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Nurjannah, Jayanti S, Tanoerahardjo FS, Al Musyahadah US, Sukowati CHC, Massi MN. Major Drug Resistance Mutations on Reverse Transcriptase Gene in Human Immunodeficiency Virus Type-1 in Indonesia: A Systematic Review. Curr HIV/AIDS Rep 2024; 21:31-39. [PMID: 38244171 DOI: 10.1007/s11904-023-00687-5] [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] [Accepted: 12/29/2023] [Indexed: 01/22/2024]
Abstract
PURPOSE OF REVIEW The prevalence of HIV-1 in Indonesia is on a concerning upward trajectory, with a concurrent rise in the development of drug-resistant strains, challenging the efficacy of antiretroviral therapy (ART). Many mutations have been found in the pol gene that makes HIV resistant to ART. We aim to review the major drug resistance mutations (DRMs) of reverse transcriptase (RT) of pol gene in HIV-1 cases in Indonesia. RECENT FINDINGS A total of eleven articles reporting DRMs in HIV-1 subjects from various regions between 2015-2020 in Indonesia are included. The prevalence of major DRMs on the RT gene in studies included varies from 3.4% to 34%. The CRF01_AE subtype stands out as the predominant variant. Notably, the prevalence of major DRMs in ART-experienced individuals is 22.1%, while ART-naïve individuals show a lower rate of 4.4%. Among the RT gene mutations, M184I/V emerges as the most prevalent (10.5%) within the nucleos(t)ide reverse transcriptase inhibitors (NRTI) group, while K103N leads among the non-NRTI (NNRTI) group, with a frequency of 6.4%. Regionally, North Sulawesi records the highest prevalence of major DRMs in the RT gene at 21.1%, whereas Riau and Central Papua exhibit the lowest rates at 3.4%. Significant variations in drug resistance mutations within the RT gene across Indonesian regions highlight the importance of closely monitoring and evaluating the effectiveness of current antiretroviral therapy (ART) regimens. Considerably, more studies are needed to understand better and overcome the emergence of DRMs on HIV-1 patients in Indonesia.
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Affiliation(s)
- Nurjannah
- Postgraduate School, Hasanuddin University, Makassar, 90245, Indonesia
- Ministry of Health of Republic Indonesia, Jakarta Selatan, 12950, Indonesia
| | - Sri Jayanti
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, 16911, Indonesia
| | | | - Ummu Syauqah Al Musyahadah
- Department of Bioinformatics, Faculty of Health Technology, University of Megarezky, Makassar, 90234, Indonesia
| | - Caecilia Hapsari Ceriapuri Sukowati
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, 16911, Indonesia
- Liver Cancer Unit, Fondazione Italiana Fegato ONLUS, AREA Science Park, 34149, Trieste, Italy
| | - Muhammad Nasrum Massi
- Department of Clinical Microbiology, Hasanuddin University, Makassar, 90245, Indonesia.
- Microbiology Laboratory, Hasanuddin University Hospital, Makassar, 90245, Indonesia.
- Hasanuddin University Medical Research Center Laboratory, Faculty of Medicine, Hasanuddin University, Makassar, 90245, Indonesia.
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Kiros M, Biset S, Gebremariam B, Yalew GT, Abegaz WE, Geteneh A. Trends in HIV-1 pretreatment drug resistance and HIV-1 variant dynamics among antiretroviral therapy-naive Ethiopians from 2003 to 2018: a pooled sequence analysis. Virol J 2023; 20:243. [PMID: 37880705 PMCID: PMC10601210 DOI: 10.1186/s12985-023-02205-w] [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: 05/29/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Ethiopia is among the highly HIV-affected countries, with reported 12,000 and 12,000 AIDS-related deaths and incidents as per reports from 2021. Although the country has made a promising progress in antiretroviral therapy, recent studies have indicated that pretreatment drug resistance (PDR) is alarmingly increasing, which has become a challenge for the effectiveness of HIV treatment. Epidemiologic data on PDR is necessary to help establish ART regimens with good efficacy. Thus, this systematic review aimed to determine the trend analysis of PDR among ART-naïve individuals along with HIV variant dynamics in Ethiopia. METHOD HIV-1 pol sequences from studies conducted between 2003 and 2018 among ART-naïve Ethiopian individuals were retrieved from GenBank and analyzed for the presence of PDR mutations (PDRM) along with the analysis of HIV-1 variant dynamics. The Calibrated Population Resistance (CPR) tool Version 8.1 and the REGA HIV-1 Subtyping Tool Version 3 were used to determine the PDRM and HIV-1 genetic diversity, respectively. RESULT We identified nine studies and analyzed 1070 retrieved HIV-1 pol sequences in this systematic review. The pooled prevalence of PDR was 4.8% (51/1070), including 1.4% (15/1070), 2.8% (30/1070), and 0.8% (9/1070) for nucleoside reverse transcriptase inhibitor (NRTI), non-NRTI (NNRTI), and protease inhibitor (PI) resistance, respectively. NRTI and NNRTI concurrent PDRM were observed among 0.2% (2/799) of the analyzed sequences. The overall PDR prevalence has been increasing over the years. Though the prevalence of the NNRTI, NRTI, and PI PDR also increased over the years, the NNRTI increment was more pronounced than the others, reaching 7.84% in 2018 from 2.19% in 2003. The majority (97%; 1038/1070) of the genetic diversity was HIV-1 subtype C virus, followed by subtype C' (2%; 20/1038) and other subtypes (1%; 10/1038). CONCLUSIONS According to this systematic review, the overall pooled prevalence of PDR is low. Despite the low prevalence, there has been an increasing trend of PDR over the years, which implies the need for routine surveillance of PDRMs along with preventive measures. Hence, this supports the recently endorsed transition of ART regimens from NNRTI to integrase strand transfer inhibitor-based regimens recommended by the WHO. In addition, this finding underscores the need for routine baseline genotypic drug resistance testing for all newly diagnosed HIV-infected patients before initiating treatment to halt the upward trend of PDR.
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Affiliation(s)
- Mulugeta Kiros
- Department of Medical Laboratory Science, CollegeofMedicineandHealth Sciences, Aksum University, Aksum, Ethiopia.
| | - Sirak Biset
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Birhane Gebremariam
- Department of Medical Laboratory Science, CollegeofMedicineandHealth Sciences, Aksum University, Aksum, Ethiopia
| | - Gebrehiwet Tesfay Yalew
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Adigrat University, Adigrat, Ethiopia
| | - Woldaregay Erku Abegaz
- Department of Microbiology, Parasitology, and Immunology, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Alene Geteneh
- Department of Medical Laboratory Sciences, College of Health Sciences, Woldia University, Woldia, Ethiopia
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Kouamou V, Washaya T, Ndhlovu CE, Manasa J. Low Prevalence of Pre-Treatment and Acquired Drug Resistance to Dolutegravir among Treatment Naïve Individuals Initiating on Tenofovir, Lamivudine and Dolutegravir in Zimbabwe. Viruses 2023; 15:1882. [PMID: 37766288 PMCID: PMC10534864 DOI: 10.3390/v15091882] [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: 08/11/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Dolutegravir (DTG) use in combination with tenofovir and lamivudine (TLD) is scaling up in Africa. However, HIV drug resistance (HIVDR) data to DTG remain scarce in Zimbabwe. We assessed the prevalence and genetic mechanisms of DTG resistance in people living with HIV initiating on TLD. A prospective cohort study was conducted between October 2021 and April 2023 among antiretroviral therapy (ART) naïve adults (≥18 years) attending care at an HIV clinic in Zimbabwe. Pre-treatment drug resistance (PDR) was assessed prior to TLD initiation and viral load (VL) outcome and acquired drug resistance (ADR) to TLD were described after 24 weeks follow-up. In total, 172 participants were enrolled in the study. The median (IQR) age and log10 VL were 39 (29-48) years and 5.41 (4.80-5.74) copies/mL, respectively. At baseline, no PDR to DTG was found. However, as previously reported, PDR to non-nucleotide reverse transcriptase inhibitor (NNRTI) was high (15%) whilst PDR to NRTI was low (4%). After a median duration of 27 (25-30) weeks on TLD, virological suppression (VL < 1000 copies/mL) was 98% and among the 2 participants with VL ≥ 1000 copies/mL, no ADR was found. HIVDR to DTG is rare among ART naïve individuals. DTG is more likely to address the problems of HIVDR in Africa.
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Affiliation(s)
- Vinie Kouamou
- Unit of Internal Medicine, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare P.O. Box A178, Zimbabwe;
- Biomedical Research and Training Institute, Harare P.O. Box A178, Zimbabwe; (T.W.); (J.M.)
| | - Tendai Washaya
- Biomedical Research and Training Institute, Harare P.O. Box A178, Zimbabwe; (T.W.); (J.M.)
| | - Chiratidzo Ellen Ndhlovu
- Unit of Internal Medicine, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare P.O. Box A178, Zimbabwe;
| | - Justen Manasa
- Biomedical Research and Training Institute, Harare P.O. Box A178, Zimbabwe; (T.W.); (J.M.)
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Jennings L, West RL, Halim N, Kaiser JL, Gwadz M, MacLeod WB, Gifford AL, Haberer JE, Orrell C, Sabin LL. Protocol for an evaluation of adherence monitoring and support interventions among people initiating antiretroviral therapy in Cape Town, South Africa-a multiphase optimization strategy (MOST) approach using a fractional factorial design. Trials 2023; 24:310. [PMID: 37147725 PMCID: PMC10163747 DOI: 10.1186/s13063-023-07322-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/21/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND South Africa bears a large HIV burden with 7.8 million people with HIV (PWH). However, due to suboptimal antiretroviral therapy (ART) adherence and retention in care, only 66% of PWH in South Africa are virally suppressed. Standard care only allows for suboptimal adherence detection when routine testing indicates unsuppressed virus. Several adherence interventions are known to improve HIV outcomes, yet few are implemented in routinely due to the resources required. Therefore, determining scalable evidence-based adherence support interventions for resource-limited settings (RLS) is a priority. The multiphase optimization strategy (MOST) framework allows for simultaneous evaluation of multiple intervention components and their interactions. We propose to use MOST to identify the intervention combination with the highest levels of efficacy and cost-effectiveness that is feasible and acceptable in primary care clinics in Cape Town. METHODS We will employ a fractional factorial design to identify the most promising intervention components for inclusion in a multi-component intervention package to be tested in a future randomized controlled trial. We will recruit 512 participants initiating ART between March 2022 and February 2024 in three Cape Town clinics and evaluate acceptability, feasibility, and cost-effectiveness of intervention combinations. Participants will be randomized to one of 16 conditions with different combinations of three adherence monitoring components: rapid outreach following (1) unsuppressed virus, (2) missed pharmacy refill collection, and/or (3) missed doses as detected by an electronic adherence monitoring device; and two adherence support components: (1) weekly check-in texts and (2) enhanced peer support. We will assess viral suppression (<50 copies/mL) at 24 months as the primary outcome; acceptability, feasibility, fidelity, and other implementation outcomes; and cost-effectiveness. We will use logistic regression models to estimate intervention effects with an intention-to-treat approach, employ descriptive statistics to assess implementation outcomes, and determine an optimal intervention package. DISCUSSION To our knowledge, ours will be the first study to use the MOST framework to determine the most effective combination of HIV adherence monitoring and support intervention components for implementation in clinics in a RLS. Our findings will provide direction for pragmatic, ongoing adherence support that will be key to ending the HIV epidemic. TRIAL REGISTRATION ClinicalTrials.gov NCT05040841. Registered on 10 September 2021.
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Affiliation(s)
- Lauren Jennings
- Desmond Tutu Health Foundation, Institute of Infectious Diseases and Molecular Medicine and the Department of Medicine, University of Cape Town, Cape Town, South Africa.
| | - Rebecca L West
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | - Nafisa Halim
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | - Jeanette L Kaiser
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | - Marya Gwadz
- Silver School of Social Work, New York University, New York, NY, USA
| | - William B MacLeod
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
- Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Allen L Gifford
- Section of General Internal Medicine, Department of Medicine, Boston University School of Medicine, 72 E Concord Street, Boston, MA, 02118, USA
- Center for Healthcare Organization and Implementation Research, VA Boston Healthcare System, 150 S. Huntington Ave, Boston, MA, 02130, USA
- Department of Health Policy and Management, Boston University School of Public Health, Talbot Building, T348W, Boston, MA, 02118, USA
| | - Jessica E Haberer
- Center for Global Health, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Catherine Orrell
- Desmond Tutu Health Foundation, Institute of Infectious Diseases and Molecular Medicine and the Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Lora L Sabin
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
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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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Jennings L, Kellermann T, Spinelli M, Nkantsu Z, Cogill D, van Schalkwyk M, Decloedt E, van Zyl G, Orrell C, Gandhi M. Drug Resistance, Rather than Low Tenofovir Levels in Blood or Urine, Is Associated with Tenofovir, Emtricitabine, and Efavirenz Failure in Resource-Limited Settings. AIDS Res Hum Retroviruses 2022; 38:455-462. [PMID: 34779228 PMCID: PMC9225825 DOI: 10.1089/aid.2021.0135] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The high cost of viral load (VL) testing limits its use for antiretroviral therapy (ART) adherence support. A low-cost lateral flow urine tenofovir (TFV) rapid assay predicts pre-exposure prophylaxis breakthroughs, but has not yet been investigated in HIV treatment. We therefore evaluated its utility in a pilot cross-sectional study of TFV-containing ART recipients at an increased risk of virologic failure (VF). Participants who had a treatment interruption ≥30 days or had ≥1 episode of viremia (VL ≥400 copies/mL) in the previous year were recruited from a public health setting in Cape Town, South Africa. Self-reported adherence data were collected, the urine TFV assay performed, and concurrent TFV-diphosphate analyzed in dried blood spots. VL testing was done concurrently and, if viremic, genotypic HIV drug resistance testing was performed. Of 48 participants, 18 (37.5%) had VL (>400 copies/mL) at the time of the study, including 16 of 39 receiving efavirenz (EFV), 2 of 6 receiving protease inhibitors, and 0 of 3 receiving dolutegravir. Resistance testing succeeded in 17/18, of which 14 had significant mutations compromising ≥2 agents of the current EFV-based regimen. Of these 14, all had detected urine TFV. Urine TFV was undetectable in two out of three without regimen-relevant resistance; p = .02. In participants on EFV-based regimens returning to care, VF was largely due to viral resistance, where detectable urine TFV had 100% sensitivity (14/14 participants) in predicting resistance. Conversely, when undetectable, the urine-based assay could be used to preclude participants with poor adherence from undergoing costly HIV drug resistance testing.
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Affiliation(s)
- Lauren Jennings
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, South Africa
| | - Tracy Kellermann
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Matthew Spinelli
- Division of HIV, Infectious Diseases, and Global Medicine at UCSF/San Francisco General Hospital, San Francisco, California, USA
| | - Zukiswa Nkantsu
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, South Africa
| | - Dolphina Cogill
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, South Africa
| | - Marije van Schalkwyk
- Division of Infectious Diseases, Department of Medicine, Stellenbosch University, Cape Town, South Africa
| | - Eric Decloedt
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gert van Zyl
- Division of Medical Virology, Stellenbosch University, Faculty of Medicine and Health Sciences, Cape Town, South Africa
- National Health Laboratory Service, Tygerberg Business Unit, Cape Town, South Africa
| | - Catherine Orrell
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, South Africa
| | - Monica Gandhi
- Division of HIV, Infectious Diseases, and Global Medicine at UCSF/San Francisco General Hospital, San Francisco, California, USA
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Bateman M, Wolf A, Chimukangara B, Brust JCM, Lessells R, Amico R, Boodhram R, Singh N, Orrell C, Friedland G, Naidoo K, Padayatchi N, O'Donnell MR. Adherence measured using electronic dose monitoring is associated with emergent antiretroviral resistance and poor outcomes in patients co-infected with HIV/AIDS and multidrug-resistant tuberculosis. Clin Infect Dis 2022; 75:1489-1496. [PMID: 35352097 PMCID: PMC9617578 DOI: 10.1093/cid/ciac232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Medication adherence is known to challenge treatment of HIV/AIDS and multidrug-resistant tuberculosis (MDR-TB). We hypothesized that electronic dose adherence monitoring (EDM) would identify an ART adherence threshold for emergent ART resistance and predict treatment outcomes in patients with MDR-TB and HIV on ART and bedaquiline-containing TB regimens. METHODS A prospective cohort of adults with MDR-TB and HIV, on ART and initiating MDR-TB treatment with bedaquiline, were enrolled at a public TB referral hospital in KwaZulu-Natal, South Africa (PRAXIS Study, Clinicaltrials.gov NCT03162107). Participants received separate EDM devices measuring adherence to bedaquiline and ART (nevirapine or lopinavir/ritonavir). Adherence was calculated cumulatively over six months. Participants were followed through completion of MDR-TB treatment. HIV genome sequencing was performed at baseline, 2 and 6 months on samples with HIV RNA ≥1000 copies/mL. FINDINGS From November 2016 through February 2018, 198 MDR-TB and HIV co-infected participants were enrolled and followed (median 17.2 months, IQR 12.2 - 19.6). Eleven percent had baseline ART resistance mutations, and 7.5% developed emergent ART resistance at 6 months. ART adherence was independently associated with both emergent ART resistance and mortality. Modeling identified a significant (p<0.001), but linear association between ART adherence and emergent resistance, suggesting a strong association without a specific threshold. INTERPRETATION Our findings highlight the need for ART resistance testing, especially in MDR-TB HIV co-infected patients, which is currently not standard of care in resource-limited settings. Despite short follow-up duration, reduced ART adherence was significantly associated with emergent resistance and increased mortality.
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Affiliation(s)
- Mark Bateman
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Allison Wolf
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Benjamin Chimukangara
- Critical Care Medicine Department, NIH Clinical Center, Bethesda, Maryland, USA.,CAPRISA MRC- HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - James C M Brust
- Department of Medicine, Albert Einstein College of Medicine, New York, NY, USA
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rivet Amico
- Department of Health Behavior & Health Education, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Resha Boodhram
- CAPRISA MRC- HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Nalini Singh
- King Dinuzulu Hospital Complex, Durban, South Africa
| | | | | | - Kogieleum Naidoo
- CAPRISA MRC- HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Nesri Padayatchi
- CAPRISA MRC- HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Max R O'Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Irving Medical Center, New York, New York, USA.,Department of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York, New York, USA.,CAPRISA MRC- HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
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Ogola B, Matume ND, Mavhandu-Ramarumo LG, Tebit DM, Bessong PO. Drug Resistance Mutations in a Population Before Antiretroviral Therapy Initiation in Northern South Africa. AIDS Res Hum Retroviruses 2022; 38:248-256. [PMID: 34107774 DOI: 10.1089/aid.2021.0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
South Africa introduced the "diagnose and treat" universal HIV treatment program in September 2016. This program enables all identified HIV-positive patients to immediately start first-line antiretroviral therapy (ART). However, the presence of drug-resistant (DR) viruses in the drug-naive population complicates the choice of ART. We used next-generation sequencing (NGS) to determine the prevalence and diversity of HIV DR mutations in patients entering HIV treatment programs in northern South Africa. RNA was isolated from plasma of drug-naive HIV-1-infected patients. Using reverse transcriptase polymerase chain reaction, the HIV-1-pol gene comprising the complete protease (PR) and the first 900 bp of reverse transcriptase (RT) was amplified and sequenced on an Illumina MiniSeq platform. Consensus sequences were derived at >20% threshold and at >5% threshold using Geneious PRIME® software version 2020.1.2. HIV-1 surveillance drug resistance mutations (SDRM) were inferred using Calibrated Population Resistance tool in HIV Drug Resistance Database. Viral subtypes were determined using REGA and RIP genotyping tools. The HIV PR/RT region was successfully sequenced from 241 patients. From these, 23 (9.5%) had at least one SDRM detected at >20% threshold, with a prevalence of 9.5% (n = 18), 3% (n = 7), and 0.4% (n = 1) for non-nucleoside reverse transcriptase inhibitors (NNRTI), nucleoside reverse transcriptase inhibitors (NRTI), and protease inhibitors (PI), respectively. The number of patients with SDRM increased to 31 (12.9%) when minority variants were accounted for at >5% threshold. The most frequent SDRMs based on drug class were; K103N (7.9%-NNRTI), K65R (2.5%-NRTI), and D30N (0.8%-PI). Four cases of dual NRTI/NNRTI mutations were identified. All consensus sequences were subtype C, except three, which were C/A1, C/F1, and C/G recombinants. NGS analysis confirms that individuals entering HIV treatment programs in northern South Africa, habor moderate levels of SDRM, including cases of dual-class drug resistance. Further SDRM studies may be required to better understand resistance in the drug-naive population in the era of "diagnose and treat" in Limpopo Province, South Africa.
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Affiliation(s)
- Bixa Ogola
- HIV/AIDS & Global Health Research Program, University of Venda, Thohoyandou, South Africa
| | - Nontokozo D. Matume
- HIV/AIDS & Global Health Research Program, University of Venda, Thohoyandou, South Africa
| | | | - Denis M. Tebit
- HIV/AIDS & Global Health Research Program, University of Venda, Thohoyandou, South Africa
- Global Biomed Scientific LLC, PO Box 2368, Forest, VA 24551, USA
| | - Pascal O. Bessong
- HIV/AIDS & Global Health Research Program, University of Venda, Thohoyandou, South Africa
- Center for Global Health Equity, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
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Sabin LL, Gifford AL, Haberer JE, Harvey K, Sarkisova N, Martin K, West RL, Stephens J, Killian C, Halim N, Berkowitz N, Jennings K, Jennings L, Orrell C. Patients' and Providers' Views on Optimal Evidence-Based and Scalable Interventions for Individuals at High Risk of HIV Treatment Failure: Sequential Explorations Among Key Stakeholders in Cape Town, South Africa. AIDS Behav 2022; 26:2783-2797. [PMID: 35190943 DOI: 10.1007/s10461-022-03623-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2022] [Indexed: 11/25/2022]
Abstract
To support translation of evidence-based interventions into practice for HIV patients at high risk of treatment failure, we conducted qualitative research in Cape Town, South Africa. After local health officials vetted interventions as potentially scalable, we held 41 in-depth interviews with patients with elevated viral load or a 3-month treatment gap at community clinics, followed by focus group discussions (FGDs) with 20 providers (physicians/nurses, counselors, and community health care workers). Interviews queried treatment barriers, solutions, and specific intervention options, including motivational text messages, data-informed counseling, individual counseling, peer support groups, check-in texts, and treatment buddies. Based on patients' preferences, motivational texts and treatment buddies were removed from consideration in subsequent FGDs. Patients most preferred peer support groups and check-in texts while individual counseling garnered the broadest support among providers. Check-in texts, peer support groups, and data-informed counseling were also endorsed by provider sub-groups. These strategies warrant attention for scale-up in South Africa and other resource-constrained settings.
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Affiliation(s)
- Lora L Sabin
- Department of Global Health, Boston University School of Public Health, 801 Massachusetts Avenue, Crosstown, 3rd Floor, Boston, MA, 02118, USA.
| | - Allen L Gifford
- Section of General Internal Medicine, Boston University School of Medicine and Department of Health Law, Policy, and Management, Boston University School of Public Health, Boston, MA, 02118, USA
- Center for Healthcare Organization and Implementation Research, VA Boston Healthcare System, Boston, MA, 02130, USA
| | - Jessica E Haberer
- Center of Global Health, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02114, USA
| | - Kelsee Harvey
- Department of Global Health, Boston University School of Public Health, 801 Massachusetts Avenue, Crosstown, 3rd Floor, Boston, MA, 02118, USA
| | - Natalya Sarkisova
- Department of Global Health, Boston University School of Public Health, 801 Massachusetts Avenue, Crosstown, 3rd Floor, Boston, MA, 02118, USA
| | - Kyle Martin
- Department of Global Health, Boston University School of Public Health, 801 Massachusetts Avenue, Crosstown, 3rd Floor, Boston, MA, 02118, USA
| | - Rebecca L West
- Department of Global Health, Boston University School of Public Health, 801 Massachusetts Avenue, Crosstown, 3rd Floor, Boston, MA, 02118, USA
| | - Jessie Stephens
- Department of Global Health, Boston University School of Public Health, 801 Massachusetts Avenue, Crosstown, 3rd Floor, Boston, MA, 02118, USA
| | - Clare Killian
- Department of Global Health, Boston University School of Public Health, 801 Massachusetts Avenue, Crosstown, 3rd Floor, Boston, MA, 02118, USA
| | - Nafisa Halim
- Department of Global Health, Boston University School of Public Health, 801 Massachusetts Avenue, Crosstown, 3rd Floor, Boston, MA, 02118, USA
| | | | - Karen Jennings
- City of Cape Town Health Department, Cape Town, South Africa
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10
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Park SY, Faraci G, Murphy G, Pilcher C, Busch MP, Lee HY. Microdrop Human Immunodeficiency Virus Sequencing for Incidence and Drug Resistance Surveillance. J Infect Dis 2021; 224:1048-1059. [PMID: 33517458 DOI: 10.1093/infdis/jiab060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/26/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Precise and cost-efficient human immunodeficiency virus (HIV) incidence and drug resistance surveillances are in high demand for the advancement of the 90-90-90 "treatment for all" target. METHODS We developed microdrop HIV sequencing for the HIV incidence and drug resistance assay (HIDA), a single-blood-draw surveillance tool for incidence and drug resistance mutation (DRM) detection. We amplified full-length HIV envelope and pol gene sequences within microdroplets, and this compartmental amplification with long-read high-throughput sequencing enabled us to recover multiple unique sequences. RESULTS We achieved greater precision in determining the stage of infection than current incidence assays, with a 1.2% false recency rate (proportion of misclassified chronic infections) and a 262-day mean duration of recent infection (average time span of recent infection classification) from 83 recently infected and 81 chronically infected individuals. Microdrop HIV sequencing demonstrated an increased capacity to detect minority variants and linked DRMs. By screening all 93 World Health Organization surveillance DRMs, we detected 6 pretreatment drug resistance mutations with 2.6%-13.2% prevalence and cross-linked mutations. CONCLUSIONS HIDA with microdrop HIV sequencing may promote global HIV real-time surveillance by serving as a precise and high-throughput cross-sectional survey tool that can be generalized for surveillance of other pathogens.
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Affiliation(s)
- Sung Yong Park
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Gina Faraci
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Gary Murphy
- Public Health England, London, United Kingdom
| | - Christopher Pilcher
- Department of Medicine, University of California, San Francisco, California, USA
| | - Michael P Busch
- Research and Scientific Programs, Vitalant Research Institute, San Francisco, California, USA.,Deparment of Laboratory Medicine, University of California, California, San Francisco, USA
| | - Ha Youn Lee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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11
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Steegen K, Moorhouse M, Wensing AMJ, Venter WDF, Hans L. Is there a role for doravirine in African HIV treatment programmes? A large observational resistance study in South Africa. J Int AIDS Soc 2021; 24:e25706. [PMID: 33943000 PMCID: PMC8094661 DOI: 10.1002/jia2.25706] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/05/2021] [Accepted: 03/17/2021] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Dolutegravir has replaced efavirenz in most low- and middle-income countries, due to better tolerability and formidable resistance profile, but dolutegravir side effects suggest alternatives are needed. We evaluated doravirine resistance in South Africa as a first step to assess whether doravirine may replace dolutegravir. METHODS A retrospective dataset was analysed for predicted doravirine susceptibility, including sequences obtained from three patient groups. First, data from 277 patients initiating antiretroviral treatment (ART) were collected between February 2013 and October 2014 as part of a national survey. Second, data from 788 patients experiencing NNRTI-based ART failure were obtained between February 2013 and October 2014 as part of a national survey. Third, data derived from 584 patients who had genotypic drug resistance testing requested after NNRT-based failure as part of individual patient management between January 2016 and December 2019. Pol sequences were generated using validated population-based in-house genotyping and submitted to Stanford HIVdb v8.9. RESULTS AND DISCUSSION Less than 5% of patients initiating ART presented with genotypic doravirine resistance, whereas most patients experiencing NNRTI-based ART failure presented with predicted intermediate (41.0%) or high-level resistance (43.8%) to doravirine. High-level resistance to doravirine was commonly predicted by the presence of at least three DRMs (79.7%). The predicted resistance profile to doravirine in ART-naïve patients is promising, but less so in those experiencing failure to first-generation NNRTIs. Accumulation of NNRTI DRMs seems to be an important factor in the poor resistance prediction for doravirine. CONCLUSIONS Although doravirine is approved as initial therapy in patients who are ART-naïve, it is currently recommended to obtain a genotype prior to the initiation of ART. Clinical studies are needed to ascertain whether predicted resistance profiles in ART naïve and NNRTI-treated patients translate into poor clinical outcomes, especially in settings where genotypic resistance testing is not available.
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Affiliation(s)
- Kim Steegen
- Department of Molecular Medicine and HaematologyNational Health Laboratory ServicesJohannesburgSouth Africa
- Department of Molecular Medicine and HaematologyUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Michelle Moorhouse
- Ezintsha, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Global Medical AffairsViiV HealthCareJohannesburgSouth Africa
| | - Annemarie MJ Wensing
- Ezintsha, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Translational VirologyDepartment of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Willem DF Venter
- Ezintsha, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Lucia Hans
- Department of Molecular Medicine and HaematologyNational Health Laboratory ServicesJohannesburgSouth Africa
- Department of Molecular Medicine and HaematologyUniversity of the WitwatersrandJohannesburgSouth Africa
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12
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Obasa AE, Ambikan AT, Gupta S, Neogi U, Jacobs GB. Increased acquired protease inhibitor drug resistance mutations in minor HIV-1 quasispecies from infected patients suspected of failing on national second-line therapy in South Africa. BMC Infect Dis 2021; 21:214. [PMID: 33632139 PMCID: PMC7908688 DOI: 10.1186/s12879-021-05905-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND HIV-1C has been shown to have a greater risk of virological failure and reduced susceptibility towards boosted protease inhibitors (bPIs), a component of second-line combination antiretroviral therapy (cART) in South Africa. This study entailed an evaluation of HIV-1 drug resistance-associated mutations (RAMs) among minor viral populations through high-throughput sequencing genotypic resistance testing (HTS-GRT) in patients on the South African national second-line cART regimen receiving bPIs. METHODS During 2017 and 2018, 67 patient samples were sequenced using high-throughput sequencing (HTS), of which 56 samples were included in the final analysis because the patient's treatment regimen was available at the time of sampling. All patients were receiving bPIs as part of their cART. Viral RNA was extracted, and complete pol genes were amplified and sequenced using Illumina HiSeq2500, followed by bioinformatics analysis to quantify the RAMs according to the Stanford HIV Drug Resistance Database. RESULTS Statistically significantly higher PI RAMs were observed in minor viral quasispecies (25%; 14/56) compared to non-nucleoside reverse transcriptase inhibitors (9%; 5/56; p = 0.042) and integrase inhibitor RAM (4%; 2/56; p = 0.002). The majority of the drug resistance mutations in the minor viral quasispecies were observed in the V82A mutation (n = 13) in protease and K65R (n = 5), K103N (n = 7) and M184V (n = 5) in reverse transcriptase. CONCLUSIONS HTS-GRT improved the identification of PI and reverse transcriptase inhibitor (RTI) RAMs in second-line cART patients from South Africa compared to the conventional GRT with ≥20% used in Sanger-based sequencing. Several RTI RAMs, such as K65R, M184V or K103N and PI RAM V82A, were identified in < 20% of the population. Deep sequencing could be of greater value in detecting acquired resistance mutations early.
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Affiliation(s)
- Adetayo Emmanuel Obasa
- Department of Pathology, Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, 7505, South Africa.
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institute, Stockholm, Sweden.
| | - Anoop T Ambikan
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institute, Stockholm, Sweden
| | - Soham Gupta
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institute, Stockholm, Sweden
| | - Ujjwal Neogi
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institute, Stockholm, Sweden
| | - Graeme Brendon Jacobs
- Department of Pathology, Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, 7505, South Africa
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13
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Nel A, van Niekerk N, Van Baelen B, Malherbe M, Mans W, Carter A, Steytler J, van der Ryst E, Craig C, Louw C, Gwetu T, Mabude Z, Kotze P, Moraba R, Tempelman H, Gill K, Kusemererwa S, Bekker LG, Devlin B, Rosenberg Z. Safety, adherence, and HIV-1 seroconversion among women using the dapivirine vaginal ring (DREAM): an open-label, extension study. Lancet HIV 2021; 8:e77-e86. [PMID: 33539761 DOI: 10.1016/s2352-3018(20)30300-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/13/2020] [Accepted: 10/21/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND The Ring Study, a phase 3 trial in 1959 sexually active women (randomised 2:1), showed a favourable safety profile and a 31% HIV-1 infection risk reduction for a vaginal ring containing 25 mg of dapivirine, compared with a placebo ring. We report here the DREAM study, which aimed to evaluate safety, adherence, and HIV-1 incidence in those using the dapivirine vaginal ring (DVR) in open-label use. METHODS The DREAM study is an open-label extension of The Ring Study, done at five research centres in South Africa and one research centre in Uganda. Former participants from The Ring Study, who remained HIV-negative and who did not discontinue the study due to an adverse event or safety concern that was considered to be related to the investigational product, were eligible. Women who were pregnant, planning to become pregnant, or breastfeeding at screening for DREAM were excluded. All participants received the DVR for insertion at the enrolment visit. Participants attended a 1-month follow-up visit and could either proceed with visits once every 3 months or attend monthly visits up to month 3 and then continue with visits once every 3 months. At each visit, HIV testing and safety evaluations were done, and residual dapivirine measured in used rings (approximately 4 mg is released from the DVR over 28 days of consistent use). HIV-1 incidence was compared descriptively with the simulated incidence rate obtained from bootstrap sampling of participants in the placebo group of The Ring Study, matched for research centre, age, and presence of sexually transmitted infections at enrolment. This study is registered with ClinicalTrials.gov, NCT02862171. FINDINGS Between July 12, 2016, and Jan 11, 2019, 1034 former participants from The Ring Study were screened, 941 were enrolled and 848 completed the trial. 616 (65·5%) of 941 participants reported treatment-emergent adverse events. Of these, six (0·6%) had events considered to be treatment-related. No treatment-related serious adverse events were reported. Measurements of monthly ring residual amounts in participants enrolled in both trials showed consistently lower mean values in DREAM than in The Ring Study. Arithmetic mean ring residual amounts of participants in The Ring Study DVR group who enrolled in DREAM were 0·25 mg lower (95% CI 0·03-0·47; p=0·027) than the mean ring residual amounts of these participants in The Ring Study. 18 (1·9%) HIV-1 infections were confirmed during DVR use, resulting in an incidence of 1·8 (95% CI 1·1-2·6) per 100 person-years, 62% lower than the simulated placebo rate. INTERPRETATION Although efficacy estimation is limited by the absence of a placebo group, the observed low HIV-1 incidence and improved adherence observed in DREAM support the hypothesis that increased efficacy due to improved adherence occurs when women know the demonstrated safety and efficacy of the DVR. The feasibility of a visit schedule of once every 3 months was shown, indicating that the DVR can be used in a real-world situation in usual clinical practice. FUNDING The Ministry of Foreign Affairs (MFA) Denmark, Flanders MFA, Irish Aid, Dutch MFA, UK Aid from the UK Government's Foreign, Commonwealth and Development Office, and the US President's Emergency Plan for AIDS Relief through the US Agency for International Development.
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Affiliation(s)
- Annalene Nel
- Medinel CC Clinical Consulting, Paarl, South Africa
| | | | | | | | - Winél Mans
- Independent Consultant, Paarl, South Africa
| | | | - John Steytler
- International Partnership for Microbicides, Paarl, South Africa
| | | | | | - 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
| | | | | | - Katherine Gill
- Desmond Tutu HIV Centre, University of Cape Town, Observatory, Cape Town, South Africa
| | - Sylvia Kusemererwa
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Linda-Gail Bekker
- Desmond Tutu HIV Centre, University of Cape Town, Observatory, Cape Town, South Africa
| | - Brid Devlin
- International Partnership for Microbicides, Silver Spring, MD, USA
| | - Zeda Rosenberg
- International Partnership for Microbicides, Silver Spring, MD, USA.
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Bessong PO, Matume ND, Tebit DM. Potential challenges to sustained viral load suppression in the HIV treatment programme in South Africa: a narrative overview. AIDS Res Ther 2021; 18:1. [PMID: 33407664 PMCID: PMC7788882 DOI: 10.1186/s12981-020-00324-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 11/16/2020] [Indexed: 12/14/2022] Open
Abstract
Background South Africa, with one of the highest HIV prevalences in the world, introduced the universal test and treat (UTT) programme in September 2016. Barriers to sustained viral suppression may include drug resistance in the pre-treated population, non-adherence, acquired resistance; pharmacokinetics and pharmacodynamics, and concurrent use of alternative treatments. Objective The purpose of this review is to highlight potential challenges to achieving sustained viral load suppression in South Africa (SA), a major expectation of the UTT initiative. Methodology Through the PRISMA approach, published articles from South Africa on transmitted drug resistance; adherence to ARV; host genetic factors in drug pharmacokinetics and pharmacodynamics, and interactions between ARV and herbal medicine were searched and reviewed. Results The level of drug resistance in the pre-treated population in South Africa has increased over the years, although it is heterogeneous across and within Provinces. At least one study has documented a pre-treated population with moderate (> 5%) or high (> 15%) levels of drug resistance in eight of the nine Provinces. The concurrent use of ARV and medicinal herbal preparation is fairly common in SA, and may be impacting negatively on adherence to ARV. Only few studies have investigated the association between the genetically diverse South African population and pharmacokinetics and pharmacodynamics of ARVs. Conclusion The increasing levels of drug resistant viruses in the pre-treated population poses a threat to viral load suppression and the sustainability of first line regimens. Drug resistance surveillance systems to track the emergence of resistant viruses, study the burden of prior exposure to ARV and the parallel use of alternative medicines, with the goal of minimizing resistance development and virologic failure are proposed for all the Provinces of South Africa. Optimal management of the different drivers of drug resistance in the pre-treated population, non-adherence, and acquired drug resistance will be beneficial in ensuring sustained viral suppression in at least 90% of those on treatment, a key component of the 90-90-90 strategy.
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15
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Moyo S, Hunt G, Zuma K, Zungu M, Marinda E, Mabaso M, Kana V, Kalimashe M, Ledwaba J, Naidoo I, Takatshana S, Matjokotja T, Dietrich C, Raizes E, Diallo K, Kindra G, Mugore L, Rehle T. HIV drug resistance profile in South Africa: Findings and implications from the 2017 national HIV household survey. PLoS One 2020; 15:e0241071. [PMID: 33147285 PMCID: PMC7641411 DOI: 10.1371/journal.pone.0241071] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND HIV drug resistance (HIVDR) testing was included in the 2017 South African national HIV household survey. We describe the prevalence of HIVDR by drug class, age, sex and antiretroviral drugs (ARV) status. METHODS Dried blood were spots tested for HIV, with Viral load (VL), exposure to ARVs and HIVDR testing among those HIV positive. HIVDR testing was conducted on samples with VL ≥1000 copies/ml using Next Generation Sequencing. Weighted percentages of HIVDR are reported. RESULTS 697/1,105 (63%) of HIV positive samples were sequenced. HIVDR was detected in samples from 200 respondents (27.4% (95% confidence interval (CI) 22.8-32.6)). Among these 130 (18.9% (95% CI 14.8-23.8)), had resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) only, 63 (7.8% (95% CI 5.6-10.9)) resistance to NNRTIs and nucleoside reverse transcriptase inhibitors, and 3 (0.5% (95% CI 0.1-2.1)) resistance to protease inhibitors. Sixty-five (55.7% (95% CI 42.6-67.9) of ARV-positive samples had HIVDR compared to 112 (22.8% (95% CI 17.7-28.7)), in ARV-negative samples. HIVDR was found in 75.6% (95% CI 59.2-87.3), n = 27, samples from respondents who reported ARV use but tested ARV-negative, and in 15.3% (95% CI 6.3-32.8), n = 7, respondents who reported no ARV use and tested ARV-negative. There were no significant age and sex differences in HIVDR. CONCLUSION 27% of virally unsuppressed respondents had HIVDR, increasing to 75% among those who had discontinued ARV. Our findings support strengthening first-line ARV regimens by including drugs with a higher resistance barrier and treatment adherence strategies, and close monitoring of HIVDR.
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Affiliation(s)
- Sizulu Moyo
- Human Sciences Research Council, Pretoria, South Africa
- School of Public Health, University of Cape Town, Cape Town, South Africa
| | - Gillian Hunt
- Centre for HIV and STIs, National Institute of Communicable Diseases, Johannesburg, South Africa
| | | | - Mpumi Zungu
- Human Sciences Research Council, Pretoria, South Africa
| | - Edmore Marinda
- Human Sciences Research Council, Pretoria, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Vibha Kana
- Centre for HIV and STIs, National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Monalisa Kalimashe
- Centre for HIV and STIs, National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Johanna Ledwaba
- Centre for HIV and STIs, National Institute of Communicable Diseases, Johannesburg, South Africa
| | | | | | | | - Cheryl Dietrich
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Elliot Raizes
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Karidia Diallo
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Gurpreet Kindra
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Linnetie Mugore
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Thomas Rehle
- School of Public Health, University of Cape Town, Cape Town, South Africa
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16
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Lippman SA, Mooney AC, Puren A, Hunt G, Grignon JS, Prach LM, Gilmore HJ, Truong HHM, Barnhart S, Liegler T. The role of drug resistance in poor viral suppression in rural South Africa: findings from a population-based study. BMC Infect Dis 2020; 20:248. [PMID: 32216752 PMCID: PMC7099808 DOI: 10.1186/s12879-020-4933-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/28/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Understanding factors driving virological failure, including the contribution of HIV drug resistance mutations (DRM), is critical to ensuring HIV treatment remains effective. We examine the contribution of drug resistance mutations for low viral suppression in HIV-positive participants in a population-based sero-prevalence survey in rural South Africa. METHODS We conducted HIV drug resistance genotyping and ART analyte testing on dried blood spots (DBS) from HIV-positive adults participating in a 2014 survey in North West Province. Among those with virologic failure (> 5000 copies/mL), we describe frequency of DRM to protease inhibitors (PI), nucleoside reverse transcriptase inhibitors (NRTI), and non-nucleoside reverse transcriptase inhibitors (NNRTI), report association of resistance with antiretroviral therapy (ART) status, and assess resistance to first and second line therapy. Analyses are weighted to account for sampling design. RESULTS Overall 170 DBS samples were assayed for viral load and ART analytes; 78.4% of men and 50.0% of women had evidence of virologic failure and were assessed for drug resistance, with successful sequencing of 76/107 samples. We found ≥1 DRM in 22% of participants; 47% were from samples with detectable analyte (efavirenz, nevirapine or lopinavir). Of those with DRM and detectable analyte, 60% showed high-level resistance and reduced predicted virologic response to ≥1 NRTI/NNRTI typically used in first and second-line regimens. CONCLUSIONS DRM and predicted reduced susceptibility to first and second-line regimens were common among adults with ART exposure in a rural South African population-based sample. Results underscore the importance of ongoing virologic monitoring, regimen optimization and adherence counseling to optimize durable virologic suppression.
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Affiliation(s)
- Sheri A Lippman
- Division of Prevention Science, Department of Medicine, University of California San Francisco, 550 16th Street, 3rd Floor, San Francisco, CA, 94158-2549, USA.
| | - Alyssa C Mooney
- Department of Epidemiology, University of California San Francisco, San Francisco, USA
| | - Adrian Puren
- National Institute for Communicable Diseases/NHLS, Johannesburg, South Africa
- Division of Virology, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Gillian Hunt
- National Institute for Communicable Diseases/NHLS, Johannesburg, South Africa
- Division of Virology, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Jessica S Grignon
- Department of Global Health, University of Washington, Seattle, USA
- International Training and Education Center for Health (I-TECH) South Africa, Pretoria, Republic of South Africa
| | - Lisa M Prach
- Division of Prevention Science, Department of Medicine, University of California San Francisco, 550 16th Street, 3rd Floor, San Francisco, CA, 94158-2549, USA
| | - Hailey J Gilmore
- Division of Prevention Science, Department of Medicine, University of California San Francisco, 550 16th Street, 3rd Floor, San Francisco, CA, 94158-2549, USA
| | - Hong-Ha M Truong
- Division of Prevention Science, Department of Medicine, University of California San Francisco, 550 16th Street, 3rd Floor, San Francisco, CA, 94158-2549, USA
| | - Scott Barnhart
- Department of Global Health, University of Washington, Seattle, USA
- International Training and Education Center for Health (I-TECH) South Africa, Pretoria, Republic of South Africa
| | - Teri Liegler
- Department of Medicine, University of California San Francisco, San Francisco, USA
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17
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Obasa AE, Mikasi SG, Brado D, Cloete R, Singh K, Neogi U, Jacobs GB. Drug Resistance Mutations Against Protease, Reverse Transcriptase and Integrase Inhibitors in People Living With HIV-1 Receiving Boosted Protease Inhibitors in South Africa. Front Microbiol 2020; 11:438. [PMID: 32265875 PMCID: PMC7099763 DOI: 10.3389/fmicb.2020.00438] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/02/2020] [Indexed: 12/17/2022] Open
Abstract
The South African national combination antiretroviral therapy (cART) roll-out program started in 2006, with over 4.4 million people accessing treatment since it was first introduced. HIV-1 drug resistance can hamper the success of cART. This study determined the patterns of HIV-1 drug-resistance associated mutations (RAMs) in People Living with HIV-1 (PLHIV-1). Receiving first (for children below 3 years of age) and second-line (for adults) cART regimens in South Africa. During 2017 and 2018, 110 patients plasma samples were selected, 96 samples including those of 17 children and infants were successfully analyzed. All patients were receiving a boosted protease inhibitor (bPI) as part of their cART regimen. The viral sequences were analyzed for RAMs through genotypic resistance testing. We performed genotypic resistance testing (GRT) for Protease inhibitors (PIs), Reverse transcriptase inhibitors (RTIs) and Integrase strand transfer inhibitors (InSTIs). Viral sequences were subtyped using REGAv3 and COMET. Based on the PR/RT sequences, HIV-1 subtypes were classified as 95 (99%) HIV-1 subtype C (HIV-1C) while one sample as 02_AG. Integrase sequencing was successful for 89 sequences, and all the sequences were classified as HIV-1C (99%, 88/89) except one sequence classified CRF02_AG, as observed in PR/RT. Of the 96 PR/RT sequences analyzed, M184V/I (52/96; 54%) had the most frequent RAM nucleoside reverse transcriptase inhibitor (NRTI). The most frequent non-nucleoside reverse transcriptase inhibitor (NNRTI) RAM was K103N/S (40/96, 42%). Protease inhibitor (PI) RAMs M46I and V82A were present in 12 (13%) of the sequences analyzed. Among the InSTI major RAM two (2.2%) sequences have Y143R and T97A mutations while one sample had T66I. The accessory RAM E157Q was identified in two (2.2%). The data indicates that the majority of the patients failed on bPIs didn't have any mutation; therefore adherence could be major issue in these groups of individuals. We propose continued viral load monitoring for better management of infected PLHIV.
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Affiliation(s)
- Adetayo Emmanuel Obasa
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm University, Stockholm, Sweden
| | - Sello Given Mikasi
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Dominik Brado
- Division of Virology, Institute for Virology and Immunobiology, Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Kamlendra Singh
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm University, Stockholm, Sweden
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm University, Stockholm, Sweden
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Machado LY, Blanco M, López LS, Díaz HM, Dubed M, Valdés N, Noa E, Martínez L, Pérez MT, Romay DM, Rivero CB, Joanes J, Cancio I, Lantero MI, Rodríguez M. National survey of pre-treatment HIV drug resistance in Cuban patients. PLoS One 2019; 14:e0221879. [PMID: 31479466 PMCID: PMC6719847 DOI: 10.1371/journal.pone.0221879] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/17/2019] [Indexed: 11/22/2022] Open
Abstract
Background The World Health Organization (WHO) recommends a method to estimate nationally representative pretreatment HIV drug resistance (PDR) in order to evaluate the effectiveness of first -line treatments. The objective of the present study was to determine the prevalence of PDR in Cuban adults infected with HIV-1. Materials and methods A cross-sectional study in Cuban adults infected with HIV-1 over 18 years was conducted. The probability proportional to size method for the selection of municipalities and patients without a prior history of antiretroviral treatment during the period from January 2017 to June 2017 was used. The plasma from 141 patients from 15 municipalities for the determination of viral subtype and HIV drug resistance was collected. Some clinical and epidemiological variables were evaluated. Results 80. 9% of the patients corresponded to the male sex and 76.3% were men who have sex with other men (MSM). The median CD4 count was 371 cells / mm3 and the median viral load was 68000 copies / mL. The predominant genetic variants were subtype B (26.9%), CRF19_cpx (24.1%), CRF 20, 23, 24_BG (23.4%) and CRF18_cpx (12%). Overall, the prevalence of PDR was 29.8% (95%, CI 22.3–38.1). The prevalence was 12.8% (95%, CI 6.07–16.9) for any nucleoside reverse transcriptase inhibitor (NRTI), 23.4% (95%, CI 16.7–31.3) for any non-reverse transcriptase inhibitor (NNRTI) and 1.4% (95%, CI 0.17–5.03) for any protease inhibitor (PI). The most frequent mutations detected were K103N (12.9%), G190A (6.4%) and Y181C (4.8%). Conclusions The NNRTI prevalence above 10% in our study indicates that the first-line antiretroviral therapy in Cuba may be less effective and supports the need to look for new treatment options that contribute to therapeutic success and help the country achieve the global goals 90-90-90 set forth by UNAIDS.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - José Joanes
- Department of STI/HIV/AIDS, Ministry of Public Health, Havana, Cuba
| | - Isis Cancio
- Department of STI/HIV/AIDS, Ministry of Public Health, Havana, Cuba
| | - María I. Lantero
- Department of STI/HIV/AIDS, Ministry of Public Health, Havana, Cuba
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Abbas UL, Glaubius RL, Ding Y, Hood G. Drug resistance from preferred antiretroviral regimens for HIV infection in South Africa: A modeling study. PLoS One 2019; 14:e0218649. [PMID: 31269034 PMCID: PMC6609148 DOI: 10.1371/journal.pone.0218649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 06/06/2019] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Tenofovir-containing regimens comprise the preferred first-line antiretroviral therapy (ART) in many countries including South Africa, where utilization of second-line regimens is limited. Considerable HIV drug resistance has occurred among persons failing tenofovir-containing first-line ART. We evaluated drug resistance at the population level using mathematical modeling. SETTING Heterosexual HIV epidemic in KwaZulu-Natal, South Africa. METHODS We constructed a stochastic individual-based model and simulated scenarios of ART implementation, either CD4-based (threshold < 500 cells/mL) or Fast-track (81% coverage by 2020), with consideration of major drug-associated mutations (M184V, K65R and non-nucleoside reverse transcriptase inhibitor (NNRTI)). Using base case and uncertainty analyses, we assessed (majority) drug resistance levels. RESULTS By 2030, the median total resistance (proportion of HIV-infected persons with drug resistance) is predicted to reach 31.4% (interquartile range (IQR): 16.5%-50.2%) with CD4-based ART, decreasing to 14.5% (IQR: 7.7%-25.8%) with Fast-track implementation. In both scenarios, we find comparably high prevalence (~80%) of acquired NNRTI-associated, M184V and K65R mutations. Over 48% of individuals with acquired resistance harbor dual, 44% triple and 7% just single drug mutations. Drug-resistant HIV is predicted to comprise 40% (IQR: 27%-50%) of incident infections, while 70% of prevalent transmitted resistance is NNRTI-associated. At 2018, the projected total resistance is 15% (IQR: 7.5%-25%), with 18% (IQR: 13%-24%) of incident infections from transmitted drug-resistant HIV. CONCLUSIONS WHO-recommended preferred first-line ART could lead to substantial drug resistance. Effective surveillance of HIV drug resistance and utilization of second-line as well as alternative first-line regimens is crucial.
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Affiliation(s)
- Ume L. Abbas
- Department of Medicine, Section of Infectious Diseases and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Departments of Quantitative Health Sciences and Infectious Disease, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Robert L. Glaubius
- Departments of Quantitative Health Sciences and Infectious Disease, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Yajun Ding
- Department of Medicine, Section of Infectious Diseases and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Gregory Hood
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
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Derache A, Iwuji CC, Baisley K, Danaviah S, Marcelin AG, Calvez V, de Oliveira T, Dabis F, Porter K, Pillay D. Impact of Next-generation Sequencing Defined Human Immunodeficiency Virus Pretreatment Drug Resistance on Virological Outcomes in the ANRS 12249 Treatment-as-Prevention Trial. Clin Infect Dis 2019; 69:207-214. [PMID: 30321314 PMCID: PMC6603266 DOI: 10.1093/cid/ciy881] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 10/09/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Previous studies in human immunodeficiency virus (HIV)-positive individuals on thymidine analogue backbone antiretroviral therapy (ART) with either nevirapine or efavirenz have suggested poorer virological outcomes in the presence of pretreatment drug resistance (PDR). We assessed the impact of PDR on virological suppression (VS; <50 copies/mL) in individuals prescribed primarily tenofovir/emtricitabine/efavirenz in rural KwaZulu-Natal within a treatment-as-prevention trial. METHODS Among 1557 HIV-positive individuals who reported no prior ART at study entry and provided plasma samples, 1328 individuals with entry viral load (VL) >1000 copies/mL had next-generation sequencing (NGS) of the HIV pol gene with MiSeq technology. Results were obtained for 1148 individuals, and the presence of PDR was assessed at 5% and 20% detection thresholds. Virological outcome was assessed using Cox regression in 837 of 920 ART initiators with at least 1 follow-up VL after ART initiation. RESULTS PDR prevalence was 9.5% (109/1148) and 12.8% (147/1148) at 20% and 5% thresholds, respectively. After a median of 1.36 years (interquartile range, 0.91-2.13), mostly on fixed-dose combination tenofovir/emtricitabine/efavirenz, presence of both nonnucleoside reverse transcriptase inhibitor (NNRTI)/nucleoside reverse transcriptase inhibitor PDR vs no PDR was associated with longer time to VS (adjusted hazard ratio [aHR], 0.32; 95% confidence interval [CI], 0.12-0.86), while there was no difference between those with only NNRTI PDR vs no PDR (aHR, 1.05; 95% CI, 0.82-1.34) at the 5% threshold. Similar differences were observed for mutations detected at the 20% threshold, although without statistical significance. CONCLUSIONS NGS uncovered a high prevalence of PDR among participants enrolled in trial clinics in rural KwaZulu-Natal. Dual-class PDR to a mainly tenofovir/emtricitabine/efavirenz regimen was associated with poorer VS. However, there was no impact of NNRTI PDR alone. CLINICAL TRIALS TEGISTRATION NCT01509508; South African National Clinical Trials Register: DOH-27-0512-3974.
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Affiliation(s)
- Anne Derache
- Africa Health Research Institute, Mtubatuba, South Africa
- Sorbonne University, l’université Pierre et Marie Curie, Institut national de la santé et de la recherche médicale, Institut Pierre Louis d’Epidémiologie et de Santé Publique Unité Mixte de Recherche en Santé (IPLESP UMRS 1136), Paris, France
| | - Collins C Iwuji
- Africa Health Research Institute, Mtubatuba, South Africa
- Department of Global Health and Infection, Brighton and Sussex Medical School
- Institute for Global Health, University College London, United Kingdom
| | - Kathy Baisley
- Sorbonne University, l’université Pierre et Marie Curie, Institut national de la santé et de la recherche médicale, Institut Pierre Louis d’Epidémiologie et de Santé Publique Unité Mixte de Recherche en Santé (IPLESP UMRS 1136), Paris, France
| | - Siva Danaviah
- Africa Health Research Institute, Mtubatuba, South Africa
| | - Anne-Geneviève Marcelin
- Sorbonne University, l’université Pierre et Marie Curie, Institut national de la santé et de la recherche médicale, Institut Pierre Louis d’Epidémiologie et de Santé Publique Unité Mixte de Recherche en Santé (IPLESP UMRS 1136), Paris, France
| | - Vincent Calvez
- Sorbonne University, l’université Pierre et Marie Curie, Institut national de la santé et de la recherche médicale, Institut Pierre Louis d’Epidémiologie et de Santé Publique Unité Mixte de Recherche en Santé (IPLESP UMRS 1136), Paris, France
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - François Dabis
- Université de Bordeaux, Institut de Santé Publique d’Epidémiologie et de Développement, Centre Institut national de la santé et de la recherche médicale 1219, France
| | - Kholoud Porter
- Institute for Global Health, University College London, United Kingdom
| | - Deenan Pillay
- Africa Health Research Institute, Mtubatuba, South Africa
- Division of Infection and Immunity, University College London, United Kingdom
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Hauser A, Kusejko K, Johnson LF, Wandeler G, Riou J, Goldstein F, Egger M, Kouyos RD. Bridging the gap between HIV epidemiology and antiretroviral resistance evolution: Modelling the spread of resistance in South Africa. PLoS Comput Biol 2019; 15:e1007083. [PMID: 31233494 PMCID: PMC6611642 DOI: 10.1371/journal.pcbi.1007083] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 07/05/2019] [Accepted: 05/06/2019] [Indexed: 11/19/2022] Open
Abstract
The scale-up of antiretroviral therapy (ART) in South Africa substantially reduced AIDS-related deaths and new HIV infections. However, its success is threatened by the emergence of resistance to non-nucleoside reverse-transcriptase inhibitors (NNRTI). The MARISA (Modelling Antiretroviral drug Resistance In South Africa) model presented here aims at investigating the time trends and factors driving NNRTI resistance in South Africa. MARISA is a compartmental model that includes the key aspects of the local HIV epidemic: continuum of care, disease progression, and gender. The dynamics of NNRTI resistance emergence and transmission are then added to this framework. Model parameters are informed using data from HIV cohorts participating in the International epidemiology Databases to Evaluate AIDS (IeDEA) and literature estimates, or fitted to UNAIDS estimates. Using this novel approach of triangulating clinical and resistance data from various sources, MARISA reproduces the time trends of HIV in South Africa in 2005–2016, with a decrease in new infections, undiagnosed individuals, and AIDS-related deaths. MARISA captures the dynamics of the spread of NNRTI resistance: high levels of acquired drug resistance (ADR, in 83% of first-line treatment failures in 2016), and increasing transmitted drug resistance (TDR, in 8.1% of ART initiators in 2016). Simulation of counter-factual scenarios reflecting alternative public health policies shows that increasing treatment coverage would have resulted in fewer new infections and deaths, at the cost of higher TDR (11.6% in 2016 for doubling the treatment rate). Conversely, improving switching to second-line treatment would have led to lower TDR (6.5% in 2016 for doubling the switching rate) and fewer new infections and deaths. Implementing drug resistance testing would have had little impact. The rapid ART scale-up and inadequate switching to second-line treatment were the key drivers of the spread of NNRTI resistance in South Africa. However, even though some interventions could have substantially reduced the level of NNRTI resistance, no policy including NNRTI-based first line regimens could have prevented this spread. Thus, by combining epidemiological data on HIV in South Africa with biological data on resistance evolution, our modelling approach identified key factors driving NNRTI resistance, highlighting the need of alternative first-line regimens. Resistance to non-nucleoside reverse transcriptase inhibitors (NNRTI) threatens the long-term success of antiretroviral therapy (ART) roll-out in South Africa. We developed a compartmental model integrating the local HIV epidemiology with biological mechanisms of drug resistance. A first dimension of the model accounts for the continuum of care: infection, diagnosis, first-line treatment with suppression or failure, and second-line treatment. Other dimensions include: disease progression (CD4 counts), gender, and acquisition and transmission of NNRTI resistance. Whenever possible, we informed the parameters using the data available from local cohorts. Other parameters were informed using literature or UNAIDS estimates. The model captured the rise of NNRTI resistance during the period. We assessed the impact of counter-factual scenarios reflecting alternative countrywide policies during the period 2005 to 2016, considering either increasing ART coverage, improving management of treatment failure, broadening ART eligibility, or implementing drug resistance testing before ART initiation. We identified key drivers of the NNRTI resistance epidemic: large-scale ART roll-out and insufficient monitoring of first-line treatment failure. The model also suggested that no policy including NNRTI-based first line regimens could have prevented the spread of NNRTI resistance.
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Affiliation(s)
- Anthony Hauser
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Leigh F. Johnson
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town, South Africa
| | - Gilles Wandeler
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Julien Riou
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
| | - Fardo Goldstein
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town, South Africa
| | - Roger D. Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- * E-mail:
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22
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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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Black V, Schwartz SR. Issues about periconception use of dolutegravir are reminiscent of early concerns about efavirenz. Lancet HIV 2019; 5:e732-e736. [PMID: 30527330 DOI: 10.1016/s2352-3018(18)30249-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/24/2018] [Accepted: 09/04/2018] [Indexed: 11/19/2022]
Abstract
South Africa intends to include dolutegravir in its first-line antiretroviral therapy (ART) regimen because of cost savings, the drug's high barrier to resistance, and efficacy. However, recent data from Botswana suggest potential teratogenicity of dolutegravir. WHO recommends that non-pregnant women of childbearing age who are not using an effective form of contraception and women in early pregnancy should not initiate treatment with dolutegravir. Similar concerns about efavirenz once existed; the 2010 South African ART guidelines recommended that pregnant women and women at-risk of pregnancy should not be given efavirenz. Screening of fertility intentions and contraceptive use were poor, and protocols for regimen changes were unevenly implemented across South Africa. High incidence of unplanned pregnancies and late pregnancy diagnosis resulted in delays in efavirenz substitution. In the absence of reassuring safety data on dolutegravir, South Africa should learn from past mistakes and develop systems to ensure improved communication with patients and better integration of comprehensive reproductive health services.
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Affiliation(s)
- Vivian Black
- Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Sheree R Schwartz
- Center for Public Health and Human Rights, Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Bester PA, De Vries A, Riekert S, Steegen K, van Zyl G, Goedhals D. PhyloPi: An affordable, purpose built phylogenetic pipeline for the HIV drug resistance testing facility. PLoS One 2019; 14:e0213241. [PMID: 30835760 PMCID: PMC6400384 DOI: 10.1371/journal.pone.0213241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 02/19/2019] [Indexed: 12/05/2022] Open
Abstract
INTRODUCTION Phylogenetic analysis plays a crucial role in quality control in the HIV drug resistance testing laboratory. If previous patient sequence data is available sample swaps can be detected and investigated. As Antiretroviral treatment coverage is increasing in many developing countries, so is the need for HIV drug resistance testing. In countries with multiple languages, transcription errors are easily made with patient identifiers. Here a self-contained blastn integrated phylogenetic pipeline can be especially useful. Even though our pipeline can run on any unix based system, a Raspberry Pi 3 is used here as a very affordable and integrated solution. PERFORMANCE BENCHMARKS The computational capability of this single board computer is demonstrated as well as the utility thereof in the HIV drug resistance laboratory. Benchmarking analysis against a large public database shows excellent time performance with minimal user intervention. This pipeline also contains utilities to find previous sequences as well as phylogenetic analysis and a graphical sequence mapping utility against the pol area of the HIV HXB2 reference genome. Sequence data from the Los Alamos HIV database was analyzed for inter- and intra-patient diversity and logistic regression was conducted on the calculated genetic distances. These findings show that allowable clustering and genetic distance between viral sequences from different patients is very dependent on subtype as well as the area of the viral genome being analyzed. AVAILABILITY The Raspberry Pi image for PhyloPi, source code of the pipeline, sequence data, bash-, python- and R-scripts for the logistic regression, benchmarking as well as helper scripts are available at http://scholar.ufs.ac.za:8080/xmlui/handle/11660/7638 and https://github.com/ArmandBester/phylopi. The PhyloPi image and the source code are published under the GPLv3 license. A demo version of the PhyloPi pipeline is available at http://phylopi.hpc.ufs.ac.za/.
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Affiliation(s)
- Phillip Armand Bester
- Division of Virology, University of the Free State and National Health Laboratory Service (NHLS), Bloemfontein, South Africa
| | - Andrie De Vries
- RStudio Team (2016). RStudio: Integrated Development for R. RStudio, Inc., Boston, MA, United States of America
| | - Stephanus Riekert
- Information and Communication Technology Services, University of the Free State, Bloemfontein, South Africa
| | - Kim Steegen
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Gert van Zyl
- Division of Medical Virology, Stellenbosch University and National Health Laboratory Service (NHLS) Tygerberg, Cape Town, South Africa
| | - Dominique Goedhals
- Division of Virology, University of the Free State and National Health Laboratory Service (NHLS), Bloemfontein, South Africa
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Burman C, Aphane M. Improved adherence to anti-retroviral therapy among traditionalists: reflections from rural South Africa. Afr Health Sci 2019; 19:1422-1432. [PMID: 31148969 PMCID: PMC6531950 DOI: 10.4314/ahs.v19i1.15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Medical pluralism is common place in sub-Saharan Africa. The South African pluralistic health care environment is varied and includes traditionalist beliefs relating to the efficacy of African traditional medicine. Prior research indicates that traditionalism is associated with delays in testing for HIV and treatment interruption. Despite numerous reports about this in South Africa, there is a paucity of documented strategies to counter this trend. OBJECTIVES To develop a strategy to reduce the impact of non-adherence to antiretroviral therapy among traditionalists in Waterberg district, Limpopo Province, South Africa. METHODS Qualitative information was elicited from five face-to-face, dual moderated, semi-structured homogenous group discussions. The groups comprised of 50 purposively selected, rurally based, mixed gender traditionalists living with HIV. Grounded theory was applied to analyse qualitative findings that emerged from the group discussions. FINDINGS Self-reported increases in adherence to anti-retroviral therapy and a reduction in internalised stigma by the respondents. Both are attributed by the respondents to disease causation differentiation from a traditional explanation to an allopathic explanation. CONCLUSION A nascent strategy has been developed which is contributing to improved adherence and a reduction in internalised stigma among traditionalists living with HIV in Waterberg district, South Africa.
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Affiliation(s)
- Christopher Burman
- University of Limpopo, Rural Development and Innovation Hub, affiliated to the Turfloop Graduate School of Leadership
| | - Marota Aphane
- University of Venda, Department of Research and Innovation
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Chimukangara B, Lessells RJ, Rhee SY, Giandhari J, Kharsany AB, Naidoo K, Lewis L, Cawood C, Khanyile D, Ayalew KA, Diallo K, Samuel R, Hunt G, Vandormael A, Stray-Pedersen B, Gordon M, Makadzange T, Kiepiela P, Ramjee G, Ledwaba J, Kalimashe M, Morris L, Parikh UM, Mellors JW, Shafer RW, Katzenstein D, Moodley P, Gupta RK, Pillay D, Abdool Karim SS, de Oliveira T. Trends in Pretreatment HIV-1 Drug Resistance in Antiretroviral Therapy-naive Adults in South Africa, 2000-2016: A Pooled Sequence Analysis. EClinicalMedicine 2019; 9:26-34. [PMID: 31143879 PMCID: PMC6510720 DOI: 10.1016/j.eclinm.2019.03.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND South Africa has the largest public antiretroviral therapy (ART) programme in the world. We assessed temporal trends in pretreatment HIV-1 drug resistance (PDR) in ART-naïve adults from South Africa. METHODS We included datasets from studies conducted between 2000 and 2016, with HIV-1 pol sequences from more than ten ART-naïve adults. We analysed sequences for the presence of 101 drug resistance mutations. We pooled sequences by sampling year and performed a sequence-level analysis using a generalized linear mixed model, including the dataset as a random effect. FINDINGS We identified 38 datasets, and retrieved 6880 HIV-1 pol sequences for analysis. The pooled annual prevalence of PDR remained below 5% until 2009, then increased to a peak of 11·9% (95% confidence interval (CI) 9·2-15·0) in 2015. The pooled annual prevalence of non-nucleoside reverse-transcriptase inhibitor (NNRTI) PDR remained below 5% until 2011, then increased to 10.0% (95% CI 8.4-11.8) by 2014. Between 2000 and 2016, there was a 1.18-fold (95% CI 1.13-1.23) annual increase in NNRTI PDR (p < 0.001), and a 1.10-fold (95% CI 1.05-1.16) annual increase in nucleoside reverse-transcriptase inhibitor PDR (p = 0.001). INTERPRETATION Increasing PDR in South Africa presents a threat to the efforts to end the HIV/AIDS epidemic. These findings support the recent decision to modify the standard first-line ART regimen, but also highlights the need for broader public health action to prevent the further emergence and transmission of drug-resistant HIV. SOURCE OF FUNDING This research project was funded by the South African Medical Research Council (MRC) with funds from National Treasury under its Economic Competitiveness and Support Package. DISCLAIMER The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of CDC.
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Affiliation(s)
- Benjamin Chimukangara
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
- Corresponding authors at: KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Science, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa.
| | - Richard J. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Soo-Yon Rhee
- Department of Medicine, Stanford University, Stanford, CA, United States of America
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ayesha B.M. Kharsany
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC)-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Lara Lewis
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Cherie Cawood
- Epicentre AIDS Risk Management (Pty) Limited, PO Box 3484, Paarl, Cape Town, South Africa
| | - David Khanyile
- Epicentre AIDS Risk Management (Pty) Limited, PO Box 3484, Paarl, Cape Town, South Africa
| | | | - Karidia Diallo
- Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Reshmi Samuel
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Gillian Hunt
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Alain Vandormael
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Babill Stray-Pedersen
- Institute of Clinical Medicine, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Michelle Gordon
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Tariro Makadzange
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, MA, United States of America
| | - Photini Kiepiela
- HIV Prevention Research Unit, Medical Research Council, Durban, South Africa
| | - Gita Ramjee
- HIV Prevention Research Unit, Medical Research Council, Durban, South Africa
| | - Johanna Ledwaba
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | - Monalisa Kalimashe
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | - Lynn Morris
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Urvi M. Parikh
- Department of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - John W. Mellors
- Department of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Robert W. Shafer
- Department of Medicine, Stanford University, Stanford, CA, United States of America
| | - David Katzenstein
- Department of Medicine, Stanford University, Stanford, CA, United States of America
| | - Pravi Moodley
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Ravindra K. Gupta
- Department of Infection, University College London, United Kingdom of Great Britain and Northern Ireland
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Deenan Pillay
- Department of Infection, University College London, United Kingdom of Great Britain and Northern Ireland
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Corresponding authors at: KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Science, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa.
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Chimukangara B, Kharsany AB, Lessells RJ, Naidoo K, Rhee SY, Manasa J, Gräf T, Lewis L, Cawood C, Khanyile D, Diallo K, Ayalew KA, Shafer RW, Hunt G, Pillay D, Abdool SK, de Oliveira T. Moderate-to-High Levels of Pretreatment HIV Drug Resistance in KwaZulu-Natal Province, South Africa. AIDS Res Hum Retroviruses 2019; 35:129-138. [PMID: 30430843 DOI: 10.1089/aid.2018.0202] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
There is evidence of increasing levels of pretreatment HIV drug resistance (PDR) in Southern Africa. We used data from two large population-based HIV surveillance studies to estimate prevalence of PDR in KwaZulu-Natal, the province with the highest HIV prevalence in South Africa. Sanger sequencing was performed on samples obtained from a longitudinal HIV surveillance program (study A, 2013-2014) and the HIV Incidence Provincial Surveillance System (study B, 2014-2015). Sequences were included for adult HIV positive participants (age ≥15 years for study A, age 15-49 years for study B) with no documented prior exposure to antiretroviral therapy (ART). Overall and drug class-specific PDR was estimated using the World Health Organization 2009 surveillance drug resistance mutation (SDRM) list, and phylogenetic analysis was performed to establish evidence of drug resistance transmission linkage. A total of 1,845 sequences were analyzed (611 study A; 1,234 study B). An overall PDR prevalence of 9.2% [95% confidence interval (CI) 7.0-11.7] was observed for study A and 11.0% (95% CI 8.9-13.2) for study B. In study B, the prevalence of non-nucleoside reverse-transcriptase inhibitor (NNRTI) PDR exceeded 10% for sequences collected in 2014 (10.2%, 95% CI 7.5-12.9). The most prevalent SDRMs were K103NS (7.5%), M184VI (2.4%), and V106AM (1.4%). There was no evidence of large transmission chains of drug-resistant virus. High level NNRTI PDR (>10%) suggests a need to modify the standard first-line ART regimen and to focus attention on improving the quality of HIV prevention, treatment, and care.
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Affiliation(s)
- Benjamin Chimukangara
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Ayesha B.M. Kharsany
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard J. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Soo-Yon Rhee
- Department of Medicine, Stanford University, Stanford, California
| | - Justen Manasa
- Department of Medicine, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - Tiago Gräf
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Lara Lewis
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Cherie Cawood
- Epicentre AIDS Risk Management (Pty) Limited, Paarl, Cape Town, South Africa
| | - David Khanyile
- Epicentre AIDS Risk Management (Pty) Limited, Paarl, Cape Town, South Africa
| | - Karidia Diallo
- Centers for Disease Control and Prevention (CDC), Pretoria, South Africa
| | - Kassahun A. Ayalew
- Centers for Disease Control and Prevention (CDC), Pretoria, South Africa
| | - Robert W. Shafer
- Department of Medicine, Stanford University, Stanford, California
| | - Gillian Hunt
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Deenan Pillay
- Africa Health Research Institute, KwaZulu-Natal, South Africa
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Salim Karim Abdool
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
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Vermeulen M, Lelie N, Coleman C, Sykes W, Jacobs G, Swanevelder R, Busch M, van Zyl G, Grebe E, Welte A, Reddy R. Assessment of HIV transfusion transmission risk in South Africa: a 10-year analysis following implementation of individual donation nucleic acid amplification technology testing and donor demographics eligibility changes. Transfusion 2019; 59:267-276. [PMID: 30265757 PMCID: PMC10419327 DOI: 10.1111/trf.14959] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 08/15/2018] [Accepted: 08/15/2018] [Indexed: 01/12/2023]
Abstract
BACKGROUND In 1998 we estimated that 34/million infectious window period donations were entering the blood supply at the South African National Blood Service. Selective use of donations based on donor race-ethnicity reduced this risk to 26/million donations but was deemed unethical. Consequently, in 2005 South African National Blood Service eliminated race-ethnicity-based collection policies and implemented individual-donation nucleic acid testing (ID-NAT). We describe the change in donor base demographics, human immunodeficiency virus (HIV) detection rates, and transfusion-transmissible HIV risk. STUDY DESIGN AND METHODS In ten years 7.7 million donations were tested for anti-HIV and HIV RNA. Number of donations, HIV prevalence, ID-NAT yield rate, serology yield rate and residual transfusion-transmissible HIV risk were analyzed by donor type, race-ethnicity, age, and sex. Multiple regression analysis was performed to investigate the determinants of HIV-positive and nucleic acid testing yield donations. RESULTS The combined strategy of increasing donations from black donors and implementing ID-NAT increased the proportion of donations from black donors from 6% in 2005 to 30% in 2015 (p < 0.00001), and reduced the transfusion-transmissible risk from 24 to 13 per million transfusions. ID-NAT interdicted 481 (1:16,100) seronegative window period donations, while one transfusion-transmissible case (0.13 per million) was documented. Race-ethnicity and donor type were highly significant predictors of HIV positivity, with adjusted odds ratio for first-time donors of 12.5 (95% confidence interval, 11.9-13.1) and for black race-ethnicity of 31.1 (95% confidence interval, 28.9-33.4). The proportion of serology yields among HIV-infected donors increased from 0.27% to 2.4%. CONCLUSION ID-NAT enabled the South African National Blood Service to increase the number of donations from black donors fivefold while enhancing the safety of the blood supply.
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Affiliation(s)
- Marion Vermeulen
- The South African National Blood Service, 1 Constantia Boulevard, Constantia kloof, Roodepoort, South Africa
| | - Nico Lelie
- Lelie Research, Parkstraat 2, 1811DK, Alkmaar
| | - Charl Coleman
- The South African National Blood Service, 1 Constantia Boulevard, Constantia kloof, Roodepoort, South Africa
| | - Wendy Sykes
- The South African National Blood Service, 1 Constantia Boulevard, Constantia kloof, Roodepoort, South Africa
| | - Genevieve Jacobs
- The South African National Blood Service, 1 Constantia Boulevard, Constantia kloof, Roodepoort, South Africa
| | - Ronel Swanevelder
- The South African National Blood Service, 1 Constantia Boulevard, Constantia kloof, Roodepoort, South Africa
| | - Michael Busch
- Blood Systems Research Institute, 270 Masonic Avenue, San Francisco, California, USA
| | - Gert van Zyl
- Division of Medical Virology, Stellenbosch University, Faculty of Medicine and Health Sciences, Francie van Zijl Drive, Parow, 7500, South Africa
- National Health Laboratory Service, Tygerberg Business Unit, Francie van Zijl Drive, Parow, 7500, South Africa
| | - Eduard Grebe
- Division of Medical Virology, Stellenbosch University, Faculty of Medicine and Health Sciences, Francie van Zijl Drive, Parow, 7500, South Africa
| | - Alex Welte
- Division of Medical Virology, Stellenbosch University, Faculty of Medicine and Health Sciences, Francie van Zijl Drive, Parow, 7500, South Africa
| | - Ravi Reddy
- The South African National Blood Service, 1 Constantia Boulevard, Constantia kloof, Roodepoort, South Africa
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Chagomerana MB, Miller WC, Tang JH, Hoffman IF, Harrington BJ, DiPrete B, Wallie S, Jumbe A, Limarzi L, Hosseinipour MC. Prevalence of antiretroviral therapy treatment failure among HIV-infected pregnant women at first antenatal care: PMTCT Option B+ in Malawi. PLoS One 2018; 13:e0209052. [PMID: 30543685 PMCID: PMC6292583 DOI: 10.1371/journal.pone.0209052] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/27/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND In Malawi's PMTCT Option B+ program, HIV-infected pregnant women who are already receiving ART are continued on their current therapy regimen without testing for treatment failure at the first antenatal care (ANC) visit. HIV RNA screening at ANC may identify women with treatment failure and ensure that viral suppression is maintained throughout the pregnancy. METHODS We conducted a cross-sectional study of HIV-infected pregnant women who had been receiving ART for at least 6 months at the first ANC visit under the PMTCT Option B+ program at Bwaila Hospital in Lilongwe, Malawi from June 2015 to December 2017. Poisson regression models with robust variance were used to investigate the predictors of ART treatment failure defined as viral load ≥1000 copies/ml. RESULTS The median age of 864 women tested for ART failure was 31.1 years (interquartile range: 26.9-34.5). The prevalence of treatment failure was 7.6% (95% confidence interval (CI): 6.0-9.6). CD4 cell count (adjusted prevalence ratio (aPR) = 0.57; 95% CI: 0.50-0.65) was strongly associated with treatment failure. CONCLUSION The low prevalence of treatment failure among women presenting for their first ANC in urban Malawi demonstrates success of Option B+ in maintaining viral suppression and suggests progress towards the last 90% of the UNAIDS 90-90-90 targets. Women failing on ART should be identified early for adherence counseling and may require switching to an alternative ART regimen.
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Affiliation(s)
| | - William C. Miller
- Division of Epidemiology, College of Public Health, The Ohio State University, Columbus, Ohio, United States of America
| | - Jennifer H. Tang
- UNC Project-Malawi, Kamuzu Central Hospital, Lilongwe, Malawi
- Department of Obstetrics and Gynecology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Irving F. Hoffman
- UNC Project-Malawi, Kamuzu Central Hospital, Lilongwe, Malawi
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Bryna J. Harrington
- UNC Project-Malawi, Kamuzu Central Hospital, Lilongwe, Malawi
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Bethany DiPrete
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Shaphil Wallie
- UNC Project-Malawi, Kamuzu Central Hospital, Lilongwe, Malawi
| | - Allan Jumbe
- UNC Project-Malawi, Kamuzu Central Hospital, Lilongwe, Malawi
| | - Laura Limarzi
- UNC Project-Malawi, Kamuzu Central Hospital, Lilongwe, Malawi
| | - Mina C. Hosseinipour
- UNC Project-Malawi, Kamuzu Central Hospital, Lilongwe, Malawi
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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30
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Zhang Y, Sivay MV, Hudelson SE, Clarke W, Breaud A, Wang J, Piwowar-Manning E, Agyei Y, Fogel JM, Hamilton EL, Selin A, MacPhail C, Kahn K, Gomez-Olive FX, Hughes JP, Pettifor A, Eshleman SH. Antiretroviral Drug Use and HIV Drug Resistance Among Young Women in Rural South Africa: HPTN 068. J Acquir Immune Defic Syndr 2018; 79:315-322. [PMID: 29985265 PMCID: PMC6185777 DOI: 10.1097/qai.0000000000001793] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Antiretroviral (ARV) drugs are used for HIV treatment and prevention. We analyzed ARV drug use and HIV drug resistance in a cohort of young women in rural South Africa enrolled in the HIV Prevention Trials Network (HPTN) 068 study, which evaluated the use of a cash transfer conditional on school attendance to reduce HIV incidence. METHODS ARV drug testing was performed using plasma samples from 2526 young women. This included 2526 enrollment samples (80 HIV-infected and 2446 HIV-uninfected) and 162 seroconversion samples (first HIV-positive study visit). Testing was performed using a qualitative assay that detects 20 ARV drugs from 5 drug classes. HIV drug resistance testing was performed with the ViroSeq HIV-1 Genotyping System for samples that had HIV viral loads ≥400 copies per milliliter. RESULTS At enrollment, ARV drugs were detected in 10 (12.5%) of 80 HIV-infected young women. None of 2446 HIV-uninfected young women had ARV drugs detected at enrollment. ARV drugs were also detected in 16 (9.9%) of 162 seroconverters. At enrollment, 9 (13.4%) of 67 young women with genotyping results had HIV drug resistance; resistance was also detected in 9 (6.9%) of 131 seroconverters with genotyping results. CONCLUSIONS Most of the HIV-infected young women in this cohort from rural South Africa were not taking ARV drugs, suggesting they were unaware of their HIV status or were not in care. HIV drug resistance was detected in young women with both prevalent and new HIV infection.
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Affiliation(s)
- Yinfeng Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mariya V. Sivay
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah E. Hudelson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - William Clarke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Autumn Breaud
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jing Wang
- Statistical Center for HIV/AIDS Research & Prevention (SCHARP), Seattle, WA, USA
| | | | - Yaw Agyei
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jessica M. Fogel
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Amanda Selin
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Catherine MacPhail
- School of Health and Society, University of Wollongong, Australia; MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - F. Xavier Gomez-Olive
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - James P. Hughes
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Audrey Pettifor
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC; MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan H. Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
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Jordan MR, Penazzato M, Cournil A, Vubil A, Jani I, Hunt G, Carmona S, Maphalala G, Mthethwa N, Watera C, Kaleebu P, Musanhu CC, Mtapuri-Zinyowera S, Dzangare J, Peeters M, Yang C, Parkin N, Bertagnolio S. Human Immunodeficiency Virus (HIV) Drug Resistance in African Infants and Young Children Newly Diagnosed With HIV: A Multicountry Analysis. Clin Infect Dis 2018; 65:2018-2025. [PMID: 29020335 DOI: 10.1093/cid/cix698] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/03/2017] [Indexed: 11/12/2022] Open
Abstract
Background Programs for the prevention of mother-to-child transmission (PMTCT) of human immunodeficiency virus (HIV) have been scaled up in many low- and middle-income countries. However, HIV drug resistance (HIVDR) data among HIV-1-infected young children remain limited. Methods Surveys of pretreatment HIVDR among children aged <18 months who were diagnosed with HIV through early infant diagnosis were conducted in 5 sub-Saharan African countries (Mozambique, Swaziland, South Africa, Uganda, and Zimbabwe) between 2011 and 2014 following World Health Organization (WHO) guidance. Deidentified demographic and clinical data were used to explore risk factors associated with nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance. Results Among the 1450 genotypes analyzed, 1048 had accompanying demographic and clinical data. The median age of children was 4 months; 50.4% were female. HIV from 54.1% showed resistance to 1 or more antiretroviral (ARV) drugs, with 53.0% and 8.8% having resistance to 1 or more NNRTI or nucleoside reverse transcriptase inhibitors, respectively. NNRTI resistance was particularly high in children exposed to ARV drugs through PMTCT; adjusted odds ratios were 1.8 (95% confidence interval [CI], 1.3-2.6) for maternal exposure only and 2.4 (CI, 1.6-3.6) for neonatal exposure only. Conclusions Protease inhibitor-based regimens in children aged <3 years are currently recommended by WHO, but the implementation of this recommendation is suboptimal. These results reinforce the urgent need to overcome barriers to scaling up pediatric protease inhibitor-based regimens in sub-Saharan Africa and underscore the need to accelerate the study and approval of integrase inhibitors for use in young children.
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Affiliation(s)
- Michael R Jordan
- Tufts University School of Medicine and Tufts Medical Center, Boston, Massachusetts
| | - Martina Penazzato
- Department of HIV/AIDS, World Health Organization, Geneva, Switzerland
| | - Amandine Cournil
- IRD UMI 233, INSERM U1175, Université de Montpellier, Unité TransVIHMI, France
| | | | - Ilesh Jani
- Instituto Nacional de Saúde, Maputo, Mozambique
| | | | | | | | | | | | | | | | | | | | - Martine Peeters
- IRD UMI 233, INSERM U1175, Université de Montpellier, Unité TransVIHMI, France
| | - Chunfu Yang
- Division of Global HIV and TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
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Brado D, Obasa AE, Ikomey GM, Cloete R, Singh K, Engelbrecht S, Neogi U, Jacobs GB. Analyses of HIV-1 integrase sequences prior to South African national HIV-treatment program and available of integrase inhibitors in Cape Town, South Africa. Sci Rep 2018; 8:4709. [PMID: 29549274 PMCID: PMC5856838 DOI: 10.1038/s41598-018-22914-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/01/2018] [Indexed: 01/16/2023] Open
Abstract
HIV-Integrase (IN) has proven to be a viable target for highly specific HIV-1 therapy. We aimed to characterize the HIV-1 IN gene in a South African context and identify resistance-associated mutations (RAMs) against available first and second generation Integrase strand-transfer inhibitors (InSTIs). We performed genetic analyses on 91 treatment-naïve HIV-1 infected patients, as well as 314 treatment-naive South African HIV-1 IN-sequences, downloaded from Los Alamos HIV Sequence Database. Genotypic analyses revealed the absence of major RAMs in the cohort collected before the broad availability of combination antiretroviral therapy (cART) and INSTI in South Africa, however, occurred at a rate of 2.85% (9/314) in database derived sequences. RAMs were present at IN-positions 66, 92, 143, 147 and 148, all of which may confer resistance to Raltegravir (RAL) and Elvitegravir (EVG), but are unlikely to affect second-generation Dolutegravir (DTG), except mutations in the Q148 pathway. Furthermore, protein modeling showed, naturally occurring polymorphisms impact the stability of the intasome-complex and therefore may contribute to an overall potency against InSTIs. Our data suggest the prevalence of InSTI RAMs, against InSTIs, is low in South Africa, but natural polymorphisms and subtype-specific differences may influence the effect of individual treatment regimens.
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Affiliation(s)
- Dominik Brado
- Division of Virology, Institute for Virology and Immunobiology, Faculty of Medicine, University of Wuerzburg, 97080, Wuerzburg, Germany
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Adetayo Emmanuel Obasa
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa.
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, University of Stockholm, Stockholm, Sweden.
| | - George Mondinde Ikomey
- CSCCD, Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Western Cape, South Africa
| | - Kamalendra Singh
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, University of Stockholm, Stockholm, Sweden
- Department of Molecular Microbiology and Immunology, Columbia, MO, 65211, USA
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Susan Engelbrecht
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, University of Stockholm, Stockholm, Sweden
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
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Brenner BG, Ibanescu RI, Oliveira M, Roger M, Hardy I, Routy JP, Kyeyune F, Quiñones-Mateu ME, Wainberg MA. HIV-1 strains belonging to large phylogenetic clusters show accelerated escape from integrase inhibitors in cell culture compared with viral isolates from singleton/small clusters. J Antimicrob Chemother 2018; 72:2171-2183. [PMID: 28472323 PMCID: PMC7263826 DOI: 10.1093/jac/dkx118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/22/2017] [Indexed: 12/20/2022] Open
Abstract
Objectives: Viral phylogenetics revealed two patterns of HIV-1 spread among
MSM in Quebec. While most HIV-1 strains (n = 2011) were
associated with singleton/small clusters (cluster size 1–4), 30 viral lineages formed
large networks (cluster size 20–140), contributing to 42% of diagnoses between 2011 and
2015. Herein, tissue culture selections ascertained if large cluster lineages possessed
higher replicative fitness than singleton/small cluster isolates, allowing for viral
escape from integrase inhibitors. Methods: Primary HIV-1 isolates from large 20+ cluster
(n = 11) or singleton/small cluster
(n = 6) networks were passagedin
vitro in escalating concentrations of dolutegravir, elvitegravir and lamivudine
for 24–36 weeks. Sanger and deep sequencing assessed genotypic changes under selective
drug pressure. Results: Large cluster HIV-1 isolates selected for resistance to
dolutegravir, elvitegravir and lamivudine faster than HIV-1 strains forming small
clusters. With dolutegravir, large cluster HIV-1 variants acquired solitary R263K
(n = 7), S153Y
(n = 1) or H51Y
(n = 1) mutations as the dominant quasi-species within
8–12 weeks as compared with small cluster lineages where R263K
(n = 1/6), S153Y (1/6) or WT species (4/6) were
observed after 24 weeks. Interestingly, dolutegravir-associated mutations compromised
viral replicative fitness, precluding escalations in concentrations beyond 5–10 nM. With
elvitegravir, large cluster variants more rapidly acquired first mutations (T66I, A92G,
N155H or S147G) by week 8 followed by sequential accumulation of multiple mutations
leading to viral escape (>10 μM) by week 24. Conclusions: Further studies are needed to understand virological features of
large cluster viruses that may favour their transmissibility, replicative competence and
potential to escape selective antiretroviral drug pressure.
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Affiliation(s)
- Bluma G Brenner
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Ruxandra-Ilinca Ibanescu
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Maureen Oliveira
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Michel Roger
- Département de Microbiologie et d'Immunologie et Centre de Recherche du Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Isabelle Hardy
- Département de Microbiologie et d'Immunologie et Centre de Recherche du Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | | | - Fred Kyeyune
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Miguel E Quiñones-Mateu
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA.,University Hospitals Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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Thanprasertsuk S, Phokhasawad K, Teeraratkul A, Chasombat S, Pattarapayoon N, Saeng-aroon S, Yuktanon P, Kohreanudom S, Lertpiriyasuwat C. HIV Drug Resistance among Pre-treatment Cases in Thailand: Four Rounds of Surveys during 2006-2013. OUTBREAK, SURVEILLANCE AND INVESTIGATION REPORTS 2018; 11:6-13. [PMID: 30847451 PMCID: PMC6400074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In Thailand, antiretroviral therapy (ART) was initiated to treat human immunodeficiency virus infection and acquired immune deficiency syndrome (HIV/AIDS) cases using the empirical regimen with no prior genotypic test to determine drug resistance. In order to assess prevalence rate of HIV drug resistance (HIVDR) among pre-treatment cases, four rounds of survey were carried out in ART clinics, including six, eight, 33 and four ART clinics in each round during 2006-2013. For which, HIVDR testing results were available in 310, 350, 797, and 413 cases in four rounds. It was revealed that HIVDR rates among naive cases were 2.0%, 2.8%, 4.0% and 4.8%, while in experienced cases, the rates were 0, 3.3%, 11.4% and 13.9%. The rates among all cases were 1.9%, 2.9%, 4.4% and 5.6%. Resistant drugs with the highest rates among all cases in the survey round 4 were nevirapine (3.6%) and efavirenz (3.1%). The results indicated the need to continue surveillance for pre-treatment HIVDR, and posed challenges to implement activities for protecting efficacy and prolong the use of empirical first-line regimen. A strategy to apply genotyping test, in a cost-effective approach, should be considered to prepare for situation when HIVDR increases beyond a critical level.
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Affiliation(s)
| | | | - Achara Teeraratkul
- Thailand MOPH-US CDC collaboration, Division of Global HIV and Tuberculosis, Thailand
| | - Sanchai Chasombat
- Bureau of Vector Borne Diseases, Department of Disease Control, Ministry of Public Health, Thailand
| | - Naparat Pattarapayoon
- Bureau of AIDS, TB and STIs, Department of Disease Control, Ministry of Public Health, Thailand
| | - Siriphan Saeng-aroon
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Porntip Yuktanon
- Bureau of AIDS, TB and STIs, Department of Disease Control, Ministry of Public Health, Thailand
| | - Surapol Kohreanudom
- Bureau of AIDS, TB and STIs, Department of Disease Control, Ministry of Public Health, Thailand
| | - Cheewanan Lertpiriyasuwat
- Institute of Research, Knowledge Management and Standards for Disease Control, Department of Disease Control, Ministry of Public Health, Thailand
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Coetzee J, Hunt G, Jaffer M, Otwombe K, Scott L, Bongwe A, Ledwaba J, Molema S, Jewkes R, Gray GE. HIV-1 viraemia and drug resistance amongst female sex workers in Soweto, South Africa: A cross sectional study. PLoS One 2017; 12:e0188606. [PMID: 29244809 PMCID: PMC5731765 DOI: 10.1371/journal.pone.0188606] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/09/2017] [Indexed: 12/25/2022] Open
Abstract
Background HIV drug resistance (HIVDR) poses a threat to future antiretroviral therapy success. Monitoring HIVDR patterns is of particular importance in populations such as sex workers (SWs), where documented HIV prevalence is between 34–89%, and in countries with limited therapeutic options. Currently in South Africa, there is a dearth in evidence and no ongoing surveillance of HIVDR amongst sex work populations. This study aims to describe the prevalence of HIVDR amongst a sample of female sex workers (FSWs) from Soweto, South Africa. Methodology A cross-sectional, respondent driven sampling (RDS) recruitment methodology was used to enrol FSWs based in Soweto. Participants were tested for HIV and undertook a survey that included HIV knowledge and treatment status. Whole blood specimens were collected from HIV positive FSWs to measure for CD4 counts, viral load (VL) and perform HIVDR genotyping. Frequencies were determined for categorical variables and medians and interquartile ranges (IQR) for the continuous. Results Of the 508 enrolled participants, 55% (n = 280) were HIV positive and of median age 32 (IQR: 20–51) years. Among the HIV positive, 51.8% (132/269) were defined as virologically suppressed (VL < 400 copies/ml). Of the 119 individuals with unsuppressed viral loads who were successfully genotyped for resistance testing 37.8% (45/119) had detectable drug resistance. In this group, HIVDR mutations were found amongst 73.7% (14/19) of individuals on treatment, 27.4% (26/95) of individuals who were treatment naïve, and 100% (5/5) of defaulters. One phylogenetic cluster was found amongst treatment naïve FSWs. The K103N mutation was detected most commonly in 68.9% (31/45) individuals with HIVDR mutations, with 20/26 (76.9%) of treatment naïve FSW with detectable resistance having this mutation. The M184V mutation was found in both FSWs on treatment (12/14, 85.7%) and those defaulting (1/5, 20.0%). Discussion More than one third (45/119) of the genotyped sample had HIVDR, with resistance to the NNRTI class being the most common. Almost half of HIV positive FSWs had unsuppressed viral loads, increasing the likelihood for onward transmission of HIV. Disturbingly, more than 1:4 treatment naïve women with unsuppressed viral loads had HIVDR suggesting that possible sexual transmission of drug resistance is occurring in this high-risk population. Given the high burden of HIVDR in a population with a high background prevalence of HIV, it is imperative that routine monitoring of HIVDR be implemented. Understanding transmission dynamics of HIVDR in FSW and its impact on treatment success should be urgently elucidated.
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Affiliation(s)
- Jenny Coetzee
- Perinatal HIV Research Unit (PHRU), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
| | - Gillian Hunt
- National Institute for Communicable Diseases (NICD), Sandringham, South Africa
| | - Maya Jaffer
- Perinatal HIV Research Unit (PHRU), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kennedy Otwombe
- Perinatal HIV Research Unit (PHRU), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lesley Scott
- Department of Molecular Medicine and Haematology, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Asiashu Bongwe
- National Institute for Communicable Diseases (NICD), Sandringham, South Africa
| | - Johanna Ledwaba
- National Institute for Communicable Diseases (NICD), Sandringham, South Africa
| | - Sephonono Molema
- Perinatal HIV Research Unit (PHRU), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Rachel Jewkes
- Gender and Health Research Unit, South African Medical Research Council, Pretoria, South Africa
| | - Glenda E. Gray
- Perinatal HIV Research Unit (PHRU), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Office of the President, South African Medical Research Council, Cape Town, South Africa
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Moderate levels of pre-therapy drug resistance (PDR) in a generalised epidemic: time for better first-line ART? AIDS 2017; 31:2387-2391. [PMID: 28857824 DOI: 10.1097/qad.0000000000001629] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND The WHO-recommended first-line antiretroviral therapy (ART) as a fixed dose combination (FDC) of efavirenz (EFV) and tenofovir disoproxil fumarate (TDF) with lamivudine (3TC) or emtricitabine (FTC) has been preferred in the large scale unprecedented ART roll out in Southern Africa. Models and recent reports suggest that pre-ART
HIV drug resistance (PDR) is increasing with high treatment coverage. METHOD We therefore investigated PDR and any local transmission clusters in a setting where high treatment coverage was further enhanced by universal test and treat (UTT). Surveillance drug resistance mutations (SDRMs) were identified with an in-house PCR and population sequencing method and calibrated population resistance (CPR) tool. RESULTS Of 60 patients, six (10%) had an SDRM mutation: five (8.3%) had nonnucleoside reverse transcriptase (NNRT) mutations, one had an nucleos(t)ide reverse transcriptase inhibitor mutation and none had protease inhibitor (PI) mutations. Phylogenetic analysis revealed no large transmission clusters. CONCLUSION An increase to the current moderate PDR levels and the better tolerability and durability, may support a recent drive to avail FDC integrase strand transfer inhibitor (ISTI)-based regimens as the new preferred first-line ART in the Southern African region for individual benefit and to contribute to limiting transmission of infection and drug resistant virus.
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Guo J, Yan Y, Zhang J, Ji J, Ge Z, Ge R, Zhang X, Wang H, Chen Z, Luo J. Genetic characterization and antiretroviral resistance mutations among treatment-naive HIV-infected individuals in Jiaxing, China. Oncotarget 2017; 8:18271-18279. [PMID: 28407682 PMCID: PMC5392326 DOI: 10.18632/oncotarget.15382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 01/11/2017] [Indexed: 12/23/2022] Open
Abstract
The aim of this study was to characterize HIV-1 genotypes and antiretroviral resistance mutations among treatment-naive HIV-infected individuals in Jiaxing, China. The HIV-1 partial polymerase (pol) genes in 93 of the 99 plasma samples were successfully amplified and analyzed. Phylogenetic analysis revealed the existence of five HIV-1 genotypes, of which the most prevalent genotype was CRF01_AE (38.7%), followed by CRF07_BC (34.4%), CRF08_BC (16.1%), subtype B/B' (5.4%), and CRF55_01B (2.1%). Besides, three types of unique recombination forms (URFs) were also observed, including C/F2/A1, CRF01_AE/B, and CRF08_BC/CRF07_BC. Among 93 amplicons, 46.2% had drug resistance-associated mutations, including 23.7% for protease inhibitors (PIs) mutations, 1.1% for nucleoside reverse transcriptase inhibitors (NRTIs) mutations, and 20.4% for non-nucleoside reverse transcriptase inhibitors (NNRTIs) mutations. Six (6.5%) out of 93 treatment-naive subjects were identified to be resistant to one or more NNRTIs, while resistance to NRTIs or PIs was not observed. Our study showed the genetic diversity of HIV-1 strains circulating in Jiaxing and a relative high proportion of antiretroviral resistance mutations among treatment-naive patients, indicating a serious challenge for HIV prevention and treatment program.
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Affiliation(s)
- Jinlei Guo
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Yong Yan
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Jiafeng Zhang
- Institute of AIDS Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, PR China
| | - Jimei Ji
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Zhijian Ge
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Rui Ge
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Xiaofei Zhang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Henghui Wang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Zhongwen Chen
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Jianyong Luo
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
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Multimethod Longitudinal HIV Drug Resistance Analysis in Antiretroviral-Therapy-Naive Patients. J Clin Microbiol 2017; 55:2785-2800. [PMID: 28659324 DOI: 10.1128/jcm.00634-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 06/27/2017] [Indexed: 11/20/2022] Open
Abstract
The global intensification of antiretroviral therapy (ART) can lead to increased rates of HIV drug resistance (HIVDR) mutations in treated and also in ART-naive patients. ART-naive HIV-1-infected patients from Cameroon were subjected to a multimethod HIVDR analysis using amplification-refractory mutation system (ARMS)-PCR, Sanger sequencing, and longitudinal next-generation sequencing (NGS) to determine their profiles for the mutations K103N, Y181C, K65R, M184V, and T215F/Y. We processed 66 ART-naive HIV-1-positive patients with highly diverse subtypes that underlined the predominance of CRF02_AG and the increasing rate of F2 and other recombinant forms in Cameroon. We compared three resistance testing methods for 5 major mutation sites. Using Sanger sequencing, the overall prevalence of HIVDR mutations was 7.6% (5/66) and included all studied mutations except K65R. Comparing ARMS-PCR with Sanger sequencing as a reference, we obtained a sensitivity of 100% (5/5) and a specificity of 95% (58/61), caused by three false-positive calls with ARMS-PCR. For 32/66 samples, we obtained NGS data and we observed two additional mismatches made up of minority variants (7% and 18%) that might not be clinically relevant. Longitudinal NGS analyses revealed changes in HIVDR mutations in all five positive subjects that could not be attributed to treatment. In one of these cases, superinfection led to the temporary masking of a resistant virus. HIVDR mutations can be sensitively detected by ARMS-PCR and sequencing methods with comparable performances. Longitudinal changes in HIVDR mutations have to be considered even in the absence of treatment.
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