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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: 0] [Impact Index Per Article: 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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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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Oliveira RC, Gräf T, Rego FFDA, Silva GPSA, Giovanetti M, Monteiro Cunha JP. Dynamic Dispersion of HIV-1 Subtype C Toward Brazilian Northeastern Region. AIDS Res Hum Retroviruses 2021; 37:913-921. [PMID: 34036794 DOI: 10.1089/aid.2020.0308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The subtype C accounts for >50% of HIV type 1 (HIV-1) infections worldwide and it is currently the predominant viral form in South Brazil. Subtype C has been reported in all Brazilian regions; however, the phylogenetic relationship among strains circulating in those regions still remains unclear. This study aimed to investigate the origin and dynamic dispersion of HIV-1 subtype C toward Northeast Brazil. Our phylogenetic analysis suggests that most subtype C strains circulating in Brazil (99%) are descendant from the main lineage whose entrance in the country was previously described in the 1970s. According to the literature, additional introductions of subtype C were reported in the country through the Southeast region and in this study we identified another entry event that occurred most likely through the North region. Furthermore, our analysis suggests that the spread of subtype C to Brazilian Northeastern states occurred through multiple independent introductions of the main lineage that originated in South Brazil between mid-1980s and late 1990s. Despite the observation of eventual new HIV-1 subtype C introductions, our results highlight the predominance of a single lineage of this subtype in Brazil and the importance of South region in its dissemination throughout the country.
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Affiliation(s)
- Rodrigo Cunha Oliveira
- Núcleo de Bioinformática, Departamento de Bioquímica e Biofísica, Universidade Federal da Bahia, Salvador, Brazil
| | - Tiago Gräf
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz—FIOCRUZ, Salvador, Brazil
| | | | | | - Marta Giovanetti
- Instituto Oswaldo Cruz, Fundação Oswaldo Cruz—FIOCRUZ, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Joana Paixão Monteiro Cunha
- Núcleo de Bioinformática, Departamento de Bioquímica e Biofísica, Universidade Federal da Bahia, Salvador, Brazil
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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: 2] [Impact Index Per Article: 0.7] [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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