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Folgosi VÂ, Komninakis SV, Lopes L, Monteiro MA, Assone T, Fonseca LAM, Domingues W, Leite PD, Victor JR, Casseb J. Unraveling clinical outcomes of long-term cART treatment in HIV-1 patients with or without the Brazilian GWGR motif in the V3 loop. Rev Inst Med Trop Sao Paulo 2024; 66:e38. [PMID: 39052025 PMCID: PMC11251515 DOI: 10.1590/s1678-9946202466038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/06/2024] [Indexed: 07/27/2024] Open
Abstract
The presence of genetic mutations in HIV poses a significant challenge, potentially leading to antiretroviral resistance and hampering therapeutic development. The Brazilian population has presented variations in the HIV envelope V3 loop gene, especially the GWGR motif. This motif has been linked to reduced transmission potential and slower CD4+ T cell decline. This study aimed to assess clinical outcomes in patients with HIV-1 infected with strains containing the GWGR motif compared with those without it during long-term cART. A cohort of 295 patients with HIV was examined for the GWGR motif presence in the V3 loop. A total of 58 samples showed the GWGR signature, while 237 had other signatures. Multifactorial analyses showed no significant differences in demographic characteristics, CD4+ cell count, AIDS progression, or mortality between GWGR carriers and others. However, the mean interval between the first positive HIV test and the initial AIDS-defining event was more than two times longer for women carrying the GWGR signature (p = 0.0231). We emphasize the positive impact of cART on HIV/AIDS treatment, including viral suppression, CD4+ cell preservation, and immune function maintenance. Although no significant differences were found during cART, residual outcomes reflecting adherence challenges were observed between diagnosis and the first AIDS-defining event. The previously described outcomes, highlighting statistically significant differences between individuals carrying the GPGR motif compared with those with the Brazilian GWGR motif, may be directly linked to the natural progression of infection before advancements in cART. Presently, these physicochemical aspects may no longer hold the same relevance.
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Affiliation(s)
- Victor Ângelo Folgosi
- Universidade de São Paulo, Faculdade de Medicina, Instituto de
Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM-56), São
Paulo, São Paulo, Brazil
| | - Shirley Vasconcelos Komninakis
- Universidade de São Paulo, Faculdade de Medicina, Instituto de
Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM-56), São
Paulo, São Paulo, Brazil
- Universidade Federal de São Paulo, Laboratório de Retrovirologia,
São Paulo, São Paulo, Brazil
| | - Luciano Lopes
- Universidade Federal de São Paulo, Departamento de Informática em
Saúde, Divisão de Bioinformática e Ciência de Dados em Biologia, São Paulo, São
Paulo, Brazil
| | - Mariana Amélia Monteiro
- Universidade de São Paulo, Faculdade de Medicina, Instituto de
Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM-56), São
Paulo, São Paulo, Brazil
| | - Tatiane Assone
- Universidade de São Paulo, Faculdade de Medicina, Instituto de
Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM-56), São
Paulo, São Paulo, Brazil
| | - Luiz Augusto Marcondes Fonseca
- Universidade de São Paulo, Faculdade de Medicina, Instituto de
Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM-56), São
Paulo, São Paulo, Brazil
| | - Wilson Domingues
- Universidade de São Paulo, Faculdade de Medicina, Instituto de
Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM-56), São
Paulo, São Paulo, Brazil
| | - Pedro Domingos Leite
- Universidade de São Paulo, Faculdade de Medicina, Instituto de
Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM-56), São
Paulo, São Paulo, Brazil
| | - Jefferson Russo Victor
- Universidade de São Paulo, Faculdade de Medicina, Instituto de
Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM-56), São
Paulo, São Paulo, Brazil
- Universidade Santo Amaro, Programa de Pós-Graduação em Ciências da
Saúde, São Paulo, São Paulo, Brazil
| | - Jorge Casseb
- Universidade de São Paulo, Faculdade de Medicina, Instituto de
Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM-56), São
Paulo, São Paulo, Brazil
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Lee GQ, Khadka P, Gowanlock SN, Copertino DC, Duncan MC, Omondi FH, Kinloch NN, Kasule J, Kityamuweesi T, Buule P, Jamiru S, Tomusange S, Anok A, Chen Z, Jones RB, Galiwango RM, Reynolds SJ, Quinn TC, Brumme ZL, Redd AD, Prodger JL. HIV-1 subtype A1, D, and recombinant proviral genome landscapes during long-term suppressive therapy. Nat Commun 2024; 15:5480. [PMID: 38956017 PMCID: PMC11219899 DOI: 10.1038/s41467-024-48985-9] [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: 01/18/2023] [Accepted: 05/13/2024] [Indexed: 07/04/2024] Open
Abstract
The primary obstacle to curing HIV-1 is a reservoir of CD4+ cells that contain stably integrated provirus. Previous studies characterizing the proviral landscape, which have been predominantly conducted in males in the United States and Europe living with HIV-1 subtype B, have revealed that most proviruses that persist during antiretroviral therapy (ART) are defective. In contrast, less is known about proviral landscapes in females with non-B subtypes, which represents the largest group of individuals living with HIV-1. Here, we analyze genomic DNA from resting CD4+ T-cells from 16 female and seven male Ugandans with HIV-1 receiving suppressive ART (n = 23). We perform near-full-length proviral sequencing at limiting dilution to examine the proviral genetic landscape, yielding 607 HIV-1 subtype A1, D, and recombinant proviral sequences (mean 26/person). We observe that intact genomes are relatively rare and clonal expansion occurs in both intact and defective genomes. Our modification of the primers and probes of the Intact Proviral DNA Assay (IPDA), developed for subtype B, rescues intact provirus detection in Ugandan samples for which the original IPDA fails. This work will facilitate research on HIV-1 persistence and cure strategies in Africa, where the burden of HIV-1 is heaviest.
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Affiliation(s)
- Guinevere Q Lee
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA.
| | - Pragya Khadka
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Sarah N Gowanlock
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Dennis C Copertino
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Maggie C Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - F Harrison Omondi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | | | | | - Paul Buule
- Rakai Health Sciences Program, Kalisizo, Uganda
| | | | | | - Aggrey Anok
- Rakai Health Sciences Program, Kalisizo, Uganda
| | - Zhengming Chen
- Department of Population Health Sciences, Division of Biostatistics, Weill Cornell Medicine, New York, NY, USA
| | - R Brad Jones
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | | | - Steven J Reynolds
- Rakai Health Sciences Program, Kalisizo, Uganda
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas C Quinn
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Andrew D Redd
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Western University, London, ON, Canada
- Department of Epidemiology and Biostatistics, Western University, London, ON, Canada
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3
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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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Lemonovich TL, Watkins RR, Morrison CS, Kwok C, Chipato T, Musoke R, Arts EJ, Nankya I, Salata RA. Differences in Clinical Manifestations of Acute and Early HIV-1 Infection between HIV-1 Subtypes in African Women. J Int Assoc Provid AIDS Care 2015; 14:415-22. [PMID: 24106054 PMCID: PMC4511722 DOI: 10.1177/2325957413504827] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Little is known about the differences in clinical manifestations between women with various HIV-1 subtypes during acute (AI) and early (EI) HIV infection. In a longitudinal cohort study, clinical signs and symptoms among Uganda and Zimbabwe women with AI and EI were compared with HIV-negative controls; symptoms were assessed quarterly for 15 to 24 months. Early HIV infection was defined as the first visit during which a woman tested HIV antibody positive. Women who were HIV negative serologically but DNA polymerase chain reaction positive were considered AI. In all, 26 women were classified AI and 192 EI, with 654 HIV-negative controls. Primary HIV infection (AI and EI) was associated with unexplained fever (P <.01), weight loss (P <.01), fatigue (P <.01), inguinal adenopathy (P <.01), and cervical friability (P =.01). More women with subtype C infection had unexplained fever, fatigue, and abnormal vaginal discharge compared to subtype A or D infection. Inguinal adenopathy occurred less often in women with subtype A infection than those with subtype C or D infection.
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Affiliation(s)
- Tracy L Lemonovich
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, University Hospitals Case Medical Center, Cleveland, OH, USA
| | - Richard R Watkins
- Division of Infectious Diseases, Akron General Medical Center, Akron, OH, USA
| | | | | | - Tsungai Chipato
- Department of Obstetrics and Gynaecology, University of Zimbabwe Medical School, Harare, Zimbabwe
| | - Robert Musoke
- Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Eric J Arts
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, University Hospitals Case Medical Center, Cleveland, OH, USA
| | - Immaculate Nankya
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, University Hospitals Case Medical Center, Cleveland, OH, USA
| | - Robert A Salata
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, University Hospitals Case Medical Center, Cleveland, OH, USA
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6
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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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7
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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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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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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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10
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Westrop SJ, Jackson A, Gazzard B, Imami N. HIV-1 clade A infection and viral control: an immunological perspective on a case of underquantification. Int J STD AIDS 2012; 22:690-2. [PMID: 22096061 DOI: 10.1258/ijsa.2009.009045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Although a vast majority of HIV-1-positive patients in the UK are infected with clade B virus, a large number of newly diagnosed cases of heterosexually transmitted HIV-1 are acquired abroad, in countries where non-B clade HIV-1 predominates. Since the development of the viral load assay in 1988, assessment of HIV-1 plasma viraemia has become an integral part of HIV clinical care; however, the contemporary viral load assay was developed and optimized for clade B HIV-1. Here we report the underquantification of viraemia in an individual infected with clade A virus, and the consequent initial classification of the patient as an HIV controller (HIC). Immunological investigations of interferon (IFN)-γ and lymphoproliferative responses to HIV-1 clade B antigens and peptides, in parallel with mitogenic stimulation, were performed. Subsequent comparison with responses observed within clade B-infected HIC led to viral sequencing, confirmation of infecting clade and recommendation of antiretroviral therapy initiation. We emphasize the growing need for awareness of possible limitations of the commonly used viral load assays, which cannot be relied upon unreservedly in a clinical setting. Furthermore, this case highlights the increasing need for more detailed investigation into both viral genetics and fitness when defining patients as HIC.
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Morrison CS, Chen PL, Nankya I, Rinaldi A, Van Der Pol B, Ma YR, Chipato T, Mugerwa R, Dunbar M, Arts E, Salata RA. Hormonal contraceptive use and HIV disease progression among women in Uganda and Zimbabwe. J Acquir Immune Defic Syndr 2011; 57:157-64. [PMID: 21358412 PMCID: PMC3164299 DOI: 10.1097/qai.0b013e318214ba4a] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND HIV-infected women need highly effective contraception to reduce unintended pregnancies and mother-to-child HIV transmission. Previous studies report conflicting results regarding the effect of hormonal contraception on HIV disease progression. METHODS HIV-infected women in Uganda and Zimbabwe were recruited immediately after seroconversion; CD4 testing and clinical examinations were conducted quarterly. The study end point was time to AIDS (two successive CD4 200 cells/mm or less or World Health Organization advanced Stage 3 or Stage 4 disease). We used marginal structural Cox survival models to estimate the effect of cumulative exposure to depot-medroxyprogesterone acetate and oral contraceptives on time to AIDS. RESULTS Three hundred three HIV-infected women contributed 1408 person-years. One hundred eleven women (37%) developed AIDS. Cumulative probability of AIDS was 50% at 7 years and did not vary by country. AIDS incidence was 6.6, 9.3, and 8.8 per 100 person-years for depot-medroxyprogesterone acetate, oral contraceptive, and nonhormonal users. Neither depot-medroxyprogesterone acetate (adjusted hazard ratio, 0.90; 95% confidence interval, 0.76-1.08) nor oral contraceptives ( adjusted hazard ratio, 1.07; 95% confidence interval, 0.89-1.29) were associated with HIV disease progression. Alternative exposure definitions of hormonal contraception use during the year before AIDS or at the time of HIV infection produced similar results. Sexually transmitted infection symptoms were associated with faster progression, whereas young age at HIV infection (18-24 years) was associated with slower progression. Adding baseline CD4 level and set point viral load to models did not change the hormonal contraception results, but Subtype D infection became associated with disease progression. CONCLUSION Hormonal contraceptive use was not associated with more rapid HIV disease progression, but older age, sexually transmitted infection symptoms, and Subtype D infection were.
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Affiliation(s)
- Charles S Morrison
- Department of Clinical Sciences, Family Health International, Research Triangle Park, NC, USA.
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HIV-subtype A is associated with poorer neuropsychological performance compared with subtype D in antiretroviral therapy-naive Ugandan children. AIDS 2010; 24:1163-70. [PMID: 20425886 DOI: 10.1097/qad.0b013e3283389dcc] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND HIV-subtype D is associated with more rapid disease progression and higher rates of dementia in Ugandan adults compared with HIV-subtype A. There are no data comparing neuropsychological function by HIV subtype in Ugandan children. DESIGN One hundred and two HIV-infected antiretroviral therapy (ART) naive Ugandan children 6-12 years old (mean 8.9) completed the Kaufman Assessment Battery for Children, second edition (KABC-2), the Test of Variables of Attention (TOVA), and the Bruininks-Oseretsky Test for Motor Proficiency, second edition (BOT-2). Using a PCR-based multiregion assay with probe hybridization in five different regions (gag, pol, vpu, env, gp-41), HIV subtype was defined by hybridization in env and by total using two or more regions. Analysis of covariance was used for multivariate comparison. RESULTS The env subtype was determined in 54 (37 A, 16 D, 1 C) children. Subtype A and D groups were comparable by demographics, CD4 status, and WHO stage. Subtype A infections had higher log viral loads (median 5.0 vs. 4.6, P = 0.02). Children with A performed more poorly than those with D on all measures, especially on KABC-2 Sequential Processing (memory) (P = 0.01), Simultaneous Processing (visual-spatial analysis) (P = 0.005), Learning (P = 0.02), and TOVA visual attention (P = 0.04). When adjusted for viral load, Sequential and Simultaneous Processing remained significantly different. Results were similar comparing by total HIV subtype. CONCLUSION HIV subtype A children demonstrated poorer neurocognitive performance than those with HIV subtype D. Subtype-specific neurocognitive deficits may reflect age-related differences in the neuropathogenesis of HIV. This may have important implications for when to initiate ART and the selection of drugs with greater central nervous system penetration.
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Teeravechyan S, Essex M, Lee TH. Conserved determinants of enhanced CCR5 binding in the human immunodeficiency virus subtype D envelope third variable loop. AIDS Res Hum Retroviruses 2010; 26:481-8. [PMID: 20377425 DOI: 10.1089/aid.2009.0086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human immunodeficiency virus 1 subtype D (HIV-1D) contributes to a significant portion of the HIV-1 disease burden in eastern and central Africa, and is associated with more rapid disease progression. Its viral envelope sequences, particularly in the third variable region (V3), are highly divergent from other major subtypes yet have rarely been studied to date. We evaluated the V3 and select bridging sheet residues of the HIV-1D 94UG114 envelope by alanine-scanning mutagenesis to determine the residues involved in CCR5 usage conservation in the face of sequence variability. We found most single alanine mutations capable of abolishing CCR5 binding, suggesting binding contacts that are highly sensitive to mutation. Despite drastic binding defects across the board, most mutants mediated fusion at or near wild-type levels, demonstrating an ability to accommodate changes in CCR5 affinity while maintaining the ability to complete entry. Three of the alanine mutations did not abolish CCR5 binding but rather resulted in enhanced CCR5 binding. The positions of these residues were found to be conserved between strains of two subtypes, revealing similar V3 elements that suggest a conservation of constraints in V3 loop conformation.
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Affiliation(s)
- Samaporn Teeravechyan
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts
| | - M. Essex
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts
| | - Tun-Hou Lee
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts
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14
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Plasma and cervical viral loads among Ugandan and Zimbabwean women during acute and early HIV-1 infection. AIDS 2010; 24:573-82. [PMID: 20154581 DOI: 10.1097/qad.0b013e32833433df] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES High levels of HIV-1 viremia exist in peripheral blood during acute and early infection; however, data on HIV-1 viral loads in female genital secretions during this period are sparse. DESIGN Prospective cohort of 188 African women with primary HIV-1 infection. METHODS HIV-uninfected and infected women were followed quarterly; we tested serial plasma specimens by HIV PCR to estimate infection dates. We used the Loess procedure to estimate the magnitude and timing of viral setpoints in plasma and cervical secretions and generalized estimating equations (GEE) to identify predictors of plasma and cervical viral setpoints. RESULTS We estimated the mean HIV-1 plasma setpoint to be 4.20 log10 HIV-1 RNA copies/ml [95% confidence interval (CI) 4.04-4.35] at 121 days (95% CI 91-137) from infection; an analogous mean cervical viral setpoint was 1.64 log10 HIV-1 RNA copies/swab (95% CI 1.46-1.82) at 174 days (95% CI 145-194) from infection. Cervical loads were significantly higher (0.7-1.1 log10 copies/swab) during acute infection than subsequently. Subtype D infection, pregnancy, breastfeeding, and older age at the time of infection were associated with higher plasma viral setpoint. Subtype C infection, nonviral sexually transmitted infections, having a partner spending nights away from home, recent unprotected sex, and shorter time since infection were associated with higher cervical HIV-1 loads. Hormonal contraception was not associated with either the HIV-1 plasma setpoint or cervical loads during early infection. CONCLUSION Cervical HIV-1 viral loads were highest during acute infection and then declined up to 6 months following infection, when a 'setpoint' was attained. The prognostic value of a cervical 'setpoint' on future transmission risk remains unclear.
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Yirrell DL, Shaw L, Campbell E, Burns SM, Cameron SO, Goldberg D. HIV subtypes in Scotland, 2000-2006. Epidemiol Infect 2008; 136:1069-75. [PMID: 17922931 PMCID: PMC2870891 DOI: 10.1017/s0950268807009545] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2007] [Indexed: 11/06/2022] Open
Abstract
The purpose of this study was to document the dynamics of HIV-1 subtypes in Scotland over a 6-year period. Viral RNA from all-new diagnoses was amplified by nested PCR and sequenced in the gag and/or env regions. Subtype was assigned by phylogenetic analysis, and aligned with demographic data including likely route and geographical origin of infection. We present data on 80% of all new diagnoses in Scotland between April 2000 and April 2006. Within the background of an expanding epidemic, subtype B predominates in men who have sex with men and intravenous drug users but there is a small but consistent number of UK-acquired infections in these risk groups caused by non-B subtypes. In heterosexuals, non-B subtypes acquired abroad, especially Africa, are still the largest group but again UK-acquired numbers are rising. The social and clinical significance of the spread of non-B subtypes in different ethnic and risk groups remains to be established.
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Affiliation(s)
- D L Yirrell
- Department of Medical Microbiology, Ninewells Hospital, Dundee, Scotland, UK.
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16
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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: 204] [Impact Index Per Article: 12.8] [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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The natural history of HIV-1 subtype E infection in young men in Thailand with up to 14 years of follow-up. AIDS 2007; 21 Suppl 6:S39-46. [PMID: 18032937 DOI: 10.1097/01.aids.0000299409.29528.23] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE We evaluated the progression to AIDS and death among 228 men who seroconverted within a 6-month window when in the Royal Thai Army between 1991 and 1995. DESIGN AND METHODS Men (N = 228) who seroconverted to HIV at 21-23 years of age between 1991 and 1995 were evaluated up to 14 years after HIV seroconversion. The seroconverters were matched with men who were seronegative when they were discharged from the military. In 2005-2006, the vital status was determined through the national mortality database and survivors were contacted for follow-up clinical and immunological assessment. Death certificates, medical records and next of kin interviews were used to evaluate the causes of death. RESULTS As of March 2006, among 228 seroconverters, 56 (24.6%) were alive, 171 (75.0%) had died and one (0.4%) had undetermined status. Among 255 HIV-seronegative individuals at baseline, 15 (5.9%) had died. The median time from HIV seroconversion to death was 7.8 years. The median time to AIDS death was 8.4 years. The median times from seroconversion to clinical AIDS and a CD4 cell count less than 200 cells/mul were 7.2 years and 6.5 years, respectively. The median time from seroconversion to World Health Organization criteria for antiretroviral therapy was 6.3 years. CONCLUSION Our data indicate a more rapid progression to AIDS and death after HIV-1 infection among young Thai men than has been reported in similar aged men who were HAART-naive in western high income countries.
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18
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Survival and mortality of people infected with HIV in low and middle income countries: results from the extended ALPHA network. AIDS 2007; 21 Suppl 6:S1-4. [PMID: 18032932 DOI: 10.1097/01.aids.0000299404.99033.bf] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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Survival of HIV-infected treatment-naive individuals with documented dates of seroconversion in Rakai, Uganda. AIDS 2007; 21 Suppl 6:S15-9. [PMID: 18032934 DOI: 10.1097/01.aids.0000299406.44775.de] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
OBJECTIVE To estimate the survival time from HIV infection to death. METHODS A community cohort in Rakai district, Uganda, identified 837 seroconverters followed annually between 1995 and 2003 until they died, were censored by outmigration or truncated on 31 December 2003 because antiretroviral treatment became available. HIV-1 subtype was determined by multiple hybridization assay for 396 seroconverters. The median interval from infection to death was estimated by Kaplan-Meier survival analyses and Weibull models. Hazard ratios (HR) and their 95% confidence intervals (CI) associated with survival were estimated using Cox proportional hazards modeling RESULTS There were 122 deaths over 2330 person-years (py), an average mortality of 5.2/100 py. The median survival time was 8.7 years (95% CI 8.1-9.3), and did not differ by sex, place of residence or time period of seroconversion. Survival time decreased significantly with older age at infection (P = 0.01). Survival was shorter with subtypes D, AD recombinant or multiple infections compared with subtype A (log rank P = 0.04), but this was of borderline significance after adjustment (adjusted HR 3.47, 95% CI 0.89-15.44, P = 0.07). Non-A subtypes constituted 84.6% of all identifiable infections and had a median survival time of 7.5 years (95% CI 6.4-8.5), whereas over 90% of those infected with subtype A were still alive 7 years post-infection. CONCLUSION The median survival time in Rakai was shorter than reported in other African populations, and we hypothesize that this may be a result of the predominance of non-A subtypes with faster disease progression in this population.
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20
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Survival of blood donors and their spouses with HIV-1 subtype E (CRF01 A_E) infection in northern Thailand, 1992-2007. AIDS 2007; 21 Suppl 6:S47-54. [PMID: 18032938 DOI: 10.1097/01.aids.0000299410.37152.17] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To evaluate the survival patterns among adults in Thailand 8-14 years after HIV-1 subtype E (CRF01 A_E) infection. DESIGN Follow-up for the current vital status of adults who were estimated to have had incident HIV-1 subtype E infection 8-14 years previously. METHODS Data on the survival of a population of HIV-1-infected male blood donors and their seropositive wives was obtained during March-April 2007. These subjects were identified from a subpopulation of 150 individuals whose seroconversion interval was estimated to be less than 2 years and who were enrolled in 1992-1997. National registration, vital records, and death certificates, as appropriate, were obtained and Kaplan-Meier survival curves were constructed for the entire population, for males and females, and for individuals above and equal to or below the median age at infection. RESULTS The vital status was obtained for 138 of 150 subjects (92%). The overall median survival was 8.2 [95% confidence interval (CI) 7.1-9.4] years. The median survival did not differ significantly between men and women or in those above or below the median age. CONCLUSION The median survival of 8.2 years in this population of young adults in Thailand was significantly less than that reported among persons of similar age in high-income countries or in eastern or southern Africa. The survival among individuals in Thailand infected with HIV-1 subtype E appears to be similar to that reported among individuals in Africa infected with HIV-1 subtype D.
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21
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Campbell GR, Senkaali D, Watkins J, Esquieu D, Opi S, Yirrell DL, Kaleebu P, Loret EP. Tat mutations in an African cohort that do not prevent transactivation but change its immunogenic properties. Vaccine 2007; 25:8441-7. [PMID: 17997200 DOI: 10.1016/j.vaccine.2007.09.070] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Revised: 03/04/2007] [Accepted: 09/20/2007] [Indexed: 11/26/2022]
Abstract
Humoral responses against extra-cellular HIV-1 Tat may be beneficial as Tat has been implicated in the viral pathogenesis associated with HIV-1 disease progression. We determined the levels of anti-Tat IgG in sera of HIV-1 seropositive individuals from the Rural Clinical Cohort in Uganda using nine different Tat proteins representative of the major subtypes presently accounting for 97% of infections worldwide. We observed the presence of anti-Tat IgG able to react against the various subtypes tested, although none cross-reacted against all nine variants. We show that 46.25% of seropositive patients were able to recognise at least one Tat variant with 1:1000 sera dilution. We also show that the C terminus of Tat is the most variable region and an important epitope that might explain the limitation of cross-recognition of Tat antibodies regarding Tat variants. This study shows in seropositive patients that Tat can tolerate mutations without modification of its primary function but with changes in its immunogenic properties. These findings should be considered when designing Tat-based HIV-1 vaccines.
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Affiliation(s)
- Grant R Campbell
- CNRS Formation de Recherche en Evolution 2737, Faculté de Pharmacie, Université de la Méditerranée, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
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22
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Abstract
The enormous genetic diversity of HIV-1 is a major challenge to vaccine development and may have important clinical consequences. HIV-1 group M predominates globally, with nine subtypes, several sub-subtypes and over 30 circulating recombinant forms that may exhibit differences with respect to transmissibility, pathogenicity and development of antiretroviral resistance. Subtype D appears to be more virulent than other subtypes, in particular subtype A. Subtype C may be less virulent and more transmissible, although the evidence for this is inconclusive. All group M non-B subtypes appear to be equally susceptible to combination antiretroviral therapy, but development of resistance mutations may vary significantly between subtypes. Further research into the clinical implications of HIV-1 diversity is crucial for effective HIV-1 prevention and treatment.
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Affiliation(s)
- Susan M Graham
- University of Washington, Box 359909, 325 Ninth Avenue, Seattle, WA 98104, USA
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Sankalé JL, Langevin S, Odaibo G, Meloni ST, Ojesina AI, Olaleye D, Kanki P. The complexity of circulating HIV type 1 strains in Oyo state, Nigeria. AIDS Res Hum Retroviruses 2007; 23:1020-5. [PMID: 17725419 DOI: 10.1089/aid.2006.0304] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Multiple HIV-1 subtypes and circulating recombinant forms (CRFs) are known to circulate in West Africa. We undertook a survey of HIVs in Oyo state, in southwestern Nigeria. We analyzed 71 samples from Ibadan, the capital city, and 33 samples from Saki, 100 miles west of Ibadan. We sequenced part of the gag gene and the envelope C2V3 region from 102 and 89 samples, respectively. In the 87 samples for which both genes were sequenced, subtype G and CRF02_AG were found in equal proportions (32.2% each). Other samples included CRF06_cpx (8.0%), subtype A (2.3%), C (1.1%), unclassified (1.1%), or discordant sequences suggesting the presence of a large number of recombinants involving CRF02_AG and/or subtype G (20.7%) or other subtypes (2.3%). The subtype/CRF designation was concordant in two gene fragments in the majority of samples evaluated. However, we observed differences in subtype distribution between the two locations with a predominance of subtype G in Ibadan and CRF02 in Saki. This is the first in-depth analysis of HIV variability at a state level in Nigeria. Our analysis revealed a significant level of viral heterogeneity and a geographical difference in subtype distribution, and demonstrated that CRF02_AG does not account for the majority of circulating strains.
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Affiliation(s)
- Jean-Louis Sankalé
- Department of Immunology and Infectious Diseases, Harvard School of Public Health AIDS Initiative, Boston, Massachusetts 02115, USA
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Campbell GR, Watkins JD, Singh KK, Loret EP, Spector SA. Human immunodeficiency virus type 1 subtype C Tat fails to induce intracellular calcium flux and induces reduced tumor necrosis factor production from monocytes. J Virol 2007; 81:5919-28. [PMID: 17376903 PMCID: PMC1900281 DOI: 10.1128/jvi.01938-06] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Over 50% of all human immunodeficiency virus type 1 (HIV-1) infections worldwide are caused by subtype C strains, yet most research to date focuses on subtype B, the subtype most commonly found in North America and Europe. The HIV-1 trans-acting regulatory protein (Tat) is essential for regulating productive replication of HIV-1. Tat is secreted by HIV-infected cells and alters several functions of uninfected bystander cells. One such function is that, by acting at the cell membrane, subtype B Tat stimulates the production of tumor necrosis factor (TNF) and chemokine (C-C motif) ligand 2 (CCL2) from human monocytes and can act as a chemoattractant. In this study, we show that the mutation of a cysteine to a serine at residue 31 of Tat commonly found in subtype C variants significantly inhibits the abilities of the protein to bind to chemokine (C-C motif) receptor 2 (CCR2), induce intracellular calcium flux, stimulate TNF and CCL2 production, and inhibit its chemoattractant properties. We also show that TNF is important in mediating some effects of extracellular Tat. This report therefore demonstrates the important functional differences between subtype C and subtype B Tat and highlights the need for further investigation into the different strains of HIV-1.
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Affiliation(s)
- Grant R Campbell
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0672, USA
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25
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Abstract
During the rapid spread of HIV-1 in humans, the main (M) group of HIV-1 has evolved into ten distinct subtypes, undergone countless recombination events and diversified extensively. The impact of this extreme genetic diversity on the phenotype of HIV-1 has only recently become a research focus, but early findings indicate that the dominance of HIV-1 subtype C in the current epidemic might be related to the lower virulence of this subtype compared with other subtypes. Here, we explore whether HIV-1 has reached peak virulence or has already started the slow path to attenuation.
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Affiliation(s)
- Kevin K. Ariën
- the Department of Microbiology, HIV and Retrovirology Research Unit, Institute of Tropical Medicine, Nationalestraat 155, Antwerp, B2000 Belgium
- Present Address: the Department of Clinical Chemistry, Microbiology and Immunology, Faculty of Medicine and Health Sciences, Ghent University, De Pintelaan 185, Ghent, B-9000 Belgium
| | - Guido Vanham
- the Department of Microbiology, HIV and Retrovirology Research Unit, Institute of Tropical Medicine, Nationalestraat 155, Antwerp, B2000 Belgium
| | - Eric J. Arts
- the Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 2109, Adelbert Rd, Cleveland, 44195 Ohio USA
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Gale CV, Yirrell DL, Campbell E, Van der Paal L, Grosskurth H, Kaleebu P. Genotypic variation in the pol gene of HIV type 1 in an antiretroviral treatment-naive population in rural southwestern Uganda. AIDS Res Hum Retroviruses 2006; 22:985-92. [PMID: 17067268 DOI: 10.1089/aid.2006.22.985] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The majority of studies of HIV-1 drug resistance have involved subtype B viruses. Here we have characterized subtype distribution and determined the levels of polymorphism at protease (PR) and reverse transcriptase (RT) drug resistance positions, in antiretroviral treatment-naive HIV-positive Ugandan patients. We have also investigated codon usage variability at these positions and assessed intersubtype recombination within the pol gene. The study population consisted of 187 patients, from a cohort established by the UK Medical Research Council Programme on AIDS in Uganda in 1990. Results indicate that 28.3% of patients were infected with subtype A (n = 53), 64.2% subtype D (n = 120), 6.4% A/D recombinant (n = 12), and 1.1% subtype C (n = 2). Variation in amino acid usage at drug resistance-associated positions was minimal between the two main subtypes (A and D) in RT, but there was appreciable variation in PR. Codon usage, however, was considerably more variable between subtypes A and D in both PR and RT. Thus, while no natural high-level resistance to antiretroviral therapy was detected in this cohort, subtypes A and D may possess different genetic barriers to be overcome in order to achieve resistance. With the increasing introduction of antiretroviral therapy into Africa, such information will be vital in our understanding and evaluation of the development of drug resistance as it occurs, and how to interpret resistance data the type of which has rarely previously been seen. This analysis also significantly increases the number of Ugandan PR and RT sequences characterized to date.
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Campbell GR, Watkins JD, Esquieu D, Pasquier E, Loret EP, Spector SA. The C terminus of HIV-1 Tat modulates the extent of CD178-mediated apoptosis of T cells. J Biol Chem 2005; 280:38376-82. [PMID: 16155003 DOI: 10.1074/jbc.m506630200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
HIV infection and the progression to AIDS are characterized by the depletion of CD4(+) T cells through apoptosis of the uninfected bystander cells and the direct killing of HIV-infected cells. This is mediated in part by the human immunodeficiency virus, type 1 Tat protein, which is secreted by virally infected cells and taken up by uninfected cells and CD178 gene expression, which is critically involved in T cell apoptosis. The differing ability of HIV strains to induce death of infected and uninfected cells may play a role in the clinical and biological differences displayed by HIV strains. We chemically synthesized the 86-residue truncated short variant of Tat and its full-length form. We show that the trans-activation ability of Tat at the long terminal repeat does not correlate with T cell apoptosis but that the ability of Tat to up-regulate CD178 mRNA expression and induce apoptosis in T cells is critically dependent on the C terminus of Tat. Moreover, the greater 86-residue Tat-induced apoptosis is via the extrinsic pathway of CD95-CD178.
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Affiliation(s)
- Grant R Campbell
- Department of Pediatrics, Division of Infectious Diseases, University of California San Diego, La Jolla, California 92093-0672, USA
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