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Branda F, Giovanetti M, Sernicola L, Farcomeni S, Ciccozzi M, Borsetti A. Comprehensive Analysis of HIV-1 Integrase Resistance-Related Mutations in African Countries. Pathogens 2024; 13:102. [PMID: 38392840 PMCID: PMC10892843 DOI: 10.3390/pathogens13020102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
The growing emergence of non-nucleoside reverse transcriptase inhibitor (NNRTI) HIV drug resistance in sub-Saharan Africa (SSA) led to the World Health Organization (WHO) recommending, in 2018, a transition to dolutegravir (DTG) as a first-line antiretroviral therapy (ART) in SSA. The broad HIV-1 genetic diversity in SSA could shape DTG effectiveness and the pattern of drug resistance mutations (DRMs) in this region. This study evaluated HIV-1 integrase (IN) DRMs and conserved regions among published groups M, N, O, and P HIV-1 sequences spanning forty years of the HIV epidemic during the transition of DTG-based ART. Overall, we found low levels of integrase strand transfer inhibitor (INSTI)-DRMs (<1%) across HIV groups between the years 1983 and 2023; however, it was unexpected to detect DRMs at statistically significantly higher frequencies in pre-INSTI (1983-2007) than in the INSTI (2008-2023) era. The variability of accessory INSTI-DRMs depended on the HIV subtypes, with implications for susceptibility to DTG. Our findings provide new perspectives on the molecular epidemiology and drug resistance profiles of INSTIs in SSA, emphasizing the need for ongoing surveillance and customized treatment approaches to address the continent's varied HIV subtypes and changing resistance patterns.
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Affiliation(s)
- Francesco Branda
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy; (F.B.); (M.C.)
| | - Marta Giovanetti
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Rome, Italy;
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, Brazil
- Climate Amplified Diseases and Epidemics (CLIMADE), Brasilia 70070-130, Brazil
| | - Leonardo Sernicola
- National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, 00161 Rome, Italy; (L.S.); (S.F.)
| | - Stefania Farcomeni
- National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, 00161 Rome, Italy; (L.S.); (S.F.)
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy; (F.B.); (M.C.)
| | - Alessandra Borsetti
- National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, 00161 Rome, Italy; (L.S.); (S.F.)
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Kiros M, Tefera DA, Andualem H, Geteneh A, Tesfaye A, Woldemichael TS, Kidane E, Alemayehu DH, Maier M, Mihret A, Abegaz WE, Mulu A. Low level of HIV-1C integrase strand transfer inhibitor resistance mutations among recently diagnosed ART-naive Ethiopians. Sci Rep 2023; 13:6546. [PMID: 37085698 PMCID: PMC10121640 DOI: 10.1038/s41598-023-33850-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/19/2023] [Indexed: 04/23/2023] Open
Abstract
With the widespread use of Integrase strand transfer inhibitors (INSTIs), surveillance of HIV-1 pretreatment drug resistance is critical in optimizing antiretroviral treatment efficacy. However, despite the introduction of these drugs, data concerning their resistance mutations (RMs) is still limited in Ethiopia. Thus, this study aimed to assess INSTI RMs and polymorphisms at the gene locus coding for Integrase (IN) among viral isolates from ART-naive HIV-1 infected Ethiopian population. This was a cross-sectional study involving isolation of HIV-1 from plasma of 49 newly diagnosed drug-naive HIV-1 infected individuals in Addis-Ababa during the period between June to December 2018. The IN region covering the first 263 codons of blood samples was amplified and sequenced using an in-house assay. INSTIs RMs were examined using calibrated population resistance tool version 8.0 from Stanford HIV drug resistance database while both REGA version 3 online HIV-1 subtyping tool and the jumping profile Hidden Markov Model from GOBICS were used to examine HIV-1 genetic diversity. Among the 49 study participants, 1 (1/49; 2%) harbored a major INSTIs RM (R263K). In addition, blood specimens from 14 (14/49; 28.5%) patients had accessory mutations. Among these, the M50I accessory mutation was observed in a highest frequency (13/49; 28.3%) followed by L74I (1/49; 2%), S119R (1/49; 2%), and S230N (1/49; 2%). Concerning HIV-1 subtype distribution, all the entire study subjects were detected to harbor HIV-1C strain as per the IN gene analysis. This study showed that the level of primary HIV-1 drug resistance to INSTIs is still low in Ethiopia reflecting the cumulative natural occurrence of these mutations in the absence of selective drug pressure and supports the use of INSTIs in the country. However, continues monitoring of drug resistance should be enhanced since the virus potentially develop resistance to this drug classes as time goes by.
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Affiliation(s)
- Mulugeta Kiros
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Aksum University, Aksum, Ethiopia.
| | | | - Henok Andualem
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Alene Geteneh
- Department of Medical Laboratory Science, College of Health Sciences, Woldia University, Woldia, Ethiopia
| | | | | | - Eleni Kidane
- The Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Melanie Maier
- Department Virology, Institute Medical Microbiology and Virology, Leipzig University, Leipzig, Germany
| | - Adane Mihret
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Woldaregay Erku Abegaz
- Department of Microbiology, Parasitology, and Immunology, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
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Henerico S, Lyimo E, Makubi AN, Magesa D, Desderius B, Mueller A, Changalucha J, Kalluvya SE, Van Zyl G, Preiser W, Mshana SE, Kasang C. Primary resistance against integrase strand transfer inhibitors in integrase strand transfer inhibitor-naive patients failing first- and second-line ART in Tanzania. J Antimicrob Chemother 2022; 77:3138-3143. [PMID: 36101479 PMCID: PMC9616539 DOI: 10.1093/jac/dkac295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
INTRODUCTION Sub-Saharan African countries are introducing integrase strand transfer inhibitors (INSTIs) in their ART programmes as the preferred first-line regimen, and dolutegravir is the INSTI of choice due to its potency, tolerability and high genetic barrier to resistance. Dolutegravir was introduced into the first-line ART regimen in Tanzania in 2019. However, there is a paucity of data on the occurrence of mutations in HIV lineages circulating in Tanzania. This study aimed to determine the prevalence of INSTI primary resistance mutations in Tanzanian patients exposed to ART but not INSTIs. METHODS Plasma samples from 50 INSTI-naive patients failing first- or second-line ART [median (IQR) age: 40 (21.93-46.41) years; 68% women] were subjected to Sanger sequencing of the HIV integrase gene. Participants had been on ART for a median (IQR) duration of 7.32 (4.73-9.29) years, with 80% and 20% failing first- and second-line ART, respectively. RESULTS No major INSTI mutations were found, but 2 (4%) participants had the accessory mutation T97A. Using the REGA HIV-1 subtyping tool, HIV subtype A1 (53.1%) was found to be dominant, followed by subtypes C (30.6%) and D (16.3%). CONCLUSIONS This study found no current evidence for transmitted resistance against INSTIs among unexposed patients failing ART and supports the scale-up of INSTI-based regimens. However, the presence of accessory mutations calls for the surveillance of INSTI resistance mutations to ensure that the anticipated long-term desired outcomes are achieved.
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Affiliation(s)
| | - Eric Lyimo
- National Institute for Medical Research, Mwanza Research Centre, Mwanza, United Republic of Tanzania
| | - Abel N Makubi
- The Ministry of Health, Dodoma, United Republic of Tanzania
| | - Daniel Magesa
- Centers for Disease Control and Prevention, United Republic of Tanzania branch, Dar es Salaam, United Republic of Tanzania
| | - Bernard Desderius
- Bugando Medical Centre, Mwanza, United Republic of Tanzania
- Catholic University of Health and Allied Sciences-Bugando, Mwanza, United Republic of Tanzania
| | - Andreas Mueller
- Klinikum Wuerzburg Mitte gGmbH, Missioklinik, Department of Tropical Medicine, Würzburg, Germany
| | - John Changalucha
- National Institute for Medical Research, Mwanza Research Centre, Mwanza, United Republic of Tanzania
| | | | - Gert Van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University/National Health Laboratory Service (NHLS) Tygerberg, Cape Town, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University/National Health Laboratory Service (NHLS) Tygerberg, Cape Town, South Africa
| | - Stephen E Mshana
- Catholic University of Health and Allied Sciences-Bugando, Mwanza, United Republic of Tanzania
| | - Christa Kasang
- German Leprosy and Tuberculosis Relief Association (DAHW), Würzburg, Germany
- Medmissio, Würzburg, Germany
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Ghasabi F, Hashempour A, Khodadad N, Bemani S, Keshani P, Shekiba MJ, Hasanshahi Z. First report of computational protein-ligand docking to evaluate susceptibility to HIV integrase inhibitors in HIV-infected Iranian patients. Biochem Biophys Rep 2022; 30:101254. [PMID: 35368742 PMCID: PMC8968007 DOI: 10.1016/j.bbrep.2022.101254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 12/04/2022] Open
Abstract
Background Iran has recently included integrase (INT) inhibitors (INTIs) in the first-line treatment regimen in human immunodeficiency virus (HIV)-infected patients. However, there is no bioinformatics data to elaborate the impact of resistance-associated mutations (RAMs) and naturally occurring polymorphisms (NOPs) on INTIs treatment outcome in Iranian patients. Method In this cross-sectional survey, 850 HIV-1-infected patients enrolled; of them, 78 samples had successful sequencing results for INT gene. Several analyses were performed including docking screening, genotypic resistance, secondary/tertiary structures, post-translational modification (PTM), immune epitopes, etc. Result The average docking energy (E value) of different samples with elvitegravir (EVG) and raltegravir (RAL) was more than other INTIs. Phylogenetic tree analysis and Stanford HIV Subtyping program revealed HIV-1 CRF35-AD was the predominant subtype (94.9%) in our cases; in any event, online subtyping tools confirmed A1 as the most frequent subtype. For the first time, CRF-01B and BF were identified as new subtypes in Iran. Decreased CD4 count was associated with several factors: poor or unstable adherence, naïve treatment, and drug user status. Conclusion As the first bioinformatic report on HIV-integrase from Iran, this study indicates that EVG and RAL are the optimal INTIs in first-line antiretroviral therapy (ART) in Iranian patients. Some conserved motifs and specific amino acids in INT-protein binding sites have characterized that mutation(s) in them may disrupt INT-drugs interaction and cause a significant loss in susceptibility to INTIs. Good adherence, treatment of naïve patients, and monitoring injection drug users are fundamental factors to control HIV infection in Iran effectively.
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Key Words
- Antiretroviral therapy, ART
- Behavioral Diseases Consultation Center, BDCC
- Bictegravir, BIC
- C-terminal domain, CTD
- CRF35-AD
- Cabotegravir, CBT
- Catalytic core domain, CCD
- Dolutegravir, DTG
- Drug resistance
- Elvitegravir, EVG
- Grand average hydropathy, GRAVY
- HIV
- Human immunodeficiency virus, HIV
- INT, Integrase
- INTIs, Integrase inhibitors (INTIs)
- Injecting drug users, IDUs
- Integrase
- Integrase inhibitors
- Molecular docking
- N-terminal domain, NTD
- Naturally occurring polymorphisms, NOPs
- Post-translational modification, PTM
- Raltegravir, RAL
- Resistance-associated mutations, RAMs
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Affiliation(s)
- Farzane Ghasabi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ava Hashempour
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nastaran Khodadad
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Soudabeh Bemani
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Parisa Keshani
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohamad Javad Shekiba
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Hasanshahi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
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Kouamou V, Mavetera J, Manasa J, Ndhlovu CE, Katzenstein D, McGregor AM. Pretreatment HIV Drug Resistance Among Adults Initiating or Re-Initiating First-Line Antiretroviral Therapy in Zimbabwe: Fast-Tracking the Transition to Dolutegravir-Based First-Line Regimens? AIDS Res Hum Retroviruses 2021; 37:776-783. [PMID: 33430681 DOI: 10.1089/aid.2020.0242] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pretreatment drug resistance (PDR) can compromise antiretroviral therapy (ART) efficacy and undermine the WHO targets to end the AIDS epidemic as a public health threat by 2030. Thus, we examined the level of PDR in Harare, Zimbabwe. Eligible study participants were adults who were ART naive or individuals with previous ART exposure reinitiating treatment, recruited between October 2018 and February 2020 in a HIV ART treatment clinic, in Harare. HIV drug resistance tests were performed for all specimens with viral load ≥400 copies/mL and interpreted using the Stanford HIVDB Algorithm. Chi-square test or Fisher's exact test was used for comparison of proportions of PDR across ART-naive or prior ART-exposed participants. All statistical analyses were performed using Stata version 14. Overall, 120 samples were genotyped of whom 104 were ART naive and 16 reported previous ART exposure. The overall PDR frequency among all participants was 31% [95% confidence interval (CI): 22.5-39.6]. PDR to any non-nucleotide reverse transcriptase inhibitor (NNRTI) was reported in 29% (95% CI: 21.0-37.9). PDR to nucleotide reverse transcriptase inhibitors (NRTIs) and protease inhibitors were low, found in 3% (95% CI: 0.9-8.2) and 1% (95% CI: 0.02-4.52), respectively. PDR to NNRTIs [efavirenz/nevirapine (EFV/NVP)] was found in 17% (95% CI: 10.5-24.6) and was more than six times higher among people with previous ART exposure than ART-naive people: 63% versus 10%, p < .001. Our study shows that PDR to NNRTIs in Zimbabwe has remarkably increased from the 10.9% prevalence reported in the 2016 WHO survey. Addressing PDR at a national level is a critical need and will be facilitated by fast-tracking the transition to dolutegravir in first-line ART regimens.
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Affiliation(s)
- Vinie Kouamou
- Department of Medicine, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Justice Mavetera
- Department of Medicine, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Justen Manasa
- Department of Medical Microbiology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | | | - David Katzenstein
- Department of Molecular Biology, Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Alan Michael McGregor
- Department of Medicine, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
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Yendewa GA, Lakoh S, Yendewa SA, Bangura K, Tabernilla A, Patiño L, Jiba DF, Vandy AO, Massaquoi SP, Osório NS, Deen GF, Sahr F, Salata RA, Poveda E. Characterizing HIV-1 Genetic Subtypes and Drug Resistance Mutations among Children, Adolescents and Pregnant Women in Sierra Leone. Genes (Basel) 2021; 12:1314. [PMID: 34573296 PMCID: PMC8469552 DOI: 10.3390/genes12091314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/15/2021] [Accepted: 08/24/2021] [Indexed: 11/17/2022] Open
Abstract
Human immunodeficiency virus (HIV) drug resistance (HIVDR) is widespread in sub-Saharan Africa. Children and pregnant women are particularly vulnerable, and laboratory testing capacity remains limited. We, therefore, used a cross-sectional design and convenience sampling to characterize HIV subtypes and resistance-associated mutations (RAMs) in these groups in Sierra Leone. In total, 96 children (age 2-9 years, 100% ART-experienced), 47 adolescents (age 10-18 years, 100% ART-experienced), and 54 pregnant women (>18 years, 72% ART-experienced) were enrolled. Median treatment durations were 36, 84, and 3 months, respectively, while the sequencing success rates were 45%, 70%, and 59%, respectively, among children, adolescents, and pregnant women. Overall, the predominant HIV-1 subtype was CRF02_AG (87.9%, 95/108), with minority variants constituting 12%. Among children and adolescents, the most common RAMs were M184V (76.6%, n = 49/64), K103N (45.3%, n = 29/64), Y181C/V/I (28.1%, n = 18/64), T215F/Y (25.0%, n = 16/64), and V108I (18.8%, n = 12/64). Among pregnant women, the most frequent RAMs were K103N (20.6%, n = 7/34), M184V (11.8%, n = 4/34), Y181C/V/I (5.9%, n = 2/34), P225H (8.8%, n = 3/34), and K219N/E/Q/R (5.9%, n = 2/34). Protease and integrase inhibitor-RAMs were relatively few or absent. Based on the genotype susceptibility score distributions, 73%, 88%, and 14% of children, adolescents, and pregnant women, respectively, were not susceptible to all three drug components of the WHO preferred first-line regimens per 2018 guidelines. These findings suggest that routine HIVDR surveillance and access to better ART choices may improve treatment outcomes in Sierra Leone.
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Affiliation(s)
- George A. Yendewa
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA;
- Division of Infectious Diseases and HIV Medicine, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Sulaiman Lakoh
- Department of Medicine, College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone; (S.L.); (S.A.Y.); (G.F.D.); (F.S.)
- Ministry of Health and Sanitation, University of Sierra Leone Teaching Hospitals Complex, Freetown, Sierra Leone; (K.B.); (D.F.J.); (A.O.V.); (S.P.M.)
| | - Sahr A. Yendewa
- Department of Medicine, College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone; (S.L.); (S.A.Y.); (G.F.D.); (F.S.)
- Ministry of Health and Sanitation, University of Sierra Leone Teaching Hospitals Complex, Freetown, Sierra Leone; (K.B.); (D.F.J.); (A.O.V.); (S.P.M.)
| | - Khadijah Bangura
- Ministry of Health and Sanitation, University of Sierra Leone Teaching Hospitals Complex, Freetown, Sierra Leone; (K.B.); (D.F.J.); (A.O.V.); (S.P.M.)
| | - Andrés Tabernilla
- Group of Virology and Pathogenesis, Galicia Sur Health Research Institute (IIS Galicia Sur), Complexo Hospitalario Universitario de Vigo, SERGAS-UVigo, 36213 Vigo, Spain; (A.T.); (L.P.); (E.P.)
| | - Lucia Patiño
- Group of Virology and Pathogenesis, Galicia Sur Health Research Institute (IIS Galicia Sur), Complexo Hospitalario Universitario de Vigo, SERGAS-UVigo, 36213 Vigo, Spain; (A.T.); (L.P.); (E.P.)
| | - Darlinda F. Jiba
- Ministry of Health and Sanitation, University of Sierra Leone Teaching Hospitals Complex, Freetown, Sierra Leone; (K.B.); (D.F.J.); (A.O.V.); (S.P.M.)
| | - Alren O. Vandy
- Ministry of Health and Sanitation, University of Sierra Leone Teaching Hospitals Complex, Freetown, Sierra Leone; (K.B.); (D.F.J.); (A.O.V.); (S.P.M.)
| | - Samuel P. Massaquoi
- Ministry of Health and Sanitation, University of Sierra Leone Teaching Hospitals Complex, Freetown, Sierra Leone; (K.B.); (D.F.J.); (A.O.V.); (S.P.M.)
| | - Nuno S. Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal;
| | - Gibrilla F. Deen
- Department of Medicine, College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone; (S.L.); (S.A.Y.); (G.F.D.); (F.S.)
- Ministry of Health and Sanitation, University of Sierra Leone Teaching Hospitals Complex, Freetown, Sierra Leone; (K.B.); (D.F.J.); (A.O.V.); (S.P.M.)
| | - Foday Sahr
- Department of Medicine, College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone; (S.L.); (S.A.Y.); (G.F.D.); (F.S.)
| | - Robert A. Salata
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA;
- Division of Infectious Diseases and HIV Medicine, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Eva Poveda
- Group of Virology and Pathogenesis, Galicia Sur Health Research Institute (IIS Galicia Sur), Complexo Hospitalario Universitario de Vigo, SERGAS-UVigo, 36213 Vigo, Spain; (A.T.); (L.P.); (E.P.)
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Li JZ, Stella N, Choudhary MC, Javed A, Rodriguez K, Ribaudo H, Moosa MY, Brijkumar J, Pillay S, Sunpath H, Noguera-Julian M, Paredes R, Johnson B, Edwards A, Marconi VC, Kuritzkes DR. Impact of pre-existing drug resistance on risk of virological failure in South Africa. J Antimicrob Chemother 2021; 76:1558-1563. [PMID: 33693678 DOI: 10.1093/jac/dkab062] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/10/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES There is conflicting evidence on the impact of pre-existing HIV drug resistance mutations (DRMs) in patients infected with non-B subtype virus. METHODS We performed a case-cohort substudy of the AIDS Drug Resistance Surveillance Study, which enrolled South African patients initiating first-line efavirenz/emtricitabine/tenofovir. Pre-ART DRMs were detected by Illumina sequencing of HIV pol and DRMs present at <20% of the viral population were labelled as minority variants (MVs). Weighted Cox proportional hazards models estimated the association between pre-ART DRMs and risk of virological failure (VF), defined as confirmed HIV-1 RNA ≥1000 copies/mL after ≥5 months of ART. RESULTS The evaluable population included 178 participants from a randomly selected subcohort (16 with VF, 162 without VF) and 83 additional participants with VF. In the subcohort, 16% of participants harboured ≥1 majority DRM. The presence of any majority DRM was associated with a 3-fold greater risk of VF (P = 0.002), which increased to 9.2-fold (P < 0.001) in those with <2 active drugs. Thirteen percent of participants harboured MV DRMs in the absence of majority DRMs. Presence of MVs alone had no significant impact on the risk of VF. Inclusion of pre-ART MVs with majority DRMs improved the sensitivity but reduced the specificity of predicting VF. CONCLUSIONS In a South African cohort, the presence of majority DRMs increased the risk of VF, especially for participants receiving <2 active drugs. The detection of drug-resistant MVs alone did not predict an increased risk of VF, but their inclusion with majority DRMs affected the sensitivity/specificity of predicting VF.
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Affiliation(s)
- Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Natalia Stella
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Aneela Javed
- Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | | | | | | | | | | | | | | | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain
| | | | - Alex Edwards
- Emory University School of Medicine and Rollins School of Public Health, Atlanta, GA, USA
| | - Vincent C Marconi
- Emory University School of Medicine and Rollins School of Public Health, Atlanta, GA, USA
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Calza L, Colangeli V, Borderi M, Testi D, Granozzi B, Bon I, Re MC, Viale P. Simplification to dual therapy containing lamivudine and raltegravir or dolutegravir in HIV-infected patients on virologically suppressive antiretroviral therapy. J Antimicrob Chemother 2021; 75:3327-3333. [PMID: 32728708 DOI: 10.1093/jac/dkaa319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 06/25/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Antiretroviral dual regimens including lamivudine and one boosted PI or dolutegravir are warranted in order to optimize combination ART (cART), prevent long-term toxicity and reduce the cost of treatments. OBJECTIVES We hypothesized that a maintenance dual regimen of lamivudine plus raltegravir would be effective and as well tolerated as the dual maintenance combination of lamivudine plus dolutegravir. METHODS We performed an observational, retrospective study of HIV-infected patients on suppressive ART who switched to a dual regimen containing lamivudine 300 mg once daily plus raltegravir 1200 mg once daily or dolutegravir 50 mg once daily. RESULTS In total, 109 patients (79 men; mean age 46.4 years; mean CD4+ T lymphocyte count 605 cells/mm3) were enrolled. Overall, 50 subjects switched to lamivudine plus raltegravir (Group A) and 59 to lamivudine plus dolutegravir (Group B). After 12 months, 45 patients (90%) in Group A and 52 (88.1%) in Group B had HIV RNA <20 copies/mL. No patients had severe adverse effects in either group, and the percentages of patients with mild adverse effects were comparable, except for a higher incidence of headache and sleeping disturbances in Group B than in Group A (30.5% versus 14%, P < 0.001). A comparable and non-significant weight increase was reported in both groups (+1.91 kg in Group A and +2.28 kg in Group B). CONCLUSIONS In our study, dual therapies containing lamivudine plus raltegravir or dolutegravir in virologically suppressed patients showed high and comparable efficacy, as well as good tolerability.
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Affiliation(s)
- Leonardo Calza
- Clinic of Infectious Diseases, 'Alma Mater Studiorum' University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Vincenzo Colangeli
- Clinic of Infectious Diseases, 'Alma Mater Studiorum' University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Marco Borderi
- Clinic of Infectious Diseases, 'Alma Mater Studiorum' University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Diletta Testi
- Clinic of Infectious Diseases, 'Alma Mater Studiorum' University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Bianca Granozzi
- Clinic of Infectious Diseases, 'Alma Mater Studiorum' University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Isabella Bon
- Unit of Microbiology, 'Alma Mater Studiorum' University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Maria Carla Re
- Unit of Microbiology, 'Alma Mater Studiorum' University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Pierluigi Viale
- Clinic of Infectious Diseases, 'Alma Mater Studiorum' University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
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Mikasi SG, Isaacs D, Chitongo R, Ikomey GM, Jacobs GB, Cloete R. Interaction analysis of statistically enriched mutations identified in Cameroon recombinant subtype CRF02_AG that can influence the development of Dolutegravir drug resistance mutations. BMC Infect Dis 2021; 21:379. [PMID: 33892628 PMCID: PMC8063366 DOI: 10.1186/s12879-021-06059-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 04/08/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND The Integrase (IN) strand transfer inhibitor (INSTI), Dolutegravir (DTG), has been given the green light to form part of first-line combination antiretroviral therapy (cART) by the World Health Organization (WHO). DTG containing regimens have shown a high genetic barrier against HIV-1 isolates carrying specific resistance mutations when compared with other class of regimens. METHODS We evaluated the HIV-1 CRF02_AG IN gene sequences from Cameroon for the presence of resistance-associated mutations (RAMs) against INSTIs and naturally occurring polymorphisms (NOPs), using study sequences (n = 20) and (n = 287) sequences data derived from HIV Los Alamos National Laboratory database. The possible impact of NOPs on protein structure caused by HIV-1 CRF02_AG variations was addressed within the context of a 3D model of the HIV-1 IN complex and interaction analysis was performed using PyMol to validate DTG binding to the Wild type and seven mutant structures. RESULTS We observed 12.8% (37/287) sequences to contain RAMs, with only 1.0% (3/287) of the sequences having major INSTI RAMs: T66A, Q148H, R263K and N155H. Of these,11.8% (34/287) of the sequences contained five different IN accessory mutations; namely Q95K, T97A, G149A, E157Q and D232N. NOPs occurred at a frequency of 66% on the central core domain (CCD) position, 44% on the C-terminal domain (CTD) position and 35% of the N-terminal domain (NTD) position. The interaction analysis revealed that DTG bound to DNA, 2MG ions and DDE motif residues for T66A, T97A, Q148H, N155H and R263K comparable to the WT structure. Except for accessory mutant structure E157Q, only one MG contact was made with DTG, while DTG had no MG ion contacts and no DDE motif residue contacts for structure D232N. CONCLUSIONS Our analysis indicated that all RAM's that resulted in a change in the number of interactions with encompassing residues does not affect DTG binding, while accessory mutations E157Q and D232N could affect DTG binding leading to possible DTG resistance. However, further experimental validation is required to validate the in silico findings of our study.
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Affiliation(s)
- Sello Given Mikasi
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Darren Isaacs
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Robert Sobukwe Rd, Bellville, P.O. Box X17, Cape Town, 7535, South Africa
| | - Rumbidzai Chitongo
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Robert Sobukwe Rd, Bellville, P.O. Box X17, Cape Town, 7535, South Africa
| | - George Mondide Ikomey
- Centre for the Study and Control of Communicable Diseases, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Robert Sobukwe Rd, Bellville, P.O. Box X17, Cape Town, 7535, South Africa.
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Mikasi SG, Isaacs D, Ikomey GM, Shimba H, Cloete R, Jacobs GB. Short Communication: HIV-1 Drug Resistance Mutation Analyses of Cameroon-Derived Integrase Sequences. AIDS Res Hum Retroviruses 2021; 37:54-56. [PMID: 32640829 DOI: 10.1089/aid.2020.0022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
HIV-1 integrase (IN) is a primary target for combination antiretroviral therapy. Only a limited number of studies report on the emergence of resistance-associated mutations (RAMs) in Cameroon. We observed that 1.4% of sequence from treatment-naive patients had IN strand transfer inhibitor (INSTI) RAMs. These mutations confer resistance to raltegravir and elvitegravir. We also observed that 10.1% of the sequences have INSTI accessory RAMs. HIV-1 CRF02_AG was the predominant subtype (44.7%) in this study analyses. The occurrence of INSTI RAMs among the sequences at baseline needs to be monitored carefully.
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Affiliation(s)
- Sello Given Mikasi
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Darren Isaacs
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - George Mondinde Ikomey
- Centre for the Study and Control of Communicable Diseases, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaounde, Cameroon
| | - Henerico Shimba
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Bugando Medical Centre, Mwanza, United Republic of Tanzania
| | - Ruben Cloete
- Centre for the Study and Control of Communicable Diseases, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaounde, Cameroon
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Structural Comparison of Diverse HIV-1 Subtypes using Molecular Modelling and Docking Analyses of Integrase Inhibitors. Viruses 2020; 12:v12090936. [PMID: 32858802 PMCID: PMC7552036 DOI: 10.3390/v12090936] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/27/2020] [Accepted: 08/05/2020] [Indexed: 12/27/2022] Open
Abstract
The process of viral integration into the host genome is an essential step of the HIV-1 life cycle. The viral integrase (IN) enzyme catalyzes integration. IN is an ideal therapeutic enzyme targeted by several drugs; raltegravir (RAL), elvitegravir (EVG), dolutegravir (DTG), and bictegravir (BIC) having been approved by the USA Food and Drug Administration (FDA). Due to high HIV-1 diversity, it is not well understood how specific naturally occurring polymorphisms (NOPs) in IN may affect the structure/function and binding affinity of integrase strand transfer inhibitors (INSTIs). We applied computational methods of molecular modelling and docking to analyze the effect of NOPs on the full-length IN structure and INSTI binding. We identified 13 NOPs within the Cameroonian-derived CRF02_AG IN sequences and further identified 17 NOPs within HIV-1C South African sequences. The NOPs in the IN structures did not show any differences in INSTI binding affinity. However, linear regression analysis revealed a positive correlation between the Ki and EC50 values for DTG and BIC as strong inhibitors of HIV-1 IN subtypes. All INSTIs are clinically effective against diverse HIV-1 strains from INSTI treatment-naïve populations. This study supports the use of second-generation INSTIs such as DTG and BIC as part of first-line combination antiretroviral therapy (cART) regimens, due to a stronger genetic barrier to the emergence of drug resistance.
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12
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Kirichenko A, Lapovok I, Baryshev P, van de Vijver DAMC, van Kampen JJA, Boucher CAB, Paraskevis D, Kireev D. Genetic Features of HIV-1 Integrase Sub-Subtype A6 Predominant in Russia and Predicted Susceptibility to INSTIs. Viruses 2020; 12:v12080838. [PMID: 32752001 PMCID: PMC7472261 DOI: 10.3390/v12080838] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023] Open
Abstract
The increasing use of the integrase strand transfer inhibitor (INSTI) class for the treatment of HIV-infection has pointed to the importance of analyzing the features of HIV-1 subtypes for an improved understanding of viral genetic variability in the occurrence of drug resistance (DR). In this study, we have described the prevalence of INSTI DR in a Russian cohort and the genetic features of HIV-1 integrase sub-subtype A6. We included 408 HIV infected patients who were not exposed to INSTI. Drug resistance mutations (DRMs) were detected among 1.3% of ART-naïve patients and among 2.7% of INSTI-naïve patients. The prevalence of 12 polymorphic mutations was significantly different between sub-subtypes A6 and A1. Analysis of the genetic barriers determined two positions in which subtype A (A1 and A6) showed a higher genetic barrier (G140C and V151I) compared with subtype B, and one position in which subtypes A1 and B displayed a higher genetic barrier (L74M and L74I) than sub-subtype A6. Additionally, we confirmed that the L74I mutation was selected at the early stage of the epidemic and subsequently spread as a founder effect in Russia. Our data have added to the overall understanding of the genetic features of sub-subtype A6 in the context of drug resistance.
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Affiliation(s)
- Alina Kirichenko
- Central Research Institute of Epidemiology, 111123 Moscow, Russia; (I.L.); (P.B.); (D.K.)
- Correspondence:
| | - Ilya Lapovok
- Central Research Institute of Epidemiology, 111123 Moscow, Russia; (I.L.); (P.B.); (D.K.)
| | - Pavel Baryshev
- Central Research Institute of Epidemiology, 111123 Moscow, Russia; (I.L.); (P.B.); (D.K.)
| | - David A. M. C. van de Vijver
- Viroscience Department, Erasmus Medical Centre, 3015 CE Rotterdam, The Netherlands; (D.A.M.C.v.d.V.); (J.J.A.v.K.); (C.A.B.B.)
| | - Jeroen J. A. van Kampen
- Viroscience Department, Erasmus Medical Centre, 3015 CE Rotterdam, The Netherlands; (D.A.M.C.v.d.V.); (J.J.A.v.K.); (C.A.B.B.)
| | - Charles A. B. Boucher
- Viroscience Department, Erasmus Medical Centre, 3015 CE Rotterdam, The Netherlands; (D.A.M.C.v.d.V.); (J.J.A.v.K.); (C.A.B.B.)
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Goudi, Athens, Greece;
| | - Dmitry Kireev
- Central Research Institute of Epidemiology, 111123 Moscow, Russia; (I.L.); (P.B.); (D.K.)
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