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Oluniyi PE, Ajogbasile FV, Zhou S, Fred-Akintunwa I, Polyak CS, Ake JA, Tovanabutra S, Iroezindu M, Rolland M, Happi CT. HIV-1 drug resistance and genetic diversity in a cohort of people with HIV-1 in Nigeria. AIDS 2022; 36:137-146. [PMID: 34628443 PMCID: PMC8654252 DOI: 10.1097/qad.0000000000003098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 09/13/2021] [Accepted: 09/20/2021] [Indexed: 12/25/2022]
Abstract
OBJECTIVE This study was designed to provide information on the genetic diversity of HIV-1 and drug resistance mutations in Nigeria, as there is limited understanding of variants circulating in the country. METHODS We used an advanced next-generation sequencing platform, Primer ID, to: investigate the presence of high and low abundance drug resistance mutations; characterize preexisting Integrase Strand Transfer Inhibitor (INSTI) mutations in antiretroviral therapy (ART)-experienced but dolutegravir-naive individuals; detect recent HIV-1 infections and characterize subtype diversity from a cohort of people with HIV-1 (PWH). RESULTS HIV-1 subtype analysis revealed the predominance of CRF02_AG and subtype G in our study population. At detection sensitivity of 30% abundance, drug resistance mutations (DRMs) were identified in 3% of samples. At a sensitivity level of 10%, DRMs were identified in 27.3% of samples. We did not detect any major INSTI mutation associated with dolutegravir-resistance. Only one recent infection was detected in our study population. CONCLUSION Our study suggests that dolutegravir-containing antiretroviral regimens will be effective in Nigeria. Our study also further emphasizes the high genetic diversity of HIV-1 in Nigeria and that CRF02_AG and subtype G are the dominant circulating forms of HIV-1 in Nigeria. These two circulating forms of the virus are largely driving the epidemic in the country.
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Affiliation(s)
- Paul E. Oluniyi
- Department of Biological Sciences, Faculty of Natural Sciences
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Fehintola V. Ajogbasile
- Department of Biological Sciences, Faculty of Natural Sciences
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Shuntai Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Iyanuoluwa Fred-Akintunwa
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Christina S. Polyak
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA
| | - Julie A. Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA
| | - Michael Iroezindu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
- HJF Medical Research International, Abuja, Nigeria
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA
| | - Christian T. Happi
- Department of Biological Sciences, Faculty of Natural Sciences
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
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Olusola BA, Olaleye DO, Odaibo GN. New infections and HIV-1 subtypes among febrile persons and blood donors in Oyo State, Nigeria. J Med Virol 2021; 93:4891-4900. [PMID: 33590935 DOI: 10.1002/jmv.26872] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 12/28/2022]
Abstract
PURPOSE There were approximately 37.9 million persons infected with HIV in 2018 globally, resulting in 770,000 deaths annually. Over 50% of this infection and deaths occur in sub-Saharan Africa, with countries like Nigeria being seriously affected. Nigeria has one of the highest rates of new infections globally. To control HIV infection in Nigeria, there is a need to continually screen high-risk groups for early HIV infection and subtypes using very sensitive methods. In this study, new HIV-1 infection and circulating HIV-1 subtypes among febrile persons and blood donors were determined. Performance characteristics of three commercial EIA kits were also evaluated. METHODS In total, 1028 participants were recruited for the study. New HIV-1 infection and subtypes were determined using enzyme immunoassays and molecular techniques, respectively. Sensitivity, specificity, predictive values, and agreements were compared among the EIA kits using PCR-confirmed HIV-positive and negative samples. RESULTS The overall prevalence of HIV infection in this study was 5.35%. The rate of new HIV infection was significantly different (p < .03674) among 1028 febrile persons (Ibadan: 2.22%; Saki: 1.36%) and blood donors (5.07%) studied. Three subtypes, CRF02_AG, A, and G, were found among those with new HIV infection. Whereas the commercial ELISA kits had very high specificities (94.12%, 100%, and 100%) for HIV-1 detection, Alere Determine HIV-1 antibody rapid kit had the lowest sensitivity score (50%). CONCLUSION Genetic diversity of HIV-1 strains among infected individuals in Oyo State, Nigeria, is still relatively high. This high level of diversity of HIV-1 strains may impact the reliability of diagnosis of the virus in Nigeria and other African countries where many of the virus strains co-circulate.
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Affiliation(s)
- Babatunde A Olusola
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - David O Olaleye
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Georgina N Odaibo
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
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Ogbenna AA, Meloni S, Inzaule S, Hamers RL, Sigaloff K, Osibogun A, Adeyemo TA, Okonkwo P, Samuels JO, Kanki PJ, Rinke de Wit TF, Akanmu AS. The impact of HIV-1 subtypes on virologic and immunologic treatment outcomes at the Lagos University Teaching Hospital: A longitudinal evaluation. PLoS One 2020; 15:e0238027. [PMID: 32841264 PMCID: PMC7447033 DOI: 10.1371/journal.pone.0238027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 08/10/2020] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION HIV is a highly diverse virus with significant genetic variability which may confer biologic differences that could impact on treatment outcomes. MATERIALS AND METHODS We studied the association between HIV subtypes and immunologic and virologic outcomes in a longitudinal cohort of 169 patients on combination antiretroviral therapy. Participants were followed up for 5 years. Demographic data, CD4 cell count and viral loads (VL) were extracted from medical records. Whole protease gene and codon 1-300 of the reverse transcriptase gene were sequenced and analysed. RESULTS Sixty-four percent of participants were females with a median age of 35 years. Twelve different subtypes were observed, the commonest being CRF 02_AG (55.0%) and subtypes G (23.1%). All subtypes showed steady rise in CD4 count and there was no difference in proportion who achieved CD4+ cell count rise of ≥100 cells/μL from baseline within 12 months' post-initiation of ART, or ≥350 cells/μL at 60 months' post-initiation. Median time to attaining a rise of ≥350 cells/μL was 24 months (6-48 months). The proportion that achieved undetectable VL at month 6 and 12 post-initiation of ART were comparable across subtypes. At end of 5th year, there was no statistical difference in proportion with virologic failure. CONCLUSION No association between HIV subtypes and immunologic or virologic response to therapy was observed, suggesting that current first-line ART may have similar efficacy across subtype predominating in South-West Nigeria.
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Affiliation(s)
- Ann Abiola Ogbenna
- Department of Haematology and Blood Transfusion, Faculty of Clinical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Seema Meloni
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Seth Inzaule
- Department of Global Health, Amsterdam UMC, Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, Netherlands
| | - Raph L. Hamers
- Department of Global Health, Amsterdam UMC, Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, Netherlands
- Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Kim Sigaloff
- Department of Global Health, Amsterdam UMC, Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, Netherlands
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam UMC, Amsterdam, Netherlands
| | - Akin Osibogun
- Department of Community Health and Primary Care, College of Medicine, Faculty of Clinical Sciences, University of Lagos, Lagos, Nigeria
| | - Titilope Adenike Adeyemo
- Department of Haematology and Blood Transfusion, Faculty of Clinical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
| | | | | | - Phyllis J. Kanki
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Tobias F. Rinke de Wit
- Department of Global Health, Amsterdam UMC, Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, Netherlands
| | - Alani Sulaimon Akanmu
- Department of Haematology and Blood Transfusion, Faculty of Clinical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
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Udeze AO, Olaleye DO, Odaibo GN. Phylogeny of partial gag, pol and env genes show predominance of HIV-1G and CRF02_AG with emerging recombinants in south-eastern Nigeria. Heliyon 2020; 6:e04310. [PMID: 32775738 PMCID: PMC7403892 DOI: 10.1016/j.heliyon.2020.e04310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/06/2020] [Accepted: 06/22/2020] [Indexed: 12/20/2022] Open
Abstract
Human Immunodeficiency Virus is characterized by high degree of genetic diversity with marked differences in its geographic distribution even within a country. This study was designed to identify the strains of HIV-1 circulating among infected individuals in southeastern parts of Nigeria. Genomic DNA was extracted from blood samples of 30 HIV-1 infected individuals from Anambra, Delta and Imo states of southeastern Nigeria. Portions of the genome corresponding to entire p24 gag, entire protease and C2-V3 env genes were amplified by nested PCR, sequenced using Sanger's method and phylogenetically analysed. Out of the 30 samples sequenced, 17, 28 and 14 readable sequences were obtained for gag, pol and env regions respectively. The most prevalent subtypes were CRF02_AG (41.2% in gag, 57.1% in pol protease and 50.0% in env) and G (29.4% in gag, 35.7% in pol protease and 35.7% in env). Other subtypes identified include A (17.7% in gag, 7.1% in env) and J (7.1% in env). Also 2 sequences each in gag (11.8%) and pol protease (7.1%) regions were unclassified but preliminary analysis showed they are recombinants. Furthermore, 71.4% of the isolates with sequences in the 3 regions and 26.7% of those with sequences in 2 genomic regions were recombinant forms. CRF02_AG and subtype G are the predominant HIV-1 strains circulating among infected individuals in southeastern Nigeria. Preliminary analysis results of unclassified sequences suggest that they are new recombinants.
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Affiliation(s)
- Augustine O Udeze
- Department of Virology, College of Medicine, University College Hospital, Ibadan, Nigeria.,Virology Unit, Department of Microbiology, University of Ilorin, P.M.B 1515, Ilorin, Nigeria
| | - David O Olaleye
- Department of Virology, College of Medicine, University College Hospital, Ibadan, Nigeria
| | - Georgina N Odaibo
- Department of Virology, College of Medicine, University College Hospital, Ibadan, Nigeria
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Folayan MO, Durueke F, Gofwen W, Godo-Odemijie G, Okonkwo C, Nanmak B, Osawe S, Okporoko E, Abimiku A. Community stakeholder engagement during a vaccine demonstration project in Nigeria: lessons on implementation of the good participatory practice guidelines. Pan Afr Med J 2019; 34:179. [PMID: 32153719 PMCID: PMC7046105 DOI: 10.11604/pamj.2019.34.179.18458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 09/23/2019] [Indexed: 11/11/2022] Open
Abstract
Introduction To report on the successes and challenges with implementing the good participatory practice guidelines for the Nigerian Canadian Collaboration on AIDS Vaccine (NICCAV) project. Methods An open and close ended questionnaire was administered to 25 randomly selected community stakeholders on the project. The questions sought information on perception about the community entry, constitution and function of the community advisory board (CAB) and community based organization (CBO), media engagement process, and research literacy programmes. The quantitative and qualitative data were analysed and findings triangulated. Results The project exceeded its targets on CBO engagement and community members reached. Stakeholders had significant improvement in knowledge about HIV vaccine research design and implementation (p=0.004). All respondents felt satisfied with the community entry, CAB constitution process, function and level of media engagement; 40% were satisfied with the financial support provided; 70% felt the community awareness and education coverage was satisfactory; and 40% raised concerns about the study site selection with implications for study participants' recruitment. Conclusion The NICCAV community stakeholder engagement model produced satisfactory outcomes for both researchers and community stakeholders. The inclusion of an advocacy and monitoring plan enabled it to identify important challenges that were of ethical concerns for the study.
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Affiliation(s)
- Morenike Oluwatoyin Folayan
- New HIV Vaccine and Microbicide Advocacy Society, Abuja, Nigeria.,Institute of Public Health, Obafemi Awolowo University, Ile-Ife, Nigeria.,Department of Child Dental Health, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Florita Durueke
- New HIV Vaccine and Microbicide Advocacy Society, Abuja, Nigeria
| | - Wika Gofwen
- New HIV Vaccine and Microbicide Advocacy Society, Abuja, Nigeria
| | | | - Chuks Okonkwo
- New HIV Vaccine and Microbicide Advocacy Society, Abuja, Nigeria
| | - Bali Nanmak
- New HIV Vaccine and Microbicide Advocacy Society, Abuja, Nigeria
| | - Sophia Osawe
- Plateau State Human Virology Research Center, Jos Institute of Human Virology, Abuja, Nigeria
| | - Evaezi Okporoko
- Plateau State Human Virology Research Center, Jos Institute of Human Virology, Abuja, Nigeria
| | - Alash'le Abimiku
- Plateau State Human Virology Research Center, Jos Institute of Human Virology, Abuja, Nigeria.,Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, USA
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Early HIV infection among persons referred for malaria parasite testing in Nigeria. Arch Virol 2017; 163:439-445. [PMID: 29119359 DOI: 10.1007/s00705-017-3599-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/01/2017] [Indexed: 10/18/2022]
Abstract
Persons in the early stages of HIV infection are the major drivers of new infections. These individuals may also develop renal dysfunctions at this time. Nigeria, as other African countries, has one of the highest prevalence of newly diagnosed HIV infections. Despite this, limited information exists on early HIV detection in the continent. This may be related to difficulties in providing early HIV diagnosis and treatment. Patients referred for malaria testing may provide a unique opportunity for early HIV detection. In this study, a method for identifying early HIV-infected individuals was assessed. HIV-1 subtype and renal function biomarkers were also analyzed in these persons. To identify early HIV infection, over a period of 18 months blood samples were collected from persons referred by clinicians for malaria parasite tests in Nigeria. A total of 671 samples were collected and analyzed for HIV antigen/antibody and subtypes. 101 of these samples were categorized into one of four groups: early HIV, chronic HIV, malaria infection and control groups for renal function analysis. 29% of HIV infected individuals were at the early stages of infection. The predominant subtype detected was CRF02_AG (57.14%). The early HIV group had the highest mean serum creatinine (95 µmol/L) and urea (5.7 mmol/L) values across all groups with the difference significant at P < 0.05. There was no significant difference between the circulating subtype and the stage of HIV infection. Our results show the feasibility of screening persons referred for malaria tests for early HIV. This can be used to control new HIV infections in sub-Saharan Africa.
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Motayo BO, Olusola BA, Faneye AO, Aturaka S, Oluwasemowo O, Ogiogwa JI. Dynamics of CD4 cell count among HIV-infected individuals in Lagos, Nigeria. J Immunoassay Immunochem 2017; 38:569-578. [PMID: 28699851 DOI: 10.1080/15321819.2017.1350706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Human immunodeficiency virus (HIV) infection leads to progressive loss of CD4 T cells. Antiretroviral therapy has been able to inhibit this process, resulting in significant level of immune recovery and function. Our aim is to investigate the dynamics of CD4 recovery among HIV patients in Lagos, Nigeria. A total of 213 HIV-positive individuals were enrolled between October 2007 and May 2008, and followed up for 9 months based on CD4 count. CD4 analysis was done by flow cytometry at enrollment and after every 3 months. Data were grouped according to age range, antiretroviral treatment (ART), and time between infection and diagnosis. Kaplan-Meier survival analysis was used for data analysis. There was a significant difference in CD4 count between antiretroviral (ART) naïve and ART experienced subjects (P < 0.001). About 50% of the ART experienced population was identified to show poor CD4 reconstitution unable to achieve a CD4 of 500 cells/µl after 9 months of therapy. Time interval between infection and therapy was also identified to contribute to poor CD4 restoration. Further studies need to be done to classify immunological nonresponders among HIV patients in Nigeria. We also recommend introduction of programs that will facilitate early detection of HIV infection.
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Affiliation(s)
- Babatunde O Motayo
- a Microbiology Unit , Pathology Department, Federal Medical Center , Abeokuta , Nigeria
| | | | - Adedayo O Faneye
- b Department of Virology , University of Ibadan , Ibadan , Nigeria
| | - Solomon Aturaka
- c Igbenedion University, Department of Medical laboratory Science , Okada , Nigeria
| | | | - Joseph I Ogiogwa
- a Microbiology Unit , Pathology Department, Federal Medical Center , Abeokuta , Nigeria.,c Igbenedion University, Department of Medical laboratory Science , Okada , Nigeria
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An Evaluation of Selected Populations for HIV-1 Vaccine Cohort Development in Nigeria. PLoS One 2016; 11:e0166711. [PMID: 27936236 PMCID: PMC5147844 DOI: 10.1371/journal.pone.0166711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/18/2016] [Indexed: 11/19/2022] Open
Abstract
Development of a globally effective HIV-1 vaccine will need to encompass Nigeria, one of the hardest hit areas, with an estimated 3.2 million people living with HIV. This cross-sectional Institutional Review Board (IRB) approved study was conducted in 2009-12 at four market sites and two highway settlements sites in Nigeria to identify and characterize populations at high risk for HIV; engage support of local stakeholders; and assess the level of interest in future vaccine studies. Demographic, HIV risk data were collected by structured interviewer-administered questionnaires. Blood samples were tested on site by HIV rapid diagnostic tests, followed by rigorous confirmatory testing, subtype evaluation and testing for HBV and HCV markers in a clinical reference laboratory. Of 3229 study participants, 326 were HIV infected as confirmed by Western Blot or RNA, with a HIV prevalence of 15.4%-23.9% at highway settlements and 3.1%-9.1% at market sites. There was no observable correlation of prevalence of HIV-1 (10.1%) with HBV (10.9%) or HCV (2.9%). Major HIV-1 subtypes included CRF02_AG (37.5%); G (27.5%); G/CRF02_AG (25.9%); and non-typeable (8.9%), with 0.3% HIV-2. Univariate analysis found age, gender, marital status, level of education, and sex under substance influence as significant risk factors for HIV (p<0.001). Educating and winning the trust of local community leadership ensured high level of participation (53.3-77.9%) and willingness to participate in future studies (95%). The high HIV prevalence and high risk of HIV infection at highway settlement and mammy markets make them well suited for targeting future vaccine trials in Nigeria.
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Heipertz RA, Ayemoba O, Sanders-Buell E, Poltavee K, Pham P, Kijak GH, Lei E, Bose M, Howell S, O'Sullivan AM, Bates A, Cervenka T, Kuroiwa J, Akintunde A, Ibezim O, Alabi A, Okoye O, Manak M, Malia J, Peel S, Maisaka M, Singer D, O’Connell RJ, Robb ML, Kim JH, Michael NL, Njoku O, Tovanabutra S. Significant contribution of subtype G to HIV-1 genetic complexity in Nigeria identified by a newly developed subtyping assay specific for subtype G and CRF02_AG. Medicine (Baltimore) 2016; 95:e4346. [PMID: 27512845 PMCID: PMC4985300 DOI: 10.1097/md.0000000000004346] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
While abundant sequence information is available from human immunodeficiency virus type 1 (HIV-1) subtypes A, B, C and CRF01_AE for HIV-1 vaccine design, sequences from West Africa are less represented. We sought to augment our understanding of HIV-1 variants circulating in 6 Nigerian cities as a step to subsequent HIV-1 vaccine development.The G/CRF02_AG multi-region hybridization assay (MHA) was developed to differentiate subtype G, CRF02_AG and their recombinants from other subtypes based on 7 HIV-1 segments. Plasma from 224 HIV-1 infected volunteers enrolled in a cohort examining HIV-1 prevalence, risk factor, and subtype from Makurdi (30), Abuja (18), Enugu (11), Kaduna (12), Tafa (95), and Ojo/Lagos (58) was analyzed using MHA. HIV-1 genomes from 42 samples were sequenced to validate the MHA and fully explore the recombinant structure of G and CRF02_AG variants.The sensitivity and specificity of MHA varied between 73-100% and 90-100%, respectively. The subtype distribution as identified by MHA among 224 samples revealed 38% CRF02_AG, 28% G, and 26% G/CRF02_AG recombinants while 8% remained nontypeable strains. In envelope (env) gp120, 38.84% of the samples reacted to a G probe while 31.25% reacted to a CRF02 (subtype A) probe. Full genome characterization of 42 sequences revealed the complexity of Nigerian HIV-1 variants.CRF02_AG, subtype G, and their recombinants were the major circulating HIV-1 variants in 6 Nigerian cities. High proportions of samples reacted to a G probe in env gp120 confirms that subtype G infections are abundant and should be considered in strategies for global HIV-1 vaccine development.
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Affiliation(s)
- Richard A. Heipertz
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Ojor Ayemoba
- Emergency Plan Implementation Committee, Nigerian Ministry of Defense, Abuja, Nigeria
| | - Eric Sanders-Buell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Kultida Poltavee
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Phuc Pham
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Gustavo H. Kijak
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Esther Lei
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Meera Bose
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Shana Howell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Anne Marie O'Sullivan
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Adam Bates
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Taylor Cervenka
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Janelle Kuroiwa
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | | | - Onyekachukwu Ibezim
- Emergency Plan Implementation Committee, Nigerian Ministry of Defense, Abuja, Nigeria
| | - Abraham Alabi
- US Military HIV Research Program (HJF-MRI), Abuja, Nigeria
- Centre de Recherches Medicales de Lambarene (CERMEL) Fondation Internationale de l’Hôpital Albert Schweitzer Lambarene, Gabon
| | - Obumneke Okoye
- Emergency Plan Implementation Committee, Nigerian Ministry of Defense, Abuja, Nigeria
| | - Mark Manak
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Jennifer Malia
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- United States Public Health Service, Rockville, Maryland
| | - Sheila Peel
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | - Darrell Singer
- United States Public Health Service, Rockville, Maryland
- Department of Defense HIV Program, Abuja, Nigeria
| | - Robert J. O’Connell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Merlin L. Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Jerome H. Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Nelson L. Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | - Sodsai Tovanabutra
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
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Adewumi OM, Odaibo GN, Olaleye OD. Efficacy of generic highly active antiretroviral therapy in HIV-1 infected individuals in Nigeria. J Immunoassay Immunochem 2016; 36:464-77. [PMID: 25436763 DOI: 10.1080/15321819.2014.969436] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
CD4 T lymphocyte and plasma HIV RNA parameters have been used to monitor disease progression, and predict clinical course in HIV infection. Initial evaluation of these parameters was conducted in the western countries where accessible ARVs, circulating HIV subtypes and mode of transmission are different from the situation in Nigeria. This study appraised these parameters, and efficacy of generic ARVs. Consenting 106 HIV infected ARV naïve patients were enrolled. CD4 T lymphocyte and plasma HIV RNA levels were determined at interval for 24 months. Ninety eight (92.5%) of the patients who completed the follow up in strict adherence to therapy guideline were included in the analysis. Baseline median CD4 T lymphocyte increased from 114 (Range: 6-330) to highest 357 (Range: 15-1036) cells/ μ L at 18 months of therapy, while baseline median plasma viral RNA declined from 4.6 (Range: 2.6-6.0) Log10 copies/mL to undetectable level within three months of therapy. Significant CD4 T-cell restoration and plasma viral RNA decline in the study population demonstrate efficacy of the generic HAART. The importance of combined use of both parameters for evaluation of immunologic and virologic responses to ART was confirmed.
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Affiliation(s)
- Olubusuyi M Adewumi
- a Department of Virology , College of Medicine, University of Ibadan , Ibadan , Oyo State , Nigeria
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de Pina-Araujo IIM, Delatorre E, Guimarães ML, Morgado MG, Bello G. Origin and Population Dynamics of a Novel HIV-1 Subtype G Clade Circulating in Cape Verde and Portugal. PLoS One 2015; 10:e0127384. [PMID: 25993094 PMCID: PMC4439163 DOI: 10.1371/journal.pone.0127384] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 04/15/2015] [Indexed: 01/04/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) subtype G is the most prevalent and second most prevalent HIV-1 clade in Cape Verde and Portugal, respectively; but there is no information about the origin and spatiotemporal dispersal pattern of this HIV-1 clade circulating in those countries. To this end, we used Maximum Likelihood and Bayesian coalescent-based methods to analyze a collection of 578 HIV-1 subtype G pol sequences sampled throughout Portugal, Cape Verde and 11 other countries from West and Central Africa over a period of 22 years (1992 to 2013). Our analyses indicate that most subtype G sequences from Cape Verde (80%) and Portugal (95%) branched together in a distinct monophyletic cluster (here called GCV-PT). The GCV-PT clade probably emerged after a single migration of the virus out of Central Africa into Cape Verde between the late 1970s and the middle 1980s, followed by a rapid dissemination to Portugal a couple of years later. Reconstruction of the demographic history of the GCV-PT clade circulating in Cape Verde and Portugal indicates that this viral clade displayed an initial phase of exponential growth during the 1980s and 1990s, followed by a decline in growth rate since the early 2000s. Our data also indicate that during the exponential growth phase the GCV-PT clade recombined with a preexisting subtype B viral strain circulating in Portugal, originating the CRF14_BG clade that was later disseminated to Spain and Cape Verde. Historical and recent human population movements between Angola, Cape Verde and Portugal probably played a key role in the origin and dispersal of the GCV-PT and CRF14_BG clades.
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Affiliation(s)
| | - Edson Delatorre
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Monick L. Guimarães
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Mariza G. Morgado
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- * E-mail:
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12
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Diallo K, Zheng DP, Rottinghaus EK, Bassey O, Yang C. Viral Genetic Diversity and Polymorphisms in a Cohort of HIV-1-Infected Patients Eligible for Initiation of Antiretroviral Therapy in Abuja, Nigeria. AIDS Res Hum Retroviruses 2015; 31:564-75. [PMID: 25582324 DOI: 10.1089/aid.2014.0168] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Studying the genetic diversity and natural polymorphisms of HIV-1 would benefit our understanding of HIV drug resistance (HIVDR) development and predict treatment outcomes. In this study, we have characterized the HIV-1 genetic diversity and natural polymorphisms at the 5' region of the pol gene encompassing the protease (PR) and reverse transcriptase (RT) from 271 plasma specimens collected in 2008 from HIV-1-infected patients who were eligible for initiating antiretroviral therapy in Abuja (Nigeria). The analysis indicated that the predominant subtype was subtype G (31.0%), followed by CRF02-AG (19.2 %), CRF43-02G (18.5%), and A/CRF36-cpx (11.4%); the remaining (19.9%) were other subtypes and circulating (CRF) and unique (URF) recombinant forms. Recombinant viruses (68.6%) were the major viral strains in the region. Eighty-four subtype G sequences were further mainly classified into two major and two minor clusters; sequences in the two major clusters were closely related to the HIV-1 strains in two of the three major subtype G clusters detected worldwide. Those in the two minor clusters appear to be new subtype G strains circulating only in Abuja. The pretreatment DR prevalence was <3%; however, numerous natural polymorphisms were present. Eleven polymorphic mutations (G16E, K20I, L23P, E35D, M36I, N37D/S/T, R57K, L63P, and V82I) were detected in the PR that were subtype or CRF specific while only three mutations (D123N, I135T, and I135V) were identified in the RT. Overall, this study indicates an evolving HIV-1 epidemic in Abuja with recombinant viruses becoming the dominant strains and the emergence of new subtype G strains; pretreatment HIVDR was low and the occurrence of natural polymorphism in the PR region was subtype or CRF dependent.
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Affiliation(s)
- Karidia Diallo
- International Laboratory Branch, Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Du-Ping Zheng
- International Laboratory Branch, Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Erin K. Rottinghaus
- International Laboratory Branch, Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Orji Bassey
- Centers for Disease Control and Prevention, Abuja, Nigeria
| | - Chunfu Yang
- International Laboratory Branch, Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
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13
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Delatorre E, Mir D, Bello G. Spatiotemporal dynamics of the HIV-1 subtype G epidemic in West and Central Africa. PLoS One 2014; 9:e98908. [PMID: 24918930 PMCID: PMC4053352 DOI: 10.1371/journal.pone.0098908] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 05/03/2014] [Indexed: 01/25/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) subtype G is the second most prevalent HIV-1 clade in West Africa, accounting for nearly 30% of infections in the region. There is no information about the spatiotemporal dynamics of dissemination of this HIV-1 clade in Africa. To this end, we analyzed a total of 305 HIV-1 subtype G pol sequences isolated from 11 different countries from West and Central Africa over a period of 20 years (1992 to 2011). Evolutionary, phylogeographic and demographic parameters were jointly estimated from sequence data using a Bayesian coalescent-based method. Our analyses indicate that subtype G most probably emerged in Central Africa in 1968 (1956–1976). From Central Africa, the virus was disseminated to West and West Central Africa at multiple times from the middle 1970s onwards. Two subtype G strains probably introduced into Nigeria and Togo between the middle and the late 1970s were disseminated locally and to neighboring countries, leading to the origin of two major western African clades (GWA-I and GWA-II). Subtype G clades circulating in western and central African regions displayed an initial phase of exponential growth followed by a decline in growth rate since the early/middle 1990s; but the mean epidemic growth rate of GWA-I (0.75 year−1) and GWA-II (0.95 year−1) clades was about two times higher than that estimated for central African lineages (0.47 year−1). Notably, the overall evolutionary and demographic history of GWA-I and GWA-II clades was very similar to that estimated for the CRF06_cpx clade circulating in the same region. These results support the notion that the spatiotemporal dissemination dynamics of major HIV-1 clades circulating in western Africa have probably been shaped by the same ecological factors.
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Affiliation(s)
- Edson Delatorre
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Daiana Mir
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- * E-mail:
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14
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Imade GE, Sagay AS, Chaplin B, Chebu P, Musa J, Okpokwu J, Hamel DJ, Pam IC, Agbaji O, Samuels J, Meloni S, Sankale JL, Okonkwo P, Kanki P. Short communication: Transmitted HIV drug resistance in antiretroviral-naive pregnant women in north central Nigeria. AIDS Res Hum Retroviruses 2014; 30:127-33. [PMID: 24164431 DOI: 10.1089/aid.2013.0074] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The World Health Organization (WHO) recommends periodic surveillance of transmitted drug resistance (TDR) in communities in which antiretroviral therapy (ART) has been scaled-up for greater than 3 years. We conducted a survey of TDR mutations among newly detected HIV-infected antiretroviral (ARV)-naive pregnant women. From May 2010 to March 2012, 38 ARV-naive pregnant women were recruited in three hospitals in Jos, Plateau state, north central Nigeria. Eligible subjects were recruited using a modified version of the binomial sequential sampling technique recommended by WHO. HIV-1 genotyping was performed and HIV-1 drug resistance mutations were characterized according to the WHO 2009 surveillance drug resistance mutation (SDRM) list. HIV subtypes were determined by phylogenetic analysis. The women's median age was 25.5 years; the median CD4(+) cell count was 317 cells/μl and the median viral load of 16 was 261 copies/ml. Of the 38 samples tested, 34 (89%) were successfully genotyped. The SDRM rate was <5% for all ART drug classes, with 1/34 (2.9%) for NRTIs/NNRTIs and none for protease inhibitors 0/31 (0%). The specific SDRMs detected were M41L for nucleoside reverse transcriptase inhibitors (NRTIs) and G190A for nonnucleoside reverse transcriptase inhibitors (NNRTIs). HIV-1 subtypes detected were CRF02_AG (38.2%), G' (41.2%), G (14.7%), CRF06-CPX (2.9%), and a unique AG recombinant form (2.9%). The single ARV-native pregnant woman with SDRMs was infected with HIV-1 subtype G'. Access to ART has been available in the Jos area for over 8 years. The prevalence of TDR lower than 5% suggests proper ART administration, although continued surveillance is warranted.
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Affiliation(s)
- Godwin E. Imade
- Jos University Teaching Hospital (JUTH), APIN Centre, Jos, Nigeria
- Department of Obstetrics and Gynecology, Faculty of Medical Sciences, University of Jos, Jos, Nigeria
| | - Atiene S. Sagay
- Jos University Teaching Hospital (JUTH), APIN Centre, Jos, Nigeria
- Department of Obstetrics and Gynecology, Faculty of Medical Sciences, University of Jos, Jos, Nigeria
| | - Beth Chaplin
- Harvard School of Public Health, Boston, Massachusetts
| | - Philippe Chebu
- Jos University Teaching Hospital (JUTH), APIN Centre, Jos, Nigeria
| | - Jonah Musa
- Jos University Teaching Hospital (JUTH), APIN Centre, Jos, Nigeria
| | - Jonathan Okpokwu
- Jos University Teaching Hospital (JUTH), APIN Centre, Jos, Nigeria
| | | | - Ishaya C. Pam
- Department of Obstetrics and Gynecology, Faculty of Medical Sciences, University of Jos, Jos, Nigeria
| | - Oche Agbaji
- Jos University Teaching Hospital (JUTH), APIN Centre, Jos, Nigeria
| | - Jay Samuels
- AIDS Prevention Initiative in Nigeria Ltd, Abuja, Nigeria
| | - Seema Meloni
- Harvard School of Public Health, Boston, Massachusetts
| | | | | | - Phyllis Kanki
- Harvard School of Public Health, Boston, Massachusetts
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15
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Odaibo GN, Adewole IF, Olaleye DO. High Rate of Non-detectable HIV-1 RNA Among Antiretroviral Drug Naive HIV Positive Individuals in Nigeria. Virology (Auckl) 2013; 4:35-40. [PMID: 25512693 PMCID: PMC4222343 DOI: 10.4137/vrt.s12677] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Plasma HIV-1 RNA concentration, or viral load, is an indication of the magnitude of virus replication and largely correlates with disease progression in an infected person. It is a very useful guide for initiation of therapy and monitoring of response to antiretroviral drugs. Although the majority of patients who are not on antiretroviral therapy (ART) have a high viral load, a small proportion of ART naive patients are known to maintain low levels or even undetectable viral load levels. In this study, we determined the rate of undetectable HIV-1 RNA among ART naive HIV positive patients who presented for treatment at the University College Hospital (UCH), Ibadan, Nigeria from 2005 to 2011. Baseline viral load and CD4 lymphocyte cell counts of 14,662 HIV positive drug naive individuals were determined using the Roche Amplicor version 1.5 and Partec easy count kit, respectively. The detection limits of the viral load assay are 400 copies/mL and 750,000 copies/mL for lower and upper levels, respectively. A total of 1,399 of the 14,662 (9.5%) HIV-1 positive drug naive individuals had undetectable viral load during the study period. In addition, the rate of non-detectable viral load increased over the years. The mean CD4 counts among HIV-1 infected individuals with detectable viral load (266 cells/μL; range = 1 to 2,699 cells/μL) was lower than in patients with undetectable viral load (557 cells/μL; range = 1 to 3,102 cells/μL). About 10% of HIV-1 infected persons in our study population had undetectable viral load using the Roche Amplicor version 1.5.
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Affiliation(s)
- Georgina N Odaibo
- Department of Virology College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Isaac F Adewole
- Department of Obstetrics and Gynecology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - David O Olaleye
- Department of Virology College of Medicine, University of Ibadan, Ibadan, Nigeria
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16
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Ajoge HO, Gordon ML, de Oliveira T, Green TN, Ibrahim S, Shittu OS, Olonitola SO, Ahmad AA, Ndung'u T. Genetic characteristics, coreceptor usage potential and evolution of Nigerian HIV-1 subtype G and CRF02_AG isolates. PLoS One 2011; 6:e17865. [PMID: 21423811 PMCID: PMC3056731 DOI: 10.1371/journal.pone.0017865] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 02/16/2011] [Indexed: 11/22/2022] Open
Abstract
HIV-1 CRF02_AG and subtype G (HIV-1G) account for most HIV infections in Nigeria, but their evolutionary trends have not been well documented. To better elucidate the dynamics of the epidemic in Nigeria we characterised the gag and env genes of North-Central Nigerian HIV-1 isolates from pregnant women. Of 28 samples sequenced in both genes, the predominant clades were CRF02_AG (39%) and HIV-1G (32%). Higher predicted proportion of CXCR4-tropic (X4) HIV-1G isolates was noted compared to CRF02_AG (p = 0.007, Fisher's exact test). Phylogenetic and Bayesian analysis conducted on our sequences and all the dated available Nigerian sequences on the Los Alamos data base showed that CRF02_AG and HIV-1G entered into Nigeria through multiple entries, with presence of HIV-1G dating back to early 1980s. This study underlines the genetic complexity of the HIV-1 epidemic in Nigeria, possible subtype-specific differences in co-receptor usage, and the evolutionary trends of the predominant HIV-1 strains in Nigeria, which may have implications for the design of biomedical interventions and better understanding of the epidemic.
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Affiliation(s)
- Hannah O. Ajoge
- Department of Microbiology, Ahmadu Bello University, Zaria, Nigeria
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Michelle L. Gordon
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tulio de Oliveira
- Nelson R. Mandela School of Medicine, Africa Centre for Health and Population Studies, University of KwaZulu-Natal, Durban, South Africa
| | - Taryn N. Green
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Sani Ibrahim
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Oladapo S. Shittu
- Department of Gyneacology and Obstetrics, Ahmadu Bello University Teaching Hospital, Ahmadu Bello University, Zaria, Nigeria
| | | | - Aliyu A. Ahmad
- Department of Microbiology, Ahmadu Bello University, Zaria, Nigeria
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- * E-mail:
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17
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Chaplin B, Eisen G, Idoko J, Onwujekwe D, Idigbe E, Adewole I, Gashau W, Meloni S, Sarr A, Sankalé J, Ekong E, Murphy R, Kanki P. Impact of HIV type 1 subtype on drug resistance mutations in Nigerian patients failing first-line therapy. AIDS Res Hum Retroviruses 2011; 27:71-80. [PMID: 20964479 DOI: 10.1089/aid.2010.0050] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A diverse array of non-subtype B HIV-1 viruses circulates in Africa and dominates the global pandemic. It is important to understand how drug resistance mutations in non-B subtypes may develop differently from the patterns described in subtype B. HIV-1 reverse transcriptase and protease sequences from 338 patients with treatment failure to first-line ART regimens were evaluated. Multivariate logistic regression was used to examine the effect of subtype on each mutation controlling for regimen, time on therapy, and total mutations. The distribution of HIV-1 subtypes included CRF02_AG (45.0%), G (37.9%), CRF06_cpx (4.4%), A (3.6%), and other subtypes or recombinant sequences (9.2%). The most common NRTI mutations were M184V (89.1%) and thymidine analog mutations (TAMs). The most common NNRTI mutations were Y181C (49.7%), K103N (36.4%), G190A (26.3%), and A98G (19.5%). Multivariate analysis showed that CRF02_AG was less likely to have the M41L mutation compared to other subtypes [adjusted odds ratio (AOR) = 0.35; p = 0.022]. Subtype A patients showed a 42.5-fold increased risk (AOR = 42.5, p = 0.001) for the L210W mutation. Among NNRTI mutations, subtype G patients had an increased risk for A98G (AOR = 2.40, p = 0.036) and V106I (AOR = 6.15, p = 0.010), whereas subtype CRF02_AG patients had an increased risk for V90I (AOR = 3.16; p = 0.003) and a decreased risk for A98G (AOR = 0.48, p = 0.019). Five RT mutations were found to vary significantly between different non-B West African subtypes. Further study to understand the clinical impact of subtype-specific diversity on drug resistance will be critically important to the continued success of ART scale-up in resource-limited settings.
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Affiliation(s)
- B. Chaplin
- Harvard School of Public Health, Boston, Massachusetts
| | - G. Eisen
- Harvard School of Public Health, Boston, Massachusetts
| | - J. Idoko
- Jos University Teaching Hospital, Plateau State, Nigeria
| | - D. Onwujekwe
- National Institute of Medical Research, Lagos, Nigeria
| | - E. Idigbe
- National Institute of Medical Research, Lagos, Nigeria
| | - I. Adewole
- University College Hospital, Ibadan, Nigeria
| | - W. Gashau
- University Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | - S. Meloni
- Harvard School of Public Health, Boston, Massachusetts
| | - A.D. Sarr
- Harvard School of Public Health, Boston, Massachusetts
| | - J.L. Sankalé
- Harvard School of Public Health, Boston, Massachusetts
| | - E. Ekong
- Harvard School of Public Health, Boston, Massachusetts
| | | | - P. Kanki
- Harvard School of Public Health, Boston, Massachusetts
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Galimand J, Frange P, Rouzioux C, Deveau C, Avettand-Fenoël V, Ghosn J, Lascoux C, Goujard C, Meyer L, Chaix ML. Short communication: evidence of HIV type 1 complex and second generation recombinant strains among patients infected in 1997-2007 in France: ANRS CO06 PRIMO Cohort. AIDS Res Hum Retroviruses 2010; 26:645-51. [PMID: 20560794 DOI: 10.1089/aid.2009.0201] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although subtype B strains are still predominant in France, non-B viruses have been isolated from 26% of patients with a primary HIV-1 infection in 2005-2006. The objective of this study was to characterize recombinant-HIV-1 strains by a subtyping based on the phylogenetic analysis of both pol and env sequences. We studied 591 patients who were part of the French PRIMO-Cohort between 1997 and 2007. The RT and V3 regions were sequenced and phylogenetic analyses were performed. Phylogenetic analyses showed concordant subtype results for 91.7% of viruses: 71.6% of the viruses were subtype B and 28.4% belonged to non-B subtypes or circulating recombinant forms (CRFs). Forty-nine strains showed different phylogenies between the two genes (pol and env), indicating that recombinations were observed in 8.3% of the cases. These recombinants were observed in patients from sub-Saharan Africa (28.3%) and in white patients (6.3%). Moreover, among the 49 recombinant viruses, 15 (30.6%) contained a B sequence in the pol or in the env gene compared to 34 (69.4%), which contained non-B or CRF sequences. Twenty-six different recombination patterns involving subtypes, CRFs, or undetermined strains were observed. We have reported the occurrence of new recombinant forms between the two major viral types of strains circulating in France: subtype B and CRF02_AG. Our study confirms a high HIV-1 diversity among patients infected in France within the past 10 years, with a high proportion of non-B strains and the circulation of complex recombinant strains among both sub-Saharan patients and French patients.
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Affiliation(s)
- Julie Galimand
- Université Paris Descartes EA 3620, Paris, France
- AP-HP, Laboratoire de Virologie, CHU Necker-Enfants Malades, Paris, France
| | - Pierre Frange
- Université Paris Descartes EA 3620, Paris, France
- Unité d'Immunologie, Hématologie et Rhumatologie Pédiatriques, CHU Necker–Enfants Malades, AP-HP, Paris, France
| | - Christine Rouzioux
- Université Paris Descartes EA 3620, Paris, France
- AP-HP, Laboratoire de Virologie, CHU Necker-Enfants Malades, Paris, France
| | - Christiane Deveau
- INSERM, U822, Le Kremlin-Bicêtre, Université Paris-Sud, Faculté de Médecine Paris-Sud, AP-HP, Le Kremlin-Bicêtre, France
| | - Véronique Avettand-Fenoël
- Université Paris Descartes EA 3620, Paris, France
- AP-HP, Laboratoire de Virologie, CHU Necker-Enfants Malades, Paris, France
| | - Jade Ghosn
- Université Paris Descartes EA 3620, Paris, France
- Service de Médecine Interne et Maladies Infectieuses, Hôpital Bicêtre, AP-HP, Le Kremlin–Bicêtre, France
| | - Caroline Lascoux
- Service de Médecine Interne, Hôpital Saint-Louis, AP-HP, Paris, France
| | - Cécile Goujard
- Service de Médecine Interne et Maladies Infectieuses, Hôpital Bicêtre, AP-HP, Le Kremlin–Bicêtre, France
| | - Laurence Meyer
- INSERM, U822, Le Kremlin-Bicêtre, Université Paris-Sud, Faculté de Médecine Paris-Sud, AP-HP, Le Kremlin-Bicêtre, France
| | - Marie-Laure Chaix
- Université Paris Descartes EA 3620, Paris, France
- AP-HP, Laboratoire de Virologie, CHU Necker-Enfants Malades, Paris, France
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Yamaguchi J, Ndembi N, Ngansop C, Mbanya D, Kaptué L, Gürtler LG, Devare SG, Brennan CA. HIV type 1 group M subtype G in Cameroon: five genome sequences. AIDS Res Hum Retroviruses 2009; 25:469-73. [PMID: 19361281 DOI: 10.1089/aid.2008.0296] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Near full-length viral genome sequences were obtained for five putative subtype G candidates identified in HIV-infected Cameroonian blood donors, based on partial genome sequences for the gag, pol, and env regions. Phylogenetic analysis of the genome sequences shows that all five strains are pure subtype G with no indication of intersubtype recombination. The Cameroon subtype G sequences did not form a geographically based subcluster and were intermixed within the subtype G branch with isolates from several different countries. HIV-1 group M subtype G accounts for only 4.5% of HIV infections in Cameroon. However, genome segments of subtype G are present in 67% of all infections and 80% of infections due to intersubtype recombinant strains in Cameroon. The addition of five subtype G genome sequences to the HIV database may contribute to a better understanding of the origins and classification of HIV-1 subtypes and CRFs.
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Affiliation(s)
| | | | | | | | - Lazare Kaptué
- University of Yaoundé I, Yaoundé, Cameroon
- Université des Montagnes, Bangangté, Cameroon
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20
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Imamichi H, Koita O, Dabitao D, Dao S, Ibrah M, Sogoba D, Dewar RL, Berg SC, Jiang MK, Parta M, Washington JA, Polis MA, Lane HC, Tounkara A. Identification and characterization of CRF02_AG, CRF06_cpx, and CRF09_cpx recombinant subtypes in Mali, West Africa. AIDS Res Hum Retroviruses 2009; 25:45-55. [PMID: 19182920 DOI: 10.1089/aid.2008.0111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract Multiple HIV-1 subtypes and circulating recombinant forms (CRFs) are known to cocirculate in Africa. In West Africa, the high prevalence of CRF02_AG, and cocirculation of subtype A, CRF01_AE, CRF06_cpx, and other complex intersubtype recombinants has been well documented. Mali, situated in the heart of West Africa, is likely to be affected by the spread of recombinant subtypes. However, the dynamics of the spread of HIV-1 recombinant subtypes as well as nonrecombinant HIV-1 group M subtypes in this area have not been systematically assessed. Herein, we undertook genetic analyses on full-length env sequences derived from HIV-1-infected individuals living in the capital city of Mali, Bamako. Of 23 samples we examined, 16 were classified as CRF02_AG and three had a subsubtype A3. Among the remaining HIV-1 strains, CRF06_cpx and CRF09_cpx were each found in two patients. Comparison of phylogenies for six matched pol and full-length env sequences revealed that two strains had discordant subtype/CRF designations between the pol and env regions: one had A3(pol)CRF02_AG(env) and the other had CRF02_AG(pol)A3(env). Taken together, our study demonstrated the high prevalence of CRF02_AG and complexity of circulating HIV-1 strains in Mali. It also provided evidence of ongoing virus evolution of CRF02_AG, as illustrated by the emergence of more complex CRF02_AG/A3 intersubtype recombinants in this area.
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Affiliation(s)
- Hiromi Imamichi
- Clinical Services Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702
| | - Ousmane Koita
- Center for Research and Training on HIV and Tuberculosis, Faculty of Medicine, Pharmacy and Odontostomatology, University of Bamako, Bamako, Mali
| | - Djeneba Dabitao
- Center for Research and Training on HIV and Tuberculosis, Faculty of Medicine, Pharmacy and Odontostomatology, University of Bamako, Bamako, Mali
| | - Sounkalo Dao
- Center for Research and Training on HIV and Tuberculosis, Faculty of Medicine, Pharmacy and Odontostomatology, University of Bamako, Bamako, Mali
| | - Mahamadou Ibrah
- Center for Research and Training on HIV and Tuberculosis, Faculty of Medicine, Pharmacy and Odontostomatology, University of Bamako, Bamako, Mali
| | - Dramane Sogoba
- Center for Research and Training on HIV and Tuberculosis, Faculty of Medicine, Pharmacy and Odontostomatology, University of Bamako, Bamako, Mali
| | - Robin L. Dewar
- Clinical Services Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702
| | - Steve C. Berg
- Clinical Services Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702
| | - Min-Kang Jiang
- Clinical Services Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702
| | - Mark Parta
- Clinical Services Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702
| | - Janice A. Washington
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Michael A. Polis
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - H. Clifford Lane
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Anatole Tounkara
- Center for Research and Training on HIV and Tuberculosis, Faculty of Medicine, Pharmacy and Odontostomatology, University of Bamako, Bamako, Mali
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21
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Yamaguchi J, Badreddine S, Swanson P, Bodelle P, Devare SG, Brennan CA. Identification of new CRF43_02G and CRF25_cpx in Saudi Arabia based on full genome sequence analysis of six HIV type 1 isolates. AIDS Res Hum Retroviruses 2008; 24:1327-35. [PMID: 18844465 DOI: 10.1089/aid.2008.0101] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recently, we reported a high level of HIV-1 strain diversity in patients at the King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia. Based on phylogenetic analysis of gag p24, pol integrase, and env gp41 sequences, subtypes A, B, C, D, and G, and CRF02_AG, as well as unique recombinant forms were identified. Subtype G accounted for 25% of the infections in the Saudi population and this high prevalence was unexpected. Although subtype G is found in west central Africa, pure subtype G strains are uncommon. To further characterize the subtype G infections in Saudi Arabia, six strains that appeared to be pure subtype G were selected for full genome sequencing. Near full-length genomes were obtained using RT-PCR amplification to generate overlapping fragments from viral RNA extracted from plasma. The six strains are not subtype G throughout their entire genome. Four isolates have a recombinant structure composed of CRF02_AG and subtype G and share three identical breakpoints. This recombinant form defines a new CRF designated CRF43_02G. The remaining two isolates are CRF25_cpx, a circulating recombinant form identified in Cameroon composed of subtypes A and G and unclassified segments. Reanalysis of the previously reported Saudi HIV-1 partial genome sequences revealed additional isolates classified as CRF43_02G and CRF25_cpx and one isolate was reclassified to CRF22_01A. Identification of CRF43_02G in Saudi Arabia could indicate a transmission network within the country. Alternatively, the new CRF could have been introduced from an external source where this CRF is not yet recognized.
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Affiliation(s)
| | - Samar Badreddine
- King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
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22
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Ojesina AI, Mullins C, Imade G, Samuels J, Sankalé JL, Pam S, Sagay S, Idoko J, Kanki PJ. Characterization of HIV type 1 reverse transcriptase mutations in infants infected by mothers who received peripartum nevirapine prophylaxis in Jos, Nigeria. AIDS Res Hum Retroviruses 2007; 23:1587-92. [PMID: 18160018 DOI: 10.1089/aid.2007.0064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This study was carried out to characterize HIV-1 reverse transcriptase (RT) mutations in vertically infected infants in Jos, Nigeria. DNA was extracted from peripheral blood mononuclear cells of 102 infants, aged 0 to 6 months, born to HIV-1-infected mothers who had received peripartum single-dose nevirapine prophylaxis. PCR-based diagnosis revealed that 14 infants (13.7%) were infected with HIV-1. Phylogenetic analyses of RT revealed wide viral diversity, with CRF02_AG, subtype G, subsubtype A3, CRF06_cpx, and a subtype D recombinant present in the population. Four of 13 (31%) infants had NNRTI resistance mutations--V179I (2 infants), Y181C, and V179E. Intriguingly, subtype G sequences did not have NNRTI mutations but rather carried a Q207N mutation, which may undergo negative selection under drug pressure. Our data suggest wide diversity for vertically transmitted HIV-1 viruses in Nigeria and highlight the potential significance of transmitting rare mutations in subtype G.
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Affiliation(s)
- Akinyemi I. Ojesina
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts 02115
| | - Christopher Mullins
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts 02115
| | - Godwin Imade
- Jos University Teaching Hospital, Jos, Plateau State, Nigeria
| | - Jay Samuels
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts 02115
| | - Jean-Louis Sankalé
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts 02115
| | - Sunday Pam
- Jos University Teaching Hospital, Jos, Plateau State, Nigeria
| | - Solomon Sagay
- Jos University Teaching Hospital, Jos, Plateau State, Nigeria
| | - John Idoko
- Jos University Teaching Hospital, Jos, Plateau State, Nigeria
| | - Phyllis J. Kanki
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts 02115
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