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Rakotomalala FA, Butel C, Rasamoelina T, Serrano L, Vidal N, Randriarimanana SHD, Maharavo L, Randriamananjara HN, Fernandez-Nuñez N, Rabetokotany FR, Rakoto DAD, Delaporte E, Peeters M, Babin FX, Samison LH, Nerrienet E, Ayouba A. High HIV-1 genetic diversity and low prevalence of transmitted drug resistance among treatment-naive people living with HIV in Madagascar. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 125:105679. [PMID: 39368593 DOI: 10.1016/j.meegid.2024.105679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2024] [Revised: 09/30/2024] [Accepted: 10/02/2024] [Indexed: 10/07/2024]
Abstract
BACKGROUND AND OBJECTIVES Data on HIV drug resistance in Madagascar are rare and outdated. In this study, we assessed the prevalence of HIV drug resistance mutations to antiretrovirals (ARVs) and genetic diversity of circulating strains in treatment-naive people living with HIV (PLHIV) in Madagascar. MATERIALS AND METHODS We amplified the protease (PR), fragments of the Reverse Transcriptase (RT) and Integrase (IN) genes according to the French ANRS protocol. The amplicons were sequenced using next-generation sequencing technology on an Illumina platform (MiSeq). We determined HIV-1 subtypes through phylogenetic analysis using maximum likelihood in PhyML. Resistance interpretation was performed using the Stanford algorithm (version 9.5.1). RESULTS We included 239 HIV-infected adults and children, sampled between January 2019 and November 2023, with a median age of 30 years and a mean plasma HIV viral load of 6.3 Log copies/mL. We sequenced at least one genomic fragment (PR or RT or IN) of the 239 samples, but 9 were excluded from analysis (mean depth < 10,000×). Phylogenetic analysis of 230 sequences revealed the presence of subtype C (33.91 %), A1 (11.30 %), B (11.30 %), CRF02_AG (9.56 %), subtype G (3.04 %), subtype D (0.43 %), CRF01_AE (0.43 %), and a significant proportion of unique recombinant forms (URFs) (30.30 %). The prevalence of transmitted drug resistance (TDR) was 4.95 % (10/202) among patients aged 15 years and older. When stratified by ARV class, this prevalence was 4.79 % for non-nucleoside reverse transcriptase inhibitors (NNRTIs), 0.59 % for Nucleoside Reverse Transcriptase inhibitors (NRTIs), and 0.50 % for integrase strand transfer inhibitors (INSTIs). Among children under 15 years old (n = 28), the prevalence of TDR was 14.28 % (4/28), with all mutations conferring resistance to NNRTIs. No mutation conferring resistance to protease inhibitors was found, neither in children nor in adults. CONCLUSION Our results show a low prevalence of ARV resistance mutations among adult treatment-naive PLHIV in Madagascar. In children under 15 years old, 92 % were infants under two years old, the high resistance rate is likely related to mother-to-child transmission. No resistance mutation to dolutegravir was detected. We also observed high frequencies of subtypes C, B, A1 and a high proportion of URFs, highlighting an ongoing dynamic epidemic.
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Affiliation(s)
- Fetra Angelot Rakotomalala
- Centre d'Infectiologie Charles Mérieux, Université d'Antananarivo, Antananarivo, Madagascar; TransVIHMI, Université de Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD), Montpellier, France; Ecole Doctorale Sciences de la Vie et de l'Environnement, Université d'Antananarivo, Antananarivo, Madagascar
| | - Christelle Butel
- TransVIHMI, Université de Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD), Montpellier, France.
| | | | - Laetitia Serrano
- TransVIHMI, Université de Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD), Montpellier, France.
| | - Nicole Vidal
- TransVIHMI, Université de Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD), Montpellier, France.
| | | | - Luca Maharavo
- Centre d'Infectiologie Charles Mérieux, Université d'Antananarivo, Antananarivo, Madagascar
| | | | - Nicolas Fernandez-Nuñez
- TransVIHMI, Université de Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD), Montpellier, France.
| | | | - Danielle Aurore Doll Rakoto
- Ecole Doctorale Sciences de la Vie et de l'Environnement, Université d'Antananarivo, Antananarivo, Madagascar
| | - Eric Delaporte
- TransVIHMI, Université de Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD), Montpellier, France.
| | - Martine Peeters
- TransVIHMI, Université de Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD), Montpellier, France.
| | | | - Luc Hervé Samison
- Centre d'Infectiologie Charles Mérieux, Université d'Antananarivo, Antananarivo, Madagascar
| | | | - Ahidjo Ayouba
- TransVIHMI, Université de Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD), Montpellier, France.
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Mimtsoudis I, Tsachouridou O, Akinosoglou K, Metallidis S. Treatment Management Challenges in Naïve and Experienced HIV-1-Infected Individuals Carrying the M184V Mutation. Viruses 2024; 16:1392. [PMID: 39339868 PMCID: PMC11437411 DOI: 10.3390/v16091392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 08/12/2024] [Accepted: 08/22/2024] [Indexed: 09/30/2024] Open
Abstract
M184V is a single-base mutation in the YMDD domain of reverse transcriptase (RT). The M184V resistance-associated mutation (RAM) is related to virological unresponsiveness to lamivudine (3TC) and emtricitabine (FTC) and induces high-level resistance to these two antiretroviral agents. M184V is rapidly selected in the setting of non-suppressive antiretroviral therapy (ART) and accumulates in the HIV reservoir. There were continuous efforts to evaluate the impact of the M184V mutation on the treatment outcomes in people living with HIV (PLWH). Since 3TC remains an extensively used part of recommended antiretroviral combinations, M184V is commonly detected in patients with virological failure (VF). ART guidelines do not recommend the use of drugs impacted by RAMs as they have been confirmed to comprise a risk factor for VF. However, there is evidence that 3TC/FTC can remain active even in the presence of M184V. Given the potential benefits of 3TC in ART combinations, the investigation of M184V remains of high interest to clinicians and researchers, especially in certain regions with limited resources, and especially for its unusual effects. This is a review of the literature on the challenges in treating both naïve and experienced individuals carrying the M184V mutation, including virological failure, virological suppression, and resistance to ART.
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Affiliation(s)
- Iordanis Mimtsoudis
- Infectious Diseases Division 1st Internal Medicine Department, AHEPA University Hospital Thessaloniki, 54636 Thessaloniki, Greece; (I.M.); (S.M.)
| | - Olga Tsachouridou
- Infectious Diseases Division 1st Internal Medicine Department, AHEPA University Hospital Thessaloniki, 54636 Thessaloniki, Greece; (I.M.); (S.M.)
| | - Karolina Akinosoglou
- Department of Internal Medicine and Infectious Diseases, University General Hospital of Patras, 26504 Patras, Greece;
| | - Symeon Metallidis
- Infectious Diseases Division 1st Internal Medicine Department, AHEPA University Hospital Thessaloniki, 54636 Thessaloniki, Greece; (I.M.); (S.M.)
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Boyce CL, Sils T, Milne RS, Wallner JJ, Hardy SR, Ko D, Wong-On-Wing A, Mackey M, Higa N, Beck IA, Styrchak SM, DeMarrais P, Tierney C, Fowler MG, Frenkel LM. Impact of Human Immunodeficiency Virus Drug Resistance Mutations Detected in Women Prior to Antiretroviral Therapy With Efavirenz + Tenofovir Disoproxil Fumarate + Lamivudine (or Emtricitabine). Open Forum Infect Dis 2024; 11:ofae383. [PMID: 39050228 PMCID: PMC11267229 DOI: 10.1093/ofid/ofae383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 07/05/2024] [Indexed: 07/27/2024] Open
Abstract
Background Two large studies suggest that resistance mutations to only nonnucleoside reverse transcriptase inhibitors (NNRTI) did not increase the risk of virologic failure during antiretroviral therapy (ART) with efavirenz/tenofovir disoproxil fumarate/lamivudine (or emtricitabine). We retrospectively evaluated a third cohort to determine the impact of NNRTI resistance on the efficacy of efavirenz-based ART. Methods Postpartum women living with human immunodeficiency virus (HIV) were studied if they initiated efavirenz-based ART because of the World Health Organization's recommendation for universal ART. Resistance was detected by Sanger genotyping plasma prior to efavirenz-based ART and at virologic failure (HIV RNA >400 copies/mL). Logistic regression examined relationships between pre-efavirenz genotypes and virologic failure. Results Pre-efavirenz resistance was detected in 169 of 1223 (13.8%) participants. By month 12 of efavirenz-based ART, 189 of 1233 (15.3%) participants had virologic failure. Rates of virologic failure did not differ by pre-efavirenz NNRTI resistance. However, while pre-efavirenz nucleos(t)ide reverse transcriptase inhibitors (NRTI) and NNRTI resistance was rare (8/1223 [0.7%]) this genotype increased the odds (adjusted odds ratio, 11.2 [95% confidence interval, 2.21-72.2]) of virologic failure during efavirenz-based ART. Age, time interval between last viremic visit and efavirenz initiation, clinical site, viremia at delivery, hepatitis B virus coinfection, and antepartum regimen were also associated with virologic failure. Conclusions Resistance to NNRTI alone was prevalent and dual-class (NRTI and NNRTI) resistance was rare in this cohort, with only the latter associated with virologic failure. This confirms others' findings that, if needed, efavirenz-based ART offers most people an effective alternative to dolutegravir-based ART.
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Affiliation(s)
- Ceejay L Boyce
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Tatiana Sils
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Ross S Milne
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Jackson J Wallner
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Samantha R Hardy
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Daisy Ko
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Annie Wong-On-Wing
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Malia Mackey
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Nikki Higa
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Ingrid A Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Sheila M Styrchak
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Patricia DeMarrais
- Center for Biostatistics in AIDS Research, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Camlin Tierney
- Center for Biostatistics in AIDS Research, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Mary G Fowler
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Lisa M Frenkel
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
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Chen H, Hao J, Hu J, Song C, Zhou Y, Li M, Chen J, Liu X, Wang D, Xu X, Xin P, Zhang J, Liao L, Feng Y, Li D, Pan SW, Shao Y, Ruan Y, Xing H. Pretreatment HIV Drug Resistance and the Molecular Transmission Network Among HIV-Positive Individuals in China in 2022: Multicenter Observational Study. JMIR Public Health Surveill 2023; 9:e50894. [PMID: 37976080 PMCID: PMC10692882 DOI: 10.2196/50894] [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: 07/17/2023] [Revised: 09/10/2023] [Accepted: 10/06/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Emerging HIV drug resistance caused by increased usage of antiretroviral drugs (ARV) could jeopardize the success of standardized HIV management protocols in resource-limited settings. OBJECTIVE We aimed to characterize pretreatment HIV drug resistance (PDR) among HIV-positive individuals and risk factors in China in 2022. METHODS This cross-sectional study was conducted using 2-stage systematic sampling according to the World Health Organization's surveillance guidelines in 8 provincial-level administrative divisions in 2022. Demographic information and plasma samples were obtained from study participants. PDR was analyzed using the Stanford HIV drug resistance database, and the Tamura-Nei 93 model in HIV-TRACE was used to calculate pairwise matches with a genetic distance of 0.01 substitutions per site. Logistic regression was used to identify and estimate factors associated with PDR. RESULTS PDR testing was conducted on 2568 participants in 2022. Of the participants, 34.8% (n=893) were aged 30-49 years, 81.4% (n=2091) were male, and 3.2% (n=81) had prior ARV exposure. The prevalence of PDR to protease and reverse transcriptase regions, nonnucleoside reverse transcriptase inhibitors, nucleoside reverse transcriptase inhibitors, and protease inhibitors were 7.4% (n=190), 6.3% (n=163), 1.2% (n=32), and 0.2% (n=5), respectively. Yunnan, Jilin, and Zhejiang had much higher PDR incidence than did Sichuan. The prevalence of nonnucleoside reverse transcriptase inhibitor-related drug resistance was 6.1% (n=157) for efavirenz and 6.3% (n=163) for nevirapine. Multivariable logistic regression models indicated that participants who had prior ARV exposure (odds ratio [OR] 7.45, 95% CI 4.50-12.34) and the CRF55_01B HIV subtype (OR 2.61, 95% CI 1.41-4.83) were significantly associated with PDR. Among 618 (24.2%) sequences (nodes) associated with 253 molecular transmission clusters (size range 2-13), drug resistance mutation sites included K103, E138, V179, P225, V106, V108, L210, T215, P225, K238, and A98. CONCLUSIONS The overall prevalence of PDR in China in 2022 was modest. Targeted genotypic PDR testing and medication compliance interventions must be urgently expanded to address PDR among newly diagnosed people living with HIV in China.
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Affiliation(s)
- Hongli Chen
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
- Sichuan Nursing Vocational College, Chengdu, China
| | - Jingjing Hao
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Jing Hu
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Chang Song
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Yesheng Zhou
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Miaomiao Li
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Jin Chen
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Xiu Liu
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Dong Wang
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Xiaoshan Xu
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Peixian Xin
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Jiaxin Zhang
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Lingjie Liao
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Yi Feng
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Dan Li
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Stephen W Pan
- Department of Public Health, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Yiming Shao
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Yuhua Ruan
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Hui Xing
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
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Fokam J, Chenwi CA, Tala V, Takou D, Santoro MM, Teto G, Dambaya B, Anubodem F, Semengue ENJ, Beloumou G, Djupsa S, Assomo E, Fokunang C, Alteri C, Billong S, Bouba NP, Ajeh R, Colizzi V, Mbanya D, Ceccherini-Silberstein F, Perno CF, Ndjolo A. Pre-Treatment HIV Drug Resistance and Genetic Diversity in Cameroon: Implications for First-Line Regimens. Viruses 2023; 15:1458. [PMID: 37515146 PMCID: PMC10385257 DOI: 10.3390/v15071458] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/30/2023] Open
Abstract
The efficacy of first-line antiretroviral therapy (ART) may be hampered by the presence of HIV drug resistance (HIVDR). We described HIV-1 pre-treatment drug resistance (PDR) patterns, effect of viral clades on PDR, and programmatic implications on first-line regimens in Cameroon. A sentinel surveillance of PDR was conducted from 2014 to 2019. Sequencing of HIV-1 protease and reverse transcriptase was performed, and HIVDR was interpreted using Stanford HIVdb.v.9.4. In total, 379 sequences were obtained from participants (62% female, mean age 36 ± 10 years). The overall PDR rate was 15.0% [95% CI: 11.8-19.0] nationwide, with significant disparity between regions (p = 0.03). NNRTI PDR was highest (12.4%), of which 7.9% had DRMs to EFV/NVP. Two regions had EFV/NVP PDR above the 10% critical threshold, namely the Far North (15%) and East (10.9%). Eighteen viral strains were identified, predominated by CRF02_AG (65.4%), with no influence of genetic diversity PDR occurrence. TDF-3TC-DTG predictive efficacy was superior (98.4%) to TDF-3TC-EFV (92%), p < 0.0001. The overall high rate of PDR in Cameroon, not substantially affected by the wide HIV-1 genetic diversity, underscores the poor efficacy of EFV/NVP-based first-line ART nationwide, with major implications in two regions of the country. This supports the need for a rapid transition to NNRTI-sparing regimens, with TDF-3TC-DTG having optimal efficacy at the programmatic level.
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Affiliation(s)
- Joseph Fokam
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Messa, Yaoundé P.O. Box 3077, Cameroon
- Faculty of Health Science, University of Buea, Buea P.O. Box 0063, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé P.O. Box 1364, Cameroon
- National HIV Drug Resistance Prevention and Surveillance Working Group, Ministry of Public Health, Yaoundé P.O. Box 3038, Cameroon
| | - Collins Ambe Chenwi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Messa, Yaoundé P.O. Box 3077, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé P.O. Box 1364, Cameroon
- Department of Experimental Medicine, Faculty of Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
| | - Valère Tala
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Messa, Yaoundé P.O. Box 3077, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé P.O. Box 1364, Cameroon
| | - Désiré Takou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Messa, Yaoundé P.O. Box 3077, Cameroon
| | - Maria Mercedes Santoro
- Department of Experimental Medicine, Faculty of Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
| | - George Teto
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Messa, Yaoundé P.O. Box 3077, Cameroon
| | - Beatrice Dambaya
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Messa, Yaoundé P.O. Box 3077, Cameroon
| | - Felix Anubodem
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Messa, Yaoundé P.O. Box 3077, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé P.O. Box 1364, Cameroon
| | - Ezechiel Ngoufack Jagni Semengue
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Messa, Yaoundé P.O. Box 3077, Cameroon
- Department of Experimental Medicine, Faculty of Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
- Faculty of Sciences and Technologies, Evangelical University of Cameroon, Bandjoun P.O. Box 0127, Cameroon
| | - Grace Beloumou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Messa, Yaoundé P.O. Box 3077, Cameroon
| | - Sandrine Djupsa
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Messa, Yaoundé P.O. Box 3077, Cameroon
| | - Edgar Assomo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Messa, Yaoundé P.O. Box 3077, Cameroon
| | - Charles Fokunang
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé P.O. Box 1364, Cameroon
| | - Claudia Alteri
- Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122 Milano, Italy
| | - Serge Billong
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé P.O. Box 1364, Cameroon
- National HIV Drug Resistance Prevention and Surveillance Working Group, Ministry of Public Health, Yaoundé P.O. Box 3038, Cameroon
| | - Nounouce Pamen Bouba
- Department of Disease, Epidemic and Pandemic Control, Ministry of Public Health, Yaounde P.O. Box 3038, Cameroon
| | - Rogers Ajeh
- Central Technical Group, National AIDS Control Committee, Yaoundé P.O. Box 2005, Cameroon
| | - Vittorio Colizzi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Messa, Yaoundé P.O. Box 3077, Cameroon
- Department of Experimental Medicine, Faculty of Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
- Faculty of Sciences and Technologies, Evangelical University of Cameroon, Bandjoun P.O. Box 0127, Cameroon
| | - Dora Mbanya
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé P.O. Box 1364, Cameroon
- National Blood Transfusion Service, Ministry of Public Health, Yaoundé P.O. Box 3038, Cameroon
- Haematology and Transfusion Service, Centre Hospitalier et Universitaire (CHU), Yaoundé P.O. Box 30335, Cameroon
| | - Francesca Ceccherini-Silberstein
- Department of Experimental Medicine, Faculty of Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
| | - Carlo-Federico Perno
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Messa, Yaoundé P.O. Box 3077, Cameroon
- Bambino Gesu' Children's Research Hospital, Piazza S. Onofrio 4, 00165 Rome, Italy
| | - Alexis Ndjolo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Messa, Yaoundé P.O. Box 3077, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé P.O. Box 1364, Cameroon
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Switching to coformulated bictegravir, emtricitabine, and tenofovir alafenamide maintained viral suppression in adults with historical virological failures and K65N/R mutation. Int J Infect Dis 2023; 126:39-47. [PMID: 36384186 DOI: 10.1016/j.ijid.2022.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/27/2022] [Accepted: 11/08/2022] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Real-world experience with coformulated bictegravir, emtricitabine, and tenofovir alafenamide (BIC/FTC/TAF) is sparse as a switch regimen among people living with HIV (PLWH) having achieved viral suppression after previous virologic failures with the emergence of K65N/R. METHODS In this retrospective study, PLWH aged ≥20 years who had previous virologic failures with emergent K65N/R were included for switching to BIC/FTC/TAF after having achieved plasma HIV RNA load (PVL) <200 copies/ml for ≥3 months. PLWH were excluded if integrase inhibitor resistance-associated mutations were detected. The primary end point was losing virologic control (PVL >50 copies/ml) at week 48 using a modified US Food and Drug Administration snapshot algorithm. RESULTS A total of 72 PLWH with K65N/R who switched to BIC/FTC/TAF were identified. A total of 42 (59.7%) had concurrent M184V/I, and 9 (12.5%) had ≥1 thymidine analog mutations. The median duration of viral suppression was 4.7 years (interquartile range 2.3-5.8), and 97.2% (n = 70) had PVL <50 copies/ml before switching. After a median observation of 98.6 weeks (interquartile range 77.9-120.3), 94.4% (n = 68) continued BIC/FTC/TAF. At week 48, the rate of losing virologic control was 2.8% (2/72). M184V/I was not associated with viral rebound. CONCLUSION Despite the emergence of K65N/R +/- M184V/I after virologic failures, BIC/FTC/TAF could be an option for simplification after viral suppression.
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Ntamatungiro AJ, Kagura J, Weisser M, Francis JM. Pre-treatment HIV-1 drug resistance in antiretroviral therapy-naive adults in Eastern Africa: a systematic review and meta-analysis. J Antimicrob Chemother 2022; 77:3231-3241. [PMID: 36225089 DOI: 10.1093/jac/dkac338] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/12/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Pre-treatment HIV drug resistance (PDR) may result in increased risk of virological failure and acquisition of new resistance mutations. With recently increasing ART coverage and periodic modifications of the guidelines for HIV treatment, there is a need for an updated systematic review to assess the levels of the PDR among adults newly initiating ART in Eastern Africa. METHODS We conducted a systematic search for studies published between 1 January 2017 and 30 April 2022 in the MEDLINE Complete and CINAHL Complete, searched simultaneously using EBSCOhost, and Web of Science. To determine the overall PDR prevalence estimates, we extracted data from eligible articles and analysed prevalence estimates using Stata 14.2. RESULTS A total of 22 eligible observation studies were selected. The studies included a total of 5852 ART-naive people living with HIV. The overall pooled prevalence of PDR was 10.0% (95% CI: 7.9%-12.0%, I2 = 88.9%) and 9.4% (95% CI: 7.0%-11.9%, I2 = 90.4%) for NNRTIs, 2.6% (95% CI: 1.8%-3.4%, I2 = 69.2%) for NRTIs and 0.7% (95% CI: 0.3%-1.2%, I2 = 29.0%) for PIs. No major integrase strand transfer inhibitors (INSTI)-related mutations were identified. CONCLUSIONS We observed a moderate overall PDR prevalence among new ART initiators in this study. PDR to NNRTIs is more prevalent, underscoring the importance of the current WHO recommendation for replacement of NNRTIs by INSTIs. PDR to NRTIs was low but notable, which warrants continuous surveillance of pre-existing resistance to the dolutegravir co-administered NRTI in Eastern Africa.
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Affiliation(s)
- Alex J Ntamatungiro
- Ifakara Health Institute, Ifakara, Tanzania.,Division of Epidemiology and Biostatistics, University of the Witwatersrand, Johannesburg, South Africa
| | - Juliana Kagura
- Division of Epidemiology and Biostatistics, University of the Witwatersrand, Johannesburg, South Africa
| | - Maja Weisser
- Ifakara Health Institute, Ifakara, Tanzania.,Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Basel, Basel, Switzerland.,Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Joel M Francis
- Department of Family Medicine and Primary Care, University of the Witwatersrand, Johannesburg, South Africa
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8
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MILNE RS, BECK IA, LEVINE M, SO I, ANDERSEN N, DENG W, PANPRADIST N, KINGOO J, KIPTINNESS C, YATICH N, KIARIE JN, SAKR SR, CHUNG MH, FRENKEL LM. Low-frequency pre-treatment HIV drug resistance: effects on 2-year outcome of first-line efavirenz-based antiretroviral therapy. AIDS 2022; 36:1949-1958. [PMID: 36305180 PMCID: PMC9623471 DOI: 10.1097/qad.0000000000003361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Assess the impact of pre-treatment high-frequency and low-frequency drug-resistant HIV variants on long-term outcomes of first-line efavirenz-based antiretroviral therapy (ART). DESIGN Prospective observational study. METHODS Participants' pre-treatment plasma RNA had two sections of HIV pol encoding reverse transcriptase sequenced (Illumina, MiSeq) using unique molecular identifiers to detect wild-type (pre-treatment drug-resistant variants less than 1% of viral quasispecies), low-frequency (1-9%) or high-frequency drug-resistant variants (10-100%). Associations between pre-treatment drug resistance and virologic outcomes over 24 months of efavirenz-based ART were assessed for the number and frequency of mutations by drug class and other resistance parameters. RESULTS Virologic failure was detected in 30 of 352 (9%) and pre-treatment drug-resistant variants were detected in the viral quasispecies of 31 of 352 (9%) participants prescribed efavirenz-based ART. Survival analyses revealed statistically significant associations between pre-treatment drug resistance at low (P < 0.0001) and high (P < 0.001) frequencies, at oligonucleotide ligation assay (OLA) (P < 0.00001) and non-OLA (P < 0.01) codons, to a single-antiretroviral class (P < 0.00001), and a shorter time to virologic failure of efavirenz-based ART. Regression analyses detected independent effects across resistance categories, including both low-frequency (P < 0.01) and high-frequency (P < 0.001) drug-resistant variants. CONCLUSION We observed that pre-treatment HIV drug resistance detected at low frequencies increased the risk of virologic failure over 24 months of efavirenz-based ART, but that most failures, regardless of drug-resistant variants' frequencies, were detected within a year of ART initiation. These observations suggest that when efavirenz-based ART is prescribed, screening for pre-treatment drug resistance by an assay capable of detecting low-frequency variants, including OLA, may guide clinicians to prescribe more effective ART.
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Affiliation(s)
- Ross S. MILNE
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Ingrid A. BECK
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Molly LEVINE
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Isaac SO
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Nina ANDERSEN
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Wenjie DENG
- University of Washington, Seattle, Washington, USA
| | | | - James KINGOO
- University of Washington, Seattle, Washington, USA
- Coptic Hospital, Nairobi, Kenya
| | | | - Nelly YATICH
- University of Washington, Seattle, Washington, USA
| | | | | | | | - Lisa M. FRENKEL
- Seattle Children’s Research Institute, Seattle, Washington, USA
- University of Washington, Seattle, Washington, USA
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9
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Beesham I, Parikh UM, Mellors JW, Joseph Davey DL, Heffron R, Palanee-Phillips T, Bosman SL, Beksinska M, Smit J, Ahmed K, Makkan H, Selepe P, Louw C, Kotze P, Hofmeyr GJ, Singata‐Madliki M, Rees H, Baeten JM, Wallis C. High Levels of Pretreatment HIV-1 Drug Resistance Mutations Among South African Women Who Acquired HIV During a Prospective Study. J Acquir Immune Defic Syndr 2022; 91:130-137. [PMID: 36094478 PMCID: PMC9651927 DOI: 10.1097/qai.0000000000003027] [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: 10/21/2021] [Accepted: 04/07/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Pretreatment HIV drug resistance (PDR) undermines individual treatment success and threatens the achievement of UNAIDS 95-95-95 targets. In many African countries, limited data are available on PDR as detection of recent HIV infection is uncommon and access to resistance testing is limited. We describe the prevalence of PDR among South African women with recent HIV infection from the Evidence for Contraceptive Options and HIV Outcomes (ECHO) Trial. METHODS HIV-uninfected, sexually active women, aged 18-35 years, and seeking contraception were enrolled in the ECHO Trial at sites in South Africa, from 2015 to 2018. HIV testing was done at trial entry and repeated quarterly. We tested stored plasma samples collected at HIV diagnosis from women who seroconverted during follow-up and had a viral load >1000 copies/mL for antiretroviral resistant mutations using a validated laboratory-developed population genotyping assay, which sequences the full protease and reverse transcriptase regions. Mutation profiles were determined using the Stanford Drug Resistance Database. RESULTS We sequenced 275 samples. The median age was 23 years, and majority (98.9%, n = 272) were infected with HIV-1 subtype C. The prevalence of surveillance drug resistance mutations (SDRMs) was 13.5% (n = 37). Nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations were found in 12.4% of women (n = 34). Few women had NRTI (1.8%, n = 5) and protease inhibitor (1.1%, n = 3) mutations. Five women had multiple NRTI and NNRTI SDRMs. CONCLUSIONS The high levels of PDR, particularly to NNRTIs, strongly support the recent change to the South African national HIV treatment guidelines to transition to a first-line drug regimen that excludes NNRTIs.
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Affiliation(s)
- Ivana Beesham
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | - Urvi M. Parikh
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - John W. Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Dvora L. Joseph Davey
- Division of Epidemiology and Biostatistics, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
- Department of Epidemiology, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA
| | - Renee Heffron
- Department of Global Health and Department of Epidemiology, University of Washington, Seattle, WA
| | - Thesla Palanee-Phillips
- Wits Reproductive Health and HIV Institute (Wits RHI), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shannon L. Bosman
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | - Mags Beksinska
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | - Jennifer Smit
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | - Khatija Ahmed
- Setshaba Research Centre, Soshanguve, South Africa
- Faculty of Health Sciences, Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Heeran Makkan
- The Aurum Institute, Klerksdorp, South Africa
- Department of Interdisciplinary Social Science, Public Health, Utrecht University, Utrecht, The Netherlands
| | | | - Cheryl Louw
- Madibeng Centre for Research, Brits, South Africa
- Department of Family Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Philip Kotze
- Qhakaza Mbokodo Research Clinic, Ladysmith, South Africa
| | - G. Justus Hofmeyr
- Effective Care Research Unit, Universities of the Witwatersrand, Walter Sisulu and Fort Hare and Eastern Cape Department of Health, East London, South Africa
- Department of Obstetrics and Gynaecology, University of Botswana, Gaborone, Botswana
| | - Mandisa Singata‐Madliki
- Effective Care Research Unit, Universities of the Witwatersrand, Walter Sisulu and Fort Hare and Eastern Cape Department of Health, East London, South Africa
- Effective Care Research Unit, Universities of the Witwatersrand and Fort Hare and Eastern Cape Department of Health, East London, South Africa
| | - Helen Rees
- Wits Reproductive Health and HIV Institute (Wits RHI), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jared M. Baeten
- Department of Global Health, Department of Epidemiology, Department of Medicine, University of Washington, Seattle, WA
- Currently, Gilead Sciences, Foster City, CA; and
| | - Carole Wallis
- BARC-SA and Lancet Laboratories, Johannesburg, South Africa
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10
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Boyce CL, Beck IA, Styrchak SM, Hardy SR, Wallner JJ, Milne RS, Morrison RL, Shapiro DE, João EC, Mirochnick MH, Frenkel LM. Assessment of minority frequency pretreatment HIV drug-resistant variants in pregnant women and associations with virologic non-suppression at term. PLoS One 2022; 17:e0275254. [PMID: 36166463 PMCID: PMC9514603 DOI: 10.1371/journal.pone.0275254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
Objective
To assess in ART-naïve pregnant women randomized to efavirenz- versus raltegravir-based ART (IMPAACT P1081) whether pretreatment drug resistance (PDR) with minority frequency variants (<20% of individual’s viral quasispecies) affects antiretroviral treatment (ART)-suppression at term.
Design
A case-control study design compared PDR minority variants in cases with virologic non-suppression (plasma HIV RNA >200 copies/mL) at delivery to randomly selected ART-suppressed controls.
Methods
HIV pol genotypes were derived from pretreatment plasma specimens by Illumina sequencing. Resistance mutations were assessed using the HIV Stanford Database, and the proportion of cases versus controls with PDR to their ART regimens was compared.
Results
PDR was observed in 7 participants (11.3%; 95% CI 4.7, 21.9) and did not differ between 21 cases and 41 controls (4.8% vs 14.6%, p = 0.4061). PDR detected only as minority variants was less common (3.2%; 95% CI 0.2, 11.7) and also did not differ between groups (0% vs. 4.9%; p = 0.5447). Cases’ median plasma HIV RNA at delivery was 347c/mL, with most (n = 19/22) showing progressive diminution of viral load but not ≤200c/mL. Among cases with viral rebound (n = 3/22), none had PDR detected. Virologic non-suppression at term was associated with higher plasma HIV RNA at study entry (p<0.0001), a shorter duration of ART prior to delivery (p<0.0001), and randomization to efavirenz- (versus raltegravir-) based ART (p = 0.0085).
Conclusions
We observed a moderate frequency of PDR that did not significantly contribute to virologic non-suppression at term. Rather, higher pretreatment plasma HIV RNA, randomization to efavirenz-based ART, and shorter duration of ART were associated with non-suppression. These findings support early prenatal care engagement of pregnant women and initiation of integrase inhibitor-based ART due to its association with more rapid suppression of plasma RNA levels. Furthermore, because minority variants appeared infrequent in ART-naïve pregnant women and inconsequential to ART-suppression, testing for minority variants may be unwarranted.
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Affiliation(s)
- Ceejay L. Boyce
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Ingrid A. Beck
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Sheila M. Styrchak
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Samantha R. Hardy
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Jackson J. Wallner
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Ross S. Milne
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - R. Leavitt Morrison
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - David E. Shapiro
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Esaú C. João
- Infectious Diseases Department, Hospital Federal dos Servidores do Estado, Rio de Janeiro, Brazil
| | - Mark H. Mirochnick
- Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Lisa M. Frenkel
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Departments of Pediatrics, Laboratory Medicine and Pathology and Medicine, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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11
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Mwangi A, van Wyk B. Factors Associated with Viral Suppression Among Adolescents on Antiretroviral Therapy in Homa Bay County, Kenya: A Retrospective Cross-Sectional Study. HIV AIDS (Auckl) 2021; 13:1111-1118. [PMID: 34992469 PMCID: PMC8713714 DOI: 10.2147/hiv.s345731] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/01/2021] [Indexed: 12/03/2022] Open
Abstract
Background Despite the success in initiating adolescents living with HIV on antiretroviral therapy (ART), questions remain about factors affecting viral suppression. In Kenya, only 63% of adolescents (aged 10–19 years) on ART had achieved viral suppression in 2016. We investigated factors associated with viral suppression among adolescents initiated on ART before November 30, 2017 in Homa Bay County, Kenya. Methods A retrospective cross-sectional analysis of 908 adolescents registered on ART for at least 6 months and with at least one documented viral load in the last 12 months, in six health facilities in Homa Bay County was conducted. Data were extracted from the electronic medical records and exported into an excel spreadsheet. Bivariate and multivariate logistic regression analyses were conducted to identify factors associated with viral suppression and adjust for confounding, using Stata 12.0. Results Out of all participants, 80% (726) had achieved viral suppression (<1,000 copies of viral RNA/mL of blood at latest viral load count). After adjusting for other covariates, adolescents with good adherence to ART (AOR=2.3, 95% CI=1.38–3.84) and a most recent CD4 count of above 500 cells/mm3 (AOR=1.87, 95% CI=1.13–3.08), were more likely to be virally suppressed. Adolescents on second line ART treatment (AOR=0.45, 95% CI=0.28–0.73) and having inadequate adherence to ART (AOR=0.26, 95% CI=0.11–63) were less likely to be virally suppressed. Conclusion Viral suppression for adolescents on ART in this study is significantly higher than the national prevalence in 2016 (80% vs 63%), but it is still below the WHO target of 90%. Enhanced adherence support for adolescents on ART should be implemented to improve long-term adherence. Specific interventions are needed to “rescue” adolescents on second-line ART regimens who may have a history of poor adherence.
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Affiliation(s)
- Anne Mwangi
- School of Public Health, University of the Western Cape, Bellville, Western Cape Province, South Africa
| | - Brian van Wyk
- School of Public Health, University of the Western Cape, Bellville, Western Cape Province, South Africa
- Correspondence: Brian van Wyk Tel +27 82 8049055 Email
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12
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Boyce CL, Sils T, Ko D, Wong-On-Wing A, Beck IA, Styrchak SM, DeMarrais P, Tierney C, Stranix-Chibanda L, Flynn PM, Taha TE, Owor M, Fowler MG, Frenkel LM. Maternal HIV drug resistance is associated with vertical transmission and is prevalent in infected infants. Clin Infect Dis 2021; 74:2001-2009. [PMID: 34467974 DOI: 10.1093/cid/ciab744] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND We aimed to assess if maternal HIV drug resistance is associated with an increased risk of HIV vertical transmission and to describe the dynamics of drug resistance in HIV-infected infants. METHODS A case-control study of PROMISE study participants. "Cases" were mother-infant pairs with HIV vertical transmission during pregnancy or breastfeeding and "controls" were mother-infant pairs without transmission matched 1:3 by delivery date and clinical site. Genotypic HIV drug resistance analyses were performed on mothers' and their infants' plasma at or near the time of infant HIV diagnosis. Longitudinal analysis of genotypic resistance was assessed in available specimens from infants, from diagnosis and beyond, including ART initiation and last study visits. RESULTS Our analyses included 85 cases and 255 matched controls. Maternal HIV drug resistance, adjusted for plasma HIV RNA load at infant HIV diagnosis, enrollment CD4 count, and antepartum regimens, was not associated with in utero/peripartum HIV transmission. In contrast, both maternal plasma HIV RNA load and HIV drug resistance were independent risk factors associated with vertical transmission during breastfeeding. Furthermore, HIV drug resistance was selected across infected infants during infancy. CONCLUSIONS Maternal HIV drug resistance and maternal viral load were independent risk factors for vertical transmission during breastfeeding, suggesting that nevirapine alone may be insufficient infant prophylaxis against drug-resistant variants in maternal breast milk. These findings support efforts to achieve suppression of HIV replication during pregnancy and suggest that breastfeeding infants may benefit from prophylaxis with a greater barrier to drug resistance than nevirapine alone.
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Affiliation(s)
- Ceejay L Boyce
- Department of Global Health, University of Washington, Seattle, WA, USA.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Tatiana Sils
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Daisy Ko
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Annie Wong-On-Wing
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Ingrid A Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Sheila M Styrchak
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Patricia DeMarrais
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Camlin Tierney
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Patricia M Flynn
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Taha E Taha
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | - Maxensia Owor
- Makerere University-Johns Hopkins University Research Collaboration, Kampala, Uganda
| | - Mary Glenn Fowler
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Lisa M Frenkel
- Department of Global Health, University of Washington, Seattle, WA, USA.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA.,Department of Pediatrics and Laboratory Medicine, University of Washington, Seattle, WA, USA
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13
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Application of next generation sequencing in HIV drug resistance studies in Africa, 2005–2019: A systematic review. SCIENTIFIC AFRICAN 2021. [DOI: 10.1016/j.sciaf.2021.e00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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14
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Liu L, Dong A, Liao L, Feng Y, Shao Y, Liang S, Ruan Y, Xing H. Survey of Pretreatment HIV Drug Resistance and Genetic Transmission Network Analysis Among HIV Patients in a High Drug-Use Area of Southwest China. Curr HIV Res 2021; 17:441-451. [PMID: 31778107 PMCID: PMC7497539 DOI: 10.2174/1570162x17666191128101426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/21/2019] [Accepted: 11/23/2019] [Indexed: 11/22/2022]
Abstract
Background: Pretreatment drug resistance (PDR) poses an increasing threat to the success of antiretroviral treatment (ART) programs in China. We aimed to conduct a survey of PDR among HIV patients in an area in Southwest China with extensive drug trafficking. Methods: Consecutive cross-sectional surveys were conducted in Liangshan Prefecture of Sichuan Province from 2009 to 2018 based on the WHO-recommended method. PDR was identified by testing pol region sequences with the Stanford HIVdb algorithm (version 7.0). PDR prevalence and related factors were assessed by multivariable logistic regression. The transmission of HIV drug resistance was analyzed using a genetic transmission network. Results: HIV-1 pol genes from 1889 patients were successfully amplified. The distribution of HIV-1 genotypes was as follows: CRF07_BC (94.0%), CRF08_BC (2.3%), CRF01_AE (2.0%) and others (1.4%). Of the participants, 6.9% (95% CI: 4.1-8.1%) had pretreatment resistance to 12 antiretroviral drugs recommended by the WHO, and nucleoside reverse transcriptase inhibitor (NRTI), non-nucleoside reverse transcriptase inhibitor (NNRTI) and protease inhibitors (PI) resistance were identified among 1.4% (95% CI: 0.7-3.4%), 5.8% (95% CI: 1.2-8.7%) and 0.4% (95% CI: 0.1-3.0%) of the patients, respectively. In the multivariate logistic model, the prevalence of PDR was 1.52-fold higher among intravenous drug users (IDUs) than among patients infected by heterosexual transmission (95% CI: 1.07-2.38; P=0.049), and the prevalence of PDR among patients diagnosed from 2017-2018 was 2.03-fold higher than that among patients diagnosed from 2009-2016 (95% CI: 1.18-5.76; P=0.018). A total of 26 clusters containing PDR and a rapidly growing drug resistance-related cluster containing the E138Q and V179D mutations were identified by genetic transmission network analysis. Conclusion: The results show a moderate overall level of PDR prevalence and rapidly growing drug resistance over time. Preventive intervention should be focused on controlling the HIV epidemic among drug users, and surveillance is urgently needed to monitor the trend of PDR.
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Affiliation(s)
- Lei Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Aobo Dong
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Lingjie Liao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Shu Liang
- Sichuan Provincial Center for Disease Control and Prevention, Chengdu, Sichuan, China
| | - Yuhua Ruan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
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15
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Crowell TA, Danboise B, Parikh A, Esber A, Dear N, Coakley P, Kasembeli A, Maswai J, Khamadi S, Bahemana E, Iroezindu M, Kiweewa F, Owuoth J, Freeman J, Jagodzinski LL, Malia JA, Eller LA, Tovanabutra S, Peel SA, Ake JA, Polyak CS. Pretreatment and Acquired Antiretroviral Drug Resistance Among Persons Living With HIV in Four African Countries. Clin Infect Dis 2020; 73:e2311-e2322. [PMID: 32785695 PMCID: PMC8492117 DOI: 10.1093/cid/ciaa1161] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Emerging HIV drug resistance (HIVDR) could jeopardize the success of standardized HIV management protocols in resource-limited settings. We characterized HIVDR among antiretroviral therapy (ART)-naive and experienced participants in the African Cohort Study (AFRICOS). METHODS From January 2013 to April 2019, adults with HIV-1 RNA >1000 copies/mL underwent ART history review and HIVDR testing upon enrollment at 12 clinics in Uganda, Kenya, Tanzania, and Nigeria. We calculated resistance scores for specific drugs and tallied major mutations to non-nucleoside reverse transcriptase inhibitors (NNRTIs), nucleoside reverse transcriptase inhibitors (NRTIs), and protease inhibitors (PIs) using Stanford HIVDB 8.8 and SmartGene IDNS software. For ART-naive participants, World Health Organization surveillance drug resistance mutations (SDRMs) were noted. RESULTS HIVDR testing was performed on 972 participants with median age 35.7 (interquartile range [IQR] 29.7-42.7) years and median CD4 295 (IQR 148-478) cells/mm3. Among 801 ART-naive participants, the prevalence of SDRMs was 11.0%, NNRTI mutations 8.2%, NRTI mutations 4.7%, and PI mutations 0.4%. Among 171 viremic ART-experienced participants, NNRTI mutation prevalence was 83.6%, NRTI 67.8%, and PI 1.8%. There were 90 ART-experienced participants with resistance to both efavirenz and lamivudine, 33 (36.7%) of whom were still prescribed these drugs. There were 10 with resistance to both tenofovir and lamivudine, 8 (80.0%) of whom were prescribed these drugs. CONCLUSIONS Participants on failing ART regimens had a high burden of HIVDR that potentially limited the efficacy of standardized first- and second-line regimens. Management strategies that emphasize adherence counseling while delaying ART switch may promote drug resistance and should be reconsidered.
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Affiliation(s)
- Trevor A Crowell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Brook Danboise
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Ajay Parikh
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Allahna Esber
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Nicole Dear
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Peter Coakley
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Alex Kasembeli
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,HJF Medical Research International, Kericho, Kenya
| | - Jonah Maswai
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,HJF Medical Research International, Kericho, Kenya
| | - Samoel Khamadi
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,HJF Medical Research International, Mbeya, Tanzania
| | - Emmanuel Bahemana
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,HJF Medical Research International, Mbeya, Tanzania
| | - Michael Iroezindu
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,HJF Medical Research International, Abuja, Nigeria
| | | | - John Owuoth
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,HJF Medical Research International, Kisumu, Kenya
| | - Joanna Freeman
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Linda L Jagodzinski
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Jennifer A Malia
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Leigh Ann Eller
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Sodsai Tovanabutra
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Sheila A Peel
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Julie A Ake
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Christina S Polyak
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
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Zuo L, Peng K, Hu Y, Xu Q. Genotypic Methods for HIV Drug Resistance Monitoring: The Opportunities and Challenges Faced by China. Curr HIV Res 2020; 17:225-239. [PMID: 31560290 DOI: 10.2174/1570162x17666190927154110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/05/2019] [Accepted: 09/20/2019] [Indexed: 12/18/2022]
Abstract
AIDS is a globalized infectious disease. In 2014, UNAIDS launched a global project of "90-90-90" to end the HIV epidemic by 2030. The second and third 90 require 90% of HIV-1 infected individuals receiving antiretroviral therapy (ART) and durable virological suppression. However, wide use of ART will greatly increase the emergence and spreading of HIV drug resistance and current HIV drug resistance test (DRT) assays in China are seriously lagging behind, hindering to achieve virological suppression. Therefore, recommending an appropriate HIV DRT method is critical for HIV routine surveillance and prevention in China. In this review, we summarized the current existing HIV drug resistance genotypic testing methods around the world and discussed the advantages and disadvantages of these methods.
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Affiliation(s)
- Lulu Zuo
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212002, China.,Pathogen Discovery & Big Data Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences; Shanghai 200031, China
| | - Ke Peng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yihong Hu
- Pathogen Discovery & Big Data Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences; Shanghai 200031, China
| | - Qinggang Xu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212002, China
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17
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Vannappagari V, Ragone L, Henegar C, van Wyk J, Brown D, Demarest J, Quercia R, St Clair M, Underwood M, Gatell JM, de Ruiter A, Aboud M. Prevalence of pretreatment and acquired HIV-1 mutations associated with resistance to lamivudine or rilpivirine: a systematic review. Antivir Ther 2020; 24:393-404. [PMID: 31503008 DOI: 10.3851/imp3331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND Pretreatment and acquired drug resistance mutations (DRMs) can limit antiretroviral therapy effectiveness. METHODS We review prevalence of DRMs with resistance to nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs), focusing on lamivudine and rilpivirine, from 127 articles with >100,000 individuals with HIV-1 infection. RESULTS Estimated global prevalence of pretreatment resistance to any NRTI was 4% and to any NNRTI was 6%. Most prevalent DRMs resistant to lamivudine or rilpivirine were at positions E138 (4%), V179 (1%) and M184 (1%). Estimated acquired DRM prevalence was 58% for any NRTIs and 67% for any NNRTIs, most frequently at positions M184 (58%) and Y181 (21%). CONCLUSIONS This review suggests low risk of lamivudine- or rilpivirine-resistant mutations in treatment-naive, HIV-1-infected individuals.
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Affiliation(s)
| | - Leigh Ragone
- ViiV Healthcare, Research Triangle Park, NC, USA
| | | | | | | | | | | | | | | | - Jose M Gatell
- Hospital Clinic/IDIBAPS, University of Barcelona, Barcelona, Spain.,ViiV Healthcare, Barcelona, Spain
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18
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Pretreatment HIV drug resistance in adults initiating antiretroviral therapy in China, 2017. Infect Dis Poverty 2020; 9:54. [PMID: 32448388 PMCID: PMC7247188 DOI: 10.1186/s40249-020-00668-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/06/2020] [Indexed: 12/05/2022] Open
Abstract
Background After the scale-up of antiretroviral therapy (ART) for HIV infected people, increasing numbers of patients have pretreatment drug resistance (PDR). In this study, the prevalence of PDR was evaluated in adults initiating antiretroviral therapy in China. Methods Blood samples were obtained from 1943 patients who initiated antiretroviral therapy (ART) in 2017 from 13 provinces or cities in China. Pol sequences were used to analyze drug resistance and construct transmission networks. Logistic regression model was used to estimate the potential factors associated with PDR. Results In total, 1711 eligible patients (76.0% male; 87.8% aged ≥ 25 years) were included, of which 117 (6.8%) had PDR. The highest rates of PDR were 12.2% in Liangshan Prefecture of Sichuan and 9.3 and 8.9% in Dehong and Lincang Prefecture of Yunnan. A multivariate logistic regression analysis revealed that PDR was significantly higher among intravenous drug users (adjusted Odds Ratio (aOR) = 2.64, 95% CI: 1.57–4.44) and individuals from Liangshan, Dehong, and Lincang (aOR = 2.04, 95% CI: 1.26–3.30). In total, 754 sequences were used to generate 164 transmission networks. Five transmission networks had two or three sequences containing the same mutations, two networks contained subjects from Liangshan, and one network contained subjects from Dehong. Conclusions Overall, the PDR prevalence was moderate, with a particularly high prevalence in areas with severe HIV epidemics. These results indicate the importance of continuous PDR monitoring in patients initiating antiretroviral therapy.
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19
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Beck IA, Levine M, McGrath CJ, Bii S, Milne RS, Kingoo JM, So I, Andersen N, Dross S, Coombs RW, Kiarie J, Chohan B, Sakr SR, Chung MH, Frenkel LM. Pre-treatment HIV-drug resistance associated with virologic outcome of first-line NNRTI-antiretroviral therapy: A cohort study in Kenya. EClinicalMedicine 2020; 18:100239. [PMID: 31956856 PMCID: PMC6962698 DOI: 10.1016/j.eclinm.2019.100239] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Pre-treatment HIV-drug-resistance (PDR) to WHO-recommended 1st-line non-nucleoside reverse transcriptase inhibitors (NNRTI)-based antiretroviral treatment (ART) is increasing in low-resource communities. We evaluated the risk of PDR on treatment failure if detected at single or multiple codons, at minority (2-9%) or higher (≥10%) frequencies during efavirenz- vs. nevirapine-ART. METHODS We conducted a pooled analysis across three cohorts of Kenyans initiating 1st-line NNRTI-ART between 2006 and 2014. Mutations K103N, Y181C, G190A, M184V and K65R were detected by an oligonucleotide ligation assay (OLA) and confirmed by Sanger and next-generation sequencing (NGS). PDR was defined as detection of any mutation by OLA when confirmed by NGS. Treatment failure, defined as plasma HIV RNA ≥400 copies/mL at month-12 of ART, was compared by PDR genotypes. FINDINGS PDR was detected in 59/1231 (4·8%) participants. Compared to wild-type genotypes, PDR in participants prescribed nevirapine-ART was associated with increased treatment failure [PDR 69·2% (27/39) vs. wild-type 10·4% (70/674); p = 0·0001], whether detected as minority [66·7% (4/6)] or higher [69·7% (23/33)] frequencies in an individual's HIV quasispecies (p = 0·002 and p < 0·0001, respectively), or mutations at single [50·0% (12/24)] or multiple [100·0% (15/15)] codons (p < 0·0001). During efavirenz-ART, PDR was also associated with increased virologic failure [PDR 25·0% (5/20) vs. wild-type 5·0% (25/498); p = 0·005], but only if detected at multiple drug-resistant codons [50·0% (3/6); p = 0·003] or high frequencies PDR [33·3% (5/15); p = 0·001]. INTERPRETATION The risk that PDR confers for treatment failure varies by number of mutant codons and their frequency in the quasispecies, with a lower risk for efavirenz- compared to nevirapine-based regimens. PDR detection and management could extend the effective use of efavirenz-ART in low-resource settings. FUNDING NIH, PEPFAR.
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Affiliation(s)
- Ingrid A. Beck
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Molly Levine
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Christine J. McGrath
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Steve Bii
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Ross S. Milne
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - James M. Kingoo
- Department of Global Health, University of Washington, Seattle, WA, United States
- Coptic Hope Center for Infectious Diseases, Coptic Hospital, Nairobi, Kenya
| | - Isaac So
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Nina Andersen
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Sandra Dross
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Robert W. Coombs
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States
| | - James Kiarie
- Department of Obstetrics and Gynecology, University of Nairobi, Nairobi, Kenya
| | - Bhavna Chohan
- Department of Global Health, University of Washington, Seattle, WA, United States
- Kenya Medical Research Institute, Nairobi, Kenya
| | - Samah R. Sakr
- Coptic Hope Center for Infectious Diseases, Coptic Hospital, Nairobi, Kenya
| | - Michael H. Chung
- Department of Global Health, University of Washington, Seattle, WA, United States
- Department of Medicine, Aga Khan University, Nairobi, Kenya
| | - Lisa M. Frenkel
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
- Corresponding author at: Seattle Children's Research Institute, 307 Westlake Ave N, Seattle, WA 98109, United States.
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20
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Chung MH, McGrath CJ, Beck IA, Levine M, Milne RS, So I, Andersen N, Dross S, Coombs RW, Chohan B, Yatich N, Kiptinness C, Sakr SR, Kiarie JN, Frenkel LM. Evaluation of the management of pretreatment HIV drug resistance by oligonucleotide ligation assay: a randomised controlled trial. Lancet HIV 2019; 7:e104-e112. [PMID: 31818716 DOI: 10.1016/s2352-3018(19)30337-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 08/14/2019] [Accepted: 08/27/2019] [Indexed: 11/30/2022]
Abstract
BACKGROUND Although experts have recommended testing for pretreatment drug resistance (PDR) before antiretroviral therapy (ART) initiation, there is little evidence to support its implementation. We aimed to establish whether an inexpensive point mutation assay can improve virological suppression by identifying PDR to guide drug selection for ART in a lower-middle income country. METHODS Investigators did an open-label, randomised controlled trial at three HIV treatment sites in Kenya: two in Nairobi and one in rural Maseno. Individuals (aged ≥2 years) were eligible to participate if they were confirmed HIV-seropositive, qualified for first-line ART, planned to reside in the area for more than 1 year, and provided informed consent. We randomly assigned participants (1:1) to either PDR testing by oligonucleotide ligation assay (OLA) to guide selection of ART or to standard of care, which did not include OLA testing. The OLA-guided therapy group had pre-ART peripheral blood mononuclear cells evaluated for drug resistance to non-nucleoside reverse transcriptase inhibitor (NNRTI) at codons Lys103Asn, Tyr181Cys, Gly190Ala, and to lamivudine at Met184Val, and when at least one drug-resistant codon was detected in a participant's pre-ART specimen, clinicians were directed to prescribe protease inhibitor-based second-line ART. Those without detected resistance and those who were randomised to standard of care received NNRTI-based first-line ART. The primary outcome was plasma HIV-1 RNA of at least 400 copies per mL at 4, 8, or 12 months after ART initiation, which defined virological failure, assessed in all participants who received treatment (data were censored for those lost-to-follow-up or who died). The study has been completed and is registered with ClinicalTrials.gov, NCT01898754. FINDINGS We screened 1198 participants between May 28, 2013, and Nov 4, 2014, of whom 991 (83%) were enrolled (492 received OLA and 495 received standard of care; four did not begin treatment). 93 participants (prevalence 9·4%) had PDR (95% CI 7·7-11·4). 34 (8·5%) of 400 participants in the OLA group had virological failure at month 12 of ART (95% CI 6·0-11·7) compared with 39 (9·7%) of 402 (7·0-13·0) in the standard-of-care group (log-rank p=0·26). Among participants with PDR, virological failure was lower in the OLA-guided therapy group than in the standard-of-care group: five (14%) of 35 compared with 13 (50%) of 26; p=0·0020). Among those prescribed NNRTI-based ART, participants given efavirenz were less likely to have virological failure than were those receiving nevirapine (odds ratio 0·37, 95% CI 0·22-0·62; p<0·0001). The OLA-guided therapy group had 39 serious non-lethal adverse events and 34 deaths. The standard-of-care group had 34 severe adverse events and 43 deaths, differences that were not significant. Adverse events judged to potentially be due to ART were few and similar between groups, with 17 (16%) in the OLA-guided therapy group and 16 (16%) in the standard-of-care group (p=0·90). INTERPRETATION Our finding that OLA testing for PDR reduced virological failure in only those with specific PDR mutations suggests that PDR poses less of a risk for virological failure than that predicted by past prevalence estimates, and that the value of PDR testing to reduce virological failure should be assessed for antiretroviral treatment regimens. FUNDING US National Institutes of Health.
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Affiliation(s)
- Michael H Chung
- Department of Global Health, University of Washington, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA
| | | | - Ingrid A Beck
- Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Molly Levine
- Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Ross S Milne
- Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Isaac So
- Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Nina Andersen
- Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Sandra Dross
- Department of Global Health, University of Washington, Seattle, WA, USA; Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Robert W Coombs
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Bhavna Chohan
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Nelly Yatich
- Department of Global Health, University of Washington, Seattle, WA, USA
| | | | | | - James N Kiarie
- Department of Obstetrics and Gynaecology, University of Nairobi, Nairobi, Kenya
| | - Lisa M Frenkel
- Department of Global Health, University of Washington, Seattle, WA, USA; Department of Laboratory Medicine, University of Washington, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA; Seattle Children's Research Institute, University of Washington, Seattle, WA, USA.
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21
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Panpradist N, Beck IA, Vrana J, Higa N, McIntyre D, Ruth PS, So I, Kline EC, Kanthula R, Wong-On-Wing A, Lim J, Ko D, Milne R, Rossouw T, Feucht UD, Chung M, Jourdain G, Ngo-Giang-Huong N, Laomanit L, Soria J, Lai J, Klavins ED, Frenkel LM, Lutz BR. OLA-Simple: A software-guided HIV-1 drug resistance test for low-resource laboratories. EBioMedicine 2019; 50:34-44. [PMID: 31767540 PMCID: PMC6921160 DOI: 10.1016/j.ebiom.2019.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 01/21/2023] Open
Abstract
Background HIV drug resistance (HIVDR) testing can assist clinicians in selecting treatments. However, high complexity and cost of genotyping assays limit routine testing in settings where HIVDR prevalence has reached high levels. Methods The oligonucleotide ligation assay (OLA)-Simple kit was developed for detection of HIVDR against first-line non-nucleoside/nucleoside reverse transcriptase inhibitors and validated on 672 codons (168 specimens) from subtypes A, B, C, D, and AE. The kit uses dry reagents to facilitate assay setup, lateral flow devices for visual HIVDR detections, and in-house software with an interface for guiding users and analyzing results. Findings HIVDR analysis of specimens by OLA-Simple compared to Sanger sequencing revealed 99.6 ± 0.3% specificity and 98.2 ± 0.9% sensitivity, and compared to high-sensitivity assays, 99.6 ± 0.6% specificity and 86.2 ± 2.5% sensitivity, with 2.6 ± 0.9% indeterminate results. OLA-Simple was performed more rapidly compared to Sanger sequencing (<4 h vs. 35–72 h). Forty-one untrained volunteers blindly tested two specimens each with 96.8 ± 0.8% accuracy. Interpretation OLA-Simple compares favorably with HIVDR genotyping by Sanger and sensitive comparators. Instructional software enabled inexperienced, first-time users to perform the assay with high accuracy. The reduced complexity, cost, and training requirements of OLA-Simple could improve access to HIVDR testing in low-resource settings and potentially allow same-day selection of appropriate antiretroviral therapy. Fund USA National Institutes of Health R01; the Clinical and Retrovirology Research Core and the Molecular Profiling and Computational Biology Core of the UW CFAR; Seattle Children's Research Institute; UW Holloman Innovation Challenge Award; Pilcher Faculty Fellowship.
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Affiliation(s)
- Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Global WACh Program, Department of Global Health, University of Washington, Seattle, WA 98104, USA
| | - Ingrid A Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Justin Vrana
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Nikki Higa
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - David McIntyre
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Parker S Ruth
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Departments of Electrical Engineering and Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Isaac So
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Enos C Kline
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Ruth Kanthula
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Medstar Georgetown University Hospital, DC, 20007, USA
| | - Annie Wong-On-Wing
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Jonathan Lim
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Daisy Ko
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Ross Milne
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Theresa Rossouw
- Department of Immunology, University of Pretoria, Pretoria 0002, South Africa
| | - Ute D Feucht
- Research Centre for Maternal, Fetal, Newborn and Child Health Care Strategies, Department of Paediatrics, University of Pretoria, Pretoria 0002, South Africa; Research Unit for Maternal and Infant Health Care Strategies, South African Medical Research Council, Kalafong Hospital, Atteridgeville 0008, South Africa
| | - Michael Chung
- Department of Global Health, University of Washington, Seattle, WA 98195, USA; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Department of Epidemiology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Department of Medicine, Aga Khan University, Nairobi, Kenya
| | - Gonzague Jourdain
- Institut de Recherche pour le Développement IRD U174 PHPT, Chiang Mai 50000, Thailand; Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
| | - Nicole Ngo-Giang-Huong
- Institut de Recherche pour le Développement IRD U174 PHPT, Chiang Mai 50000, Thailand; Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
| | - Laddawan Laomanit
- Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
| | - Jaime Soria
- Department of Infectious Diseases, Hospital Nacional Dos de Mayo, Av. Miguel Grau 13, Cercado de Lima 15003, Peru
| | - James Lai
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Eric D Klavins
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Departments of Electrical Engineering and Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Lisa M Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Division of Infectious Diseases, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Division of Virology, Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
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Meriki HD, Tufon KA, Anong DN, Atanga PN, Anyangwe IA, Cho-Ngwa F, Nkuo-Akenji T. Genetic diversity and antiretroviral resistance-associated mutation profile of treated and naive HIV-1 infected patients from the Northwest and Southwest regions of Cameroon. PLoS One 2019; 14:e0225575. [PMID: 31751428 PMCID: PMC6874083 DOI: 10.1371/journal.pone.0225575] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 11/07/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Antiretroviral therapy (ART) has improved the survival of HIV infected persons. However, rapid scale-up of ART and the high HIV-1 genetic variability, has greatly influenced the emergence of drug-resistant strains. This constitutes a potential threat to achieving the UNAIDS' 90-90-90 goals by 2020. We investigated the prevalent HIV-1 genotypes, drug resistance-associated mutations and assessed some predictors of the occurrence of these mutations. METHODS This was a hospital-based cross-sectional study conducted between October 2010 and June 2012. Participants were consecutively enrolled from selected HIV treatment centers of the Southwest and Northwest regions of Cameroon. Viral load was determined with the automated Abbott Real-time HIV-1 m2000rt System. HIV genotyping and antiretroviral resistance mutations analysis were performed using Bayer's HIV-1 TRUGENE™ Genotyping Kit and OpenGene DNA Sequencing system. The drug resistance mutation was interpreted with the Stanford HIV database. Epidemiological data were obtained using pre-tested semi-structured questionnaires. RESULTS Of the 387 participants, 239 were successfully genotyped. The median age of these participants was 33 years (interquartile range, IQR: 28-40 years), and a majority (65.7%) were female. A total of 29.3% of the participants were receiving ART. The median duration of ART was 10.5 months (IQR: 4-17.25 months). The median CD4 count and log10 viral load of study participants were 353.5 cells/ml (IQR:145-471) and 4.89 copies/ml (IQR: 3.91-5.55) respectively. CRF02 (A/G) (69%) was the most prevalent subtype followed by G (8.2%) and F (6.7%). Overall, resistance mutations were present in 37.1% of ART-experienced and 10.7% of ART-naive patients. Nucleoside reverse transcriptase inhibitors (NRTI) mutations occurred in 30% of ART-experienced and 2.4% of ART-naïve patients, while non-nucleoside reverse transcriptase inhibitors (NNRTI) mutations occurred in 34.2% of ART-experienced and 10.1% of -naïve patients. M184V (8.4%, 20/239) and K103N (5.4%, 13/239) were the most prevalent mutations. Major protease inhibitor mutations occurred in 3 (1.3%) out of the 239 sequences. The duration of ART independently predicted the occurrence of resistance mutation among ART-experienced patients. CONCLUSION The high resistance to NNRTIs, which are the main support to the backbone (NRTIs) first-line antiretroviral regimen in Cameroon, has prompted the need to rollout an integrase strand transfer inhibitor regimen (containing Dolutegravir) with a higher genetic barrier to resistance as the preferred first line regimen.
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Affiliation(s)
- Henry Dilonga Meriki
- Department of Microbiology and Parasitology, University of Buea, Buea, SW Region, Cameroon
- BioCollections Worldwide Inc., Regional Office, Buea, SW Region, Cameroon
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, SW Region, Cameroon
| | - Kukwah Anthony Tufon
- Department of Microbiology and Parasitology, University of Buea, Buea, SW Region, Cameroon
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, SW Region, Cameroon
| | - Damian Nota Anong
- Department of Microbiology and Parasitology, University of Buea, Buea, SW Region, Cameroon
| | - Pascal Nji Atanga
- Cameroon Baptist Convention Health Service, Mutengene, South West Region, Cameroon
| | - Irene Ane Anyangwe
- Department of Microbiology and Parasitology, University of Buea, Buea, SW Region, Cameroon
| | - Fidelis Cho-Ngwa
- Laboratory Department, Buea Regional Hospital, Buea, SW Region, Cameroon
| | - Theresa Nkuo-Akenji
- Department of Microbiology and Parasitology, University of Buea, Buea, SW Region, Cameroon
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Silverman RA, John-Stewart GC, Beck IA, Milne R, Kiptinness C, McGrath CJ, Richardson BA, Chohan B, Sakr SR, Frenkel LM, Chung MH. Predictors of mortality within the first year of initiating antiretroviral therapy in urban and rural Kenya: A prospective cohort study. PLoS One 2019; 14:e0223411. [PMID: 31584992 PMCID: PMC6777822 DOI: 10.1371/journal.pone.0223411] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/21/2019] [Indexed: 12/25/2022] Open
Abstract
Introduction Despite increased treatment availability, HIV-infected individuals continue to start antiretroviral therapy (ART) late in disease progression, increasing early mortality risk. Materials and methods Nested prospective cohort study within a randomized clinical trial of adult patients initiating ART at clinics in urban Nairobi and rural Maseno, Kenya, between 2013–2014. We estimated mortality incidence rates following ART initiation and used Cox proportional hazards regression to identify predictors of mortality within 12 months of ART initiation. Analyses were stratified by clinic site to examine differences in mortality correlates and risk by location. Results Among 811 participants initiated on ART, the mortality incidence rate within a year of initiating ART was 7.44 per 100 person-years (95% CI 5.71, 9.69). Among 207 Maseno and 612 Nairobi participants initiated on ART, the mortality incidence rates (per 100 person-years) were 12.78 (95% CI 8.49, 19.23) and 5.72 (95% CI 4.05, 8.09). Maseno had a 2.20-fold greater risk of mortality than Nairobi (95% CI 1.29, 3.76; P = 0.004). This association remained [adjusted hazard ratio (HR) = 2.09 (95% CI 1.17, 3.74); P = 0.013] when adjusting for age, gender, education, pre-treatment drug resistance (PDR), and CD4 count, but not when adjusting for BMI. In unadjusted analyses, other predictors (P<0.05) of mortality included male gender (HR = 1.74), age (HR = 1.04 for 1-year increase), fewer years of education (HR = 0.92 for 1-year increase), unemployment (HR = 1.89), low body mass index (BMI<18.5 m/kg2; HR = 4.99), CD4 count <100 (HR = 11.67) and 100–199 (HR = 3.40) vs. 200–350 cells/μL, and pre-treatment drug resistance (PDR; HR = 2.49). The increased mortality risk associated with older age, males, and greater education remained when adjusted for location, age, education and PDR, but not when adjusted for BMI and CD4 count. PDR remained associated with increased mortality risk when adjusted for location, age, gender, education, and BMI, but not when adjusted for CD4 count. CD4 and BMI associations with increased mortality risk persisted in multivariable analyses. Despite similar baseline CD4 counts across locations, mortality risk associated with low CD4 count, low BMI, and PDR was greater in Maseno than Nairobi in stratified analyses. Conclusions High short-term post-ART mortality was observed, partially due to low CD4 count and BMI at presentation, especially in the rural setting. Male gender, older age, and markers of lower socioeconomic status were also associated with greater mortality risk. Engaging patients earlier in HIV infection remains critical. PDR may influence short-term mortality and further studies to optimize management will be important in settings with increasing PDR.
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Affiliation(s)
- Rachel A. Silverman
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Population Health Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- * E-mail:
| | - Grace C. John-Stewart
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Ingrid A. Beck
- Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Ross Milne
- Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Catherine Kiptinness
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Christine J. McGrath
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Barbra A. Richardson
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Bhavna Chohan
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | | | - Lisa M. Frenkel
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Pediatrics, University of Washington, Seattle, Washington, United States of America
- Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Michael H. Chung
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
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Minority and majority pretreatment HIV-1 drug resistance associated with failure of first-line nonnucleoside reverse-transcriptase inhibitor antiretroviral therapy in Kenyan women. AIDS 2019; 33:941-951. [PMID: 30946148 DOI: 10.1097/qad.0000000000002134] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Among women initiating first-line nonnucleoside reverse-transcriptase inhibitor (NNRTI)-based-ART with and without a history of single-dose nevirapine (sdNVP) with or without zidovudine with or without lamivudine (ZDV with and without 3TC) for prevention of mother-to-child HIV transmission (PMTCT), we hypothesized that pre-ART HIV-drug resistance would be associated with virologic failure DESIGN/METHODS:: In a prospectively enrolled study, three genotypic drug-resistance assays [oligonucleotide-ligation-assay (OLA), consensus sequencing, and next-generation sequencing by Illumina] were retrospectively performed to detect pre-ART drug resistance. Minority or majority drug-resistant variants identified in pre-ART RNA and/or DNA, a history of antiretrovirals for PMTCT, and other risk factors were assessed for association with virologic failure. RESULTS Failure occurred in 38/169 (22.5%) women, and was associated with pre-ART drug resistance detected by any assay (OLA of plasma or PBMC, consensus sequencing of PBMC and/or plasma, and next-generation sequencing of PBMC at frequencies of at least 10% and as minority variants; all P < 0.0001). Failure was also associated with PMTCT using sdNVP and ZDV with or without 3TC, but not sdNVP only; however, the longer time-interval between PMTCT and ART initiation observed for sdNVP-only women showed no interaction with failure. Viral loads and OLA of PBMC in longitudinal specimens demonstrated rapid failure and emergence of drug resistance, particularly among sdNVP and ZDV with or without 3TC-experienced women with pre-ART drug-resistant minority variants by next-generation sequencing but without drug resistance by OLA or consensus sequencing. CONCLUSION Pre-ART drug resistance was detected similarly by OLA of PBMC or plasma and by consensus sequencing, and was associated with virologic failure soon after initiation of first-line NVP-based ART. A history of sdNVP and ZDV with or without 3TC for PMTCT or minority variants detected by next-generation sequencing identified additional women with failure. These findings emphasize the value of assessing individual antiretroviral history, particularly nonsuppressive antiretrovirals with at least two drug classes, and testing for pre-ART drug resistance, including minority variants.
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Chimukangara B, Kharsany AB, Lessells RJ, Naidoo K, Rhee SY, Manasa J, Gräf T, Lewis L, Cawood C, Khanyile D, Diallo K, Ayalew KA, Shafer RW, Hunt G, Pillay D, Abdool SK, de Oliveira T. Moderate-to-High Levels of Pretreatment HIV Drug Resistance in KwaZulu-Natal Province, South Africa. AIDS Res Hum Retroviruses 2019; 35:129-138. [PMID: 30430843 DOI: 10.1089/aid.2018.0202] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
There is evidence of increasing levels of pretreatment HIV drug resistance (PDR) in Southern Africa. We used data from two large population-based HIV surveillance studies to estimate prevalence of PDR in KwaZulu-Natal, the province with the highest HIV prevalence in South Africa. Sanger sequencing was performed on samples obtained from a longitudinal HIV surveillance program (study A, 2013-2014) and the HIV Incidence Provincial Surveillance System (study B, 2014-2015). Sequences were included for adult HIV positive participants (age ≥15 years for study A, age 15-49 years for study B) with no documented prior exposure to antiretroviral therapy (ART). Overall and drug class-specific PDR was estimated using the World Health Organization 2009 surveillance drug resistance mutation (SDRM) list, and phylogenetic analysis was performed to establish evidence of drug resistance transmission linkage. A total of 1,845 sequences were analyzed (611 study A; 1,234 study B). An overall PDR prevalence of 9.2% [95% confidence interval (CI) 7.0-11.7] was observed for study A and 11.0% (95% CI 8.9-13.2) for study B. In study B, the prevalence of non-nucleoside reverse-transcriptase inhibitor (NNRTI) PDR exceeded 10% for sequences collected in 2014 (10.2%, 95% CI 7.5-12.9). The most prevalent SDRMs were K103NS (7.5%), M184VI (2.4%), and V106AM (1.4%). There was no evidence of large transmission chains of drug-resistant virus. High level NNRTI PDR (>10%) suggests a need to modify the standard first-line ART regimen and to focus attention on improving the quality of HIV prevention, treatment, and care.
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Affiliation(s)
- Benjamin Chimukangara
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Ayesha B.M. Kharsany
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard J. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Soo-Yon Rhee
- Department of Medicine, Stanford University, Stanford, California
| | - Justen Manasa
- Department of Medicine, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - Tiago Gräf
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Lara Lewis
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Cherie Cawood
- Epicentre AIDS Risk Management (Pty) Limited, Paarl, Cape Town, South Africa
| | - David Khanyile
- Epicentre AIDS Risk Management (Pty) Limited, Paarl, Cape Town, South Africa
| | - Karidia Diallo
- Centers for Disease Control and Prevention (CDC), Pretoria, South Africa
| | - Kassahun A. Ayalew
- Centers for Disease Control and Prevention (CDC), Pretoria, South Africa
| | - Robert W. Shafer
- Department of Medicine, Stanford University, Stanford, California
| | - Gillian Hunt
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Deenan Pillay
- Africa Health Research Institute, KwaZulu-Natal, South Africa
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Salim Karim Abdool
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
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HIV-genetic diversity and drug resistance transmission clusters in Gondar, Northern Ethiopia, 2003-2013. PLoS One 2018; 13:e0205446. [PMID: 30304061 PMCID: PMC6179264 DOI: 10.1371/journal.pone.0205446] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/25/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The HIV-1 epidemic in Ethiopia has been shown to be dominated by two phylogenetically distinct subtype C clades, the Ethiopian (C'-ET) and East African (C-EA) clades, however, little is known about the temporal dynamics of the HIV epidemic with respect to subtypes and distinct clades. Moreover, there is only limited information concerning transmission of HIV-1 drug resistance (TDR) in the country. METHODS A cross-sectional survey was conducted among young antiretroviral therapy (ART)-naïve individuals recently diagnosed with HIV infection, in Gondar, Ethiopia, 2011-2013 using the WHO recommended threshold survey. A total of 84 study participants with a median age of 22 years were enrolled. HIV-1 genotyping was performed and investigated for drug resistance in 67 individuals. Phylogenetic analyses were performed on all available HIV sequences obtained from Gondar (n = 301) which were used to define subtype C clades, temporal trends and local transmission clusters. Dating of transmission clusters was performed using BEAST. RESULT Four of 67 individuals (6.0%) carried a HIV drug resistance mutation strain, all associated with non-nucleoside reverse transcriptase inhibitors (NNRTI). Strains of the C-EA clade were most prevalent as we found no evidence of temporal changes during this time period. However, strains of the C-SA clade, prevalent in Southern Africa, have been introduced in Ethiopia, and became more abundant during the study period. The oldest Gondar transmission clusters dated back to 1980 (C-EA), 1983 (C-SA) and 1990 (C'-ET) indicating the presence of strains of different subtype C clades at about the same time point in Gondar. Moreover, some of the larger clusters dated back to the 1980s but transmissions within clusters have been ongoing up till end of the study period. Besides being associated with more sequences and larger clusters, the C-EA clade sequences were also associated with clustering of HIVDR sequences. One cluster was associated with the G190A mutation and showed onward transmissions at high rate. CONCLUSION TDR was detected in 6.0% of the sequenced samples and confirmed pervious reports that the two subtype C clades, C-EA and C'-ET, are common in Ethiopia. Moreover, the findings indicated an increased diversity in the epidemic as well as differences in transmission clusters sizes of the different clades and association with resistance mutations. These findings provide epidemiological insights not directly available using standard surveillance and may inform the adjustment of public health strategies in HIV prevention in Ethiopia.
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