resistance testing for selected patient groups to guide clinical management. The scale-up of resistance testing will require substantial expansion of clinical and laboratory capacity in the region, but the expertise and resources exist in Africa to support this. The long-term population health impact and cost-effectiveness of resistance testing in the region will also require further investigation.
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Affiliation(s)
- Richard J. Lessells
- Africa Centre for Health and Population Studies, University of KwaZulu-Natal, Mtubatuba, South Africa
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
| | - Ava Avalos
- Ministry of Health (MOH), Republic of Botswana, Gaborone, Botswana
| | - Tulio de Oliveira
- Africa Centre for Health and Population Studies, University of KwaZulu-Natal, Mtubatuba, South Africa
- Research Department of Infection, University College London, London, UK
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Bronze M, Aitken SC, Wallis CL, Steegen K, Stuyver LJ, de Wit TFR, Stevens W. Evaluation of an affordable HIV-1 virological failure assay and antiretroviral drug resistance genotyping protocol. J Virol Methods 2013; 194:300-7. [PMID: 23994150 DOI: 10.1016/j.jviromet.2013.08.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 08/08/2013] [Accepted: 08/15/2013] [Indexed: 11/28/2022]
Abstract
HIV-1 RNA viral load is the preferred tool to monitor virological failure during antiretroviral therapy (ART) exposure. Timely detection of virological failure can reduce the prevalence and complexity of HIV-1 drug resistance. This field evaluation further characterizes a two-step approach to identify virological failure, as a measure of ART adherence, and detect HIVDR mutations in the reverse transcriptase (RT) gene of HIV-1. Two hundred and forty-eight (248) samples were tested; 225 from South African HIV-1 participants enrolled in the PharmAccess African Studies to Evaluate Resistance (PASER) cohort, forty of which had paired dried blood spot (DBS) samples and 23 HIV-1 negative samples. A newly developed virological failure assay (ARTA-VFA) was used on all samples, and those with a viral load >5000 RNA copies/ml were genotyped with a shortened RT protocol to detect HIVDR (ARTA-HIVDR(ultralight)). The ARTA-VFA showed good precision and linearity as compared to a commercial reference assay (NucliSENS EasyQ v1.2, Roche) with an R(2) of 0.99. Accuracy studies illustrated standard deviations of <1 log RNA copies/ml for plasma and DBS ARTA-VFA results compared to the reference method. The ARTA-VFA's intended use was to deliver qualitative results either < or >5000 RNA copies/ml. No significant differences in the proportion of results < or > either the 5000 RNA copies/ml or 1000 RNA copies/ml cut-off were noted for plasma indicating either cut-off to be useful. Significant differences were noted in these proportions when DBS were used (P=0.0002), where a 5000 RNA copies/ml cut-off was deemed more appropriate. The sensitivity and specificity of the ARTA-VFA with plasma were 95% and 93% and 91% and 95% for DBS using a 5000 RNA copies/ml cut-off. The ARTA HIVDR(ultralight) assay was reliable for plasma and DBS samples with a viral load >5000 RNA copies/ml, with amplification and sequencing success rates of 91% and 92% respectively for plasma, and 95% and 80% respectively for DBS. HIVDR profiles for plasma and DBS were 100% concordant with the reference assay. This study evaluated a previously described combination of two assays potentially useful in assessing HIV-1 virological failure and resistance, showing good concordance with reference assays. These assays are simple to perform and are affordable, viable options to detect virological failures in certain resource limited settings. The assays' compatibility with DBS sampling extends the access of HIV-1 virological monitoring to more remote settings.
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Affiliation(s)
- M Bronze
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa; Department of Molecular Medicine and Haematology, National Health Laboratory Services, Charlotte Maxeke Johannesburg Academic Hospital, South Africa.
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To SWC, Chen JHK, Yam WC. Current assays for HIV-1 diagnostics and antiretroviral therapy monitoring: challenges and possibilities. Future Virol 2013. [DOI: 10.2217/fvl.13.21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In 2011, there were over 34 million people living with HIV infections, placing a heavy burden on public health sectors. HIV infection is a lifelong threat that cannot be prevented by vaccination or cured by antiretroviral drugs. The infected patients rely on daily antiretroviral therapy to suppress HIV viral replication. Hence, it is important to diagnose HIV infections as early as possible and to monitor the efficacy of antiretroviral therapy every 3–6 months. Different immunoassays detecting HIV antigens and antibodies have been modified to offer better sensitivity and more rapid diagnosis. Several clinical and virological parameters, including CD4+ cell counts, viral load and drug resistance mutations, are also used for treatment monitoring. Many molecular assay optimizations are now being utilized to improve patient care. This review will focus on the most updated HIV diagnostic assays, as well as discussing the upcoming possibilities of other advanced technologies.
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Affiliation(s)
- Sabrina Wai-Chi To
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Jonathan Hon-Kwan Chen
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Wing-Cheong Yam
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China.
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A pragmatic approach to HIV-1 drug resistance determination in resource-limited settings by use of a novel genotyping assay targeting the reverse transcriptase-encoding region only. J Clin Microbiol 2013; 51:1757-61. [PMID: 23536405 DOI: 10.1128/jcm.00118-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In resource-limited settings (RLS), reverse transcriptase (RT) inhibitors form the backbone of first-line treatment regimens. We have developed a simplified HIV-1 drug resistance genotyping assay targeting the region of RT harboring all major RT inhibitor resistance mutation positions, thus providing all relevant susceptibility data for first-line failures, coupled with minimal cost and labor. The assay comprises a one-step RT-PCR amplification reaction, followed by sequencing using one forward and one reverse primer, generating double-stranded coverage of RT amino acids (aa) 41 to 238. The assay was optimized for all major HIV-1 group M subtypes in plasma and dried blood spot (DBS) samples using a panel of reference viruses for HIV-1 subtypes A to D, F to H, and circulating recombinant form 01_AE (CRF01_AE) and applied to 212 clinical plasma samples and 25 DBS samples from HIV-1-infected individuals from Africa and Europe. The assay was subsequently transferred to Uganda and applied locally on clinical plasma samples. All major HIV-1 subtypes could be detected with an analytical sensitivity of 5.00E+3 RNA copies/ml for plasma and DBS. Application of the assay on 212 clinical samples from African subjects comprising subtypes A to D, F to H (rare), CRF01_AE, and CRF02_AG at a viral load (VL) range of 6.71E+2 to 1.00E+7 (median, 1.48E+5) RNA copies/ml was 94.8% (n = 201) successful. Application on clinical samples in Uganda demonstrated a comparable success rate. Genotyping of clinical DBS samples, all subtype C with a VL range of 1.02E+3 to 4.49E+5 (median, 1.42E+4) RNA copies/ml, was 84.0% successful. The described assay greatly reduces hands-on time and the costs required for genotyping and is ideal for use in RLS, as demonstrated in a reference laboratory in Uganda and its successful application on DBS samples.
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Chaturbhuj DN, Deshmukh PS, Hingankar NK, Siddhaarth K, Deshpande SN, Sen S, Kabra S, Paranjape RS, Tripathy SP. Evaluations of an in-house drug resistance method for HIV-1 drug resistance using ViroSeq™ 2.0 genotyping system as a gold standard. J Virol Methods 2013; 189:87-92. [PMID: 23353551 DOI: 10.1016/j.jviromet.2013.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 12/14/2012] [Accepted: 01/02/2013] [Indexed: 02/08/2023]
Abstract
An in-house method was evaluated for its efficiency to detect the HIV-1 drug resistance mutations. This method was compared with the ViroSeq™ Genotyping System 2.0 (Celera Diagnostics, US) a gold standard. Sixty-five stored plasma samples, previously tested for HIV-1 drug resistance using the ViroSeq™ method were used to evaluate the in-house method. Out of the sixty five plasma samples, sixty were HIV-1 positive clinical samples; four samples from the Virology Quality Assessment (VQA) program and one positive control from the ViroSeq™ kit were used in this study. The sequences generated by the ViroSeq™ and an in-house method showed 99.5±0.5% and 99.7±0.4% (mean±SD) nucleotide and amino acid identity, respectively. Out of 214 Stanford HIVdb listed HIV-1 drug resistance mutations in the protease and reverse transcriptase regions, concordance was observed in 203 (94.9%), partial discordance in 11 (5.1%) and complete discordance was absent. The in-house primers are broadly sensitive in genotyping multiple HIV-1 group M subtypes. The amplification sensitivity of the in-house method was 1000 copies/ml. The evaluation of the in-house method provides results comparable with that of ViroSeq™ method thus, making the in-house method suitable for HIV-1 drug resistance testing in the developing countries.
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Affiliation(s)
- Devidas N Chaturbhuj
- National AIDS Research Institute, Plot 73, 'G' Block, M.I.D.C., Bhosari, Pune 411 026, India.
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Lee CK, Lee HK, Loh TP, Sethi SK, Koay ESC, Tang JWT. An in-house HIV genotyping assay for the detection of drug resistance mutations in Southeast Asian patients infected with HIV-1. J Med Virol 2012; 84:394-401. [PMID: 22246824 DOI: 10.1002/jmv.23202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Genotyping for HIV drug resistance is costly and beyond the means for many Southeast Asian patients, who are self-funded. This prompted the development of a more cost-effective, in-house assay for an ethnically diverse, Southeast Asian population at the National University Hospital in Singapore, using Sanger-based sequencing. Plasma samples from 20 treatment-failure patients with a broad spectrum of HIV drug resistance mutations were used to validate this assay clinically. Blinded testing gave concordant results for 7/7 (100%) protease drug resistance-related mutations, including one major and six minor mutations, and 111/116 (95.7%) reverse-transcriptase (RT) drug resistance-related mutations, including 65 nucleoside RT inhibitors (NRTI) and 46 non-nucleoside RT inhibitors (NNRTI) mutations. There were five discordant results, involving three NRTI- and two NNRTI-resistance-associated mutations. Highly conserved primers designed to have a wide coverage of the HIV pol gene (covering the entire protease and 395 codons of the RT region) enabled efficient multi-ethnic population-based genotyping. Reagents for this in-house test cost around 60% less than those for commercially available assays (SGD150 vs. SGD350 per sample). In addition, this assay also identified mutations located within the C-terminal domain (codons 312-560) of RT that are beyond the reach of most published and commercial GRTs. Currently, most research on C-terminal drug-resistance-related mutations has been conducted on HIV subtype B infections. Therefore this assay enables further study of these C-terminal mutations in Southeast Asian populations, where there is a high prevalence of CRF01_AE and other non-subtype B HIV infections.
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Affiliation(s)
- Chun Kiat Lee
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
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Bronze M, Steegen K, Wallis CL, De Wolf H, Papathanasopoulos MA, Van Houtte M, Stevens WS, de Wit TR, Stuyver LJ. HIV-1 phenotypic reverse transcriptase inhibitor drug resistance test interpretation is not dependent on the subtype of the virus backbone. PLoS One 2012; 7:e34708. [PMID: 22496845 PMCID: PMC3322145 DOI: 10.1371/journal.pone.0034708] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 03/08/2012] [Indexed: 11/18/2022] Open
Abstract
To date, the majority of HIV-1 phenotypic resistance testing has been performed with subtype B virus backbones (e.g. HXB2). However, the relevance of using this backbone to determine resistance in non-subtype B HIV-1 viruses still needs to be assessed. From 114 HIV-1 subtype C clinical samples (36 ARV-naïve, 78 ARV-exposed), pol amplicons were produced and analyzed for phenotypic resistance using both a subtype B- and C-backbone in which the pol fragment was deleted. Phenotypic resistance was assessed in resulting recombinant virus stocks (RVS) for a series of antiretroviral drugs (ARV's) and expressed as fold change (FC), yielding 1660 FC comparisons. These Antivirogram® derived FC values were categorized as having resistant or sensitive susceptibility based on biological cut-off values (BCOs). The concordance between resistance calls obtained for the same clinical sample but derived from two different backbones (i.e. B and C) accounted for 86.1% (1429/1660) of the FC comparisons. However, when taking the assay variability into account, 95.8% (1590/1660) of the phenotypic data could be considered as being concordant with respect to their resistance call. No difference in the capacity to detect resistance associated with M184V, K103N and V106M mutations was noted between the two backbones. The following was concluded: (i) A high level of concordance was shown between the two backbone phenotypic resistance profiles; (ii) Assay variability is largely responsible for discordant results (i.e. for FC values close to BCO); (iii) Confidence intervals should be given around the BCO's, when assessing resistance in HIV-1 subtype C; (iv) No systematic resistance under- or overcalling of subtype C amplicons in the B-backbone was observed; (v) Virus backbone subtype sequence variability outside the pol region does not contribute to phenotypic FC values. In conclusion the HXB2 virus backbone remains an acceptable vector for phenotyping HIV-1 subtype C pol amplicons.
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Affiliation(s)
- Michelle Bronze
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa.
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Struck D, Wallis CL, Denisov G, Lambert C, Servais JY, Viana RV, Letsoalo E, Bronze M, Aitken SC, Schuurman R, Stevens W, Schmit JC, Rinke de Wit T, Perez Bercoff D. Automated sequence analysis and editing software for HIV drug resistance testing. J Clin Virol 2012; 54:30-5. [PMID: 22425336 DOI: 10.1016/j.jcv.2012.01.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 01/20/2012] [Accepted: 01/23/2012] [Indexed: 11/25/2022]
Abstract
BACKGROUND Access to antiretroviral treatment in resource-limited-settings is inevitably paralleled by the emergence of HIV drug resistance. Monitoring treatment efficacy and HIV drugs resistance testing are therefore of increasing importance in resource-limited settings. Yet low-cost technologies and procedures suited to the particular context and constraints of such settings are still lacking. The ART-A (Affordable Resistance Testing for Africa) consortium brought together public and private partners to address this issue. OBJECTIVES To develop an automated sequence analysis and editing software to support high throughput automated sequencing. STUDY DESIGN The ART-A Software was designed to automatically process and edit ABI chromatograms or FASTA files from HIV-1 isolates. RESULTS The ART-A Software performs the basecalling, assigns quality values, aligns query sequences against a set reference, infers a consensus sequence, identifies the HIV type and subtype, translates the nucleotide sequence to amino acids and reports insertions/deletions, premature stop codons, ambiguities and mixed calls. The results can be automatically exported to Excel to identify mutations. Automated analysis was compared to manual analysis using a panel of 1624 PR-RT sequences generated in 3 different laboratories. Discrepancies between manual and automated sequence analysis were 0.69% at the nucleotide level and 0.57% at the amino acid level (668,047 AA analyzed), and discordances at major resistance mutations were recorded in 62 cases (4.83% of differences, 0.04% of all AA) for PR and 171 (6.18% of differences, 0.03% of all AA) cases for RT. CONCLUSIONS The ART-A Software is a time-sparing tool for pre-analyzing HIV and viral quasispecies sequences in high throughput laboratories and highlighting positions requiring attention.
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Levison JH, Orrell C, Gallien S, Kuritzkes DR, Fu N, Losina E, Freedberg KA, Wood R. Virologic failure of protease inhibitor-based second-line antiretroviral therapy without resistance in a large HIV treatment program in South Africa. PLoS One 2012; 7:e32144. [PMID: 22427821 PMCID: PMC3302781 DOI: 10.1371/journal.pone.0032144] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 01/20/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND We investigated the prevalence of wild-type virus (no major drug resistance) and drug resistance mutations at second-line antiretroviral treatment (ART) failure in a large HIV treatment program in South Africa. METHODOLOGY/ PRINCIPAL FINDINGS HIV-infected patients ≥ 15 years of age who had failed protease inhibitor (PI)-based second-line ART (2 consecutive HIV RNA tests >1000 copies/ml on lopinavir/ritonavir, didanosine, and zidovudine) were identified retrospectively. Patients with virologic failure were continued on second-line ART. Genotypic testing for drug resistance was performed on frozen plasma samples obtained closest to and after the date of laboratory confirmed second-line ART failure. Of 322 HIV-infected patients on second-line ART, 43 were adults with confirmed virologic failure, and 33 had available plasma for viral sequencing. HIV-1 RNA subtype C predominated (n = 32, 97%). Mean duration on ART (SD) prior to initiation of second-line ART was 23 (17) months, and time from second-line ART initiation to failure was 10 (9) months. Plasma samples were obtained 7(9) months from confirmed failure. At second-line failure, 22 patients (67%) had wild-type virus. There was no major resistance to PIs found. Eleven of 33 patients had a second plasma sample taken 8 (5.5) months after the first. Median HIV-1 RNA and the genotypic resistance profile were unchanged. CONCLUSIONS/ SIGNIFICANCE Most patients who failed second-line ART had wild-type virus. We did not observe evolution of resistance despite continuation of PI-based ART after failure. Interventions that successfully improve adherence could allow patients to continue to benefit from second-line ART therapy even after initial failure.
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Affiliation(s)
- Julie H Levison
- Division of General Medicine Massachusetts General Hospital, Boston, Massachusetts, United States of America.
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Aitken SC, Kliphuis A, Wallis CL, Chu ML, Fillekes Q, Barth R, Stevens W, Rinke de Wit TF, Schuurman R. Development and evaluation of an assay for HIV-1 protease and reverse transcriptase drug resistance genotyping of all major group-M subtypes. J Clin Virol 2012; 54:21-5. [PMID: 22306272 DOI: 10.1016/j.jcv.2012.01.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 01/07/2012] [Accepted: 01/12/2012] [Indexed: 10/14/2022]
Abstract
BACKGROUND High cost and varying sensitivity for non-B HIV-1 subtypes limits application of current commercial kits for HIV-1 drug resistance genotyping of all major HIV-1 group-M subtypes. OBJECTIVES Our research aimed to develop and validate an assay specific for all major HIV-1 group-M subtypes for use as an alternative to commercial assays for HIV-1 protease (PR) and reverse transcriptase (RT) drug resistance genotyping. STUDY DESIGN A nested RT-PCR encompassing the entire PR and RT up to amino acid 321 of HIV-1 was designed to detect HIV-1 group-M subtypes. Primers compatible with group-M subtypes were defined and analytical sensitivity of the assay evaluated using a panel of reference viruses for subtypes A-H and CRF01_AE. The assay was subsequently evaluated on 246 plasma samples from HIV-1 infected individuals harboring various group-M subtypes and viral loads (VLs). RESULTS All major group-M HIV-1 subtypes were detected with an overall analytical sensitivity of 1.00E+03 RNA copies/ml. Application of the genotyping assay on 246 primarily African clinical samples comprising subtypes A (n=52; 21.7%), B (n=12; 5.0%), C (n=127; 52.9%), D (n=25; 10.4%), CRF01_AE (n=10; 4.2%), and CRF02_AG (n=10; 4.2%), and unassigned variants (n=10; 4.2%), VL range 4.32E+02-8.63E+06 (median 2.66E+04) RNA copies/ml, was ∼98% successful. CONCLUSIONS A group-M subtype-independent genotyping assay for detection of HIV-1 drug resistance was developed. The described assay can serve as an alternative to commercial assays for HIV-1 drug resistance genotyping in routine diagnostics, and for surveillance and monitoring of drug resistance in resource-limited settings (RLS).
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Affiliation(s)
- Susan C Aitken
- Department of Medical Microbiology, University Medical Centre Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands.
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Sigaloff KC, Ramatsebe T, Viana R, de Wit TFR, Wallis CL, Stevens WS. Accumulation of HIV drug resistance mutations in patients failing first-line antiretroviral treatment in South Africa. AIDS Res Hum Retroviruses 2012; 28:171-5. [PMID: 21819219 DOI: 10.1089/aid.2011.0136] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Patients failing antiretroviral treatment for extended periods of time are at risk of accumulating HIV drug resistance mutations (DRMs), which negatively influences second-line treatment. This retrospective study assessed the rate of DRM accumulation among South African patients with continued virological failure. Serial genotypic resistance testing was performed and DRMs were scored according to the 2009 IAS-USA list. Among 43 patients, 38 (88.4%) harbored ≥1 DRM. The median time between two sequential resistance tests was 5 months (IQR: 3-10). Thymidine analogue mutations accumulated at a rate of 0.07 mutation per month of drug exposure, which is faster than previously reported. Routine virological monitoring should be implemented in resource-limited settings to preserve susceptibility to second-line regimens.
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Affiliation(s)
- Kim C.E. Sigaloff
- PharmAccess Foundation, Amsterdam, The Netherlands
- Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | - Tina Ramatsebe
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Raquel Viana
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Tobias F. Rinke de Wit
- PharmAccess Foundation, Amsterdam, The Netherlands
- Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | - Carole L. Wallis
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Wendy S. Stevens
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
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Zhou Z, Wagar N, DeVos JR, Rottinghaus E, Diallo K, Nguyen DB, Bassey O, Ugbena R, Wadonda-Kabondo N, McConnell MS, Zulu I, Chilima B, Nkengasong J, Yang C. Optimization of a low cost and broadly sensitive genotyping assay for HIV-1 drug resistance surveillance and monitoring in resource-limited settings. PLoS One 2011; 6:e28184. [PMID: 22132237 PMCID: PMC3223235 DOI: 10.1371/journal.pone.0028184] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 11/02/2011] [Indexed: 11/29/2022] Open
Abstract
Commercially available HIV-1 drug resistance (HIVDR) genotyping assays are expensive and have limitations in detecting non-B subtypes and circulating recombinant forms that are co-circulating in resource-limited settings (RLS). This study aimed to optimize a low cost and broadly sensitive in-house assay in detecting HIVDR mutations in the protease (PR) and reverse transcriptase (RT) regions of pol gene. The overall plasma genotyping sensitivity was 95.8% (N = 96). Compared to the original in-house assay and two commercially available genotyping systems, TRUGENE® and ViroSeq®, the optimized in-house assay showed a nucleotide sequence concordance of 99.3%, 99.6% and 99.1%, respectively. The optimized in-house assay was more sensitive in detecting mixture bases than the original in-house (N = 87, P<0.001) and TRUGENE® and ViroSeq® assays. When the optimized in-house assay was applied to genotype samples collected for HIVDR surveys (N = 230), all 72 (100%) plasma and 69 (95.8%) of the matched dried blood spots (DBS) in the Vietnam transmitted HIVDR survey were genotyped and nucleotide sequence concordance was 98.8%; Testing of treatment-experienced patient plasmas with viral load (VL) ≥ and <3 log10 copies/ml from the Nigeria and Malawi surveys yielded 100% (N = 46) and 78.6% (N = 14) genotyping rates, respectively. Furthermore, all 18 matched DBS stored at room temperature from the Nigeria survey were genotyped. Phylogenetic analysis of the 236 sequences revealed that 43.6% were CRF01_AE, 25.9% subtype C, 13.1% CRF02_AG, 5.1% subtype G, 4.2% subtype B, 2.5% subtype A, 2.1% each subtype F and unclassifiable, 0.4% each CRF06_CPX, CRF07_BC and CRF09_CPX.
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Affiliation(s)
- Zhiyong Zhou
- Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Nick Wagar
- Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Joshua R. DeVos
- Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Erin Rottinghaus
- Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Karidia Diallo
- Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Duc B. Nguyen
- Department of Health and Human Services/US CDC, Hanoi, Vietnam
| | | | | | | | - Michelle S. McConnell
- Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
- Thailand Ministry of Public Health/US CDC Collaboration, Nonthaburi, Thailand
| | - Isaac Zulu
- Global AIDS Program CDC-Zambia, Lusaka, Zambia
| | - Benson Chilima
- Community Health Sciences Unit, Malawi Ministry of Health, Lilongwe, Malawi
| | - John Nkengasong
- Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Chunfu Yang
- Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
- * E-mail:
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Wallis CL, Papathanasopolous MA, Fox M, Conradie F, Ive P, Orrell C, Zeinecker J, Sanne I, Wood R, McIntyre J, Stevens W. Low rates of nucleoside reverse transcriptase inhibitor resistance in a well-monitored cohort in South Africa on antiretroviral therapy. Antivir Ther 2011; 17:313-20. [PMID: 22293461 DOI: 10.3851/imp1985] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2011] [Indexed: 10/15/2022]
Abstract
BACKGROUND The emergence of complex HIV-1 drug resistance mutations has been linked to the duration of time patients are on a failing antiretroviral drug regimen. This study reports on resistance profiles in a closely monitored subtype C infected cohort. METHODS A total of 812 participants were enrolled into the CIPRA-SA 'safeguard the household' study, viral loads were determined at 12-weekly intervals for 96 weeks. Virological failure was defined as either a <1.5 log decrease in viral load at week 12 or two consecutive viral load measurements of >1,000 RNA copies/ml after week 24. Regimens prescribed were in line with the South African roll-out programme (stavudine, lamivudine, efavirenz or nevirapine). Viral RNA was extracted from patients with virological failure, and pol reverse-transcriptase PCR and sequence analysis were performed to determine drug-resistant mutations. RESULTS Virological failure was observed in 83 participants on the first-line regimen during the study period, of which 61 (73%) had HIV-1 drug-resistant mutations. The M184V mutation was the most frequent (n=46; 65%), followed by K103N (46%) and Y181C (21%). Thymidine analogue mutations were infrequent (1%) and Q151M was not observed. CONCLUSIONS Drug resistance profiles were less complex than has been previously reported in South Africa using the same antiretroviral drug regimens. These data suggest that frequent viral load monitoring limits the level and complexity of resistance observed in HIV-1 subtype C, preserving susceptibility to second-line options.
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Affiliation(s)
- Carole L Wallis
- University of the Witwatersrand, Johannesburg, South Africa.
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Unnecessary Antiretroviral Treatment Switches and Accumulation of HIV Resistance Mutations; Two Arguments for Viral Load Monitoring in Africa. J Acquir Immune Defic Syndr 2011; 58:23-31. [DOI: 10.1097/qai.0b013e318227fc34] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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46
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Hamers RL, Wallis CL, Kityo C, Siwale M, Mandaliya K, Conradie F, Botes ME, Wellington M, Osibogun A, Sigaloff KCE, Nankya I, Schuurman R, Wit FW, Stevens WS, van Vugt M, de Wit TFR. HIV-1 drug resistance in antiretroviral-naive individuals in sub-Saharan Africa after rollout of antiretroviral therapy: a multicentre observational study. THE LANCET. INFECTIOUS DISEASES 2011; 11:750-9. [PMID: 21802367 DOI: 10.1016/s1473-3099(11)70149-9] [Citation(s) in RCA: 235] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND There are few data on the epidemiology of primary HIV-1 drug resistance after the roll-out of antiretroviral treatment (ART) in sub-Saharan Africa. We aimed to assess the prevalence of primary resistance in six African countries after ART roll-out and if wider use of ART in sub-Saharan Africa is associated with rising prevalence of drug resistance. METHODS We did a cross-sectional study in antiretroviral-naive adults infected with HIV-1 who had not started first-line ART, recruited between 2007 and 2009 from 11 regions in Kenya, Nigeria, South Africa, Uganda, Zambia, and Zimbabwe. We did population-based sequencing of the pol gene on plasma specimens with greater than 1000 copies per mL of HIV RNA. We identified drug-resistance mutations with the WHO list for transmitted resistance. The prevalence of sequences containing at least one drug-resistance mutation was calculated accounting for the sampling weights of the sites. We assessed the risk factors of resistance with multilevel logistic regression with random coefficients. FINDINGS 2436 (94.1%) of 2590 participants had a pretreatment genotypic resistance result. 1486 participants (57.4%) were women, 1575 (60.8%) had WHO clinical stage 3 or 4 disease, and the median CD4 count was 133 cells per μL (IQR 62-204). Overall sample-weighted drug-resistance prevalence was 5.6% (139 of 2436; 95% CI 4.6-6.7), ranging from 1.1% (two of 176; 0.0-2.7) in Pretoria, South Africa, to 12.3% (22 of 179; 7.5-17.1) in Kampala, Uganda. The pooled prevalence for all three Ugandan sites was 11.6% (66 of 570; 8.9-14.2), compared with 3.5% (73 of 1866; 2.5-4.5) for all other sites. Drug class-specific resistance prevalence was 2.5% (54 of 2436; 1.8-3.2) for nucleoside reverse-transcriptase inhibitors (NRTIs), 3.3% (83 of 2436; 2.5-4.2) for non-NRTIs (NNRTIs), 1.3% (31 of 2436; 0.8-1.8) for protease inhibitors, and 1.2% (25 of 2436; 0.7-1.7) for dual-class resistance to NRTIs and NNRTIs. The most common drug-resistance mutations were K103N (43 [1.8%] of 2436), thymidine analogue mutations (33 [1.6%] of 2436), M184V (25 [1.2%] of 2436), and Y181C/I (19 [0.7%] of 2436). The odds ratio for drug resistance associated with each additional year since the start of the ART roll-out in a region was 1.38 (95% CI 1.13-1.68; p=0.001). INTERPRETATION The higher prevalence of primary drug resistance in Uganda than in other African countries is probably related to the earlier start of ART roll-out in Uganda. Resistance surveillance and prevention should be prioritised in settings where ART programmes are scaled up. FUNDING Ministry of Foreign Affairs of the Netherlands.
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Affiliation(s)
- Raph L Hamers
- PharmAccess Foundation, Department of Global Health, Academic Medical Centre of University of Amsterdam, Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands.
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Peeters M, Aghokeng AF, Delaporte E. Genetic diversity among human immunodeficiency virus-1 non-B subtypes in viral load and drug resistance assays. Clin Microbiol Infect 2011; 16:1525-31. [PMID: 20649800 DOI: 10.1111/j.1469-0691.2010.03300.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tremendous diversity of human immunodeficiency virus (HIV)-1 strains circulating worldwide has an important impact on almost all aspects of the management of this infection, from the identification of infected persons, through treatment efficacy and monitoring, and prevention strategies such as vaccine design. The areas where HIV-1 genetic diversity is highest are those where the majority of patients in need of treatment and biological monitoring live. With increased access to treatment in these areas, it is expected that the demand for monitoring tools such as viral load assays and resistance tests will also increase, and their reliability will be critical. Regular updates of these assays during the last two decades have aimed at improving their performances in different ways that include their reliability with different HIV-1 strains. We here review to what extent HIV-1 genetic diversity still limits or not the use of currently available viral load and resistance tests.
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Affiliation(s)
- M Peeters
- UMR 145 VIH et Maladies Associées Institut de Recherche pour le Développement (IRD) and University of Montpellier 1, Montpellier, France.
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Fokam J, Salpini R, Santoro MM, Cento V, D’Arrigo R, Gori C, Perno CF, Colizzi V, Nanfack A, Gwom LC, Cappelli G, Takou D. Performance evaluation of an in-house human immunodeficiency virus type-1 protease-reverse transcriptase genotyping assay in Cameroon. Arch Virol 2011; 156:1235-43. [DOI: 10.1007/s00705-011-0982-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 03/14/2011] [Indexed: 11/29/2022]
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High failure rate of the ViroSeq HIV-1 genotyping system for drug resistance testing in Cameroon, a country with broad HIV-1 genetic diversity. J Clin Microbiol 2011; 49:1635-41. [PMID: 21270223 DOI: 10.1128/jcm.01478-10] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ViroSeq HIV-1 genotyping system is used in many African countries for drug resistance testing. In this study, we used a panel of diverse HIV-1 group M isolates circulating in Cameroon to show that the performance of this assay can be altered by the sequence variation of non-B HIV-1 strains that predominate in African settings.
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Price MA, Wallis CL, Lakhi S, Karita E, Kamali A, Anzala O, Sanders EJ, Bekker LG, Twesigye R, Hunter E, Kaleebu P, Kayitenkore K, Allen S, Ruzagira E, Mwangome M, Mutua G, Amornkul PN, Stevens G, Pond SLK, Schaefer M, Papathanasopoulos MA, Stevens W, Gilmour J. Transmitted HIV type 1 drug resistance among individuals with recent HIV infection in East and Southern Africa. AIDS Res Hum Retroviruses 2011; 27:5-12. [PMID: 21091377 PMCID: PMC3045073 DOI: 10.1089/aid.2010.0030] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To characterize WHO-defined transmitted HIV drug resistance mutation (TDRM) data from recently HIV-infected African volunteers, we sequenced HIV (pol) and evaluated for TDRM the earliest available specimens from ARV-naive volunteers diagnosed within 1 year of their estimated date of infection at eight research centers in sub-Saharan Africa. TDRMs were detected in 19/408 (5%) volunteers. The prevalence of TDRMs varied by research center, from 5/26 (19%) in Entebbe, 6/78 (8%) in Kigali, 2/49 (4%) in Kilifi, to 3/106 (3%) in Lusaka. One of five volunteers from Cape Town (20%) had TDRMs. Despite small numbers, our data suggest an increase in DRMs by year of infection in Zambia (p = 0.004). The prevalence observed in Entebbe was high across the entire study. ARV history data from 12 (63%) HIV-infected sexual partners were available; 3 reported ARV use prior to transmission. Among four partners with sequence data available, transmission linkage was confirmed and two had the same TDRMs as the newly infected volunteer (both K103N). As ARV therapy continues to increase in availability throughout Africa, monitoring incident virus strains for the presence of TDRMs should be a priority. Early HIV infection cohorts provide an excellent and important platform to monitor the development of TDRMs to inform treatment guidelines, drug choices, and strategies for secondary prevention of TDRM transmission.
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Affiliation(s)
- Matt A Price
- International AIDS Vaccine Initiative, San Francisco, California, USA.
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