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Khan A, Pillay M, Chimukangara B, Gounder L, Manyana S, Francois KL, Chipango K. Identification of HIV-1 subtype CRF18_cpx in a patient with multidrug resistance in KwaZulu-Natal, South Africa: An epidemiological worry? JOURNAL OF CLINICAL VIROLOGY PLUS 2023. [DOI: 10.1016/j.jcvp.2023.100143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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The differences in functional recovery between HIV-positive and HIV-negative stroke survivors. Turk J Phys Med Rehabil 2019; 64:314-321. [PMID: 31453528 DOI: 10.5606/tftrd.2018.1708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 02/05/2018] [Indexed: 11/21/2022] Open
Abstract
Objectives This study aims to identify the differences in functional abilities between stroke survivors who are human immunodeficiency virus (HIV)-positive and HIV-negative. Patients and methods This was a retrospective, longitudinal record review of stroke survivors' files between April 2005 and December 2010. Of a total of 173 stroke survivors who were admitted to the rehabilitation unit, 141 (75 males, 66 females; mean age 52.7±14.3 years; range, 19 to 86 years) met the inclusion criteria. The patients were divided into two groups as HIV-positive (n=21) and HIV-negative (n=120). Functional ability was recorded using the admission and discharge BETA® scores. Results Ischemic strokes were more prevalent than hemorrhagic strokes (74.5% vs. 25.5%, respectively) with hypertension as the most common (31.9%) stroke risk factor. The mean age of stroke onset for HIV-positive patients and HIV-negative patients was 39.6 years and 54.9 years, respectively. In HIV-positive patients, the mean duration of rehabilitation was 7.5-day shorter than HIV-negative patients. After receiving rehabilitation from a multidisciplinary team, the HIV-positive group improved with a mean of 40 points and the HIV-negative group improved with a mean of 38 points. The similarities in functional outcome between the HIV-positive and HIV-negative group were related to the fact that HIV-positive stroke survivors were relatively younger than the HIV-negative group. Conclusion Our study results show that patients who sustain a stroke, are HIV-positive, are receiving antiretroviral therapy and rehabilita- tion may recover similar to those who are HIV-negative, spending a similar length of stay in a rehabilitation clinic. Therefore, stroke survivors who are HIV-positive should receive full rehabilitation similar to any other stroke survivors.
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Anderson SG, McCaul M, Khoo S, Wiesner L, Sacktor N, Joska JA, Decloedt EH. The neurologic phenotype of South African patients with HIV-associated neurocognitive impairment. Neurol Clin Pract 2019; 10:15-22. [PMID: 32190416 DOI: 10.1212/cpj.0000000000000687] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/30/2019] [Indexed: 11/15/2022]
Abstract
Background The neurologic manifestations of HIV include a spectrum of HIV-associated neurocognitive disorders, as well as a cluster of neurologic symptoms and signs. The neurologic manifestations have been modified but not eradicated by antiretroviral therapy (ART). We describe the neurologic phenotype in South African patients with predominant HIV-1 subtype C infection on ART and its association with neurocognitive impairment and efavirenz and 8-hydroxy-efavirenz concentrations. Methods We conducted a cross-sectional analysis of the neurologic examination findings of HIV+ patients with neurocognitive impairment and used multiple linear regression to explore associations with neurocognitive impairment, efavirenz, and 8-hydroxy-efavirenz pharmacokinetics (plasma and CSF). Results We included 80 participants established on ART (median 40 months) of which 72 (90%) were female. The median age was 35 (interquartile range [IQR], 32-42) and the median Global Deficit Score was 0.94 (IQR 0.63-1.36). We found associations between neurocognitive impairment and neurologic signs: gait (slow walking speed [p = 0.03; R2 = 0.06], gait ataxia [p < 0.01; R2 = 0.21], and abnormal gait appearance [p < 0.01; R2 = 0.18]); coordination (upper limb bradykinesia [p < 0.01; R2 = 0.10] and lower limb bradykinesia [p = 0.01; R2 = 0.10]); reflexes (jaw jerk [p = 0.04; R2 = 0.05] and palmomental response [p = 0.03; R2 = 0.06]); ocular signs (impaired smooth pursuit [p = 0.01; R2 = 0.09] and impaired saccades [p < 0.01; R2 = 0.15]); and motor signs (spasticity [p ≤ 0.01; R2 = 0.15] and muscle weakness [p = 0.01; R2 = 0.08]). No significant associations were found between plasma and CSF efavirenz or 8-hydroxy efavirenz concentrations and any neurologic sign. Conclusion We found that individual neurologic signs were associated with neurocognitive impairment in South African HIV+ patients with predominant HIV-1 subtype C infection on ART and could be used in clinical practice to assess severity. Registration number PACTR201310000635418.
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Affiliation(s)
- Sean G Anderson
- Division of Clinical Pharmacology (SGA, EHD), Faculty of Medicine and Health Sciences, University of Stellenbosch; Biostatistics Unit (MM), Division of Epidemiology and Biostatistics, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa; Institute of Translational Medicine (SK), University of Liverpool, and Royal Liverpool University Hospital, United Kingdom; Division of Clinical Pharmacology (LW), Department of Medicine, University of Cape Town, South Africa; Department of Neurology (NS), Johns Hopkins University School of Medicine, Baltimore, MD; and Division of Neuropsychiatry (JAJ), Department of Psychiatry and Mental Health, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Michael McCaul
- Division of Clinical Pharmacology (SGA, EHD), Faculty of Medicine and Health Sciences, University of Stellenbosch; Biostatistics Unit (MM), Division of Epidemiology and Biostatistics, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa; Institute of Translational Medicine (SK), University of Liverpool, and Royal Liverpool University Hospital, United Kingdom; Division of Clinical Pharmacology (LW), Department of Medicine, University of Cape Town, South Africa; Department of Neurology (NS), Johns Hopkins University School of Medicine, Baltimore, MD; and Division of Neuropsychiatry (JAJ), Department of Psychiatry and Mental Health, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Saye Khoo
- Division of Clinical Pharmacology (SGA, EHD), Faculty of Medicine and Health Sciences, University of Stellenbosch; Biostatistics Unit (MM), Division of Epidemiology and Biostatistics, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa; Institute of Translational Medicine (SK), University of Liverpool, and Royal Liverpool University Hospital, United Kingdom; Division of Clinical Pharmacology (LW), Department of Medicine, University of Cape Town, South Africa; Department of Neurology (NS), Johns Hopkins University School of Medicine, Baltimore, MD; and Division of Neuropsychiatry (JAJ), Department of Psychiatry and Mental Health, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Lubbe Wiesner
- Division of Clinical Pharmacology (SGA, EHD), Faculty of Medicine and Health Sciences, University of Stellenbosch; Biostatistics Unit (MM), Division of Epidemiology and Biostatistics, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa; Institute of Translational Medicine (SK), University of Liverpool, and Royal Liverpool University Hospital, United Kingdom; Division of Clinical Pharmacology (LW), Department of Medicine, University of Cape Town, South Africa; Department of Neurology (NS), Johns Hopkins University School of Medicine, Baltimore, MD; and Division of Neuropsychiatry (JAJ), Department of Psychiatry and Mental Health, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Ned Sacktor
- Division of Clinical Pharmacology (SGA, EHD), Faculty of Medicine and Health Sciences, University of Stellenbosch; Biostatistics Unit (MM), Division of Epidemiology and Biostatistics, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa; Institute of Translational Medicine (SK), University of Liverpool, and Royal Liverpool University Hospital, United Kingdom; Division of Clinical Pharmacology (LW), Department of Medicine, University of Cape Town, South Africa; Department of Neurology (NS), Johns Hopkins University School of Medicine, Baltimore, MD; and Division of Neuropsychiatry (JAJ), Department of Psychiatry and Mental Health, Faculty of Health Sciences, University of Cape Town, South Africa
| | - John A Joska
- Division of Clinical Pharmacology (SGA, EHD), Faculty of Medicine and Health Sciences, University of Stellenbosch; Biostatistics Unit (MM), Division of Epidemiology and Biostatistics, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa; Institute of Translational Medicine (SK), University of Liverpool, and Royal Liverpool University Hospital, United Kingdom; Division of Clinical Pharmacology (LW), Department of Medicine, University of Cape Town, South Africa; Department of Neurology (NS), Johns Hopkins University School of Medicine, Baltimore, MD; and Division of Neuropsychiatry (JAJ), Department of Psychiatry and Mental Health, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Eric H Decloedt
- Division of Clinical Pharmacology (SGA, EHD), Faculty of Medicine and Health Sciences, University of Stellenbosch; Biostatistics Unit (MM), Division of Epidemiology and Biostatistics, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa; Institute of Translational Medicine (SK), University of Liverpool, and Royal Liverpool University Hospital, United Kingdom; Division of Clinical Pharmacology (LW), Department of Medicine, University of Cape Town, South Africa; Department of Neurology (NS), Johns Hopkins University School of Medicine, Baltimore, MD; and Division of Neuropsychiatry (JAJ), Department of Psychiatry and Mental Health, Faculty of Health Sciences, University of Cape Town, South Africa
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Rogers L, Obasa AE, Jacobs GB, Sarafianos SG, Sönnerborg A, Neogi U, Singh K. Structural Implications of Genotypic Variations in HIV-1 Integrase From Diverse Subtypes. Front Microbiol 2018; 9:1754. [PMID: 30116231 PMCID: PMC6083056 DOI: 10.3389/fmicb.2018.01754] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 07/13/2018] [Indexed: 01/02/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) integrase (IN) integrates viral DNA into the host genome using its 3′-end processing and strand-transfer activities. Due to the importance of HIV-1 IN, it is targeted by the newest class of approved drugs known as integrase strand transfer inhibitors (INSTIs). INSTIs are efficient in maintaining low viral load; however, as with other approved antivirals, resistance mutations emerge in patients receiving INSTI-containing therapy. As INSTIs are becoming increasingly accessible worldwide, it is important to understand the mechanism(s) of INSTI susceptibility. There is strong evidence suggesting differences in the patterns and mechanisms of drug resistance between HIV-1 subtype B, which dominates in United States, Western Europe and Australia, and non-B infections that are most prevalent in countries of Africa and Asia. IN polymorphisms and other genetic differences among diverse subtypes are likely responsible for these different patterns, but lack of a full-length high-resolution structure of HIV-1 IN has been a roadblock in understanding the molecular mechanisms of INSTI resistance and the impact of polymorphisms on therapy outcome. A recently reported full-length medium-resolution cryoEM structure of HIV-1 IN provides insights into understanding the mechanism of integrase function and the impact of genetic variation on the effectiveness of INSTIs. Here we use molecular modeling to explore the structural impact of IN polymorphisms on the IN reaction mechanism and INSTI susceptibility.
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Affiliation(s)
- Leonard Rogers
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Adetayo E Obasa
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa.,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Graeme B Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Kamalendra Singh
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
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Brado D, Obasa AE, Ikomey GM, Cloete R, Singh K, Engelbrecht S, Neogi U, Jacobs GB. Analyses of HIV-1 integrase sequences prior to South African national HIV-treatment program and available of integrase inhibitors in Cape Town, South Africa. Sci Rep 2018; 8:4709. [PMID: 29549274 PMCID: PMC5856838 DOI: 10.1038/s41598-018-22914-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/01/2018] [Indexed: 01/16/2023] Open
Abstract
HIV-Integrase (IN) has proven to be a viable target for highly specific HIV-1 therapy. We aimed to characterize the HIV-1 IN gene in a South African context and identify resistance-associated mutations (RAMs) against available first and second generation Integrase strand-transfer inhibitors (InSTIs). We performed genetic analyses on 91 treatment-naïve HIV-1 infected patients, as well as 314 treatment-naive South African HIV-1 IN-sequences, downloaded from Los Alamos HIV Sequence Database. Genotypic analyses revealed the absence of major RAMs in the cohort collected before the broad availability of combination antiretroviral therapy (cART) and INSTI in South Africa, however, occurred at a rate of 2.85% (9/314) in database derived sequences. RAMs were present at IN-positions 66, 92, 143, 147 and 148, all of which may confer resistance to Raltegravir (RAL) and Elvitegravir (EVG), but are unlikely to affect second-generation Dolutegravir (DTG), except mutations in the Q148 pathway. Furthermore, protein modeling showed, naturally occurring polymorphisms impact the stability of the intasome-complex and therefore may contribute to an overall potency against InSTIs. Our data suggest the prevalence of InSTI RAMs, against InSTIs, is low in South Africa, but natural polymorphisms and subtype-specific differences may influence the effect of individual treatment regimens.
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Affiliation(s)
- Dominik Brado
- Division of Virology, Institute for Virology and Immunobiology, Faculty of Medicine, University of Wuerzburg, 97080, Wuerzburg, Germany
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Adetayo Emmanuel Obasa
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa.
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, University of Stockholm, Stockholm, Sweden.
| | - George Mondinde Ikomey
- CSCCD, Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Western Cape, South Africa
| | - Kamalendra Singh
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, University of Stockholm, Stockholm, Sweden
- Department of Molecular Microbiology and Immunology, Columbia, MO, 65211, USA
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Susan Engelbrecht
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, University of Stockholm, Stockholm, Sweden
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
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Ikomey GM, Assoumou MCO, Gichana JO, Njenda D, Mikasi SG, Mesembe M, Lyonga E, Jacobs GB. Observed HIV drug resistance associated mutations amongst naïve immunocompetent children in Yaoundé, Cameroon. Germs 2017; 7:178-185. [PMID: 29264355 DOI: 10.18683/germs.2017.1124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/29/2017] [Accepted: 10/19/2017] [Indexed: 11/08/2022]
Abstract
Introduction The emergence of drug resistance mutations (DRMs) has been a major threat for successful lifelong combination antiretroviral therapy (cART), especially for HIV-vertically infected children within the context of the prevention of mother-to-child transmission (PMTCT). This study aimed to evaluate DRMs amongst immune competent treatment-naïve children in Cameroon. Methods A cross-sectional study was conducted between 2015 and 2016 amongst 55 proxy consented HIV-1 positive children, aged 9 months to 6 years. They were all immune competent, cART naïve and with unknown history of PMTCT. CD4 cell counts and genotypic drug resistance testing were performed using standard methods. Results Levels of DRMs to protease (PR) inhibitors (PIs), nucleoside reverse transcriptase inhibitors (NRTIs) and non-NRTIs were 27.6%, 3.7% and 40.7%, respectively. Only minor DRMs were observed for PR. The observed mutations for NRTI were K65R, T215I and K219E (33.0% each) and for NNRTI: V106M, Y181C and Y188H (6.0% each). Only minor accessory mutations were found in the integrase (IN) region. Conclusion Despite widely available cART we still observe naïve HIV children, especially from the rural communities. We observe that a proportion of study participants had HIV-1 drug resistance associated mutations (RAMs). Data generated could help strengthen the current PMTCT programmes within the country. There is a need to upscale approaches for drug resistance testing for children in Cameroon and many other resource-limited settings.
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Affiliation(s)
- George Mondinde Ikomey
- PhD, Center for the Study and Control of Communicable Diseases (CSCCD), Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, PO Box 8445, Yaoundé, Cameroon
| | - Marie Claire Okomo Assoumou
- PhD, Center for the Study and Control of Communicable Diseases (CSCCD) Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, PO Box 8445, Yaoundé, Cameroon
| | - Josiah Otwoma Gichana
- BSc, Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Tygerberg 7505, South Africa
| | - Duncan Njenda
- MSc, Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Tygerberg 7505, South Africa
| | - Sello Given Mikasi
- MSc, Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Tygerberg 7505, South Africa
| | - Martha Mesembe
- BSc, Center for the Study and Control of Communicable Diseases (CSCCD) Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, PO Box 8445, Yaoundé, Cameroon
| | - Emilia Lyonga
- MSc, Center for the Study and Control of Communicable Diseases (CSCCD) Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, PO Box 8445, Yaoundé, Cameroon
| | - Graeme Brendon Jacobs
- PhD, Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Tygerberg 7505, South Africa
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Wilkinson E, Holzmayer V, Jacobs GB, de Oliveira T, Brennan CA, Hackett J, van Rensburg EJ, Engelbrecht S. Sequencing and phylogenetic analysis of near full-length HIV-1 subtypes A, B, G and unique recombinant AC and AD viral strains identified in South Africa. AIDS Res Hum Retroviruses 2015; 31:412-20. [PMID: 25492033 PMCID: PMC4378615 DOI: 10.1089/aid.2014.0230] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
By the end of 2012, more than 6.1 million people were infected with HIV-1 in South Africa. Subtype C was responsible for the majority of these infections and more than 300 near full-length genomes (NFLGs) have been published. Currently very few non-subtype C isolates have been identified and characterized within the country, particularly full genome non-C isolates. Seven patients from the Tygerberg Virology (TV) cohort were previously identified as possible non-C subtypes and were selected for further analyses. RNA was isolated from five individuals (TV047, TV096, TV101, TV218, and TV546) and DNA from TV016 and TV1057. The NFLGs of these samples were amplified in overlapping fragments and sequenced. Online subtyping tools REGA version 3 and jpHMM were used to screen for subtypes and recombinants. Maximum likelihood (ML) phylogenetic analysis (phyML) was used to infer subtypes and SimPlot was used to confirm possible intersubtype recombinants. We identified three subtype B (TV016, TV047, and TV1057) isolates, one subtype A1 (TV096), one subtype G (TV546), one unique AD (TV101), and one unique AC (TV218) recombinant form. This is the first NFLG of subtype G that has been described in South Africa. The subtype B sequences described also increased the NFLG subtype B sequences in Africa from three to six. There is a need for more NFLG sequences, as partial HIV-1 sequences may underrepresent viral recombinant forms. It is also necessary to continue monitoring the evolution and spread of HIV-1 in South Africa, because understanding viral diversity may play an important role in HIV-1 prevention strategies.
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Affiliation(s)
- Eduan Wilkinson
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Academic Hospital, Tygerberg, Cape Town, South Africa
- Africa Centre for Health and Population Studies, University of KwaZulu-Natal, Mtubatuba, South Africa
| | | | - Graeme B. Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Academic Hospital, Tygerberg, Cape Town, South Africa
| | - Tulio de Oliveira
- Africa Centre for Health and Population Studies, University of KwaZulu-Natal, Mtubatuba, South Africa
| | | | | | | | - Susan Engelbrecht
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Academic Hospital, Tygerberg, Cape Town, South Africa
- National Health Laboratory Services (NHLS), Western Cape Region, Tygerberg Hospital (Coastal), Cape Town, South Africa
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Msimanga PW, Vardas E, Engelbrecht S. HIV-1 diversity in an antiretroviral treatment naïve cohort from Bushbuckridge, Mpumalanga Province, South Africa. Virol J 2015; 12:24. [PMID: 25889106 PMCID: PMC4340098 DOI: 10.1186/s12985-015-0244-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 01/19/2015] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND South Africa has a generalized and explosive HIV/AIDS epidemic with the largest number of people infected with HIV-1 in the world. Molecular investigations of HIV-1 diversity can help enhance interventions to contain and combat the HIV/AIDS epidemic. However, many studies of HIV-1 diversity in South Africa tend to be limited to the major metropolitan centers and their surrounding provinces. Hardly any studies of HIV diversity have been undertaken in Mpumalanga Province, and this study sought to investigate the HIV-1 diversity in this province, as well as establish the occurrence and extent of transmitted antiretroviral drug resistance mutations. METHODS HIV-1 gag p24, pol p10 and p66/p51, pol p31 and env gp41 gene fragments from 43 participants were amplified and sequenced. Quality control on the sequences was carried out using the LANL QC online tool. HIV-1 subtype was preliminary assigned using the REGA 3.0 and jpHMM online tools. Subtype for the pol gene fragment was further designated using the SCUEAL online tool. Phylogenetic analysis was inferred using the Maximum Likelihood methods in MEGA version 6. HIV-1 antiretroviral drug resistance mutations were determined using the Stanford database. RESULTS Phylogenetic analysis using Maximum Likelihood methods indicated that all sequences in the study clustered with HIV-1 subtype C. The exception was one putative subtype BC unique recombinant form. Antiretroviral drug resistance mutations K103N and E138A were also detected, indicating possible transmission of anti-retroviral drug resistance mutations. CONCLUSIONS The phylogenetic analysis of the HIV sequences revealed that, by 2009, patients in the Bushbuckridge, Mpumalanga were predominantly infected with HIV-1 subtype C. However, the generalized, explosive nature of the HIV/AIDS epidemic in South Africa, in the context of extensive mobility by South Africans who inhabit rural areas, renders the continued molecular monitoring and surveillance of the epidemic imperative.
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Affiliation(s)
- Patrick Wela Msimanga
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Hospital, P.O. Box 241, Cape Town, 8000, South Africa.
- Current Address: National Department of Health, Civitas Building, Corner Thabo Sehume and Struben Streets, P.O. Box X828, Pretoria, 0001, South Africa.
| | - Efthyia Vardas
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Hospital, P.O. Box 241, Cape Town, 8000, South Africa.
- Lancet Laboratories, P.O. Box 8475, Johannesburg, 2000, South Africa.
| | - Susan Engelbrecht
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Hospital, P.O. Box 241, Cape Town, 8000, South Africa.
- National Health Laboratory Services (NHLS), Western Cape Region, Tygerberg Hospital (Coastal), Tygerberg, Cape Town, South Africa.
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Detection of transmission clusters of HIV-1 subtype C over a 21-year period in Cape Town, South Africa. PLoS One 2014; 9:e109296. [PMID: 25357201 PMCID: PMC4214637 DOI: 10.1371/journal.pone.0109296] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 08/31/2014] [Indexed: 11/19/2022] Open
Abstract
Introduction Despite recent breakthroughs in the fight against the HIV/AIDS epidemic within South Africa, the transmission of the virus continues at alarmingly high rates. It is possible, with the use of phylogenetic methods, to uncover transmission events of HIV amongst local communities in order to identify factors that may contribute to the sustained transmission of the virus. The aim of this study was to uncover transmission events of HIV amongst the infected population of Cape Town. Methods and Results We analysed gag p24 and RT-pol sequences which were generated from samples spanning over 21-years with advanced phylogenetic techniques. We identified two transmission clusters over a 21-year period amongst randomly sampled patients from Cape Town and the surrounding areas. We also estimated the origin of each of the identified transmission clusters with the oldest cluster dating back, on average, 30 years and the youngest dating back roughly 20 years. Discussion and Conclusion These transmission clusters represent the first identified transmission events among the heterosexual population in Cape Town. By increasing the number of randomly sampled specimens within a dataset over time, it is possible to start to uncover transmission events of HIV amongst local communities in generalized epidemics. This information can be used to produce targeted interventions to decrease transmission of HIV in Africa.
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Middelkoop K, Rademeyer C, Brown BB, Cashmore TJ, Marais JC, Scheibe AP, Bandawe GP, Myer L, Fuchs JD, Williamson C, Bekker LG. Epidemiology of HIV-1 subtypes among men who have sex with men in Cape Town, South Africa. J Acquir Immune Defic Syndr 2014; 65:473-80. [PMID: 24583617 DOI: 10.1097/qai.0000000000000067] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Early studies in Cape Town identified independent HIV-1 epidemics, with distinct viral subtypes, among men who have sex with men (MSM) and the heterosexual population. However, few recent HIV-1 subtype data are available for MSM in South Africa. We examined HIV-1 subtypes among MSM in Cape Town. DESIGN Cross-sectional survey. METHODS Self-identified MSM were recruited from geographically and racially disparate communities across Cape Town. Participants completed behavioral questionnaires and underwent HIV testing. Virus isolated from infected participants underwent complete env gp160 sequencing, and HIV-1 subtypes were assigned through phylogenetic analysis. RESULTS In total, 194 HIV-infected MSM were enrolled: 67% black African, 24% colored, and 9% white men. More black African men identified as bisexual or heterosexual compared with other races. Overall, 31%-66% of men reported a recent partner of another race. HIV-1 subtypes were confirmed for 143 participants: 81% were subtype C, 14% B, 1% A1, 1% F2, and 3 recombinant viruses. Subtype C virus was associated with black African race (P = 0.003 compared with colored; P < 0.001 compared with white), men who identified as bisexual/heterosexual (P = 0.01), and reported a female sexual partner in the last year (P = 0.02). Compared with previous studies, an increasing prevalence of subtype C virus was noted among white MSM. CONCLUSIONS This molecular epidemiology study provides novel evidence of sexual network links between the heterosexual and MSM epidemics and between historically racially disparate communities. These findings provide insights into the drivers of HIV epidemics in different population groups and may have implications for prevention strategies.
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Affiliation(s)
- Keren Middelkoop
- *Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine and †Department of Medicine, University of Cape Town, Cape Town, South Africa; ‡Division of Medical Virology and §Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; ‖Division of Epidemiology & Biostatistics, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa; ¶Center for Learning and Innovation, San Francisco Department of Public Health, San Francisco, CA; #University of California, San Francisco; and **National Health Laboratory Services, Cape Town, South Africa
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11
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Jacobs GB, Wilkinson E, Isaacs S, Spies G, de Oliveira T, Seedat S, Engelbrecht S. HIV-1 subtypes B and C unique recombinant forms (URFs) and transmitted drug resistance identified in the Western Cape Province, South Africa. PLoS One 2014; 9:e90845. [PMID: 24609015 PMCID: PMC3946584 DOI: 10.1371/journal.pone.0090845] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 02/04/2014] [Indexed: 12/31/2022] Open
Abstract
South Africa has the largest worldwide HIV/AIDS population with 5.6 million people infected and at least 2 million people on antiretroviral therapy. The majority of these infections are caused by HIV-1 subtype C. Using genotyping methods we characterized HIV-1 subtypes of the gag p24 and pol PR and RT fragments, from a cohort of female participants in the Western Cape Province, South Africa. These participants were recruited as part of a study to assess the combined brain and behavioural effects of HIV and early childhood trauma. The partial HIV-1 gag and pol fragments of 84 participants were amplified by PCR and sequenced. Different online tools and manual phylogenetic analysis were used for HIV-1 subtyping. Online tools included: REGA HIV Subtyping tool version 3; Recombinant Identification Program (RIP); Context-based Modeling for Expeditious Typing (COMET); jumping profile Hidden Markov Models (jpHMM) webserver; and subtype classification using evolutionary algorithms (SCUEAL). HIV-1 subtype C predominates within the cohort with a prevalence of 93.8%. We also show, for the first time, the presence of circulating BC strains in at least 4.6% of our study cohort. In addition, we detected transmitted resistance associated mutations in 4.6% of analysed sequences. With tourism and migration rates to South Africa currently very high, we are detecting more and more HIV-1 URFs within our study populations. It is stil unclear what role these unique strains will play in terms of long term antiretroviral treatment and what challenges they will pose to vaccine development. Nevertheless, it remains vitally important to monitor the HIV-1 diversity in South Africa and worldwide as the face of the epidemic is continually changing.
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Affiliation(s)
| | - Eduan Wilkinson
- Division of Medical Virology, Stellenbosch University, Tygerberg, South Africa
- Africa Center for Health and Population Studies, University of KwaZulu-Natal, Mtubatuba, South Africa
| | - Shahieda Isaacs
- Division of Medical Virology, Stellenbosch University, Tygerberg, South Africa
| | - Georgina Spies
- Department of Psychiatry, Stellenbosch University, Tygerberg, South Africa
| | - Tulio de Oliveira
- Africa Center for Health and Population Studies, University of KwaZulu-Natal, Mtubatuba, South Africa
| | - Soraya Seedat
- Department of Psychiatry, Stellenbosch University, Tygerberg, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Stellenbosch University, Tygerberg, South Africa
- National Health Laboratory Services (NHLS), Tygerberg Coastal, South Africa
- * E-mail:
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12
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Horn A, Scheller C, du Plessis S, Arendt G, Nolting T, Joska J, Sopper S, Maschke M, Obermann M, Husstedt IW, Hain J, Maponga T, Riederer P, Koutsilieri E. Increases in CSF dopamine in HIV patients are due to the dopamine transporter 10/10-repeat allele which is more frequent in HIV-infected individuals. J Neural Transm (Vienna) 2013; 120:1411-9. [PMID: 24057505 PMCID: PMC3779317 DOI: 10.1007/s00702-013-1086-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 08/23/2013] [Indexed: 11/30/2022]
Abstract
Dysfunction of dopaminergic neurotransmission has been implicated in HIV infection. We showed previously increased dopamine (DA) levels in CSF of therapy-naïve HIV patients and an inverse correlation between CSF DA and CD4 counts in the periphery, suggesting adverse effects of high levels of DA on HIV infection. In the current study including a total of 167 HIV-positive and negative donors from Germany and South Africa (SA), we investigated the mechanistic background for the increase of CSF DA in HIV individuals. Interestingly, we found that the DAT 10/10-repeat allele is present more frequently within HIV individuals than in uninfected subjects. Logistic regression analysis adjusted for gender and ethnicity showed an odds ratio for HIV infection in DAT 10/10 allele carriers of 3.93 (95% CI 1.72-8.96; p = 0.001, Fishers exact test). 42.6% HIV-infected patients harbored the DAT 10/10 allele compared to only 10.5% uninfected DAT 10/10 carriers in SA (odds ratio 6.31), whereas 68.1 versus 40.9%, respectively, in Germany (odds ratio 3.08). Subjects homozygous for the 10-repeat allele had higher amounts of CSF DA and reduced DAT mRNA expression but similar disease severity compared with those carrying other DAT genotypes. These intriguing and novel findings show the mutual interaction between DA and HIV, suggesting caution in the interpretation of CNS DA alterations in HIV infection solely as a secondary phenomenon to the virus and open the door for larger studies investigating consequences of the DAT functional polymorphism on HIV epidemiology and progression of disease.
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Affiliation(s)
- Anne Horn
- Institute of Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
| | - Carsten Scheller
- Institute of Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
| | - Stefan du Plessis
- Department of Psychiatry, Stellenbosch University, Stellenbosch, South Africa
| | - Gabriele Arendt
- Department of Neurology, University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Thorsten Nolting
- Department of Neurology, University Hospital of Düsseldorf, Düsseldorf, Germany
| | - John Joska
- Department of Psychiatry, University of Cape Town, Cape Town, South Africa
| | | | - Matthias Maschke
- Department of Neurology, University Hospital of Duisburg-Essen, Essen, Germany
| | - Mark Obermann
- Department of Neurology, University Hospital of Duisburg-Essen, Essen, Germany
| | - Ingo W. Husstedt
- Department of Neurology, University Hospital of Münster, Münster, Germany
| | - Johannes Hain
- Institute of Mathematics and Informatics, Chair of Mathematics VIII (Statistics), University of Würzburg, Würzburg, Germany
| | - Tongai Maponga
- Department of Virology, Stellenbosch University, Stellenbosch, South Africa
| | - Peter Riederer
- Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Eleni Koutsilieri
- Institute of Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
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Pineda-Peña AC, Faria NR, Imbrechts S, Libin P, Abecasis AB, Deforche K, Gómez-López A, Camacho RJ, de Oliveira T, Vandamme AM. Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools. INFECTION GENETICS AND EVOLUTION 2013; 19:337-48. [PMID: 23660484 DOI: 10.1016/j.meegid.2013.04.032] [Citation(s) in RCA: 277] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 04/10/2013] [Accepted: 04/28/2013] [Indexed: 12/26/2022]
Abstract
BACKGROUND To investigate differences in pathogenesis, diagnosis and resistance pathways between HIV-1 subtypes, an accurate subtyping tool for large datasets is needed. We aimed to evaluate the performance of automated subtyping tools to classify the different subtypes and circulating recombinant forms using pol, the most sequenced region in clinical practice. We also present the upgraded version 3 of the Rega HIV subtyping tool (REGAv3). METHODOLOGY HIV-1 pol sequences (PR+RT) for 4674 patients retrieved from the Portuguese HIV Drug Resistance Database, and 1872 pol sequences trimmed from full-length genomes retrieved from the Los Alamos database were classified with statistical-based tools such as COMET, jpHMM and STAR; similarity-based tools such as NCBI and Stanford; and phylogenetic-based tools such as REGA version 2 (REGAv2), REGAv3, and SCUEAL. The performance of these tools, for pol, and for PR and RT separately, was compared in terms of reproducibility, sensitivity and specificity with respect to the gold standard which was manual phylogenetic analysis of the pol region. RESULTS The sensitivity and specificity for subtypes B and C was more than 96% for seven tools, but was variable for other subtypes such as A, D, F and G. With regard to the most common circulating recombinant forms (CRFs), the sensitivity and specificity for CRF01_AE was ~99% with statistical-based tools, with phylogenetic-based tools and with Stanford, one of the similarity based tools. CRF02_AG was correctly identified for more than 96% by COMET, REGAv3, Stanford and STAR. All the tools reached a specificity of more than 97% for most of the subtypes and the two main CRFs (CRF01_AE and CRF02_AG). Other CRFs were identified only by COMET, REGAv2, REGAv3, and SCUEAL and with variable sensitivity. When analyzing sequences for PR and RT separately, the performance for PR was generally lower and variable between the tools. Similarity and statistical-based tools were 100% reproducible, but this was lower for phylogenetic-based tools such as REGA (~99%) and SCUEAL (~96%). CONCLUSIONS REGAv3 had an improved performance for subtype B and CRF02_AG compared to REGAv2 and is now able to also identify all epidemiologically relevant CRFs. In general the best performing tools, in alphabetical order, were COMET, jpHMM, REGAv3, and SCUEAL when analyzing pure subtypes in the pol region, and COMET and REGAv3 when analyzing most of the CRFs. Based on this study, we recommend to confirm subtyping with 2 well performing tools, and be cautious with the interpretation of short sequences.
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Affiliation(s)
- Andrea-Clemencia Pineda-Peña
- Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, University of Leuven, Belgium; Clinical and Molecular Infectious Diseases Group, Faculty of Sciences and Mathematics, Universidad del Rosario, Bogotá, Colombia.
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14
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Kabue JP, de Swardt D, de Beer C, Glashoff RH. Short-term antiretroviral therapy fails to reduce the expanded activated CCR5-expressing CD4+ T lymphocyte population or to restore the depleted naive population in chronically HIV-infected individuals with active pulmonary tuberculosis. AIDS Res Hum Retroviruses 2013; 29:769-77. [PMID: 23259904 DOI: 10.1089/aid.2012.0153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The effective role of antiretroviral (ARV) therapy in the regulation of CD4 T cell subset distribution, coreceptor expression, and activation status in individuals with chronic HIV also presenting with active pulmonary TB is not clearly understood. A cross-sectional analysis was performed on a total of 137 South African individuals. CCR5, CXCR4, and CD38 expression of CD4 T cell subsets in HIV-infected individuals with and without active pulmonary tuberculosis (TB) disease, pre- and post-ARV therapy, were determined by flow cytometry. In treatment-naive patients, CD4 T cells showed elevated surface expression of CCR5 and CD38 in TB/HIV coinfection as compared to HIV infection alone despite the overall percentage of CD4 T cells expressing CCR5 being reduced. Total CD38+ CD4 T cells were not significantly increased in either group; however, mean CD38 fluorescence was significantly higher in the context of TB infection. HIV/TB-coinfected individuals also displayed an increased percentage of activated (CD38+) CCR5+ CD4 T cells as compared to HIV patients alone. The naive CD4 T cell subset was depleted similarly in both HIV and HIV/TB groups. Only the HIV treatment group and not the TB-coinfected treatment group showed significantly decreased activated CCR5+ CD4 T cells, an increased percentage of naive T cells, and a decreased percentage of antigen-experienced T cells. This study highlighted an association of TB disease with immune activation, particularly of the CCR5+ CD4 T cell subset in HIV infection and the differential impact of ARV treatment. Further studies are needed to understand how TB coinfection confounds normal responses to ARV.
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Affiliation(s)
- Jean Pierre Kabue
- Medical Virology Division, Department of Pathology, Faculty of Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Dalene de Swardt
- Medical Virology Division, Department of Pathology, Faculty of Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Corena de Beer
- Medical Virology Division, Department of Pathology, Faculty of Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Richard H. Glashoff
- Medical Virology Division, Department of Pathology, Faculty of Health Sciences, Stellenbosch University, Cape Town, South Africa
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Construction of a high titer infectious HIV-1 subtype C proviral clone from South Africa. Viruses 2012; 4:1830-43. [PMID: 23170185 PMCID: PMC3499832 DOI: 10.3390/v4091830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 09/13/2012] [Accepted: 09/13/2012] [Indexed: 12/13/2022] Open
Abstract
The Human Immunodeficiency Virus type 1 (HIV-1) subtype C is currently the predominant subtype worldwide. Cell culture studies of Sub-Saharan African subtype C proviral plasmids are hampered by the low replication capacity of the resulting viruses, although viral loads in subtype C infected patients are as high as those from patients with subtype B. Here, we describe the sequencing and construction of a new HIV-1 subtype C proviral clone (pZAC), replicating more than one order of magnitude better than the previous subtype C plasmids. We identify the env-region for being the determinant for the higher viral titers and the pZAC Env to be M-tropic. This higher replication capacity does not lead to a higher cytotoxicity compared to previously described subtype C viruses. In addition, the pZAC Vpu is also shown to be able to down-regulate CD4, but fails to fully counteract CD317.
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16
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Neuroimaging markers of human immunodeficiency virus infection in South Africa. J Neurovirol 2012; 18:151-6. [PMID: 22528474 DOI: 10.1007/s13365-012-0090-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Revised: 02/28/2012] [Accepted: 03/07/2012] [Indexed: 12/13/2022]
Abstract
Previous studies have reported cognitive deficits among HIV-positive individuals infected with clade C virus. However, no study has examined whether individuals predominately infected with clade C virus exhibit brain atrophy relative to healthy controls. This study examined volumetric differences between 28 HIV+ individuals and 23 HIV- controls from South Africa. Volumetric measures were obtained from six regions of interest -- caudate, thalamus, corpus callosum, total cortex, total gray matter, and total white matter. HIV+ participants had significantly lower volumes in the total white matter (p<0.01), thalamus (p<0.01) and total gray matter (inclusive of cortical and subcortical regions, p<0.01). This study is the first to provide evidence of brain atrophy among HIV+ individuals in South Africa, where HIV clade C predominates. Additional research that integrates neuroimaging, comprehensive neuropsychological testing, genetic variance in clade-specific proteins, and the impact of treatment with Antiretrovirals (ARV) are necessary to understand the development of HIV-related neurocognitive disorders in South Africa.
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Iweriebor BC, Mavhandu LG, Masebe T, Rekosh D, Hammarskjold ML, Mphahlele JM, Bessong PO. Molecular epidemiology of HIV in two highly endemic areas of northeastern South Africa. Arch Virol 2011; 157:455-65. [PMID: 22189822 DOI: 10.1007/s00705-011-1180-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Accepted: 11/19/2011] [Indexed: 11/28/2022]
Abstract
There is paucity of data on the genetic landscape of HIV-1 viruses circulating in the Limpopo Province of northeastern South Africa. Here, we examine the genetic diversity of viruses from Bela-Bela and Musina, two towns with high HIV prevalence. Between June 2007 and March 2008, blood samples were collected from antiretroviral-drug-naïve individuals. Viruses were analyzed for genetic subtypes and drug resistance mutations. All of the viruses in these samples were shown by phylogenetic analysis based on gag p17, gag p24, reverse transcriptase, protease and envelope C2-C3 gene regions to belong to HIV-1 subtype C. Two of 44 reverse transcriptase sequences (4.5%) contained N rather than the consensus K at position 103. The K103N mutation is normally associated with resistance to NNRTIs. No major mutations were observed in the protease gene. However, several polymorphisms and amino acid changes normally considered to be minor drug resistance mutations were observed in the protease sequences. These results suggest that HIV-1 subtype C remains the predominant variant responsible for the epidemic in northeastern South Africa and that the prevalence of drug-resistant viruses among the naïve population is low.
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Affiliation(s)
- Benson Chuks Iweriebor
- AIDS Virus Research Laboratory, Department of Microbiology, University of Venda, PMB X5050, Thohoyandou 0950, South Africa
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Joska JA, Westgarth-Taylor J, Myer L, Hoare J, Thomas KGF, Combrinck M, Paul RH, Stein DJ, Flisher AJ. Characterization of HIV-Associated Neurocognitive Disorders among individuals starting antiretroviral therapy in South Africa. AIDS Behav 2011; 15:1197-203. [PMID: 20614176 DOI: 10.1007/s10461-010-9744-6] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
HIV-Associated Neurocognitive Disorders (HAND) exert an impact on everyday functions, including adherence. The prevalence of and risk factors for HAND in patients commencing anti-retroviral therapy in Southern Africa are unknown. Participants from primary care clinics in Cape Town, South Africa underwent detailed neuropsychological, neuropsychiatric, and neuromedical evaluation. Using the updated American Academy of Neurology (AAN) criteria, participants were classified into categories of HAND, and demographic and clinical risk factors for HIV-dementia (HIV-D) were assessed. The prevalence of mild neurocognitive disorder (MND) and HIV-D were 42.4 and 25.4%, respectively. There were significant associations between lower levels of education and older age with HIV-D, and a trend to association with HIV-D and lower CD4 count. In a regression model, a lower level of education and male gender were predictive of HIV-D. These findings suggest that HAND are highly prevalent in primary care settings in South Africa where clade C HIV is predominant.
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Joska JA, Combrinck M, Valcour VG, Hoare J, Leisegang F, Mahne AC, Myer L, Stein DJ. Association between apolipoprotein E4 genotype and human immunodeficiency virus-associated dementia in younger adults starting antiretroviral therapy in South Africa. J Neurovirol 2011; 16:377-83. [PMID: 20825268 DOI: 10.3109/13550284.2010.513365] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
It is not known whether the apolipoprotein E (ApoE) ε4 allelic variant is associated with human immunodeficiency virus (HIV)-associated dementia (HAD) in a South African population, where HIV clade C is predominant. ApoE genotyping was performed on 144 participants in a larger study of HIV-associated neurocognitive disorders (HAND). There was a lower frequency of the ε2 and ε3 alleles in the HIV-positive group, compared to a group of 300 community-based newborn infants. There were no differences in ApoE genotype across different categories of HAND. The ε4 allelic variant was less common in individuals with HAD than in those without HAD. These findings suggest that the ε4 allelic variant in HIV-positive individuals is not associated with the development of HAD in Southern Africa.
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Affiliation(s)
- John A Joska
- Department of Psychiatry and Mental Health, University of Cape Town, South Africa.
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