|
1
|
Yan C, Yu F, Li M, Yang X, Sun R, Liang X, Lao X, Zhang H, Lv W, Hu Y, Lai Y, Ding Y, Zhang F. A bibliometric analysis of HIV-1 drug-resistant minority variants from 1999 to 2024. AIDS Res Ther 2025; 22:47. [PMID: 40211381 PMCID: PMC11984210 DOI: 10.1186/s12981-025-00739-3] [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: 12/07/2024] [Accepted: 03/29/2025] [Indexed: 04/14/2025] Open
Abstract
BACKGROUND The rapid initiation of antiretroviral therapy has become an international trend, necessitating lifelong medication for all HIV patients. Sanger sequencing, as the gold standard for clinically detecting HIV drug resistance, often fails to detect mutations comprising less than 20% of the total viral population. With the advancement of detection technologies, HIV-1 drug-resistant minority variants have garnered increasing attention. Few studies have analyzed the hotspots and trends in this field, which bibliometrics can effectively address. METHODS Publications related to HIV-1 DRMinVs from 1999 to 2024 were searched on the Web of Science Core Collection database. Visual knowledge maps and bibliometric analyses were generated using VOSviewer and Bibliometrix. RESULTS In total, 289 publications concerning HIV-1 drug-resistant minority variants were identified from 1999 to 2024, demonstrating a steady increase in publication output over the years. Although developed countries, led by the United States, are the main contributors, 9.57% and 2.48% of the research from the top five publishing countries focus on populations in Africa and other developing countries, respectively. Most contributing institutions are universities and public health organizations, with the University of Washington having the highest publication output. The Journal of Antimicrobial Chemotherapy holds the highest prominence among journals in this domain. The main hotspots include "drug classes," "drug resistance surveillance," "mother-to-child transmission," "treatment outcomes," and "targets of HIV-1 drug resistance testing," And we found several noteworthy shifts in research trends in HIV-1 drug-resistant minority variants studies, including changes in drug resistance testing technologies, the primary study population, and drug classes. CONCLUSIONS This is the first bibliometric analysis of publications related to HIV-1 DRMinVs from 1999 to 2024. We analyzed the key research contributions across countries, institutions and journals. Based on keyword co-occurrence and cluster analysis, we identified several noteworthy shifts in research trends in HIV-1 DRMinVs studies, including changes in drug resistance testing technologies, the primary study population, and drug classes.
Collapse
Affiliation(s)
- Chang Yan
- Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
| | - Fengting Yu
- Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Medical School, University of Chinese Academy of Sciences, Beijing, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
| | - Mengying Li
- Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Medical School, University of Chinese Academy of Sciences, Beijing, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
| | - Xiaojie Yang
- Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
| | - Rui Sun
- Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
| | - Xuelei Liang
- Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
| | - Xiaojie Lao
- Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
| | - Hanxi Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- WHO Collaborating Centre for Comprehensive Management of HIV Treatment and Care, Beijing Ditan Hospital Capital Medical University, Beijing, China
| | - Wenhao Lv
- Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
| | - Ying Hu
- Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
| | - Yuan Lai
- Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
| | - Yi Ding
- Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
| | - Fujie Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China.
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China.
| |
Collapse
|
|
2
|
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.
Collapse
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
| |
Collapse
|
|
3
|
Branda F, Giovanetti M, Sernicola L, Farcomeni S, Ciccozzi M, Borsetti A. Comprehensive Analysis of HIV-1 Integrase Resistance-Related Mutations in African Countries. Pathogens 2024; 13:102. [PMID: 38392840 PMCID: PMC10892843 DOI: 10.3390/pathogens13020102] [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: 12/30/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
The growing emergence of non-nucleoside reverse transcriptase inhibitor (NNRTI) HIV drug resistance in sub-Saharan Africa (SSA) led to the World Health Organization (WHO) recommending, in 2018, a transition to dolutegravir (DTG) as a first-line antiretroviral therapy (ART) in SSA. The broad HIV-1 genetic diversity in SSA could shape DTG effectiveness and the pattern of drug resistance mutations (DRMs) in this region. This study evaluated HIV-1 integrase (IN) DRMs and conserved regions among published groups M, N, O, and P HIV-1 sequences spanning forty years of the HIV epidemic during the transition of DTG-based ART. Overall, we found low levels of integrase strand transfer inhibitor (INSTI)-DRMs (<1%) across HIV groups between the years 1983 and 2023; however, it was unexpected to detect DRMs at statistically significantly higher frequencies in pre-INSTI (1983-2007) than in the INSTI (2008-2023) era. The variability of accessory INSTI-DRMs depended on the HIV subtypes, with implications for susceptibility to DTG. Our findings provide new perspectives on the molecular epidemiology and drug resistance profiles of INSTIs in SSA, emphasizing the need for ongoing surveillance and customized treatment approaches to address the continent's varied HIV subtypes and changing resistance patterns.
Collapse
Affiliation(s)
- Francesco Branda
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy; (F.B.); (M.C.)
| | - Marta Giovanetti
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Rome, Italy;
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, Brazil
- Climate Amplified Diseases and Epidemics (CLIMADE), Brasilia 70070-130, Brazil
| | - Leonardo Sernicola
- National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, 00161 Rome, Italy; (L.S.); (S.F.)
| | - Stefania Farcomeni
- National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, 00161 Rome, Italy; (L.S.); (S.F.)
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy; (F.B.); (M.C.)
| | - Alessandra Borsetti
- National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, 00161 Rome, Italy; (L.S.); (S.F.)
| |
Collapse
|
|
4
|
Loosli T, Hossmann S, Ingle SM, Okhai H, Kusejko K, Mouton J, Bellecave P, van Sighem A, Stecher M, d'Arminio Monforte A, Gill MJ, Sabin CA, Maartens G, Günthard HF, Sterne JAC, Lessells R, Egger M, Kouyos RD. HIV-1 drug resistance in people on dolutegravir-based antiretroviral therapy: a collaborative cohort analysis. Lancet HIV 2023; 10:e733-e741. [PMID: 37832567 PMCID: PMC10913014 DOI: 10.1016/s2352-3018(23)00228-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 08/08/2023] [Accepted: 08/25/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND The widespread use of the integrase strand transfer inhibitor (INSTI) dolutegravir in first-line and second-line antiretroviral therapy (ART) might facilitate emerging resistance. The DTG RESIST study combined data from HIV cohorts to examine patterns of drug resistance mutations (DRMs) and identify risk factors for dolutegravir resistance. METHODS We included cohorts with INSTI resistance data from two collaborations (ART Cohort Collaboration, International epidemiology Databases to Evaluate AIDS in Southern Africa), and the UK Collaborative HIV Cohort. Eight cohorts from Canada, France, Germany, Italy, the Netherlands, Switzerland, South Africa, and the UK contributed data on individuals who were viraemic on dolutegravir-based ART and underwent genotypic resistance testing. Individuals with unknown dolutegravir initiation date were excluded. Resistance levels were categorised using the Stanford algorithm. We identified risk factors for resistance using mixed-effects ordinal logistic regression models. FINDINGS We included 599 people with genotypic resistance testing on dolutegravir-based ART between May 22, 2013, and Dec 20, 2021. Most had HIV-1 subtype B (n=351, 59%), a third had been exposed to first-generation INSTIs (n=193, 32%), 70 (12%) were on dolutegravir dual therapy, and 18 (3%) were on dolutegravir monotherapy. INSTI DRMs were detected in 86 (14%) individuals; 20 (3%) had more than one mutation. Most (n=563, 94%) were susceptible to dolutegravir, seven (1%) had potential low, six (1%) low, 17 (3%) intermediate, and six (1%) high-level dolutegravir resistance. The risk of dolutegravir resistance was higher on dolutegravir monotherapy (adjusted odds ratio [aOR] 34·1, 95% CI 9·93-117) and dolutegravir plus lamivudine dual therapy (aOR 9·21, 2·20-38·6) compared with combination ART, and in the presence of potential low or low (aOR 5·23, 1·32-20·7) or intermediate or high-level (aOR 13·4, 4·55-39·7) nucleoside reverse transcriptase inhibitor (NRTI) resistance. INTERPRETATION Among people with viraemia on dolutegravir-based ART, INSTI DRMs and dolutegravir resistance were rare. NRTI resistance substantially increased the risk of dolutegravir resistance, which is of concern, notably in resource-limited settings. Monitoring is important to prevent resistance at the individual and population level and ensure the long-term sustainability of ART. FUNDING US National Institutes of Health, Swiss National Science Foundation.
Collapse
Affiliation(s)
- Tom Loosli
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Stefanie Hossmann
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
| | - Suzanne M Ingle
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hajra Okhai
- Institute for Global Health, University College London, London, UK
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Johannes Mouton
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Melanie Stecher
- German Center for Infection Research (DZIF), Partner-Site Cologne-Bonn, Cologne, Germany; Department I of Internal Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | | | - M John Gill
- Southern Alberta Clinic, Calgary, AB, Canada; Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Caroline A Sabin
- Institute for Global Health, University College London, London, UK
| | - Gary Maartens
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jonathan A C Sterne
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Matthias Egger
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Centre for Infectious Disease Epidemiology and Research, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
|
5
|
Loosli T, Hossmann S, Ingle SM, Okhai H, Kusejko K, Mouton J, Bellecave P, van Sighem A, Stecher M, d’Arminio Monforte A, Gill MJ, Sabin CA, Maartens G, Günthard HF, Sterne JAC, Lessells R, Egger M, Kouyos R. sHIV-1 drug resistance in people on dolutegravir-based ART: Collaborative analysis of cohort studies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.05.23288183. [PMID: 37066200 PMCID: PMC10104228 DOI: 10.1101/2023.04.05.23288183] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Background The widespread use of the integrase strand transfer inhibitor (INSTI) dolutegravir (DTG) in first- and second-line antiretroviral therapy (ART) may facilitate emerging resistance. We combined data from HIV cohorts to examine patterns of drug resistance mutations (DRMs) and identify risk factors for DTG resistance. Methods Eight cohorts from Canada, Europe, and South Africa contributed data on individuals with genotypic resistance testing on DTG-based ART. Resistance levels were categorised using the Stanford algorithm. We identified risk factors for resistance using mixed-effects ordinal logistic regression models. Results We included 750 people with genotypic resistance testing on DTG-based ART between 2013 and 2022. Most had HIV subtype B (N=444, 59·2%) and were treatment-experienced; 134 (17.9%) were on DTG dual and 19 (2.5%) on DTG monotherapy. INSTI DRMs were detected in 100 (13·3%) individuals; 21 (2·8%) had more than one mutation. Most (N=713, 95·1%) were susceptible to DTG, 8 (1·1%) had potential-low, 5 (0·7%) low, 18 (2·4%) intermediate and 6 (0·8%) high-level DTG resistance. The risk of DTG resistance was higher on DTG monotherapy (adjusted odds ratio (aOR) 37·25, 95% CI 11·17 to 124·2) and DTG lamivudine dual therapy (aOR 6·59, 95% CI 1·70 to 25·55) compared to combination ART, and higher in the presence of potential-low/low (aOR 4.62, 95% CI 1.24 to 17.2) or intermediate/high-level (aOR 7·01, 95% CI 2·52 to 19·48) nucleoside reverse transcriptase inhibitors (NRTI) resistance. Viral load on DTG showed a trend towards increased DTG resistance (aOR 1·42, 95% CI 0·92 to 2·19 per standard deviation of log10 area under the viral load curve). Interpretation Among people experiencing virological failure on DTG-based ART, INSTI DRMs were uncommon, and DTG resistance was rare. DTG monotherapy and NRTI resistance substantially increased the risk for DTG resistance, which is of concern, notably in resource-limited settings.
Collapse
Affiliation(s)
- Tom Loosli
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Stefanie Hossmann
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Switzerland
| | - Suzanne M. Ingle
- Population Health Sciences, Bristol Medical School, University of Bristol, UK
| | - Hajra Okhai
- Institute for Global Health, University College London, UK
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Johannes Mouton
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Melanie Stecher
- German Center for Infection Research (DZIF), Partner-Site Cologne-Bonn, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf
| | - Antonella d’Arminio Monforte
- Italian Cohort Naive Antiretrovirals, (ICONA) L’Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Milano, Italy
| | - M. John Gill
- Southern Alberta Clinic, Calgary, AB, Canada
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Gary Maartens
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Huldrych F. Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Richard Lessells
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Centre for Infectious Disease Epidemiology and Research, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Matthias Egger
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Switzerland
- Population Health Sciences, Bristol Medical School, University of Bristol, UK
- Centre for Infectious Disease Epidemiology and Research, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Roger Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
|
6
|
Fofana DB, Diarra H, Guindo I, Savadogo MK, d’Almeida M, Diallo FI, Baldé A, Soulié C, Kone A, Marcelin AG, Maiga AI, Lambert-Niclot S, Maiga M, McFall S, Hawkins CA, Murphy RL, Sylla M, Katlama C, Holl JL, Calvez V, Morand-Joubert L. Prevalence of HIV-1 Natural Polymorphisms and Integrase-Resistance-Associated Mutations in African Children. Viruses 2023; 15:v15020546. [PMID: 36851760 PMCID: PMC9964382 DOI: 10.3390/v15020546] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/05/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023] Open
Abstract
Integrase inhibitors (INIs) are a potent option for HIV treatment. Limited data exist on INI resistance in West Africa, particularly in children living with HIV/AIDS. We determined the prevalence of integrase gene polymorphisms and the frequency of naturally occurring amino acid (aa) substitutions at positions associated with INI resistance. Dried blood spot (DBS) samples were obtained from one hundred and seven (107) HIV-1-infected children aged less than 15 years old in two West African countries, Benin and Mali. All children were naïve to INI treatment, 56 were naïve to anti-retroviral therapy (ART), and 51 had received ART. Genetic sequencing of HIV integrase was successful in 75 samples. The aa changes at integrase positions associated with INI resistance were examined according to the Stanford HIV Genotypic Resistance database. The median ages were 2.6 and 10 years for ART-naïve and -treated children, respectively. The most common subtypes observed were CRF02_AG (74.7%) followed by CRF06_cpx (20%). No major INI-resistance mutations at positions 66, 92, 121, 143, 147, 148, 155, and 263 were detected. The most prevalent INI accessory resistance mutations were: L74I/M (14/75, 18.6%) followed by E157Q (8/75, 10.6%), G163E/N/T/Q (5/75, 6.6%), Q95A/H/P (2/75, 2.6%), and T97A (4/75, 5.3%). Other substitutions observed were M50I/L/P, H51E/P/S/Q, I72V, T112V, V201I, and T206S. Polymorphisms at positions which may influence the genetic barrier and/or drive the selection of specific INI-resistance pathways were detected. However, no transmitted drug resistance (TDR) to INI was detected among samples of INI-naïve patients. These findings support the use of this treatment class for children with HIV-1, particularly in West Africa.
Collapse
Affiliation(s)
- Djeneba B. Fofana
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-Hôpitaux de Paris (AP-HP), Saint-Antoine Hospital, F-75012 Paris, France
- Correspondence:
| | - Houdou Diarra
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Ibrahima Guindo
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | | | - Marceline d’Almeida
- Département Mère Enfant, Faculté Des Sciences De La Santé, Université Abomey-Calavi, CNHU—HKM, Cotonou 229, Benin
| | - Fatoumata I. Diallo
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Aliou Baldé
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
| | - Cathia Soulié
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-HÔpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, F-75013 Paris, France
| | - Amadou Kone
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-HÔpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, F-75013 Paris, France
| | - Almoustapha I. Maiga
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Sidonie Lambert-Niclot
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-Hôpitaux de Paris (AP-HP), Saint-Antoine Hospital, F-75012 Paris, France
| | - Mamoudou Maiga
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Sally McFall
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Claudia A. Hawkins
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Robert L. Murphy
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Mariam Sylla
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Christine Katlama
- Service des Maladies Infectieuses, Hôpital Pitié-Salpêtrière APHP, F-75013 Paris, France
| | - Jane L. Holl
- Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-HÔpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, F-75013 Paris, France
| | - Laurence Morand-Joubert
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-Hôpitaux de Paris (AP-HP), Saint-Antoine Hospital, F-75012 Paris, France
| |
Collapse
|
|
7
|
Henerico S, Lyimo E, Makubi AN, Magesa D, Desderius B, Mueller A, Changalucha J, Kalluvya SE, Van Zyl G, Preiser W, Mshana SE, Kasang C. Primary resistance against integrase strand transfer inhibitors in integrase strand transfer inhibitor-naive patients failing first- and second-line ART in Tanzania. J Antimicrob Chemother 2022; 77:3138-3143. [PMID: 36101479 PMCID: PMC9616539 DOI: 10.1093/jac/dkac295] [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: 04/27/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
INTRODUCTION Sub-Saharan African countries are introducing integrase strand transfer inhibitors (INSTIs) in their ART programmes as the preferred first-line regimen, and dolutegravir is the INSTI of choice due to its potency, tolerability and high genetic barrier to resistance. Dolutegravir was introduced into the first-line ART regimen in Tanzania in 2019. However, there is a paucity of data on the occurrence of mutations in HIV lineages circulating in Tanzania. This study aimed to determine the prevalence of INSTI primary resistance mutations in Tanzanian patients exposed to ART but not INSTIs. METHODS Plasma samples from 50 INSTI-naive patients failing first- or second-line ART [median (IQR) age: 40 (21.93-46.41) years; 68% women] were subjected to Sanger sequencing of the HIV integrase gene. Participants had been on ART for a median (IQR) duration of 7.32 (4.73-9.29) years, with 80% and 20% failing first- and second-line ART, respectively. RESULTS No major INSTI mutations were found, but 2 (4%) participants had the accessory mutation T97A. Using the REGA HIV-1 subtyping tool, HIV subtype A1 (53.1%) was found to be dominant, followed by subtypes C (30.6%) and D (16.3%). CONCLUSIONS This study found no current evidence for transmitted resistance against INSTIs among unexposed patients failing ART and supports the scale-up of INSTI-based regimens. However, the presence of accessory mutations calls for the surveillance of INSTI resistance mutations to ensure that the anticipated long-term desired outcomes are achieved.
Collapse
Affiliation(s)
| | - Eric Lyimo
- National Institute for Medical Research, Mwanza Research Centre, Mwanza, United Republic of Tanzania
| | - Abel N Makubi
- The Ministry of Health, Dodoma, United Republic of Tanzania
| | - Daniel Magesa
- Centers for Disease Control and Prevention, United Republic of Tanzania branch, Dar es Salaam, United Republic of Tanzania
| | - Bernard Desderius
- Bugando Medical Centre, Mwanza, United Republic of Tanzania
- Catholic University of Health and Allied Sciences-Bugando, Mwanza, United Republic of Tanzania
| | - Andreas Mueller
- Klinikum Wuerzburg Mitte gGmbH, Missioklinik, Department of Tropical Medicine, Würzburg, Germany
| | - John Changalucha
- National Institute for Medical Research, Mwanza Research Centre, Mwanza, United Republic of Tanzania
| | | | - Gert Van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University/National Health Laboratory Service (NHLS) Tygerberg, Cape Town, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University/National Health Laboratory Service (NHLS) Tygerberg, Cape Town, South Africa
| | - Stephen E Mshana
- Catholic University of Health and Allied Sciences-Bugando, Mwanza, United Republic of Tanzania
| | - Christa Kasang
- German Leprosy and Tuberculosis Relief Association (DAHW), Würzburg, Germany
- Medmissio, Würzburg, Germany
| |
Collapse
|
|
8
|
OUP accepted manuscript. J Antimicrob Chemother 2022; 77:979-988. [DOI: 10.1093/jac/dkab498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 12/20/2021] [Indexed: 11/15/2022] Open
|
|
9
|
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.
Collapse
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
| |
Collapse
|
|
10
|
Semengue ENJ, Armenia D, Inzaule S, Santoro MM, Dambaya B, Takou D, Teto G, Nka AD, Yagai B, Fabeni L, Chenwi C, Angong Beloumou G, Djupsa Ndjeyep SC, Colizzi V, Perno CF, Ceccherini-Silberstein F, Fokam J. Baseline integrase drug resistance mutations and conserved regions across HIV-1 clades in Cameroon: implications for transition to dolutegravir in resource-limited settings. J Antimicrob Chemother 2021; 76:1277-1285. [PMID: 33501504 DOI: 10.1093/jac/dkab004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/28/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Transition to dolutegravir-based regimens in resource-limited settings (RLS) requires prior understanding of HIV-1 integrase variants and conserved regions. Therefore, we evaluated integrase drug resistance mutations (DRMs) and conserved regions amongst integrase strand transfer inhibitor (INSTI)-naive patients harbouring diverse HIV-1 clades in Cameroon. METHODS A cross-sectional study was conducted amongst 918 INSTI-naive patients from Cameroon (89 ART-naive and 829 ART-experienced patients). HIV-1 sequences were interpreted regarding INSTI-DRMs using the Stanford HIVdb v8.9-1 and the 2019 IAS-USA list. Amino acid positions with <1% variability were considered as highly conserved. Subtyping was performed by phylogeny. RESULTS Overall prevalence (95% CI) of INSTI-DRMs was 0.8% (0.4-1.7), with 0.0% (0.0-4.0) amongst ART-naive versus 0.9% (0.5-1.9) amongst ART-experienced patients; P = 0.44. Accessory mutations (95% CI) were found in 33.8% (30.9-37.0), with 38.2% (28.1-49.1) amongst ART-naive versus 33.4% (30.4-36.7) amongst ART-experienced patients; P = 0.21. Of 288 HIV-1 integrase amino acid positions, 58.3% were highly conserved across subtypes in the following major regions: V75-G82, E85-P90, H114-G118, K127-W132, E138-G149, Q168-L172, T174-V180, W235-A239 and L241-D253. Wide genetic diversity was found (37 clades), including groups M (92.3%), N (1.4%), O (6.2%) and P (0.1%). Amongst group M, CRF02_AG was predominant (47.4%), with a significantly higher frequency (95% CI) of accessory mutations compared with non-AG [41.4% (36.8-46.0) versus 27.1% (23.3-31.2) respectively; P < 0.001]. CONCLUSIONS The low baseline of INSTI-DRMs (<1%) in Cameroon suggests effectiveness of dolutegravir-based regimens. In spite of high conservation across clades, the variability of accessory mutations between major circulating strains underscores the need for monitoring the selection of INSTI-DRMs while scaling up dolutegravir-based regimens in RLS.
Collapse
Affiliation(s)
- Ezechiel Ngoufack Jagni Semengue
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Evangelical University of Cameroon, Bandjoun, Cameroon
| | - Daniele Armenia
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Saint Camillus International University of Health and Medical Sciences, Rome, Italy
| | - Seth Inzaule
- Department of Global Health, Academic Medical Center of the University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | | | - Béatrice Dambaya
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Désiré Takou
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Georges Teto
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Alex Durand Nka
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Evangelical University of Cameroon, Bandjoun, Cameroon
| | - Bouba Yagai
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani" - IRCCS, Rome, Italy
| | - Collins Chenwi
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Grâce Angong Beloumou
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Sandrine Claire Djupsa Ndjeyep
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Vittorio Colizzi
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Evangelical University of Cameroon, Bandjoun, Cameroon
| | - Carlo-Federico Perno
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Bambino Gesu Children's Hospital, IRCCS, Rome, Italy
| | | | - Joseph Fokam
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon.,National HIV Drug Resistance Working Group, Ministry of Public Health, Cameroon.,Faculty of Health Sciences, University of Buea, Buea, Cameroon
| |
Collapse
|
|
11
|
Mbisa JL, Ledesma J, Kirwan P, Bibby DF, Manso C, Skingsley A, Murphy G, Brown A, Dunn DT, Delpech V, Geretti AM. Surveillance of HIV-1 transmitted integrase strand transfer inhibitor resistance in the UK. J Antimicrob Chemother 2021; 75:3311-3318. [PMID: 32728703 PMCID: PMC7566560 DOI: 10.1093/jac/dkaa309] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022] Open
Abstract
Background HIV treatment guidelines have traditionally recommended that all HIV-positive individuals are tested for evidence of drug resistance prior to starting ART. Testing for resistance to reverse transcriptase inhibitors and PIs is well established in routine care. However, testing for integrase strand transfer inhibitor (InSTI) resistance is less consistent. Objectives To inform treatment guidelines by determining the prevalence of InSTI resistance in a national cohort of recently infected individuals. Patients and methods Recent (within 4 months) HIV-1 infections were identified using a Recent Infection Testing Algorithm of new HIV-1 diagnoses in the UK. Resistance-associated mutations (RAMs) in integrase, protease and reverse transcriptase were detected by ultradeep sequencing, which allows for the sensitive estimation of the frequency of each resistant variant in a sample. Results The analysis included 655 randomly selected individuals (median age = 33 years, 95% male, 83% MSM, 78% white) sampled in the period 2014 to 2016 and determined to have a recent infection. These comprised 320, 138 and 197 samples from 2014, 2015 and 2016, respectively. None of the samples had major InSTI RAMs occurring at high variant frequency (≥20%). A subset (25/640, 3.9%) had major InSTI RAMs occurring only as low-frequency variants (2%–20%). In contrast, 47/588 (8.0%) had major reverse transcriptase inhibitor and PI RAMs at high frequency. Conclusions Between 2014 and 2016, major InSTI RAMs were uncommon in adults with recent HIV-1 infection, only occurring as low-frequency variants of doubtful clinical significance. Continued surveillance of newly diagnosed patients for evidence of transmitted InSTI resistance is recommended to inform clinical practice.
Collapse
Affiliation(s)
- Jean L Mbisa
- National Infection Service, Public Health England, London, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, UK
| | - Juan Ledesma
- National Infection Service, Public Health England, London, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, UK
| | - Peter Kirwan
- National Infection Service, Public Health England, London, UK
| | - David F Bibby
- National Infection Service, Public Health England, London, UK
| | - Carmen Manso
- National Infection Service, Public Health England, London, UK
| | | | - Gary Murphy
- National Infection Service, Public Health England, London, UK
| | - Alison Brown
- National Infection Service, Public Health England, London, UK
| | - David T Dunn
- Institute for Global Health, University College London, London, UK
| | - Valerie Delpech
- National Infection Service, Public Health England, London, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, UK
| | - Anna Maria Geretti
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| |
Collapse
|
|
12
|
Chehadeh W, Albaksami O, Al-Shammari S. Virologic failure after 48 weeks of raltegravir-based regimen in low HIV-1 incidence setting. Antivir Chem Chemother 2021; 28:2040206620927908. [PMID: 32434393 PMCID: PMC7241205 DOI: 10.1177/2040206620927908] [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] [Indexed: 11/24/2022] Open
Abstract
Background With the advent of next generation integrase strand transfer inhibitors, the rates of virologic failure in treated subjects are expected to decrease. In this study, we analyzed the mutation patterns leading to virologic failure before and after starting integrase strand transfer inhibitor-based regimen as first-line or salvage therapy. Methods Between 2016 and 2019, blood samples were received from 258 patients with HIV-1 infection. Plasma HIV-1 RNA concentrations, and pol gene sequences were determined at baseline, and 16–48 weeks of treatment with integrase strand transfer inhibitor-based regimen. Only patients who did not achieve viral suppression at 48 weeks of integrase strand transfer inhibitor-based treatment were eligible for the current study. Results Virologic failure was observed in seven patients on raltegravir-based regimen. All patients with virologic failure but one were infected with CRF01_AE virus subtype. Raltegravir based-regimen was offered as first-line therapy for four patients, and as salvage therapy for three patients. M184V mutation associated with high level resistance to lamivudine and emtricitabine was detected in six out of seven patients. Primary mutations (Y143C, N155H, T66I, G118R, E138K) conferring high level resistance to raltegravir were detected in only three patients. Pre-existing polymorphic integrase mutation (T97A) was detected in two patients. Furthermore, two patients reported low adherence to treatment. Conclusions Emergence of primary mutations in the integrase gene can account for virologic failure in less than half of patients on raltegravir-based regimen. Low adherence to treatment, pre-existing accessory mutations, and resistance to reverse transcriptase inhibitors may have some role in virologic outcome.
Collapse
Affiliation(s)
- Wassim Chehadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Osama Albaksami
- Infectious Diseases Hospital, Ministry of Health, Safat, Kuwait
| | - Shaikhah Al-Shammari
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| |
Collapse
|
|
13
|
Borghetti A, Giacomelli A, Borghi V, Ciccullo A, Dusina A, Fabbiani M, Rusconi S, Zazzi M, Mussini C, Di Giambenedetto S. Nucleoside Reverse-Transcriptase Inhibitor Resistance Mutations Predict Virological Failure in Human Immunodeficiency Virus-Positive Patients During Lamivudine Plus Dolutegravir Maintenance Therapy in Clinical Practice. Open Forum Infect Dis 2021; 8:ofab103. [PMID: 34327247 PMCID: PMC8314943 DOI: 10.1093/ofid/ofab103] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/03/2021] [Indexed: 11/13/2022] Open
Abstract
The TANGO trial demonstrated the efficacy of lamivudine plus dolutegravir in virologically suppressed patients without previous virological failures (VFs). In this dataset from clinical practice investigating the impact of past nucleoside reverse-transcriptase inhibitor resistance on this strategy, the combination of M184V/I plus at least 1 thymidine analog-associated mutation significantly increased the risk of VF.
Collapse
Affiliation(s)
- Alberto Borghetti
- Fondazione Policlinico Universitario A. Gemelli IRCCS, UOC Malattie Infettive, Roma, Italia
| | - Andrea Giacomelli
- Luigi Sacco Department of Biomedical and Clinical Sciences, University of Milan, Italy.,Department of Infectious Diseases, ASST Fatebenefratelli-Sacco, Milan, Italy
| | - Vanni Borghi
- Clinica Malattie Infettive e Tropicali, Azienda Ospedaliero Universitaria di Modena, Modena, Italia
| | - Arturo Ciccullo
- Dipartimento di Sicurezza e Bioetica Sezione Malattie Infettive, Università Cattolica del Sacro Cuore, Roma, Italia
| | - Alex Dusina
- Dipartimento di Sicurezza e Bioetica Sezione Malattie Infettive, Università Cattolica del Sacro Cuore, Roma, Italia
| | - Massimiliano Fabbiani
- Tropical and Infectious Diseases Unit, Department of Specialized and Internal Medicine, University Hospital of Siena, Siena, Italy
| | - Stefano Rusconi
- Luigi Sacco Department of Biomedical and Clinical Sciences, University of Milan, Italy.,Department of Infectious Diseases, ASST Fatebenefratelli-Sacco, Milan, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Cristina Mussini
- Clinica Malattie Infettive e Tropicali, Azienda Ospedaliero Universitaria di Modena, Modena, Italia
| | - Simona Di Giambenedetto
- Fondazione Policlinico Universitario A. Gemelli IRCCS, UOC Malattie Infettive, Roma, Italia.,Dipartimento di Sicurezza e Bioetica Sezione Malattie Infettive, Università Cattolica del Sacro Cuore, Roma, Italia
| |
Collapse
|
|
14
|
Pyngottu A, Scherrer AU, Kouyos R, Huber M, Hirsch H, Perreau M, Yerly S, Calmy A, Cavassini M, Stöckle M, Furrer H, Vernazza P, Bernasconi E, Günthard HF. Predictors of virological failure and time to viral suppression of first line integrase inhibitor based antiretroviral treatment. Clin Infect Dis 2020; 73:e2134-e2141. [PMID: 33095848 PMCID: PMC8492202 DOI: 10.1093/cid/ciaa1614] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/19/2020] [Indexed: 11/12/2022] Open
Abstract
Background Integrase strand transfer inhibitors (InSTIs) are recommended for first-line treatment of persons with human immunodeficiency virus (HIV). We identified risk factors, including baseline minor InSTI resistance mutations, for treatment failure of InSTI-based regimens. Methods We studied time-to-treatment failure and time to viral suppression among 1419 drug-naive patients in the Swiss HIV Cohort Study. We performed Cox regression models adjusted for demographic factors, baseline HIV RNA/CD4 cell counts, AIDS-defining events, and the type of InSTI. In 646 patients with a baseline genotypic resistance test of the integrase, we studied the impact of minor integrase resistance mutations. Results We observed 121 virological failures during 18 447 person-years of follow-up. A baseline viral load ≥100 000 copies/mL (multivariable hazard ratio [mHR], 2.2; 95% confidence interval [CI], 1.3–3.6) and an AIDS-defining event (mHR, 1.8; 95% CI. 1.1–3.0) were associated with treatment failure. CD4 counts between 200 and 500 cells/µL (mHR, 0.5; 95% CI, .3–.8) and >500 cells/µL (mHR, 0.4; 95% CI, .2–.7) were protective. Time to suppression was shorter in lower viral load strata (mHR, 0.7; 95% CI, .6–.8) and in dolutegravir-based therapy (mHR, 1.2; 95% CI, 1.0–1.4). Minor resistance mutations were found at baseline in 104 of 646 (16%) patients with no effect on treatment outcome. Conclusions Factors associated with treatment failure on InSTI-based first-line regimen remained similar to those of older treatments, in particular high viral load and low CD4 counts.
Collapse
Affiliation(s)
- Ashima Pyngottu
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra U Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Hans Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Sabine Yerly
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Alexandra Calmy
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Marcel Stöckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Pietro Vernazza
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St. Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | |
Collapse
|
|
15
|
Structural Comparison of Diverse HIV-1 Subtypes using Molecular Modelling and Docking Analyses of Integrase Inhibitors. Viruses 2020; 12:v12090936. [PMID: 32858802 PMCID: PMC7552036 DOI: 10.3390/v12090936] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/27/2020] [Accepted: 08/05/2020] [Indexed: 12/27/2022] Open
Abstract
The process of viral integration into the host genome is an essential step of the HIV-1 life cycle. The viral integrase (IN) enzyme catalyzes integration. IN is an ideal therapeutic enzyme targeted by several drugs; raltegravir (RAL), elvitegravir (EVG), dolutegravir (DTG), and bictegravir (BIC) having been approved by the USA Food and Drug Administration (FDA). Due to high HIV-1 diversity, it is not well understood how specific naturally occurring polymorphisms (NOPs) in IN may affect the structure/function and binding affinity of integrase strand transfer inhibitors (INSTIs). We applied computational methods of molecular modelling and docking to analyze the effect of NOPs on the full-length IN structure and INSTI binding. We identified 13 NOPs within the Cameroonian-derived CRF02_AG IN sequences and further identified 17 NOPs within HIV-1C South African sequences. The NOPs in the IN structures did not show any differences in INSTI binding affinity. However, linear regression analysis revealed a positive correlation between the Ki and EC50 values for DTG and BIC as strong inhibitors of HIV-1 IN subtypes. All INSTIs are clinically effective against diverse HIV-1 strains from INSTI treatment-naïve populations. This study supports the use of second-generation INSTIs such as DTG and BIC as part of first-line combination antiretroviral therapy (cART) regimens, due to a stronger genetic barrier to the emergence of drug resistance.
Collapse
|
|
16
|
Mikasi SG, Gichana JO, Van der Walt C, Brado D, Obasa AE, Njenda D, Messembe M, Lyonga E, Assoumou O, Cloete R, Ikomey GM, Jacobs GB. HIV-1 Integrase Diversity and Resistance-Associated Mutations and Polymorphisms Among Integrase Strand Transfer Inhibitor-Naive HIV-1 Patients from Cameroon. AIDS Res Hum Retroviruses 2020; 36:450-455. [PMID: 31830799 DOI: 10.1089/aid.2019.0264] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The World Health Organization (WHO) has put forth recommendations for the use of integrase (IN) strand transfer inhibitors (INSTIs) to be part of the first-line combination antiretroviral therapy regimen to treat HIV infections. The knowledge of pretreatment drug resistance against INSTIs is still scarce in resource-limited settings (RLS). We characterized the integrase gene to identify resistance-associated mutations (RAMs) in 56 INSTI-naive patient viral sequences from Cameroon. Study analysis used 37 sequences with fragment size ≥500 bp or of good quality .The majority of the sequences were identified as CRF02_AG 54.% (n = 20/37) and 45.9% (n = 17/37), other subtype viral sequences include (A, CRF36_cpx, F,G, and C). A total of 18.9% (n = 7/37) of the sequences had RAMs, with only 5.4% (n = 2/37) having major RAMs (Y143R/C/D/G and P145S), against INSTIs. Accessory RAMs were present in 8.1% (n = 3/37) of the sequences, of which one sequence contained solely E157Q, and another Q95K. One patient sequence had three accessory RAMs (G140E, E157Q, and G163R). We identified major RAMs to INSTIs, which might have a potential clinical impact to dolutegravir rollout in RLS, including Cameroon. This is the first study to describe RAMs among INSTI-naive people living with HIV-1 (PLHIV-1) infected with CRF02_AG and other subtypes in Cameroon.
Collapse
Affiliation(s)
- Sello Given Mikasi
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Josiah Otwoma Gichana
- Division of Oral Surgery, Department of Pathology Laboratory, University of Nairobi, Nairobi, Kenya
| | - Cheri Van der Walt
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Dominik Brado
- Division of Virology, Faculty of Medicine, Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany
| | - Adetayo Emmanuel Obasa
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Duncan Njenda
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, University of Stockholm, Stockholm, Sweden
| | - Martha Messembe
- Faculty of Medicine and Biomedical Sciences, Centre for the Study and Control of Communicable Diseases, University of Yaoundé I, Yaoundé, Cameroon
| | - Emilia Lyonga
- Faculty of Medicine and Biomedical Sciences, Centre for the Study and Control of Communicable Diseases, University of Yaoundé I, Yaoundé, Cameroon
| | - Okomo Assoumou
- Faculty of Medicine and Biomedical Sciences, Centre for the Study and Control of Communicable Diseases, University of Yaoundé I, Yaoundé, Cameroon
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - George Mondinde Ikomey
- Faculty of Medicine and Biomedical Sciences, Centre for the Study and Control of Communicable Diseases, University of Yaoundé I, Yaoundé, Cameroon
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| |
Collapse
|
|
17
|
Lack of HIV-1 integrase inhibitor resistance among 392 antiretroviral-naïve individuals in a tertiary care hospital in Beijing, China. AIDS 2019; 33:1945-1947. [PMID: 31491787 DOI: 10.1097/qad.0000000000002282] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
: Reports of resistance to integrase strand transfer inhibitors (INSTIs) are now not uncommon. We analyzed the HIV int gene from plasma of antiretroviral-naïve individuals during acute and chronic HIV-1 infection. No individual with major INSTI mutations was identified. Two individuals harbored INSTI accessory mutations E157Q/T97A were detected for the first time. Our results emphasize the need to consider testing for INSTI resistance at baseline as this class of drugs is increasingly used in clinical routine.
Collapse
|
|
18
|
Margot NA, Ram RR, White KL, Abram ME, Callebaut C. Antiviral activity of HIV-1 integrase strand-transfer inhibitors against mutants with integrase resistance-associated mutations and their frequency in treatment-naïve individuals. J Med Virol 2019; 91:2188-2194. [PMID: 31389026 DOI: 10.1002/jmv.25564] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/31/2019] [Indexed: 11/08/2022]
Abstract
The development of resistance to human immunodeficiency virus 1 (HIV-1) integrase strand-transfer inhibitors (INSTI) has been documented; however, knowledge of the impact of pre-existing integrase (IN) mutations on INSTI resistance (INSTI-R) is still evolving. The frequency of HIV-1 IN mutations in 2177 treatment-naïve subjects was investigated, along with the INSTI susceptibility of site-directed mutant viruses containing major and minor INSTI-R mutations. Total 6 of 39 minor INSTI-R mutations (M50I, S119P/G/T/R, and E157Q) were found in >1% of IN-treatment-naïve subjects with no impact on INSTI susceptibility. When each combined with major INSTI-R mutation, M50I, S119P, and E157Q led to decreased susceptibility to elvitegravir but remained sensitive to dolutegravir and bictegravir.
Collapse
Affiliation(s)
- Nicolas A Margot
- Gilead Sciences, Inc., Clinical virology, Foster City, California
| | - Renee R Ram
- Gilead Sciences, Inc., Clinical virology, Foster City, California
| | - Kirsten L White
- Gilead Sciences, Inc., Clinical virology, Foster City, California
| | - Michael E Abram
- Gilead Sciences, Inc., Clinical virology, Foster City, California
| | | |
Collapse
|
|
19
|
Günthard HF, Calvez V, Paredes R, Pillay D, Shafer RW, Wensing AM, Jacobsen DM, Richman DD. Reply to Ambrosioni et al. Clin Infect Dis 2019; 68:1977-1978. [PMID: 30520997 DOI: 10.1093/cid/ciy1022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 12/03/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Huldrych F Günthard
- University Hospital Zürich and Institute of Medical Virology, University of Zurich, Switzerland
| | - Vincent Calvez
- Pierre et Marie Curie University and Pitié-Salpêtrieŕe Hospital, Paris, France
| | - Roger Paredes
- Infectious Diseases Service and IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Deenan Pillay
- Africa Health Research Institute, KwaZulu Natal, South Africa.,University College London, United Kingdom
| | | | | | | | - Douglas D Richman
- Veterans Affairs San Diego Healthcare System.,University of California San Diego
| |
Collapse
|
|
20
|
George JM, Kuriakose SS, Dee N, Stoll P, Lalani T, Dewar R, Khan MA, Rehman MT, Grossman Z, Maldarelli F, Pau AK. Rapid Development of High-Level Resistance to Dolutegravir With Emergence of T97A Mutation in 2 Treatment-Experienced Individuals With Baseline Partial Sensitivity to Dolutegravir. Open Forum Infect Dis 2018; 5:ofy221. [PMID: 30568974 PMCID: PMC6172925 DOI: 10.1093/ofid/ofy221] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/30/2018] [Indexed: 11/14/2022] Open
Abstract
HIV integrase mutation T97A emerges after suboptimal therapy with integrase strand transfer inhibitors (INSTIs), but the contribution of T97A to dolutegravir resistance remains uncertain. Here we report >10-fold increase in dolutegravir resistance after the single addition of T97A in 2 individuals with prior INSTI resistance receiving dolutegravir salvage therapy.
Collapse
Affiliation(s)
- Jomy M George
- Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Safia S Kuriakose
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland
| | - Nicola Dee
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland
| | - Pam Stoll
- Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Tahaniyat Lalani
- Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Robin Dewar
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland
| | - Muhammad A Khan
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland
| | - Muhammad T Rehman
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland
| | - Zehava Grossman
- National Cancer Institute, Frederick, Maryland
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Alice K Pau
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|
|
21
|
Ndashimye E, Avino M, Kyeyune F, Nankya I, Gibson RM, Nabulime E, Poon AF, Kityo C, Mugyenyi P, Quiñones-Mateu ME, Arts EJ. Absence of HIV-1 Drug Resistance Mutations Supports the Use of Dolutegravir in Uganda. AIDS Res Hum Retroviruses 2018; 34:404-414. [PMID: 29353487 DOI: 10.1089/aid.2017.0205] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To screen for drug resistance and possible treatment with Dolutegravir (DTG) in treatment-naive patients and those experiencing virologic failure during first-, second-, and third-line combined antiretroviral therapy (cART) in Uganda. Samples from 417 patients in Uganda were analyzed for predicted drug resistance upon failing a first- (N = 158), second- (N = 121), or third-line [all 51 involving Raltegravir (RAL)] treatment regimen. HIV-1 pol gene was amplified and sequenced from plasma samples. Drug susceptibility was interpreted using the Stanford HIV database algorithm and SCUEAL was used for HIV-1 subtyping. Frequency of resistance to nucleoside reverse transcriptase inhibitors (NRTIs) (95%) and non-NRTI (NNRTI, 96%) was high in first-line treatment failures. Despite lack of NNRTI-based treatment for years, NNRTI resistance remained stable in 55% of patients failing second-line or third-line treatment, and was also at 10% in treatment-naive Ugandans. DTG resistance (n = 366) was not observed in treatment-naive individuals or individuals failing first- and second-line cART, and only found in two patients failing third-line cART, while 47% of the latter had RAL- and Elvitegravir-resistant HIV-1. Secondary mutations associated with DTG resistance were found in 2%-10% of patients failing third-line cART. Of 14 drugs currently available for cART in Uganda, resistance was readily observed to all antiretroviral drugs (except for DTG) in Ugandan patients failing first-, second-, or even third-line treatment regimens. The high NNRTI resistance in first-line treatment in Uganda even among treatment-naive patients calls for the use of DTG to reach the UNAIDS 90:90:90 goals.
Collapse
Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Mariano Avino
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Fred Kyeyune
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Immaculate Nankya
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Richard M. Gibson
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Eva Nabulime
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Art F.Y. Poon
- Department of Microbiology and Immunology, Western University, London, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Cissy Kityo
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Peter Mugyenyi
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Miguel E. Quiñones-Mateu
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Eric J. Arts
- Department of Microbiology and Immunology, Western University, London, Canada
| |
Collapse
|
|
22
|
Brado D, Obasa AE, Ikomey GM, Cloete R, Singh K, Engelbrecht S, Neogi U, Jacobs GB. Analyses of HIV-1 integrase sequences prior to South African national HIV-treatment program and available of integrase inhibitors in Cape Town, South Africa. Sci Rep 2018; 8:4709. [PMID: 29549274 PMCID: PMC5856838 DOI: 10.1038/s41598-018-22914-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/01/2018] [Indexed: 01/16/2023] Open
Abstract
HIV-Integrase (IN) has proven to be a viable target for highly specific HIV-1 therapy. We aimed to characterize the HIV-1 IN gene in a South African context and identify resistance-associated mutations (RAMs) against available first and second generation Integrase strand-transfer inhibitors (InSTIs). We performed genetic analyses on 91 treatment-naïve HIV-1 infected patients, as well as 314 treatment-naive South African HIV-1 IN-sequences, downloaded from Los Alamos HIV Sequence Database. Genotypic analyses revealed the absence of major RAMs in the cohort collected before the broad availability of combination antiretroviral therapy (cART) and INSTI in South Africa, however, occurred at a rate of 2.85% (9/314) in database derived sequences. RAMs were present at IN-positions 66, 92, 143, 147 and 148, all of which may confer resistance to Raltegravir (RAL) and Elvitegravir (EVG), but are unlikely to affect second-generation Dolutegravir (DTG), except mutations in the Q148 pathway. Furthermore, protein modeling showed, naturally occurring polymorphisms impact the stability of the intasome-complex and therefore may contribute to an overall potency against InSTIs. Our data suggest the prevalence of InSTI RAMs, against InSTIs, is low in South Africa, but natural polymorphisms and subtype-specific differences may influence the effect of individual treatment regimens.
Collapse
Affiliation(s)
- Dominik Brado
- Division of Virology, Institute for Virology and Immunobiology, Faculty of Medicine, University of Wuerzburg, 97080, Wuerzburg, Germany
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Adetayo Emmanuel Obasa
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa.
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, University of Stockholm, Stockholm, Sweden.
| | - George Mondinde Ikomey
- CSCCD, Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Western Cape, South Africa
| | - Kamalendra Singh
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, University of Stockholm, Stockholm, Sweden
- Department of Molecular Microbiology and Immunology, Columbia, MO, 65211, USA
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Susan Engelbrecht
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, University of Stockholm, Stockholm, Sweden
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| |
Collapse
|
|
23
|
Abstract
OBJECTIVE We sought to define the prevalence of pretreatment integrase strand transfer inhibitor (INSTI) resistance and assess the transmission networks of those with pretreatment INSTI resistance. DESIGN A retrospective cohort study of HIV-positive patients with genotypic resistance testing sent to a single referral laboratory in North Carolina between 2010 and 2016. METHODS We linked genotype and public health data for in-care HIV-positive individuals to determine the prevalence of INSTI resistance among treatment-naive (defined as those with a first genotype ≤3 months after diagnosis) and treatment-experienced (defined as those with a first genotype >3 months after diagnosis) patients. We performed molecular and phylogenetic analyses to assess whether pretreatment INSTI resistance mutations represented clustered HIV transmission. RESULTS Of 8825 individuals who contributed sequences for protease, reverse transcriptase, or INSTI genotypic resistance testing during the study period, 2784 (31%) contributed at least one sequence for INSTI resistance testing. Of these, 840 were treatment-naive individuals and 20 [2.4%, 95% confidence interval (CI): 1.5, 3.6%] had INSTI mutations; only two (0.2%, 95% CI: 0.02, 0.9%) had major mutations. Of 1944 treatment-experienced individuals, 9.6% (95% CI: 8.3, 11.0%) had any INSTI mutation and 7.0% (95% CI: 5.9, 8.3%) had major mutations; the prevalence of INSTI mutations among treatment-experienced patients decreased overtime (P < 0.001). In total 12 of 20 individuals with pretreatment INSTI mutations were part of 10 molecular transmission clusters; only one cluster shared identical minor mutations. CONCLUSION The prevalence of major pretreatment INSTI resistance is very low. Pretreatment INSTI mutations do not appear to represent clustered HIV transmission.
Collapse
|
|
24
|
Paredes R, Tzou PL, van Zyl G, Barrow G, Camacho R, Carmona S, Grant PM, Gupta RK, Hamers RL, Harrigan PR, Jordan MR, Kantor R, Katzenstein DA, Kuritzkes DR, Maldarelli F, Otelea D, Wallis CL, Schapiro JM, Shafer RW. Collaborative update of a rule-based expert system for HIV-1 genotypic resistance test interpretation. PLoS One 2017; 12:e0181357. [PMID: 28753637 PMCID: PMC5533429 DOI: 10.1371/journal.pone.0181357] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 06/27/2017] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION HIV-1 genotypic resistance test (GRT) interpretation systems (IS) require updates as new studies on HIV-1 drug resistance are published and as treatment guidelines evolve. METHODS An expert panel was created to provide recommendations for the update of the Stanford HIV Drug Resistance Database (HIVDB) GRT-IS. The panel was polled on the ARVs to be included in a GRT report, and the drug-resistance interpretations associated with 160 drug-resistance mutation (DRM) pattern-ARV combinations. The DRM pattern-ARV combinations included 52 nucleoside RT inhibitor (NRTI) DRM pattern-ARV combinations (13 patterns x 4 NRTIs), 27 nonnucleoside RT inhibitor (NNRTI) DRM pattern-ARV combinations (9 patterns x 3 NNRTIs), 39 protease inhibitor (PI) DRM pattern-ARV combinations (13 patterns x 3 PIs) and 42 integrase strand transfer inhibitor (INSTI) DRM pattern-ARV combinations (14 patterns x 3 INSTIs). RESULTS There was universal agreement that a GRT report should include the NRTIs lamivudine, abacavir, zidovudine, emtricitabine, and tenofovir disoproxil fumarate; the NNRTIs efavirenz, etravirine, nevirapine, and rilpivirine; the PIs atazanavir/r, darunavir/r, and lopinavir/r (with "/r" indicating pharmacological boosting with ritonavir or cobicistat); and the INSTIs dolutegravir, elvitegravir, and raltegravir. There was a range of opinion as to whether the NRTIs stavudine and didanosine and the PIs nelfinavir, indinavir/r, saquinavir/r, fosamprenavir/r, and tipranavir/r should be included. The expert panel members provided highly concordant DRM pattern-ARV interpretations with only 6% of NRTI, 6% of NNRTI, 5% of PI, and 3% of INSTI individual expert interpretations differing from the expert panel median by more than one resistance level. The expert panel median differed from the HIVDB 7.0 GRT-IS for 20 (12.5%) of the 160 DRM pattern-ARV combinations including 12 NRTI, two NNRTI, and six INSTI pattern-ARV combinations. Eighteen of these differences were updated in HIVDB 8.1 GRT-IS to reflect the expert panel median. Additionally, HIVDB users are now provided with the option to exclude those ARVs not considered to be universally required. CONCLUSIONS The HIVDB GRT-IS was updated through a collaborative process to reflect changes in HIV drug resistance knowledge, treatment guidelines, and expert opinion. Such a process broadens consensus among experts and identifies areas requiring further study.
Collapse
Affiliation(s)
| | - Philip L. Tzou
- Division of Infectious Diseases, Stanford University, Stanford, CA, United States of America
| | - Gert van Zyl
- Division of Medical Virology, Stellenbosch University and NHLS Tygerberg, Cape Town, South Africa
| | - Geoff Barrow
- Centre for HIV/AIDS Research, Education and Services (CHARES), Department of Medicine, University of the West Indies, Kingston Jamaica
| | - Ricardo Camacho
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sergio Carmona
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Philip M. Grant
- Division of Infectious Diseases, Stanford University, Stanford, CA, United States of America
| | | | - Raph L. Hamers
- Amsterdam Institute for Global Health and Development, Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | | | - Michael R. Jordan
- Tufts University School of Medicine, Boston, MA, United States of America
| | - Rami Kantor
- Division of Infectious Diseases, Alpert Medical School, Brown University, Providence, RI, United States of America
| | - David A. Katzenstein
- Division of Infectious Diseases, Stanford University, Stanford, CA, United States of America
| | - Daniel R. Kuritzkes
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, NIH, Translational Research Unit, Frederick, MD, United States of America
| | - Dan Otelea
- Molecular Diagnostics Laboratory, National Institute for Infectious Diseases, Bucharest, Romania
| | | | | | - Robert W. Shafer
- Division of Infectious Diseases, Stanford University, Stanford, CA, United States of America
| |
Collapse
|