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Zaki EA, El-Daly MM, Abdulhaq A, Al-Subhi TL, Hassan AM, El-Kafrawy SA, Alhazmi MM, Darraj MA, Azhar EI. Genotyping and antiretroviral drug resistance of human immunodeficiency Virus-1 in Jazan, Saudi Arabia. Medicine (Baltimore) 2020; 99:e23274. [PMID: 33285702 PMCID: PMC7717766 DOI: 10.1097/md.0000000000023274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Determination of human immunodeficiency virus-1 (HIV-1) genotypes and identification of antiretroviral drug-resistant mutations. Among treatment naïve HIV patients in Jazan, Saudi Arabia. HIV is a major public health problem. HIV genotyping and antiretroviral resistance testing is an important guide for better management of treatment-naive. Antiretroviral resistance testing before starting of treatment regimen leads to a better virological response. A total of 57 samples of treatment-naive patients were collected from King Fahd Central Hospital in Jazan, Saudi Arabia. Samples were tested for HIV-1 antibodies, western blot, viral load, HIV-1 genotypes through direct sequencing, and antiretroviral resistance testing. The HIV-1 Genotypes were as follow; C: 66.6%, D: 10.5%, G: 8.8%, B: 7.0%, CRF01_AE: 3.5%, A and CRF02_AG: 1.8% each. 77.2% of cases showed susceptibility to the 3 major classes of antiretroviral drugs; Protease inhibitor (PI), Nucleoside reverse transcriptase inhibitor (NRTI), and non-nucleoside reverse transcriptase inhibitors (NNRTI); while 8.8% had mutations conferring resistance to NRTI. Mutations conferring resistance to PI were detected in 7.0% of cases, and 1.8% of cases had mutations conferring resistance to both NRTI and PI. Mutations conferring resistance to NNRTI were detected in 5.3% of cases. Mutations associated with antiretroviral drugs include (V82A+I84IV), (L10F+Q58E), (L10F+V82Y), L10FV, L33LF, L89LMV, M184V, E138A, V106I, and V179VD. The prevalence of HIV-1 antiretroviral resistance mutations is 22.8% in the studied population, which may warrant antiretroviral drug resistance testing as a pretreatment to help and guide physicians for the proper HIV treatment.
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Affiliation(s)
- Eitezaz A. Zaki
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University
- Department of Virology, Jeddah Regional Lab, Ministry of Health
| | - Mai M. El-Daly
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Clinical Pathology Department, National Liver Institute, Menoufia University, Shebin El-Kom, Egypt
| | - Ahmed Abdulhaq
- Deanship of Scientific Affairs and Research, Jazan University
| | - Tagreed L. Al-Subhi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed M. Hassan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sherif A. El-Kafrawy
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Clinical Pathology Department, National Liver Institute, Menoufia University, Shebin El-Kom, Egypt
| | | | - Majid A. Darraj
- Department of Infectious Diseases, King Fahd Central Hospital
- Department of Medicine, College of Medicine, Jazan University, Jazan, Saudi Arabia
| | - Esam I. Azhar
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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Polymorphisms and drug resistance analysis of HIV-1 isolates from patients on first line antiretroviral therapy (ART) in South-eastern Nigeria. PLoS One 2020; 15:e0231031. [PMID: 32267869 PMCID: PMC7141668 DOI: 10.1371/journal.pone.0231031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 03/15/2020] [Indexed: 11/25/2022] Open
Abstract
Acquisition of resistance mutations by HIV-1 isolates causes treatment failure among infected patients receiving antiretroviral therapy (ART). This study determined patterns of drug-resistance mutations (DRMs) among HIV-1 isolates from patients receiving first-line ART in South-eastern Nigeria. Blood samples were collected from HIV-1 infected patients accessing antiretroviral treatment centers at General Hospital Awo-Omamma, Imo state, State Hospital Asaba, Delta state and St Joseph’s Catholic Hospital Adazi, Anambra state and used for HIV-1 DNA sequencing and phylogenetic analysis. DRMs were scored using combination of Stanford algorithm and the 2015 International Antiviral Society-USA list while drug susceptibility was predicted using Stanford algorithm. Twenty eight of the HIV-1 isolates were sequenced and identified as subtypes G (35.7%), CRF02_AG (57.1%) and unclassifiable, UG (7.1%). Major PI resistance-associated mutations were identified at two sites including M46L (16.7% of subtype G/UG) and V82L (6.3% of CRF02_AG). Minor PI resistance-associated mutations identified among subtype G/UG are L10V/I (8.3%) and K20I (100%) while L10V/I (50%), K20I (100%), L33F (6.3%) and N88D (6.3%) were identified among CRF02_AG. Other polymorphisms found include; I13V/A, E35Q, M36I/L, N37D/S/E/H, R57K/G, L63T/P/S/Q, C67E/S, H69K/R, K70R, V82I and L89M in the range of 28.6% to 100% among the different subtypes. Interpretation based on Stanford algorithm showed that Darunavir/ritonavir is the only regimen whose potency was not compromised by the circulating mutations. Identification of major and minor PI resistance mutations in this study underscores the need for drug resistance testing prior to initiation of second line antiretroviral therapy in Nigeria.
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Abongwa LE, Nyamache AK, Torimiro JN, Okemo P, Charles F. Human immunodeficiency virus type 1 ((HIV-1) subtypes in the northwest region, Cameroon. Virol J 2019; 16:103. [PMID: 31416460 PMCID: PMC6694531 DOI: 10.1186/s12985-019-1209-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/05/2019] [Indexed: 12/01/2022] Open
Abstract
Background The high genetic diversity of HIV-1 has been shown to influence the global distribution, disease progression, treatment success, and the development of an effective vaccine. Despite the low HIV prevalence in Cameroon, all the major HIV subtypes alongside several circulating recombinant forms (CRFs) and unique recombinant forms (URFs) have been reported in Cameroon. To date, HIV-1 diversity in some parts of Cameroon has been largely studied however, information on circulating HIV-1 subtypes in the Northwest region (NWR) of Cameroon is dearth. Therefore the aim of this study was to determine the current circulating HIV-1 subtypes among adults in the NWR of Cameroon. Methods The genetic analysis of the reverse transcriptase region of the pol gene was performed on 81 samples. The samples were collected from drug naïve patients aged between 18 and 61 years residing within the rural and urban towns in the NWR during the period between February and April 2016. Viral RNA was extracted from plasma, reverse-transcribed, further amplified by nested-PCR before sequencing using an in-house protocol. Generated sequences were then phylogenetically analyzed together with references using MEGA 7. Results Phylogenetic analysis revealed a broad viral diversity including CRF02 _AG (74.1%), F2 (7.4%), D (7.4%), G (3.7%), A1 (1.2%), CRF22_01A1 (2.5%), CRF06_cpx (1.2%), CRF09_cpx (1.2%), CRF11_cpx (1.2%). Three close epidemic clusters were found among F2 (1) and CRF02_AG (2) variants. For the first time we are reporting the CRF22_01A1 subtype in this region. Conclusion Our findings update HIV-1 subtypes information in Cameroon and uphold previous studies that CRF02_AG is the most prevalent subtype. This CRF02_AG subtype may have important public health, research, and clinical consequences.
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Affiliation(s)
- Lem Edith Abongwa
- Department of Biochemistry, Biotechnology, and Microbiology, School of Pure and Applied Sciences, Kenyatta University, Nairobi, Kenya. .,Department of Biological Sciences, Faculty of Science, University of Bamenda, Northwest, Region, Bamenda, Cameroon. .,Laboratory of Molecular Biology, Chantal Biya International Center for Research on the Prevention and Management of HIV / AIDS (CIRCB), Yaounde, Cameroon.
| | - Anthony Kebira Nyamache
- Department of Biochemistry, Biotechnology, and Microbiology, School of Pure and Applied Sciences, Kenyatta University, Nairobi, Kenya
| | - Judith Ndongo Torimiro
- Laboratory of Molecular Biology, Chantal Biya International Center for Research on the Prevention and Management of HIV / AIDS (CIRCB), Yaounde, Cameroon.,Department of Biochemistry, Faculty of Medicine and Biomedical Science, University of Yaounde I, Yaounde, Cameroon
| | - Paul Okemo
- Department of Biochemistry, Biotechnology, and Microbiology, School of Pure and Applied Sciences, Kenyatta University, Nairobi, Kenya
| | - Fokunang Charles
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, University of Yaounde, Yaounde, Cameroon
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Rosemary A, Chika O, Jonathan O, Godwin I, Georgina O, Azuka O, Zaidat M, Philippe C, Oliver E, Oche A, David O, Jay S, Ibrahim D, Mukhtar A, Joshua D, Chunfu Y, Elliot R, Beth C, Phyllis K, Emmanuel I. Genotyping performance evaluation of commercially available HIV-1 drug resistance test. PLoS One 2018; 13:e0198246. [PMID: 29953436 PMCID: PMC6023177 DOI: 10.1371/journal.pone.0198246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/16/2018] [Indexed: 11/18/2022] Open
Abstract
Background ATCC HIV-1 drug resistance test kit was designed to detect HIV-1 drug resistance (HIVDR) mutations in the protease and reverse transcriptase genes for all HIV-1 group M subtypes and circulating recombinant forms. The test has been validated for both plasma and dried blood spot specimen types with viral load (VL) of ≥1000 copies/ml. We performed an in-country assessment on the kit to determine the genotyping sensitivity and its accuracy in detecting HIVDR mutations using plasma samples stored under suboptimal conditions. Methods Among 572 samples with VL ≥1000 copies/ml that had been genotyped by ViroSeq assay, 183 were randomly selected, including 85 successful genotyped and 98 unsuccessful genotyped samples. They were tested with ATCC kits following the manufacturer’s instructions. Sequence identity and HIVDR patterns were analysed with Stanford University HIV Drug Resistance HIVdb program. Results Of the 183 samples, 127 (69.4%) were successfully genotyped by either method. While ViroSeq system genotyped 85/183 (46.5%) with median VL of 32,971 (IQR: 11,150–96,506) copies/ml, ATCC genotyped 115/183 (62.8%) samples with median VL of 23,068 (IQR: 7,397–86,086) copies/ml. Of the 98 unsuccessful genotyped samples with ViroSeq assay, 42 (42.9%) samples with lower median VL of 13,906 (IQR: 6,122–72,329) copies/ml were successfully genotyped using ATCC. Sequence identity analysis revealed that the sequences generated by both methods were >98% identical and yielded similar HIVDR profiles at individual patient level. Conclusion This study confirms that ATCC kit showed greater sensitivity in genotyping plasma samples stored in suboptimal conditions experiencing frequent and prolonged power outage. Thus, it is more sensitive particularly for subtypes A and A/G HIV-1 in resource-limited settings.
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Affiliation(s)
- Audu Rosemary
- Nigerian Institute of Medical Research, Lagos, Nigeria
- * E-mail:
| | | | | | | | | | | | - Musa Zaidat
- Nigerian Institute of Medical Research, Lagos, Nigeria
| | | | - Ezechi Oliver
- Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Agbaji Oche
- Jos University Teaching Hospital, Jos, Nigeria
| | | | - Samuel Jay
- AIDS Prevention Initiative in Nigeria, Abuja, Nigeria
| | | | - Ahmed Mukhtar
- Centers for Disease Control and Prevention, Abuja, Nigeria
| | - DeVos Joshua
- Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Yang Chunfu
- Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Raizes Elliot
- Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Chaplin Beth
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States of America
| | - Kanki Phyllis
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States of America
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