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Gouissi Anguechia DH, Bouba Y, Semengue ENJ, Ka’e AC, Takou D, Ambe Chenwi C, Beloumou G, Nka AD, Basseck Wome UR, Santoro MM, Ceccherini-Silberstein F, Chatté A, Montesano C, Cappelli G, Colizzi V, Ndjolo A, Mbanya D, Ndembi N, Perno CF, Fokam J. Predictive Efficacy of Dual Therapies Combining Integrase Strand Transfer Inhibitors with Second-Generation Non-Nucleoside Reverse Transcriptase Inhibitors Following HIV-1 Treatment Failure in Cameroon: Implications for the Use of a Long-Acting Therapeutic Strategy in Low- and Middle-Income Countries. Viruses 2024; 16:1853. [PMID: 39772163 PMCID: PMC11680099 DOI: 10.3390/v16121853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Revised: 11/09/2024] [Accepted: 11/14/2024] [Indexed: 01/30/2025] Open
Abstract
Dual therapies (DT) combining integrase strand transfer inhibitors (INSTIs) with second-generation non-nucleoside reverse transcriptase inhibitors (2nd-Gen-NNRTIs) offer new possibilities for HIV treatment to improve adherence. However, drug resistance associated mutations (RAMs) to prior antiretrovirals may jeopardize the efficacy of DT. We herein describe the predicted efficacy of DT combining INSTIs + 2nd-Gen-NNRTI following treatment failure among Cameroonian patients. We genotyped the HIV-1 pol gene using Sanger sequencing and assessed acquired RAMs to NNRTIs and INSTIs in patients failing treatment from March 2019 to December 2023. Drug susceptibility was interpreted using Stanford HIVdb v9.5, and statistical analyses were performed using SPSS v22. Of 130 successfully genotyped participants (median age (IQR): 38 (27-46) years; 59.2% female), 92.3% had RAMs to NNRTIs and 1.5% to INSTIs. Prevailing RAMs were Y181C (32.3%) among NNRTIs and R263K (0.7%) among INSTIs. Among 2nd-Gen-NNRTIs, etravirine, doravirine and rilpivirine had 43.85%, 41.54% and 38.46% genotypic sensitivity, respectively. Among INSTIs, we found 97.69% efficacy for dolutegravir/bictegravir, 96.15% for cabotegravir and 92.31% for elvitegravir/raltegravir. The overall predictive efficacy of DT was lower among participants who failed 1st-Gen-NNRTI (p < 0.001); with etravirine + dolutegravir/bictegravir combination showing the highest score (43.8%). Conclusively, DT combining INSTIs + 2nd-Gen-NNRTIs might be suboptimal in the context of previous ART failure, especially with NNRTI-based treatment in low- and middle-income countries. The general data clearly indicate that without resistance testing, it is nearly impossible to use long-acting dual therapies in previously failing patients.
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Affiliation(s)
- Davy-Hyacinthe Gouissi Anguechia
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé P.O. Box 3077, Cameroon; (D.-H.G.A.); (Y.B.); (E.N.J.S.); (A.C.K.); (D.T.); (C.A.C.); (G.B.); (A.D.N.); (U.R.B.W.); (V.C.); (A.N.); (C.-F.P.)
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé P.O. Box 337, Cameroon;
| | - Yagai Bouba
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé P.O. Box 3077, Cameroon; (D.-H.G.A.); (Y.B.); (E.N.J.S.); (A.C.K.); (D.T.); (C.A.C.); (G.B.); (A.D.N.); (U.R.B.W.); (V.C.); (A.N.); (C.-F.P.)
- Faculty of Medicine, UniCamillus-Saint Camillus International University of Health Sciences, 00131 Rome, Italy
| | - Ezechiel Ngoufack Jagni Semengue
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé P.O. Box 3077, Cameroon; (D.-H.G.A.); (Y.B.); (E.N.J.S.); (A.C.K.); (D.T.); (C.A.C.); (G.B.); (A.D.N.); (U.R.B.W.); (V.C.); (A.N.); (C.-F.P.)
- National HIV Drug Resistance Working Group, Yaoundé P.O. Box 1459, Cameroon
| | - Aude Christelle Ka’e
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé P.O. Box 3077, Cameroon; (D.-H.G.A.); (Y.B.); (E.N.J.S.); (A.C.K.); (D.T.); (C.A.C.); (G.B.); (A.D.N.); (U.R.B.W.); (V.C.); (A.N.); (C.-F.P.)
| | - Désiré Takou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé P.O. Box 3077, Cameroon; (D.-H.G.A.); (Y.B.); (E.N.J.S.); (A.C.K.); (D.T.); (C.A.C.); (G.B.); (A.D.N.); (U.R.B.W.); (V.C.); (A.N.); (C.-F.P.)
- National HIV Drug Resistance Working Group, Yaoundé P.O. Box 1459, Cameroon
| | - Collins Ambe Chenwi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé P.O. Box 3077, Cameroon; (D.-H.G.A.); (Y.B.); (E.N.J.S.); (A.C.K.); (D.T.); (C.A.C.); (G.B.); (A.D.N.); (U.R.B.W.); (V.C.); (A.N.); (C.-F.P.)
- National HIV Drug Resistance Working Group, Yaoundé P.O. Box 1459, Cameroon
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (M.M.S.); (F.C.-S.)
| | - Grace Beloumou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé P.O. Box 3077, Cameroon; (D.-H.G.A.); (Y.B.); (E.N.J.S.); (A.C.K.); (D.T.); (C.A.C.); (G.B.); (A.D.N.); (U.R.B.W.); (V.C.); (A.N.); (C.-F.P.)
| | - Alex Durand Nka
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé P.O. Box 3077, Cameroon; (D.-H.G.A.); (Y.B.); (E.N.J.S.); (A.C.K.); (D.T.); (C.A.C.); (G.B.); (A.D.N.); (U.R.B.W.); (V.C.); (A.N.); (C.-F.P.)
| | - Ulrich Roland Basseck Wome
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé P.O. Box 3077, Cameroon; (D.-H.G.A.); (Y.B.); (E.N.J.S.); (A.C.K.); (D.T.); (C.A.C.); (G.B.); (A.D.N.); (U.R.B.W.); (V.C.); (A.N.); (C.-F.P.)
| | - Maria Mercedes Santoro
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (M.M.S.); (F.C.-S.)
| | | | - Adawaye Chatté
- Project Management Unit, Ministry of Health, N’djamena P.O. Box 548, Chad;
| | - Carla Montesano
- Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy;
| | - Giulia Cappelli
- National Research Council, 00185 Rome, Italy;
- LAGET, Centre Hospitalo-Universitaire (CHU), N’djamena P.O. Box 456, Chad
| | - Vittorio Colizzi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé P.O. Box 3077, Cameroon; (D.-H.G.A.); (Y.B.); (E.N.J.S.); (A.C.K.); (D.T.); (C.A.C.); (G.B.); (A.D.N.); (U.R.B.W.); (V.C.); (A.N.); (C.-F.P.)
- LAGET, Centre Hospitalo-Universitaire (CHU), N’djamena P.O. Box 456, Chad
- EUROBIOPARK and UNSECO Board for Biotechnology, University of Rome “Tor Vergata”, 00133 Rome, Italy
- Faculty of Sciences and Technology, Evangelical University of Cameroon, Bandjoun P.O. Box 127, Cameroon
| | - Alexis Ndjolo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé P.O. Box 3077, Cameroon; (D.-H.G.A.); (Y.B.); (E.N.J.S.); (A.C.K.); (D.T.); (C.A.C.); (G.B.); (A.D.N.); (U.R.B.W.); (V.C.); (A.N.); (C.-F.P.)
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé P.O. Box 337, Cameroon;
| | - Dora Mbanya
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé P.O. Box 337, Cameroon;
| | - Nicaise Ndembi
- Africa Centres for Disease Control and Prevention, Addis Ababa P.O. Box 3243, Ethiopia
- Institute of Human Virology, Baltimore, MD 21201, USA
| | - Carlo-Federico Perno
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé P.O. Box 3077, Cameroon; (D.-H.G.A.); (Y.B.); (E.N.J.S.); (A.C.K.); (D.T.); (C.A.C.); (G.B.); (A.D.N.); (U.R.B.W.); (V.C.); (A.N.); (C.-F.P.)
- Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Joseph Fokam
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé P.O. Box 3077, Cameroon; (D.-H.G.A.); (Y.B.); (E.N.J.S.); (A.C.K.); (D.T.); (C.A.C.); (G.B.); (A.D.N.); (U.R.B.W.); (V.C.); (A.N.); (C.-F.P.)
- National HIV Drug Resistance Working Group, Yaoundé P.O. Box 1459, Cameroon
- Faculty of Health Sciences, University of Buea, Buea P.O. Box 63, Cameroon
- Central Technical Group, National AIDS Control Committee, Yaoundé P.O. Box 1459, Cameroon
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Kemp SA, Kamelian K, Cuadros DF, Cheng MTK, Okango E, Hanekom W, Ndung'u T, Pillay D, Bonsall D, Wong EB, Tanser F, Siedner MJ, Gupta RK. HIV transmission dynamics and population-wide drug resistance in rural South Africa. Nat Commun 2024; 15:3644. [PMID: 38684655 PMCID: PMC11059351 DOI: 10.1038/s41467-024-47254-z] [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: 11/20/2023] [Accepted: 03/20/2024] [Indexed: 05/02/2024] Open
Abstract
Despite expanded antiretroviral therapy (ART) in South Africa, HIV-1 transmission persists. Integrase strand transfer inhibitors (INSTI) and long-acting injectables offer potential for superior viral suppression, but pre-existing drug resistance could threaten their effectiveness. In a community-based study in rural KwaZulu-Natal, prior to widespread INSTI usage, we enroled 18,025 individuals to characterise HIV-1 drug resistance and transmission networks to inform public health strategies. HIV testing and reflex viral load quantification were performed, with deep sequencing (20% variant threshold) used to detect resistance mutations. Phylogenetic and geospatial analyses characterised transmission clusters. One-third of participants were HIV-positive, with 21.7% having detectable viral loads; 62.1% of those with detectable viral loads were ART-naïve. Resistance to older reverse transcriptase (RT)-targeting drugs was found, but INSTI resistance remained low (<1%). Non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance, particularly to rilpivirine (RPV) even in ART-naïve individuals, was concerning. Twenty percent of sequenced individuals belonged to transmission clusters, with geographic analysis highlighting higher clustering in peripheral and rural areas. Our findings suggest promise for INSTI-based strategies in this setting but underscore the need for RPV resistance screening before implementing long-acting cabotegravir (CAB) + RPV. The significant clustering emphasises the importance of geographically targeted interventions to effectively curb HIV-1 transmission.
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Affiliation(s)
- Steven A Kemp
- Department of Medicine, University of Cambridge, Cambridge, UK
- Pandemic Science Institute, Big Data Institute, University of Oxford, Oxford, UK
| | - Kimia Kamelian
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Diego F Cuadros
- Digital Epidemiology Laboratory, Digital Futures, University of Cincinnati, Cincinnati, OH, USA
| | - Mark T K Cheng
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Elphas Okango
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
| | - Willem Hanekom
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
- University College London, London, UK
| | - Thumbi Ndung'u
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
- University College London, London, UK
| | | | - David Bonsall
- Pandemic Science Institute, Big Data Institute, University of Oxford, Oxford, UK
| | - Emily B Wong
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
| | - Frank Tanser
- University of Stellenbosch, Cape Town, South Africa
| | - Mark J Siedner
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- University of KwaZulu-Natal, Durban, South Africa
- Harvard University, Cambridge, MA, England
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa.
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Gupta R, Kemp S, Kamelian K, Cuadros D, Gupta R, Cheng M, Okango E, Hanekom W, Ndung'u T, Pillay D, Bonsall D, Wong E, Tanser F, Siedner M. HIV transmission dynamics and population-wide drug resistance in rural South Africa. RESEARCH SQUARE 2023:rs.3.rs-3640717. [PMID: 38076835 PMCID: PMC10705695 DOI: 10.21203/rs.3.rs-3640717/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Despite the scale-up of antiretroviral therapy (ART) in South Africa, HIV-1 incidence remains high. The anticipated use of potent integrase strand transfer inhibitors and long-acting injectables aims to enhance viral suppression at the population level and diminish transmission. Nevertheless, pre-existing drug resistance could impede the efficacy of long-acting injectable ART combinations, such as rilpivirine (an NNRTI) and cabotegravir (an INSTI). Consequently, a thorough understanding of transmission networks and geospatial distributions is vital for tailored interventions, including pre-exposure prophylaxis with long-acting injectables. However, empirical data on background resistance and transmission networks remain limited. In a community-based study in rural KwaZulu-Natal (2018-2019), prior to the widespread use of integrase inhibitor-based first-line ART, we performed HIV testing with reflex HIV-1 RNA viral load quantification on 18,025 participants. From this cohort, 6,096 (33.9%) tested positive for HIV via ELISA, with 1,323 (21.7%) exhibiting detectable viral loads (> 40 copies/mL). Of those with detectable viral loads, 62.1% were ART-naïve, and the majority of the treated were on an efavirenz + cytosine analogue + tenofovir regimen. Deep sequencing analysis, with a variant abundance threshold of 20%, revealed NRTI resistance mutations such as M184V in 2% of ART-naïve and 32% of treated individuals. Tenofovir resistance mutations K65R and K70E were found in 12% and 5% of ART-experienced individuals, respectively, and in less than 1% of ART-naïve individuals. Integrase inhibitor resistance mutations were notably infrequent (< 1%). Prevalence of pre-treatment drug resistance to NNRTIs was 10%, predominantly consisting of the K103N mutation. Among those with viraemic ART, NNRTI resistance was 50%, with rilpivirine-associated mutations observed in 9% of treated and 6% of untreated individuals. Cluster analysis revealed that 20% (205/1,050) of those sequenced were part of a cluster. We identified 171 groups with at least two linked participants; three quarters of clusters had only two individuals, and a quarter had 3-6 individuals. Integrating phylogenetic with geospatial analyses, we revealed a complex transmission network with significant clustering in specific regions, notably peripheral and rural areas. These findings derived from population scale genomic analyses are encouraging in terms of the limited resistance to DTG, but indicate that transitioning to long-acting cabotegravir + rilpivirine for transmission reduction should be accompanied by prior screening for rilpivirine resistance. Whole HIV-1 genome sequencing allowed identification of significant proportions of clusters with multiple individuals, and geospatial analyses suggesting decentralised networks can inform targeting public health interventions to effectively curb HIV-1 transmission.
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Kemp SA, Charles OJ, Derache A, Smidt W, Martin DP, Iwuji C, Adamson J, Govender K, de Oliveira T, Dabis F, Pillay D, Goldstein RA, Gupta RK. HIV-1 Evolutionary Dynamics under Nonsuppressive Antiretroviral Therapy. mBio 2022; 13:e0026922. [PMID: 35446121 PMCID: PMC9239331 DOI: 10.1128/mbio.00269-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/28/2022] [Indexed: 12/19/2022] Open
Abstract
Prolonged virologic failure on 2nd-line protease inhibitor (PI)-based antiretroviral therapy (ART) without emergence of major protease mutations is well recognized and provides an opportunity to study within-host evolution in long-term viremic individuals. Using next-generation sequencing and in silico haplotype reconstruction, we analyzed whole-genome sequences from longitudinal plasma samples of eight chronically infected HIV-1-positive individuals failing 2nd-line regimens from the French National Agency for AIDS and Viral Hepatitis Research (ANRS) 12249 Treatment as Prevention (TasP) trial. On nonsuppressive ART, there were large fluctuations in synonymous and nonsynonymous variant frequencies despite stable viremia. Reconstructed haplotypes provided evidence for selective sweeps during periods of partial adherence, and viral haplotype competition, during periods of low drug exposure. Drug resistance mutations in reverse transcriptase (RT) were used as markers of viral haplotypes in the reservoir, and their distribution over time indicated recombination. We independently observed linkage disequilibrium decay, indicative of recombination. These data highlight dramatic changes in virus population structure that occur during stable viremia under nonsuppressive ART. IMPORTANCE HIV-1 infections are most commonly initiated with a single founder virus and are characterized by extensive inter- and intraparticipant genetic diversity. However, existing literature on HIV-1 intrahost population dynamics is largely limited to untreated infections, predominantly in subtype B-infected individuals. The manuscript characterizes viral population dynamics in long-term viremic treatment-experienced individuals, which has not been previously characterized. These data are particularly relevant for understanding HIV dynamics but can also be applied to other RNA viruses. With this unique data set we propose that the virus is highly unstable, and we have found compelling evidence of HIV-1 within-host viral diversification, recombination, and haplotype competition during nonsuppressive ART.
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Affiliation(s)
- Steven A. Kemp
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
| | - Oscar J. Charles
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Anne Derache
- Africa Health Research Institute, Durban, South Africa
| | - Werner Smidt
- Africa Health Research Institute, Durban, South Africa
| | - Darren P. Martin
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Collins Iwuji
- Africa Health Research Institute, Durban, South Africa
- Research Department of Infection and Population Health, University College London, United Kingdom
| | - John Adamson
- Africa Health Research Institute, Durban, South Africa
| | | | - Tulio de Oliveira
- Africa Health Research Institute, Durban, South Africa
- KRISP - KwaZulu-Natal Research and Innovation Sequencing Platform, UKZN, Durban, South Africa
| | - Francois Dabis
- INSERM U1219-Centre Inserm Bordeaux Population Health, Université de Bordeaux, France
- Université de Bordeaux, ISPED, Centre INSERM U1219-Bordeaux Population Health, France
| | - Deenan Pillay
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Richard A. Goldstein
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Ravindra K. Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
- Africa Health Research Institute, Durban, South Africa
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McCluskey SM, Pepperrell T, Hill A, Venter WDF, Gupta RK, Siedner MJ. Adherence, resistance, and viral suppression on dolutegravir in sub-Saharan Africa: implications for the TLD era. AIDS 2021; 35:S127-S135. [PMID: 34848579 PMCID: PMC8647784 DOI: 10.1097/qad.0000000000003082] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Dolutegravir (DTG) is now a component of preferred first-line antiretroviral therapy (ART) worldwide. ADVANCE and NAMSAL were two landmark clinical trials conducted exclusively in sub-Saharan Africa, which studied the effectiveness of DTG-based first-line regimens for ART-naive individuals. In this review, we examine the data from these studies to consider the contributions of adherence and HIV drug resistance to treatment failure on DTG-based ART, as compared with efavirenz (EFV)-based ART, which has a lower genetic barrier to resistance. We also discuss the implications of virologic failure on DTG and consolidate currently available data to conclude with recommendations for virologic monitoring on DTG-based ART.
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Affiliation(s)
- Suzanne M McCluskey
- Medical Practice Evaluation Center
- Division of Infectious Diseases, Massachusetts General Hospital
- Harvard Medical School, Boston, MA, USA
| | | | - Andrew Hill
- Department of Translational Medicine, Liverpool University, Liverpool, United Kingdom
| | - Willem D F Venter
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| | - Ravindra K Gupta
- Africa Health Research Institute, Durban, South Africa
- Cambridge University, Cambridge, United Kingdom
| | - Mark J Siedner
- Medical Practice Evaluation Center
- Division of Infectious Diseases, Massachusetts General Hospital
- Harvard Medical School, Boston, MA, USA
- Africa Health Research Institute, Durban, South Africa
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Fokam J, Ngoufack Jagni Semengue E, Armenia D, Takou D, Dambaya B, Teto G, Chenwi CA, Nka AD, Beloumou GA, Ndjeyep SCD, Tchouaket MCT, Fainguem N, Sosso SM, Colizzi V, Perno CF, Ndjolo A, Ceccherini-Silberstein F, Santoro MM. High performance of integrase genotyping on diverse HIV-1 clades circulating in Cameroon: toward a successful transition to dolutegravir-based regimens in low and middle-income countries. Diagn Microbiol Infect Dis 2021; 102:115574. [PMID: 34864527 DOI: 10.1016/j.diagmicrobio.2021.115574] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/08/2021] [Accepted: 10/17/2021] [Indexed: 11/03/2022]
Abstract
A successful transition to dolutegravir-based regimens in low and middle-income countries (LMICs) requires an integrase genotyping assay effective on diverse HIV-1 clades. We herein developed and validated an in-house integrase genotyping protocol on plasma samples from 195 HIV-infected patients in Cameroon. Median [IQR] viremia was 23,574 (518-109,235) copies/mL; 128/195 participants had ≥1000copies/mL (i.e., WHO-threshold for genotypic resistance testing in LMICs). A total of 18 viral clades were detected: 72(51.1%) CRF02_AG, 38(26.9%) pure subtypes and 31(22.0%) other recombinants. Following WHO-threshold (≥1000copies/ml), sequencing performance was 82.81%(106/128). Regarding viremia, performance was 85.00%(68/80) with ≥100,000copies/mL versus 76.67%(23/30) with 10,000 to 99,999copies/mL (P = 0.22); 83.33%(15/18) with 1,000 to 99,999copies/mL (P = 0.55); 73.68%(14/19) with 500 to 999copies/mL (P = 0.19); 50%(13/26) for 200 to 499copies/mL (P = 0.0005) and 36.36%(8/22) for <200copies/mL (P < 0.0001). The developed in-house integrase-genotyping is highly effective on both pure and recombinant viral clades, even at low-level viremia. This performance underscores its usefulness in monitoring integrase-resistance mutations and supporting the scale-up of dolutegravir-based regimens in LMICs.
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Affiliation(s)
- Joseph Fokam
- Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon; Faculty of Health Sciences, University of Buea, Buea, Cameroon; Faculty of Medicine and biomedical Sciences, University of Yaounde I, Yaounde, Cameroon.
| | - Ezechiel Ngoufack Jagni Semengue
- Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon; University of Rome Tor Vergata, Rome, Italy; Evangelical University of Cameroon, Bandjoun, Cameroon.
| | - Daniele Armenia
- Saint Camillus International University of Health and Medical Sciences, Rome Italy
| | - Désiré Takou
- Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon
| | - Béatrice Dambaya
- Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon; Faculty of Sciences, University of Yaounde I, Yaounde, Cameroon
| | - Georges Teto
- Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon
| | - Collins Ambe Chenwi
- Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon; Faculty of Medicine and biomedical Sciences, University of Yaounde I, Yaounde, Cameroon
| | - Alex Durand Nka
- Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon; University of Rome Tor Vergata, Rome, Italy; Evangelical University of Cameroon, Bandjoun, Cameroon
| | - Grâce Angong Beloumou
- Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon
| | - Sandrine Claire Djupsa Ndjeyep
- Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon
| | - Michel Carlos Tommo Tchouaket
- Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon
| | - Nadine Fainguem
- Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon
| | - Samuel Martin Sosso
- Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon
| | - Vittorio Colizzi
- Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon; University of Rome Tor Vergata, Rome, Italy; Evangelical University of Cameroon, Bandjoun, Cameroon
| | - Carlo-Federico Perno
- Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon; Bambino Gesu Children's Hospital, Rome, Italy
| | - Alexis Ndjolo
- Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon; Faculty of Medicine and biomedical Sciences, University of Yaounde I, Yaounde, Cameroon
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Yendewa GA, Lakoh S, Yendewa SA, Bangura K, Tabernilla A, Patiño L, Jiba DF, Vandy AO, Massaquoi SP, Osório NS, Deen GF, Sahr F, Salata RA, Poveda E. Characterizing HIV-1 Genetic Subtypes and Drug Resistance Mutations among Children, Adolescents and Pregnant Women in Sierra Leone. Genes (Basel) 2021; 12:1314. [PMID: 34573296 PMCID: PMC8469552 DOI: 10.3390/genes12091314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/15/2021] [Accepted: 08/24/2021] [Indexed: 11/17/2022] Open
Abstract
Human immunodeficiency virus (HIV) drug resistance (HIVDR) is widespread in sub-Saharan Africa. Children and pregnant women are particularly vulnerable, and laboratory testing capacity remains limited. We, therefore, used a cross-sectional design and convenience sampling to characterize HIV subtypes and resistance-associated mutations (RAMs) in these groups in Sierra Leone. In total, 96 children (age 2-9 years, 100% ART-experienced), 47 adolescents (age 10-18 years, 100% ART-experienced), and 54 pregnant women (>18 years, 72% ART-experienced) were enrolled. Median treatment durations were 36, 84, and 3 months, respectively, while the sequencing success rates were 45%, 70%, and 59%, respectively, among children, adolescents, and pregnant women. Overall, the predominant HIV-1 subtype was CRF02_AG (87.9%, 95/108), with minority variants constituting 12%. Among children and adolescents, the most common RAMs were M184V (76.6%, n = 49/64), K103N (45.3%, n = 29/64), Y181C/V/I (28.1%, n = 18/64), T215F/Y (25.0%, n = 16/64), and V108I (18.8%, n = 12/64). Among pregnant women, the most frequent RAMs were K103N (20.6%, n = 7/34), M184V (11.8%, n = 4/34), Y181C/V/I (5.9%, n = 2/34), P225H (8.8%, n = 3/34), and K219N/E/Q/R (5.9%, n = 2/34). Protease and integrase inhibitor-RAMs were relatively few or absent. Based on the genotype susceptibility score distributions, 73%, 88%, and 14% of children, adolescents, and pregnant women, respectively, were not susceptible to all three drug components of the WHO preferred first-line regimens per 2018 guidelines. These findings suggest that routine HIVDR surveillance and access to better ART choices may improve treatment outcomes in Sierra Leone.
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Affiliation(s)
- George A. Yendewa
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA;
- Division of Infectious Diseases and HIV Medicine, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Sulaiman Lakoh
- Department of Medicine, College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone; (S.L.); (S.A.Y.); (G.F.D.); (F.S.)
- Ministry of Health and Sanitation, University of Sierra Leone Teaching Hospitals Complex, Freetown, Sierra Leone; (K.B.); (D.F.J.); (A.O.V.); (S.P.M.)
| | - Sahr A. Yendewa
- Department of Medicine, College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone; (S.L.); (S.A.Y.); (G.F.D.); (F.S.)
- Ministry of Health and Sanitation, University of Sierra Leone Teaching Hospitals Complex, Freetown, Sierra Leone; (K.B.); (D.F.J.); (A.O.V.); (S.P.M.)
| | - Khadijah Bangura
- Ministry of Health and Sanitation, University of Sierra Leone Teaching Hospitals Complex, Freetown, Sierra Leone; (K.B.); (D.F.J.); (A.O.V.); (S.P.M.)
| | - Andrés Tabernilla
- Group of Virology and Pathogenesis, Galicia Sur Health Research Institute (IIS Galicia Sur), Complexo Hospitalario Universitario de Vigo, SERGAS-UVigo, 36213 Vigo, Spain; (A.T.); (L.P.); (E.P.)
| | - Lucia Patiño
- Group of Virology and Pathogenesis, Galicia Sur Health Research Institute (IIS Galicia Sur), Complexo Hospitalario Universitario de Vigo, SERGAS-UVigo, 36213 Vigo, Spain; (A.T.); (L.P.); (E.P.)
| | - Darlinda F. Jiba
- Ministry of Health and Sanitation, University of Sierra Leone Teaching Hospitals Complex, Freetown, Sierra Leone; (K.B.); (D.F.J.); (A.O.V.); (S.P.M.)
| | - Alren O. Vandy
- Ministry of Health and Sanitation, University of Sierra Leone Teaching Hospitals Complex, Freetown, Sierra Leone; (K.B.); (D.F.J.); (A.O.V.); (S.P.M.)
| | - Samuel P. Massaquoi
- Ministry of Health and Sanitation, University of Sierra Leone Teaching Hospitals Complex, Freetown, Sierra Leone; (K.B.); (D.F.J.); (A.O.V.); (S.P.M.)
| | - Nuno S. Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal;
| | - Gibrilla F. Deen
- Department of Medicine, College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone; (S.L.); (S.A.Y.); (G.F.D.); (F.S.)
- Ministry of Health and Sanitation, University of Sierra Leone Teaching Hospitals Complex, Freetown, Sierra Leone; (K.B.); (D.F.J.); (A.O.V.); (S.P.M.)
| | - Foday Sahr
- Department of Medicine, College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone; (S.L.); (S.A.Y.); (G.F.D.); (F.S.)
| | - Robert A. Salata
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA;
- Division of Infectious Diseases and HIV Medicine, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Eva Poveda
- Group of Virology and Pathogenesis, Galicia Sur Health Research Institute (IIS Galicia Sur), Complexo Hospitalario Universitario de Vigo, SERGAS-UVigo, 36213 Vigo, Spain; (A.T.); (L.P.); (E.P.)
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Genetic characteristics of HIV-1 CRF06_cpx and CRF56_cpx strains isolated in Guangzhou, China. Arch Virol 2021; 166:2853-2857. [PMID: 34373969 DOI: 10.1007/s00705-021-05198-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/14/2021] [Indexed: 10/20/2022]
Abstract
Strains of the HIV-1 circulating recombinant forms (CRFs) 06_cpx and 56_cpx were identified for the first time in Guangzhou, China. The nearly full-length genome (NFLG) sequence was amplified, and the PCR products were sequenced by the Sanger method. The CRF06_cpx and CRF56_cpx strains were identified using the Basic Local Alignment Search Tool (BLAST) and confirmed by neighbour-joining (NJ) phylogenetic analysis. Additionally, these strains were found to contain transmitted drug resistance mutations that have little effect on first-line efavirenz (EFV)-based treatment. Genetic analysis of the detailed sequence data will provide more information on the HIV-1 epidemic in China.
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