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Kotokwe K, Moyo S, Zahralban-Steele M, Holme MP, Melamu P, Koofhethile CK, Choga WT, Mohammed T, Nkhisang T, Mokaleng B, Maruapula D, Ditlhako T, Bareng O, Mokgethi P, Boleo C, Makhema J, Lockman S, Essex M, Ragonnet-Cronin M, Novitsky V, Gaseitsiwe S. Prediction of Coreceptor Tropism in HIV-1 Subtype C in Botswana. Viruses 2023; 15:403. [PMID: 36851617 PMCID: PMC9963705 DOI: 10.3390/v15020403] [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: 12/31/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
It remains unknown whether the C-C motif chemokine receptor type 5 (CCR5) coreceptor is still the predominant coreceptor used by Human Immunodeficiency Virus-1 (HIV-1) in Botswana, where the HIV-1 subtype C predominates. We sought to determine HIV-1C tropism in Botswana using genotypic tools, taking into account the effect of antiretroviral treatment (ART) and virologic suppression. HIV-1 gp120 V3 loop sequences from 5602 participants were analyzed for viral tropism using three coreceptor use predicting algorithms/tools: Geno2pheno, HIV-1C Web Position-Specific Score Matrices (WebPSSM) and the 11/25 charge rule. We then compared the demographic and clinical characteristics of people living with HIV (PLWH) harboring R5- versus X4-tropic viruses using χ2 and Wilcoxon rank sum tests for categorical and continuous data analysis, respectively. The three tools congruently predicted 64% of viruses as either R5-tropic or X4-tropic. Geno2pheno and the 11/25 charge rule had the highest concordance at 89%. We observed a significant difference in ART status between participants harboring X4- versus R5-tropic viruses. X4-tropic viruses were more frequent among PLWH receiving ART (χ2 test, p = 0.03). CCR5 is the predominant coreceptor used by HIV-1C strains circulating in Botswana, underlining the strong potential for CCR5 inhibitor use, even in PLWH with drug resistance. We suggest that the tools for coreceptor prediction should be used in combination.
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Affiliation(s)
- Kenanao Kotokwe
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Melissa Zahralban-Steele
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Molly Pretorius Holme
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Pinkie Melamu
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Catherine Kegakilwe Koofhethile
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | | | - Terence Mohammed
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Tapiwa Nkhisang
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Baitshepi Mokaleng
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Tsotlhe Ditlhako
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Ontlametse Bareng
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Patrick Mokgethi
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Corretah Boleo
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Joseph Makhema
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Shahin Lockman
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Max Essex
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Manon Ragonnet-Cronin
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
| | - Vlad Novitsky
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
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2
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Judicate GP, Barabona G, Kamori D, Mahiti M, Tan TS, Ozono S, Mgunya AS, Kuwata T, Matsushita S, Sunguya B, Lyamuya E, Tokunaga K, Ueno T. Phenotypic and Genotypic Co-receptor Tropism Testing in HIV-1 Epidemic Region of Tanzania Where Multiple Non-B Subtypes Co-circulate. Front Microbiol 2021; 12:703041. [PMID: 34305873 PMCID: PMC8292895 DOI: 10.3389/fmicb.2021.703041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
HIV human immunodeficiency virus type I (HIV-1) entry inhibitor potency is dependent on viral co-receptor tropisms and thereby tropism determination is clinically important. However, phenotypic tropisms of HIV-1 non-B subtypes have been poorly investigated and the genotypic prediction algorithms remain insufficiently validated. To clarify this issue, we recruited 52 treatment-naïve, HIV-1-infected patients in Tanzania, where multiple HIV-1 non-B subtypes co-circulate. Sequence analysis of 93 infectious envelope clones isolated from their plasma viral RNA revealed the co-circulation of subtypes A1, C, D, and inter-subtype recombinant forms (isRFs). Phenotypic tropism assays revealed that lentivirus reporters pseudotyped with 75 (80.6%) and 5 (5.4%) envelope clones could establish infection toward U87.CD4 cells expressing CCR5 (R5) and CXCR4 (X4), respectively; whereas the remaining 13 (14%) clones could infect both cells. Genotypic analyses by widely used algorithms including V3 net charge, Geno2pheno, WebPSSM, and PhenoSeq showed that almost all phenotypic X4-tropic clones and only 15 of 75 phenotypic R5-tropic clones were concordantly predicted. However, the remaining 60 phenotypic R5-tropic clones were discordantly predicted by at least one algorithm. In particular, 2 phenotypic R5-tropic clones were discordantly predicted by all algorithms tested. Taken together, the results demonstrate the limitation of currently available genotypic algorithms for predicting co-receptor inference among co-circulating multiple non-B subtypes and emerging isRFs. Also, the phenotypic tropism dataset presented here could be valuable for retraining of the widely used genotypic prediction algorithms to enhance their performance.
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Affiliation(s)
- George P Judicate
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Godfrey Barabona
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Doreen Kamori
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Macdonald Mahiti
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Toong Seng Tan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Seiya Ozono
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Takeo Kuwata
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Shuzo Matsushita
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Bruno Sunguya
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Eligius Lyamuya
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Kenzo Tokunaga
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takamasa Ueno
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
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3
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Kelentse N, Moyo S, Mogwele ML, Ditshwanelo D, Mokaleng B, Moraka NO, Lechiile K, Leeme TB, Lawrence DS, Musonda R, Kasvosve I, Harrison TS, Jarvis JN, Gaseitsiwe S. HIV-1C env and gag Variation in the Cerebrospinal Fluid and Plasma of Patients with HIV-Associated Cryptococcal Meningitis in Botswana. Viruses 2020; 12:E1404. [PMID: 33297399 PMCID: PMC7762280 DOI: 10.3390/v12121404] [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: 10/25/2020] [Revised: 11/26/2020] [Accepted: 11/26/2020] [Indexed: 12/19/2022] Open
Abstract
HIV-1 compartmentalization in reservoir sites remains a barrier to complete HIV eradication. It is unclear whether there is variation in HIV-1 env and gag between cerebrospinal fluid (CSF) and plasma of individuals with HIV-associated cryptococcal meningitis (CM). We compared HIV-1 env characteristics and the gag cytotoxic T-lymphocyte (CTL) escape mutations from CSF and plasma samples. Employing population-based Sanger sequencing, we sequenced HIV-1 env from CSF of 25 patients and plasma of 26 patients. For gag, 15 CSF and 21 plasma samples were successfully sequenced. Of these, 18 and 9 were paired env and gag CSF/plasma samples, respectively. There was no statistically significant difference in the proportion of CCR5-using strains in the CSF and plasma, (p = 0.50). Discordant CSF/plasma virus co-receptor use was found in 2/18 pairs (11.1%). The polymorphisms in the HIV-1 V3 loop were concordant between the two compartments. From the HIV-1 gag sequences, three pairs had discordant CTL escape mutations in three different epitopes of the nine analyzed. These findings suggest little variation in the HIV-1 env between plasma and CSF and that the CCR5-using strains predominate in both compartments. HIV-1 gag CTL escape mutations also displayed little variation in CSF and plasma suggesting similar CTL selective pressure.
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MESH Headings
- AIDS-Related Opportunistic Infections/blood
- AIDS-Related Opportunistic Infections/cerebrospinal fluid
- AIDS-Related Opportunistic Infections/diagnosis
- AIDS-Related Opportunistic Infections/metabolism
- Adult
- Amino Acid Sequence
- Amino Acid Substitution
- Botswana
- CD4 Lymphocyte Count
- Cross-Sectional Studies
- Disease Susceptibility
- Female
- HIV Infections/complications
- HIV Infections/virology
- Humans
- Immunocompromised Host
- Male
- Meningitis, Cryptococcal/blood
- Meningitis, Cryptococcal/cerebrospinal fluid
- Meningitis, Cryptococcal/etiology
- Meningitis, Cryptococcal/metabolism
- Middle Aged
- Mutation
- RNA, Viral
- Viral Load
- env Gene Products, Human Immunodeficiency Virus/blood
- env Gene Products, Human Immunodeficiency Virus/cerebrospinal fluid
- env Gene Products, Human Immunodeficiency Virus/metabolism
- gag Gene Products, Human Immunodeficiency Virus/blood
- gag Gene Products, Human Immunodeficiency Virus/cerebrospinal fluid
- gag Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Nametso Kelentse
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana;
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Mompati L. Mogwele
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Doreen Ditshwanelo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
| | - Baitshepi Mokaleng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana;
| | - Natasha O. Moraka
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- Department of Pathology, Stellenbosch University, Stellenbosch 7505, South Africa
| | - Kwana Lechiile
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - Tshepo B. Leeme
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - David S. Lawrence
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, The London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Rosemary Musonda
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Ishmael Kasvosve
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana;
| | - Thomas S. Harrison
- Centre for Global Health, Institute for Infection and Immunity, St. George’s University of London, London SW17 0RE, UK;
| | - Joseph N. Jarvis
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, The London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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4
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Connell BJ, Hermans LE, Wensing AMJ, Schellens I, Schipper PJ, van Ham PM, de Jong DTCM, Otto S, Mathe T, Moraba R, Borghans JAM, Papathanasopoulos MA, Kruize Z, Venter FWD, Kootstra NA, Tempelman H, Tesselaar K, Nijhuis M. Immune activation correlates with and predicts CXCR4 co-receptor tropism switch in HIV-1 infection. Sci Rep 2020; 10:15866. [PMID: 32985522 PMCID: PMC7522993 DOI: 10.1038/s41598-020-71699-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/10/2020] [Indexed: 12/31/2022] Open
Abstract
HIV-1 cell entry is mediated by binding to the CD4-receptor and chemokine co-receptors CCR5 (R5) or CXCR4 (X4). R5-tropic viruses are predominantly detected during early infection. A switch to X4-tropism often occurs during the course of infection. X4-tropism switching is strongly associated with accelerated disease progression and jeopardizes CCR5-based HIV-1 cure strategies. It is unclear whether host immunological factors play a causative role in tropism switching. We investigated the relationship between immunological factors and X4-tropism in a cross-sectional study in HIV-1 subtype C (HIV-1C)-infected patients and in a longitudinal HIV-1 subtype B (HIV-1B) seroconverter cohort. Principal component analysis identified a cluster of immunological markers (%HLA-DR+ CD4+ T-cells, %CD38+HLA-DR+ CD4+ T-cells, %CD38+HLA-DR+ CD8+ T-cells, %CD70+ CD4+ T-cells, %CD169+ monocytes, and absolute CD4+ T-cell count) in HIV-1C patients that was independently associated with X4-tropism (aOR 1.044, 95% CI 1.003–1.087, p = 0.0392). Analysis of individual cluster contributors revealed strong correlations of two markers of T-cell activation (%HLA-DR+ CD4+ T-cells, %HLA-DR+CD38+ CD4+ T-cells) with X4-tropism, both in HIV-1C patients (p = 0.01;p = 0.03) and HIV-1B patients (p = 0.0003;p = 0.0001). Follow-up data from HIV-1B patients subsequently revealed that T-cell activation precedes and independently predicts X4-tropism switching (aHR 1.186, 95% CI 1.065–1.321, p = 0.002), providing novel insights into HIV-1 pathogenesis and CCR5-based curative strategies.
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Affiliation(s)
- Bridgette J Connell
- Department of Medical Microbiology, Virology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - Lucas E Hermans
- Department of Medical Microbiology, Virology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands.,Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Ndlovu Research Consortium, Elandsdoorn, Limpopo Province, South Africa
| | - Annemarie M J Wensing
- Department of Medical Microbiology, Virology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands.,Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Ndlovu Research Consortium, Elandsdoorn, Limpopo Province, South Africa
| | - Ingrid Schellens
- Center for Translational Immunology, UMCU, Utrecht, The Netherlands
| | - Pauline J Schipper
- Department of Medical Microbiology, Virology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - Petra M van Ham
- Department of Medical Microbiology, Virology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - Dorien T C M de Jong
- Department of Medical Microbiology, Virology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - Sigrid Otto
- Center for Translational Immunology, UMCU, Utrecht, The Netherlands
| | - Tholakele Mathe
- Ndlovu Research Consortium, Elandsdoorn, Limpopo Province, South Africa
| | - Robert Moraba
- Ndlovu Research Consortium, Elandsdoorn, Limpopo Province, South Africa
| | | | - Maria A Papathanasopoulos
- HIV Pathogenesis Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zita Kruize
- Amsterdam University Medical Center, Amsterdam Infection and Immunity Institute, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Francois W D Venter
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Neeltje A Kootstra
- Amsterdam University Medical Center, Amsterdam Infection and Immunity Institute, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Hugo Tempelman
- Ndlovu Research Consortium, Elandsdoorn, Limpopo Province, South Africa
| | - Kiki Tesselaar
- Center for Translational Immunology, UMCU, Utrecht, The Netherlands
| | - Monique Nijhuis
- Department of Medical Microbiology, Virology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands. .,Ndlovu Research Consortium, Elandsdoorn, Limpopo Province, South Africa. .,HIV Pathogenesis Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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5
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Gartner MJ, Gorry PR, Tumpach C, Zhou J, Dantanarayana A, Chang JJ, Angelovich TA, Ellenberg P, Laumaea AE, Nonyane M, Moore PL, Lewin SR, Churchill MJ, Flynn JK, Roche M. Longitudinal analysis of subtype C envelope tropism for memory CD4 + T cell subsets over the first 3 years of untreated HIV-1 infection. Retrovirology 2020; 17:24. [PMID: 32762760 PMCID: PMC7409430 DOI: 10.1186/s12977-020-00532-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/27/2020] [Indexed: 12/14/2022] Open
Abstract
Background HIV-1 infects a wide range of CD4+ T cells with different phenotypic properties and differing expression levels of entry coreceptors. We sought to determine the viral tropism of subtype C (C-HIV) Envelope (Env) clones for different CD4+ T cell subsets and whether tropism changes during acute to chronic disease progression. HIV-1 envs were amplified from the plasma of five C-HIV infected women from three untreated time points; less than 2 months, 1-year and 3-years post-infection. Pseudoviruses were generated from Env clones, phenotyped for coreceptor usage and CD4+ T cell subset tropism was measured by flow cytometry. Results A total of 50 C-HIV envs were cloned and screened for functionality in pseudovirus infection assays. Phylogenetic and variable region characteristic analysis demonstrated evolution in envs between time points. We found 45 pseudoviruses were functional and all used CCR5 to mediate entry into NP2/CD4/CCR5 cells. In vitro infection assays showed transitional memory (TM) and effector memory (EM) CD4+ T cells were more frequently infected (median: 46% and 25% of total infected CD4+ T cells respectively) than naïve, stem cell memory, central memory and terminally differentiated cells. This was not due to these subsets contributing a higher proportion of the CD4+ T cell pool, rather these subsets were more susceptible to infection (median: 5.38% EM and 2.15% TM cells infected), consistent with heightened CCR5 expression on EM and TM cells. No inter- or intra-participant changes in CD4+ T cell subset tropism were observed across the three-time points. Conclusions CD4+ T cell subsets that express more CCR5 were more susceptible to infection with C-HIV Envs, suggesting that these may be the major cellular targets during the first 3 years of infection. Moreover, we found that viral tropism for different CD4+ T cell subsets in vitro did not change between Envs cloned from acute to chronic disease stages. Finally, central memory, naïve and stem cell memory CD4+ T cell subsets were susceptible to infection, albeit inefficiently by Envs from all time-points, suggesting that direct infection of these cells may help establish the latent reservoir early in infection.
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Affiliation(s)
- Matthew J Gartner
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Melbourne, VIC, Australia.,The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Paul R Gorry
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Melbourne, VIC, Australia
| | - Carolin Tumpach
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Jingling Zhou
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Melbourne, VIC, Australia
| | - Ashanti Dantanarayana
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - J Judy Chang
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Thomas A Angelovich
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Melbourne, VIC, Australia.,Life Sciences, Burnet Institute, Melbourne, VIC, Australia
| | - Paula Ellenberg
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Annemarie E Laumaea
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Melbourne, VIC, Australia.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Molati Nonyane
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Penny L Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Sharon R Lewin
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia.,Department of Infectious Diseases, Monash University and Alfred Hospital, Melbourne, Australia
| | - Melissa J Churchill
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Melbourne, VIC, Australia
| | - Jacqueline K Flynn
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Melbourne, VIC, Australia. .,The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia. .,School of Clinical Sciences, Monash University, Melbourne, VIC, Australia.
| | - Michael Roche
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Melbourne, VIC, Australia. .,The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia.
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6
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Gartner MJ, Roche M, Churchill MJ, Gorry PR, Flynn JK. Understanding the mechanisms driving the spread of subtype C HIV-1. EBioMedicine 2020; 53:102682. [PMID: 32114391 PMCID: PMC7047180 DOI: 10.1016/j.ebiom.2020.102682] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/29/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) subtype C (C-HIV) is the most prevalent form of HIV-1 globally, accounting for approximately 50% of infections worldwide. C-HIV is the predominant and near-exclusive subtype in the low resource regions of India and Southern Africa. Given the vast diversity of HIV-1 subtypes, it is curious as to why C-HIV constitutes such a large proportion of global infections. This enriched prevalence may be due to phenotypic differences between C-HIV isolates and other viral strains that permit enhanced transmission efficiency or, pathogenicity, or might due to the socio-demographics of the regions where C-HIV is endemic. Here, we compare the mechanisms of C-HIV pathogenesis to less prominent HIV-1 subtypes, including viral genetic and phenotypic characteristics, and host genetic variability, to understand whether evolutionary factors drove C-HIV to predominance.
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Affiliation(s)
- Matthew J Gartner
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
| | - Michael Roche
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia; The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Melissa J Churchill
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia; Department of Microbiology, Monash University, Melbourne, Australia
| | - Paul R Gorry
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia.
| | - Jacqueline K Flynn
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia; The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia; School of Clinical Sciences at Monash Health, Monash University, Melbourne, Australia.
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Sojane K, Kangethe RT, Chang CC, Moosa MYS, Lewin SR, French MA, Ndung'u T. Individuals with HIV-1 Subtype C Infection and Cryptococcal Meningitis Exhibit Viral Genetic Intermixing of HIV-1 Between Plasma and Cerebrospinal Fluid and a High Prevalence of CXCR4-Using Variants. AIDS Res Hum Retroviruses 2018; 34:607-620. [PMID: 29658309 PMCID: PMC6314437 DOI: 10.1089/aid.2017.0209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genotypic properties of human immunodeficiency virus type 1 (HIV-1) subtype C in individuals presenting with cryptococcal meningitis (CM) are not well established. Employing single-genome amplification as well as bulk PCR, cloning and sequencing strategies, we evaluated the genetic properties of HIV-1 subtype C env in 16 antiretroviral therapy-naive study participants with CM. Eleven of the 16 participants had matched blood plasma and cerebrospinal fluid (CSF) evaluated, with the rest having either a plasma or CSF sample evaluated. Before antiretroviral therapy initiation, matched plasma and CSF-derived env sequences of all 11 participants displayed genetic intermixing between the two compartments. Overall, 7 of the 16 (∼43.8%) participants harbored CXCR4-using variants in plasma and/or CSF, according to coreceptor usage prediction algorithms. This study suggests that HIV-1 subtype C genetic intermixing between peripheral blood and the central nervous system is common in individuals presenting with CM, and that CXCR4 usage is present in one or both compartments in approximately 44% of individuals.
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Affiliation(s)
- Katlego Sojane
- 1 HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal , Durban, South Africa
| | - Richard T Kangethe
- 1 HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal , Durban, South Africa
| | - Christina C Chang
- 2 Department of Infectious Diseases, Alfred Hospital and Monash University , Melbourne, Australia
| | - Mahomed-Yunus S Moosa
- 3 Department of Infectious Diseases, King Edward VIII Hospital, University of KwaZulu-Natal , Durban, South Africa
| | - Sharon R Lewin
- 2 Department of Infectious Diseases, Alfred Hospital and Monash University , Melbourne, Australia
- 4 The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital , Melbourne, Australia
| | - Martyn A French
- 5 Medical School and School of Biomedical Sciences, University of Western Australia , Perth, Australia
- 6 Department of Clinical Immunology, Royal Perth Hospital and PathWest Laboratory Medicine , Perth, Australia
| | - Thumbi Ndung'u
- 1 HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal , Durban, South Africa
- 7 Africa Health Research Institute , Durban, South Africa
- 8 Ragon Institute of MGH, MIT and Harvard University , Cambridge, Massachusetts
- 9 Max Planck Institute for Infection Biology , Berlin, Germany
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Lin N, Gonzalez OA, Registre L, Becerril C, Etemad B, Lu H, Wu X, Lockman S, Essex M, Moyo S, Kuritzkes DR, Sagar M. Humoral Immune Pressure Selects for HIV-1 CXC-chemokine Receptor 4-using Variants. EBioMedicine 2016; 8:237-247. [PMID: 27428434 PMCID: PMC4919596 DOI: 10.1016/j.ebiom.2016.04.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 11/26/2022] Open
Abstract
Although both C-C chemokine receptor 5 (CCR5)- and CXC chemokine receptor 4 (CXCR4)-using HIV-1 strains cause AIDS, the emergence of CXCR4-utilizing variants is associated with an accelerated decline in CD4+ T cells. It remains uncertain if CXCR4-using viruses hasten disease or if these variants only emerge after profound immunological damage. We show that exclusively CXCR4- as compared to cocirculating CCR5-utilizing variants are less sensitive to neutralization by both contemporaneous autologous plasma and plasma pools from individuals that harbor only CCR5-using HIV-1. The CXCR4-utilizing variants, however, do not have a global antigenic change because they remain equivalently susceptible to antibodies that do not target coreceptor binding domains. Studies with envelope V3 loop directed antibodies and chimeric envelopes suggest that the neutralization susceptibility differences are potentially influenced by the V3 loop. In vitro passage of a neutralization sensitive CCR5-using virus in the presence of autologous plasma and activated CD4+ T cells led to the emergence of a CXCR4-utilizing virus in 1 of 3 cases. These results suggest that in some but not necessarily all HIV-1 infected individuals humoral immune pressure against the autologous virus selects for CXCR4-using variants, which potentially accelerates disease progression. Our observations have implications for using antibodies for HIV-1 immune therapy.
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Affiliation(s)
- Nina Lin
- Section of Infectious Diseases, Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Oscar A Gonzalez
- Section of Infectious Diseases, Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Ludy Registre
- Section of Infectious Diseases, Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Carlos Becerril
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, United States
| | - Behzad Etemad
- Section of Infectious Diseases, Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Hong Lu
- Aaron Diamond AIDS Research Center, New York, NY, United States
| | - Xueling Wu
- Aaron Diamond AIDS Research Center, New York, NY, United States
| | - Shahin Lockman
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, United States; Harvard School of Public Health, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - Myron Essex
- Harvard School of Public Health, Boston, MA, United States; Botswana Harvard AIDS Institute, Gaborone, Botswana
| | | | - Daniel R Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - Manish Sagar
- Section of Infectious Diseases, Department of Medicine, Boston University School of Medicine, Boston, MA, United States.
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Dauwe K, Mortier V, Schauvliege M, Van Den Heuvel A, Fransen K, Servais JY, Bercoff DP, Seguin-Devaux C, Verhofstede C. Characteristics and spread to the native population of HIV-1 non-B subtypes in two European countries with high migration rate. BMC Infect Dis 2015; 15:524. [PMID: 26572861 PMCID: PMC4647655 DOI: 10.1186/s12879-015-1217-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/14/2015] [Indexed: 12/13/2022] Open
Abstract
Background Non-B subtypes account for at least 50 % of HIV-1 infections diagnosed in Belgium and Luxembourg. They are considered to be acquired through heterosexual contacts and infect primarily individuals of foreign origin. Information on the extent to which non-B subtypes spread to the local population is incomplete. Methods Pol and env gene sequences were collected from 410 non-subtype B infections. Profound subtyping was performed using 5 subtyping tools and sequences of both pol and env. Demographic information, disease markers (viral load, CD4 count) and viral characteristics (co-receptor tropism) were compared between subtypes. Maximum likelihood phylogenetic trees were constructed and examined for clustering. Results The majority of non-B infections were diagnosed in patients originating from Africa (55.8 %), individuals born in Western Europe represented 30.5 %. Heterosexual transmission was the most frequently reported transmission route (79.9 %), MSM transmission accounted for 12.2 % and was significantly more frequently reported for Western Europeans (25.7 % versus 4.3 % for individuals originating from other regions; p < 0.001). Subtypes A and C and the circulating recombinant forms CRF01_AE and CRF02_AG were the most represented and were included in the comparative analysis. Native Western Europeans were underrepresented for subtype A (14.5 %) and overrepresented for CRF01_AE (38.6 %). The frequency of MSM transmission was the highest for CRF01_AE (18.2 %) and the lowest for subtype A (0 %). No differences in age, gender, viral load or CD4 count were observed. Prevalence of CXCR4-use differed between subtypes but largely depended on the tropism prediction algorithm applied. Indications for novel intersubtype recombinants were found in 20 patients (6.3 %). Phylogenetic analysis revealed only few and small clusters of local transmission but could document one cluster of CRF02_AG transmission among Belgian MSM. Conclusions The extent to which non-B subtypes spread in the native Belgian-Luxembourg population is higher than expected, with 30.5 % of the non-B infections diagnosed in native Western Europeans. These infections resulted from hetero- as well as homosexual transmission. Introduction of non-B variants in the local high at risk population of MSM may lead to new sub-epidemics and/or increased genetic variability and is an evolution that needs to be closely monitored.
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Affiliation(s)
- Kenny Dauwe
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
| | - Marlies Schauvliege
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
| | - Annelies Van Den Heuvel
- Aids Reference laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Nationalestraat 155, B-2000, Antwerp, Belgium.
| | - Katrien Fransen
- Aids Reference laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Nationalestraat 155, B-2000, Antwerp, Belgium.
| | - Jean-Yves Servais
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Val Fleuri 84, L-1526, Luxembourg, Luxembourg.
| | - Danielle Perez Bercoff
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Val Fleuri 84, L-1526, Luxembourg, Luxembourg.
| | - Carole Seguin-Devaux
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Val Fleuri 84, L-1526, Luxembourg, Luxembourg.
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
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Sollerkvist LP, Gaseitsiwe S, Mine M, Sebetso G, Mphoyakgosi T, Diphoko T, Essex M, Ehrnst A. Increased CXCR4 use of HIV-1 subtype C identified by population sequencing in patients failing antiretroviral treatment compared with treatment-naive patients in Botswana. AIDS Res Hum Retroviruses 2014; 30:436-45. [PMID: 24205895 DOI: 10.1089/aid.2013.0203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
HIV-1 uses the coreceptors CCR5 and/or CXCR4 for cell entry. Monotropic CCR5-using variants are found early in the infection while CXCR4-using variants may appear after progression to AIDS. CXCR4 use may consist of both monotropic and dualtropic viruses. The viral phenotype is important in evaluating the response to CCR5 inhibitors, a new class of antiviral drugs. The coreceptor use of HIV-1 was investigated using population sequencing in 24 patients from Botswana, carrying HIV-1 subtype C and failing antiretroviral treatment, while 26 treatment-naive patients acted as controls. Single genome sequencing was used to discern minor HIV-1 populations in the treatment-experienced group. The Geno2Pheno method was employed to predict the coreceptor use phenotype from HIV-1 env gp120 V3 DNA sequences. The glycan-charge model adjusted for subtype C was also used for phenotype prediction. The viral phenotype of population sequences was predicted using Geno2Pheno in 24/24 treatment-experienced patients, of whom eight (33%) were predicted to harbor CXCR4-using strains as compared to 2/26 in the treatment-naive group (p=0.03). Single genome sequencing generated 4-23 clones/patient in the treatment-experienced group. Altogether, 90/295 (31%) putative CXCR4-using clones were identified. In 10/24 (42%) treated patients at least one clone was predicted to be CXCR4-using, further increasing the amount of identified treatment-experienced patients with CXCR4 use. Although subtype C is usually associated with comparatively little CXCR4 use, the frequency of CXCR4 use in treatment-experienced patients with subtype C can be higher, which may have implications for the administration of CCR5 inhibitors in this patient group.
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Affiliation(s)
| | - Simani Gaseitsiwe
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
- Botswana-Harvard School of Public Health AIDS Initiative Partnership for HIV Research and Education, Gaborone, Botswana
| | - Madisa Mine
- Ministry of Health, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Gaseene Sebetso
- Ministry of Health, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | | | - Thabo Diphoko
- Botswana-Harvard School of Public Health AIDS Initiative Partnership for HIV Research and Education, Gaborone, Botswana
| | - Max Essex
- Botswana-Harvard School of Public Health AIDS Initiative Partnership for HIV Research and Education, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, and the Harvard School of Public Health AIDS Initiative, Harvard School of Public Health, Boston, Massachusetts
| | - Anneka Ehrnst
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
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11
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Cenci A, D'Avenio G, Tavoschi L, Chiappi M, Becattini S, Narino MDP, Picconi O, Bernasconi D, Fanales-Belasio E, Vardas E, Sukati H, Lo Presti A, Ciccozzi M, Monini P, Ensoli B, Grigioni M, Buttò S. Molecular characterization of HIV-1 subtype C gp-120 regions potentially involved in virus adaptive mechanisms. PLoS One 2014; 9:e95183. [PMID: 24788065 PMCID: PMC4005737 DOI: 10.1371/journal.pone.0095183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/24/2014] [Indexed: 11/17/2022] Open
Abstract
The role of variable regions of HIV-1 gp120 in immune escape of HIV has been investigated. However, there is scant information on how conserved gp120 regions contribute to virus escaping. Here we have studied how molecular sequence characteristics of conserved C3, C4 and V3 regions of clade C HIV-1 gp120 that are involved in HIV entry and are target of the immune response, are modulated during the disease course. We found an increase of “shifting” putative N-glycosylation sites (PNGSs) in the α2 helix (in C3) and in C4 and an increase of sites under positive selection pressure in the α2 helix during the chronic stage of disease. These sites are close to CD4 and to co-receptor binding sites. We also found a negative correlation between electric charges of C3 and V4 during the late stage of disease counteracted by a positive correlation of electric charges of α2 helix and V5 during the same stage. These data allow us to hypothesize possible mechanisms of virus escape involving constant and variable regions of gp120. In particular, new mutations, including new PNGSs occurring near the CD4 and CCR5 binding sites could potentially affect receptor binding affinity and shield the virus from the immune response.
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Affiliation(s)
| | - Giuseppe D'Avenio
- Istituto Superiore di Sanità, Department of Technology and Health, Rome, Italy
| | - Lara Tavoschi
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | - Michele Chiappi
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | | | | | - Orietta Picconi
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | | | | | - Eftyhia Vardas
- Stellenbosch University, Division of Medical Virology, Stellenbosch, South Africa; Lancet Laboratories, Johannesburg, South Africa
| | - Hosea Sukati
- National Center Public Health Laboratory, Manzini, Swaziland
| | - Alessandra Lo Presti
- Istituto Superiore di Sanità, Department of Infectious, Parasitic and Immunomediated Diseases, Rome, Italy
| | - Massimo Ciccozzi
- Istituto Superiore di Sanità, Department of Infectious, Parasitic and Immunomediated Diseases, Rome, Italy; University of Biomedical Campus, Rome, Italy
| | - Paolo Monini
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | - Barbara Ensoli
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | - Mauro Grigioni
- Istituto Superiore di Sanità, Department of Technology and Health, Rome, Italy
| | - Stefano Buttò
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
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Abstract
PURPOSE OF REVIEW Primary HIV-1 infection is usually initiated by viruses with an exclusive affinity for the C-C chemokine receptor type 5 (CCR5) coreceptor. Viral variants that are also able to bind the C-X-C chemokine receptor type 4 (CXCR4) coreceptor arise during the course of the disease in about 50% of the infected individuals and their emergence is associated with a faster disease progression. In this article we provide a historical overview of the events that led to the discovery of the relationship between viral phenotype, coreceptor tropism and pathogenesis. RECENT FINDINGS The prevalence of CCR5 and CXCR4-using viruses differs from study to study, but overall percentages of CXCR4 use fluctuate between 2.0 and 63.0%. The association between coreceptor use and disease stage is recognized, with the lowest X4 prevalence in seroconverters and the highest in the final stage of the disease. Up to date there are insufficient arguments to support an impact of coreceptor tropism on response to combined antiretroviral therapy (cART) or an impact of cART on coreceptor tropism evolution. SUMMARY This review provides an overview of available data on coreceptor use in the different stages of the HIV-1 infection process. Although it is clear that CXCR4-using viruses emerge during the course of infection, the driving forces and mechanisms behind coreceptor switch remain largely unknown.
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Lin NH, Becerril C, Giguel F, Novitsky V, Moyo S, Makhema J, Essex M, Lockman S, Kuritzkes DR, Sagar M. Env sequence determinants in CXCR4-using human immunodeficiency virus type-1 subtype C. Virology 2012; 433:296-307. [PMID: 22954962 DOI: 10.1016/j.virol.2012.08.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/12/2012] [Accepted: 08/01/2012] [Indexed: 02/09/2023]
Abstract
HIV-1 subtype C (HIV-1C) CXCR4-using virus is isolated infrequently and is poorly characterized. Understanding HIV-1C env characteristics has implications for the clinical use of antiretrovirals that target viral entry. A total of 209 env clones derived from 10 samples with mixed CCR5-(R5), CXCR4-using (X4) or dual-tropic HIV-1C were phenotyped for coreceptor usage. Intra-patient X4 and R5 variants generally formed distinct monophyletic phylogenetic clusters. X4 compared to R5 envs had significantly greater amino acid variability and insertions, higher net positive charge, fewer glycosylation sites and increased basic amino acid substitutions in the GPGQ crown. Basic amino acid substitution and/or insertion prior to the crown are highly sensitive characteristics for predicting X4 viruses. Chimeric env functional studies suggest that the V3 loop is necessary but often not sufficient to impart CXCR4 utilization. Our studies provide insights into the unique genotypic characteristics of X4 variants in HIV-1C.
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Affiliation(s)
- Nina H Lin
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
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14
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Ataher Q, Portsmouth S, Napolitano LA, Eng S, Greenacre A, Kambugu A, Wood R, Badal-Faesen S, Tressler R. The epidemiology and clinical correlates of HIV-1 co-receptor tropism in non-subtype B infections from India, Uganda and South Africa. J Int AIDS Soc 2012; 15:2. [PMID: 22281097 PMCID: PMC3298508 DOI: 10.1186/1758-2652-15-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 01/26/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The introduction of C-C chemokine receptor type-5 (CCR5) antagonists as antiretroviral therapy has led to the need to study HIV co-receptor tropism in different HIV-1 subtypes and geographical locations. This study was undertaken to evaluate HIV-1 co-receptor tropism in the developing world where non-B subtypes predominate, in order to assess the therapeutic and prophylactic potential of CCR5 antagonists in these regions. METHODS HIV-1-infected patients were recruited into this prospective, cross-sectional, epidemiologic study from HIV clinics in South Africa, Uganda and India. Patients were infected with subtypes C (South Africa, India) or A or D (Uganda). HIV-1 subtype and co-receptor tropism were determined and analyzed with disease characteristics, including viral load and CD4(+) and CD8(+) T cell counts. RESULTS CCR5-tropic (R5) HIV-1 was detected in 96% of treatment-naïve (TN) and treatment-experienced (TE) patients in India, 71% of TE South African patients, and 86% (subtype A/A1) and 71% (subtype D) of TN and TE Ugandan patients. Dual/mixed-tropic HIV-1 was found in 4% of Indian, 25% of South African and 13% (subtype A/A1) and 29% (subtype D) of Ugandan patients. Prior antiretroviral treatment was associated with decreased R5 tropism; however, this decrease was less in subtype C from India (TE: 94%, TN: 97%) than in subtypes A (TE: 59%; TN: 91%) and D (TE: 30%; TN: 79%). R5 virus infection in all three subtypes correlated with higher CD4(+) count. CONCLUSIONS R5 HIV-1 was predominant in TN individuals with HIV-1 subtypes C, A, and D and TE individuals with subtypes C and A. Higher CD4(+) count correlated with R5 prevalence, while treatment experience was associated with increased non-R5 infection in all subtypes.
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15
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Mehlotra RK, Dazard JE, John B, Zimmerman PA, Weinberg A, Jurevic RJ. Copy Number Variation within Human β-Defensin Gene Cluster Influences Progression to AIDS in the Multicenter AIDS Cohort Study. ACTA ACUST UNITED AC 2012; 3. [PMID: 23543857 DOI: 10.4172/2155-6113.1000184] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
STUDY BACKGROUND DEFB4/103A encoding β-defensin 2 and 3, respectively, inhibit CXCR4-tropic (X4) viruses in vitro. We determined whether DEFB4/103A Copy Number Variation (CNV) influences time-to-X4 and time-to-AIDS outcomes. METHODS We utilized samples from a previously published Multicenter AIDS Cohort Study (MACS), which provides longitudinal account of viral tropism in relation to the full spectrum of rates of disease progression. Using traditional models for time-to-event analysis, we investigated association between DEFB4/103A CNV and the two outcomes, and interaction between DEFB4/103A CNV and disease progression groups, Fast and Slow. RESULTS Time-to-X4 and time-to-AIDS were weakly correlated. There was a stronger relationship between these two outcomes for the fast progressors. DEFB4/103A CNV was associated with time-to-AIDS, but not time-to-X4. The association between higher DEFB4/103A CNV and time-to-AIDS was more pronounced for the slow progressors. CONCLUSION DEFB4/103A CNV was associated with time-to-AIDS in a disease progression group-specific manner in the MACS cohort. Our findings may contribute to enhancing current understanding of how genetic predisposition influences AIDS progression.
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Affiliation(s)
- Rajeev K Mehlotra
- Center for Global Health and Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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