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Schulz VE, Tuff JF, Tough RH, Lewis L, Chimukangara B, Garrett N, Abdool Karim Q, Abdool Karim SS, McKinnon LR, Kharsany ABM, McLaren PJ. Host genetic variation at a locus near CHD1L impacts HIV sequence diversity in a South African population. J Virol 2023; 97:e0095423. [PMID: 37747237 PMCID: PMC10617395 DOI: 10.1128/jvi.00954-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/04/2023] [Indexed: 09/26/2023] Open
Abstract
IMPORTANCE It has been previously shown that genetic variants near CHD1L on chromosome 1 are associated with reduced HIV VL in African populations. However, the impact of these variants on viral diversity and how they restrict viral replication are unknown. We report on a regional association analysis in a South African population and show evidence of selective pressure by variants near CHD1L on HIV RT and gag. Our findings provide further insight into how genetic variability at this locus contributes to host control of HIV in a South African population.
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Affiliation(s)
- Vanessa E. Schulz
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Jeffrey F. Tuff
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Riley H. Tough
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Lara Lewis
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Benjamin Chimukangara
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
- Department of Virology, University of KwaZulu-Natal, Durban, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Lyle R. McKinnon
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Ayesha B. M. Kharsany
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Science, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Paul J. McLaren
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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Manyana S, Pillay M, Gounder L, Khan A, Moodley P, Naidoo K, Chimukangara B. Affordable drug resistance genotyping of HIV-1 reverse transcriptase, protease and integrase genes, for resource limited settings. AIDS Res Ther 2023; 20:9. [PMID: 36759801 PMCID: PMC9912687 DOI: 10.1186/s12981-023-00505-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND As use of dolutegravir (DTG) becomes more common in resource limited settings (RLS), the demand for integrase resistance testing is increasing. Affordable methods for genotyping all relevant HIV-1 pol genes (i.e., protease (PR), reverse transcriptase (RT) and integrase (IN)) are required to guide choice of future antiretroviral therapy (ART). We designed an in-house HIV-1 drug resistance (HIVDR) genotyping method that is affordable and suitable for use in RLS. METHODS We obtained remnant plasma samples from CAPRISA 103 study and amplified HIV-1 PR, RT and IN genes, using an innovative PCR assay. We validated the assay using remnant plasma samples from an external quality assessment (EQA) programme. We genotyped samples by Sanger sequencing and assessed HIVDR mutations using the Stanford HIV drug resistance database. We compared drug resistance mutations with previous genotypes and calculated method cost-estimates. RESULTS From 96 samples processed, we obtained sequence data for 78 (81%), of which 75 (96%) had a least one HIVDR mutation, with no major-IN mutations observed. Only one sample had an E157Q INSTI-accessory mutation. When compared to previous genotypes, 18/78 (23%) had at least one discordant mutation, but only 2/78 (3%) resulted in different phenotypic predictions that could affect choice of subsequent regimen. All CAPRISA 103 study sequences were HIV-1C as confirmed by phylogenetic analysis. Of the 7 EQA samples, 4 were HIV-1C, 2 were HIV-1D, and 1 was HIV-1A. Genotypic resistance data generated using the IDR method were 100% concordant with EQA panel results. Overall genotyping cost per sample was estimated at ~ US$43-$US49, with a processing time of ~ 2 working days. CONCLUSIONS We successfully designed an in-house HIVDR method that is suitable for genotyping HIV-1 PR, RT and IN genes, at an affordable cost and shorter turnaround time. This HIVDR genotyping method accommodates changes in ART regimens and will help to guide HIV-1 treatment decisions in RLS.
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Affiliation(s)
- Sontaga Manyana
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, 800 Vusi Mzimela Road, Durban, 4058, South Africa
| | - Melendhran Pillay
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, 800 Vusi Mzimela Road, Durban, 4058, South Africa
| | - Lilishia Gounder
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, 800 Vusi Mzimela Road, Durban, 4058, South Africa
| | - Aabida Khan
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, 800 Vusi Mzimela Road, Durban, 4058, South Africa
| | - Pravi Moodley
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, 800 Vusi Mzimela Road, Durban, 4058, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, South African Medical Research Council (SAMRC), Durban, South Africa
| | - Benjamin Chimukangara
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, 800 Vusi Mzimela Road, Durban, 4058, South Africa.
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.
- Critical Care Medicine Department, NIH Clinical Center, Bethesda, MD, USA.
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Khan A, Pillay M, Chimukangara B, Gounder L, Manyana S, Francois KL, Chipango K. Identification of HIV-1 subtype CRF18_cpx in a patient with multidrug resistance in KwaZulu-Natal, South Africa: An epidemiological worry? Journal of Clinical Virology Plus 2023. [DOI: 10.1016/j.jcvp.2023.100143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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Tyagi A, Tong Y, Rabideau DJ, Reynolds Z, De Oliveira T, Lessells R, Amanyire G, Orrell C, Asiimwe S, Chimukangara B, Giandhari J, Pillay S, Haberer JE, Siedner MJ. Antiretroviral therapy adherence patterns, virological suppression, and emergence of drug resistance: A nested case–control study from Uganda and South Africa. Antivir Ther 2022; 27:13596535221114822. [DOI: 10.1177/13596535221114822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background Relationships between distinct antiretroviral therapy (ART) adherence patterns and risk of drug resistance are not well understood. Methods We conducted a nested case–control analysis within a longitudinal cohort study of individuals initiating efavirenz-based ART. Primary outcomes of interest, measured at 6 and 12 months after treatment initiation, were: 1) virologic suppression, 2) virologic failure with resistance, and 3) virologic failure without resistance. Our primary exposure of interest was ART adherence, measured over the 6 months before each visit with electronic pill monitors, and categorized in three ways: 1) 6 months average adherence; 2) running adherence, defined as the proportion of days with average adherence over 9 days of less than or equal to 10%, 20%, and 30%; and 3) number of 3-, 7-, and 28-day treatment gaps in the prior 6 months Results We analyzed data from 166 individuals (107 had virologic failure during observation and 59 had virologic suppression at 6 and 12 months). Average adherence was higher among those with virologic suppression (median 83%, IQR 58–96%) versus those with virologic failure with resistance (median 35%, IQR 20–77%, pairwise P < 0.01) and those with virologic failure without resistance (median 21%, IQR 2–54%, pairwise P < 0.01). Although treatment gaps generally predicted virologic failure ( P < 0.01), they did not differentiate failure with and without drug resistance ( P > 0.6). Conclusions Average adherence patterns, but not the assessed frequency of treatment gaps, differentiated failure with versus without drug resistance among individuals initiating efavirenz-based ART. Future work should explore adherence-resistance relationships for integrase inhibitor-based regimens.
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Affiliation(s)
- Anisha Tyagi
- Massachusetts General Hospital, Medical Practice Evaluation Center, Boston, MA, USA
| | - Yao Tong
- Massachusetts General Hospital, Medical Practice Evaluation Center, Boston, MA, USA
| | - Dustin J Rabideau
- Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Biostatistics, Boston, MA, USA
| | - Zahra Reynolds
- Massachusetts General Hospital, Medical Practice Evaluation Center, Boston, MA, USA
| | - Tulio De Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Gideon Amanyire
- Africa Health Research Institute, Durban, South Africa
- Global Health Collaborative, Mbarara, Uganda
- Makerere University Joint AIDS Program, Kampala, Uganda
| | - Catherine Orrell
- Desmond Tutu Health Foundation, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Stephen Asiimwe
- Global Health Collaborative, Mbarara, Uganda
- Kabwohe Clinical Research Center, Kabwohe, Uganda
| | - Benjamin Chimukangara
- KwaZulu-Natal Research Innovation and Sequencing Platform, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Critical Care Medicine Department, NIH Clinical Center, Bethesda, MD, USA
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Jessica E Haberer
- Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Center for Global Health, Boston, MA, USA
| | - Mark J Siedner
- Massachusetts General Hospital, Medical Practice Evaluation Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Africa Health Research Institute, Durban, South Africa
- Massachusetts General Hospital Center for Global Health, Boston, MA, USA
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Lau CY, Adan MA, Earhart J, Seamon C, Nguyen T, Savramis A, Adams L, Zipparo ME, Madeen E, Huik K, Grossman Z, Chimukangara B, Wulan WN, Millo C, Nath A, Smith BR, Ortega-Villa AM, Proschan M, Wood BJ, Hammoud DA, Maldarelli F. Imaging and biopsy of HIV-infected individuals undergoing analytic treatment interruption. Front Med (Lausanne) 2022; 9:979756. [PMID: 36072945 PMCID: PMC9441850 DOI: 10.3389/fmed.2022.979756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Background HIV persistence during antiretroviral therapy (ART) is the principal obstacle to cure. Lymphoid tissue is a compartment for HIV, but mechanisms of persistence during ART and viral rebound when ART is interrupted are inadequately understood. Metabolic activity in lymphoid tissue of patients on long-term ART is relatively low, and increases when ART is stopped. Increases in metabolic activity can be detected by 18F-fluorodeoxyglucose Positron Emission Tomography (FDG-PET) and may represent sites of HIV replication or immune activation in response to HIV replication. Methods FDG-PET imaging will be used to identify areas of high and low metabolic uptake in lymphoid tissue of individuals undergoing long-term ART. Baseline tissue samples will be collected. Participants will then be randomized 1:1 to continue or interrupt ART via analytic treatment interruption (ATI). Image-guided biopsy will be repeated 10 days after ATI initiation. After ART restart criteria are met, image-guided biopsy will be repeated once viral suppression is re-achieved. Participants who continued ART will have a second FDG-PET and biopsies 12–16 weeks after the first. Genetic characteristics of HIV populations in areas of high and low FDG uptake will be assesed. Optional assessments of non-lymphoid anatomic compartments may be performed to evaluate HIV populations in distinct anatomic compartments. Anticipated results We anticipate that PET standardized uptake values (SUV) will correlate with HIV viral RNA in biopsies of those regions and that lymph nodes with high SUV will have more viral RNA than those with low SUV within a patient. Individuals who undergo ATI are expected to have diverse viral populations upon viral rebound in lymphoid tissue. HIV populations in tissues may initially be phylogenetically diverse after ATI, with emergence of dominant viral species (clone) over time in plasma. Dominant viral species may represent the same HIV population seen before ATI. Discussion This study will allow us to explore utility of PET for identification of HIV infected cells and determine whether high FDG uptake respresents areas of HIV replication, immune activation or both. We will also characterize HIV infected cell populations in different anatomic locations. The protocol will represent a platform to investigate persistence and agents that may target HIV populations. Study protocol registration Identifier: NCT05419024.
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Affiliation(s)
- Chuen-Yen Lau
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
- *Correspondence: Chuen-Yen Lau
| | - Matthew A. Adan
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Jessica Earhart
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Cassie Seamon
- Critical Care Medicine Department, Clinical Center (CC), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Thuy Nguyen
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD, United States
| | - Ariana Savramis
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Lindsey Adams
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD, United States
| | - Mary-Elizabeth Zipparo
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD, United States
| | - Erin Madeen
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD, United States
| | - Kristi Huik
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD, United States
| | - Zehava Grossman
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD, United States
| | - Benjamin Chimukangara
- Critical Care Medicine Department, Clinical Center (CC), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Wahyu Nawang Wulan
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD, United States
| | - Corina Millo
- PET Department, Clinical Center (CC), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Avindra Nath
- Division of Neuroimmunology and Neurovirology, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Bryan R. Smith
- Division of Neuroimmunology and Neurovirology, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Ana M. Ortega-Villa
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Michael Proschan
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Bradford J. Wood
- Interventional Radiology, Radiology and Imaging Sciences, Clinical Center (CC), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Dima A. Hammoud
- Radiology and Imaging Sciences, Clinical Center (CC), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD, United States
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Msomi N, Parboosing R, Wilkinson E, Giandhari J, Govender K, Chimukangara B, Mlisana KP. Persistent Hepatitis B Viraemia with Polymerase Mutations among HIV/HBV Co-Infected Patients on HBV-Active ART in KwaZulu-Natal, South Africa. Viruses 2022; 14:v14040788. [PMID: 35458518 PMCID: PMC9026734 DOI: 10.3390/v14040788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/02/2022] [Accepted: 04/07/2022] [Indexed: 12/25/2022] Open
Abstract
To understand the problem of persistent Hepatitis B virus (HBV) viraemia in HIV/HBV co-infected patients on HBV-active antiretroviral therapy (ART), we assessed the rate of HBV virological response in patients on HBV-active ART in KwaZulu-Natal, South Africa, and analysed factors associated with persistent HBV viraemia. One hundred and fifty eligible participants with a chronic HBV diagnosis, with or without HIV coinfection, were enrolled and followed up after 6 months. The HBV pol gene was sequenced by next-generation sequencing and mutations were determined using the Stanford HBVseq database. Logistic regression analysis was used to assess factors associated with HBV viraemia at 6-month follow-up. The mean duration of HBV-active ART was 24 months. Thirty-seven of one hundred and six (35%) participants receiving HBV-active ART for longer than 6 months had virological failure. Advanced immunosuppression with CD4+ cell counts <200 cells/μL was independently associated with persistent HBV viraemia, aOR 5.276 (95% CI 1.575−17.670) p = 0.007. A high proportion of patients on HBV-active ART are unsuppressed, which will ultimately have an impact on global elimination goals. Better monitoring should be implemented, especially in HIV-coinfected patients with low CD4+ cell counts and followed by early HBV drug-resistance testing.
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Affiliation(s)
- Nokukhanya Msomi
- Discipline of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (R.P.); (K.G.); (B.C.)
- National Health Laboratory Service, Inkosi Albert Luthuli Central Hospital, Durban 4091, South Africa
- Correspondence:
| | - Raveen Parboosing
- Discipline of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (R.P.); (K.G.); (B.C.)
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa; (E.W.); (J.G.)
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa; (E.W.); (J.G.)
| | - Kerusha Govender
- Discipline of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (R.P.); (K.G.); (B.C.)
- National Health Laboratory Service, Inkosi Albert Luthuli Central Hospital, Durban 4091, South Africa
| | - Benjamin Chimukangara
- Discipline of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (R.P.); (K.G.); (B.C.)
| | - Koleka P. Mlisana
- National Health Laboratory Service (Academic Affairs, Research and Quality Assurance), Johannesburg 2131, South Africa;
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Madyadi A, Dhoro M, Shamu T, Washaya T, Kouamou V, Chimukangara B, Katzenstein D, Manasa J. HIV-1 Genetic Diversity and Natural Polymorphisms of the Integrase Gene in Integrase Inhibitor-Naive Patients in Harare, Zimbabwe. AIDS Res Hum Retroviruses 2021; 37:954-961. [PMID: 34714124 DOI: 10.1089/aid.2021.0084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Previously used as part of salvage therapy, integrase strand transfer inhibitors (INSTIs) have become part of the preferred antiretroviral therapy (ART) first-line regimen in most low- to middle-income countries. With the extensive use of dolutegravir in first-line ART, drug resistance mutations to INSTIs are inevitable. Therefore, active monitoring and surveillance of INSTI drug resistance is required. The aim of this study was to evaluate the genetic diversity of the integrase gene and determine pretreatment INSTI resistance in Harare, Zimbabwe. Forty-four HIV-1 Integrase sequences from 65 were obtained from treatment-naive individuals using a custom genotyping method. Drug resistance mutations were determined using the Stanford HIV Drug Resistance Interpretation program. Viral subtyping was done by phylogenetic analysis and the REGA HIV subtyping tool determined recombinants. Natural polymorphisms were evaluated relative to the global subtype B and C consensus sequences. One hundred ninety-two sequences from the region were accessed from GenBank to assess differences between the Zimbabwean sequences and those from neighboring countries. No major INSTI resistance mutations were detected; however, the L74I polymorphism was detected in three sequences of the 44 (6.8%). There was little genetic variability in the Integrase gene, with a mean genetic distance range of 0.053015. The subtype C consensus was identical to the global subtype C consensus and varied from the global subtype B consensus at five major positions: T124A, V201I, T218I, D278A, and S283G. This study has provided baseline sequence data on the presence of HIV-1 subtype C Integrase gene drug resistance mutations from Harare, Zimbabwe.
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Affiliation(s)
- Amanda Madyadi
- Department of Molecular Biology, Biomedical Research and Training Institute, Harare, Zimbabwe
- Department of Clinical Pharmacology and Department of Medical Microbiology, University of Zimbabwe, Mt Pleasant, Harare, Zimbabwe
| | - Milcah Dhoro
- Department of Clinical Pharmacology and Department of Medical Microbiology, University of Zimbabwe, Mt Pleasant, Harare, Zimbabwe
| | - Tinei Shamu
- Department of Molecular Biology, Newlands Clinic, Harare, Zimbabwe
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Graduate School of Health Sciences, University of Bern, Bern, Switzerland
| | - Tendai Washaya
- Department of Molecular Biology, Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Vinie Kouamou
- Department of Clinical Pharmacology and Department of Medical Microbiology, University of Zimbabwe, Mt Pleasant, Harare, Zimbabwe
| | - Benjamin Chimukangara
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Virology, University of KwaZulu-Natal, Durban, South Africa
- Critical Care Medicine Department, NIH Clinical Center, Bethesda, Maryland, USA
| | - David Katzenstein
- Department of Molecular Biology, Biomedical Research and Training Institute, Harare, Zimbabwe
- School of Medicine, University of Stanford, Stanford, California, USA
| | - Justen Manasa
- Department of Clinical Pharmacology and Department of Medical Microbiology, University of Zimbabwe, Mt Pleasant, Harare, Zimbabwe
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Chimukangara B, Lessells RJ, Sartorius B, Gounder L, Manyana S, Pillay M, Singh L, Giandhari J, Govender K, Samuel R, Msomi N, Naidoo K, de Oliveira T, Moodley P, Parboosing R. HIV-1 drug resistance in adults and adolescents on protease inhibitor-based antiretroviral treatment in KwaZulu-Natal Province, South Africa. J Glob Antimicrob Resist 2021; 29:468-475. [PMID: 34785393 DOI: 10.1016/j.jgar.2021.10.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/19/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND In low- and middle-income countries, increasing levels of HIV drug resistance (HIVDR) on second-line protease inhibitor (PI)-based regimens are a cause for concern, given limited drug options for third-line antiretroviral therapy (ART). OBJECTIVES We conducted a retrospective analysis of routine HIV-1 genotyping laboratory data from KwaZulu-Natal, in South Africa, to describe the frequency and patterns of HIVDR mutations and their consequent impact on standardized third-line regimens. METHODS This was a cross-sectional analysis of all HIV-1 genotypic resistance tests conducted by the National Health Laboratory Service in KwaZulu-Natal, South Africa (Jan 2015 - Dec 2016), for adults and adolescents (age ≥10 years) on second-line PI-based ART with virological failure. We assigned a third-line regimen to each record, based on a national treatment algorithm and calculated the genotypic susceptibility score (GSS) for that regimen. RESULTS Of 348 samples analyzed, 287 (83%) had at least one drug resistance mutation (DRM) and 114 (33%) had at least one major PI DRM. Major PI resistance was associated with longer duration on second-line ART (aOR per 6-months, 1.11, 95% CI 1.04-1.19) and older age (aOR 1.03, 95% CI 1.01-1.05). Of 112 patients requiring third-line ART, 12 (11%) had a GSS of <2 for the algorithm-assigned third-line regimen. CONCLUSIONS One in three people failing second-line ART had significant PI DRMs. A subgroup of these individuals had extensive HIVDR, where the predicted activity of third-line ART was suboptimal, highlighting the need for continuous evaluation of outcomes on third-line regimens and close monitoring for emergent HIV-1 integrase-inhibitor resistance.
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Affiliation(s)
- Benjamin Chimukangara
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; Critical Care Medicine Department, NIH Clinical Center, Bethesda, MD, USA.
| | - Richard J Lessells
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Benn Sartorius
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Lilishia Gounder
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Sontaga Manyana
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Melendhran Pillay
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kerusha Govender
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Reshmi Samuel
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Nokukhanya Msomi
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Tulio de Oliveira
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Global Health, University of Washington, Seattle, United States
| | - Pravi Moodley
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Raveen Parboosing
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
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10
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Chimukangara B, Lessells RJ, Singh L, Grigalionyte I, Yende-Zuma N, Adams R, Dawood H, Dlamini L, Buthelezi S, Chetty S, Diallo K, Duffus WA, Mogashoa M, Hagen MB, Giandhari J, de Oliveira T, Moodley P, Padayatchi N, Naidoo K. Acquired HIV drug resistance and virologic monitoring in a HIV hyper-endemic setting in KwaZulu-Natal Province, South Africa. AIDS Res Ther 2021; 18:74. [PMID: 34656129 PMCID: PMC8520607 DOI: 10.1186/s12981-021-00393-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 09/22/2021] [Indexed: 11/17/2022] Open
Abstract
Background Introduction of tenofovir (TDF) plus lamivudine (3TC) and dolutegravir (DTG) in first- and second-line HIV treatment regimens in South Africa warrants characterization of acquired HIV-1 drug resistance (ADR) mutations that could impact DTG-based antiretroviral therapy (ART). In this study, we sought to determine prevalence of ADR mutations and their potential impact on susceptibility to drugs used in combination with DTG among HIV-positive adults (≥ 18 years) accessing routine care at a selected ART facility in KwaZulu-Natal, South Africa. Methods We enrolled adult participants in a cross-sectional study between May and September 2019. Eligible participants had a most recent documented viral load (VL) ≥ 1000 copies/mL after at least 6 months on ART. We genotyped HIV-1 reverse transcriptase and protease genes by Sanger sequencing and assessed ADR. We characterized the effect of ADR mutations on the predicted susceptibility to drugs used in combination with DTG. Results From 143 participants enrolled, we obtained sequence data for 115 (80%), and 92.2% (95% CI 85.7–96.4) had ADR. The proportion with ADR was similar for participants on first-line ART (65/70, 92.9%, 95% CI 84.1–97.6) and those on second-line ART (40/44, 90.9%, 95% CI 78.3–97.5), and was present for the single participant on third-line ART. Approximately 89% (62/70) of those on first-line ART had dual class NRTI and NNRTI resistance and only six (13.6%) of those on second-line ART had major PI mutations. Most participants (82%) with first-line viraemia maintained susceptibility to Zidovudine (AZT), and the majority of them had lost susceptibility to TDF (71%) and 3TC (84%). Approximately two in every five TDF-treated individuals had thymidine analogue mutations (TAMs). Conclusions Susceptibility to AZT among most participants with first-line viraemia suggests that a new second-line regimen of AZT + 3TC + DTG could be effective. However, atypical occurrence of TAMs in TDF-treated individuals suggests a less effective AZT + 3TC + DTG regimen in a subpopulation of patients. As most patients with first-line viraemia had at least low-level resistance to TDF and 3TC, identifying viraemia before switch to TDF + 3TC + DTG is important to avoid DTG functional monotherapy. These findings highlight a need for close monitoring of outcomes on new standardized treatment regimens. Supplementary Information The online version contains supplementary material available at 10.1186/s12981-021-00393-5.
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11
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Chimukangara B, Giandhari J, Lessells R, Yende-Zuma N, Sartorius B, Samuel R, Khanyile KS, Stray-Pedersen B, Moodley P, Metzner KJ, Padayatchi N, Naidoo K, De Oliveira T. Impact of pretreatment low-abundance HIV-1 drug-resistant variants on virological failure among HIV-1/TB-co-infected individuals. J Antimicrob Chemother 2021; 75:3319-3326. [PMID: 32772079 PMCID: PMC7566390 DOI: 10.1093/jac/dkaa343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/03/2020] [Indexed: 11/23/2022] Open
Abstract
Objectives To determine the impact of pretreatment low-abundance HIV-1 drug-resistant variants (LA-DRVs) on virological failure (VF) among HIV-1/TB-co-infected individuals treated with NNRTI first-line ART. Methods We conducted a case–control study of 170 adults with HIV-1/TB co-infection. Cases had at least one viral load (VL) ≥1000 RNA copies/mL after ≥6 months on NNRTI-based ART, and controls had sustained VLs <1000 copies/mL. We sequenced plasma viruses by Sanger and MiSeq next-generation sequencing (NGS). We assessed drug resistance mutations (DRMs) using the Stanford drug resistance database, and analysed NGS data for DRMs at ≥20%, 10%, 5% and 2% thresholds. We assessed the effect of pretreatment drug resistance (PDR) on VF. Results We analysed sequences from 45 cases and 125 controls. Overall prevalence of PDR detected at a ≥20% threshold was 4.7% (8/170) and was higher in cases than in controls (8.9% versus 3.2%), P = 0.210. Participants with PDR at ≥20% had almost 4-fold higher odds of VF (adjusted OR 3.7, 95% CI 0.8–18.3) compared with those without, P = 0.104. PDR prevalence increased to 18.2% (31/170) when LA-DRVs at ≥2% were included. Participants with pretreatment LA-DRVs only had 1.6-fold higher odds of VF (adjusted OR 1.6, 95% CI 0.6–4.3) compared with those without, P = 0.398. Conclusions Pretreatment DRMs and LA-DRVs increased the odds of developing VF on NNRTI-based ART, although without statistical significance. NGS increased detection of DRMs but provided no additional benefit in identifying participants at risk of VF at lower thresholds. More studies assessing mutation thresholds predictive of VF are required to inform use of NGS in treatment decisions.
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Affiliation(s)
- Benjamin Chimukangara
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.,Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa
| | - Nonhlanhla Yende-Zuma
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.,South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Benn Sartorius
- Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa.,Health Metrics Sciences, University of Washington, Seattle, USA
| | - Reshmi Samuel
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Khulekani S Khanyile
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa
| | - Babill Stray-Pedersen
- Institute of Clinical Medicine, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Pravi Moodley
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.,South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.,South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Tulio De Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
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12
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Manyana S, Gounder L, Pillay M, Manasa J, Naidoo K, Chimukangara B. HIV-1 Drug Resistance Genotyping in Resource Limited Settings: Current and Future Perspectives in Sequencing Technologies. Viruses 2021; 13:1125. [PMID: 34208165 PMCID: PMC8230827 DOI: 10.3390/v13061125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 12/14/2022] Open
Abstract
Affordable, sensitive, and scalable technologies are needed for monitoring antiretroviral treatment (ART) success with the goal of eradicating HIV-1 infection. This review discusses use of Sanger sequencing and next generation sequencing (NGS) methods for HIV-1 drug resistance (HIVDR) genotyping, focusing on their use in resource limited settings (RLS). Sanger sequencing remains the gold-standard method for detecting HIVDR mutations of clinical relevance but is mainly limited by high sequencing costs and low-throughput. NGS is becoming a more common sequencing method, with the ability to detect low-abundance drug-resistant variants and reduce per sample costs through sample pooling and massive parallel sequencing. However, use of NGS in RLS is mainly limited by infrastructure costs. Given these shortcomings, our review discusses sequencing technologies for HIVDR genotyping, focusing on common in-house and commercial assays, challenges with Sanger sequencing in keeping up with changes in HIV-1 treatment programs, as well as challenges with NGS that limit its implementation in RLS and in clinical diagnostics. We further discuss knowledge gaps and offer recommendations on how to overcome existing barriers for implementing HIVDR genotyping in RLS, to make informed clinical decisions that improve quality of life for people living with HIV.
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Affiliation(s)
- Sontaga Manyana
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Lilishia Gounder
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Melendhran Pillay
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Justen Manasa
- Department of Laboratory Medicine and Investigative Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe;
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa;
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban 4013, South Africa
| | - Benjamin Chimukangara
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa;
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13
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Mbhele N, Chimukangara B, Gordon M. HIV-1 integrase strand transfer inhibitors: a review of current drugs, recent advances and drug resistance. Int J Antimicrob Agents 2021; 57:106343. [PMID: 33852932 DOI: 10.1016/j.ijantimicag.2021.106343] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 03/30/2021] [Accepted: 04/03/2021] [Indexed: 12/22/2022]
Abstract
Antiretroviral therapy has been imperative in controlling the human immunodeficiency virus (HIV) epidemic. Most low- and middle-income countries have used nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs) and protease inhibitors extensively in the treatment of HIV. However, integrase strand transfer inhibitors (INSTIs) are becoming more common. Since their identification as a promising therapeutic drug, significant progress has been made that has led to the approval of five INSTIs by the US Food and Drug Administration (FDA), i.e. dolutegravir (DTG), raltegravir (RAL), elvitegravir (EVG), bictegravir (BIC) and cabotegravir (CAB). INSTIs have been shown to effectively halt HIV-1 replication and are commended for having a higher genetic barrier to resistance compared with NRTIs and NNRTIs. More interestingly, DTG has shown a higher genetic barrier to resistance compared with RAL and EVG, and CAB is being used as the first long-acting agent in HIV-1 treatment. Considering the increasing interest in INSTIs for HIV-1 treatment, we focus our review on the retroviral integrase, development of INSTIs and their mode of action. We also discuss each of the INSTI drugs, including potential drug resistance and known side effects.
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Affiliation(s)
- Nokuzola Mbhele
- KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa
| | - Benjamin Chimukangara
- KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa; Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Michelle Gordon
- KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa.
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14
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Giandhari J, Pillay S, Wilkinson E, Tegally H, Sinayskiy I, Schuld M, Lourenço J, Chimukangara B, Lessells R, Moosa Y, Gazy I, Fish M, Singh L, Sedwell Khanyile K, Fonseca V, Giovanetti M, Carlos Junior Alcantara L, Petruccione F, de Oliveira T. Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report. Int J Infect Dis 2021; 103:234-241. [PMID: 33189939 PMCID: PMC7658561 DOI: 10.1016/j.ijid.2020.11.128] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES The Network for Genomic Surveillance in South Africa (NGS-SA) was formed to investigate the introduction and understand the early transmission dynamics of the SARS-CoV-2 epidemic in South-Africa. DESIGN This paper presents the first results from this group, which is a molecular epidemiological study of the first 21 SARS-CoV-2 whole genomes sampled in the first port of entry - KwaZulu-Natal (KZN) - during the first month of the epidemic. By combining this with calculations of the effective reproduction number (R), it aimed to shed light on the patterns of infections in South Africa. RESULTS Two of the largest provinces - Gauteng and KZN - had a slow growth rate for the number of detected cases, while the epidemic spread faster in the Western Cape and Eastern Cape. The estimates of transmission potential suggested a decrease towards R = 1 since the first cases and deaths, but a subsequent estimated R average of 1.39 between 6-18 May 2020. It was also demonstrated that early transmission in KZN was associated with multiple international introductions and dominated by lineages B1 and B. Evidence for locally acquired infections in a hospital in Durban within the first month of the epidemic was also provided. CONCLUSION The COVID-19 pandemic in South Africa was very heterogeneous in its spatial dimension, with many distinct introductions of SARS-CoV2 in KZN and evidence of nosocomial transmission, which inflated early mortality in KZN. The epidemic at the local level was still developing and NGS-SA aimed to clarify the dynamics in South Africa and devise the most effective measures as the outbreak evolved.
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Affiliation(s)
- Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ilya Sinayskiy
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa; National Institute for Theoretical Physics (NITheP), KwaZulu-Natal, South Africa
| | - Maria Schuld
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, UK
| | - Benjamin Chimukangara
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Zoology, University of Oxford, Oxford, UK
| | - Yunus Moosa
- Department of Zoology, University of Oxford, Oxford, UK
| | - Inbal Gazy
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Maryam Fish
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Khulekani Sedwell Khanyile
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Laboratorio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil
| | - Luiz Carlos Junior Alcantara
- Laboratorio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil
| | - Francesco Petruccione
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa; National Institute for Theoretical Physics (NITheP), KwaZulu-Natal, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Centre for Aids Programme of Research in South Africa (CAPRISA), Durban, South Africa; Department of Global Health, University of Washington, Seattle, Washington, USA.
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15
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San JE, Ngcapu S, Kanzi AM, Tegally H, Fonseca V, Giandhari J, Wilkinson E, Nelson CW, Smidt W, Kiran AM, Chimukangara B, Pillay S, Singh L, Fish M, Gazy I, Martin DP, Khanyile K, Lessells R, de Oliveira T. Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa. Virus Evol 2021; 7:veab041. [PMID: 34035952 PMCID: PMC8135343 DOI: 10.1093/ve/veab041] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes acute, highly transmissible respiratory infection in humans and a wide range of animal species. Its rapid global spread has resulted in a major public health emergency, necessitating commensurately rapid research to improve control strategies. In particular, the ability to effectively retrace transmission chains in outbreaks remains a major challenge, partly due to our limited understanding of the virus' underlying evolutionary dynamics within and between hosts. We used high-throughput sequencing whole-genome data coupled with bottleneck analysis to retrace the pathways of viral transmission in two nosocomial outbreaks that were previously characterised by epidemiological and phylogenetic methods. Additionally, we assessed the mutational landscape, selection pressures, and diversity at the within-host level for both outbreaks. Our findings show evidence of within-host selection and transmission of variants between samples. Both bottleneck and diversity analyses highlight within-host and consensus-level variants shared by putative source-recipient pairs in both outbreaks, suggesting that certain within-host variants in these outbreaks may have been transmitted upon infection rather than arising de novo independently within multiple hosts. Overall, our findings demonstrate the utility of combining within-host diversity and bottleneck estimations for elucidating transmission events in SARS-CoV-2 outbreaks, provide insight into the maintenance of viral genetic diversity, provide a list of candidate targets of positive selection for further investigation, and demonstrate that within-host variants can be transferred between patients. Together these results will help in developing strategies to understand the nature of transmission events and curtail the spread of SARS-CoV-2.
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Affiliation(s)
- James E San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Sinaye Ngcapu
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban, South Africa
| | - Aquillah M Kanzi
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Chase W Nelson
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Werner Smidt
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Anmol M Kiran
- Malawi-Liverpool-Wellcome Trust, Queen Elizabeth Central Hospital, College of Medicine, Blantyre, Malawi
- Centre for Inflammation Research, Queens Research Institute, University of Edinburgh, Edinburgh, UK
| | - Benjamin Chimukangara
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Maryam Fish
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Inbal Gazy
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Darren P Martin
- Institute of Infectious Diseases and Molecular Medicine, Division of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Khulekani Khanyile
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
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16
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James SE, Ngcapu S, Kanzi AM, Tegally H, Fonseca V, Giandhari J, Wilkinson E, Chimukangara B, Pillay S, Singh L, Fish M, Gazy I, Khanyile K, Lessells R, de Oliveira T. High Resolution analysis of Transmission Dynamics of Sars-Cov-2 in Two Major Hospital Outbreaks in South Africa Leveraging Intrahost Diversity. medRxiv 2020:2020.11.15.20231993. [PMID: 33236025 PMCID: PMC7685338 DOI: 10.1101/2020.11.15.20231993] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes acute, highly transmissible respiratory infection in both humans and wide range of animal species. Its rapid spread globally and devasting effects have resulted into a major public health emergency prompting the need for methodological interventions to understand and control its spread. In particular, The ability to effectively retrace its transmission pathways in outbreaks remains a major challenge. This is further exacerbated by our limited understanding of its underlying evolutionary mechanism. Using NGS whole-genome data, we determined whether inter- and intra-host diversity coupled with bottleneck analysis can retrace the pathway of viral transmission in two epidemiologically well characterised nosocomial outbreaks in healthcare settings supported by phylogenetic analysis. Additionally, we assessed the mutational landscape, selection pressure and diversity of the identified variants. Our findings showed evidence of intrahost variant transmission and evolution of SARS-CoV-2 after infection These observations were consistent with the results from the bottleneck analysis suggesting that certain intrahost variants in this study could have been transmitted to recipients. In both outbreaks, we observed iSNVs and SNVs shared by putative source-recipients pairs. Majority of the observed iSNVs were positioned in the S and ORF1ab region. AG, CT and TC nucleotide changes were enriched across SARS-COV-2 genome. Moreover, SARS-COV-2 genome had limited diversity in some loci while being highly conserved in others. Overall, Our findings show that the synergistic effect of combining withinhost diversity and bottleneck estimations greatly enhances resolution of transmission events in Sars-Cov-2 outbreaks. They also provide insight into the genome diversity suggesting purifying selection may be involved in the transmission. Together these results will help in developing strategies to elucidate transmission events and curtail the spread of Sars-Cov-2.
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Affiliation(s)
- San Emmanuel James
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sinaye Ngcapu
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban, South Africa
| | - Aquillah M Kanzi
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Benjamin Chimukangara
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Maryam Fish
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Inbal Gazy
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Khulekani Khanyile
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Department of Global Health, University of Washington, Seattle, USA
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
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17
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Kanzi AM, San JE, Chimukangara B, Wilkinson E, Fish M, Ramsuran V, de Oliveira T. Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance. Front Genet 2020; 11:544162. [PMID: 33193618 PMCID: PMC7649788 DOI: 10.3389/fgene.2020.544162] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/21/2020] [Indexed: 12/29/2022] Open
Abstract
Mendelian and complex genetic trait diseases continue to burden and affect society both socially and economically. The lack of effective tests has hampered diagnosis thus, the affected lack proper prognosis. Mendelian diseases are caused by genetic mutations in a singular gene while complex trait diseases are caused by the accumulation of mutations in either linked or unlinked genomic regions. Significant advances have been made in identifying novel diseases associated mutations especially with the introduction of next generation and third generation sequencing. Regardless, some diseases are still without diagnosis as most tests rely on SNP genotyping panels developed from population based genetic analyses. Analysis of family genetic inheritance using whole genomes, whole exomes or a panel of genes has been shown to be effective in identifying disease-causing mutations. In this review, we discuss next generation and third generation sequencing platforms, bioinformatic tools and genetic resources commonly used to analyze family based genomic data with a focus on identifying inherited or novel disease-causing mutations. Additionally, we also highlight the analytical, ethical and regulatory challenges associated with analyzing personal genomes which constitute the data used for family genetic inheritance.
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Affiliation(s)
- Aquillah M. Kanzi
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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18
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Pillay S, Giandhari J, Tegally H, Wilkinson E, Chimukangara B, Lessells R, Moosa Y, Mattison S, Gazy I, Fish M, Singh L, Khanyile KS, San JE, Fonseca V, Giovanetti M, Alcantara LC, de Oliveira T. Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic. Genes (Basel) 2020; 11:E949. [PMID: 32824573 PMCID: PMC7464704 DOI: 10.3390/genes11080949] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/16/2020] [Accepted: 07/24/2020] [Indexed: 12/22/2022] Open
Abstract
The COVID-19 pandemic has spread very fast around the world. A few days after the first detected case in South Africa, an infection started in a large hospital outbreak in Durban, KwaZulu-Natal (KZN). Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes can be used to trace the path of transmission within a hospital. It can also identify the source of the outbreak and provide lessons to improve infection prevention and control strategies. This manuscript outlines the obstacles encountered in order to genotype SARS-CoV-2 in near-real time during an urgent outbreak investigation. This included problems with the length of the original genotyping protocol, unavailability of reagents, and sample degradation and storage. Despite this, three different library preparation methods for Illumina sequencing were set up, and the hands-on library preparation time was decreased from twelve to three hours, which enabled the outbreak investigation to be completed in just a few weeks. Furthermore, the new protocols increased the success rate of sequencing whole viral genomes. A simple bioinformatics workflow for the assembly of high-quality genomes in near-real time was also fine-tuned. In order to allow other laboratories to learn from our experience, all of the library preparation and bioinformatics protocols are publicly available at protocols.io and distributed to other laboratories of the Network for Genomics Surveillance in South Africa (NGS-SA) consortium.
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Affiliation(s)
- Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - Benjamin Chimukangara
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
- Centre for AIDS Programme of Research in South Africa (CAPRISA), Durban 4001, South Africa
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
- Infectious Diseases Department, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa;
| | - Yunus Moosa
- Infectious Diseases Department, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa;
| | - Stacey Mattison
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - Inbal Gazy
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - Maryam Fish
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - Khulekani Sedwell Khanyile
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
- Laboratorio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil;
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro 21045-900, Brazil;
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro 21045-900, Brazil;
| | - Luiz Carlos Alcantara
- Laboratorio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil;
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro 21045-900, Brazil;
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
- Centre for AIDS Programme of Research in South Africa (CAPRISA), Durban 4001, South Africa
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
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19
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Giandhari J, Pillay S, Wilkinson E, Tegally H, Sinayskiy I, Schuld M, Lourenco J, Chimukangara B, Lessells R, Moosa Y, Gazy I, Fish M, Singh L, Khanyile KS, Fonseca V, Giovanetti M, Alcantara LC, Petruccione F, de Oliveira T. Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report. medRxiv 2020:2020.05.29.20116376. [PMID: 32511505 PMCID: PMC7273273 DOI: 10.1101/2020.05.29.20116376] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background The emergence of a novel coronavirus, SARS-CoV-2, in December 2019, progressed to become a world pandemic in a few months and reached South Africa at the beginning of March. To investigate introduction and understand the early transmission dynamics of the virus, we formed the South African Network for Genomics Surveillance of COVID (SANGS_COVID), a network of ten government and university laboratories. Here, we present the first results of this effort, which is a molecular epidemiological study of the first twenty-one SARS-CoV-2 whole genomes sampled in the first port of entry, KwaZulu-Natal (KZN), during the first month of the epidemic. By combining this with calculations of the effective reproduction number (R), we aim to shed light on the patterns of infections that define the epidemic in South Africa. Methods R was calculated using positive cases and deaths from reports provided by the four major provinces. Molecular epidemiology investigation involved sequencing viral genomes from patients in KZN using ARCTIC protocols and assembling whole genomes using meticulous alignment methods. Phylogenetic analysis was performed using maximum likelihood (ML) and Bayesian trees, lineage classification and molecular clock calculations. Findings The epidemic in South Africa has been very heterogeneous. Two of the largest provinces, Gauteng, home of the two large metropolis Johannesburg and Pretoria, and KwaZulu-Natal, home of the third largest city in the country Durban, had a slow growth rate on the number of detected cases. Whereas, Western Cape, home of Cape Town, and the Eastern Cape provinces the epidemic is spreading fast. Our estimates of transmission potential for South Africa suggest a decreasing transmission potential towards R=1 since the first cases and deaths have been reported. However, between 06 May and 18 May 2020, we estimate that R was on average 1.39 (1.04 - 2.15, 95% CI). We also demonstrate that early transmission in KZN, and most probably in all main regions of SA, was associated with multiple international introductions and dominated by lineages B1 and B. The study also provides evidence for locally acquired infections in a hospital in Durban within the first month of the epidemic, which inflated early mortality in KZN. Interpretation This first report of SANGS_COVID consortium focuses on understanding the epidemic heterogeneity and introduction of SARS-CoV-2 strains in the first month of the epidemic in South Africa. The early introduction of SARS-CoV-2 in KZN included caused a localized outbreak in a hospital, provides potential explanations for the initially high death rates in the province. The current high rate of transmission of COVID-19 in the Western Cape and Eastern Cape highlights the crucial need to strength local genomic surveillance in South Africa. Funding UKZN Flagship Program entitled: Afrocentric Precision Approach to Control Health Epidemic, by a research Flagship grant from the South African Medical Research Council (MRC-RFA-UFSP-01-2013/UKZN HIVEPI, by the the Technology Innovation Agency and the the Department of Science and Innovation and by National Human Genome Re- search Institute of the National Institutes of Health under Award Number U24HG006941. H3ABioNet is an initiative of the Human Health and Heredity in Africa Consortium (H3Africa).
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Affiliation(s)
- Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ilya Sinayskiy
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
- National Institute for Theoretical Physics (NITheP), KwaZulu-Natal, 4001, South Africa
| | - Maria Schuld
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
| | - Jose Lourenco
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Benjamin Chimukangara
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Infectious Diseases Department, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Yunus Moosa
- Infectious Diseases Department, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Inbal Gazy
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Maryam Fish
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Khulekani Sedwell Khanyile
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Laboratorio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil
| | - Luiz Carols Alcantara
- Laboratorio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil
| | - Francesco Petruccione
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
- National Institute for Theoretical Physics (NITheP), KwaZulu-Natal, 4001, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Aids Programme of Research in South Africa (CAPRISA), Durban South Africa
- Department of Global Health, University of Washington, Seattle, Washington, USA
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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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Naidoo K, Dookie N, Naidoo K, Yende-Zuma N, Chimukangara B, Bhushan A, Govender D, Gengiah S, Padayatchi N. Recurrent tuberculosis among HIV-coinfected patients: a case series from KwaZulu-Natal. Infect Drug Resist 2018; 11:1413-1421. [PMID: 30233220 PMCID: PMC6130302 DOI: 10.2147/idr.s150644] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Recurrent tuberculosis (TB) following TB treatment completion in HIV-infected individuals remains a major public health burden. We assessed the role of various risk factors in mediating the development of recurrent TB and subsequent resistance to antiretroviral therapy and anti-TB drugs. Patients and methods We analyzed secondary demographic, clinical, and laboratory data from medical records of five HIV-infected TB patients enrolled between 2009 and 2014 in a prospective observational study investigating TB recurrence. Paired clinical isolates of Myco-bacterium tuberculosis were typed by IS6110 restriction fragment length polymorphism analysis to determine the mechanism of TB recurrence. Plasma samples were genotyped to determine acquisition of HIV drug resistance mutations on antiretroviral treatment (ART). Results All five patients were HIV-coinfected, with a previous history of TB infection and prior exposure to anti-TB treatment, and residual lung damage, and demonstrated poor treatment adherence – significant risk factors linked to the development of recurrent TB disease. Furthermore, three of the five patients had multiple episodes of drug-susceptible TB infection with subsequent drug-resistant TB infection. Genotyping of the initial and recurrent M. tuberculosis isolates demonstrated three cases of recurrent TB because of relapse and two because of reinfection. All five patients had no mutations at ART initiation; however, by the end of the study follow-up, all patients developed dual class resistance. Conclusion This series demonstrates the complexity of recurrent TB in HIV coinfection. We highlight the challenges of managing coinfected patients and the increased propensity for the development of drug resistance. We report on the role of various risk factors mediating the development of resistance and subsequent clinical impact. This report underscores the need for structural clinical and adherence interventions for the management of complex treatment and dosing.
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Affiliation(s)
- Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa, .,South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa,
| | - Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa, .,KwaZulu Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa
| | - Kasavan Naidoo
- South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa,
| | - Nonhlanhla Yende-Zuma
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa,
| | - Benjamin Chimukangara
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa, .,KwaZulu Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa.,Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Ambika Bhushan
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa,
| | - Dhineshree Govender
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa,
| | - Santhanalakshmi Gengiah
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa,
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa, .,South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa,
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Chimukangara B, Manasa J, Mitchell R, Nyabadza G, Katzenstein D, Masimirembwa C. Community Based Antiretroviral Treatment in Rural Zimbabwe. AIDS Res Hum Retroviruses 2017; 33:1185-1191. [PMID: 28899102 DOI: 10.1089/aid.2017.0029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Treatment of HIV has reduced HIV/AIDS-related mortality. Sustaining >90% virologic suppression in sub-Saharan Africa requires decentralized care and prevention services to rural communities. In Zimbabwe, the number of people receiving antiretroviral treatment (ART) has increased rapidly. However, access to treatment monitoring tools such as viral load and drug resistance testing is limited. We assessed virologic treatment outcomes among ART recipients in Nyamutora, a rural community receiving bimonthly ART and prevention services. We enrolled all ART recipients (143) at 6-monthly visits in the Nyamutora community in 2014 and 2015. Whole blood samples were collected in K-EDTA tubes, transported to Harare for CD4 counts and viral load testing, and genotype was obtained in participants with viral loads >1,000 copies/ml. Ages ranged from 2 to 75 years (median 43 years) with a median 42 months on ART at follow-up. Eight of 143 (6%) had viral loads >1,000 copies/ml at one of the 3 visits, 7 on first-line nevirapine (NVP)-based ART and 1 on second-line LPV/r-based ART. Seven participants had sequence data available, and five had drug resistance mutations, K65R, T69N, K101E, K103N, Y181C/I, M184V, and G190A. Virologic failure (p = .001) and drug resistance mutations (p = .01) on first-line NVP-based ART were associated with younger age by univariate exact logistic regression. The participants had high viral suppression (94%) despite less than optimal (NVP based) ART regimens without laboratory monitoring. Virologic failure and drug resistance were higher among children and adolescents. Effective ART delivery to the community achieved high rates of virologic suppression and minimal drug resistance.
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Affiliation(s)
- Benjamin Chimukangara
- Department of Molecular Biology, Biomedical Research and Training Institute, Harare, Zimbabwe
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Justen Manasa
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Rebecca Mitchell
- Department of Mathematics and Computer Science, Emory University, Atlanta, Georgia
| | - Georgina Nyabadza
- African Institute of Biomedical Science and Technology, Harare, Zimbabwe
| | - David Katzenstein
- Department of Medicine, Stanford University School of Medicine, Stanford, California
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Makadzange AT, Boyd FK, Chimukangara B, Masimirembwa C, Katzenstein D, Ndhlovu CE. A Simple Phosphate-Buffered-Saline-Based Extraction Method Improves Specificity of HIV Viral Load Monitoring Using Dried Blood Spots. J Clin Microbiol 2017; 55:2172-2179. [PMID: 28468852 PMCID: PMC5483919 DOI: 10.1128/jcm.00176-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 04/19/2017] [Indexed: 12/30/2022] Open
Abstract
Although Roche COBAS Ampliprep/COBAS TaqMan (CAP/CTM) systems are widely used in sub-Saharan Africa for early infant diagnosis of HIV from dried blood spots (DBS), viral load monitoring with this system is not practical due to nonspecific extraction of both cell-free and cell-associated viral nucleic acids. A simplified DBS extraction technique for cell-free virus elution using phosphate-buffered saline (PBS) may provide an alternative analyte for lower-cost quantitative HIV virus load (VL) testing to monitor antiretroviral therapy (ART). We evaluated the CAP/CTM v2.0 assay in 272 paired plasma and DBS specimens using the cell-free virus elution method and determined the level of agreement, sensitivity, and specificity at thresholds of target not detected (TND), target below the limit of quantification (BLQ) (<20 copies/ml in plasma or <400 copies/ml in DBS), and VL of <1,000 copies/ml, and VL of <5,000 copies/ml. Reported plasma VL ranged from TND, or <20, to 5,781,592 copies/ml, and DBS VL ranged from TND, or <400, to 467,600 copies/ml. At <1000 copies/ml, agreement between DBS and plasma was 96.7% (kappa coefficient, 0.93; P < 0.0001). The mean difference between DBS and plasma VL values was -1.06 log10 copies/ml (95% confidence interval [CI], -1.17, -0.97; P < 0.0001). At a treatment failure threshold of >1,000 copies/ml, the sensitivities, specificities, positive predictive values (PPV), and negative predictive values (NPV) were 92.7%, 100%, 100%, and 94.3%, respectively. PBS elution of DBS offers a sensitive and specific method for monitoring plasma viremia among adults and children on ART at the WHO-recommended threshold of >1,000 copies/ml on the Roche CAP/CTM system.
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Affiliation(s)
- A Tariro Makadzange
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachussetts, USA
- Department of Medicine, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - F Kathryn Boyd
- Department of Medicine, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - Benjamin Chimukangara
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | | | - David Katzenstein
- Division of Infectious Diseases, Stanford University, Palo Alto, California, USA
| | - Chiratidzo E Ndhlovu
- Department of Medicine, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
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25
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Chimukangara B, Varyani B, Shamu T, Mutsvangwa J, Manasa J, White E, Chimbetete C, Luethy R, Katzenstein D. HIV drug resistance testing among patients failing second line antiretroviral therapy. Comparison of in-house and commercial sequencing. J Virol Methods 2017; 243:151-157. [PMID: 27894862 PMCID: PMC5393912 DOI: 10.1016/j.jviromet.2016.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 11/07/2016] [Accepted: 11/23/2016] [Indexed: 01/05/2023]
Abstract
INTRODUCTION HIV genotyping is often unavailable in low and middle-income countries due to infrastructure requirements and cost. We compared genotype resistance testing in patients with virologic failure, by amplification of HIV pol gene, followed by "in-house" sequencing and commercial sequencing. METHODS Remnant plasma samples from adults and children failing second-line ART were amplified and sequenced using in-house and commercial di-deoxysequencing, and analyzed in Harare, Zimbabwe and at Stanford, U.S.A, respectively. HIV drug resistance mutations were determined using the Stanford HIV drug resistance database. RESULTS Twenty-six of 28 samples were amplified and 25 were successfully genotyped. Comparison of average percent nucleotide and amino acid identities between 23 pairs sequenced in both laboratories were 99.51 (±0.56) and 99.11 (±0.95), respectively. All pairs clustered together in phylogenetic analysis. Sequencing analysis identified 6/23 pairs with mutation discordances resulting in differences in phenotype, but these did not impact future regimens. CONCLUSIONS The results demonstrate our ability to produce good quality drug resistance data in-house. Despite discordant mutations in some sequence pairs, the phenotypic predictions were not clinically significant.
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Affiliation(s)
- Benjamin Chimukangara
- Department of Molecular Biology, Biomedical Research and Training Institute, Harare, Zimbabwe; Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa.
| | - Bhavini Varyani
- Department of Molecular Biology, Biomedical Research and Training Institute, Harare, Zimbabwe.
| | - Tinei Shamu
- Newlands Clinic, Newlands, Harare, Zimbabwe.
| | - Junior Mutsvangwa
- Department of Molecular Biology, Biomedical Research and Training Institute, Harare, Zimbabwe.
| | - Justen Manasa
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Elizabeth White
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Cleophas Chimbetete
- Newlands Clinic, Newlands, Harare, Zimbabwe; Institute of Social and Preventive Medicine, University of Bern, Switzerland.
| | | | - David Katzenstein
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Musingwini TV, Zhou DT, Mhandire D, Duri K, Gomo E, Oktedalen O, Chimukangara B, Shamu T, Shawarira-Bote S, Dandara C, Stray-Pedersen B. Use of Proviral DNA to Investigate Virus Resistance Mutations in HIV-infected Zimbabweans. Open Microbiol J 2017; 11:45-52. [PMID: 28553415 PMCID: PMC5427698 DOI: 10.2174/1874285801711010045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/27/2017] [Accepted: 02/28/2017] [Indexed: 11/23/2022] Open
Abstract
Background: Antiretroviral therapy (ART) to suppress HIV replication has reduced morbidity and mortality yet effectiveness of current HIV drugs is threatened by HIV drug resistance (HIVDR) mutations. Objective: To determine HIVDR mutations using proviral DNA from specimens of patients presenting to an HIV treatment clinic. Methods: DNA from 103 patients, 86 treatment-experienced, 17 treatment-naïve, were genotyped for the HIV-1C reverse transcriptase gene (RT; codons 21-304) using Sanger sequencing and sequences analyzed using Sequencher software. Resistance mutations were interpreted using Stanford HIVDR reference database. Results: Median age was 39 (IQR, 33-46) years and 80% of patients were female. Six-percent (n=6) had at least one HIVDR mutation, comprising NRTI-associated mutations, (M184V, T69D, T69N and V75I); NNRTI-associated mutations (G190A, K103N, V106M, Y181C) and thymidine analogue associated mutations (D67N, K70R, K219Q, L210W, M41L, T215Y). Of the six participants, with at least one HIVDR mutation, all were treatment experienced, five were on tenofovir, lamivudine and nevirapine and one was on tenofovir, lamivudine and atazanavir. There was no difference in median CD4 count and viral loads when patients were compared by presence of HIVDR mutations. Conclusion: We demonstrated the use of proviral DNA in HIVDR testing in adult patients and present that all the patients with various kinds of HIVDR mutations were treatment experienced, pointing to the role of drug regimens in driving viral mutations. Thus, the use of proviral DNA has potential to help provide surveillance on risk of HIVDR in HIV-infected individuals who are on treatment, which may assist in corrective treatment.
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Affiliation(s)
- Tutsirai V Musingwini
- University of Zimbabwe, College of Health Sciences, Department of Medical Laboratory Sciences, Harare, Zimbabwe
| | - Danai T Zhou
- University of Zimbabwe, College of Health Sciences, Department of Medical Laboratory Sciences, Harare, Zimbabwe.,Institute of Clinical Medicine, University in Oslo, Oslo University Hospital, Oslo, Norway
| | - Doreen Mhandire
- University of Zimbabwe, College of Health Sciences, Department of Chemical Pathology, Harare, Zimbabwe
| | - Kerina Duri
- Universisty of Zimbabwe, College of Health Sciences, Department of Immunology, Harare, Zimbabwe
| | - Exnevia Gomo
- University of Zimbabwe, College of Health Sciences, Department of Medical Laboratory Sciences, Harare, Zimbabwe
| | - Olav Oktedalen
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Benjamin Chimukangara
- Africa Centre for Health and Population Studies, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
| | | | | | - Collet Dandara
- Division of Human Genetics, Department of Clinical Laboratory Sciences & Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Babill Stray-Pedersen
- Institute of Clinical Medicine, University in Oslo and Women's Clinic, Oslo University Hospital, Oslo, Norway
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Chimukangara B, Samuel R, Naidoo K, de Oliveira T. Primary HIV-1 Drug Resistant Minority Variants. AIDS Rev 2017; 19:89-96. [PMID: 28182621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Primary HIV drug resistant mutations are mutations that occur in an HIV-infected individual prior to the initiation of antiretroviral therapy (ART). These mutations may arise by de novo mutagenesis or result from transmission. Drug resistant mutations (DRMs) may reduce the effectiveness of ART leading to inadequate virological outcomes. Currently, Sanger sequencing is the standard method for detection of DRMs to inform treatment decisions, but does not detect minor variant mutations. Drug resistant minority variants (DRMVs) can be detected by next generation sequencing (NGS). However, several challenges including cost of infrastructure and the need for complex data analysis bioinformatics tools remain major setbacks for NGS use. More importantly, the clinical impact of DRMVs on ART is not well understood, underscoring the importance for understanding whether the levels of primary DRMVs for different mutations impact on the effectiveness of ART and the rationale for inclusion in routine diagnostics. Understanding the impact of primary DRMVs will help inform how NGS may be utilized in the future for pre-emptive clinical ART decision making.
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Affiliation(s)
- Benjamin Chimukangara
- Africa Centre for Population Health, Doris Duke Medical Research Institute, Nelson 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
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Reshmi Samuel
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Tulio de Oliveira
- Africa Centre for Population Health, Doris Duke Medical Research Institute, Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
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Makadzange AT, Higgins-Biddle M, Chimukangara B, Birri R, Gordon M, Mahlanza T, McHugh G, van Dijk JH, Bwakura-Dangarembizi M, Ndung’u T, Masimirembwa C, Phelps B, Amzel A, Ojikutu BO, Walker BD, Ndhlovu CE. Clinical, Virologic, Immunologic Outcomes and Emerging HIV Drug Resistance Patterns in Children and Adolescents in Public ART Care in Zimbabwe. PLoS One 2015; 10:e0144057. [PMID: 26658814 PMCID: PMC4678607 DOI: 10.1371/journal.pone.0144057] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/12/2015] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE To determine immunologic, virologic outcomes and drug resistance among children and adolescents receiving care during routine programmatic implementation in a low-income country. METHODS A cross-sectional evaluation with collection of clinical and laboratory data for children (0-<10 years) and adolescents (10-19 years) attending a public ART program in Harare providing care for pediatric patients since 2004, was conducted. Longitudinal data for each participant was obtained from the clinic based medical record. RESULTS Data from 599 children and adolescents was evaluated. The participants presented to care with low CD4 cell count and CD4%, median baseline CD4% was lower in adolescents compared with children (11.0% vs. 15.0%, p<0.0001). The median age at ART initiation was 8.0 years (IQR 3.0, 12.0); median time on ART was 2.9 years (IQR 1.7, 4.5). On ART, median CD4% improved for all age groups but remained below 25%. Older age (≥ 5 years) at ART initiation was associated with severe stunting (HAZ <-2: 53.3% vs. 28.4%, p<0.0001). Virologic failure rate was 30.6% and associated with age at ART initiation. In children, nevirapine based ART regimen was associated with a 3-fold increased risk of failure (AOR: 3.5; 95% CI: 1.3, 9.1, p = 0.0180). Children (<10 y) on ART for ≥4 years had higher failure rates than those on ART for <4 years (39.6% vs. 23.9%, p = 0.0239). In those initiating ART as adolescents, each additional year in age above 10 years at the time of ART initiation (AOR 0.4 95%CI: 0.1, 0.9, p = 0.0324), and each additional year on ART (AOR 0.4, 95%CI 0.2, 0.9, p = 0.0379) were associated with decreased risk of virologic failure. Drug resistance was evident in 67.6% of sequenced virus isolates. CONCLUSIONS During routine programmatic implementation of HIV care for children and adolescents, delayed age at ART initiation has long-term implications on immunologic recovery, growth and virologic outcomes.
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Affiliation(s)
- A. T. Makadzange
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Medicine, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | | | - B. Chimukangara
- Department of Medicine, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
- African Institute of Biomedical Sciences, Harare, Zimbabwe
| | - R. Birri
- Department of Medicine, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - M. Gordon
- HIV Pathogenesis Program, University of Kwa-Zulu Natal, Durban, South Africa
| | - T. Mahlanza
- Department of Medicine, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - G. McHugh
- Department of Medicine, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - J. H. van Dijk
- Department of Medicine, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - M. Bwakura-Dangarembizi
- Department of Pediatrics, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - T. Ndung’u
- HIV Pathogenesis Program, University of Kwa-Zulu Natal, Durban, South Africa
| | | | - B. Phelps
- United States Agency for International Development (USAID), Washington, DC, United States of America
| | - A. Amzel
- United States Agency for International Development (USAID), Washington, DC, United States of America
| | - B. O. Ojikutu
- John Snow Inc, Boston, Massachusetts, United States of America
| | - B. D. Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - C. E. Ndhlovu
- Department of Medicine, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
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Chimukangara B, Gwanzura L, Mitchell R, Katzenstein D, Masimirembwa C. Drug resistance mutations from whole blood proviral DNA among patients on antiretroviral drugs in Zimbabwe. Curr HIV Res 2015; 12:309-16. [PMID: 25323793 DOI: 10.2174/1570162x12666141017100733] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 09/19/2014] [Accepted: 10/09/2014] [Indexed: 11/22/2022]
Abstract
INTRODUCTION There are more than 500 000 HIV-infected people on antiretroviral treatment (ART) in Zimbabwe with very limited laboratory monitoring. To ensure effective treatment and prevent transmission of drug resistance, affordable treatment monitoring is needed to guide individual treatment. METHODS 125 whole blood samples from patients on first-line ART were investigated for drug resistance mutations using an in-house genotypic testing method. Patients had been on HIV reverse transcriptase inhibitors only, with some having been on both HIV and TB treatment. DNA was extracted from whole blood; amplicons were generated by nested PCR and sequenced. Drug resistance mutations were determined using the Stanford HIV drug resistance database. Exact statistics were used to investigate relationships between drug resistance and predisposing factors. RESULTS From 125 samples, 108 were successfully analyzed for drug resistance mutations. 11 of the 108 sequences had drug resistance mutations; predominantly M184V and Y181C. For a 100-cell increase in CD4 count, the odds of being resistant were 61% lower than those with the baseline CD4 count (p = 0.04, CI: 0.34-0.98). There was no association between concurrent HIV/TB treatment and drug resistance (p = 0.41). DISCUSSION AND CONCLUSION Although plasma samples are recommended for genotypic testing, the cost of analyzing plasma RNA makes it less feasible in resource limited settings. Lower cost DNA drug resistance testing from whole blood samples was assessed as a treatment-monitoring tool among patients followed by CD4 and clinical monitoring only. The infrequent detection of resistance and higher CD4 is consistent with effective first-line treatment. Further investigation of proviral DNA as a tool to identify drug resistance mutations is warranted.
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Affiliation(s)
| | | | | | | | - Collen Masimirembwa
- African Institute of Biomedical Science and Technology, 211 Dominion House, Cnr H. Chitepo and Parklane, Harare, Zimbabwe.
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