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El-Daly MM, Zaher KA, Zaki EA, Bajrai LH, Alhazmi MM, Abdulhaq A, Azhar EI. Immunological and molecular assessment of HIV-1 mutations for antiretroviral drug resistance in Saudi Arabia. PLoS One 2024; 19:e0304408. [PMID: 38923958 PMCID: PMC11207162 DOI: 10.1371/journal.pone.0304408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 05/10/2024] [Indexed: 06/28/2024] Open
Abstract
Human Immunodeficiency Virus (HIV) is a significant threat to public health. HIV genotyping and antiretroviral resistance testing may have contributed to improved non-treated management. Immune markers might assist HIV-1 diagnosis and drug-resistant variant identification. HIV-1 immunogenicity and molecular characteristics of antiretroviral drug resistance are evaluated in 56 treatment-naive HIV patients. DNA sequencing and retroviral resistance testing identified HIV-1 genotypes. 55.4% of patients were susceptible to protease inhibitors (PI), nucleoside reverse transcriptase inhibitors (NRTI), and non-nucleoside reverse transcriptase inhibitors (NNRTI) antiretroviral drugs, whereas 44.6% had drug-resistance mutations against at least one antiretroviral drug. 3.6% of cases had PI-resistant mutations, while 30.4% had NRTI-resistant mutations, and 30.4% had NNRTI-resistant mutations. In patients who are susceptible to PI, the mean value of human plasma sCD80 is 2.11 ± 0.65 ng/mL; in patients with mutations, it is 3.93 ± 2.91 ng/mL. Individuals who are susceptible to PI have plasma sCD27 levels of 78.7 ± 63.2 U/mL, whereas individuals who are mutant have levels of 56.5 ± 32.1 U/mL. IP-10's mean value was 363 ± 109.2 pg/mL for the susceptible patients and 429 ± 20.7 pg/mL for the mutated patients. In susceptible patients, the plasma sCD4 level is 0.163 ± 0.229 ng/mL; in mutant patients, it is 0.084 ± 0.012 ng/mL. The data showed a relative relation between immunological parameters such as sCD80, sCD27, sCD4, and IP-10 and mutation for drug resistance.
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Affiliation(s)
- Mai M. El-Daly
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kawther A. Zaher
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Immunology Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Eitezaz A. Zaki
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Virology, Jeddah Regional Lab, Ministry of Health, Jeddah, Saudi Arabia
| | - Leena H. Bajrai
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad M. Alhazmi
- FACP, Arab Board of Internal Medicine, Saudi Board of Internal Medicine, Jazan, Saudi Arabia
| | - Ahmed Abdulhaq
- Deanship of Scientific Affairs and Research, Jazan University, Jazan, Saudi Arabia
| | - Esam I. Azhar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Rashid A, Kang L, Yi F, Chu Q, Shah SA, Mahmood SF, Getaneh Y, Wei M, Chang S, Abidi SH, Shao Y. Human Immunodeficiency Virus Type-1 Genetic Diversity and Drugs Resistance Mutations among People Living with HIV in Karachi, Pakistan. Viruses 2024; 16:962. [PMID: 38932254 PMCID: PMC11209141 DOI: 10.3390/v16060962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/07/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
The human immunodeficiency virus type-1 epidemic in Pakistan has significantly increased over the last two decades. In Karachi, Pakistan, there is a lack of updated information on the complexity of HIV-1 genetic diversity and the burden of drug resistance mutations (DRMs) that can contribute to ART failure and poor treatment outcomes. This study aimed to determine HIV-1 genetic diversity and identify drug-resistance mutations among people living with HIV in Karachi. A total of 364 HIV-positive individuals, with a median age of 36 years, were enrolled in the study. The HIV-1 partial pol gene was successfully sequenced from 268 individuals. The sequences were used to generate phylogenetic trees to determine clade diversity and also to assess the burden of DRMs. Based on the partial pol sequences, 13 distinct HIV-1 subtypes and recombinant forms were identified. Subtype A1 was the most common clade (40%), followed by CRF02_AG (33.2%). Acquired DRMs were found in 30.6% of the ART-experienced patients, of whom 70.7%, 20.7%, and 8.5% were associated with resistance to NNRTIs, NRTIs, and PIs, respectively. Transmitted DRMs were found in 5.6% of the ART-naïve patients, of whom 93% were associated with resistance against NNRTIs and 7% to PIs. The high prevalence of DRMs in ART-experienced patients poses significant challenges to the long-term benefits and sustainability of the ART program. This study emphasizes the importance of continuous HIV molecular epidemiology and drug resistance surveillance to support evidence-based HIV prevention, precise ART, and targeted AIDS care.
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Affiliation(s)
- Abdur Rashid
- School of Medicine, Nankai University, Tianjin 300071, China; (A.R.); (M.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.K.); (Q.C.); (S.C.)
| | - Li Kang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.K.); (Q.C.); (S.C.)
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Feng Yi
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.K.); (Q.C.); (S.C.)
| | - Qingfei Chu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.K.); (Q.C.); (S.C.)
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China;
| | | | | | - Yimam Getaneh
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China;
- Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia
| | - Min Wei
- School of Medicine, Nankai University, Tianjin 300071, China; (A.R.); (M.W.)
| | - Song Chang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.K.); (Q.C.); (S.C.)
| | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana 010000, Kazakhstan
| | - Yiming Shao
- School of Medicine, Nankai University, Tianjin 300071, China; (A.R.); (M.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.K.); (Q.C.); (S.C.)
- College of Life Sciences, Nankai University, Tianjin 300071, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China;
- Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing 102206, China
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3
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Kanise H, van Oosterhout JJ, Bisani P, Songo J, Matola BW, Chipungu C, Simon K, Cox C, Hosseinipour MC, Sagno JB, Hoffman RM, Wallrauch C, Phiri S, Steegen K, Jahn A, Nyirenda R, Heller T. Virological Findings and Treatment Outcomes of Cases That Developed Dolutegravir Resistance in Malawi's National HIV Treatment Program. Viruses 2023; 16:29. [PMID: 38257730 PMCID: PMC10819735 DOI: 10.3390/v16010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/28/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Millions of Africans are on dolutegravir-based antiretroviral therapy (ART), but few detailed descriptions of dolutegravir resistance and its clinical management exist. We reviewed HIV drug resistance (HIVDR) testing application forms submitted between June 2019 and October 2022, data from the national HIVDR database, and genotypic test results. We obtained standardized ART outcomes and virological results of cases with dolutegravir resistance, and explored associations with dolutegravir resistance among individuals with successful integrase sequencing. All cases were on two nucleoside reverse transcriptase inhibitors (NRTIs)/dolutegravir, and had confirmed virological failure, generally with prolonged viremia. Among 89 samples with successful integrase sequencing, 24 showed dolutegravir resistance. Dolutegravir resistance-associated mutations included R263K (16/24), E138K (7/24), and G118R (6/24). In multivariable logistic regression analysis, older age and the presence of high-level NRTI resistance were significantly associated with dolutegravir resistance. After treatment modification recommendations, four individuals (17%) with dolutegravir resistance died, one self-discontinued ART, one defaulted, and one transferred out. Of the 17 remaining individuals, 12 had follow-up VL results, and 11 (92%) were <1000 copies/mL. Twenty-four cases with dolutegravir resistance among 89 individuals with confirmed virological failure suggests a considerable prevalence in the Malawi HIV program. Successful management of dolutegravir resistance was possible, but early mortality was high. More research on the management of treatment-experienced individuals with dolutegravir resistance is needed.
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Affiliation(s)
- Hope Kanise
- Partners in Hope, Lilongwe P.O. Box 302, Malawi; (H.K.); (J.S.); (C.C.); (S.P.)
| | - Joep J. van Oosterhout
- Partners in Hope, Lilongwe P.O. Box 302, Malawi; (H.K.); (J.S.); (C.C.); (S.P.)
- Division of Infectious Diseases, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA;
| | - Pachawo Bisani
- The Lighthouse Trust, Lilongwe P.O. Box 106, Malawi; (P.B.); (C.W.); (T.H.)
| | - John Songo
- Partners in Hope, Lilongwe P.O. Box 302, Malawi; (H.K.); (J.S.); (C.C.); (S.P.)
| | - Bilaal W. Matola
- Directorate of HIV, STI and Viral Hepatitis, Ministry of Health, Lilongwe P.O. Box 30377, Malawi; (B.W.M.); (A.J.); (R.N.)
| | - Chifundo Chipungu
- Partners in Hope, Lilongwe P.O. Box 302, Malawi; (H.K.); (J.S.); (C.C.); (S.P.)
| | - Katherine Simon
- Baylor College of Medicine Children’s Foundation-Malawi, Lilongwe P.O. Box 110, Malawi; (K.S.); (C.C.)
- Baylor College of Medicine, Houston, TX 77030, USA
| | - Carrie Cox
- Baylor College of Medicine Children’s Foundation-Malawi, Lilongwe P.O. Box 110, Malawi; (K.S.); (C.C.)
- Baylor College of Medicine, Houston, TX 77030, USA
| | - Mina C. Hosseinipour
- University of North Carolina Project Malawi, Lilongwe Private Bag A-104, Malawi;
- Department of Medicine, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC 27599, USA
| | | | - Risa M. Hoffman
- Division of Infectious Diseases, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA;
| | - Claudia Wallrauch
- The Lighthouse Trust, Lilongwe P.O. Box 106, Malawi; (P.B.); (C.W.); (T.H.)
| | - Sam Phiri
- Partners in Hope, Lilongwe P.O. Box 302, Malawi; (H.K.); (J.S.); (C.C.); (S.P.)
- School of Global and Public Health, Kamuzu University of Health Sciences, Lilongwe P.O. Box 30184, Malawi
| | - Kim Steegen
- Department of Haematology & Molecular Medicine, National Health Laboratory Service, Johannesburg 2131, South Africa;
- Department of Haematology & Molecular Medicine, University of the Witwatersrand, Johannesburg 2017, South Africa
| | - Andreas Jahn
- Directorate of HIV, STI and Viral Hepatitis, Ministry of Health, Lilongwe P.O. Box 30377, Malawi; (B.W.M.); (A.J.); (R.N.)
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Rose Nyirenda
- Directorate of HIV, STI and Viral Hepatitis, Ministry of Health, Lilongwe P.O. Box 30377, Malawi; (B.W.M.); (A.J.); (R.N.)
| | - Tom Heller
- The Lighthouse Trust, Lilongwe P.O. Box 106, Malawi; (P.B.); (C.W.); (T.H.)
- International Training and Education Center for Health (ITECH), University of Washington, Seattle, WA 98104-2499, USA
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Parkin N, Harrigan PR, Inzaule S, Bertagnolio S. Need assessment for HIV drug resistance testing and landscape of current and future technologies in low- and middle-income countries. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001948. [PMID: 37851634 PMCID: PMC10584185 DOI: 10.1371/journal.pgph.0001948] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Resistance to antiretroviral drugs used to treat HIV is an important and evolving concern, particularly in low- and middle-income countries (LMICs) which have been impacted to the greatest extent by the HIV pandemic. Efforts to monitor the emergence and transmission of resistance over the past decade have shown that drug resistance-especially to the nucleoside analogue and non-nucleoside reverse transcriptase inhibitors-can (and have) increased to levels that can jeopardize the efficacy of available treatment options at the population level. The global shift to integrase-based regimens as the preferred first-line therapy as well as technological advancements in the methods for detecting resistance have had an impact in broadening and diversifying the landscape of and use case for HIV drug resistance testing. This review estimates the potential demand for HIV drug resistance tests, and surveys current testing methodologies, with a focus on their application in LMICs.
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Affiliation(s)
- Neil Parkin
- Data First Consulting, Sebastopol, CA, United States of America
| | - P. Richard Harrigan
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Seth Inzaule
- Amsterdam Institute for Global Health and Development, and Department of Global Health, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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5
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Getaneh Y, Getnet F, Ning F, Rashid A, Liao L, Yi F, Shao Y. HIV-1 Disease Progression and Drug Resistance Mutations among Children on First-Line Antiretroviral Therapy in Ethiopia. Biomedicines 2023; 11:2293. [PMID: 37626789 PMCID: PMC10452141 DOI: 10.3390/biomedicines11082293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Background: High rates of disease progression and HIV drug resistance (HIVDR) among adults taking highly active antiretroviral treatment (HAART) in Sub-Saharan Africa were previously documented. However, children were generally not considered despite their greater risk. Hence, this study was aimed to evaluate HIV-1 disease progression and drug resistance mutation among children on first-line antiretroviral therapy in Ethiopia. Method: A longitudinal study was conducted among 551 HIV-positive children (<15 years old) recruited between 2017 and 2019 at 40 antiretroviral treatment delivery sites in Ethiopia. Disease progression was retrospectively measured over a 12-year (2007-2019) follow-up as the progress towards immunosuppression. Two consecutive viral load (VL) tests were conducted in 6-month intervals to assess virologic failure (VF). For children with VF, HIV-1 genotyping and sequencing was performed for the pol gene region using in-house assay validated at the Chinese Center for Disease Control and Prevention, and the Stanford HIVDB v9.0 algorithm was used for identification of drug resistance mutations. The Kaplan-Meier analysis and Cox proportional hazards regression model were used to estimate the rate and predictors of disease progression, respectively. Results: The disease progression rate was 6.3 per 100 person-years-observation (95% CI = 4.21-8.53). Overall immunosuppression (CD4 count < 200 cells/mm3) during the 12-year follow-up was 11.3% (95% CI = 7.5-15.1). Immunosuppression was significantly increased as of the mean duration of 10.5 (95% CI = 10.1-10.8) years (38.2%) to 67.8% at 12 years (p < 0.001). Overall, 14.5% had resistance to at least one drug, and 6.2% had multi-drug resistance. A resistance of 67.8% was observed among children with VF. Resistance to non-nucleotide reverse transcriptase inhibitors (NNRTI) and nucleotide reverse transcriptase inhibitors (NRTI) drugs were 11.4% and 10.1%, respectively. Mutations responsible for NRTI resistance were M184V (30.1%), K65R (12.1%), and D67N (5.6%). Moreover, NNRTI-associated mutations were K103N (14.8%), Y181C (11.8%), and G190A (7.7%). Children who had a history of opportunistic infection [AHR (95% CI) = 3.4 (1.8-6.2)], vitamin D < 20 ng/mL [AHR (95% CI) = 4.5 (2.1-9.9)], drug resistance [AHR (95% CI) = 2.2 (1.4-3.6)], and VF [AHR (95% CI) = 2.82 (1.21, 3.53)] had a higher hazard of disease progression; whereas, being orphan [AOR (95% CI) = 1.8 (1.2-3.1)], history of drug substitution [(AOR (95% CI) = 4.8 (2.1-6.5), hemoglobin < 12 mg/dL [AOR (95% CI) = 1.2 (1.1-2.1)] had higher odds of developing drug resistance. Conclusions: Immunosuppression was increasing over time and drug resistance was also substantially high. Enhancing routine monitoring of viral load and HIVDR and providing a vitamin-D supplement during clinical management could help improve the immunologic outcome. Limiting HAART substitution is also crucial for children taking HAART in Ethiopia.
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Affiliation(s)
- Yimam Getaneh
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310027, China;
- Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia
| | - Fentabil Getnet
- Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia
- Takemi Program in International Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Feng Ning
- Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Abdur Rashid
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Lingjie Liao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Feng Yi
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yiming Shao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310027, China;
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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Hunt GM, Yousif M, Levin L, Ledwaba J, Steegen K, Kufa T, Zwane H, Kalimashe M, Kana V, Aynalem G, Perlman J, Ayalew K, Kindra G, Diallo K, Carmona S, Sherman G, Raizes EJ. Resistance is common in paediatric patients failing ART in South Africa. J Antimicrob Chemother 2023; 78:1160-1167. [PMID: 37017009 PMCID: PMC10616358 DOI: 10.1093/jac/dkac443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/05/2022] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Minimal data exist on HIV drug resistance patterns and prevalence among paediatric patients failing ART in resource-limited settings. We assessed levels of HIV drug resistance in children with virological failure. METHODS This cross-sectional study, performed from March 2017 to March 2019 in South Africa, enrolled HIV-positive children aged ≤19 years, receiving ART through public health facilities with recent evidence suggestive of virological failure (at least one viral load ≥1000 copies/mL), across 45 randomly selected high-volume clinics from all nine provinces. Resistance genotyping was performed using next-generation sequencing technologies. Descriptive analysis taking into account survey design was used to determine outcomes. RESULTS Among 899 participants enrolled, the adjusted proportion of HIV drug resistance among children with virological failure was 87.5% (95% CI 83.0%-90.9%). Resistance to NNRTIs was detected in 77.4% (95% CI 72.5%-81.7%) of participants, and resistance to NRTIs in 69.5% (95% CI 62.9%-75.4%) of participants. Overall, resistance to PIs was detected in 7.7% (95% CI 4.4%-13.0%) of children. CONCLUSIONS HIV drug resistance was highly prevalent in paediatric patients failing ART in South Africa, with 9 in 10 patients harbouring resistance to NNRTIs and/or NRTIs. PI-based regimens are predicted to be highly efficacious in achieving virological suppression amongst patients failing NNRTI-based regimens. Scaling up resistance testing amongst patients would facilitate access to second- and third-line regimens in South Africa.
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Affiliation(s)
- Gillian M. Hunt
- Centre for HIV and STIs, National Institute for Communicable Diseases, Private Bag X4, Sandringham, Johannesburg 2131, South Africa
- Department of Virology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mukhlid Yousif
- Centre for HIV and STIs, National Institute for Communicable Diseases, Private Bag X4, Sandringham, Johannesburg 2131, South Africa
- Department of Virology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Leon Levin
- Right to Care, Johannesburg, South Africa
| | - Johanna Ledwaba
- Centre for HIV and STIs, National Institute for Communicable Diseases, Private Bag X4, Sandringham, Johannesburg 2131, South Africa
| | - Kim Steegen
- National Health Laboratory Services, Johannesburg, South Africa
- Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tendesayi Kufa
- Centre for HIV and STIs, National Institute for Communicable Diseases, Private Bag X4, Sandringham, Johannesburg 2131, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Hloniphile Zwane
- Centre for HIV and STIs, National Institute for Communicable Diseases, Private Bag X4, Sandringham, Johannesburg 2131, South Africa
| | - Monalisa Kalimashe
- Centre for HIV and STIs, National Institute for Communicable Diseases, Private Bag X4, Sandringham, Johannesburg 2131, South Africa
| | - Vibha Kana
- Centre for HIV and STIs, National Institute for Communicable Diseases, Private Bag X4, Sandringham, Johannesburg 2131, South Africa
| | - Getahun Aynalem
- Division of Global HIV and Tuberculosis, Center for Global Health, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Jaclyn Perlman
- Division of Global HIV and Tuberculosis, Center for Global Health, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Kassahun Ayalew
- Division of Global HIV and Tuberculosis, Center for Global Health, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Gurpreet Kindra
- Division of Global HIV and Tuberculosis, Center for Global Health, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Karidia Diallo
- Division of Global HIV and Tuberculosis, Center for Global Health, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Sergio Carmona
- National Health Laboratory Services, Johannesburg, South Africa
- Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gayle Sherman
- Centre for HIV and STIs, National Institute for Communicable Diseases, Private Bag X4, Sandringham, Johannesburg 2131, South Africa
- Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Elliot J. Raizes
- Division of Global HIV and Tuberculosis, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
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7
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Kovalenko G, Yakovleva A, Smyrnov P, Redlinger M, Tymets O, Korobchuk A, Kolodiazieva A, Podolina A, Cherniavska S, Skaathun B, Smith LR, Strathdee SA, Wertheim JO, Friedman SR, Bortz E, Goodfellow I, Meredith L, Vasylyeva TI. Phylodynamics and migration data help describe HIV transmission dynamics in internally displaced people who inject drugs in Ukraine. PNAS NEXUS 2023; 2:pgad008. [PMID: 36896134 PMCID: PMC9991454 DOI: 10.1093/pnasnexus/pgad008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/21/2023]
Abstract
Internally displaced persons are often excluded from HIV molecular epidemiology surveillance due to structural, behavioral, and social barriers in access to treatment. We test a field-based molecular epidemiology framework to study HIV transmission dynamics in a hard-to-reach and highly stigmatized group, internally displaced people who inject drugs (IDPWIDs). We inform the framework by Nanopore generated HIV pol sequences and IDPWID migration history. In June-September 2020, we recruited 164 IDPWID in Odesa, Ukraine, and obtained 34 HIV sequences from HIV-infected participants. We aligned them to publicly available sequences (N = 359) from Odesa and IDPWID regions of origin and identified 7 phylogenetic clusters with at least 1 IDPWID. Using times to the most recent common ancestors of the identified clusters and times of IDPWID relocation to Odesa, we infer potential post-displacement transmission window when infections likely to happen to be between 10 and 21 months, not exceeding 4 years. Phylogeographic analysis of the sequence data shows that local people in Odesa disproportionally transmit HIV to the IDPWID community. Rapid transmissions post-displacement in the IDPWID community might be associated with slow progression along the HIV continuum of care: only 63% of IDPWID were aware of their status, 40% of those were in antiviral treatment, and 43% of those were virally suppressed. Such HIV molecular epidemiology investigations are feasible in transient and hard-to-reach communities and can help indicate best times for HIV preventive interventions. Our findings highlight the need to rapidly integrate Ukrainian IDPWID into prevention and treatment services following the dramatic escalation of the war in 2022.
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Affiliation(s)
- Ganna Kovalenko
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 0QN, UK
- Department of Biological Sciences, University of Alaska, Anchorage, AK 99508, USA
| | - Anna Yakovleva
- Medical Sciences Division, University of Oxford, Oxford OX3 9DU, UK
| | | | - Matthew Redlinger
- Department of Biological Sciences, University of Alaska, Anchorage, AK 99508, USA
| | - Olga Tymets
- Alliance for Public Health, Kyiv 01601, Ukraine
| | | | | | - Anna Podolina
- Odesa Regional Virology Laboratory, Odesa 65000, Ukraine
| | | | - Britt Skaathun
- Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA 92093-0507, USA
| | - Laramie R Smith
- Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA 92093-0507, USA
| | - Steffanie A Strathdee
- Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA 92093-0507, USA
| | - Joel O Wertheim
- Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA 92093-0507, USA
| | - Samuel R Friedman
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Eric Bortz
- Department of Biological Sciences, University of Alaska, Anchorage, AK 99508, USA
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 0QN, UK
| | - Luke Meredith
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 0QN, UK
| | - Tetyana I Vasylyeva
- Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA 92093-0507, USA
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8
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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] [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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9
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Getaneh Y, Ning F, He Q, Rashid A, Kassa D, Assefa Y, Yi F, Liao L, Shao Y. Survival and Predictors of Mortality among Adults Initiating Highly Active Antiretroviral Therapy in Ethiopia: A Retrospective Cohort Study (2007-2019). BIOMED RESEARCH INTERNATIONAL 2022; 2022:5884845. [PMID: 36467882 PMCID: PMC9711997 DOI: 10.1155/2022/5884845] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/22/2022] [Accepted: 11/11/2022] [Indexed: 10/14/2023]
Abstract
Background Studies have shown high early mortality after initiation of highly active antiretroviral therapy (HAART). We examined change in three-year survival and predictors of mortality of patients initiating HAART in Ethiopia since 2007 to 2019. Methods A retrospective cohort study was conducted in 47 health facilities (HFs) using records of 11,013 adult patients initiating HAART from 2007 to 2019. Study subjects were stratified as four different cohorts based on their calendar year of HAART initiation: 2007-2010, 2011-2013, 2014-2016, and 2017-2019. HFs were selected using probability proportional to size of patients. Survival rate and predictors of mortality were estimated by the calendar year using the Kaplan-Meier and Cox proportional hazard, respectively. We generated a pooled estimate of survival rate and predicators of mortality. Results Data from 1881, 3868, 3004, and 2260 patients were retrieved from each of the cohorts. Overall mortality for all cohorts at all times was 10.3%. A gradual decline of mortality was observed in the first three years of follow-up since 2007-2016 which were 21.37%, 10.03%, and 4.34% among patients who initiated HAART in 2007, 2011, and 2014 respectively. A mortality jump of 9.25% was observed among patents initiating HAART in 2017, which coincided with political instability happened in the country. Of the 21,638 person-years of follow-up among 11,013 adults, mortality was 5.23/100 person-years, while disaggregated by the cohorts, it was 14.77, 5.06, 2.12, and 4.17 per 100 person-years, respectively. Among all the cohorts, patients with CD4 count of ≤200 cells/mm3, unsuppressed viral load, poor adherence, and drug resistance in all cohorts, respectively, have overall 2.0 (95%CI = 1.35 - 2.69), 4.66 (95%CI = 2.53 - 6.72), 6.78 (95%CI = 3.4 - 10.3), and 10.02 (95%CI = 6.91 - 13.82) times of mortality risk than those without. Patients with bedridden for cohort initiating HAART during 2007 and 2011 were 2.0 (95%CI = 1.35 - 2.69) times of mortality risk than those without. Conclusion Patients initiating HAART from 2007 to 2016 have continuously improved their survival during three-year cohort follow-up in Ethiopia. The significant decline of survival among those who initiate HAART as of 2017 calls for program intervention. Low CD4 counts, unsuppressed viral load, poor adherence, and drug resistance could be used as predictors for increased mortality to monitor the quality of HAART and improve clinical management of HIV/AIDS patients.
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Affiliation(s)
- Yimam Getaneh
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Feng Ning
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Qianxin He
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Abdur Rashid
- School of Medicine, Nankai University, Tianjin, China
| | - Desta Kassa
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Yibeltal Assefa
- University of Queensland, School of Public Health, Queensland, Australia
| | - Feng Yi
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Lingjie Liao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yiming Shao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- Changping Laboratory, Beijing, China
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10
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van Zyl G, Jennings L, Kellermann T, Nkantsu Z, Cogill D, van Schalkwyk M, Spinelli M, Decloedt E, Orrell C, Gandhi M. Urine tenofovir-monitoring predicts HIV viremia in patients treated with high genetic-barrier regimens. AIDS 2022; 36:2057-2062. [PMID: 36305182 PMCID: PMC9623472 DOI: 10.1097/qad.0000000000003354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Access to viral load measurements is constrained in resource-limited settings. A lateral flow urine tenofovir (TFV) rapid assay (UTRA) for patients whose regimens include TFV offers an affordable approach to frequent adherence monitoring. DESIGN We conducted a cross-sectional study of patients to assess the utility of UTRA to predict virologic failure, defined as a viral load greater than 400 copies/ml. METHODS We assessed urine TFV among 113 participants at increased risk of viral failure (who had previous viral failure on this regimen or had previously been ≥30 days out of care), comparing low genetic-barrier efavirenz (EFV) regimens (n = 60) to dolutegravir (DTG)-boosted or ritonavir-boosted protease inhibitor (PI/r)-based high genetic-barrier regimens (n = 53). Dried blood spots (DBS) for TFV-diphosphate and plasma for TFV concentrations were collected, with drug resistance assessed if viral failure present. RESULTS Among 113 participants, 17 of 53 received DTG or PI/r had viral failure at the cross-sectional visit, with 11 (64.7%) demonstrating an undetectable urine TFV; the negative-predictive value (NPV) of undetectable UTRA for viral failure was 85% (34/40); none of the 16 sequenced had dual class drug resistance. In those treated with EFV regimens the sensitivity was lower, as only 1 (4.8%) of 21 with viral failure had an undetectable UTRA (P < 0.001). CONCLUSIONS Urine tenofovir-testing had a high negative-predictive value for viral failure in patients treated with DTG or ritonavir-boosted protease inhibitor regimens, where viral failure was largely explained by poor drug adherence. Frequent monitoring with inexpensive lateral flow urine TFV testing should be investigated prospectively in between viral load visits to improve viral load suppression on DTG-based first-line therapy in resource-limited settings.
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Affiliation(s)
- Gert van Zyl
- Division of Medical Virology, Department Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University
- National Health Laboratory Service, Tygerberg Business Unit
| | - Lauren Jennings
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town
| | | | - Zukisa Nkantsu
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town
| | - Dolphina Cogill
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town
| | - Marije van Schalkwyk
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Matthew Spinelli
- Division of HIV, Infectious Diseases, and Global Medicine at UCSF/San Francisco General Hospital, San Francisco, CA, USA
| | | | - Catherine Orrell
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town
| | - Monica Gandhi
- Division of HIV, Infectious Diseases, and Global Medicine at UCSF/San Francisco General Hospital, San Francisco, CA, USA
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11
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Minimal Cross-resistance to Tenofovir in Children and Adolescents Failing ART Makes Them Eligible for Tenofovir-Lamivudine-Dolutegravir Treatment. Pediatr Infect Dis J 2022; 41:827-834. [PMID: 35895893 PMCID: PMC9508940 DOI: 10.1097/inf.0000000000003647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Fixed-dose combination of dolutegravir (DTG) with tenofovir disoproxil fumarate (TDF) and lamivudine (3TC) likely improves adherence and has a favorable resistance profile. We evaluated predicted efficacy of TLD (TDF-3TC-DTG) in children and adolescents failing abacavir (ABC), zidovudine (AZT), or TDF containing regimens. METHODS Drug resistance mutations were analyzed in a retrospective dataset of individuals <19 years of age, failing ABC (n = 293) AZT (n = 288) or TDF (n = 69) based treatment. Pol sequences were submitted to Stanford HIVdb v8.9. Genotypic susceptibility scores were calculated for various DTG-containing regimens. RESULTS Genotypes were assessed for 650 individuals with a median age of 14 years (IQR 10-17 years). More individuals failed a protease inhibitor (PI)-based (78.3%) than a non-nucleoside reverse transcriptase inhibitors (NNRTI)-based (21.7%) regimen. Most individuals in the AZT group (n = 288; 94.4%) failed a PI-based regimen, compared with 71.0% and 64.2% in the TDF (n = 69) and ABC group (n = 293). Genotypic sensitivity scores <2 to TLD were observed in 8.5% and 9.4% of ABC- and AZT-exposed individuals, compared with 23.2% in the TDF group. The M184V mutation was most often detected in the ABC group (70.6%) versus 60.0% and 52.4% in TDF and AZT groups. The presence of K65R was rare (n = 13, 2.0%) and reduced TLD susceptibility was commonly caused by accumulation of nucleoside reverse transcriptase inhibitor (NRTI) mutations. CONCLUSIONS Cross-resistance to TDF was limited, further reducing concerns about use of transition to TLD in children and adolescents. The NADIA trial has subsequently shown that patients failing a TDF/3TC/EFV regimen can safely be transitioned to a TLD regimen but we do not have data for patients failing an ABC/3TC/NNRTI or PI regimens. Frequent virological monitoring is recommended after switch to DTG, especially in children continuing ABC in the backbone. Clinical studies correlating predicted resistance with clinical outcomes, especially in settings without access to genotyping, are required.
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12
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Evaluation of HIV-1 drug resistance among patients failing first-line antiretroviral therapy in Ethiopia. J Glob Antimicrob Resist 2022; 30:418-427. [DOI: 10.1016/j.jgar.2022.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
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13
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DeVos J, McCarthy K, Sewe V, Akinyi G, Junghae M, Opollo V, Nouhin J, Shafer R, Zeh C, Ramos A, Alexander H, Chang J. A Partially Multiplexed HIV Drug Resistance (HIVDR) Assay for Monitoring HIVDR Mutations of the Protease, Reverse-Transcriptase (PRRT), and Integrase (INT). Microbiol Spectr 2022; 10:e0177621. [PMID: 35510849 PMCID: PMC9241735 DOI: 10.1128/spectrum.01776-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/28/2022] [Indexed: 12/05/2022] Open
Abstract
As dolutegravir (DTG)-containing HIV regimens are scaled up globally, monitoring for HIV drug resistance (HIVDR) will become increasingly important. We designed a partially multiplexed HIVDR assay using Sanger sequencing technology to monitor HIVDR mutations in the protease, reverse-transcriptase (PRRT), and integrase (INT). A total of 213 clinical and analytical plasma and dried blood spot (DBS) samples were used in the evaluation. The assay detected a wide range of known HIV-1 subtypes and circulating recombinant forms (CRFs) of group M from 139 samples. INT accuracy showed that the average nucleotide (nt) sequence concordance was 99.8% for 75 plasma samples and 99.5% for 11 DBS samples compared with the reference sequences. The PRRT accuracy also demonstrated the average nucleotide sequence concordance was 99.5% for 57 plasma samples and 99.2% for 33 DBS samples. The major PRRT and INT DR mutations of all samples tested were concordant with those of the reference sequences using the Stanford HIV database (db). Amplification sensitivity of samples with viral load (VL) >5000 copies/mL showed plasma exceeded 95% of positivity, and DBS exceeded 90% for PRRT and INT. Samples with VL (1000 to 5000 copies/mL) showed plasma exceeded 90%, and DBS reached 88% positivity for PRRT and INT. Assay precision and reproducibility showed >99% nucleotide sequence concordance in each set of replicates for PRRT and INT. In conclusion, this HIVDR assay met WHO HIVDR assay performance criteria for surveillance, worked for plasma and DBS, used minimal sample volume, was sensitive, and was a potentially cost-effective tool to monitor HIVDR mutations in PRRT and INT. IMPORTANCE This HIVDR genotyping assay works for both plasma and DBS samples, requires low sample input, and is sensitive. This assay has the potential to be a user-friendly and cost-effective HIVDR assay because of its partially multiplexed design. Application of this genotyping assay will help HIVDR monitoring in HIV high-burdened countries using a DGT-based HIV drug regimen recommended by the U.S. President's Emergency Plan for AIDS Relief and the WHO.
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Affiliation(s)
- Joshua DeVos
- International Laboratory Branch, Division of Global HIV and Tuberculosis (TB), Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | | | - Victor Sewe
- HIV Research Laboratory, Kenya Medical Research Institute-Center for Global Health Research, Kisumu, Kenya
| | - Grace Akinyi
- HIV Research Laboratory, Kenya Medical Research Institute-Center for Global Health Research, Kisumu, Kenya
| | | | - Valarie Opollo
- HIV Research Laboratory, Kenya Medical Research Institute-Center for Global Health Research, Kisumu, Kenya
| | | | | | - Clement Zeh
- International Laboratory Branch, Division of Global HIV and Tuberculosis (TB), Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Artur Ramos
- International Laboratory Branch, Division of Global HIV and Tuberculosis (TB), Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Heather Alexander
- International Laboratory Branch, Division of Global HIV and Tuberculosis (TB), Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Joy Chang
- International Laboratory Branch, Division of Global HIV and Tuberculosis (TB), Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
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14
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Naidoo I, Takatshana S, Sewpaul R, Jooste S, Siyanai Z, Maseko G, Moyo S, Zuma K, Mabaso M, Nompumelelo Z. Past and current status of adolescents living with HIV in South Africa, 2005-2017. BMC Res Notes 2022; 15:132. [PMID: 35397603 PMCID: PMC8994368 DOI: 10.1186/s13104-022-06006-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/15/2022] [Indexed: 11/02/2022] Open
Abstract
OBJECTIVES This paper reports HIV prevalence, incidence, progress towards the UNAIDS (90-90-90) targets, and HIV drug resistance among adolescents living with HIV in South Africa. We conducted secondary analyses using data extracted from the South African national HIV prevalence surveys (2005-2017). Analyses were stratified by sex and age (10-14 and 15-19-years), presenting weighted descriptive statistics, and realised totals. RESULTS HIV prevalence increased from 3.0% in 2012 to 3.7% in 2017, translating to 360 582 (95% CI 302 021-419 144) HIV positive adolescents in 2017. Female adolescents bear a disproportionate HIV burden of 5.6% prevalence versus 0.7% for males. HIV incidence remained relatively stable. For the UNAIDS 90-90-90 targets, approximately 62.3% of adolescents knew their HIV status, 65.4% of whom were on antiretroviral therapy, and of these 78.1% on antiretroviral therapy had attained viral load suppression. There are knowledge gaps pertaining to the magnitude of perinatal infections and postnatal infections, and socio-behavioural risk factors for HIV transmission among adolescents in South Africa. There is still a need for focussed interventions targeting adolescent (1) gender disparities in HIV risk (2) screening for HIV, (3) sustained access and adherence to antiretroviral therapy and (3) retention in care to maintain viral load suppression.
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Affiliation(s)
- Inbarani Naidoo
- Centre for Community Based Research, Human and Social Capabilities Division, Human Sciences Research Council, Durban, South Africa.
| | - Sinovuyo Takatshana
- Health and Well-Being, Human and Social Capabilities Division, Human Sciences Research Council, Pretoria, South Africa
| | - Ronel Sewpaul
- Health and Well-Being, Human and Social Capabilities Division, Human Sciences Research Council, Cape Town, South Africa
| | - Sean Jooste
- Health and Well-Being, Human and Social Capabilities Division, Human Sciences Research Council, Cape Town, South Africa
| | - Zhou Siyanai
- AIDS and Society Research Unit, Centre for Social Science Research, University of Cape Town, Cape Town, South Africa
| | - Goitseone Maseko
- Health and Well-Being, Human and Social Capabilities Division, Human Sciences Research Council, Pretoria, South Africa
| | - Sizulu Moyo
- Health and Well-Being, Human and Social Capabilities Division, Human Sciences Research Council, Cape Town, South Africa
- School of Public Health, University of Cape Town, Cape Town, South Africa
| | - Khangelani Zuma
- Health and Well-Being, Human and Social Capabilities Division, Human Sciences Research Council, Pretoria, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Musawenkosi Mabaso
- Health and Well-Being, Human and Social Capabilities Division, Human Sciences Research Council, Durban, South Africa
| | - Zungu Nompumelelo
- Health and Well-Being, Human and Social Capabilities Division, Human Sciences Research Council, Cape Town, South Africa
- Department of Psychology, University of Pretoria, Pretoria, South Africa
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15
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van Oosterhout JJ, Chipungu C, Nkhoma L, Kanise H, Hosseinipour MC, Sagno JB, Simon K, Cox C, Hoffman R, Steegen K, Matola BW, Phiri S, Jahn A, Nyirenda R, Heller T. Dolutegravir resistance in Malawi’s national HIV treatment program. Open Forum Infect Dis 2022; 9:ofac148. [PMID: 35493118 PMCID: PMC9045949 DOI: 10.1093/ofid/ofac148] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/04/2022] [Indexed: 11/24/2022] Open
Abstract
Dolutegravir HIV drug resistance (HIVDR) data from Africa remain sparse. We reviewed HIVDR results of Malawians on dolutegravir-based antiretroviral therapy (November 2020–September 2021). Of 6462 eligible clients, 33 samples were submitted to South Africa, 27 were sequenced successfully, and 8 (30%) had dolutegravir HIVDR. Malawi urgently requires adequate HIVDR testing capacity.
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Affiliation(s)
- J J van Oosterhout
- Partners in Hope, Lilongwe, Malawi
- Division of Infectious Diseases, David Geffen School of Medicine, University of California, Los Angeles, USA
| | | | - L Nkhoma
- The Lighthouse Trust, Lilongwe, Malawi
| | - H Kanise
- Partners in Hope, Lilongwe, Malawi
| | | | - J B Sagno
- DREAM, Communion of St. Egidio, Malawi
| | - K Simon
- Baylor College of Medicine Children’s Foundation-Malawi, Lilongwe, Malawi
- Baylor International Pediatric AIDS Initiative, Houston, USA
| | - C Cox
- Baylor College of Medicine Children’s Foundation-Malawi, Lilongwe, Malawi
- Baylor International Pediatric AIDS Initiative, Houston, USA
| | - R Hoffman
- Division of Infectious Diseases, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - K Steegen
- Department of Haematology & Molecular Medicine, National Health Laboratory Service, Johannesburg, South Africa
- Department of Haematology & Molecular Medicine, University of the Witwatersrand, Johannesburg, South Africa
| | - B W Matola
- Department of Public Health and Family Medicine, Kamuzu University of Health Sciences, Lilongwe, Malawi
| | - S Phiri
- Partners in Hope, Lilongwe, Malawi
- Department of Public Health and Family Medicine, Kamuzu University of Health Sciences, Lilongwe, Malawi
| | - A Jahn
- Department of HIV-AIDS, Ministry of Health, Lilongwe, Malawi
| | - R Nyirenda
- Department of HIV-AIDS, Ministry of Health, Lilongwe, Malawi
| | - T Heller
- The Lighthouse Trust, Lilongwe, Malawi
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16
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Khamadi S, Lwembe R, Maosa N, Maloba M, Wexler C, Sandbulte M, Goggin K, Babu S, Finocchario-Kessler S. HIV Drug Resistance in Kenyan Infants Diagnosed With HIV and Their Mothers. Pediatr Infect Dis J 2022; 41:312-314. [PMID: 34955520 DOI: 10.1097/inf.0000000000003436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The presence and type of HIV drug resistance mutations among 5 infants diagnosed with HIV were assessed and compared with their mothers' viral mutations. Mother and infant blood samples were sequenced and screened for HIV drug resistance mutations using the Stanford HIV Sequence Database. Three of 5 (60%) mother-infant pairs harbored HIV drug resistance mutations.
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Affiliation(s)
- Samoel Khamadi
- From the Kenya Medical Research Institute, Center for Virus Research, Nairobi, Kenya
| | - Raphael Lwembe
- From the Kenya Medical Research Institute, Center for Virus Research, Nairobi, Kenya
| | | | - May Maloba
- Global Health Innovations, Nairobi, Kenya
| | - Catherine Wexler
- Department of Family Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Matthew Sandbulte
- Department of Family Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Kathy Goggin
- Children's Mercy Kansas City, Health Services and Outcomes Research, Kansas City, Missouri
- University of Missouri-Kansas City, School of Medicine, Kansas City, Missouri
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17
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Jordan MR, Bikinesi L, Ashipala L, Mutenda N, Brantuo M, Hunt G, Shiningavamwe A, Mutandi G, Beukes A, Beard S, Battey K, Dziuban EJ, Raizes E, Adjei P, Tang A, Giron A, Hong SY. Pretreatment HIV drug resistance among treatment naïve infants newly diagnosed with HIV in 2016 in Namibia: results of a nationally representative study. Open Forum Infect Dis 2022; 9:ofac102. [PMID: 35434174 PMCID: PMC9007920 DOI: 10.1093/ofid/ofac102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/14/2022] [Indexed: 12/02/2022] Open
Abstract
Background The World Health Organization (WHO) recommends routine surveillance of pretreatment human immunodeficiency virus (HIV) drug resistance (HIVDR) in children <18 months of age diagnosed with HIV through early infant diagnosis (EID). In 2016, 262 children <18 months of age were diagnosed with HIV in Namibia through EID. Levels of HIVDR in this population are unknown. Methods In 2016, Namibia surveyed pretreatment HIVDR among children aged <18 months following WHO guidance. Reverse transcriptase, protease, and integrase regions of HIV-1 were genotyped from remnant dried blood spot specimens from all infants diagnosed with HIV in Namibia in 2016. HIVDR was predicted using the Stanford HIVdb algorithm. Results Of 262 specimens genotyped, 198 HIV-1 protease and reverse transcriptase sequences and 118 HIV-1 integrase sequences were successfully amplified and analyzed. The prevalence of efavirenz/nevirapine (EFV/NVP), abacavir (ABC), zidovudine, lamivudine/emtricitabine (3TC/FTC), and tenofovir (TDF) resistance was 62.6%, 17.7%, 5.6%, 15.7%, and 10.1%, respectively. No integrase inhibitor resistance was detected. Conclusions The high level of EFV/NVP resistance is unsurprising; however, levels of ABC and TDF resistance are among the highest observed to date in infants in sub-Saharan Africa. The absence of resistance to dolutegravir (DTG) is reassuring but underscores the need to further study the impact of ABC and 3TC/FTC resistance on pediatric protease inhibitor– and DTG-based regimens and accelerate access to other antiretroviral drugs. Results underscore the need for antiretroviral therapy optimization and prompt management of high viral loads in infants and pregnant and breastfeeding women.
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Affiliation(s)
- Michael R Jordan
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA, USA and Levy Center for Integrated Management of Antimicrobial Resistance, Tufts University School of Medicine, Boston, MA, USA
| | - Leonard Bikinesi
- Directorate of Special Programmes, Republic of Namibia Ministry of Health and Social Services, Windhoek, Namibia
| | - Laimi Ashipala
- Directorate of Special Programmes, Republic of Namibia Ministry of Health and Social Services, Windhoek, Namibia
| | - Nicholus Mutenda
- Directorate of Special Programmes, Republic of Namibia Ministry of Health and Social Services, Windhoek, Namibia
| | | | - Gillian Hunt
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
| | | | - Gram Mutandi
- Division of Global HIV and TB, Center for Global Health, Centers for Disease Control and Prevention, Windhoek, Namibia
| | - Anita Beukes
- Division of Global HIV and TB, Center for Global Health, Centers for Disease Control and Prevention, Windhoek, Namibia
| | - Suzanne Beard
- Division of Global HIV and TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Katherine Battey
- Division of Global HIV and TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA. USA
| | - Eric J Dziuban
- Division of Global HIV and TB, Center for Global Health, Centers for Disease Control and Prevention, Windhoek, Namibia
| | - Elliot Raizes
- Division of Global HIV and TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Paul Adjei
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA, USA
| | - Alice Tang
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, USA
| | - Amalia Giron
- Department of Global HIV, Hepatitis and STI Programmes, World Health Organization, Geneva, Switzerland
| | - Steven Y Hong
- Division of Global HIV and TB, Center for Global Health, Centers for Disease Control and Prevention, Windhoek, Namibia
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Gare J, Toto B, Pokeya P, Le LV, Dala N, Lote N, John B, Yamba A, Soli K, DeVos J, Paulin H, Wagar N, Zheng DP, Nishijima T, Boas P, Kelly-Hanku A, Gurung A. High prevalence of pre-treatment HIV drug resistance in Papua New Guinea: findings from the first nationally representative pre-treatment HIV drug resistance study. BMC Infect Dis 2022; 22:266. [PMID: 35305571 PMCID: PMC8934451 DOI: 10.1186/s12879-022-07264-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 03/08/2022] [Indexed: 11/12/2022] Open
Abstract
Background Determining the prevalence of pre-treatment HIV drug resistance (PDR) is important to assess the effectiveness of first-line therapies. To determine PDR prevalence in Papua New Guinea (PNG), we conducted a nationally representative survey. Methods We used a two-stage cluster sampling method to recruit HIV treatment initiators with and without prior exposure to antiretroviral therapies (ART) in selected clinics. Dried blood spots were collected and tested for PDR. Results A total of 315 sequences were available for analysis. The overall PDR prevalence rate was 18.4% (95% CI 13.8–24.3%). The prevalence of PDR to non-nucleoside analog reverse-transcriptase inhibitors (NNRTIs) was 17.8% (95% CI 13.6–23.0%) and of PDR to nucleoside reverse transcriptase inhibitors (NRTIs) was 6.3% (95% CI 1.6–17.1%). The PDR prevalence rate among people reinitiating ART was 42.4% (95% CI 29.1–56.4%). Conclusions PNG has a high PDR prevalence rate, especially to NNRTI-based first-line therapies. Our findings suggest that removing NNRTIs as part of first-line treatment is warranted and will lead to improving viral suppression rates in PNG.
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García-Morales C, Tapia-Trejo D, Matías-Florentino M, Quiroz-Morales VS, Dávila-Conn V, Beristain-Barreda Á, Cárdenas-Sandoval M, Becerril-Rodríguez M, Iracheta-Hernández P, Macías-González I, García-Mendiola R, Guzmán-Carmona A, Zarza-Sánchez E, Cruz RA, González-Rodríguez A, Reyes-Terán G, Ávila-Ríos S. HIV Pretreatment Drug Resistance Trends in Mexico City, 2017-2020. Pathogens 2021; 10:1587. [PMID: 34959542 PMCID: PMC8708254 DOI: 10.3390/pathogens10121587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 11/19/2022] Open
Abstract
In response to increasing pretreatment drug resistance (PDR), Mexico changed its national antiretroviral treatment (ART) policy, recommending and procuring second-generation integrase strand-transfer inhibitor (INSTI)-based regimens as preferred first-line options since 2019. We present a four-year observational study describing PDR trends across 2017-2020 at the largest HIV diagnosis and primary care center in Mexico City. A total of 6688 baseline protease-reverse transcriptase and 6709 integrase sequences were included. PDR to any drug class was 14.4% (95% CI, 13.6-15.3%). A significant increasing trend for efavirenz/nevirapine PDR was observed (10.3 to 13.6%, p = 0.02). No increase in PDR to second-generation INSTI was observed, remaining under 0.3% across the study period. PDR was strongly associated with prior exposure to ART (aOR: 2.9, 95% CI: 1.9-4.6, p < 0.0001). MSM had higher odds of PDR to efavirenz/nevirapine (aOR: 2.0, 95% CI: 1.0-3.7, p = 0.04), reflecting ongoing transmission of mutations such as K103NS and E138A. ART restarters showed higher representation of cisgender women and injectable drug users, higher age, and lower education level. PDR to dolutegravir/bictegravir remained low in Mexico City, although further surveillance is warranted given the short time of ART optimization. Our study identifies demographic characteristics of groups with higher risk of PDR and lost to follow-up, which may be useful to design differentiated interventions locally.
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Affiliation(s)
- Claudia García-Morales
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Daniela Tapia-Trejo
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Margarita Matías-Florentino
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Verónica Sonia Quiroz-Morales
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Vanessa Dávila-Conn
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Ángeles Beristain-Barreda
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Miroslava Cárdenas-Sandoval
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Manuel Becerril-Rodríguez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Patricia Iracheta-Hernández
- Condesa Specialised Clinic, General Benjamín Hill 24, Colonia Condesa, Mexico City 06140, Mexico; (P.I.-H.); (I.M.-G.); (A.G.-R.)
| | - Israel Macías-González
- Condesa Specialised Clinic, General Benjamín Hill 24, Colonia Condesa, Mexico City 06140, Mexico; (P.I.-H.); (I.M.-G.); (A.G.-R.)
| | - Rebecca García-Mendiola
- Condesa Iztapalapa Specialised Clinic, Combate de Celaya s/n, Colonia Unidad Habitacional Vicente Guerrero, Mexico City 09730, Mexico; (R.G.-M.); (A.G.-C.); (R.A.C.)
| | - Alejandro Guzmán-Carmona
- Condesa Iztapalapa Specialised Clinic, Combate de Celaya s/n, Colonia Unidad Habitacional Vicente Guerrero, Mexico City 09730, Mexico; (R.G.-M.); (A.G.-C.); (R.A.C.)
| | - Eduardo Zarza-Sánchez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Raúl Adrián Cruz
- Condesa Iztapalapa Specialised Clinic, Combate de Celaya s/n, Colonia Unidad Habitacional Vicente Guerrero, Mexico City 09730, Mexico; (R.G.-M.); (A.G.-C.); (R.A.C.)
| | - Andrea González-Rodríguez
- Condesa Specialised Clinic, General Benjamín Hill 24, Colonia Condesa, Mexico City 06140, Mexico; (P.I.-H.); (I.M.-G.); (A.G.-R.)
| | - Gustavo Reyes-Terán
- Coordinating Commission of the National Institutes of Health and High Specialty Hospitals, Periférico Sur 4809, Colonia Arenal de Tepepan, Mexico City 14610, Mexico;
| | - Santiago Ávila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
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Reepalu A, Arimide DA, Balcha TT, Yeba H, Zewdu A, Medstrand P, Björkman P. Drug Resistance in HIV-Positive Adults During the Initial Year of Antiretroviral Treatment at Ethiopian Health Centers. Open Forum Infect Dis 2021; 8:ofab106. [PMID: 34805444 PMCID: PMC8597620 DOI: 10.1093/ofid/ofab106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/03/2021] [Indexed: 11/30/2022] Open
Abstract
Background The increasing prevalence of antiretroviral drug resistance in Sub-Saharan
Africa threatens the success of HIV programs. We have characterized patterns
of drug resistance mutations (DRMs) during the initial year of
antiretroviral treatment (ART) in HIV-positive adults receiving care at
Ethiopian health centers and investigated the impact of tuberculosis on DRM
acquisition. Methods Participants were identified from a cohort of ART-naïve individuals aged
≥18 years, all of whom had been investigated for active tuberculosis
at inclusion. Individuals with viral load (VL) data at 6 and/or 12 months
after ART initiation were selected for this study. Genotypic testing was
performed on samples with VLs ≥500 copies/mL obtained on these
occasions and on pre-ART samples from those with detectable DRMs during ART.
Logistic regression analysis was used to investigate the association between
DRM acquisition and tuberculosis. Results Among 621 included individuals (110 [17.5%] with concomitant tuberculosis),
101/621 (16.3%) had a VL ≥500 copies/mL at 6 and/or 12 months. DRMs
were detected in 64/98 cases with successful genotyping (65.3%). DRMs were
detected in 7/56 (12.5%) pre-ART samples from these individuals. High
pre-ART VL and low mid-upper arm circumference were associated with
increased risk of DRM acquisition, whereas no such association was found for
concomitant tuberculosis. Conclusions Among adults receiving health center–based ART in Ethiopia, most
patients without virological suppression during the first year of ART had
detectable DRM. Acquisition of DRM during this period was the dominant cause
of antiretroviral drug resistance in this setting. Tuberculosis did not
increase the risk of DRM acquisition.
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Affiliation(s)
- Anton Reepalu
- Clinical Infection Medicine, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Dawit A Arimide
- Clinical Virology, Department of Translational Medicine, Lund University, Malmö, Sweden.,Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Taye T Balcha
- Clinical Infection Medicine, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Habtamu Yeba
- Adama Public Health Research and Referral Laboratory Center, Adama, Ethiopia
| | - Adinew Zewdu
- Adama Public Health Research and Referral Laboratory Center, Adama, Ethiopia
| | - Patrik Medstrand
- Clinical Virology, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Per Björkman
- Clinical Infection Medicine, Department of Translational Medicine, Lund University, Malmö, Sweden
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21
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Hackett S, Teasdale CA, Pals S, Muttiti A, Mogashoa M, Chang J, Zeh C, Ramos A, Rivadeneira ED, DeVos J, Sleeman K, Abrams EJ. Drug Resistance Mutations Among South African Children Living With HIV on WHO-recommended ART Regimens. Clin Infect Dis 2021; 73:e2217-e2225. [PMID: 32735012 DOI: 10.1093/cid/ciaa1068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Children living with human immunodeficiency virus (HIV) (CLHIV) receiving antiretroviral therapy (ART) in resource-limited settings are susceptible to high rates of acquired HIV drug resistance (HIVDR), but few studies include children initiating age-appropriate World Health Organization (WHO)-recommended first-line regimens. We report data from a cohort of ART-naive South African children who initiated first-line ART. METHODS ART-eligible CLHIV aged 0-12 years were enrolled from 2012 to 2014 at 5 public South African facilities and were followed for up to 24 months. Enrolled CLHIV received standard-of-care WHO-recommended first-line ART. At the final study visit, a dried blood spot sample was obtained for viral load and genotypic resistance testing. RESULTS Among 72 successfully genotyped CLHIV, 49 (68.1%) received ABC/3TC/LPV/r, and 23 (31.9%) received ABC/3TC/EFV. All but 2 children on ABC/3TC/LPV/r were <3 years, and all CLHIV on ABC/3TC/EFV were ≥3 years. Overall, 80.6% (58/72) had at least one drug resistance mutation (DRM). DRMs to nonnucleoside reverse transcriptase inhibitors (NNRTIs) and nucleoside reverse transcriptase inhibitors (NRTIs) were found among 65% and 51% of all CLHIV, respectively, with no statistical difference by ART regimen. More CLHIV on ABC/3TC/EFV, 47.8% (11/23), were found to have 0 or only 1 effective antiretroviral drug remaining in their current regimen compared to 8.2% (4/49) on ABC/3TC/LPV/r. CONCLUSIONS High levels of NNRTI and NRTI DRMs among CLHIV receiving ABC/3TC/LPV/r suggests a lasting impact of failed mother-to-child transmission interventions on DRMs. However, drug susceptibility analysis reveals that CLHIV with detectable viremia on ABC/3TC/LPV/r are more likely to have maintained at least 2 effective agents on their current HIV regimen than those on ABC/3TC/EFV.
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Affiliation(s)
- Stephanie Hackett
- US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Chloe A Teasdale
- Department of Epidemiology and Biostatistics, CUNY Graduate School of Public Health & Health Policy, New York, USA.,ICAP at Columbia University, Mailman School of Public Health, Columbia University, New York, New York, USA.,Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Sherri Pals
- US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Anthony Muttiti
- ICAP at Columbia University, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Mary Mogashoa
- US Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Joy Chang
- US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Clement Zeh
- US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Artur Ramos
- US Centers for Disease Control and Prevention, Maputo, Mozambique
| | | | - Joshua DeVos
- US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Katrina Sleeman
- US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Elaine J Abrams
- ICAP at Columbia University, Mailman School of Public Health, Columbia University, New York, New York, USA.,Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA.,Department of Pediatrics, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
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22
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Onwuamah CK, Okwuraiwe AP, Ahmed RA, Sokei JO, Ponmak J, Okoli LC, Kagurusi BA, Anejo-Okopi J. Laboratory Optimization Tweaks for Sanger Sequencing in a Resource-Limited Setting. J Biomol Tech 2021; 31:157-164. [PMID: 33100921 DOI: 10.7171/jbt.20-3104-006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Despite various challenges that hinder the implementation of high-tech molecular methods in resource-limited settings, we have been able to implement and achieve International Organization for Standardization 15189:2012 accreditation for genotypic HIV drug resistance testing in our facility. At the Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Nigeria has recorded a high sequencing success rate and good quality sequence data. This was achieved by optimizing laboratory processes from 2008 to the current date. We have optimized sample preparation, RT-PCR, several post-PCR processes, and the cycle sequencing to improve the sensitivity of amplification even with limited plasma samples and low viral copy numbers. The optimized workflow maximizes output, minimizes reagent wastage, and achieves substantial cost savings without compromising the quality of the sequence data. Our performance at our last external quality assurance program is a testimonial to the efficiency of the workflow. For the 5-sample panel, each with 67-68 mutation points evaluated, we scored 100% for all 5 specimens. Our optimized laboratory workflow is thus documented to support laboratories and to help researchers achieve excellent results the first time and eliminate contamination while minimizing the wastage of costly sequencing reagents.
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Affiliation(s)
- Chika K Onwuamah
- Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba 101212, Lagos, Nigeria
| | - Azuka P Okwuraiwe
- Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba 101212, Lagos, Nigeria
| | - Rahaman A Ahmed
- Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba 101212, Lagos, Nigeria
| | - Judith O Sokei
- Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba 101212, Lagos, Nigeria
| | - Jamda Ponmak
- Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba 101212, Lagos, Nigeria
| | - Leona C Okoli
- Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba 101212, Lagos, Nigeria
| | | | - Joseph Anejo-Okopi
- AIDS Prevention Initiative in Nigeria, Jos, University Teaching Hospital, Jos, Nigeria
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Bangalee A, Hans L, Steegen K. Feasibility and clinical relevance of HIV-1 drug resistance testing in patients with low-level viraemia in South Africa. J Antimicrob Chemother 2021; 76:2659-2665. [PMID: 34278422 DOI: 10.1093/jac/dkab220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/01/2021] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To determine the feasibility of HIV genotyping at low-level viraemia (LLV) using an in-house assay in a South African population and the prevalence, as well as the clinical relevance, of drug resistance (HIVDR) in this population. METHODS We conducted an observational, retrospective, cohort study on patient samples with LLV referred for routine HIVDR testing at a public sector Johannesburg laboratory from August 2017 to October 2018. Genotyping was performed using a nested RT-PCR assay and Sanger sequencing. The genotyping success rate was evaluated for different viraemia categories. Sequences were loaded onto the Stanford HIVdb genotypic resistance tool (version 8.7) for drug resistance interpretation. RESULTS Plasma samples from 159 HIV-1-infected, treatment-experienced adults with LLV (5-999 copies/mL) were analysed. The in-house assay performed well with an overall success rate of 78.6% (125/159, 95% CI 71.6-84.3). The prevalence of drug resistance mutations in the LLV cohort was 79.2% (99/125, 95% CI 71.2-85.4) with most patients (n = 109, 68.6%) on a PI-based regimen at the time of genotyping. Of 125 sequences obtained, 73.6% (92/125) had ≥1 NRTI mutation while 70.4% (88/125) had ≥1 NNRTI mutation. Major PI mutations, including M46I and V82A, were detected in 7.2% (9/125) of patients. CONCLUSIONS Current South African virological failure guidelines may keep patients on failing regimens for longer than necessary. Our data suggest that genotyping at LLV is feasible and implementation could result in earlier identification and referral of patients requiring third-line regimens.
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Affiliation(s)
- Avania Bangalee
- Department of Medical Virology, University of the Witwatersrand, South Africa.,National Health Laboratory Service, Johannesburg, South Africa
| | - Lucia Hans
- National Health Laboratory Service, Johannesburg, South Africa.,Department of Haematology and Molecular Medicine, University of the Witwatersrand, South Africa
| | - Kim Steegen
- National Health Laboratory Service, Johannesburg, South Africa.,Department of Haematology and Molecular Medicine, University of the Witwatersrand, South Africa
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Manyana S, Gounder L, Pillay M, Manasa J, Naidoo K, Chimukangara B. HIV-1 Drug Resistance Genotyping in Resource Limited Settings: Current and Future Perspectives in Sequencing Technologies. Viruses 2021; 13:1125. [PMID: 34208165 PMCID: PMC8230827 DOI: 10.3390/v13061125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 12/14/2022] Open
Abstract
Affordable, sensitive, and scalable technologies are needed for monitoring antiretroviral treatment (ART) success with the goal of eradicating HIV-1 infection. This review discusses use of Sanger sequencing and next generation sequencing (NGS) methods for HIV-1 drug resistance (HIVDR) genotyping, focusing on their use in resource limited settings (RLS). Sanger sequencing remains the gold-standard method for detecting HIVDR mutations of clinical relevance but is mainly limited by high sequencing costs and low-throughput. NGS is becoming a more common sequencing method, with the ability to detect low-abundance drug-resistant variants and reduce per sample costs through sample pooling and massive parallel sequencing. However, use of NGS in RLS is mainly limited by infrastructure costs. Given these shortcomings, our review discusses sequencing technologies for HIVDR genotyping, focusing on common in-house and commercial assays, challenges with Sanger sequencing in keeping up with changes in HIV-1 treatment programs, as well as challenges with NGS that limit its implementation in RLS and in clinical diagnostics. We further discuss knowledge gaps and offer recommendations on how to overcome existing barriers for implementing HIVDR genotyping in RLS, to make informed clinical decisions that improve quality of life for people living with HIV.
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Affiliation(s)
- Sontaga Manyana
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Lilishia Gounder
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Melendhran Pillay
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Justen Manasa
- Department of Laboratory Medicine and Investigative Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe;
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa;
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban 4013, South Africa
| | - Benjamin Chimukangara
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa;
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Carnimeo V, Pulido Tarquino IA, Fuentes S, Vaz D, Molfino L, Tamayo Antabak N, Cuco RM, Couto A, Lobo S, de Amaral Fidelis J, Mulassua JS, Ciglenecki I, Ellman T, Schramm B. High level of HIV drug resistance informs dolutegravir roll-out and optimized NRTI backbone strategy in Mozambique. JAC Antimicrob Resist 2021; 3:dlab050. [PMID: 34223118 PMCID: PMC8209982 DOI: 10.1093/jacamr/dlab050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/21/2021] [Indexed: 11/16/2022] Open
Abstract
Background HIV drug resistance (HIV-DR) is rising in sub-Saharan Africa in both ART-naive and ART-experienced patients. Objectives To estimate the level of acquired DR (ADR) and pre-treatment DR (PDR) across selected urban and rural sites in Southern Africa, in Mozambique. Methods We conducted two cross-sectional surveys among adult HIV patients (October 2017–18) assessing ADR and PDR. In the (ADR) survey, those on NNRTI-based first-line ART for ≥6 months were recruited (three sites). In the PDR survey, those ART-naive or experienced with ≥3 months of treatment interruption prior were enrolled (eight sites). Results Among 1113 ADR survey participants 83% were receiving tenofovir (TDF)/lamivudine (3TC)/efavirenz (EFV). The median time on ART was 4.5 years (Maputo) and 3.2 years (Tete), 8.3% (95% CI 6.2%-10.6%, Maputo) and 15.5% (Tete) had a VL ≥ 1000 copies/mL, among whom 66% and 76.4% had NNRTI+NRTI resistance, and 52.8% and 66.7% had 3TC+TDF-DR. Among those on TDF regimens, 31.1% (Maputo) and 42.2% (Tete) were still TDF susceptible, whereas 24.4% and 11.5% had TDF+zidovudine (ZDV)-DR. Among those on ZDV regimens, 25% and 54.5% had TDF+ZDV-DR. The PDR survey included 735 participants: NNRTI-PDR was 16.8% (12.0–22.6) (Maputo) and 31.2% (26.2–36.6) (Tete), with a higher proportion (≥50%) among those previously on ART affected by PDR. Conclusions In Mozambique, viral failure was driven by NNRTI and NRTI resistance, with NRTI DR affecting backbone options. NNRTI-PDR levels surpassed the WHO 10% ‘alert’ threshold. Replacing NNRTI first-line drugs is urgent, as is frequent viral load monitoring and resistance surveillance. Changing NRTI backbones when switching to second-line regimens may need reconsideration.
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Affiliation(s)
| | | | - S Fuentes
- Epicentre, Paris, France.,Médecins Sans Frontières Belgium, Mozambique Mission
| | - D Vaz
- Médecins Sans Frontières Switzerland, Mozambique Mission
| | - L Molfino
- Médecins Sans Frontières Switzerland, Mozambique Mission
| | | | - R M Cuco
- National Directorate of Public Health, Ministry of Health, Maputo, Mozambique
| | - A Couto
- Ministry of Health of Mozambique, Maputo, Mozambique
| | - S Lobo
- Health Directorate of Maputo, Maputo, Mozambique
| | | | | | | | - T Ellman
- Médecins Sans Frontières, Southern Africa Medical Unit (SAMU), South Africa
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26
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Steegen K, Moorhouse M, Wensing AMJ, Venter WDF, Hans L. Is there a role for doravirine in African HIV treatment programmes? A large observational resistance study in South Africa. J Int AIDS Soc 2021; 24:e25706. [PMID: 33943000 PMCID: PMC8094661 DOI: 10.1002/jia2.25706] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/05/2021] [Accepted: 03/17/2021] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Dolutegravir has replaced efavirenz in most low- and middle-income countries, due to better tolerability and formidable resistance profile, but dolutegravir side effects suggest alternatives are needed. We evaluated doravirine resistance in South Africa as a first step to assess whether doravirine may replace dolutegravir. METHODS A retrospective dataset was analysed for predicted doravirine susceptibility, including sequences obtained from three patient groups. First, data from 277 patients initiating antiretroviral treatment (ART) were collected between February 2013 and October 2014 as part of a national survey. Second, data from 788 patients experiencing NNRTI-based ART failure were obtained between February 2013 and October 2014 as part of a national survey. Third, data derived from 584 patients who had genotypic drug resistance testing requested after NNRT-based failure as part of individual patient management between January 2016 and December 2019. Pol sequences were generated using validated population-based in-house genotyping and submitted to Stanford HIVdb v8.9. RESULTS AND DISCUSSION Less than 5% of patients initiating ART presented with genotypic doravirine resistance, whereas most patients experiencing NNRTI-based ART failure presented with predicted intermediate (41.0%) or high-level resistance (43.8%) to doravirine. High-level resistance to doravirine was commonly predicted by the presence of at least three DRMs (79.7%). The predicted resistance profile to doravirine in ART-naïve patients is promising, but less so in those experiencing failure to first-generation NNRTIs. Accumulation of NNRTI DRMs seems to be an important factor in the poor resistance prediction for doravirine. CONCLUSIONS Although doravirine is approved as initial therapy in patients who are ART-naïve, it is currently recommended to obtain a genotype prior to the initiation of ART. Clinical studies are needed to ascertain whether predicted resistance profiles in ART naïve and NNRTI-treated patients translate into poor clinical outcomes, especially in settings where genotypic resistance testing is not available.
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Affiliation(s)
- Kim Steegen
- Department of Molecular Medicine and HaematologyNational Health Laboratory ServicesJohannesburgSouth Africa
- Department of Molecular Medicine and HaematologyUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Michelle Moorhouse
- Ezintsha, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Global Medical AffairsViiV HealthCareJohannesburgSouth Africa
| | - Annemarie MJ Wensing
- Ezintsha, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Translational VirologyDepartment of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Willem DF Venter
- Ezintsha, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Lucia Hans
- Department of Molecular Medicine and HaematologyNational Health Laboratory ServicesJohannesburgSouth Africa
- Department of Molecular Medicine and HaematologyUniversity of the WitwatersrandJohannesburgSouth Africa
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27
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Ding Y, Chen M, Wang J, Yang Y, Feng Y, Wang L, Duan S, Lin Q, Xing H, Ma Y, Han M, Ma L. Increase in HIV-1-transmitted drug resistance among ART-naïve youths at the China-Myanmar border during 2009 ~ 2017. BMC Infect Dis 2021; 21:93. [PMID: 33478415 PMCID: PMC7818912 DOI: 10.1186/s12879-021-05794-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 01/12/2021] [Indexed: 11/16/2022] Open
Abstract
Background HIV-transmitted drug resistance (TDR) is found in antiretroviral therapy (ART)-naïve populations infected with HIV-1 with TDR mutations and is important for guiding future first- and second-line ART regimens. We investigated TDR and its effect on CD4 count in ART-naïve youths from the China-Myanmar border near the Golden Triangle to better understand TDR and effectively guide ART. Methods From 2009 to 2017, 10,832 HIV-1 infected individuals were newly reported along the Dehong border of China, 573 ART-naïve youths (16 ~ 25 y) were enrolled. CD4 counts were obtained from whole blood samples. HIV pol gene sequences were amplified from RNA extracted from plasma. The Stanford REGA program and jpHMM recombination prediction tool were used to determine genotypes. TDR mutations (TDRMs) were analyzed using the Stanford Calibrated Population Resistance tool. Results The most common infection route was heterosexuals (70.51%), followed by people who inject drugs (PWID, 19.20%) and men who have sex with men (MSM) (8.90%). The distribution of HIV genotypes mainly included the unique recombinant form (URF) (44.08%), 38.68% were CRFs, 13.24% were subtype C and 4.04% were subtype B. The prevalence of TDR increased significantly from 2009 to 2017 (3.48 to 9.48%) in ART-naïve youths (4.00 to 13.16% in Burmese subjects, 3.33 to 5.93% in Chinese subjects), and the resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs), nucleoside and nucleotide reverse transcriptase inhibitors (NRTIs), and protease inhibitors (PIs) were 3.49, 2.62, and 0.52%, respectively. Most (94.40%, n = 34) of HIV-1-infected patients with TDRM had mutation that conferred resistance to a single drug class. The most common mutations Y181I/C and K103N, were found in 7 and 9 youths, respectively. The mean CD4 count was significantly lower among individuals with TDRMs (373/mm3 vs. 496/mm3, p = 0.013). Conclusions The increase in the prevalence of HIV-1 TDR increase and a low CD4 count of patients with TDRMs in the China-Myanmar border suggests the need for considering drug resistance before initiating ART in HIV recombination hotspots. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-05794-5.
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Affiliation(s)
- Yibo Ding
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Min Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Jibao Wang
- Dehong Dai and Jingpo Autonomous Prefecture Center for Disease Control and Prevention, Mangshi, 678400, China
| | - Yuecheng Yang
- Dehong Dai and Jingpo Autonomous Prefecture Center for Disease Control and Prevention, Mangshi, 678400, China
| | - Yi Feng
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Lijie Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Song Duan
- Dehong Dai and Jingpo Autonomous Prefecture Center for Disease Control and Prevention, Mangshi, 678400, China
| | - Qianru Lin
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Hui Xing
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Yanling Ma
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Mengjie Han
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China.
| | - Liying Ma
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China.
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Zaki EA, El-Daly MM, Abdulhaq A, Al-Subhi TL, Hassan AM, El-Kafrawy SA, Alhazmi MM, Darraj MA, Azhar EI. Genotyping and antiretroviral drug resistance of human immunodeficiency Virus-1 in Jazan, Saudi Arabia. Medicine (Baltimore) 2020; 99:e23274. [PMID: 33285702 PMCID: PMC7717766 DOI: 10.1097/md.0000000000023274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Determination of human immunodeficiency virus-1 (HIV-1) genotypes and identification of antiretroviral drug-resistant mutations. Among treatment naïve HIV patients in Jazan, Saudi Arabia. HIV is a major public health problem. HIV genotyping and antiretroviral resistance testing is an important guide for better management of treatment-naive. Antiretroviral resistance testing before starting of treatment regimen leads to a better virological response. A total of 57 samples of treatment-naive patients were collected from King Fahd Central Hospital in Jazan, Saudi Arabia. Samples were tested for HIV-1 antibodies, western blot, viral load, HIV-1 genotypes through direct sequencing, and antiretroviral resistance testing. The HIV-1 Genotypes were as follow; C: 66.6%, D: 10.5%, G: 8.8%, B: 7.0%, CRF01_AE: 3.5%, A and CRF02_AG: 1.8% each. 77.2% of cases showed susceptibility to the 3 major classes of antiretroviral drugs; Protease inhibitor (PI), Nucleoside reverse transcriptase inhibitor (NRTI), and non-nucleoside reverse transcriptase inhibitors (NNRTI); while 8.8% had mutations conferring resistance to NRTI. Mutations conferring resistance to PI were detected in 7.0% of cases, and 1.8% of cases had mutations conferring resistance to both NRTI and PI. Mutations conferring resistance to NNRTI were detected in 5.3% of cases. Mutations associated with antiretroviral drugs include (V82A+I84IV), (L10F+Q58E), (L10F+V82Y), L10FV, L33LF, L89LMV, M184V, E138A, V106I, and V179VD. The prevalence of HIV-1 antiretroviral resistance mutations is 22.8% in the studied population, which may warrant antiretroviral drug resistance testing as a pretreatment to help and guide physicians for the proper HIV treatment.
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Affiliation(s)
- Eitezaz A. Zaki
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University
- Department of Virology, Jeddah Regional Lab, Ministry of Health
| | - Mai M. El-Daly
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Clinical Pathology Department, National Liver Institute, Menoufia University, Shebin El-Kom, Egypt
| | - Ahmed Abdulhaq
- Deanship of Scientific Affairs and Research, Jazan University
| | - Tagreed L. Al-Subhi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed M. Hassan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sherif A. El-Kafrawy
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Clinical Pathology Department, National Liver Institute, Menoufia University, Shebin El-Kom, Egypt
| | | | - Majid A. Darraj
- Department of Infectious Diseases, King Fahd Central Hospital
- Department of Medicine, College of Medicine, Jazan University, Jazan, Saudi Arabia
| | - Esam I. Azhar
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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29
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Moyo S, Hunt G, Zuma K, Zungu M, Marinda E, Mabaso M, Kana V, Kalimashe M, Ledwaba J, Naidoo I, Takatshana S, Matjokotja T, Dietrich C, Raizes E, Diallo K, Kindra G, Mugore L, Rehle T. HIV drug resistance profile in South Africa: Findings and implications from the 2017 national HIV household survey. PLoS One 2020; 15:e0241071. [PMID: 33147285 PMCID: PMC7641411 DOI: 10.1371/journal.pone.0241071] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND HIV drug resistance (HIVDR) testing was included in the 2017 South African national HIV household survey. We describe the prevalence of HIVDR by drug class, age, sex and antiretroviral drugs (ARV) status. METHODS Dried blood were spots tested for HIV, with Viral load (VL), exposure to ARVs and HIVDR testing among those HIV positive. HIVDR testing was conducted on samples with VL ≥1000 copies/ml using Next Generation Sequencing. Weighted percentages of HIVDR are reported. RESULTS 697/1,105 (63%) of HIV positive samples were sequenced. HIVDR was detected in samples from 200 respondents (27.4% (95% confidence interval (CI) 22.8-32.6)). Among these 130 (18.9% (95% CI 14.8-23.8)), had resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) only, 63 (7.8% (95% CI 5.6-10.9)) resistance to NNRTIs and nucleoside reverse transcriptase inhibitors, and 3 (0.5% (95% CI 0.1-2.1)) resistance to protease inhibitors. Sixty-five (55.7% (95% CI 42.6-67.9) of ARV-positive samples had HIVDR compared to 112 (22.8% (95% CI 17.7-28.7)), in ARV-negative samples. HIVDR was found in 75.6% (95% CI 59.2-87.3), n = 27, samples from respondents who reported ARV use but tested ARV-negative, and in 15.3% (95% CI 6.3-32.8), n = 7, respondents who reported no ARV use and tested ARV-negative. There were no significant age and sex differences in HIVDR. CONCLUSION 27% of virally unsuppressed respondents had HIVDR, increasing to 75% among those who had discontinued ARV. Our findings support strengthening first-line ARV regimens by including drugs with a higher resistance barrier and treatment adherence strategies, and close monitoring of HIVDR.
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Affiliation(s)
- Sizulu Moyo
- Human Sciences Research Council, Pretoria, South Africa
- School of Public Health, University of Cape Town, Cape Town, South Africa
| | - Gillian Hunt
- Centre for HIV and STIs, National Institute of Communicable Diseases, Johannesburg, South Africa
| | | | - Mpumi Zungu
- Human Sciences Research Council, Pretoria, South Africa
| | - Edmore Marinda
- Human Sciences Research Council, Pretoria, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Vibha Kana
- Centre for HIV and STIs, National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Monalisa Kalimashe
- Centre for HIV and STIs, National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Johanna Ledwaba
- Centre for HIV and STIs, National Institute of Communicable Diseases, Johannesburg, South Africa
| | | | | | | | - Cheryl Dietrich
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Elliot Raizes
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Karidia Diallo
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Gurpreet Kindra
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Linnetie Mugore
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Thomas Rehle
- School of Public Health, University of Cape Town, Cape Town, South Africa
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30
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Patel RC, Oyaro P, Odeny B, Mukui I, Thomas KK, Sharma M, Wagude J, Kinywa E, Oluoch F, Odhiambo F, Oyaro B, John-Stewart GC, Abuogi LL. Optimizing viral load suppression in Kenyan children on antiretroviral therapy (Opt4Kids). Contemp Clin Trials Commun 2020; 20:100673. [PMID: 33195874 PMCID: PMC7644580 DOI: 10.1016/j.conctc.2020.100673] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/26/2020] [Accepted: 10/22/2020] [Indexed: 12/16/2022] Open
Abstract
Background As many as 40% of the 1 million children living with HIV (CLHIV) receiving antiretroviral treatment (ART) in resource limited settings have not achieved viral suppression (VS). Kenya has a large burden of pediatric HIV with nearly 140,000 CLHIV. Feasible, scalable, and cost-effective approaches to ensure VS in CLHIV are urgently needed. The goal of this study is to determine the feasibility and impact of point-of-care (POC) viral load (VL) and targeted drug resistance mutation (DRM) testing to improve VS in children on ART in Kenya. Methods We are conducting a randomized controlled study to evaluate the use of POC VL and targeted DRM testing among 704 children aged 1-14 years on ART at health facilities in western Kenya. Children are randomized 1:1 to intervention (higher frequency POC VL and targeted DRM testing) vs. control (standard-of-care) arms and followed for 12 months. Our primary outcome is VS (VL < 1000 copies/mL) 12 months after enrollment by study arm. Secondary outcomes include time to VS and the impact of targeted DRM testing on VS. In addition, key informant interviews with patients and providers will generate an understanding of how the POC VL intervention functions. Finally, we will model the cost-effectiveness of POC VL combined with targeted DRM testing. Discussion This study will provide critical information on the impact of POC VL and DRM testing on VS among CLHIV on ART in a resource-limited setting and directly address the need to find approaches that maximize VS among children on ART. Trials registration NCT03820323.
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Affiliation(s)
- Rena C Patel
- Department of Medicine, University of Washington, Seattle, WA, United States.,Department of Global Health, University of Washington, Seattle, WA, United States
| | | | - Beryne Odeny
- Department of Global Health, University of Washington, Seattle, WA, United States
| | | | - Katherine K Thomas
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Monisha Sharma
- Department of Global Health, University of Washington, Seattle, WA, United States
| | | | | | | | - Francesca Odhiambo
- Family AIDS Care and Education Services, Kenya Medical Research Institute, Kisumu, Kenya
| | - Boaz Oyaro
- Kenya Medical Research Institute-CDC, Kisian, Kenya
| | - Grace C John-Stewart
- Department of Medicine, University of Washington, Seattle, WA, United States.,Department of Global Health, University of Washington, Seattle, WA, United States.,Departments of Pediatrics and Epidemiology, University of Washington, Seattle, WA, United States
| | - Lisa L Abuogi
- Department of Pediatrics, University of Colorado, Denver, CO, United States
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31
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Jordan MR, Hamunime N, Bikinesi L, Sawadogo S, Agolory S, Shiningavamwe AN, Negussie T, Fisher-Walker CL, Raizes EG, Mutenda N, Hunter CJ, Dean N, Steegen K, Kana V, Carmona S, Yang C, Tang AM, Parkin N, Hong SY. High levels of HIV drug resistance among adults failing second-line antiretroviral therapy in Namibia. Medicine (Baltimore) 2020; 99:e21661. [PMID: 32925712 PMCID: PMC7489739 DOI: 10.1097/md.0000000000021661] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
To support optimal third-line antiretroviral therapy (ART) selection in Namibia, we investigated the prevalence of HIV drug resistance (HIVDR) at time of failure of second-line ART. A cross-sectional study was conducted between August 2016 and February 2017. HIV-infected people ≥15 years of age with confirmed virological failure while receiving ritonavir-boosted protease inhibitor (PI/r)-based second-line ART were identified at 15 high-volume ART clinics representing over >70% of the total population receiving second-line ART. HIVDR genotyping of dried blood spots obtained from these individuals was performed using standard population sequencing methods. The Stanford HIVDR algorithm was used to identify sequences with predicted resistance; genotypic susceptibility scores for potential third-line regimens were calculated. Two hundred thirty-eight individuals were enrolled; 57.6% were female. The median age and duration on PI/r-based ART at time of enrolment were 37 years and 3.46 years, respectively. 97.5% received lopinavir/ritonavir-based regimens. The prevalence of nucleoside reverse transcriptase inhibitor (NRTI), non-nucleoside reverse transcriptase inhibitor (NNRTI), and PI/r resistance was 50.6%, 63.1%, and 13.1%, respectively. No significant association was observed between HIVDR prevalence and age or sex. This study demonstrates high levels of NRTI and NNRTI resistance and moderate levels of PI resistance in people receiving PI/r-based second-line ART in Namibia. Findings underscore the need for objective and inexpensive measures of adherence to identify those in need of intensive adherence counselling, routine viral load monitoring to promptly detect virological failure, and HIVDR genotyping to optimize selection of third-line drugs in Namibia.
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Affiliation(s)
- Michael R. Jordan
- Division of Geographic Medicine and Infectious Disease, Tufts Medical Center
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA, USA
| | - Ndapewa Hamunime
- Directorate of Special Programmes, Ministry of Health and Social Services, Windhoek, Namibia
| | - Leonard Bikinesi
- Directorate of Special Programmes, Ministry of Health and Social Services, Windhoek, Namibia
| | | | - Simon Agolory
- United States Centers for Disease Control and Prevention
| | | | - Taffa Negussie
- Directorate of Special Programmes, Ministry of Health and Social Services, Windhoek, Namibia
| | | | | | - Nicholus Mutenda
- Directorate of Special Programmes, Ministry of Health and Social Services, Windhoek, Namibia
| | | | - Natalie Dean
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Kim Steegen
- Department of Molecular Medicine and Haematology, University of Witwatersrand, Johannesburg, South Africa
| | - Vibha Kana
- Department of Molecular Medicine and Haematology, University of Witwatersrand, Johannesburg, South Africa
| | - Sergio Carmona
- Department of Molecular Medicine and Haematology, University of Witwatersrand, Johannesburg, South Africa
| | - Chunfu Yang
- United States Centers for Disease Control and Prevention, Atlanta, GA
| | - Alice M. Tang
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA, USA
| | - Neil Parkin
- Data First Consulting, Inc., Sebastopol, CA, USA
| | - Steven Y. Hong
- Division of Geographic Medicine and Infectious Disease, Tufts Medical Center
- United States Centers for Disease Control and Prevention
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32
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Gachogo RW, Mwai DN, Onyambu FG. Cost analysis of implementing HIV drug resistance testing in Kenya: a case study of a service delivery site at a tertiary level hospital in Kenya. F1000Res 2020; 9:793. [PMID: 32983418 PMCID: PMC7495211 DOI: 10.12688/f1000research.23379.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/15/2020] [Indexed: 01/13/2023] Open
Abstract
Background: HIV drug resistance (HIVDR) threatens progress achieved in response to the HIV epidemic. Understanding the costs of implementing HIVDR testing programs for patient management and surveillance in resource-limited settings is critical in optimizing resource allocation. Here, we estimate the unit cost of HIVDR testing and identify major cost drivers while documenting challenges and lessons learnt in implementation of HIVDR testing at a tertiary level hospital in Kenya. Methods: We employed a mixed costing approach to estimate the costs associated with performing a HIVDR test from the provider's perspective. Data collection involved a time and motion study of laboratory procedures and interviewing laboratory personnel and the management personnel. Cost analysis was based on estimated 1000 HIVDR tests per year. Data entry and analysis were done using Microsoft Excel and costs converted to US dollars (2019). Results: The estimated unit cost for a HIVDR test was $271.78 per test. The main cost drivers included capital ($102.42, 37.68%) and reagents (101.50, 37.35%). Other costs included: personnel ($46.81, 17.22%), utilities ($14.69, 5.41%), equipment maintenance costs ($2.37, 0.87%) and quality assurance program ($4, 1.47%). Costs in relation to specific laboratory processes were as follows: sample collection ($2.41, 0.89%), RNA extraction ($22.79, 8.38%), amplification ($56.14, 20.66%), gel electrophoresis ($10.34, 3.80%), sequencing ($160.94, 59.22%), and sequence analysis ($19.16, 7.05%). A user-initiated modification of halving reagent volumes for some laboratory processes (amplification and sequencing) reduced the unit cost for a HIVDR test to $233.81 (13.97%) reduction. Conclusions: Capital expenditure and reagents remain the most expensive components of HIVDR testing. This cost is bound to change as the sequencing platform is utilized towards maximum capacity or leveraged for use with other tests. Cost saving in offering HIVDR testing services is also possible through reagent volume reduction without compromising on the quality of test results.
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Affiliation(s)
- Rachael W. Gachogo
- Molecular and Infectious Diseases Research Laboratory, University of Nairobi, Nairobi, Kenya
- School of Economics, University of Nairobi, Nairobi, Kenya
| | - Daniel N. Mwai
- School of Economics, University of Nairobi, Nairobi, Kenya
| | - Frank G. Onyambu
- Molecular and Infectious Diseases Research Laboratory, University of Nairobi, Nairobi, Kenya
- School of Health Sciences, Meru University of Science and Technology, Meru, Kenya
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Zuo L, Peng K, Hu Y, Xu Q. Genotypic Methods for HIV Drug Resistance Monitoring: The Opportunities and Challenges Faced by China. Curr HIV Res 2020; 17:225-239. [PMID: 31560290 DOI: 10.2174/1570162x17666190927154110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/05/2019] [Accepted: 09/20/2019] [Indexed: 12/18/2022]
Abstract
AIDS is a globalized infectious disease. In 2014, UNAIDS launched a global project of "90-90-90" to end the HIV epidemic by 2030. The second and third 90 require 90% of HIV-1 infected individuals receiving antiretroviral therapy (ART) and durable virological suppression. However, wide use of ART will greatly increase the emergence and spreading of HIV drug resistance and current HIV drug resistance test (DRT) assays in China are seriously lagging behind, hindering to achieve virological suppression. Therefore, recommending an appropriate HIV DRT method is critical for HIV routine surveillance and prevention in China. In this review, we summarized the current existing HIV drug resistance genotypic testing methods around the world and discussed the advantages and disadvantages of these methods.
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Affiliation(s)
- Lulu Zuo
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212002, China.,Pathogen Discovery & Big Data Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences; Shanghai 200031, China
| | - Ke Peng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yihong Hu
- Pathogen Discovery & Big Data Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences; Shanghai 200031, China
| | - Qinggang Xu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212002, China
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Hermans LE, Steegen K, ter Heine R, Schuurman R, Tempelman HA, Moraba R, van Maarseveen E, Nijhuis M, Pillay T, Legg‐E’Silva D, Snyman T, Schapiro JM, Burger DM, Carmona S, Wensing AMJ. Drug level testing as a strategy to determine eligibility for drug resistance testing after failure of ART: a retrospective analysis of South African adult patients on second-line ART. J Int AIDS Soc 2020; 23:e25501. [PMID: 32515898 PMCID: PMC7282495 DOI: 10.1002/jia2.25501] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/23/2020] [Accepted: 03/27/2020] [Indexed: 01/28/2023] Open
Abstract
INTRODUCTION When protease inhibitor (PI)-based second-line ART fails, guidelines recommend drug resistance testing and individualized third-line treatment. However, PI-resistant viral strains are rare and drug resistance testing is costly. We investigated whether less costly PI-exposure testing can be used to select those patients who would benefit most from drug resistance testing. METHODS We performed a retrospective analysis of South African adults living with HIV experiencing failure of ritonavir-boosted-lopinavir (LPV/r)-based second-line ART for whom drug resistance testing results were available. We included patients who received plasma-based drug resistance testing at a central South African reference laboratory in 2017 and patients who received dried blood spots (DBS)-based drug resistance testing at a rural South African clinic between 2009 and 2017. PI-exposure testing was performed on remnant plasma or DBS using liquid chromatography mass spectrometry (LCMS). Additionally, a low-cost immunoassay was used on plasma. Population genotypic drug resistance testing of the pol region was performed on plasma and DBS using standard clinical protocols. RESULTS Samples from 544 patients (494 plasma samples and 50 DBS) were included. Median age was 41.0 years (IQR: 33.3 to 48.5) and 58.6% were women. Median HIV-RNA load was 4.9 log10 copies/mL (4.3 to 5.4). Prevalence of resistance to the NRTI-backbone was 70.6% (349/494) in plasma samples and 56.0% (28/50) in DBS. Major PI-resistance mutations conferring high-level resistance to LPV/r were observed in 26.7% (132/494) of plasma samples and 12% (6/50) of DBS. PI-exposure testing revealed undetectable LPV levels in 47.0% (232/494) of plasma samples and in 60.0% (30/50) of DBS. In pooled analysis of plasma and DBS samples, detectable LPV levels had a sensitivity of 90% (84% to 94%) and a negative predictive failure of 95% (91% to 97%) for the presence of major LPV/r resistance. CONCLUSIONS PI-exposure testing revealed non-adherence in half of patients experiencing failure on second-line ART and accurately predicted the presence or absence of clinically relevant PI resistance. PI-exposure testing constitutes a novel screening strategy in patients with virological failure of ART that can differentiate between different underlying causes of therapy failure and may allow for more effective use of limited resources available for drug resistance testing.
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Affiliation(s)
- Lucas E Hermans
- VirologyDepartment of Medical MicrobiologyUniversity Medical Center Utrecht (UMCU)UtrechtThe Netherlands
- Wits Reproductive Health and HIV Institute (Wits RHI)University of the WitwatersrandJohannesburgSouth Africa
- Ndlovu Research ConsortiumElandsdoornSouth Africa
| | - Kim Steegen
- Department of Molecular Medicine and HaematologyFaculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Department of Molecular Medicine and HaematologyNational Health Laboratory Service (NHLS)JohannesburgSouth Africa
| | - Rob ter Heine
- Department of PharmacyRadboud Institute for Health SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Rob Schuurman
- VirologyDepartment of Medical MicrobiologyUniversity Medical Center Utrecht (UMCU)UtrechtThe Netherlands
| | - Hugo A Tempelman
- Wits Reproductive Health and HIV Institute (Wits RHI)University of the WitwatersrandJohannesburgSouth Africa
- Ndlovu Research ConsortiumElandsdoornSouth Africa
| | | | | | - Monique Nijhuis
- VirologyDepartment of Medical MicrobiologyUniversity Medical Center Utrecht (UMCU)UtrechtThe Netherlands
- Wits Reproductive Health and HIV Institute (Wits RHI)University of the WitwatersrandJohannesburgSouth Africa
- Ndlovu Research ConsortiumElandsdoornSouth Africa
| | - Taryn Pillay
- Department of ChemistryUniversity of the WitwatersrandJohannesburgSouth Africa
- National Health Laboratory Service (NHLS)JohannesburgSouth Africa
| | - Derryn Legg‐E’Silva
- Department of ChemistryUniversity of the WitwatersrandJohannesburgSouth Africa
- National Health Laboratory Service (NHLS)JohannesburgSouth Africa
| | - Tracy Snyman
- Department of ChemistryUniversity of the WitwatersrandJohannesburgSouth Africa
- National Health Laboratory Service (NHLS)JohannesburgSouth Africa
| | | | - David M Burger
- Department of PharmacyRadboud Institute for Health SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Sergio Carmona
- Department of Molecular Medicine and HaematologyFaculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Department of Molecular Medicine and HaematologyNational Health Laboratory Service (NHLS)JohannesburgSouth Africa
| | - Annemarie MJ Wensing
- VirologyDepartment of Medical MicrobiologyUniversity Medical Center Utrecht (UMCU)UtrechtThe Netherlands
- Wits Reproductive Health and HIV Institute (Wits RHI)University of the WitwatersrandJohannesburgSouth Africa
- Ndlovu Research ConsortiumElandsdoornSouth Africa
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Lippman SA, Mooney AC, Puren A, Hunt G, Grignon JS, Prach LM, Gilmore HJ, Truong HHM, Barnhart S, Liegler T. The role of drug resistance in poor viral suppression in rural South Africa: findings from a population-based study. BMC Infect Dis 2020; 20:248. [PMID: 32216752 PMCID: PMC7099808 DOI: 10.1186/s12879-020-4933-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/28/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Understanding factors driving virological failure, including the contribution of HIV drug resistance mutations (DRM), is critical to ensuring HIV treatment remains effective. We examine the contribution of drug resistance mutations for low viral suppression in HIV-positive participants in a population-based sero-prevalence survey in rural South Africa. METHODS We conducted HIV drug resistance genotyping and ART analyte testing on dried blood spots (DBS) from HIV-positive adults participating in a 2014 survey in North West Province. Among those with virologic failure (> 5000 copies/mL), we describe frequency of DRM to protease inhibitors (PI), nucleoside reverse transcriptase inhibitors (NRTI), and non-nucleoside reverse transcriptase inhibitors (NNRTI), report association of resistance with antiretroviral therapy (ART) status, and assess resistance to first and second line therapy. Analyses are weighted to account for sampling design. RESULTS Overall 170 DBS samples were assayed for viral load and ART analytes; 78.4% of men and 50.0% of women had evidence of virologic failure and were assessed for drug resistance, with successful sequencing of 76/107 samples. We found ≥1 DRM in 22% of participants; 47% were from samples with detectable analyte (efavirenz, nevirapine or lopinavir). Of those with DRM and detectable analyte, 60% showed high-level resistance and reduced predicted virologic response to ≥1 NRTI/NNRTI typically used in first and second-line regimens. CONCLUSIONS DRM and predicted reduced susceptibility to first and second-line regimens were common among adults with ART exposure in a rural South African population-based sample. Results underscore the importance of ongoing virologic monitoring, regimen optimization and adherence counseling to optimize durable virologic suppression.
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Affiliation(s)
- Sheri A Lippman
- Division of Prevention Science, Department of Medicine, University of California San Francisco, 550 16th Street, 3rd Floor, San Francisco, CA, 94158-2549, USA.
| | - Alyssa C Mooney
- Department of Epidemiology, University of California San Francisco, San Francisco, USA
| | - Adrian Puren
- National Institute for Communicable Diseases/NHLS, Johannesburg, South Africa
- Division of Virology, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Gillian Hunt
- National Institute for Communicable Diseases/NHLS, Johannesburg, South Africa
- Division of Virology, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Jessica S Grignon
- Department of Global Health, University of Washington, Seattle, USA
- International Training and Education Center for Health (I-TECH) South Africa, Pretoria, Republic of South Africa
| | - Lisa M Prach
- Division of Prevention Science, Department of Medicine, University of California San Francisco, 550 16th Street, 3rd Floor, San Francisco, CA, 94158-2549, USA
| | - Hailey J Gilmore
- Division of Prevention Science, Department of Medicine, University of California San Francisco, 550 16th Street, 3rd Floor, San Francisco, CA, 94158-2549, USA
| | - Hong-Ha M Truong
- Division of Prevention Science, Department of Medicine, University of California San Francisco, 550 16th Street, 3rd Floor, San Francisco, CA, 94158-2549, USA
| | - Scott Barnhart
- Department of Global Health, University of Washington, Seattle, USA
- International Training and Education Center for Health (I-TECH) South Africa, Pretoria, Republic of South Africa
| | - Teri Liegler
- Department of Medicine, University of California San Francisco, San Francisco, USA
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Vaz P, Buck WC, Bhatt N, Bila D, Auld A, Houston J, Cossa L, Alfredo C, Jobarteh K, Sabatier J, Macassa E, Sousa A, DeVos J, Jani I, Yang C. Compromise of Second-Line Antiretroviral Therapy Due to High Rates of Human Immunodeficiency Virus Drug Resistance in Mozambican Treatment-Experienced Children With Virologic Failure. J Pediatric Infect Dis Soc 2020; 9:6-13. [PMID: 30364958 DOI: 10.1093/jpids/piy102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 09/25/2018] [Indexed: 11/12/2022]
Abstract
BACKGROUND Virologic failure (VF) is highly prevalent in sub-Saharan African children on antiretroviral therapy (ART) and is often associated with human immunodeficiency virus drug resistance (DR). Most children still lack access to routine viral load (VL) monitoring for early identification of treatment failure, with implications for the efficacy of second-line ART. METHODS Children aged 1 to 14 years on ART for ≥12 months at 6 public facilities in Maputo, Mozambique were consecutively enrolled after informed consent. Chart review and caregiver interviews were conducted. VL testing was performed, and specimens with ≥1000 copies/mL were genotyped. RESULTS Of the 715 children included, the mean age was 103 months, 85.8% had no immunosuppression, 73.1% were taking stavudine/lamivudine/nevirapine, and 20.1% had a history prevention of mother-to-child transmission exposure. The mean time on ART was 60.0 months. VF was present in 259 patients (36.3%); 248 (95.8%) specimens were genotyped, and DR mutations were found in 238 (96.0%). Severe immunosuppression and nutritional decline were associated with DR. M184V and Y181C were the most common mutations. In the 238 patients with DR, standard second-line ART would have 0, 1, 2, and 3 effective antiretrovirals in 1 (0.4%), 74 (31.1%), 150 (63.0%), and 13 (5.5%) patients, respectively. CONCLUSION This cohort had high rates of VF and DR with frequent compromise of second-line ART. There is urgent need to scale-up VL monitoring and heat-stable protease inhibitor formulations or integrase inhibitorsfor a more a durable first-line regimen that can feasibly be implemented in developing settings.
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Affiliation(s)
- Paula Vaz
- Fundação Ariel Glaser, Maputo, Mozambique
| | - W Chris Buck
- University of California Los Angeles, David Geffen School of Medicine
| | | | - Dulce Bila
- Fundação Ariel Glaser, Maputo, Mozambique.,Instituto Nacional de Saúde, Maputo, Mozambique
| | - Andrew Auld
- Division of Global HIV and TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - James Houston
- Division of Global HIV and TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Loide Cossa
- Instituto Nacional de Saúde, Maputo, Mozambique
| | - Charity Alfredo
- Centers for Disease Control and Prevention, Maputo, Mozambique
| | - Kebba Jobarteh
- Centers for Disease Control and Prevention, Maputo, Mozambique
| | - Jennifer Sabatier
- Division of Global HIV and TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Amina Sousa
- Instituto Nacional de Saúde, Maputo, Mozambique
| | - Josh DeVos
- Division of Global HIV and TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Ilesh Jani
- Instituto Nacional de Saúde, Maputo, Mozambique
| | - Chunfu Yang
- Division of Global HIV and TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
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Onwuamah CK, Okpokwu J, Audu R, Imade G, Meloni ST, Okwuraiwe A, Chebu P, Musa AZ, Chaplin B, Dalhatu I, Agbaji O, Samuels J, Ezechi O, Ahmed M, Odaibo G, Olaleye DO, Okonkwo P, Salako BL, Raizes E, Yang C, Kanki PJ, Idigbe EO. Low levels of HIV-1 drug resistance mutations in patients who achieved viral re-suppression without regimen switch: a retrospective study. BMC Microbiol 2020; 20:17. [PMID: 31959116 PMCID: PMC6971913 DOI: 10.1186/s12866-020-1706-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 01/14/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We identified a HIV-positive cohort in virologic failure (VF) who re-suppressed without drug switch. We characterized their drug resistance mutations (DRM) and adherence profiles to learn how to better manage HIV drug resistance. A retrospective cohort study utilizing clinical data and stored samples. Patients received ART at three Nigerian treatment centres. Plasma samples stored when they were in VF were genotyped. RESULT Of 126 patients with samples available, 57 were successfully genotyped. From ART initiation, the proportion of patients with adherence ≥90% increased steadily from 54% at first high viral load (VL) to 67% at confirmed VF, and 81% at time of re-suppressed VL. Sixteen (28%) patients had at least one DRM. Forty-six (81%) patients had full susceptibility to the three drugs in their first-line (1 L) regimen. Thirteen (23%) were resistant to at least one antiretroviral drug but three were resistant to drugs not used in Nigeria. Ten patients had resistance to their 1 L drug(s) and six were fully susceptible to the three drugs in the recommended second-line regimen. CONCLUSION This cohort had little drug resistance mutations. We conclude that if adherence is not assured, patients could exhibit virologic failure without having developed mutations associated with drug resistance.
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Affiliation(s)
- Chika K Onwuamah
- Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, 6 Edmund Crescent, Yaba, Lagos, 101212, Nigeria.
| | | | - Rosemary Audu
- Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, 6 Edmund Crescent, Yaba, Lagos, 101212, Nigeria
| | - Godwin Imade
- Jos University Teaching Hospital, Jos, Plateau State, Nigeria
| | - Seema T Meloni
- Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Azuka Okwuraiwe
- Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, 6 Edmund Crescent, Yaba, Lagos, 101212, Nigeria
| | - Philippe Chebu
- APIN Public Health Initiative Nigeria, Ltd./Gte, Abuja, FCT, Nigeria
| | - Adesola Z Musa
- Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, 6 Edmund Crescent, Yaba, Lagos, 101212, Nigeria
| | - Beth Chaplin
- Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | - Oche Agbaji
- Jos University Teaching Hospital, Jos, Plateau State, Nigeria
| | - Jay Samuels
- APIN Public Health Initiative Nigeria, Ltd./Gte, Abuja, FCT, Nigeria
| | - Oliver Ezechi
- Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, 6 Edmund Crescent, Yaba, Lagos, 101212, Nigeria
| | - Mukhtar Ahmed
- Centers for Disease Control-Nigeria, Abuja, FCT, Nigeria
| | | | | | - Prosper Okonkwo
- APIN Public Health Initiative Nigeria, Ltd./Gte, Abuja, FCT, Nigeria
| | - Babatunde Lawal Salako
- Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, 6 Edmund Crescent, Yaba, Lagos, 101212, Nigeria
| | - Elliot Raizes
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Chunfu Yang
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Emmanuel O Idigbe
- Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, 6 Edmund Crescent, Yaba, Lagos, 101212, Nigeria
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Panpradist N, Beck IA, Vrana J, Higa N, McIntyre D, Ruth PS, So I, Kline EC, Kanthula R, Wong-On-Wing A, Lim J, Ko D, Milne R, Rossouw T, Feucht UD, Chung M, Jourdain G, Ngo-Giang-Huong N, Laomanit L, Soria J, Lai J, Klavins ED, Frenkel LM, Lutz BR. OLA-Simple: A software-guided HIV-1 drug resistance test for low-resource laboratories. EBioMedicine 2019; 50:34-44. [PMID: 31767540 PMCID: PMC6921160 DOI: 10.1016/j.ebiom.2019.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 01/21/2023] Open
Abstract
Background HIV drug resistance (HIVDR) testing can assist clinicians in selecting treatments. However, high complexity and cost of genotyping assays limit routine testing in settings where HIVDR prevalence has reached high levels. Methods The oligonucleotide ligation assay (OLA)-Simple kit was developed for detection of HIVDR against first-line non-nucleoside/nucleoside reverse transcriptase inhibitors and validated on 672 codons (168 specimens) from subtypes A, B, C, D, and AE. The kit uses dry reagents to facilitate assay setup, lateral flow devices for visual HIVDR detections, and in-house software with an interface for guiding users and analyzing results. Findings HIVDR analysis of specimens by OLA-Simple compared to Sanger sequencing revealed 99.6 ± 0.3% specificity and 98.2 ± 0.9% sensitivity, and compared to high-sensitivity assays, 99.6 ± 0.6% specificity and 86.2 ± 2.5% sensitivity, with 2.6 ± 0.9% indeterminate results. OLA-Simple was performed more rapidly compared to Sanger sequencing (<4 h vs. 35–72 h). Forty-one untrained volunteers blindly tested two specimens each with 96.8 ± 0.8% accuracy. Interpretation OLA-Simple compares favorably with HIVDR genotyping by Sanger and sensitive comparators. Instructional software enabled inexperienced, first-time users to perform the assay with high accuracy. The reduced complexity, cost, and training requirements of OLA-Simple could improve access to HIVDR testing in low-resource settings and potentially allow same-day selection of appropriate antiretroviral therapy. Fund USA National Institutes of Health R01; the Clinical and Retrovirology Research Core and the Molecular Profiling and Computational Biology Core of the UW CFAR; Seattle Children's Research Institute; UW Holloman Innovation Challenge Award; Pilcher Faculty Fellowship.
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Affiliation(s)
- Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Global WACh Program, Department of Global Health, University of Washington, Seattle, WA 98104, USA
| | - Ingrid A Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Justin Vrana
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Nikki Higa
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - David McIntyre
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Parker S Ruth
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Departments of Electrical Engineering and Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Isaac So
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Enos C Kline
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Ruth Kanthula
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Medstar Georgetown University Hospital, DC, 20007, USA
| | - Annie Wong-On-Wing
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Jonathan Lim
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Daisy Ko
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Ross Milne
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Theresa Rossouw
- Department of Immunology, University of Pretoria, Pretoria 0002, South Africa
| | - Ute D Feucht
- Research Centre for Maternal, Fetal, Newborn and Child Health Care Strategies, Department of Paediatrics, University of Pretoria, Pretoria 0002, South Africa; Research Unit for Maternal and Infant Health Care Strategies, South African Medical Research Council, Kalafong Hospital, Atteridgeville 0008, South Africa
| | - Michael Chung
- Department of Global Health, University of Washington, Seattle, WA 98195, USA; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Department of Epidemiology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Department of Medicine, Aga Khan University, Nairobi, Kenya
| | - Gonzague Jourdain
- Institut de Recherche pour le Développement IRD U174 PHPT, Chiang Mai 50000, Thailand; Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
| | - Nicole Ngo-Giang-Huong
- Institut de Recherche pour le Développement IRD U174 PHPT, Chiang Mai 50000, Thailand; Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
| | - Laddawan Laomanit
- Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
| | - Jaime Soria
- Department of Infectious Diseases, Hospital Nacional Dos de Mayo, Av. Miguel Grau 13, Cercado de Lima 15003, Peru
| | - James Lai
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Eric D Klavins
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Departments of Electrical Engineering and Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Lisa M Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Division of Infectious Diseases, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Division of Virology, Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
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Seatla KK, Choga WT, Mogwele M, Diphoko T, Maruapula D, Mupfumi L, Musonda RM, Rowley CF, Avalos A, Kasvosve I, Moyo S, Gaseitsiwe S. Comparison of an in-house 'home-brew' and commercial ViroSeq integrase genotyping assays on HIV-1 subtype C samples. PLoS One 2019; 14:e0224292. [PMID: 31751353 PMCID: PMC6871785 DOI: 10.1371/journal.pone.0224292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/09/2019] [Indexed: 12/22/2022] Open
Abstract
Background Roll-out of Integrase Strand Transfer Inhibitors (INSTIs) such as dolutegravir for HIV combination antiretroviral therapy (cART) in sub-Saharan Africa necessitates the development of affordable HIV drug resistance (HIVDR) assays targeting the Integrase gene. We optimised and evaluated an in-house integrase HIV-1 drug resistance assay (IH-Int) and compared it to a commercially available assay, ViroSeq™ Integrase Genotyping kit (VS-Int) amongst HIV-1 clade C infected individuals. Methods We used 54 plasma samples from treatment naïve participants and one plasma sample from a patient failing INSTI based cART. Specimens were genotyped using both the VS-Int and IH-Int assays. Stanford HIV drug resistance database were used for integrase resistance interpretation. We compared the major and minor resistance mutations, pairwise nucleotide and amino-acid identity, costs and assay time. Results Among 55 specimens tested with IH-Int, 53 (96.4%) successfully amplified compared to 45/55 (81.8%) for the VS-Int assay. The mean nucleotide and amino acid similarity from 33 paired sequences was 99.8% (SD ± 0.30) and 99.8% (SD ± 0.39) for the IH-Int and VS-Int assay respectively. The reagent cost/sample were 32 USD and 147 USD for IH-Int and VS-Int assay, respectively. All sequenced samples were confirmed as HIV-1 subtype C. Conclusions The IH-Int assay had a high amplification success rate and high concordance with the commercial assay. It is significantly cheaper compared to the commercial assay. Our assay has the needed specifications for routine monitoring of participants on Dolutegravir based regimens in Botswana.
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Affiliation(s)
- Kaelo K. Seatla
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana
| | - Wonderful T. Choga
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mompati Mogwele
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana
| | - Thabo Diphoko
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana
| | - Lucy Mupfumi
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana
| | - Rosemary M. Musonda
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Christopher F. Rowley
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Ava Avalos
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Careena Centre for Health, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
| | - Ishmael Kasvosve
- Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership Gaborone, Botswana
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
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Taffa N, Roscoe C, Sawadogo S, De Klerk M, Baughman AL, Wolkon A, Mutenda N, DeVos J, Zheng DP, Wagar N, Prybylski D, Yang C, Hamunime N, Agolory S, Raizes E. Pretreatment HIV drug resistance among adults initiating ART in Namibia. J Antimicrob Chemother 2019; 73:3137-3142. [PMID: 30137412 DOI: 10.1093/jac/dky278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/19/2018] [Indexed: 11/12/2022] Open
Abstract
Background Continued use of standardized, first-line ART containing NNRTIs and NRTIs may contribute to ongoing emergence of HIV drug resistance (HIVDR) in Namibia. Methods A nationally representative cross-sectional survey was conducted during 2015-16 to estimate the prevalence of significant pretreatment HIV drug resistance (PDR) and viral load (VL) suppression rates 6-12 months after initiating standardized first-line ART. Consenting adult patients (≥18 years) initiating ART were interviewed about prior antiretroviral drug (ARV) exposure and underwent resistance testing using dried blood spot samples. PDR was defined as mutations causing low-, intermediate- and high-level resistance to ARVs according to the 2014 WHO Surveillance of HIV Drug Resistance in Adults Initiating ART. The prevalence of PDR was described by patient characteristics, ARV exposure and VL results. Results were weighted to be nationally representative. Results Successful genotyping was performed for 381 specimens; 144 (36.6%) specimens demonstrated HIVDR, of which 54 (12.7%) demonstrated PDR. Resistance to NNRTIs was most prevalent (11.9%). PDR was higher in patients with previous ARV exposure compared with no exposure (30.5% versus 9.6%) (prevalence ratio = 3.17; P < 0.01). Conclusions This survey demonstrated overall PDR at >10% among adults initiating ART in Namibia. Patients with prior ARV exposure had higher rates of PDR. Introducing a non-NNRTI-based regimen for first-line ART should be considered to maximize benefit of ART and minimize the emergence of HIVDR.
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Affiliation(s)
- Negussie Taffa
- Centers for Disease Control and Prevention (CDC), Windhoek, Namibia
| | - Clay Roscoe
- Centers for Disease Control and Prevention (CDC), Windhoek, Namibia
| | | | - Michael De Klerk
- Centers for Disease Control and Prevention (CDC), Windhoek, Namibia
| | | | - Adam Wolkon
- Centers for Disease Control and Prevention (CDC), Windhoek, Namibia
| | - Nicholus Mutenda
- Directorate of Special Programs (DSP) for HIV, TB and Malaria, Ministry of Health and Social Services (MoHSS), Windhoek, Namibia
| | - Josh DeVos
- Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Du-Ping Zheng
- Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Nick Wagar
- Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | | | - Chunfu Yang
- Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Ndapewa Hamunime
- Directorate of Special Programs (DSP) for HIV, TB and Malaria, Ministry of Health and Social Services (MoHSS), Windhoek, Namibia
| | - Simon Agolory
- Centers for Disease Control and Prevention (CDC), Windhoek, Namibia
| | - Elliot Raizes
- Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
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Circulation of multiple subtypes (A, G and CRFs 02_AG) of human immunodeficiency virus type 1 (HIV-1) in selected districts of Punjab province, Pakistan. Arch Virol 2019; 164:3081-3087. [PMID: 31576459 DOI: 10.1007/s00705-019-04422-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/30/2019] [Indexed: 10/25/2022]
Abstract
Owing to consistent genetic mutation and recombination, various escape mutants and/or drug-resistant mutants of human immunodeficiency virus (HIV-1) are now emerging worldwide. Therefore, an understanding of the genetic characteristics of prevailing strains, particularly with regard to drug-resistance-associated substitutions, is essential for devising and implementing treatments and disease control interventions in endemic settings such as Pakistan. We processed a total of 130 plasma samples originating from HIV-treatment centers in selected districts of Punjab province, Pakistan. The samples were first screened using an HIV-1 Ag/Ab Combo test followed by amplification of the pol gene (1084 bp) from samples that were positive either for the antigen or for both the antigen and antibodies simultaneously. Screening revealed that a total of 45 samples were positive (34.62%; 95% CI: 26.99-43.13) for either antigen or both antigen and antibodies (n = 18, 40%; 95% CI: 27.02-54.55) or for antibodies alone (n = 27, 60%; 95% CI: 45.45-72.98). A largest number of positive samples was from the district of Lahore (n = 19/43, 44.18%; 95% CI: 30.44-58.9) followed by Faisalabad (n= 12/36, 33.33%; 95% CI: 20.21-49.66), Gujranwala (n = 05/23, 21.7%; 95% CI: 9.66-41.9) and Sargodha (n = 09/28, 32.1%; 95% CI: 17.93-50.66). The probability of occurrence of HIV infection was significantly associated with individuals having a history of injecting drug use (68.08%; OR = 11.15; 95% CI: 53.84-79.61, p = 0.0001). Phylogenetic analysis based on the pol gene showed that the sequences from this study clustered into three distinct clades representing recombinant form 02_AG (n = 14, 77.0%; 95% CI: 54.79-91.00), and subtypes A (n = 2, 11.1%; 95% CI: 3.1-32.8) and G (n = 2, 11.1%; 95% CI: 3.1-32.8). Although we screened 18 samples for drug-resistance-associated mutations, except for an accessory mutation (M46K) in the protease (PR) region in one subject, we found a lack of drug-resistance-associated substitutions in the PR region. On the other hand, we found two subjects (2/18) carrying a resistance-associated mutation (V106I) conferring a low level of resistance against non-nucleoside reverse transcriptase inhibitors. The present study shows that multiple subtypes of HIV-1 are present in the affected population. Continuous disease surveillance coupled with evaluation of drug resistance at higher resolution should be done in future studies.
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Mzingwane ML, Hunt G, Lassauniere R, Kalimashe M, Bongwe A, Ledwaba J, Chaisson RE, Martinson N, Richter K, Bowyer SM, Tiemessen CT. Detection and molecular characterization of urinary tract HIV-1 populations. Ann Clin Microbiol Antimicrob 2019; 18:27. [PMID: 31551072 PMCID: PMC6760049 DOI: 10.1186/s12941-019-0326-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 09/16/2019] [Indexed: 11/20/2022] Open
Abstract
Background Identification of all possible HIV reservoirs is an important aspect in HIV eradication efforts. The urinary tract has however not been well studied as a potential HIV reservoir. In this pilot study we molecularly characterized HIV-1 viruses in urine and plasma samples to investigate HIV-1 replication, compartmentalization and persistence in the urinary tract. Methods Prospectively collected urine and blood samples collected over 12–36 months from 20 HIV-1 infected individuals were analysed including sampling points from prior to and after ART initiation. HIV-1 pol gene RNA and DNA from urine supernatant and urine pellets respectively were analysed and compared to plasma RNA viruses from the same individual. Results HIV-1 nucleic acid was detected in urine samples from at least one time point in 8/20 (40%) treatment-naïve subjects compared to 1/13 (7.7%) individuals on antiretroviral treatment (ART) during periods of plasma viral suppression and 1/7 (14.3%) individuals with virological failure. HIV-1 RNA was undetectable in urine samples after ART initiation but HIV-1 DNA was detectable in one patient more than 6 months after treatment initiation. There was co-clustering of urine-derived pol sequences but some urine-derived sequences were interspersed among the plasma-derived sequences. Conclusions Suppressive ART reduces HIV-1 replication in the urinary tract but HIV-1 DNA may persist in these cells despite treatment. A larger number of sequences would be required to confirm HIV compartmentalization in the urinary tract.
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Affiliation(s)
- M L Mzingwane
- Department of Pathology, Faculty of Medicine, National University of Science & Technology, Ascot, P. O Box AC 939, Bulawayo, Zimbabwe. .,Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
| | - G Hunt
- Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - R Lassauniere
- Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, Johannesburg, South Africa.,Virus Research and Development Laboratory, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - M Kalimashe
- Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - A Bongwe
- Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - J Ledwaba
- Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - R E Chaisson
- Johns Hopkins University Center for AIDS Research, Baltimore, MD, USA
| | - N Martinson
- Perinatal HIV Research Unit (PHRU), SA MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa
| | - K Richter
- Department of Medical Virology, University of Pretoria, Pretoria, South Africa.,National Health Laboratory Services Tshwane Academic Division, Pretoria, South Africa
| | - S M Bowyer
- Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - C T Tiemessen
- Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Hunt GM, Ledwaba J, Salimo A, Kalimashe M, Dinh TH, Jackson D, Sherman G, Puren A, Ngandu NK, Lombard C, Morris L, Goga A. Prevalence of HIV-1 drug resistance amongst newly diagnosed HIV-infected infants age 4-8 weeks, enrolled in three nationally representative PMTCT effectiveness surveys, South Africa: 2010, 2011-12 and 2012-13. BMC Infect Dis 2019; 19:787. [PMID: 31526373 PMCID: PMC6745779 DOI: 10.1186/s12879-019-4339-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND South Africa (SA) has expanded efforts to reduce mother-to-child transmission of HIV (MTCT) to less than 2% at six weeks after birth and to less than 5% at 18 months postpartum by 2016. Despite improved antiretroviral regimens and coverage between 2001 and 2016, there is little data on infant HIV drug resistance. This paper tracks the prevalence of HIV drug resistance patterns amongst HIV infected infants from three nationally representative studies that assessed the effectiveness of national programs to prevent MTCT (PMTCT). The first study was conducted in 2010 (under the dual therapy PMTCT policy), the second from 2011 to 12 (PMTCT Option A policy) and the third from 2012 to 13 (PMTCT Option A policy). From 2010 to 2013, infant non-nucleoside reverse transcriptase inhibitor (NNRTI) exposure increased from single dose to daily throughout breastfeeding; maternal nucleoside reverse transcriptase inhibitor (NRTI) and NNRTI exposure increased with initiation of NNRTI-and NRTI- containing triple antiretroviral therapy (ART) earlier in gestation and at higher CD4 cell counts. METHODS Three nationally representative surveys were conducted in 2010, 2011-12 and 2012-13. During the surveys, mothers with known, unknown, or no exposure to antiretrovirals for PMTCT and their infants were included, and MTCT was measured. For this paper, infant dried blood spots (iDBS) from HIV PCR positive infants aged 4-8 weeks, with consent for additional iDBS testing, were analysed for HIV drug resistance at the National Institute of Communicable Diseases (NICD), SA, using an in-house assay validated by the Centers for Disease Control and Prevention (CDC). Total viral nucleic acid was extracted from 2 spots and amplified by nested PCR to generate a ~ 1 kb amplicon that was sequenced using Sanger sequencing technologies. Sequence assembly and editing was performed using RECall v3. RESULTS Overall, HIV-1 drug resistance was detected in 51% (95% Confidence interval (CI) [45-58%]) of HIV PCR positive infants, 37% (95% CI [28-47%]) in 2010, 64% (95% CI [53-74%]) in 2011 and 63% (95% CI [47-77%]) in 2012 (p < 0.0001), particularly to the NNRTI drug class. Pooled analyses across all three surveys demonstrated that infants whose mothers received ART showed the highest prevalence of resistance (74%); 26% (21/82) of HIV PCR positive infants with no or undocumented antiretroviral drug (ARV) exposure harboured NNRTI resistance. CONCLUSIONS These data demonstrate increasing NNRTI resistance amongst newly-diagnosed infants in a high HIV prevalence setting where maternal ART coverage increased across the years, starting earlier in gestation and at higher CD4 cell counts. This is worrying as lifelong maternal ART coverage for HIV positive pregnant and lactating women is increasing. Also of concern is that resistant virus was detected in HIV positive infants whose mothers were not exposed to ARVs, raising questions about circulating resistant virus. Numbers in this group were too small to assess trends over the three years.
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Affiliation(s)
- Gillian M. Hunt
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Johanna Ledwaba
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
| | - Anna Salimo
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
| | - Monalisa Kalimashe
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
| | - Thu-Ha Dinh
- US Centers for Disease Control and Prevention, Center for Global Health, Division of Global HIV/TB, Atlanta, GA USA
| | - Debra Jackson
- School of Public Health, University of the Western Cape, Bellville, South Africa
- UNICEF, New York, NY USA
| | - Gayle Sherman
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Adrian Puren
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
| | - Nobubelo K. Ngandu
- Health Systems Research Unit, South African Medical Research Council, Cape Town, South Africa
| | - Carl Lombard
- Biostatistics Unit, South African Medical Research Council, Cape Town, South Africa
- School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ameena Goga
- Health Systems Research Unit, South African Medical Research Council, Cape Town, South Africa
- Department of Paediatrics, University of Pretoria, Pretoria, South Africa
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Strehlau R, Paximadis M, Patel F, Burke M, Technau KG, Shiau S, Abrams EJ, Sherman GG, Hunt G, Ledwaba J, Mazanderani AH, Tiemessen CT, Kuhn L. HIV diagnostic challenges in breast-fed infants of mothers on antiretroviral therapy. AIDS 2019; 33:1751-1756. [PMID: 31149944 PMCID: PMC6663570 DOI: 10.1097/qad.0000000000002276] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Prompt initiation of antiretroviral therapy (ART) for HIV-infected infants is strongly recommended but diagnostic confirmation is important as committing children to life-long ART carries serious health and social implications. METHODS Two HIV-exposed infants in Johannesburg, South Africa were identified presenting with unusual trajectories of diagnostic nucleic acid amplification tests (NAAT) and viral load results. RESULTS Case 1 had repeat indeterminate NAAT results during the first 3 weeks of life; repeat testing thereafter was negative with undetectable viral load including after daily nevirapine prophylaxis ended. ART was not initiated at this time. Case 2 had a single positive NAAT result at 1 month of age that prompted initiation of ART. Subsequent results were negative and ART was discontinued. Repeat negative NAAT with viral load below the limit of quantification or undetectable continued to be obtained. Shortly after and around weaning, positive NAAT results with high viral load (7.1 and 6.03 log10 copies/ml for Cases 1 and 2, respectively) were observed in both children. Both mothers were treated with tenofovir, emtricitabine and efavirenz during breastfeeding. Testing with ultrasensitive assays on early samples conclusively revealed HIV-1 proviral DNA in Case 1. Testing with ultrasensitive assays after the early period but prior to weaning did not detect HIV in either infant. CONCLUSION We hypothesize that breast milk from the mothers of these two rare cases had HIV-specific or nonspecific factors that led to the undetectable results in already infected infants until breastfeeding ended. Our results raise the importance of repeat testing of HIV-exposed breast-fed infants after complete cessation of all breastfeeding.
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Affiliation(s)
- Renate Strehlau
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maria Paximadis
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Faeezah Patel
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Megan Burke
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Karl-Gunter Technau
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephanie Shiau
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Elaine J Abrams
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
- ICAP at Columbia University, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Pediatrics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Gayle G Sherman
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gillian Hunt
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
| | - Johanna Ledwaba
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
| | - Ahmad Haeri Mazanderani
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Louise Kuhn
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
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Magomere EO, Nyangahu DD, Kimoloi S, Webala BA, Ondigo BN. Performance characteristics of a modified HIV-1 drug resistance genotyping method for use in resource-limited settings. F1000Res 2019; 8:1518. [PMID: 31656591 PMCID: PMC6798314 DOI: 10.12688/f1000research.20083.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/14/2019] [Indexed: 11/20/2022] Open
Abstract
Background: HIV-1 drug resistance (HIVDR) assays are critical components of HIV clinical management programs in the face of emerging drug resistance. However, the high costs associated with existing commercial HIVDR assays prohibit their routine usage in resource-limited settings. We present the performance characteristics of a modified commercial HIVDR testing assay. Methods: A total of 26 plasma samples were used to validate and assess the accuracy, precision, reproducibility and amplification sensitivity of a modified HIVDR assay by HIV genotyping. In addition, a cost comparison between the original and the modified assay was performed using the ingredient costing approach. Results: The performance characteristics of the modified assay were in agreement with the original assay. Accuracy, precision and reproducibility showed nucleotide sequence identity of 98.5% (confidence interval (CI), 97.9-99.1%), 98.67% (CI, 98.1-99.23) and 98.7% (CI, 98.1-99.3), respectively. There was no difference in the type of mutations detected by the two assays (χ 2 = 2.36, p = 0.26). Precision and reproducibility showed significant mutation agreement between replicates (kappa = 0.79 and 0.78), respectively ( p < 0.05). The amplification sensitivity of the modified assay was 100% and 62.5% for viremia ≥1000 copies/ml and <1000 copies/ml respectively. Our assay modification translates to a 39.2% reduction in the cost of reagents. Conclusions: Our findings underscore the potential of modifying commercially available HIVDR testing assays into cost-effective, yet accurate assays for use in resource-limited settings.
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Affiliation(s)
- Edwin O. Magomere
- Department of Biochemistry and Molecular Biology, Egerton University, Nakuru, Nakuru, 20115, Kenya
| | - Donald D. Nyangahu
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Seattle, Washington, USA
| | - Sammy Kimoloi
- Department of Medical Laboratory Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kakamega, Kenya
| | - Brenda A. Webala
- Faculty of Health Sciences, Egerton University, Nakuru, Nakuru, Kenya
| | - Bartholomew N. Ondigo
- Department of Biochemistry and Molecular Biology, Egerton University, Nakuru, Nakuru, 20115, Kenya
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kisumu, Kenya
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, NIH, USA, Bethesda, Maryland, USA
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Louis FJ, Segaren N, Desinor O, Beard RS, Jean-Louis R, Chang J, Boisson S, Hulland EN, Wagar N, DeVos J, François K, Buteau J, Boncy J, Marston BJ, Domerçant JW, Yang C, Charles M. High Levels of HIV-1 Drug Resistance in Children Who Acquired HIV Infection Through Mother to Child Transmission in the Era of Option B+, Haiti, 2013 to 2014. Pediatr Infect Dis J 2019; 38:503-507. [PMID: 30640198 PMCID: PMC6785839 DOI: 10.1097/inf.0000000000002270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The main objective of this study was to determine the frequency and patterns of HIV drug resistance-associated mutations among children under 18 months of age born to HIV-1-positive mothers enrolled in the prevention of mother-to-child transmission services in Haiti. METHODS Between January 1, 2013 and December 31, 2014, HIV-positive remnant dried blood spots collected from children under 18 months of age for Early Infant Diagnosis at the National Public Health Laboratory were used for HIV-1 genotyping. HIV drug resistance mutations were analyzed using the Stanford Drug Resistance HIVdb program. RESULTS Of the 3555 dried blood spots collected for Early Infant Diagnosis, 360 (10.1%) were HIV-positive and 355 were available for genotyping. Of these, 304 (85.6%) were successfully genotyped and 217 (71.4%) had ≥1 drug resistance mutation. Mutations conferring resistance to nucleoside reverse transcriptase inhibitor (NRTIs) and non-NRTIs were present in 40.5% (123) and 69.1% (210), respectively. The most frequent mutations were K103N/S (48.0%), M184V (37.5%), G190A/S (15.1%), and Y181C/G/V (14.1%). Predicted drug resistance analysis revealed that 68.8% of the children had high-level resistance to non-NRTIs and 11.5% had intermediate to high-level resistance to abacavir. CONCLUSIONS This study showed high rates of resistance to NRTIs and non-NRTIs among newly HIV-diagnosed children in Haiti, suggesting that in the era of "Option B+" (initiation of lifelong combination antiretroviral therapy to pregnant women with HIV), the majority of children who acquire HIV infection through mother-to-child transmission of HIV have resistant HIV. These results have led the National HIV Program to revise the pediatric guidelines to include protease inhibitors in first-line regimens for all HIV-positive newborns.
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Affiliation(s)
| | | | - Olbeg Desinor
- United States Agency for International Development, Port-au-Prince, Haiti
| | | | | | - Joy Chang
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Erin N. Hulland
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nick Wagar
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joshua DeVos
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kesner François
- Programme National de Lutte contre le VIH/SIDA, Ministère de la Santé Publique et de la Population, Port-au-Prince, Haiti
| | - Josiane Buteau
- Laboratoire National de Santé Publique, Ministère de la Santé Publique et de la Population, Port-au-Prince, Haiti
| | - Jacques Boncy
- Laboratoire National de Santé Publique, Ministère de la Santé Publique et de la Population, Port-au-Prince, Haiti
| | | | | | - Chunfu Yang
- Centers for Disease Control and Prevention, Atlanta, GA, USA
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Abstract
HIV diagnostics have played a central role in the remarkable progress in identifying, staging, initiating, and monitoring infected individuals on life-saving antiretroviral therapy. They are also useful in surveillance and outbreak responses, allowing for assessment of disease burden and identification of vulnerable populations and transmission "hot spots," thus enabling planning, appropriate interventions, and allocation of appropriate funding. HIV diagnostics are critical in achieving epidemic control and require a hybrid of conventional laboratory-based diagnostic tests and new technologies, including point-of-care (POC) testing, to expand coverage, increase access, and positively impact patient management. In this review, we provide (i) a historical perspective on the evolution of HIV diagnostics (serologic and molecular) and their interplay with WHO normative guidelines, (ii) a description of the role of conventional and POC testing within the tiered laboratory diagnostic network, (iii) information on the evaluations and selection of appropriate diagnostics, (iv) a description of the quality management systems needed to ensure reliability of testing, and (v) strategies to increase access while reducing the time to return results to patients. Maintaining the central role of HIV diagnostics in programs requires periodic monitoring and optimization with quality assurance in order to inform adjustments or alignment to achieve epidemic control.
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Prevalence of HIV-1 pretreatment drug resistance among treatment naïve pregnant women in Bissau, Guinea Bissau. PLoS One 2018; 13:e0206406. [PMID: 30379960 PMCID: PMC6209301 DOI: 10.1371/journal.pone.0206406] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/14/2018] [Indexed: 12/13/2022] Open
Abstract
Background With increased access to antiretroviral treatment (ART) in sub-Saharan Africa emergence of HIV-1 pretreatment drug resistance constitutes a serious risk. This may lead to rapid virological failure in subjects initiating ART, and mother-to-child transmission despite prophylaxis. Methods Treatment-naïve pregnant women from four antenatal care clinics in Bissau, Guinea-Bissau, were enrolled from October 2016 to November 2017. Genotypic resistance testing and phylogenetic subtype analysis was performed on 48 specimens. Results Forty eight women met the survey inclusion criteria. All specimens were successfully amplified and genotyped. Specimens from five women were associated with HIV-1 drug resistance mutations. Four carried mutations exclusively linked to non-nucleoside reverse transcriptase inhibitors (NNRTIs) (K103N, K103N/S) and one carried mutations to both NNRTIs (G190S, K101E) and nucleoside reverse transcriptase inhibitors (NRTIs) (M184V). These results corresponded to 10.4% (95% CI: 4.5–22.2%), 2.1% (95% CI: 0.4–10.9%) and 0% (95% CI: 0.0–7.4%) drug resistance mutations to NNRTIs, NRTIs and protease inhibitors, respectively. HIV-1 circulating recombinant form 02AG was most commonly found, followed by HIV-1 sub-subtype A3. Subtype/CRF was not associated with drug resistance mutations. Conclusion Our study reports a 10.4% prevalence of pretreatment drug resistance to NNRTIs in HIV-1-infected pregnant women in the capital Bissau, Guinea Bissau. Since NNRTIs are part of first-line ART in the country, baseline resistance screenings or adjustment of national treatment guidelines should be considered as antiretroviral treatment programs are scaled up.
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HIV-genetic diversity and drug resistance transmission clusters in Gondar, Northern Ethiopia, 2003-2013. PLoS One 2018; 13:e0205446. [PMID: 30304061 PMCID: PMC6179264 DOI: 10.1371/journal.pone.0205446] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/25/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The HIV-1 epidemic in Ethiopia has been shown to be dominated by two phylogenetically distinct subtype C clades, the Ethiopian (C'-ET) and East African (C-EA) clades, however, little is known about the temporal dynamics of the HIV epidemic with respect to subtypes and distinct clades. Moreover, there is only limited information concerning transmission of HIV-1 drug resistance (TDR) in the country. METHODS A cross-sectional survey was conducted among young antiretroviral therapy (ART)-naïve individuals recently diagnosed with HIV infection, in Gondar, Ethiopia, 2011-2013 using the WHO recommended threshold survey. A total of 84 study participants with a median age of 22 years were enrolled. HIV-1 genotyping was performed and investigated for drug resistance in 67 individuals. Phylogenetic analyses were performed on all available HIV sequences obtained from Gondar (n = 301) which were used to define subtype C clades, temporal trends and local transmission clusters. Dating of transmission clusters was performed using BEAST. RESULT Four of 67 individuals (6.0%) carried a HIV drug resistance mutation strain, all associated with non-nucleoside reverse transcriptase inhibitors (NNRTI). Strains of the C-EA clade were most prevalent as we found no evidence of temporal changes during this time period. However, strains of the C-SA clade, prevalent in Southern Africa, have been introduced in Ethiopia, and became more abundant during the study period. The oldest Gondar transmission clusters dated back to 1980 (C-EA), 1983 (C-SA) and 1990 (C'-ET) indicating the presence of strains of different subtype C clades at about the same time point in Gondar. Moreover, some of the larger clusters dated back to the 1980s but transmissions within clusters have been ongoing up till end of the study period. Besides being associated with more sequences and larger clusters, the C-EA clade sequences were also associated with clustering of HIVDR sequences. One cluster was associated with the G190A mutation and showed onward transmissions at high rate. CONCLUSION TDR was detected in 6.0% of the sequenced samples and confirmed pervious reports that the two subtype C clades, C-EA and C'-ET, are common in Ethiopia. Moreover, the findings indicated an increased diversity in the epidemic as well as differences in transmission clusters sizes of the different clades and association with resistance mutations. These findings provide epidemiological insights not directly available using standard surveillance and may inform the adjustment of public health strategies in HIV prevention in Ethiopia.
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Etoori D, Ciglenecki I, Ndlangamandla M, Edwards CG, Jobanputra K, Pasipamire M, Maphalala G, Yang C, Zabsonre I, Kabore SM, Goiri J, Teck R, Kerschberger B. Successes and challenges in optimizing the viral load cascade to improve antiretroviral therapy adherence and rationalize second-line switches in Swaziland. J Int AIDS Soc 2018; 21:e25194. [PMID: 30350392 PMCID: PMC6198167 DOI: 10.1002/jia2.25194] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 09/26/2018] [Indexed: 11/11/2022] Open
Abstract
INTRODUCTION As antiretroviral therapy (ART) is scaled up, more patients become eligible for routine viral load (VL) monitoring, the most important tool for monitoring ART efficacy. For HIV programmes to become effective, leakages along the VL cascade need to be minimized and treatment switching needs to be optimized. However, many HIV programmes in resource-constrained settings report significant shortfalls. METHODS From a public sector HIV programme in rural Swaziland, we evaluated the VL cascade of adults (≥18 years) on ART from the time of the first elevated VL (>1000 copies/mL) between January 2013 and June 2014 to treatment switching by December 2015. We additionally described HIV drug resistance for patients with virological failure. We used descriptive statistics and Kaplan-Meier estimates to describe the different steps along the cascade and regression models to determine factors associated with outcomes. RESULTS AND DISCUSSION Of 828 patients with a first elevated VL, 252 (30.4%) did not receive any enhanced adherence counselling (EAC). Six hundred and ninety-six (84.1%) patients had a follow-up VL measurement, and the predictors of receiving a follow-up VL were being a second-line patient (adjusted hazard ratio (aHR): 0.72; p = 0.051), Hlathikhulu health zone (aHR: 0.79; p = 0.013) and having received two EAC sessions (aHR: 1.31; p = 0.023). Four hundred and ten patients (58.9%) achieved VL re-suppression. Predictors of re-suppression were age 50 to 64 (adjusted odds ratio (aOR): 2.02; p = 0.015) compared with age 18 to 34 years, being on second-line treatment (aOR: 3.29; p = 0.003) and two (aOR: 1.66; p = 0.045) or three (aOR: 1.86; p = 0.003) EAC sessions. Of 278 patients eligible to switch to second-line therapy, 120 (43.2%) had switched by the end of the study. Finally, of 155 successfully sequenced dried blood spots, 144 (92.9%) were from first-line patients. Of these, 133 (positive predictive value: 92.4%) had resistance patterns that necessitated treatment switching. CONCLUSIONS Patients on ART with high VLs were more likely to re-suppress if they received EAC. Failure to re-suppress after counselling was predictive of genotypically confirmed resistance patterns requiring treatment switching. Delays in switching were significant despite the ability of the WHO algorithm to predict treatment failure. Despite significant progress in recent years, enhanced focus on quality care along the VL cascade in resource-limited settings is crucial.
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Affiliation(s)
- David Etoori
- Research DepartmentMédecins Sans FrontièresMbabaneSwaziland
- Department of Population HealthLondon School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Iza Ciglenecki
- Research DepartmentMédecins Sans FrontièresGenevaSwitzerland
| | | | | | | | | | - Gugu Maphalala
- Swaziland National Reference Laboratory (NRL)Ministry of HealthMbabaneSwaziland
| | - Chunfu Yang
- Division of Global HIV/AIDSThe Centre for Disease ControlAtlantaGAUSA
| | | | - Serge M Kabore
- Research DepartmentMédecins Sans FrontièresMbabaneSwaziland
| | - Javier Goiri
- Research DepartmentMédecins Sans FrontièresGenevaSwitzerland
| | - Roger Teck
- Research DepartmentMédecins Sans FrontièresGenevaSwitzerland
- South African Medical UnitMédecins Sans FrontièresCape TownSouth Africa
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