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Tebit DM, Nickel G, Gibson R, Rodriguez M, Hathaway NJ, Bain K, Reyes-Rodriguez AL, Ondoa P, Heeney JL, Li Y, Bongorno J, Canaday D, McDonald D, Bailey JA, Arts EJ. Replicative fitness and pathogenicity of primate lentiviruses in lymphoid tissue, primary human and chimpanzee cells: relation to possible jumps to humans. EBioMedicine 2024; 100:104965. [PMID: 38215691 PMCID: PMC10827413 DOI: 10.1016/j.ebiom.2023.104965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Simian immunodeficiency viruses (SIV) have been jumping between non-human primates in West/Central Africa for thousands of years and yet, the HIV-1 epidemic only originated from a primate lentivirus over 100 years ago. METHODS This study examined the replicative fitness, transmission, restriction, and cytopathogenicity of 22 primate lentiviruses in primary human lymphoid tissue and both primary human and chimpanzee peripheral blood mononuclear cells. FINDINGS Pairwise competitions revealed that SIV from chimpanzees (cpz) had the highest replicative fitness in human or chimpanzee peripheral blood mononuclear cells, even higher fitness than HIV-1 group M strains responsible for worldwide epidemic. The SIV strains belonging to the "HIV-2 lineage" (including SIVsmm, SIVmac, SIVagm) had the lowest replicative fitness. SIVcpz strains were less inhibited by human restriction factors than the "HIV-2 lineage" strains. SIVcpz efficiently replicated in human tonsillar tissue but did not deplete CD4+ T-cells, consistent with the slow or nonpathogenic disease observed in most chimpanzees. In contrast, HIV-1 isolates and SIV of the HIV-2 lineage were pathogenic to the human tonsillar tissue, almost independent of the level of virus replication. INTERPRETATION Of all primate lentiviruses, SIV from chimpanzees appears most capable of infecting and replicating in humans, establishing HIV-1. SIV from other Old World monkeys, e.g. the progenitor of HIV-2, replicate slowly in humans due in part to restriction factors. Nonetheless, many of these SIV strains were more pathogenic than SIVcpz. Either SIVcpz evolved into a more pathogenic virus while in humans or a rare SIVcpz, possibly extinct in chimpanzees, was pathogenic immediately following the jump into human. FUNDING Support for this study to E.J.A. was provided by the NIH/NIAID R01 AI49170 and CIHR project grant 385787. Infrastructure support was provided by the NIH CFAR AI36219 and Canadian CFI/Ontario ORF 36287. Efforts of J.A.B. and N.J.H. was provided by NIH AI099473 and for D.H.C., by VA and NIH AI AI080313.
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Affiliation(s)
- Denis M Tebit
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA; Global Biomed Scientific, LLC, P.O. Box 2368, Forest, VA, USA
| | - Gabrielle Nickel
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Richard Gibson
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Myriam Rodriguez
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Nicolas J Hathaway
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Katie Bain
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Angel L Reyes-Rodriguez
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Pascal Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia; Department of Global Health, Institute of Global Health and Development, University of Amsterdam, Amsterdam, the Netherlands
| | - Jonathan L Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Yue Li
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Jennifer Bongorno
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - David Canaday
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - David McDonald
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Eric J Arts
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Microbiology and Immunology, Western University, Ontario, Canada.
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HIV/AIDS Global Epidemic. Infect Dis (Lond) 2023. [DOI: 10.1007/978-1-0716-2463-0_522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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Rodríguez-Galet A, Ventosa-Cubillo J, Bendomo V, Eyene M, Mikue-Owono T, Nzang J, Ncogo P, Gonzalez-Alba JM, Benito A, Holguín Á. High Drug Resistance Levels Compromise the Control of HIV Infection in Pediatric and Adult Populations in Bata, Equatorial Guinea. Viruses 2022; 15:27. [PMID: 36680067 PMCID: PMC9864178 DOI: 10.3390/v15010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
A lack of HIV viral load (VL) and HIV drug resistance (HIVDR) monitoring in sub-Saharan Africa has led to an uncontrolled circulation of HIV-strains with drug resistance mutations (DRM), compromising antiretroviral therapy (ART). This study updates HIVDR data and HIV-1 variants in Equatorial Guinea (EG), providing the first data on children/adolescents in the country. From 2019−2020, 269 dried blood samples (DBS) were collected in Bata Regional Hospital (EG) from 187 adults (73 ART-naïve/114 ART-treated) and 82 children/adolescents (25 HIV-exposed-ART-naïve/57 ART-treated). HIV-1 infection was confirmed in Madrid by molecular/serological confirmatory tests and ART-failure by VL quantification. HIV-1 pol region was identified as transmitted/acquired DRM, predicted antiretroviral susceptibility (Stanfordv9.0) and HIV-1 variants (phylogeny). HIV infection was confirmed in 88.1% of the individuals and virological failure (VL > 1000 HIV-1-RNA copies/mL) in 84.2/88.9/61.9% of 169 ART-treated children/adolescents/adults. Among the 167 subjects with available data, 24.6% suffered a diagnostic delay. All 125 treated had experienced nucleoside retrotranscriptase inhibitors (NRTI); 95.2% were non-NRTI (NNRTI); 22.4% had experienced integrase inhibitors (INSTI); and 16% had experienced protease inhibitors (PI). At sampling, they had received 1 (37.6%), 2 (32%), 3 (24.8%) or 4 (5.6%) different ART-regimens. Among the 43 treated children−adolescents/37 adults with sequence, 62.8/64.9% carried viruses with major-DRM. Most harbored DRM to NNRTI (68.4/66.7%), NRTI (55.3/43.3%) or NRTI+NNRTI (50/33.3%). One adult and one child carried major-DRM to PI and none carried major-DRM to INSTI. Most participants were susceptible to INI and PI. DRM was absent in 36.2% of treated patients with VL > 1000 cp/mL, suggesting adherence failure. TDR prevalence in 59 ART-naïve adults was high (20.3%). One-half (53.9%) of the 141 subjects with pol sequence carried CRF02_AG. The observed high rate of ART-failure and transmitted/acquired HIVDR could compromise the 95-95-95-UNAIDS targets in EG. Routine VL and resistance monitoring implementation are mandatory for early detection of ART-failure and optimal rescue therapy selection ART regimens based on PI, and INSTI can improve HIV control in EG.
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Affiliation(s)
- Ana Rodríguez-Galet
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Ramón y Cajal-IRYCIS and CIBEREsp-RITIP-CoRISpe, 20834 Madrid, Spain
| | - Judit Ventosa-Cubillo
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Ramón y Cajal-IRYCIS and CIBEREsp-RITIP-CoRISpe, 20834 Madrid, Spain
- Fundación Estatal, Salud, Infancia y Bienestar Social (CSAI), 28029 Madrid, Spain
| | - Verónica Bendomo
- Unidad de Referencia de Enfermedades Infecciosas (UREI), Hospital Regional de Bata, Bata 88240, Equatorial Guinea
| | - Manuel Eyene
- Unidad de Referencia de Enfermedades Infecciosas (UREI), Hospital Regional de Bata, Bata 88240, Equatorial Guinea
| | - Teresa Mikue-Owono
- Laboratorio de Análisis Clínicos, Hospital Regional de Bata, Bata 88240, Equatorial Guinea
| | - Jesús Nzang
- Fundación Estatal, Salud, Infancia y Bienestar Social (CSAI), 28029 Madrid, Spain
| | - Policarpo Ncogo
- Fundación Estatal, Salud, Infancia y Bienestar Social (CSAI), 28029 Madrid, Spain
| | - José María Gonzalez-Alba
- Grupo de Investigación en Microbiología Translacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Microbiology Department, Hospital Universitario Central de Asturias (HUCA), 33011 Oviedo, Spain
| | - Agustín Benito
- Centro Nacional de Medicina Tropical (CNMT), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), 28029 Madrid, Spain
| | - África Holguín
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Ramón y Cajal-IRYCIS and CIBEREsp-RITIP-CoRISpe, 20834 Madrid, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
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A large population sample of African HIV genomes from the 1980s reveals a reduction in subtype D over time associated with propensity for CXCR4 tropism. Retrovirology 2022; 19:28. [PMID: 36514107 PMCID: PMC9746199 DOI: 10.1186/s12977-022-00612-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/12/2022] [Indexed: 12/15/2022] Open
Abstract
We present 109 near full-length HIV genomes amplified from blood serum samples obtained during early 1986 from across Uganda, which to our knowledge is the earliest and largest population sample from the initial phase of the HIV epidemic in Africa. Consensus sequences were made from paired-end Illumina reads with a target-capture approach to amplify HIV material following poor success with standard approaches. In comparisons with a smaller 'intermediate' genome dataset from 1998 to 1999 and a 'modern' genome dataset from 2007 to 2016, the proportion of subtype D was significantly higher initially, dropping from 67% (73/109), to 57% (26/46) to 17% (82/465) respectively (p < 0.0001). Subtype D has previously been shown to have a faster rate of disease progression than other subtypes in East African population studies, and to have a higher propensity to use the CXCR4 co-receptor ("X4 tropism"); associated with a decrease in time to AIDS. Here we find significant differences in predicted tropism between A1 and D subtypes in all three sample periods considered, which is particularly striking the 1986 sample: 66% (53/80) of subtype D env sequences were predicted to be X4 tropic compared with none of the 24 subtype A1. We also analysed the frequency of subtype in the envelope region of inter-subtype recombinants, and found that subtype A1 is over-represented in env, suggesting recombination and selection have acted to remove subtype D env from circulation. The reduction of subtype D frequency over three decades therefore appears to be a result of selective pressure against X4 tropism and its higher virulence. Lastly, we find a subtype D specific codon deletion at position 24 of the V3 loop, which may explain the higher propensity for subtype D to utilise X4 tropism.
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Farinre O, Gounder K, Reddy T, Tongo M, Hare J, Chaplin B, Gilmour J, Kanki P, Mann JK, Ndung'u T. Subtype-specific differences in Gag-protease replication capacity of HIV-1 isolates from East and West Africa. Retrovirology 2021; 18:11. [PMID: 33952315 PMCID: PMC8097975 DOI: 10.1186/s12977-021-00554-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/12/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The HIV-1 epidemic in sub-Saharan Africa is heterogeneous with diverse unevenly distributed subtypes and regional differences in prevalence. Subtype-specific differences in disease progression rate and transmission efficiency have been reported, but the underlying biological mechanisms have not been fully characterized. Here, we tested the hypothesis that the subtypes prevalent in the East Africa, where adult prevalence rate is higher, have lower viral replication capacity (VRC) than their West African counterparts where adult prevalence rates are lower. RESULTS Gag-protease sequencing was performed on 213 and 160 antiretroviral-naïve chronically infected participants from West and East Africa respectively and bioinformatic tools were used to infer subtypes and recombination patterns. VRC of patient-derived gag-protease chimeric viruses from West (n = 178) and East (n = 114) Africa were determined using a green fluorescent protein reporter-based cell assay. Subtype and regional differences in VRC and amino acid variants impacting VRC were identified by statistical methods. CRF02_AG (65%, n = 139), other recombinants (14%, n = 30) and pure subtypes (21%, n = 44) were identified in West Africa. Subtypes A1 (64%, n = 103), D (22%, n = 35), or recombinants (14%, n = 22) were identified in East Africa. Viruses from West Africa had significantly higher VRC compared to those from East Africa (p < 0.0001), with subtype-specific differences found among strains within West and East Africa (p < 0.0001). Recombination patterns showed a preference for subtypes D, G or J rather than subtype A in the p6 region of gag, with evidence that subtype-specific differences in this region impact VRC. Furthermore, the Gag A83V polymorphism was associated with reduced VRC in CRF02_AG. HLA-A*23:01 (p = 0.0014) and HLA-C*07:01 (p = 0.002) were associated with lower VRC in subtype A infected individuals from East Africa. CONCLUSIONS Although prevalent viruses from West Africa displayed higher VRC than those from East Africa consistent with the hypothesis that lower VRC is associated with higher population prevalence, the predominant CRF02_AG strain in West Africa displayed higher VRC than other prevalent strains suggesting that VRC alone does not explain population prevalence. The study identified viral and host genetic determinants of virus replication capacity for HIV-1 CRF02_AG and subtype A respectively, which may have relevance for vaccine strategies.
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Affiliation(s)
- Omotayo Farinre
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Kamini Gounder
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, 4001, South Africa
| | - Tarylee Reddy
- Biostatistics Research Unit, South African Medical Research Council, Durban, South Africa
| | - Marcel Tongo
- Centre of Research for Emerging and Re-Emerging Diseases (CREMER), Yaoundé, Cameroon
| | - Jonathan Hare
- International AIDS Vaccine Initiative (IAVI) Human Immunology Laboratory (HIL), Imperial College, London, UK
- IAVI Global Headquarters, 125 Broad Street, 9th Floor,, New York, NY, USA
| | - Beth Chaplin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jill Gilmour
- International AIDS Vaccine Initiative (IAVI) Human Immunology Laboratory (HIL), Imperial College, London, UK
- IAVI Global Headquarters, 125 Broad Street, 9th Floor,, New York, NY, USA
| | - Phyllis Kanki
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jaclyn K Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.
- Africa Health Research Institute, Durban, 4001, South Africa.
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Max Planck Institute for Infection Biology, Berlin, Germany.
- Division of Infection and Immunity, University College London, London, UK.
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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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Nazziwa J, Faria NR, Chaplin B, Rawizza H, Kanki P, Dakum P, Abimiku A, Charurat M, Ndembi N, Esbjörnsson J. Characterisation of HIV-1 Molecular Epidemiology in Nigeria: Origin, Diversity, Demography and Geographic Spread. Sci Rep 2020; 10:3468. [PMID: 32103028 PMCID: PMC7044301 DOI: 10.1038/s41598-020-59944-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 02/05/2020] [Indexed: 11/23/2022] Open
Abstract
Nigeria has the highest number of AIDS-related deaths in the world. In this study, we characterised the HIV-1 molecular epidemiology by analysing 1442 HIV-1 pol sequences collected 1999-2014 from four geopolitical zones in Nigeria using state-of-the-art maximum-likelihood and Bayesian phylogenetic analyses. The main circulating forms were the circulating recombinant form (CRF) 02_AG (44% of the analysed sequences), CRF43_02G (16%), and subtype G (8%). Twenty-three percent of the sequences represented unique recombinant forms (URFs), whereof 37 (11%) could be grouped into seven potentially novel CRFs. Bayesian phylodynamic analysis suggested that five major Nigerian HIV-1 sub-epidemics were introduced in the 1960s and 1970s, close to the Nigerian Civil War. The analysis also indicated that the number of effective infections decreased in Nigeria after the introduction of free antiretroviral treatment in 2006. Finally, Bayesian phylogeographic analysis suggested gravity-like dynamics in which virus lineages first emerge and expand within large urban centers such as Abuja and Lagos, before migrating towards smaller rural areas. This study provides novel insight into the Nigerian HIV-1 epidemic and may have implications for future HIV-1 prevention strategies in Nigeria and other severely affected countries.
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Affiliation(s)
- Jamirah Nazziwa
- Department of Translational Medicine, Lund University, Lund, Sweden
| | | | - Beth Chaplin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Holly Rawizza
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Phyllis Kanki
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Patrick Dakum
- Institute of Human Virology Nigeria, Abuja, Nigeria
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Alash'le Abimiku
- Institute of Human Virology Nigeria, Abuja, Nigeria
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Man Charurat
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Nicaise Ndembi
- Institute of Human Virology Nigeria, Abuja, Nigeria
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Lund, Sweden.
- Nuffield Department Medicine, University of Oxford, Oxford, United Kingdom.
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In-Vitro Subtype-Specific Modulation of HIV-1 Trans-Activator of Transcription (Tat) on RNAi Silencing Suppressor Activity and Cell Death. Viruses 2019; 11:v11110976. [PMID: 31652847 PMCID: PMC6893708 DOI: 10.3390/v11110976] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/06/2019] [Accepted: 10/09/2019] [Indexed: 01/22/2023] Open
Abstract
Human immunodeficiency virus (HIV) is a global health concern affecting millions of individuals with a wide variety of currently circulating subtypes affecting various regions of the globe. HIV relies on multiple regulatory proteins to modify the host cell to promote replication in infected T cells, and these regulatory proteins can have subtle phenotypic differences between subtypes. One of these proteins, HIV-1 Trans-Activator of Transcription (Tat), is capable of RNA interference (RNAi) Silencing Suppressor (RSS) activity and induction of cell death in T cells. However, the subtype-specific RSS activity and induction of cell death have not been explored. We investigated the ability of Tat subtypes and variants to induce RSS activity and cell death. TatB, from HIV-1 subtype B, was found to be a potent RSS activator by 40% whereas TatC, from HIV-1 subtype C, showed 15% RSS activity while subtype TatC variants exhibited varying levels. A high level of cell death (50–53%) was induced by subtype TatB when compared to subtype TatC (25–28%) and varying levels were observed with subtype TatC variants. These differential activities could be due to variations in the functional domains of Tat. These observations further our understanding of subtype-specific augmentation of Tat in HIV-1 replication and pathogenesis.
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Epigenetics, N-myrystoyltransferase-1 and casein kinase-2-alpha modulates the increased replication of HIV-1 CRF02_AG, compared to subtype-B viruses. Sci Rep 2019; 9:10689. [PMID: 31337802 PMCID: PMC6650493 DOI: 10.1038/s41598-019-47069-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/05/2019] [Indexed: 02/04/2023] Open
Abstract
HIV subtypes distribution varies by geographic regions; this is likely associated with differences in viral fitness but the predictors and underlying mechanisms are unknown. Using in-vitro, in-vivo, and ex-vivo approaches, we found significantly higher transactivation and replication of HIV-1-CRF02_AG (prevalent throughout West-Central Africa), compared to subtype-B. While CRF02_AG-infected animals showed higher viremia, subtype-B-infected animals showed significantly more weight loss, lower CD4+ T-cells and lower CD4/CD8 ratios, suggesting that factors other than viremia contribute to immunosuppression and wasting syndrome in HIV/AIDS. Compared to HIV-1-subtype-B and its Tat proteins(Tat.B), HIV-1-CRF02_AG and Tat.AG significantly increased histone acetyl-transferase activity and promoter histones H3 and H4 acetylation. Silencing N-myrystoyltransferase(NMT)-1 and casein-kinase-(CK)-II-alpha prevented Tat.AG- and HIV-1-CRF02_AG-mediated viral transactivation and replication, but not Tat.B- or HIV-1-subtype-B-mediated effects. Tat.AG and HIV-1-CRF02_AG induced the expression of NMT-1 and CKII-alpha in human monocytes and macrophages, but Tat.B and HIV-1-subtype-B had no effect. These data demonstrate that NMT1, CKII-alpha, histone acetylation and histone acetyl-transferase modulate the increased replication of HIV-1-CRF02_AG. These novel findings demonstrate that HIV genotype influence viral replication and provide insights into the molecular mechanisms of differential HIV-1 replication. These studies underline the importance of considering the influence of viral genotypes in HIV/AIDS epidemiology, replication, and eradication strategies.
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Bletsa M, Suchard MA, Ji X, Gryseels S, Vrancken B, Baele G, Worobey M, Lemey P. Divergence dating using mixed effects clock modelling: An application to HIV-1. Virus Evol 2019; 5:vez036. [PMID: 31720009 PMCID: PMC6830409 DOI: 10.1093/ve/vez036] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The need to estimate divergence times in evolutionary histories in the presence of various sources of substitution rate variation has stimulated a rich development of relaxed molecular clock models. Viral evolutionary studies frequently adopt an uncorrelated clock model as a generic relaxed molecular clock process, but this may impose considerable estimation bias if discrete rate variation exists among clades or lineages. For HIV-1 group M, rate variation among subtypes has been shown to result in inconsistencies in time to the most recent common ancestor estimation. Although this calls into question the adequacy of available molecular dating methods, no solution to this problem has been offered so far. Here, we investigate the use of mixed effects molecular clock models, which combine both fixed and random effects in the evolutionary rate, to estimate divergence times. Using simulation, we demonstrate that this model outperforms existing molecular clock models in a Bayesian framework for estimating time-measured phylogenies in the presence of mixed sources of rate variation, while also maintaining good performance in simpler scenarios. By analysing a comprehensive HIV-1 group M complete genome data set we confirm considerable rate variation among subtypes that is not adequately modelled by uncorrelated relaxed clock models. The mixed effects clock model can accommodate this rate variation and results in a time to the most recent common ancestor of HIV-1 group M of 1920 (1915-25), which is only slightly earlier than the uncorrelated relaxed clock estimate for the same data set. The use of complete genome data appears to have a more profound impact than the molecular clock model because it reduces the credible intervals by 50 per cent relative to similar estimates based on short envelope gene sequences.
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Affiliation(s)
- Magda Bletsa
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Xiang Ji
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
| | - Sophie Gryseels
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
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11
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Leelawiwat W, Pattanasin S, Sriporn A, Wasinrapee P, Kongpechsatit O, Mueanpai F, Tongtoyai J, Holtz TH, Curlin ME. Association between HIV genotype, viral load and disease progression in a cohort of Thai men who have sex with men with estimated dates of HIV infection. PLoS One 2018; 13:e0201386. [PMID: 30063722 PMCID: PMC6067726 DOI: 10.1371/journal.pone.0201386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/13/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Differences between HIV genotypes may affect HIV disease progression. We examined infecting HIV genotypes and their association with disease progression in a cohort of men who have sex with men with incident HIV infection in Bangkok, Thailand. METHODS We characterized the viral genotype of 189 new HIV infections among MSM identified between 2006-2014 using hybridization and sequencing. Plasma viral load (PVL) was determined by PCR, and CD4+ T-cell counts were measured by flow cytometry. We used Generalized Estimating Equations to examine factors associated with changes in CD4+ T-cell counts. Factors associated with immunologic failure were analyzed using Cox proportional hazard models. RESULTS Among 189 MSM, 84% were infected with CRF01_AE, 11% with recombinant B/CRF01_AE and 5% with subtype B. CD4+ T-cell decline rates were 68, 65, and 46 cells/μL/year for CRF01_AE, recombinants, and subtype B, respectively, and were not significantly different between HIV subtypes. CD4+ T-cell decline rate was significantly associated with baseline PVL and CD4+ T-cell counts (p <0.001). Progression to immunologic failure was associated with baseline CD4+ T-cell ≤ 500 cells/μL (AHR 1.97; 95% CI 1.14-3.40, p = 0.015) and PVL > 50,000 copies/ml (AHR 2.03; 1.14-3.63, p = 0.017). There was no difference in time to immunologic failure between HIV subtypes. CONCLUSION Among HIV-infected Thai MSM, low baseline CD4+ T-cell and high PVL are associated with rapid progression. In this cohort, no significant difference in CD4+ T-cell decline rate or time to immunologic failure was seen between CRF01_AE and other infecting HIV subtypes.
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Affiliation(s)
- Wanna Leelawiwat
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
- * E-mail:
| | - Sarika Pattanasin
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Anuwat Sriporn
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Punneeporn Wasinrapee
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Oranuch Kongpechsatit
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Famui Mueanpai
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Jaray Tongtoyai
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Timothy H. Holtz
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Marcel E. Curlin
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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12
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McCreesh N, Andrianakis I, Nsubuga RN, Strong M, Vernon I, McKinley TJ, Oakley JE, Goldstein M, Hayes R, White RG. Universal test, treat, and keep: improving ART retention is key in cost-effective HIV control in Uganda. BMC Infect Dis 2017; 17:322. [PMID: 28468605 PMCID: PMC5415795 DOI: 10.1186/s12879-017-2420-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 04/25/2017] [Indexed: 12/14/2022] Open
Abstract
Background With ambitious new UNAIDS targets to end AIDS by 2030, and new WHO treatment guidelines, there is increased interest in the best way to scale-up ART coverage. We investigate the cost-effectiveness of various ART scale-up options in Uganda. Methods Individual-based HIV/ART model of Uganda, calibrated using history matching. 22 ART scale-up strategies were simulated from 2016 to 2030, comprising different combinations of six single interventions (1. increased HIV testing rates, 2. no CD4 threshold for ART initiation, 3. improved ART retention, 4. increased ART restart rates, 5. improved linkage to care, 6. improved pre-ART care). The incremental net monetary benefit (NMB) of each intervention was calculated, for a wide range of different willingness/ability to pay (WTP) per DALY averted (health-service perspective, 3% discount rate). Results For all WTP thresholds above $210, interventions including removing the CD4 threshold were likely to be most cost-effective. At a WTP of $715 (1 × per-capita-GDP) interventions to improve linkage to and retention/re-enrolment in HIV care were highly likely to be more cost-effective than interventions to increase rates of HIV testing. At higher WTP (> ~ $1690), the most cost-effective option was ‘Universal Test, Treat, and Keep’ (UTTK), which combines interventions 1–5 detailed above. Conclusions Our results support new WHO guidelines to remove the CD4 threshold for ART initiation in Uganda. With additional resources, this could be supplemented with interventions aimed at improving linkage to and/or retention in HIV care. To achieve the greatest reductions in HIV incidence, a UTTK policy should be implemented. Electronic supplementary material The online version of this article (doi:10.1186/s12879-017-2420-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicky McCreesh
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Ioannis Andrianakis
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | | | - Mark Strong
- School of Health and Related Research, The University of Sheffield, 30 Regent Street, Sheffield, S1 4DA, UK
| | - Ian Vernon
- Department of Mathematical Sciences, Durham University, Lower Mountjoy, Stockton Road, Durham, DH1 3LE, UK
| | - Trevelyan J McKinley
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Campusm Penryn, Penryn, TR10 9FE, UK
| | - Jeremy E Oakley
- School of Mathematics and Statistics, University of Sheffield, The Hicks Building, Hounsfield Road, Sheffield, S3 7RH, UK
| | - Michael Goldstein
- Department of Mathematical Sciences, Durham University, Lower Mountjoy, Stockton Road, Durham, DH1 3LE, UK
| | - Richard Hayes
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Richard G White
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
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13
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Leite TCNF, Campos DP, Coelho AB, Teixeira SLM, Veloso V, Morgado MG, Guimarães ML. Impact of HIV-1 Subtypes on AIDS Progression in a Brazilian Cohort. AIDS Res Hum Retroviruses 2017; 33:41-48. [PMID: 27418261 DOI: 10.1089/aid.2016.0126] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Viral and host factors are known to play a role in the different patterns of AIDS progression. The cocirculation of HIV-1 subtypes B, F1, BBR, and BF1; the occasional detection of HIV-1 subtype D; and an increasing prevalence of subtype C and other recombinant forms have been described in Rio de Janeiro, Brazil. The aim of this study was to evaluate the potential association of HIV-1 subtypes circulating among HIV-1+ individuals in Rio de Janeiro with AIDS disease progression. For this purpose, 246 HIV-1 individuals under clinical and laboratory follow-up from 1986 to 2011 were classified according to their progression to AIDS in typical progressors (n = 133), rapid progressors (n = 95), and long-term nonprogressors (n = 18). The env-gp120 region was amplified and sequenced. Neighbor-joining phylogenetic inferences were performed in Mega 6 and bootscan analysis was performed in Simplot 3.5.1. The Kaplan-Meier method and Cox modeling were performed to determine the time until an AIDS-defining event based on the HIV-1 subtypes/variants. Similar AIDS progression rates were observed among individuals infected with HIV-1 subtype B and variant BBR. However, a direct association between more rapid AIDS progression and HIV-1 subtypes, D and BF1, was confirmed in the multivariate analysis, corroborating previous results. Our findings contribute to the investigation of the possible influence of HIV-1 subtypes in AIDS outcome.
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Affiliation(s)
| | - Dayse Pereira Campos
- Evandro Chagas Nacional Institute of Infectious Diseases, FIOCRUZ, Rio de Janeiro, Brazil
| | - Alessandra Brum Coelho
- Evandro Chagas Nacional Institute of Infectious Diseases, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Valdilea Veloso
- Evandro Chagas Nacional Institute of Infectious Diseases, FIOCRUZ, Rio de Janeiro, Brazil
| | - Mariza Gonçalves Morgado
- Laboratory of AIDS and Molecular Immunology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
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14
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Zhu H, Wang MC. A Semi-stationary Copula Model Approach for Bivariate Survival Data with Interval Sampling. Int J Biostat 2016; 11:151-73. [PMID: 25720090 DOI: 10.1515/ijb-2013-0060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In disease registries, bivariate survival data are typically collected under interval sampling. It refers to a situation when entry into a registry is at the time of the first failure event (i.e., HIV infection) within a calendar time window. For all the cases in the registry, time of the initiating event (i.e., birth) is retrospectively identified, and subsequently the second failure event (i.e., death) is observed during follow-up. In this paper we discuss how interval sampling introduces bias into the data. Given the sampling design that the first event occurs within a specific time interval, the first failure time is doubly truncated, and the second failure time is possibly informatively right censored. Consider semi-stationary condition that the disease progression is independent of when the initiating event occurs. Under this condition, this paper adopts copula models to assess association between the bivariate survival times with interval sampling. We first obtain bias-corrected estimators of marginal survival functions, and estimate association parameter of copula model by a two-stage procedure. In the second part of the work, covariates are incorporated into the survival distributions via the proportional hazards models. Inference of the association measure in copula model is established, where the association is allowed to depend on covariates. Asymptotic properties of proposed estimators are established, and finite sample performance is evaluated by simulation studies. The method is applied to a community-based AIDS study in Rakai to investigate dependence between age at infection and residual lifetime without and with adjustment for HIV subtype.
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15
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Palm AA, Esbjörnsson J, Månsson F, Biague A, da Silva ZJ, Norrgren H, Jansson M, Medstrand P. Cocirculation of several similar but unique HIV-1 recombinant forms in Guinea-Bissau revealed by near full-length genomic sequencing. AIDS Res Hum Retroviruses 2015; 31:938-45. [PMID: 26066756 DOI: 10.1089/aid.2015.0073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The dynamic HIV-1 epidemic has resulted in the emergence of several different subtypes and recombinant forms that may differ in biological properties. A recombinant form of CRF02_AG and subsubtype A3 (A3/02) was recently described based on env sequencing and was associated with faster disease progression rates compared with its parental strains. Here, we performed near full-length sequencing of the A3/02 variant to characterize the recombination patterns of a potential novel and more pathogenic circulating recombinant form of HIV-1 in Guinea-Bissau. HIV-1 proviral DNA was extracted from blood samples of individuals infected with the A3/02 recombinant form. The recombination patterns were investigated for six samples that were successfully amplified and sequenced. We found that all six full-length genomes were recombinant forms composed of CRF02_AG and A3 with a recombination hot-spot in the C2 region of env. However, the recombination patterns in the remaining genome differed between samples. Two samples displayed similar recombination profiles, indicative of a homogeneous recombinant form circulating in the population in Guinea-Bissau, whereas the remaining four samples represented unique recombinant forms. The characterization of five different recombination profiles indicated a high frequency of recombination. The recombination breakpoint in the C2 region was identified as the principal common feature shared between sequences, suggesting that this region may have an impact on disease progression rate. Since novel recombinant forms may have characteristics associated with a higher potential of spread in the human population, this study highlights the importance of continuous screening and surveillance of the HIV-1 epidemic.
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Affiliation(s)
- Angelica A. Palm
- Department of Experimental Medical Science Lund, Lund University, Lund, Sweden
- Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Malmö, Sweden
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Månsson
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Antonio Biague
- National Public Health Laboratory, Bissau, Guinea-Bissau
| | | | - Hans Norrgren
- Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Marianne Jansson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Laboratory Medicine Lund, Lund University, Lund, Sweden
| | - Patrik Medstrand
- Department of Translational Medicine, Lund University, Malmö, Sweden
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16
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Kaleebu P, Kamali A, Seeley J, Elliott AM, Katongole-Mbidde E. The Medical Research Council (UK)/Uganda Virus Research Institute Uganda Research Unit on AIDS--'25 years of research through partnerships'. Trop Med Int Health 2014; 20:E1-10. [PMID: 25354929 PMCID: PMC4529486 DOI: 10.1111/tmi.12415] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
For the past 25 years, the Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS has conducted research on HIV-1, coinfections and, more recently, on non-communicable diseases. Working with various partners, the research findings of the Unit have contributed to the understanding and control of the HIV epidemic both in Uganda and globally, and informed the future development of biomedical HIV interventions, health policy and practice. In this report, as we celebrate our silver jubilee, we describe some of these achievements and the Unit's multidisciplinary approach to research. We also discuss the future direction of the Unit; an exemplar of a partnership that has been largely funded from the north but led in the south.
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Affiliation(s)
- P Kaleebu
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) Uganda Research Unit on AIDS, Entebbe, Uganda; Uganda Virus Research Institute, Entebbe, Uganda; London School of Hygiene and Tropical Medicine, London, UK
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17
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Zhu H, Wang MC. Nonparametric inference on bivariate survival data with interval sampling: association estimation and testing. Biometrika 2014; 101:519-533. [PMID: 32390662 DOI: 10.1093/biomet/asu005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In many biomedical applications, interest focuses on the occurrence of two or more consecutive failure events and the relationship between event times, such as age of disease onset and residual lifetime. Bivariate survival data with interval sampling arise frequently when disease registries or surveillance systems collect data based on disease incidence occurring within a specific calendar time interval. The initial event is then retrospectively confirmed and the subsequent failure event may be observed during follow-up. In life history studies, the initial and two consecutive failure events could correspond to birth, disease onset and death. The statistical features and bias of observed data in relation to interval sampling were discussed by Zhu & Wang (2012). Here we propose nonparametric estimation of the association between bivariate failure times based on Kendall's tau for data collected with interval sampling. A nonparametric estimator is given, where the contribution of each comparable and orderable pair is weighted by the inverse of the associated selection probability. Analysis methods for bivariate survival data with interval sampling rely on the assumption of quasi-independence, i.e., that bivariate failure times and the time of the initial event are independent in the observable region. This paper develops a nonparametric test of quasi-independence based on a bivariate conditional Kendall's tau for such data. Simulation studies demonstrate that the association estimator and testing procedure perform well with moderate sample sizes. Illustrations with two real datasets are provided.
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Affiliation(s)
- Hong Zhu
- Division of Biostatistics, Department of Clinical Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, U.S.A
| | - Mei-Cheng Wang
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe St, Baltimore, Maryland 21205, U.S.A
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18
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Woollard SM, Bhargavan B, Yu F, Kanmogne GD. Differential effects of Tat proteins derived from HIV-1 subtypes B and recombinant CRF02_AG on human brain microvascular endothelial cells: implications for blood-brain barrier dysfunction. J Cereb Blood Flow Metab 2014; 34:1047-59. [PMID: 24667918 PMCID: PMC4050250 DOI: 10.1038/jcbfm.2014.54] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 02/17/2014] [Accepted: 03/05/2014] [Indexed: 01/20/2023]
Abstract
HIV-1 genetic differences influence viral replication and progression to AIDS. HIV-1 circulating recombinant form (CRF)02_AG is the predominant viral subtype infecting humans in West and Central Africa, but its effects on HIV neuropathogenesis are not known. In the present study, we investigated the effects of Tat proteins from HIV-1 subtype B (Tat.B) and HIV-1 CRF02_AG (Tat.AG) on primary human brain microvascular endothelial cells (HBMEC), the major component of the blood-brain barrier (BBB). Using Affymetrix GeneChip Human Gene 1.0.ST arrays, we showed that Tat.AG had minimal effects while Tat.B induced transcriptional upregulation of 90 genes in HBMEC, including proinflammatory chemokines, complement components C3, C7, and complement factor B, matrix metalloproteinases (MMP)-3, MMP-10, and MMP-12. These results were confirmed by real-time PCR. Compared with Tat.AG, Tat.B significantly increased MMP-3, MMP-10, and MMP-12 activities in HBMEC, and the MMPs tissue inhibitor of metalloproteinase-2 blocked Tat-induced increase in MMPs activity. Western blot analyses also showed that Tat increased the expression of C3 and its cleaved fragment C3b in HBMEC. These data suggest that genetic differences between HIV-1 subtypes B and CRF02_AG influence the effects of Tat proteins from these two clades on HBMEC, including molecular and cellular functions, and canonical pathways, which would affect BBB dysfunction and viral neuropathogenesis.
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Affiliation(s)
- Shawna M Woollard
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Biju Bhargavan
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Fang Yu
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Georgette D Kanmogne
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
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Hodcroft E, Hadfield JD, Fearnhill E, Phillips A, Dunn D, O'Shea S, Pillay D, Leigh Brown AJ. The contribution of viral genotype to plasma viral set-point in HIV infection. PLoS Pathog 2014; 10:e1004112. [PMID: 24789308 PMCID: PMC4006911 DOI: 10.1371/journal.ppat.1004112] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 03/22/2014] [Indexed: 12/24/2022] Open
Abstract
Disease progression in HIV-infected individuals varies greatly, and while the environmental and host factors influencing this variation have been widely investigated, the viral contribution to variation in set-point viral load, a predictor of disease progression, is less clear. Previous studies, using transmission-pairs and analysis of phylogenetic signal in small numbers of individuals, have produced a wide range of viral genetic effect estimates. Here we present a novel application of a population-scale method based in quantitative genetics to estimate the viral genetic effect on set-point viral load in the UK subtype B HIV-1 epidemic, based on a very large data set. Analyzing the initial viral load and associated pol sequence, both taken before anti-retroviral therapy, of 8,483 patients, we estimate the proportion of variance in viral load explained by viral genetic effects to be 5.7% (CI 2.8-8.6%). We also estimated the change in viral load over time due to selection on the virus and environmental effects to be a decline of 0.05 log10 copies/mL/year, in contrast to recent studies which suggested a reported small increase in viral load over the last 20 years might be due to evolutionary changes in the virus. Our results suggest that in the UK epidemic, subtype B has a small but significant viral genetic effect on viral load. By allowing the analysis of large sample sizes, we expect our approach to be applicable to the estimation of the genetic contribution to traits in many organisms.
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Affiliation(s)
- Emma Hodcroft
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| | - Jarrod D. Hadfield
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| | | | - Andrew Phillips
- Infection and Population Health, University College London, Royal Free Hospital, London, United Kingdom
| | - David Dunn
- MRC Clinical Trials Unit Aviation House, London, United Kingdom
| | - Siobhan O'Shea
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Deenan Pillay
- Research Department of Infection, University College London, London, United Kingdom
| | - Andrew J. Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
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20
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de Pina-Araujo IIM, Guimarães ML, Bello G, Vicente ACP, Morgado MG. Profile of the HIV epidemic in Cape Verde: molecular epidemiology and drug resistance mutations among HIV-1 and HIV-2 infected patients from distinct islands of the archipelago. PLoS One 2014; 9:e96201. [PMID: 24763617 PMCID: PMC3999145 DOI: 10.1371/journal.pone.0096201] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 04/04/2014] [Indexed: 12/12/2022] Open
Abstract
HIV-1 and HIV-2 have been detected in Cape Verde since 1987, but little is known regarding the genetic diversity of these viruses in this archipelago, located near the West African coast. In this study, we characterized the molecular epidemiology of HIV-1 and HIV-2 and described the occurrence of drug resistance mutations (DRM) among antiretroviral therapy naïve (ARTn) patients and patients under treatment (ARTexp) from different Cape Verde islands. Blood samples, socio-demographic and clinical-laboratory data were obtained from 221 HIV-positive individuals during 2010–2011. Phylogenetic and bootscan analyses of the pol region (1300 bp) were performed for viral subtyping. HIV-1 and HIV-2 DRM were evaluated for ARTn and ARTexp patients using the Stanford HIV Database and HIV-GRADE e.V. Algorithm Homepage, respectively. Among the 221 patients (169 [76.5%] HIV-1, 43 [19.5%] HIV-2 and 9 [4.1%] HIV-1/HIV-2 co-infections), 67% were female. The median ages were 34 (IQR = 1–75) and 47 (IQR = 12–84) for HIV-1 and HIV-2, respectively. HIV-1 infections were due to subtypes G (36.6%), CRF02_AG (30.6%), F1 (9.7%), URFs (10.4%), B (5.2%), CRF05_DF (3.0%), C (2.2%), CRF06_cpx (0.7%), CRF25_cpx (0.7%) and CRF49_cpx (0.7%), whereas all HIV-2 infections belonged to group A. Transmitted DRM (TDRM) was observed in 3.4% (2/58) of ARTn HIV-1-infected patients (1.7% NRTI, 1.7% NNRTI), but not among those with HIV-2. Among ARTexp patients, DRM was observed in 47.8% (33/69) of HIV-1 (37.7% NRTI, 37.7% NNRTI, 7.4% PI, 33.3% for two classes) and 17.6% (3/17) of HIV-2-infections (17.6% NRTI, 11.8% PI, 11.8% both). This study indicates that Cape Verde has a complex and unique HIV-1 molecular epidemiological scenario dominated by HIV-1 subtypes G, CRF02_AG and F1 and HIV-2 subtype A. The occurrence of TDRM and the relatively high level of DRM among treated patients are of concern. Continuous monitoring of patients on ART, including genotyping, are public policies to be implemented.
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Affiliation(s)
- Isabel Inês M. de Pina-Araujo
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
- Departamento de Ciência e Tecnologia, Universidade de Cabo Verde, Praia, Santiago, Cabo Verde
- * E-mail: (IIMPA); (MGM)
| | - Monick L. Guimarães
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Ana Carolina P. Vicente
- Laboratório de Genética Molecular de Microorganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Mariza G. Morgado
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
- * E-mail: (IIMPA); (MGM)
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Samikkannu T, Rao KVK, Kanthikeel SP, Atluri VSR, Agudelo M, Roy U, Nair MPN. Immunoneuropathogenesis of HIV-1 clades B and C: role of redox expression and thiol modification. Free Radic Biol Med 2014; 69:136-44. [PMID: 24480751 PMCID: PMC4211896 DOI: 10.1016/j.freeradbiomed.2013.12.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 12/19/2013] [Accepted: 12/22/2013] [Indexed: 12/23/2022]
Abstract
Previous studies have shown that, during infection, HIV-1 clade B and clade C differentially contribute to the neuropathogenesis and development of HIV-associated neurocognitive disorders (HANDs). The low-molecular-weight tripeptide glutathione (GSH) alters the redox balance and leads to the generation of reactive oxygen species, which play a significant role in the neuropathogenesis of HANDs. We hypothesized that the HIV-1 clade B and clade C viruses and their respective Tat proteins exert differential effects on monocyte-derived immature dendritic cells (IDCs) and neuroblastoma cells (SK-N-MC) by redox activation, which leads to immunoneuropathogenesis. The GSH/GSSG ratio and mRNA expression levels and protein modification of glutathione synthetase (GSS), glutathione peroxidase 1 (GPx1), superoxide dismutase 1 (SOD1), and catalase (CAT) were analyzed in IDCs infected with HIV-1 clade B or clade C as well as in cells treated with the respective Tat proteins. The results indicated that HIV-1 clade B virus and its Tat protein significantly increased the production of reactive oxygen species and reduced the GSH/GSSG ratio and subsequent downregulation of gene expression and protein modification of GSS, GPx1, SOD1, and CAT compared to infection with the clade C virus or treatment with the clade C Tat protein. Thus, our studies demonstrate that HIV-1 clades B and C exert differential effects of redox expression and thiol modification. HIV-1 clade B potentially induces oxidative stress, leading to more immunoneuropathogenesis than infection with HIV-1 clade C.
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Affiliation(s)
- Thangavel Samikkannu
- Department of Immunology, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Kurapati V K Rao
- Department of Immunology, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Sudhessh Pilakka Kanthikeel
- Department of Immunology, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Venkata Subba Rao Atluri
- Department of Immunology, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Marisela Agudelo
- Department of Immunology, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Upal Roy
- Department of Immunology, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Madhavan P N Nair
- Department of Immunology, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA.
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Prentice HA, Price MA, Porter TR, Cormier E, Mugavero MJ, Kamali A, Karita E, Lakhi S, Sanders EJ, Anzala O, Amornkul PN, Allen S, Hunter E, Kaslow RA, Gilmour J, Tang J. Dynamics of viremia in primary HIV-1 infection in Africans: insights from analyses of host and viral correlates. Virology 2013; 449:254-62. [PMID: 24418560 DOI: 10.1016/j.virol.2013.11.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 10/11/2013] [Accepted: 11/14/2013] [Indexed: 12/15/2022]
Abstract
In HIV-1 infection, plasma viral load (VL) has dual implications for pathogenesis and public health. Based on well-known patterns of HIV-1 evolution and immune escape, we hypothesized that VL is an evolving quantitative trait that depends heavily on duration of infection (DOI), demographic features, human leukocyte antigen (HLA) genotypes and viral characteristics. Prospective data from 421 African seroconverters with at least four eligible visits did show relatively steady VL beyond 3 months of untreated infection, but host and viral factors independently associated with cross-sectional and longitudinal VL often varied by analytical approaches and sliding time windows. Specifically, the effects of age, HLA-B(⁎)53 and infecting HIV-1 subtypes (A1, C and others) on VL were either sporadic or highly sensitive to time windows. These observations were strengthened by the addition of 111 seroconverters with 2-3 eligible VL results, suggesting that DOI should be a critical parameter in epidemiological and clinical studies.
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Affiliation(s)
- Heather A Prentice
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Matthew A Price
- International AIDS Vaccine Initiative, New York City, NY, USA; Department of Epidemiology & Biostatistics, UCSF, San Francisco, CA, USA
| | - Travis R Porter
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Emmanuel Cormier
- International AIDS Vaccine Initiative, Human Immunology Laboratory, Chelsea and Westminster Hospital, London, UK
| | - Michael J Mugavero
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anatoli Kamali
- MRC/UVRI Uganda Virus Research Unit on AIDS, Masaka Site, Masaka, Uganda
| | | | - Shabir Lakhi
- Zambia-Emory HIV Research Project, Lusaka, Zambia
| | - Eduard J Sanders
- Centre for Geographic Medicine Research, Kenya Medical Research Institute (KEMRI), Kilifi, Kenya; Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington, UK
| | - Omu Anzala
- Kenya AIDS Vaccine Initiative (KAVI), Nairobi, Kenya
| | | | - Susan Allen
- Zambia-Emory HIV Research Project, Lusaka, Zambia; Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Eric Hunter
- Vaccine Research Center, Emory University, Atlanta, GA, USA
| | - Richard A Kaslow
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jill Gilmour
- International AIDS Vaccine Initiative, Human Immunology Laboratory, Chelsea and Westminster Hospital, London, UK
| | - Jianming Tang
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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Njai HF, Ewings FM, Lyimo E, Foulongne V, Ngerageza D, Mongi A, Ssemwanga D, Andreasen A, Nyombi B, Ao T, Michael D, Urassa M, Todd J, Zaba B, Changalucha J, Hayes R, Kapiga SH. Deciphering the complex distribution of human immunodeficiency virus type 1 subtypes among different cohorts in Northern Tanzania. PLoS One 2013; 8:e81848. [PMID: 24349139 PMCID: PMC3859540 DOI: 10.1371/journal.pone.0081848] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 10/17/2013] [Indexed: 11/19/2022] Open
Abstract
Background Increased understanding of the genetic diversity of HIV-1 is challenging but important in the development of an effective vaccine. We aimed to describe the distribution of HIV-1 subtypes in northern Tanzania among women enrolled in studies preparing for HIV-1 prevention trials (hospitality facility-worker cohorts), and among men and women in an open cohort demographic surveillance system (Kisesa cohort). Methods The polymerase encompassing partial reverse transcriptase was sequenced and phylogenetic analysis performed and subtype determined. Questionnaires documented demographic data. We examined factors associated with subtype using multinomial logistic regression, adjusted for study, age, and sex. Results Among 140 individuals (125 women and 15 men), subtype A1 predominated (54, 39%), followed by C (46, 33%), D (25, 18%) and unique recombinant forms (URFs) (15, 11%). There was weak evidence to suggest different subtype frequencies by study (for example, 18% URFs in the Kisesa cohort versus 5–9% in the hospitality facility-worker cohorts; adjusted relative-risk ratio (aRR) = 2.35 [95% CI 0.59,9.32]; global p = 0.09). Compared to men, women were less likely to have subtype D versus A (aRR = 0.12 [95% CI 0.02,0.76]; global p = 0.05). There was a trend to suggest lower relative risk of subtype D compared to A with older age (aRR = 0.44 [95% CI 0.23,0.85] per 10 years; global p = 0.05). Conclusions We observed multiple subtypes, confirming the complex genetic diversity of HIV-1 strains circulating in northern Tanzania, and found some differences between cohorts and by age and sex. This has important implications for vaccine design and development, providing opportunity to determine vaccine efficacy in diverse HIV-1 strains.
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Affiliation(s)
- Harr F. Njai
- Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Fiona M. Ewings
- Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
- MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Eric Lyimo
- National Institute for Medical Research, Mwanza, Tanzania
| | - Vincent Foulongne
- Laboratoire de Virologie, University of Montpellier, Montpellier, France
| | | | - Aika Mongi
- Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
| | | | - Aura Andreasen
- Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Tony Ao
- Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Denna Michael
- National Institute for Medical Research, Mwanza, Tanzania
| | - Mark Urassa
- National Institute for Medical Research, Mwanza, Tanzania
| | - Jim Todd
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- National Institute for Medical Research, Mwanza, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Basia Zaba
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Richard Hayes
- MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Saidi H. Kapiga
- Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- * E-mail:
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Abstract
Objective: To describe immunologic, virologic, and clinical HIV disease progression by HIV-1 subtype among Africans with well documented estimated dates of HIV infection (EDIs). Design: Prospective cohort. Methods: Adults and youth with documented HIV-1 infection in the past 12 months were recruited from seroincidence cohorts in East and Southern Africa and followed at 3–6 month intervals. Blood for lymphocyte subset and viral load determination was collected at each visit. Pol was sequenced from the first positive specimen to ascertain subtype. Preantiretroviral therapy disease progression was measured by three time-to-event endpoints: CD4+ cell count 350 cells/μl or less, viral load measurement at least 1 × 105 copies/ml, and clinical AIDS. Results: From 2006 to 2011, 615 participants were enrolled at nine research centers in Kenya, Rwanda, South Africa, Uganda, and Zambia; 579 (94.1%) had viral subtyping completed. Predominant subtypes were C (256, 44.2%), A (209, 36.1%), and D (84, 14.5%). After adjustment for age, sex, and human leukocyte antigen alleles in Cox regression analyses, subtype C-infected participants progressed faster than subtype A to all three endpoints [CD4+ hazard ratio 1.60, 95% (confidence interval) CI 1.16, 2.20; viral load hazard ratio 1.59, 95% CI 1.12, 2.25; and AIDS hazard ratio 1.60, 95% CI 1.11, 2.31). Subtype D-infected participants reached high viral load more rapidly (hazard ratio 1.61, 95% CI 1.01, 2.57) and progressed nearly twice as fast to AIDS compared to subtype A (hazard ratio 1.93, 95% CI 1.21, 3.09). Conclusion: Subtype-specific differences in HIV disease progression suggest that the local subtype distribution be considered when planning HIV programs and designing and defining clinical endpoints for HIV prevention trials.
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Ssemwanga D, Nsubuga RN, Mayanja BN, Lyagoba F, Magambo B, Yirrell D, Van der Paal L, Grosskurth H, Kaleebu P. Effect of HIV-1 subtypes on disease progression in rural Uganda: a prospective clinical cohort study. PLoS One 2013; 8:e71768. [PMID: 23951241 PMCID: PMC3741119 DOI: 10.1371/journal.pone.0071768] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 07/03/2013] [Indexed: 02/04/2023] Open
Abstract
Objective We examined the association of HIV-1 subtypes with disease progression based on three viral gene regions. Design A prospective HIV-1 clinical cohort study in rural Uganda. Methods Partial gag, env and pol genes were sequenced. Cox proportional hazard regression modelling was used to estimate adjusted hazard ratios (aHRs) of progression to: CD4≤250, AIDS onset and death, adjusted for sex, age and CD4 count at enrolment. Results Between 1990 and 2010, 292 incident cases were subtyped: 25% had subtype A, 45% had D, 26% had A/D recombinants, 1% had C and 4% were other recombinant forms. Of the 278 incident cases included in the disease progression analysis, 62% progressed to CD4≤250, 32% to AIDS, and 34% died with a higher proportion being among subtype D cases. The proportions of individuals progressing to the three endpoints were significantly higher among individuals infected with subtype D. Throughout the study period, individuals infected with subtype D progressed faster to CD4≤250, adjusted HR (aHR), (95% CI) = 1.72 (1.16–2.54), but this was mainly due to events in the period before antiretroviral therapy (ART) introduction, when individuals infected with subtype D significantly progressed faster to CD4≤250 than subtype A cases; aHR (95% CI) = 1.78 (1.01–3.14). Conclusions In this population, HIV-1 subtype D was the most prevalent and was associated with faster HIV-1 disease progression than subtype A. Further studies are needed to examine the effect of HIV-1 subtypes on disease progression in the ART period and their effect on the virological and immunological ART outcomes.
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Affiliation(s)
- Deogratius Ssemwanga
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Rebecca N. Nsubuga
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Billy N. Mayanja
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Frederick Lyagoba
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Brian Magambo
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Dave Yirrell
- Department of Medical Microbiology, Ninewells Hospital, Dundee, United Kingdom
| | | | - Heiner Grosskurth
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- * E-mail:
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26
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Palm AA, Esbjörnsson J, Månsson F, Kvist A, Isberg PE, Biague A, da Silva ZJ, Jansson M, Norrgren H, Medstrand P. Faster progression to AIDS and AIDS-related death among seroincident individuals infected with recombinant HIV-1 A3/CRF02_AG compared with sub-subtype A3. J Infect Dis 2013; 209:721-8. [PMID: 23935204 DOI: 10.1093/infdis/jit416] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) is divided into subtypes and circulating recombinant forms (CRFs) but the impact of subtype/CRF on disease progression is not fully understood. METHODS We determined the HIV-1 subtype/CRF of 152 seroincident individuals from Guinea-Bissau, based on the C2-V3 region of env. Disease progression was measured as time from estimated seroconversion to AIDS and AIDS-related death. Hazard ratios (HRs) were calculated using a Cox proportional hazard model, adjusting for gender and age at seroconversion. RESULTS The major subtypes/CRFs identified were CRF02_AG (53%), A3 (29%), and A3/02 (a recombinant of A3 and CRF02_AG) (13%). Infection with A3/02 was associated with a close to 3-fold increased risk of AIDS and AIDS-related death compared to A3 (HR = 2.6 [P = 0.011] and 2.9 [P = 0.032], respectively). The estimated time from seroconversion to AIDS and AIDS-related death was 5.0 and 8.0 years for A3/02, 6.2 and 9.0 years for CRF02_AG, and 7.2 and 11.3 years for A3. CONCLUSION Our results show that there are differences in disease progression between HIV-1 A-like subtypes/CRFs. Individuals infected with A3/02 have among the fastest progression rates to AIDS reported to date. Determining the HIV-1 subtype of infected individuals could be important in the management of HIV-1 infections.
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Treatment failure and drug resistance is more frequent in HIV-1 subtype D versus subtype A-infected Ugandans over a 10-year study period. AIDS 2013; 27:1899-909. [PMID: 23727942 DOI: 10.1097/qad.0b013e3283610ec7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To determine the impact of HIV-1 subtype on treatment outcomes and the emergence of drug resistance in the resource limited setting of Kampala, Uganda. DESIGN The Joint Clinical Research Centre (JCRC) in Kampala, Uganda has provided over 2000 drug-resistant genotypes (DRGs) over the past 10 years as standard of care for patients failing therapy and 1403 from treatment-naive and experienced patients over the past 10 years have been analyzed for this study. METHOD Viral loads, CD4 cell count, treatment histories and other relevant clinical data was compared with the infecting HIV-1 subtype and DRGs of Ugandan patients failing treatment. RESULTS Patients failing HAART with DRGs (n = 937) were more frequently infected with subtype D than expected on the basis of the subtype distribution in the treatment-naive population (n = 655) in Kampala (P < 0.001). Higher proportions of treatment failures among subtype D-infected patients were driven by resistance to nucleoside reverse transcriptase inhibitors (NRTI) (P < 0.0002) more than to non-NRTIs (P > 0.04) or protease inhibitors. CONCLUSION Higher rates of treatment failure among subtype D as compared with subtype A-infected Ugandans was analogous to the faster disease progression in subtype D-infected patients. The mechanism(s) by which drug resistance may emerge faster in subtype D HIV-1 may relate to higher replicative fitness and increased propensity for a CXCR4 tropism.
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Santoro MM, Perno CF. HIV-1 Genetic Variability and Clinical Implications. ISRN MICROBIOLOGY 2013; 2013:481314. [PMID: 23844315 PMCID: PMC3703378 DOI: 10.1155/2013/481314] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 04/16/2013] [Indexed: 11/29/2022]
Abstract
Despite advances in antiretroviral therapy that have revolutionized HIV disease management, effective control of the HIV infection pandemic remains elusive. Beyond the classic non-B endemic areas, HIV-1 non-B subtype infections are sharply increasing in previous subtype B homogeneous areas such as Europe and North America. As already known, several studies have shown that, among non-B subtypes, subtypes C and D were found to be more aggressive in terms of disease progression. Luckily, the response to antiretrovirals against HIV-1 seems to be similar among different subtypes, but these results are mainly based on small or poorly designed studies. On the other hand, differences in rates of acquisition of resistance among non-B subtypes are already being observed. This different propensity, beyond the type of treatment regimens used, as well as access to viral load testing in non-B endemic areas seems to be due to HIV-1 clade specific peculiarities. Indeed, some non-B subtypes are proved to be more prone to develop resistance compared to B subtype. This phenomenon can be related to the presence of subtype-specific polymorphisms, different codon usage, and/or subtype-specific RNA templates. This review aims to provide a complete picture of HIV-1 genetic diversity and its implications for HIV-1 disease spread, effectiveness of therapies, and drug resistance development.
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Affiliation(s)
- Maria Mercedes Santoro
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Carlo Federico Perno
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
- INMI L Spallanzani Hospital, Antiretroviral Therapy Monitoring Unit, Via Portuense 292, 00149 Rome, Italy
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Touloumi G, Pantazis N, Pillay D, Paraskevis D, Chaix ML, Bucher HC, Kücherer C, Zangerle R, Kran AMB, Porter K. Impact of HIV-1 subtype on CD4 count at HIV seroconversion, rate of decline, and viral load set point in European seroconverter cohorts. Clin Infect Dis 2013; 56:888-97. [PMID: 23223594 DOI: 10.1093/cid/cis1000] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) subtype may influence disease progression. We compared CD4 lymphocyte cell count levels at seroconversion, decline rates and viral load set point in individuals infected with different HIV-1 subtypes. METHODS We used data from the Concerted Action on SeroConversion to AIDS and Death in Europe (CASCADE) collaboration, restricted to those infected since 1996, aged ≥15 years, and applied mixed effects models for CD4 cell count decline and median regression for viral load set point (mean level 6-24 months from seroconversion). RESULTS The analysis included 3364 seroconverters with known HIV-1 subtypes. Compared with subtype B, CD4 at seroconversion was significantly higher for subtype CRF01 and lower for subtype C. Subsequent CD4 decline was significantly slower for subtypes A and CRF02 and marginally slower for subtype C compared with B. Mean CD4 loss at 2 years of seroconversion for white men exposed through sex between men, aged 30-39 years, having seroconverted since 2006, enrolled within 6 months of seroconversion, and without acute infection was 88, 142, 100, 130, 103, and 167 cells/µL for subtypes A, B, C, CRF01_AE, CRF02_AG, and G, respectively. In adjusted analysis, median viral load set point and time to clinical AIDS/death did not differ significantly by subtype, although all subtypes, except C, tended to have lower levels compared with B. CONCLUSIONS HIV-1 subtype significantly influences seroconversion CD4 cell levels and decline rates but not viral load set point. These findings may be helpful to HIV-positive individuals and their attending physicians in understanding disease progression.
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Affiliation(s)
- Giota Touloumi
- Department of Hygiene, Epidemiology and Medical Statistics, Athens University Medical School, Greece.
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30
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Kapaata A, Lyagoba F, Ssemwanga D, Magambo B, Nanyonjo M, Levin J, Mayanja BN, Mugasa C, Parry CM, Kaleebu P. HIV-1 subtype distribution trends and evidence of transmission clusters among incident cases in a rural clinical cohort in southwest Uganda, 2004-2010. AIDS Res Hum Retroviruses 2013; 29:520-7. [PMID: 23046049 DOI: 10.1089/aid.2012.0170] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The high diversity of HIV-1 has been shown to affect disease progression, transmission, and response to antiretroviral therapy and may influence HIV vaccine design. We describe the distribution trends of HIV-1 subtypes over a 7-year period among incident cases in a rural clinical cohort in Southwest Uganda and identify transmission clusters. Viral RNA was extracted from cryopreserved plasma samples from 94 participants who seroconverted and enrolled between 2004 and 2010. Partial gag (p24) and env (gp41) genes were directly sequenced to identify subtypes and transmission clusters with more than 95% bootstrap values. Direct sequencing of the partial pol gene and use of individual participant sexual life histories were also used to confirm these transmission clusters. The overall gag/env subtype distribution was A 28% (n=26), C 1% (n=1), and D 45% (n=42) and 27% (n=25) were intergene unique recombinant forms. The proportions of subtype A, D, or recombinants showed no significant increasing or decreasing trend over this time period (p=0.51). Phylogenetic analysis of the three genes confirmed 13 transmission clusters of which seven clusters were confirmed sexual partners using individual participants' sexual life histories. Subtype D has remained the predominant subtype in this population. From 2004 to 2010, there was no change in the proportions of these subtypes. Phylogenetic analysis and participants' sexual life histories revealed several transmission clusters. The high proportion of transmission clusters observed suggests continued high-risk sexual behavior and mixing in some individuals and possibly super transmitters in this presumed low-risk cohort, but also indicates that many transmissions occur in early HIV infection. This calls for early and targeted effective prevention and treatment intervention in this population.
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Affiliation(s)
- Anne Kapaata
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
| | | | | | - Brian Magambo
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
| | | | | | | | - Claire Mugasa
- Faculty of Veterinary Medicine, Makerere University, Kampala, Uganda
| | | | - Pontiano Kaleebu
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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31
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Hawke KG, Waddell RG, Gordon DL, Ratcliff RM, Ward PR, Kaldor JM. HIV non-B subtype distribution: emerging trends and risk factors for imported and local infections newly diagnosed in South Australia. AIDS Res Hum Retroviruses 2013; 29:311-7. [PMID: 23098890 DOI: 10.1089/aid.2012.0082] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Monitoring HIV subtype distribution is important for understanding transmission dynamics. Subtype B has historically been dominant in Australia, but in recent years new clades have appeared. Since 2000, clade data have been collected as part of HIV surveillance in South Australia. The aim of this study was to evaluate the prevalence of and risk factors for HIV-1 non-B subtypes. The study population was composed of newly diagnosed, genotyped HIV subjects in South Australia between 2000 and 2010. We analyzed time trends and subtype patterns in this cohort; notification data were aggregated into three time periods (2000-2003, 2004-2006, and 2007-2010). Main outcome measures were number of new non-B infections by year, exposure route, and other demographic characteristics. There were 513 new HIV diagnoses; 425 had information on subtype. The majority (262/425) were in men who have sex with men (MSM), predominantly subtype B and acquired in Australia. Infections acquired in Australia decreased from 77% (2000-2003) to 64% (2007-2010) (p=0.007) and correspondingly the proportion of subtype B declined from 85% to 68% (p=0.002). Non-B infections were predominantly (83%) heterosexual contacts, mostly acquired overseas (74%). The majority (68%) of non-B patients were born outside of Australia. There was a nonsignificant increase from 1.6% to 4.2% in the proportion of locally transmitted non-B cases (p=0.3). Three non-B subtypes and two circulating recombinant forms (CRFs) were identified: CRF_AE (n=41), C (n=36), CRF_AG (n=13), A (n=9), and D (n=2). There has been a substantial increase over the past decade in diagnosed non-B infections, primarily through cases acquired overseas.
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Affiliation(s)
- Karen G. Hawke
- Discipline of Public Health, Flinders University, Adelaide, Australia
| | | | - David L. Gordon
- Department of Microbiology and Infectious Diseases, SA Pathology at Flinders Medical Centre, and Flinders University, Adelaide, Australia
| | - Rodney M. Ratcliff
- Department of Microbiology and Infectious Diseases, SA Pathology at Institute of Medical and Veterinary Science, and School of Biomedical Science, University of Adelaide, Adelaide, Australia
| | - Paul R. Ward
- Discipline of Public Health, Flinders University, Adelaide, Australia
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32
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Asiki G, Murphy G, Nakiyingi-Miiro J, Seeley J, Nsubuga RN, Karabarinde A, Waswa L, Biraro S, Kasamba I, Pomilla C, Maher D, Young EH, Kamali A, Sandhu MS. The general population cohort in rural south-western Uganda: a platform for communicable and non-communicable disease studies. Int J Epidemiol 2013; 42:129-41. [PMID: 23364209 DOI: 10.1093/ije/dys234] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The General Population Cohort (GPC) was set up in 1989 to examine trends in HIV prevalence and incidence, and their determinants in rural south-western Uganda. Recently, the research questions have included the epidemiology and genetics of communicable and non-communicable diseases (NCDs) to address the limited data on the burden and risk factors for NCDs in sub-Saharan Africa. The cohort comprises all residents (52% aged ≥13years, men and women in equal proportions) within one-half of a rural sub-county, residing in scattered houses, and largely farmers of three major ethnic groups. Data collected through annual surveys include; mapping for spatial analysis and participant location; census for individual socio-demographic and household socioeconomic status assessment; and a medical survey for health, lifestyle and biophysical and blood measurements to ascertain disease outcomes and risk factors for selected participants. This cohort offers a rich platform to investigate the interplay between communicable diseases and NCDs. There is robust infrastructure for data management, sample processing and storage, and diverse expertise in epidemiology, social and basic sciences. For any data access enquiries you may contact the director, MRC/UVRI, Uganda Research Unit on AIDS by email to mrc@mrcuganda.org or the corresponding author.
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Affiliation(s)
- Gershim Asiki
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI), Uganda Research Unit on AIDS, Entebbe, Uganda.
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HIV/AIDS Global Epidemic. Infect Dis (Lond) 2013. [DOI: 10.1007/978-1-4614-5719-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Ferreira V, Moura P, Crovella S, Sobhie Diaz R, Castelo Filho A, Ximenes R, Arraes LC. The Influence of HIV-1 Subtype in the Response to Therapeutic Dendritic Cell Vaccine. Open AIDS J 2012; 6:289-92. [PMID: 23289053 PMCID: PMC3534477 DOI: 10.2174/1874613601206010289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 06/10/2012] [Accepted: 06/12/2012] [Indexed: 11/22/2022] Open
Abstract
In the present study, we investigated the influence of HIV-1 subtype in the response to the dendritic cell (DC)
therapeutic vaccine for HIV. HIV-1 viral load and TCD8+/TCD4+ cell counts for up to 48 weeks after vaccination. Out of
19 immunized subjects, 13 were infected by subtype B, 5 by subtype F, and 1 by subtype D. Overall, 42.1% (8/19)
achieved a viral load decline of ≥ 1 log10 sustained up to 48 weeks after immunization. Such magnitude of viral load drop
was seen in 80% (4/5) of subtype F infected patients, and in 23.0% (3/13) of the subtype B infected ones (p=0.08).
Moreover, mean viral load decline was 1.32 log10, for subtype F infected individuals compared to 0.5 log10 among subtype
B infected patients (p=0.01). The variation in TCD4+ cell count was not related to HIV-1 subtype. Larger studies are
necessary to confirm the efficacy of this immunotherapy and the differential response according to the background genetic
diversity of HIV-1.
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Abstract
HIV type 1 (HIV-1) displays a greater degree of genetic and antigenic variability than any other virus studied. This diversity reflects a high mutation rate during viral replication with a large turnover of virus, and a high tolerance of variation while maintaining reproductive capacity. Generation of diversity is a common property of lentiviruses such as HIV. Differences in virulence and in transmissibility are seen between different HIV-1 strains which may have clinical implications. The great degree of HIV diversity presents challenges to maintaining sensitivity to antiretroviral therapy and to the development of preventive strategies such as microbicides and vaccines.
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Does genetic diversity of HIV-1 non-B subtypes differentially impact disease progression in treatment-naive HIV-1-infected individuals? A systematic review of evidence: 1996-2010. J Acquir Immune Defic Syndr 2012; 59:382-8. [PMID: 22269800 DOI: 10.1097/qai.0b013e31824a0628] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
With 88% of HIV-1-infected individuals living in areas of high prevalence of non-B subtypes and with expanded global access to antiretroviral treatment (ART), studying disease progression amongst non-B subtypes gains relevance. Optimized clinical management is a possibility with knowledge of non-B subtype profiles at baseline, which is currently not possible due to lack of subtype-specific point-of-care assays. In a systematic review, we synthesized global evidence on differential disease progression amongst non-B subtypes in ART-naive individuals. Due to lack of consistent effect measures, we avoided pooling data and inferred patterns with respect to disease progression outcomes (ie, AIDS, Death, CD4, viral load changes). Subtypes C and D were more aggressive, followed by G, AE, and AG, and A being the least aggressive of all HIV-1 subtypes. Evidence of greater rates of disease progression in globally prevalent C and D subtypes highlight the importance of expanding early HIV detection, and determining subtype profile at baseline with CD4 staging to optimize the quality of ART delivery and care in global settings.
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Ssemwanga D, Ndembi N, Lyagoba F, Bukenya J, Seeley J, Vandepitte J, Grosskurth H, Kaleebu P. HIV type 1 subtype distribution, multiple infections, sexual networks, and partnership histories in female sex workers in Kampala, Uganda. AIDS Res Hum Retroviruses 2012; 28:357-65. [PMID: 21749285 DOI: 10.1089/aid.2011.0024] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We investigated for the first time the subtype distribution, prevalence of multiple HIV-1 infections, sexual networks, and partnership histories in a cohort of women engaged in high-risk sexual behavior such as female sex workers (FSWs) and women employed in entertainment facilities. Viral RNA was extracted from blood samples collected from 324 HIV-1-positive women; the gp-41 and pol-IN genes were directly sequenced. Women found to have closely related viruses and those with recombinant viruses were further analyzed in the pol-IN gene by clonal sequencing to determine HIV-1 multiple infections. Individual partnership histories were used to provide information on when sex work was undertaken and where. Subtyping in both gp-41 and pol-IN was successfully done in 210/324 (64.8%) women. Subtype distribution in these two genes was 54.3% (n=114) A/A, 2.9% (n=6) C/C, 24.3% (n=51) D/D, 11.9% (n=25) A/D, 4.8% (n=10) D/A, 0.5% (n=1) C/A, 1.0% (n=2) B/A, and 0.5% (n=1) B/D. Sexual networks were identified in six pairs and one triplet of women with closely related subtype A viruses. Partnership histories showed that women having phylogenetically similar viruses had worked in the same localities. Five cases of multiple infections were confirmed: four dual infections and one triple infection. In this first molecular epidemiology study among FSWs in Kampala, subtype A was the predominant subtype. About 9% of a subgroup had multiple infections. Partnership histories and multiple infections observed in this population suggest sexual mixing of the FSWs and their clients confirming their high-risk characteristics.
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Affiliation(s)
| | | | - Fred Lyagoba
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
| | | | - Janet Seeley
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- School of International Development, University of East Anglia, Norwich, United Kingdom
| | | | - Heiner Grosskurth
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Pontiano Kaleebu
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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Samikkannu T, Agudelo M, Gandhi N, Reddy PVB, Saiyed ZM, Nwankwo D, Nair MPN. Human immunodeficiency virus type 1 clade B and C gp120 differentially induce neurotoxin arachidonic acid in human astrocytes: implications for neuroAIDS. J Neurovirol 2011; 17:230-8. [PMID: 21491143 PMCID: PMC5737634 DOI: 10.1007/s13365-011-0026-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 02/04/2011] [Accepted: 03/10/2011] [Indexed: 11/26/2022]
Abstract
HIV-1 clades (subtypes) differentially contribute to the neuropathogenesis of HIV-associated dementia (HAD) in neuroAIDS. HIV-1 envelop protein, gp120, plays a major role in neuronal function. It is not well understood how these HIV-1 clades exert these neuropathogenic differences. The N-methyl-D: -aspartate (NMDA) receptor-reduced glutamine synthesis could lead to secretion of neurotoxins such as arachidonic acid (AA) which plays a significant role in the neuropathogenic mechanisms in neuroAIDS. We hypothesize that clade B and C gp120 proteins exert differential effects on human primary astrocytes by production of the neurotoxin arachidonic acid. Our results indicate that clade B gp120 significantly downregulated NMDA receptor gene and protein expression, and level of glutamine while increasing expression of prostaglandin E2 (PGE(2)) and thromboxane A2 receptor (TBXA(2) R) compared to HIV-1 clade C gp120 protein. Thus, our studies for the first time demonstrate that HIV-1 clade B-gp120 protein appears to induce higher levels of expression of the neuropathogenic molecule cyclooxygenase-2 (COX-2)-mediated arachidonic acid by-products, PGE(2), and TBXA(2) R compared to HIV-1 clade C gp120 protein. These studies suggest that HIV-1 clade B and C gp120 proteins may play a differential role in the neuropathogenesis of HAD in neuroAIDS.
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Affiliation(s)
- Thangavel Samikkannu
- Department of Immunology, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, 11200 S.W. 8th Street, HLS-1 #418A, Miami, FL 33199, USA
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Nofemela A, Bandawe G, Thebus R, Marais J, Wood N, Hoffmann O, Maboko L, Hoelscher M, Woodman Z, Williamson C. Defining the human immunodeficiency virus type 1 transmission genetic bottleneck in a region with multiple circulating subtypes and recombinant forms. Virology 2011; 415:107-13. [PMID: 21531432 DOI: 10.1016/j.virol.2010.12.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 10/10/2010] [Accepted: 12/15/2010] [Indexed: 11/19/2022]
Abstract
The Mbeya region of Tanzania has a genetically complex HIV epidemic with multiple subtypes and recombinant forms circulating, together with a high frequency of dual infections with more than one subtype. This study aimed to determine whether this impacted the HIV-1 transmission bottleneck. A total of 210 env sequences from 22 participants were generated from recently infected women from Mbeya using the single genome amplification approach. Participants were infected with subtypes C (n=9), A (n=4), or D (n=1), and recombinants AC (n=4), CD (n=2), AD (n=1), or ACD (n=1). Sixteen participants (73%) were infected with a single variant; five (23%) with multiple variants; and one (4%) was dually infected. Thus the frequency of single variant infections was similar to cohorts located in genetically restricted subtype B or C epidemics, suggesting that multiple circulating subtypes and unique recombinant forms do not have a significant impact on the transmission bottleneck.
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Affiliation(s)
- Andile Nofemela
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
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Wong JK, Campbell GR, Spector SA. Differential induction of interleukin-10 in monocytes by HIV-1 clade B and clade C Tat proteins. J Biol Chem 2010; 285:18319-25. [PMID: 20378550 DOI: 10.1074/jbc.m110.120840] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The clade B human immunodeficiency virus, type 1 (HIV-1) Tat (trans-acting regulatory protein) induces interleukin-10 (IL-10) production in monocytes. IL-10, an anti-inflammatory cytokine, down-regulates proinflammatory cytokines and suppresses the immune response, leading to a rapid progression from HIV-1 infection to AIDS. Nine clades of HIV-1 are responsible for the majority of infections worldwide. Recent studies demonstrate that different HIV-1 clades have biological differences in relation to transmission, replication, and disease progression. In this study, we show that the cysteine to serine mutation at position 31, found in >90% of HIV-1 clade C Tat proteins, results in a marked decrease in IL-10 production in monocytes compared with clade B Tat. Additionally, the C31S mutation found in C Tat is responsible for the inability of these Tat proteins to produce high IL-10 levels in monocytes due to its inability to induce intracellular calcium flux through L-type calcium channels. Moreover, we show that p38alpha/p38beta and phosphoinositide 3-kinase are crucial to Tat-induced IL-10 production. These findings provide further evidence that HIV-1 clades differ in their biological properties that may impact HIV-1 pathogenesis and disease progression.
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Affiliation(s)
- Justine K Wong
- Department of Pediatrics, Division of Infectious Diseases, University of California, San Diego,La Jolla, California 92093, USA
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Munerato P, Sucupira MC, Oliveros MP, Janini LM, de Souza DF, Pereira AA, Inocencio LA, Diaz RS. HIV type 1 antiretroviral resistance mutations in subtypes B, C, and F in the City of São Paulo, Brazil. AIDS Res Hum Retroviruses 2010; 26:265-73. [PMID: 20210652 DOI: 10.1089/aid.2008.0288] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In Brazil, where three distinct HIV-1 subtypes (B, F, and C) cocirculate, a significant portion of the HIV-infected population has been exposed to antiretroviral drugs. This study analyzes the antiretroviral resistance profiles of HIV-1-infected individuals failing antiretroviral therapy. Genotypic resistance profiles of 2474 patients presenting virologic failure to antiretroviral therapy in the city of São Paulo, Brazil, were generated and analyzed. Resistance mutations to protease inhibitors and nucleoside reverse transcriptase inhibitors were less common in subtype C viruses, whereas nonnucleoside reverse transcriptase inhibitor resistance mutations were less common in subtype F viruses. The thymidine analog mutation pathway known as pathway 1 was more prevalent in subtype B viruses than in subtype C viruses, whereas pathway 2 was more prevalent in subtype C viruses. Selected resistance mutations varied according to subtype for all three classes of antiretrovirals. We describe two distinct pathways of nonnucleoside reverse transcriptase inhibitor resistance (to nevirapine and efavirenz). Although cross-resistance to etravirine should occur more frequently among individuals failing nevirapine treatment, the prevalence of cross-resistance to etravirine, darunavir, and tipranavir was found to be low. We found that increases in the number of resistance mutations will be related to increases in the viral load. Special attention should be given to resistance profiles in non-B subtype viruses. The accumulation of knowledge regarding such profiles in the developing world is desirable.
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Affiliation(s)
- Patricia Munerato
- Infectious Diseases Division, Federal University of São Paulo, São Paulo, Brazil
| | | | | | - Luiz Mario Janini
- National STD/AIDS Program, Brazilian National Ministry of Health, Brasilia, Brazil
| | | | | | | | - Ricardo Sobhie Diaz
- Infectious Diseases Division, Federal University of São Paulo, São Paulo, Brazil
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Easterbrook PJ, Smith M, Mullen J, O'Shea S, Chrystie I, de Ruiter A, Tatt ID, Geretti AM, Zuckerman M. Impact of HIV-1 viral subtype on disease progression and response to antiretroviral therapy. J Int AIDS Soc 2010; 13:4. [PMID: 20205896 PMCID: PMC2827379 DOI: 10.1186/1758-2652-13-4] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Accepted: 02/03/2010] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Our intention was to compare the rate of immunological progression prior to antiretroviral therapy (ART) and the virological response to ART in patients infected with subtype B and four non-B HIV-1 subtypes (A, C, D and the circulating recombinant form, CRF02-AG) in an ethnically diverse population of HIV-1-infected patients in south London. METHODS A random sample of 861 HIV-1-infected patients attending HIV clinics at King's and St Thomas' hospitals' were subtyped using an in-house enzyme-linked immunoassay and env sequencing. Subtypes were compared on the rate of CD4 cell decline using a multi-level random effects model. Virological response to ART was compared using the time to virological suppression (< 400 copies/ml) and rate of virological rebound (> 400 copies/ml) following initial suppression. RESULTS Complete subtype and epidemiological data were available for 679 patients, of whom 357 (52.6%) were white and 230 (33.9%) were black African. Subtype B (n = 394) accounted for the majority of infections, followed by subtypes C (n = 125), A (n = 84), D (n = 51) and CRF02-AG (n = 25). There were no significant differences in rate of CD4 cell decline, initial response to highly active antiretroviral therapy and subsequent rate of virological rebound for subtypes B, A, C and CRF02-AG. However, a statistically significant four-fold faster rate of CD4 decline (after adjustment for gender, ethnicity and baseline CD4 count) was observed for subtype D. In addition, subtype D infections showed a higher rate of virological rebound at six months (70%) compared with subtypes B (45%, p = 0.02), A (35%, p = 0.004) and C (34%, p = 0.01) CONCLUSIONS This is the first study from an industrialized country to show a faster CD4 cell decline and higher rate of subsequent virological failure with subtype D infection. Further studies are needed to identify the molecular mechanisms responsible for the greater virulence of subtype D.
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Affiliation(s)
- Philippa J Easterbrook
- Department of HIV/GU Medicine, King's College London School of Medicine at Guy's, King's College and St Thomas' hospitals, Weston Education Centre, 10 Cutcombe Road, London, SE5 9RJ, UK
| | - Mel Smith
- Health Protection Agency London, London South Specialist Virology Centre, Bessemer Road, London, SE5 9RS, UK
| | - Jane Mullen
- Department of Virology and HIV/GU Medicine, St Thomas' Hospital, Westminster Bridge Road, London, SE1 7EH, UK
| | - Siobhan O'Shea
- Department of Virology and HIV/GU Medicine, St Thomas' Hospital, Westminster Bridge Road, London, SE1 7EH, UK
| | - Ian Chrystie
- Department of Virology and HIV/GU Medicine, St Thomas' Hospital, Westminster Bridge Road, London, SE1 7EH, UK
| | - Annemiek de Ruiter
- Department of Virology and HIV/GU Medicine, St Thomas' Hospital, Westminster Bridge Road, London, SE1 7EH, UK
| | - Iain D Tatt
- Virus Reference Department, Health Protection Agency, Centre for Infections, 61 Colindale Avenue, London, NW9 5HT, UK
- Pharmaceuticals Division, Hofffman-La Roche AG, Basel, Switzerland
| | - Anna Maria Geretti
- Department of Virology, Royal Free Hospital and Royal Free and University College Medical School, Pond Street, London, NW3 2QG, UK
| | - Mark Zuckerman
- Health Protection Agency London, London South Specialist Virology Centre, Bessemer Road, London, SE5 9RS, UK
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Infection with different hiv subtypes is associated with CD4 activation-associated dysfunction and apoptosis. J Acquir Immune Defic Syndr 2009; 52:548-52. [PMID: 19838123 DOI: 10.1097/qai.0b013e3181c1d456] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Determination of HIV-1 subtype may be important in the management of HIV-infected individuals, particularly with regard to deciding the CD4 cell count at which to initiate antiretroviral therapy. Non-B subtypes, A and D, are prevalent in Uganda, and individuals infected with subtype D seem to have faster disease progression compared with those infected with subtype A. We examined the level of apoptosis in CD4+ T cells in a study cohort of volunteers infected with subtypes A and D infection. Although the levels of apoptosis in the activated CD4+ cells significantly decreased with viral suppression, CD4+ apoptosis in individuals infected with subtype D were found to be significantly higher compared with those infected with subtype A before antiretroviral treatment. Surface expression of PD-1 on CD4 cells in subtype D was substantially higher compared with that in subtype A (P = 0.03). This difference was not observed in the CD8 population (P > 0.05). Our findings suggest that the infecting HIV subtypes exert an independent influence on the disease outcome in response to antiretroviral treatment.
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Impact of HIV-1 viral subtype on CD4+ T-cell decline and clinical outcomes in antiretroviral naive patients receiving universal healthcare. AIDS 2009; 23:731-7. [PMID: 19279446 DOI: 10.1097/qad.0b013e328326f77f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The influence of viral subtype on the natural history of HIV is unclear and confounded by socioeconomic and host factors that vary between groups harboring different clades. We compared Canadians (clade B), with recent immigrants from Haiti (clade B) and sub-Saharan Africa (clades non-B) to determine whether there were differences in disease progression attributable to viral subtype. METHODS We conducted a retrospective cohort study in a universal healthcare setting between 1996 and 2007. The rate of CD4+ T-lymphocyte decline prior to initiation of antiretroviral therapy was determined in all participants with at least two CD4+ T-lymphocyte measures using mixed linear regression models. Time to first AIDS-defining illness was compared using adjusted Cox proportional hazards models. RESULTS Two hundred and eighty-nine Canadians, 44 Haitians, and 123 Africans were studied for a median of 260 days (2 days-11 years). Africans and Haitians were demographically and clinically similar. However, the adjusted slope of square root CD4+ T-lymphocyte decline was significantly lower in Africans [-0.04/year; 95% confidence interval (CI) = -0.08 to -0.003] compared with Canadians (-0.07/year; 95% CI = -0.11 to -0.03; P = 0.02), and Haitians (-0.10/year; 95% CI = -0.12 to -0.07; P = 0.001). Africans were also less likely to develop AIDS. CONCLUSION Despite having similar demographic, socioeconomic, and nutritional status to Haitians, Africans infected with non-B clade HIV had slower rates of disease progression compared with both Haitians and Canadians, with both groups being infected by the clade B virus. Our findings suggest that viral subtype may be an important predictor of HIV natural history in a developed medical setting.
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CCR5- and CXCR4-tropic subtype C human immunodeficiency virus type 1 isolates have a lower level of pathogenic fitness than other dominant group M subtypes: implications for the epidemic. J Virol 2009; 83:5592-605. [PMID: 19297481 DOI: 10.1128/jvi.02051-08] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) subtype C is the dominant subtype globally, due largely to the incidence of subtype C infections in sub-Saharan Africa and east Asia. We compared the relative replicative fitness (ex vivo) of the major (M) group of HIV-1 subtypes A, B, C, D, and CRF01_AE and group O isolates. To estimate pathogenic fitness, pairwise competitions were performed between CCR5-tropic (R5) or CXCR4-tropic (X4) virus isolates in peripheral blood mononuclear cells (PBMC). A general fitness order was observed among 33 HIV-1 isolates; subtype B and D HIV-1 isolates were slightly more fit than the subtype A and dramatically more fit than the 12 subtype C isolates. All group M isolates were more fit (ex vivo) than the group O isolates. To estimate ex vivo transmission fitness, a subset of primary HIV-1 isolates were examined in primary human explants from penile, cervical, and rectal tissues. Only R5 isolates and no X4 HIV-1 isolates could replicate in these tissues, whereas the spread to PM1 cells was dependent on active replication and passive virus transfer. In tissue competition experiments, subtype C isolates could compete with and, in some cases, even win over subtype A and D isolates. However, when the migratory cells from infected tissues were mixed with a susceptible cell line, the subtype C isolates were outcompeted by other subtypes, as observed in experiments with PBMC. These findings suggest that subtype C HIV-1 isolates might have equal transmission fitness but reduced pathogenic fitness relative to other group M HIV-1 isolates.
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Gurunathan S, Habib RE, Baglyos L, Meric C, Plotkin S, Dodet B, Corey L, Tartaglia J. Use of predictive markers of HIV disease progression in vaccine trials. Vaccine 2009; 27:1997-2015. [DOI: 10.1016/j.vaccine.2009.01.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Revised: 12/19/2008] [Accepted: 01/08/2009] [Indexed: 10/21/2022]
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Kiwanuka N, Laeyendecker O, Robb M, Kigozi G, Arroyo M, McCutchan F, Eller LA, Eller M, Makumbi F, Birx D, Wabwire-Mangen F, Serwadda D, Sewankambo NK, Quinn TC, Wawer M, Gray R. Effect of human immunodeficiency virus Type 1 (HIV-1) subtype on disease progression in persons from Rakai, Uganda, with incident HIV-1 infection. J Infect Dis 2008; 197:707-13. [PMID: 18266607 DOI: 10.1086/527416] [Citation(s) in RCA: 208] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) subtypes differ in biological characteristics that may affect pathogenicity. METHODS We determined the HIV-1 subtype-specific rates of disease progression among 350 HIV-1 seroconverters. Subtype, viral load, and CD4(+) cell count were determined. Cox proportional hazards regression modeling was used to estimate adjusted hazard ratios (HRs) of progression to acquired immunodeficiency syndrome (AIDS) (defined as a CD4(+) cell count of < or =250 cells/mm(3)) and to AIDS-associated death. RESULTS A total of 59.1% of study subjects had subtype D strains, 15.1% had subtype A, 21.1% had intersubtype recombinant subtypes, 4.3% had multiple subtypes, and 0.3% had subtype C. Of the 350 subjects, 129 (37%) progressed to AIDS, and 68 (19.5%) died of AIDS. The median time to AIDS onset was shorter for persons with subtype D (6.5 years), recombinant subtypes (5.6 years), or multiple subtypes (5.8 years), compared with persons with subtype A (8.0 years; P = .022). Relative to subtype A, adjusted HRs of progression to AIDS were 2.13 [95% confidence interval {CI}, 1.10-4.11] for subtype D, 2.16 [95% CI, 1.05-4.45] for recombinant subtypes, and 4.40 [95% CI, 1.71-11.3] for multiple subtypes. The risk of progression to death was significantly higher for subtype D (adjusted HR, 5.65; 95% CI, 1.37-23.4), recombinant subtypes (adjusted HR, 6.70; 95% CI, 1.56-28.8), and multiple subtypes (adjusted HR, 7.67; 95% CI, 1.27-46.3), compared with subtype A. CONCLUSIONS HIV disease progression is affected by HIV-1 subtype. This finding may impact decisions on when to initiate antiretroviral therapy and may have implications for future trials of HIV-1 vaccines aimed at slowing disease progression.
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Abdulle S, Hagberg L, Svennerholm B, Fuchs D, Gisslén M. Cerebrospinal fluid viral load and intrathecal immune activation in individuals infected with different HIV-1 genetic subtypes. PLoS One 2008; 3:e1971. [PMID: 18414666 PMCID: PMC2291576 DOI: 10.1371/journal.pone.0001971] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2007] [Accepted: 02/14/2008] [Indexed: 11/18/2022] Open
Abstract
Background HIV-1 exhibits a high degree of genetic diversity and is presently divided into 3 distinct HIV-1 genetic groups designated major (M), non-M/non-O (N) and outlier (O). Group M, which currently comprises 9 subtypes (A-D, F-H, J and K), at least 34 circulating recombinant forms (CRFs) and several unique recombinant forms (URFs) is responsible for most of the HIV-1 epidemic. Most of the current knowledge of HIV-1 central nervous system (CNS) infection is based on subtype B. However, subtypes other than subtype B account for the majority of global HIV-1 infections. Therefore, we investigated whether subtypes have any influence on cerebrospinal fluid (CSF) markers of HIV-1 CNS infection. Methodology/Principal Findings CSF HIV-1 RNA, CSF neopterin and CSF white blood cell (WBC) count were measured in patients infected with different HIV-1 subtypes. Using multivariate regression analysis, no differences in the CSF WBC count, neopterin and viral load were found between various HIV-1 subtypes. Conclusions We did not find any subtype-dependent differences in the markers evaluated in this study.
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Affiliation(s)
- Sahra Abdulle
- Department of Infectious Diseases, The Sahlgrenska Academy, Göteborg University, Göteborg, Sweden.
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Senkaali D, Kebba A, Shafer L, Campbell G, Loret E, Van Der Paal L, Grosskurth H, Yirrell D, Kaleebu P. Tat-specific binding IgG and disease progression in HIV type 1-infected Ugandans. AIDS Res Hum Retroviruses 2008; 24:587-94. [PMID: 18366309 DOI: 10.1089/aid.2007.0171] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There are data to suggest that both the humoral and cellular immune responses directed against Tat are beneficial in delaying HIV disease progression. We examined the association between the occurrence of Tat-specific binding antibodies (Abs) and different parameters of HIV-1 disease progression. We generated eight Tat proteins, derived from HIV-1 subtypes A, B, C, and D, and circulating recombinant form CRF01_AE. These proteins were used to screen for Tat-specific binding Abs by an ELISA. Using five Tat proteins, we investigated whether the occurrence of Tat-specific Abs within 2 years after seroconversion for the majority, affected disease progression over time among 126 participants using survival analysis and rate of CD4 decline. Of these, 52 participants with a sample at 1.5 and 4.5 years after seroconversion were further examined to study the effect of Tat-specific Ab loss or maintenance on disease progression. Finally, using all the eight Tat proteins, we also investigated whether specific Abs to these Tat proteins among 48 participants, grouped as rapid progressors (RP, n = 26) and long-term survivors (LTS, n = 22) according to their CD4 decline over time, affected disease progression. Survival analysis did not reveal any evidence of protection from progression by Tat-specific Abs. Comparison of rate of CD4 declines between individuals with and without Abs to any Tat protein showed only a small and borderline significant advantage of having Tat-specific Abs (p = 0.043). There was no correlation between either loss or maintenance of Tat-specific Abs and disease progression. Comparison of LTS with RP showed no evidence that Tat-specific Abs slows participants' disease progression. This study showed no evidence of a protective effect of having Tat-specific Abs among these Ugandan subjects.
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Affiliation(s)
- D. Senkaali
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe Uganda
| | - A. Kebba
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe Uganda
| | - L.A. Shafer
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe Uganda
| | - G.R. Campbell
- Department of Pediatrics, Division of Infectious Diseases, University of California San Diego, La Jolla, California 92093-0672
| | - E.P. Loret
- Centre National de la Recherche Scientifique (CNRS), Faculté de Pharmacie, Université de la Méditerranée, 13385 Marseille
| | | | - H. Grosskurth
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe Uganda
| | - D. Yirrell
- Department of Medical Microbiology, Ninewells Hospital, Dundee, UK
| | - P. Kaleebu
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe Uganda
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Baker CA, McEvers K, Byaruhanga R, Mulindwa R, Atwine D, Nantiba J, Jones NG, Ssewanyana I, Cao H. HIV subtypes induce distinct profiles of HIV-specific CD8(+) T cell responses. AIDS Res Hum Retroviruses 2008; 24:283-7. [PMID: 18284326 DOI: 10.1089/aid.2007.0183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CD8(+) T cells play an important role in controlling HIV infection and qualitative differences in HIV-specific CD8(+) responses may determine the degree of immune control. We studied 56 HIV-infected, ARV-naive Ugandans and examined the role of subtypes in modulating their HIV-specific T cell responses. Gag-specific responses were readily detectable in our study population. Interestingly, we found significantly decreased Gag-specific cytolysis (as measured by CD107 expression) in subtype D (n = 21) compared to subtype A (n = 35) HIV infection. Sequence analyses within identified epitopes suggest patterns of conservation that are subtype specific. We conclude that HIV subtypes may promote distinct profiles of T cells responses and immune control.
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Affiliation(s)
- Chris A.R. Baker
- California Department of Public Health, Richmond, California 94804
| | - Kimberly McEvers
- California Department of Public Health, Richmond, California 94804
| | | | | | | | | | - Norman G. Jones
- California Department of Public Health, Richmond, California 94804
| | | | - Huyen Cao
- California Department of Public Health, Richmond, California 94804
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