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Ndung'u T. The KT Jeang retrovirology prize 2023: Thumbi Ndung'u. Retrovirology 2023; 20:17. [PMID: 37848918 PMCID: PMC10583396 DOI: 10.1186/s12977-023-00632-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023] Open
Affiliation(s)
- Thumbi Ndung'u
- Africa Health Research Institute, Durban, South Africa.
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.
- Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA.
- Division of Infection and Immunity, University College London, London, UK.
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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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3
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Ndashimye E, Reyes PS, Arts EJ. New antiretroviral inhibitors and HIV-1 drug resistance: more focus on 90% HIV-1 isolates? FEMS Microbiol Rev 2023; 47:fuac040. [PMID: 36130204 PMCID: PMC9841967 DOI: 10.1093/femsre/fuac040] [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: 07/25/2022] [Revised: 09/13/2022] [Accepted: 09/18/2022] [Indexed: 01/21/2023] Open
Abstract
Combined HIV antiretroviral therapy (cART) has been effective except if drug resistance emerges. As cART has been rolled out in low-income countries, drug resistance has emerged at higher rates than observed in high income countries due to factors including initial use of these less tolerated cART regimens, intermittent disruptions in drug supply, and insufficient treatment monitoring. These socioeconomic factors impacting drug resistance are compounded by viral mechanistic differences by divergent HIV-1 non-B subtypes compared to HIV-1 subtype B that largely infects the high-income countries (just 10% of 37 million infected). This review compares the inhibition and resistance of diverse HIV-1 subtypes and strains to the various approved drugs as well as novel inhibitors in clinical trials. Initial sequence variations and differences in replicative fitness between HIV-1 subtypes pushes strains through different fitness landscapes to escape from drug selective pressure. The discussions here provide insight to patient care givers and policy makers on how best to use currently approved ART options and reduce the emergence of drug resistance in ∼33 million individuals infected with HIV-1 subtype A, C, D, G, and recombinants forms. Unfortunately, over 98% of the literature on cART resistance relates to HIV-1 subtype B.
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Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
- Joint Clinical Research Centre, -Center for AIDS Research Laboratories, 256, Kampala, Uganda
| | - Paul S Reyes
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
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4
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Souto B, Triunfante V, Santos-Pereira A, Martins J, Araújo PMM, Osório NS. Evolutionary dynamics of HIV-1 subtype C in Brazil. Sci Rep 2021; 11:23060. [PMID: 34845263 PMCID: PMC8629974 DOI: 10.1038/s41598-021-02428-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 11/12/2021] [Indexed: 11/29/2022] Open
Abstract
The extensive genetic diversity of HIV-1 is a major challenge for the prevention and treatment of HIV-1 infections. Subtype C accounts for most of the HIV-1 infections in the world but has been mainly localized in Southern Africa, Ethiopia and India. For elusive reasons, South Brazil harbors the largest HIV-1 subtype C epidemic in the American continent that is elsewhere dominated by subtype B. To investigate this topic, we collected clinical data and viral sequences from 2611 treatment-naïve patients diagnosed with HIV-1 in Brazil. Molecular epidemiology analysis supported 35 well-delimited transmission clusters of subtype C highlighting transmission within South Brazil but also from the South to all other Brazilian regions and internationally. Individuals infected with subtype C had lower probability to be deficient in CD4+ T cells when compared to subtype B. The HIV-1 epidemics in the South was characterized by high female-to-male infection ratios and women-to-child transmission. Our results suggest that HIV-1 subtype C probably takes advantage of longer asymptomatic periods to maximize transmission and is unlikely to outcompete subtype B in settings where the infection of women is relatively less relevant. This study contributes to elucidate factors possibly underlying the geographical distribution and expansion patterns of the most spread HIV-1 subtypes.
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Affiliation(s)
- Bernardino Souto
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal.,Department of Medicine, Federal University of São Carlos, São Carlos, Brazil
| | - Vera Triunfante
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Ana Santos-Pereira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Joana Martins
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Pedro M M Araújo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Nuno S Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal. .,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal.
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5
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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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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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Rapid CD4+ T-cell decline is associated with coreceptor switch among MSM primarily infected with HIV-1 CRF01_AE in Northeast China. AIDS 2019; 33:13-22. [PMID: 30102662 DOI: 10.1097/qad.0000000000001981] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE CRF01_AE is the most prevalent HIV-1 subtype among MSM in China. However, the characteristics and underlying mechanism of the accelerated CD4 T-cell decline in CRF01_AE-infected MSM remain incompletely understood. DESIGN A long-term prospective follow-up study was conducted with 1388 MSM at risk of HIV-1 infection in Northeast China. MSM with primary HIV-1 CRF01_AE infection were identified and followed for 3-6 years to explore the determinants of rapid CD4 T-cell decline. METHODS Tropism was determined in primary infection by both single genome amplification-based genotypic prediction using four different algorithms and phenotypic determination using clinical isolates. Serial isolates were used to determine phenotype of coreceptor switch. Human leukocyte antigen genotypes and T-cell activation markers were determined. RESULTS Fifty-nine MSM primarily infected with HIV-1 CRF01_AE were discovered and recruited for the follow-up study. CCR5-utilizing (R5) viruses accounted for up to 98% of HIV-1 CRF01_AE infections in Northeast China. Survival analysis indicated 39.5% of the patients underwent coreceptor switch within 3 years after infection. After adjustment for other potential risk factors, linear mixed-effect models demonstrated patients experienced R5 to CXCR4-utilizing/dual-tropic (X4/DM) coreceptor switch within 3 years after infection underwent a faster CD4 T-cell decline compared to those without coreceptor switch. CONCLUSIONS Primary HIV-1 CRF01_AE infection among MSM in Northeast China is characterized by R5 viral infection and early R5 to X4/DM coreceptor switch, which is associated with rapid CD4 T-cell decline. The findings highlight the importance of immediate treatment among the CRF01_AE-infected MSM.
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Subtype-Specific Differences in Gag-Protease-Driven Replication Capacity Are Consistent with Intersubtype Differences in HIV-1 Disease Progression. J Virol 2017; 91:JVI.00253-17. [PMID: 28424286 DOI: 10.1128/jvi.00253-17] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 03/30/2017] [Indexed: 11/20/2022] Open
Abstract
There are marked differences in the spread and prevalence of HIV-1 subtypes worldwide, and differences in clinical progression have been reported. However, the biological reasons underlying these differences are unknown. Gag-protease is essential for HIV-1 replication, and Gag-protease-driven replication capacity has previously been correlated with disease progression. We show that Gag-protease replication capacity correlates significantly with that of whole isolates (r = 0.51; P = 0.04), indicating that Gag-protease is a significant contributor to viral replication capacity. Furthermore, we investigated subtype-specific differences in Gag-protease-driven replication capacity using large well-characterized cohorts in Africa and the Americas. Patient-derived Gag-protease sequences were inserted into an HIV-1 NL4-3 backbone, and the replication capacities of the resulting recombinant viruses were measured in an HIV-1-inducible reporter T cell line by flow cytometry. Recombinant viruses expressing subtype C Gag-proteases exhibited substantially lower replication capacities than those expressing subtype B Gag-proteases (P < 0.0001); this observation remained consistent when representative Gag-protease sequences were engineered into an HIV-1 subtype C backbone. We identified Gag residues 483 and 484, located within the Alix-binding motif involved in virus budding, as major contributors to subtype-specific replicative differences. In East African cohorts, we observed a hierarchy of Gag-protease-driven replication capacities, i.e., subtypes A/C < D < intersubtype recombinants (P < 0.0029), which is consistent with reported intersubtype differences in disease progression. We thus hypothesize that the lower Gag-protease-driven replication capacity of subtypes A and C slows disease progression in individuals infected with these subtypes, which in turn leads to greater opportunity for transmission and thus increased prevalence of these subtypes.IMPORTANCE HIV-1 subtypes are unevenly distributed globally, and there are reported differences in their rates of disease progression and epidemic spread. The biological determinants underlying these differences have not been fully elucidated. Here, we show that HIV-1 Gag-protease-driven replication capacity correlates with the replication capacity of whole virus isolates. We further show that subtype B displays a significantly higher Gag-protease-mediated replication capacity than does subtype C, and we identify a major genetic determinant of these differences. Moreover, in two independent East African cohorts we demonstrate a reproducible hierarchy of Gag-protease-driven replicative capacity, whereby recombinants exhibit the greatest replication, followed by subtype D, followed by subtypes A and C. Our data identify Gag-protease as a major determinant of subtype differences in disease progression among HIV-1 subtypes; furthermore, we propose that the poorer viral replicative capacity of subtypes A and C may paradoxically contribute to their more efficient spread in sub-Saharan Africa.
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Danaviah S, de Oliveira T, Gordon M, Govender S, Chelule P, Pillay S, Naicker T, Cassol S, Ndung'u T. Analysis of Dominant HIV Quasispecies Suggests Independent Viral Evolution Within Spinal Granulomas Coinfected with Mycobacterium tuberculosis and HIV-1 Subtype C. AIDS Res Hum Retroviruses 2016; 32:262-70. [PMID: 26564424 DOI: 10.1089/aid.2015.0189] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Extrapulmonary tuberculosis (TB) is a significant public health challenge in South Africa and worldwide, largely fuelled by the HIV epidemic. In spinal TB, Mycobacteria infect the spinal column without dissemination to the spinal cord. The immune microenvironment, target cell characteristics, and other evolutionary forces within granulomas during HIV/TB coinfection are poorly characterized. We investigated whether spinal TB granulomas represent a sequestered anatomical site where independent HIV evolution occurs, and assessed the role of macrophages as a target cell for both HIV and mycobacteria. RNA was extracted from plasma and granulomatous tissue from six antiretroviral-naive HIV-1/spinal TB-coinfected patients, RT-PCR amplified, and the C2-V5 env segment was cloned and sequenced. Analysis of genetic diversity, phylogeny and coalescence patterns was performed on clonal sequences. To investigate their role in HIV sequestration, macrophages and the HIV-1 p24 protein were immune localized and ultrastructural features were studied. Intercompartment diversity measurements and phylogenetic reconstruction revealed anatomically distinct monophyletic HIV-1 clusters in four of six patients. Genotypic CCR5-tropic variants were predominant (98.9%) with conservation of putative N-linked glycosylation sites in both compartments. CD68(+) reactivity was associated with higher tissue viral load (r = 1.0; p < 0.01) but not greater intrapatient diversity (r = 0.60; p > 0.05). Ultrastructural imaging revealed the presence of bacterial and virus-like particles within membrane-bound intracellular compartments of macrophages. Spinal tuberculosis granulomas may form anatomically discreet sites of divergent viral evolution. Macrophages in these granulomas harbored both pathogens, suggesting that they may facilitate the process of viral sequestration within this compartment.
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Affiliation(s)
- Sivapragashini Danaviah
- Africa Centre for Health and Population Studies, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal (UKZN), Durban, South Africa
| | - Tulio de Oliveira
- Africa Centre for Health and Population Studies, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal (UKZN), Durban, South Africa
| | - Michelle Gordon
- Department of Virology, Nelson R. Mandela School of Medicine, UKZN, Durban, South Africa
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), UKZN, Durban, South Africa
| | - Shunmugam Govender
- Department of Orthopedics, Nelson R. Mandela School of Medicine, UKZN, Durban, South Africa
| | - Paul Chelule
- School of Public Health, Sefako Makgatho Health Sciences University, Medunsa, South Africa
| | - Sureshnee Pillay
- Africa Centre for Health and Population Studies, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal (UKZN), Durban, South Africa
| | - Thajasvarie Naicker
- Optics and Imaging Centre, Nelson R. Mandela School of Medicine, UKZN, Durban, South Africa
| | - Sharon Cassol
- MRC Inflammation and Immunity Unit, Department of Immunology, University of Pretoria, Pretoria, South Africa
| | - Thumbi Ndung'u
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), UKZN, Durban, South Africa
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, UKZN, Durban, South Africa
- Max Planck Institute for Infection Biology, Chariteplatz, Berlin, Germany
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, Massachusetts
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10
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Ndhlovu ZM, Kamya P, Mewalal N, Kløverpris HN, Nkosi T, Pretorius K, Laher F, Ogunshola F, Chopera D, Shekhar K, Ghebremichael M, Ismail N, Moodley A, Malik A, Leslie A, Goulder PJR, Buus S, Chakraborty A, Dong K, Ndung'u T, Walker BD. Magnitude and Kinetics of CD8+ T Cell Activation during Hyperacute HIV Infection Impact Viral Set Point. Immunity 2015; 43:591-604. [PMID: 26362266 DOI: 10.1016/j.immuni.2015.08.012] [Citation(s) in RCA: 192] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 06/02/2015] [Accepted: 06/26/2015] [Indexed: 02/07/2023]
Abstract
CD8(+) T cells contribute to the control of HIV, but it is not clear whether initial immune responses modulate the viral set point. We screened high-risk uninfected women twice a week for plasma HIV RNA and identified 12 hyperacute infections. Onset of viremia elicited a massive HIV-specific CD8(+) T cell response, with limited bystander activation of non-HIV memory CD8(+) T cells. HIV-specific CD8(+) T cells secreted little interferon-γ, underwent rapid apoptosis, and failed to upregulate the interleukin-7 receptor, known to be important for T cell survival. The rapidity to peak CD8(+) T cell activation and the absolute magnitude of activation induced by the exponential rise in viremia were inversely correlated with set point viremia. These data indicate that rapid, high magnitude HIV-induced CD8(+) T cell responses are crucial for subsequent immune control of acute infection, which has important implications for HIV vaccine design.
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Affiliation(s)
- Zaza M Ndhlovu
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Philomena Kamya
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Nikoshia Mewalal
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Henrik N Kløverpris
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa; Department of Immunology and Microbiology, University of Copenhagen, 2200-Copenhagen N, Denmark
| | - Thandeka Nkosi
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Karyn Pretorius
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Faatima Laher
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Funsho Ogunshola
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Denis Chopera
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Karthik Shekhar
- Department of Chemical Engineering, Massachusetts Institute of Technology, 25 Ames St, Cambridge, MA 02142, USA
| | - Musie Ghebremichael
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Nasreen Ismail
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Amber Moodley
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Amna Malik
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Alasdair Leslie
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Philip J R Goulder
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa; Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Søren Buus
- Department of Immunology and Microbiology, University of Copenhagen, 2200-Copenhagen N, Denmark
| | - Arup Chakraborty
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, 25 Ames St, Cambridge, MA 02142, USA
| | - Krista Dong
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa; Max Planck Institute for Infection Biology, Chariteplatz 1, 10117, Berlin, Germany
| | - Bruce D Walker
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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11
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Klein MB, Young J, Dunn D, Ledergerber B, Sabin C, Cozzi-Lepri A, Dabis F, Harrigan R, Tan DH, Walmsley S, Gill J, Cooper C, Scherrer AU, Mocroft A, Hogg RS, Smaill F. The effects of HIV-1 subtype and ethnicity on the rate of CD4 cell count decline in patients naive to antiretroviral therapy: a Canadian-European collaborative retrospective cohort study. CMAJ Open 2014; 2:E318-29. [PMID: 25485259 PMCID: PMC4251518 DOI: 10.9778/cmajo.20140017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Ethnic differences have the potential to confound associations between HIV-1 subtype and immunologic progression. We compared declines in CD4 cell counts during untreated infection for the most prevalent HIV-1 subtypes, focusing on distinguishing between the effects of viral subtype and ethnicity. METHODS We combined data from 4 European and 6 Canadian cohorts, selecting adults in the stable chronic phase of untreated HIV infection. We estimated the change in square root CD4 cell count over time for subtypes and ethnicities using mixed models, adjusting for covariates selected for their potential effect on initial CD4 cell count or its decline. RESULTS Data from 9772 patients were analyzed, contributing 79 175 measurements of CD4 cell count and 24 157 person-years of follow-up. Overall, there were no appreciable differences in CD4 cell count decline for viral subtypes A, CRF01_AE, CRF02_AG, C and G compared with viral subtype B; whereas the decline in CD4 cell count in patients of African ancestry was considerably slower than in patients of other ethnicity. When ethnic groups were studied separately, there was evidence for slower declines in CD4 cell count in viral subtypes C, and possibly A and G, compared with viral subtype B in patients of African ancestry but not among patients of other ethnicities, suggesting an interaction between subtype and ethnicity. INTERPRETATION Ethnicity is a major determinant of CD4 cell count decline; viral subtype differences may have existed but were small compared with the effect of ethnicity and were most apparent in patients of African ancestry. In developing countries, slower CD4 cell count declines among individuals of African descent may translate to a longer asymptomatic phase and increase the opportunity for HIV transmission.
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Affiliation(s)
- Marina B Klein
- Division of Infectious Diseases/Chronic Viral Illness Service, Department of Medicine, Royal Victoria Hospital, McGill University Health Centre, Montréal, Que
| | - Jim Young
- Division of Infectious Diseases/Chronic Viral Illness Service, Department of Medicine, Royal Victoria Hospital, McGill University Health Centre, Montréal, Que. ; Basel Institute for Clinical Epidemiology and Biostatistics, University Hospital Basel, Basel, Switzerland
| | - David Dunn
- Medical Research Council Clinical Trials Unit, London, UK
| | - Bruno Ledergerber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Caroline Sabin
- Research Department of Infection and Population Health, University College London, London, UK
| | - Alessandro Cozzi-Lepri
- Research Department of Infection and Population Health, University College London, London, UK
| | - Francois Dabis
- Centre du recherche INSERM U897 - Epidémiologie-Biostatistique, Institut de Santé Publique, d'Epidémioloie et de Développement (ISPED) Université Bordeaux, Bordeaux, France
| | - Richard Harrigan
- Faculty of Health Sciences, Simon Fraser University, Vancouver, BC
| | - Darrell H Tan
- Division of Infectious Diseases, St. Michael's Hospital, Toronto, Ont
| | - Sharon Walmsley
- University Health Network, University of Toronto, Toronto, Ont
| | - John Gill
- Southern Alberta HIV Clinic, Calgary, Alta
| | | | - Alexandra U Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Amanda Mocroft
- Research Department of Infection and Population Health, University College London, London, UK
| | - Robert S Hogg
- Faculty of Health Sciences, Simon Fraser University, Vancouver, BC. ; Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC
| | - Fiona Smaill
- Department of Medicine, McMaster University, Hamilton, Ont
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12
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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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13
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Fonjungo PN, Kalish ML, Schaefer A, Rayfield M, Mika J, Rose LE, Heslop O, Soudré R, Pieniazek D. Recombinant viruses initiated the early HIV-1 epidemic in Burkina Faso. PLoS One 2014; 9:e92423. [PMID: 24647246 PMCID: PMC3960253 DOI: 10.1371/journal.pone.0092423] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 02/22/2014] [Indexed: 11/28/2022] Open
Abstract
We analyzed genetic diversity and phylogenetic relationships among 124 HIV-1 and 19 HIV-2 strains in sera collected in 1986 from patients of the state hospital in Ouagadougou, Burkina Faso. Phylogenetic analysis of the HIV-1 env gp41 region of 65 sequences characterized 37 (56.9%) as CRF06_cpx strains, 25 (38.5%) as CRF02_AG, 2 (3.1%) as CRF09_cpx, and 1 (1.5%) as subtype A. Similarly, phylogenetic analysis of the protease (PR) gene region of 73 sequences identified 52 (71.2%) as CRF06_cpx, 15 (20.5%) as CRF02_AG, 5 (6.8%) as subtype A, and 1 (1.4%) was a unique strain that clustered along the B/D lineage but basal to the node connecting the two lineages. HIV-2 PR or integrase (INT) groups A (n = 17 [89.5%]) and B (n = 2 [10.5%]) were found in both monotypic (n = 11) and heterotypic HIV-1/HIV-2 (n = 8) infections, with few HIV-2 group B infections. Based on limited available sampling, evidence suggests two recombinant viruses, CRF06_cpx and CRF02_AG, appear to have driven the beginning of the mid-1980s HIV-1 epidemic in Burkina Faso.
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Affiliation(s)
- Peter N. Fonjungo
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Atlanta, Georgia, United States of America
- Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
| | - Marcia L. Kalish
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Atlanta, Georgia, United States of America
| | - Amanda Schaefer
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Atlanta, Georgia, United States of America
| | - Mark Rayfield
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Atlanta, Georgia, United States of America
| | - Jennifer Mika
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Atlanta, Georgia, United States of America
| | - Laura E. Rose
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Atlanta, Georgia, United States of America
| | - Orville Heslop
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Atlanta, Georgia, United States of America
| | - Robert Soudré
- Unité de Formation et de Recherche en Sciences de la Santé (UFR/SDS), Université de Ouagadougou, Ouagadougou, Burkina Faso
| | - Danuta Pieniazek
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Atlanta, Georgia, United States of America
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14
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Mlisana K, Sobieszczyk M, Werner L, Feinstein A, van Loggerenberg F, Naicker N, Williamson C, Garrett N. Challenges of diagnosing acute HIV-1 subtype C infection in African women: performance of a clinical algorithm and the need for point-of-care nucleic-acid based testing. PLoS One 2013; 8:e62928. [PMID: 23646162 PMCID: PMC3639937 DOI: 10.1371/journal.pone.0062928] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 03/27/2013] [Indexed: 12/13/2022] Open
Abstract
Background Prompt diagnosis of acute HIV infection (AHI) benefits the individual and provides opportunities for public health intervention. The aim of this study was to describe most common signs and symptoms of AHI, correlate these with early disease progression and develop a clinical algorithm to identify acute HIV cases in resource limited setting. Methods 245 South African women at high-risk of HIV-1 were assessed for AHI and received monthly HIV-1 antibody and RNA testing. Signs and symptoms at first HIV-positive visit were compared to HIV-negative visits. Logistic regression identified clinical predictors of AHI. A model-based score was assigned to each predictor to create a risk score for every woman. Results Twenty-eight women seroconverted after a total of 390 person-years of follow-up with an HIV incidence of 7.2/100 person-years (95%CI 4.5–9.8). Fifty-seven percent reported ≥1 sign or symptom at the AHI visit. Factors predictive of AHI included age <25 years (OR = 3.2; 1.4–7.1), rash (OR = 6.1; 2.4–15.4), sore throat (OR = 2.7; 1.0–7.6), weight loss (OR = 4.4; 1.5–13.4), genital ulcers (OR = 8.0; 1.6–39.5) and vaginal discharge (OR = 5.4; 1.6–18.4). A risk score of 2 correctly predicted AHI in 50.0% of cases. The number of signs and symptoms correlated with higher HIV-1 RNA at diagnosis (r = 0.63; p<0.001). Conclusions Accurate recognition of signs and symptoms of AHI is critical for early diagnosis of HIV infection. Our algorithm may assist in risk-stratifying individuals for AHI, especially in resource-limited settings where there is no routine testing for AHI. Independent validation of the algorithm on another cohort is needed to assess its utility further. Point-of-care antigen or viral load technology is required, however, to detect asymptomatic, antibody negative cases enabling early interventions and prevention of transmission.
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Affiliation(s)
- Koleka Mlisana
- Centre for the AIDS Programme of Research in South Africa-CAPRISA, University of KwaZulu-Natal, Durban, South Africa.
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15
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Cashin K, Gray LR, Jakobsen MR, Sterjovski J, Churchill MJ, Gorry PR. CoRSeqV3-C: a novel HIV-1 subtype C specific V3 sequence based coreceptor usage prediction algorithm. Retrovirology 2013; 10:24. [PMID: 23446039 PMCID: PMC3599735 DOI: 10.1186/1742-4690-10-24] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/12/2013] [Indexed: 12/17/2022] Open
Abstract
Background The majority of HIV-1 subjects worldwide are infected with HIV-1 subtype C (C-HIV). Although C-HIV predominates in developing regions of the world such as Southern Africa and Central Asia, C-HIV is also spreading rapidly in countries with more developed economies and health care systems, whose populations are more likely to have access to wider treatment options, including the CCR5 antagonist maraviroc (MVC). The ability to reliably determine C-HIV coreceptor usage is therefore becoming increasingly more important. In silico V3 sequence based coreceptor usage prediction algorithms are a relatively rapid and cost effective method for determining HIV-1 coreceptor specificity. In this study, we elucidated the V3 sequence determinants of C-HIV coreceptor usage, and used this knowledge to develop and validate a novel, user friendly, and highly sensitive C-HIV specific coreceptor usage prediction algorithm. Results We characterized every phenotypically-verified C-HIV gp120 V3 sequence available in the Los Alamos HIV Database. Sequence analyses revealed that compared to R5 C-HIV V3 sequences, CXCR4-using C-HIV V3 sequences have significantly greater amino acid variability, increased net charge, increased amino acid length, increased frequency of insertions and substitutions within the GPGQ crown motif, and reduced frequency of glycosylation sites. Based on these findings, we developed a novel C-HIV specific coreceptor usage prediction algorithm (CoRSeqV3-C), which we show has superior sensitivity for determining CXCR4 usage by C-HIV strains compared to all other available algorithms and prediction rules, including Geno2pheno[coreceptor] and WebPSSMSINSI-C, which has been designed specifically for C-HIV. Conclusions CoRSeqV3-C is now openly available for public use at http://www.burnet.edu.au/coreceptor. Our results show that CoRSeqV3-C is the most sensitive V3 sequence based algorithm presently available for predicting CXCR4 usage of C-HIV strains, without compromising specificity. CoRSeqV3-C may be potentially useful for assisting clinicians to decide the best treatment options for patients with C-HIV infection, and will be helpful for basic studies of C-HIV pathogenesis.
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Affiliation(s)
- Kieran Cashin
- Center for Virology, Burnet Institute, 85 Commercial Rd, Melbourne 3004VIC, Australia
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16
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Yin J, Liu S, Zhu Y. An overview of the highly pathogenic H5N1 influenza virus. Virol Sin 2013; 28:3-15. [PMID: 23325419 PMCID: PMC7090813 DOI: 10.1007/s12250-013-3294-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 12/31/2012] [Indexed: 11/17/2022] Open
Abstract
Since the first human case of H5N1 avian influenza virus infection was reported in 1997, this highly pathogenic virus has infected hundreds of people around the world and resulted in many deaths. The ability of H5N1 to cross species boundaries, and the presence of polymorphisms that enhance virulence, present challenges to developing clear strategies to prevent the pandemic spread of this highly pathogenic avian influenza (HPAI) virus. This review summarizes the current understanding of, and recent research on, the avian influenza H5N1 virus, including transmission, virulence, pathogenesis, clinical characteristics, treatment and prevention.
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Affiliation(s)
- Jingchuan Yin
- The State Key laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan 430072, China
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17
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Andrabi R, Kumar R, Bala M, Nair A, Ss P, Kushwaha V, Luthra K. Envelope diversity, characteristics of V3 region and predicted co-receptor usage of human immunodeficiency viruses infecting north Indians. J Microbiol 2012; 50:869-73. [PMID: 23124759 DOI: 10.1007/s12275-012-2136-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 06/12/2012] [Indexed: 11/27/2022]
Abstract
Subtypes of human immunodeficiency virus type 1 circulating in 21 north Indian patients were characterized based on the partial sequence of the gp120 envelope protein. A majority of viruses (85.7%, 18/21) were subtype C, while 14.3% (3/21) were subtype A. Sequence analysis revealed that the V3 region was highly conserved compared with V4 and V5. The predicted use of co-receptors indicated exclusive usage of R5, except for two subtype A viruses (AIIMS279 and AIIMS281). Our results demonstrate conservation within the V3 loop of subtype C viruses, and suggest the emergence of non-clade C viruses in the north Indian population.
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Affiliation(s)
- Raiees Andrabi
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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18
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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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19
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Dimonte S, Babakir-Mina M, Mercurio F, Di Pinto D, Ceccherini-Silberstein F, Svicher V, Perno CF. Selected amino acid changes in HIV-1 subtype-C gp41 are associated with specific gp120(V3) signatures in the regulation of co-receptor usage. Virus Res 2012; 168:73-83. [PMID: 22732432 DOI: 10.1016/j.virusres.2012.06.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 06/13/2012] [Accepted: 06/15/2012] [Indexed: 11/18/2022]
Abstract
The majority of studies have characterized the tropism of HIV-1 subtype-B isolates, but little is known about the determinants of tropism in other subtypes. So, the goal of the present study was to genetically characterize the envelope of viral proteins in terms of co-receptor usage by analyzing 356 full-length env sequences derived from HIV-1 subtype-C infected individuals. The co-receptor usage of V3 sequences was inferred by using the Geno2Pheno and PSSM algorithms, and also analyzed to the "11/25 rule". All reported env sequences were also analyzed with regard to N-linked glycosylation sites, net charge and hydrophilicity, as well as the binomial correlation phi coefficient to assess covariation among gp120(V3) and gp41 signatures and the average linkage hierarchical agglomerative clustering were also performed. Among env sequences present in Los Alamos Database, 255 and 101 sequences predicted as CCR5 and CXCR4 were selected, respectively. The classical V3 signatures at positions 11 and 25, and other specific V3 and gp41 amino acid changes were found statistically associated with different co-receptor usage. Furthermore, several statistically significant associations between V3 and gp41 signatures were also observed. The dendrogram topology showed a cluster associated with CCR5-usage composed by five gp41 mutated positions, A22V, R133M, E136G, N140L, and N166Q that clustered with T2V(V3) and G24T(V3) (bootstrap=1). Conversely, a heterogeneous cluster with CXCR4-usage, involving S11GR(V3), 13-14insIG/LG(V3), P16RQ(V3), Q18KR(V3), F20ILV(V3), D25KRQ(V3), Q32KR(V3) along with A30T(gp41), S107N(gp41), D148E(gp41), A189S(gp41) was identified (bootstrap=0.86). Our results show that as observed for HIV-1 subtype-B, also in subtype-C specific and different gp41 and gp120V3 amino acid changes are associated individually or together with CXCR4 and/or CCR5 usage. These findings strengthen previous observations that determinants of tropism may also reside in the gp41 protein.
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Affiliation(s)
- Salvatore Dimonte
- University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy.
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Green TN, Archary M, Gordon ML, Padayachi N, Lie Y, Anton ED, Reeves JD, Grobler A, Bobat R, Coovadia H, Ndung'u T. Drug resistance and coreceptor usage in HIV type 1 subtype C-infected children initiating or failing highly active antiretroviral therapy in South Africa. AIDS Res Hum Retroviruses 2012; 28:324-32. [PMID: 21819257 DOI: 10.1089/aid.2011.0106] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
HIV-1 drug resistance monitoring in resource-poor settings is crucial due to limited drug alternatives. Recent reports of the increased prevalence of CXCR4 usage in subtype C infections may have implications for CCR5 antagonists in therapy. We investigated the prevalence of drug resistance mutations and CXCR4 coreceptor utilization of viruses from HIV-1 subtype C-infected children. Fifty-one children with virological failure during highly active antiretroviral therapy (HAART) and 43 HAART-naive children were recruited. Drug resistance genotyping and coreceptor utilization assessment by phenotypic and genotypic methods were performed. At least one significant drug resistance mutation was present in 85.4% of HAART-failing children. Thymidine analogue mutations (TAMs) were detected in 58.5% of HAART-failing children and 39.0% had ≥3 TAMs. CXCR4 (X4) or dual (R5X4)/mixed (R5, X4) (D/M)-tropic viruses were found in 54.3% of HAART-failing and 9.4% of HAART-naive children (p<0.0001); however, the HAART-failing children were significantly older (p<0.0001). In multivariate logistic regression, significant predictors of CXCR4 usage included antiretroviral treatment, older age, and lower percent CD4(+) T cell counts. The majority of genotypic prediction tools had low sensitivity (≤65.0%) and high specificity (≥87.5%) for predicting CXCR4 usage. Extensive drug resistance, including the high percentage of TAMs found, may compromise future drug choices for children, highlighting the need for improved treatment monitoring and adherence counseling. Additionally, the increased prevalence of X4/D/M viruses in HAART-failing children suggests limited use of CCR5 antagonists in salvage therapy. Enhanced genotypic prediction tools are needed as current tools are not sensitive enough for predicting CXCR4 usage.
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Affiliation(s)
- Taryn N. Green
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Mohendran Archary
- Department of Paediatrics and Child Health, University of KwaZulu-Natal, Durban, South Africa
| | - Michelle L. Gordon
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Department of Virology, University of KwaZulu-Natal, Durban, South Africa
| | - Nagavelli Padayachi
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Department of Virology, University of KwaZulu-Natal, Durban, South Africa
| | - Yolanda Lie
- Monogram Biosciences, Inc., South San Francisco, California
| | | | | | - Anneke Grobler
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Raziya Bobat
- Department of Paediatrics and Child Health, University of KwaZulu-Natal, Durban, South Africa
| | - Hoosen Coovadia
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Department of Paediatrics and Child Health, University of KwaZulu-Natal, Durban, South Africa
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
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Drug resistance and viral tropism in HIV-1 subtype C-infected patients in KwaZulu-Natal, South Africa: implications for future treatment options. J Acquir Immune Defic Syndr 2011; 58:233-40. [PMID: 21709569 DOI: 10.1097/qai.0b013e318228667f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Drug resistance poses a significant challenge for the successful application of highly active antiretroviral therapy (HAART) globally. Furthermore, emergence of HIV-1 isolates that preferentially use CXCR4 as a coreceptor for cell entry, either as a consequence of natural viral evolution or HAART use, may compromise the efficacy of CCR5 antagonists as alternative antiviral therapy. METHODS We sequenced the pol gene of viruses from 45 individuals failing at least 6 months of HAART in Durban, South Africa, to determine the prevalence and patterns of drug-resistance mutations. Coreceptor use profiles of these viruses and those from 45 HAART-naive individuals were analyzed using phenotypic and genotypic approaches. RESULTS Ninety-five percent of HAART-failing patients had at least one drug-resistant mutation. Thymidine analog mutations (TAMs) were present in 55% of patients with 9% of individuals possessing mutations indicative of the TAM1 pathway, 44% had TAM2, whereas 7% had mutations common to both pathways. Sixty percent of HAART-failing subjects had X4/dual//mixed-tropic viruses compared with 30% of HAART-naïve subjects (P < 0.02). Genetic coreceptor use prediction algorithms correlated with phenotypic results with 60% of samples from HAART-failing subjects predicted to possess CXCR4-using (X4/dual/mixed viruses) versus 15% of HAART-naïve patients. CONCLUSIONS The high proportion of TAMs and X4/dual/mixed HIV-1 viruses among patients failing therapy highlight the need for intensified monitoring of patients taking HAART and the problem of diminished drug options (including CCR5 antagonists) for patients failing therapy in resource-poor settings.
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22
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Prevalence and clinical associations of CXCR4-using HIV-1 among treatment-naive subtype C-infected women in Botswana. J Acquir Immune Defic Syndr 2011; 57:46-50. [PMID: 21346588 DOI: 10.1097/qai.0b013e318214fe27] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
HIV-1 coreceptor use was determined using a phenotypic assay in plasma samples from treatment-naive women infected with subtype C virus who had CD4 cell counts below 200 cells/mm3. Of 148 women, 14.9% were infected with dual/mixed virus; the remainder had R5 virus. A greater proportion of women in the lowest CD4 cell count stratum had dual/mixed virus (P = 0.026); change in coreceptor use after antiretroviral therapy exposure was uncommon. CXCR4-using HIV-1 was less common in subtype C-infected women than reported in subtype B cohorts but was most prevalent in women with the lowest CD4 cell counts.
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Qu S, Ma L, Yuan L, Xu W, Hong K, Xing H, Huang Y, Yu X, Shao Y. Co-receptor usage and prediction of V3 genotyping algorithms in HIV-1 subtype B' from paid blood donors experienced anti-retroviral therapy in Chinese central province. Virol J 2010; 7:280. [PMID: 20969781 PMCID: PMC2988017 DOI: 10.1186/1743-422x-7-280] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2010] [Accepted: 10/22/2010] [Indexed: 11/10/2022] Open
Abstract
Background This study explored co-receptor usage and prediction of V3 genotyping algorithms in HIV-1 subtype B' from paid blood donors experienced anti-retroviral therapy in Chinese central province in order to design effectively therapeutic regimen. Methods HIV-1 strains were isolated in treatment HIV-1 infections and treatment-naïve HIV-1 infections, then co-receptor usage of HIV-1 strains was identified based on Ghost cell lines using flow cytometry. HIV-1 V3 region was amplified and submitted into web-server (WebPSSM and geno2pheno) to predict HIV-1 co-receptor usage. The feasibility of prediction HIV-1 usage with Web-server assay was analyzed by comparing prediction of V3 genotyping algorithms with HIV phenotype assay based on Ghost cell line. Results 45 HIV-1 strains and 114 HIV-1 strains were isolated from HIV-1 infections exposed anti-retroviral therapy and treatment-naïve, respectively. 41% clinical viruses from ART patients and 18% from treatment-naïve patients used CXCR4 as co-receptor. The net charge in the V3 loop was significantly difference in both groups. The sensitivity and specificity for predicting co-receptor capacity is 54.6% and 90.0% on 11/25 rule, 50.0% and 90% on Web-PSSMx4r5, 68.2% and 40.0% on Geno2pheno[co-receptor]. Conclusion Dual/mixed/X4 co-receptor utilization was higher in ART patients than treatment-naïve patients. It is should paid attention to predicting HIV-1 co-receptor usage based on V3 genotyping algorithms in HIV-1 subtype B' from paid blood donors experienced anti-retroviral therapy in Chinese central province.
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Affiliation(s)
- Shuiling Qu
- State Key Laboratory for Infectious Disease Control and Prevention, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100050, China
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Lin NH, Negusse DM, Beroukhim R, Giguel F, Lockman S, Essex M, Kuritzkes DR. The design and validation of a novel phenotypic assay to determine HIV-1 coreceptor usage of clinical isolates. J Virol Methods 2010; 169:39-46. [PMID: 20599562 PMCID: PMC2930119 DOI: 10.1016/j.jviromet.2010.06.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 06/08/2010] [Accepted: 06/17/2010] [Indexed: 10/19/2022]
Abstract
A phenotypic assay to determine coreceptor usage of HIV-1 has been developed for rapid testing of clinical samples. The assay is based on the synthesis of viral stock from full-length env amplicons isolated from patient's plasma. Pseudoviral stock is generated rapidly by using an overlapping PCR method to assemble a CMV promoter to env, followed by co-transfection into producer cells with a HIV plasmid (pNL4-3.Luc.R(-)E(-)) containing a non-functional env. The coreceptor used by the viral quasispecies is tested by infection into U87.CD4.CCR5 and U87.CD4.CXCR4 cells. Viral entry is indicated by the expression of the luciferase gene in relative light units (RLU). The use of CXCR4 coreceptor by minor variants is confirmed with sufficient suppression of RLU by a CXCR4 inhibitor. Two statistical tests are employed to confirm viral entry. This assay accurately assigned coreceptor usage of isolates of various subtypes and in the majority of samples of various viral loads. The sensitivity to detect minor species of CXCR4-using env is 1% at higher viral loads and 5% at less than 1,000 copies/ml. This assay provides a sensitive, efficient and relatively low-cost approach suitable for use by research laboratories for assessing HIV-1 coreceptor usage of plasma samples.
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Affiliation(s)
- Nina H. Lin
- Infectious Diseases Unit, Massachusetts General Hospital, 55 Fruit Street, Jackson 504, Boston, MA, 02114, USA
- Harvard Medical School, Boston, MA, 02115 USA
- Section of Retroviral Therapeutics and Division of Infectious Diseases, Brigham and Women’s Hospital, 65 Landsdowne Street Rm 449, Cambridge, MA 02139, USA
| | - Daniel M. Negusse
- Harvard School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard School of Public Health, FXB 402, 651 Huntington Avenue, Boston, MA 02115, USA
| | - Rameen Beroukhim
- Department of Medical Oncology and Cancer Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02215, USA
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Francoise Giguel
- Infectious Diseases Unit, Massachusetts General Hospital, 55 Fruit Street, Jackson 504, Boston, MA, 02114, USA
- Harvard Medical School, Boston, MA, 02115 USA
- Section of Retroviral Therapeutics and Division of Infectious Diseases, Brigham and Women’s Hospital, 65 Landsdowne Street Rm 449, Cambridge, MA 02139, USA
| | - Shahin Lockman
- Harvard Medical School, Boston, MA, 02115 USA
- Section of Retroviral Therapeutics and Division of Infectious Diseases, Brigham and Women’s Hospital, 65 Landsdowne Street Rm 449, Cambridge, MA 02139, USA
- Harvard School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard School of Public Health, FXB 402, 651 Huntington Avenue, Boston, MA 02115, USA
| | - Myron Essex
- Harvard School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard School of Public Health, FXB 402, 651 Huntington Avenue, Boston, MA 02115, USA
| | - Daniel R. Kuritzkes
- Harvard Medical School, Boston, MA, 02115 USA
- Section of Retroviral Therapeutics and Division of Infectious Diseases, Brigham and Women’s Hospital, 65 Landsdowne Street Rm 449, Cambridge, MA 02139, USA
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Iwabu Y, Kinomoto M, Tatsumi M, Fujita H, Shimura M, Tanaka Y, Ishizaka Y, Nolan D, Mallal S, Sata T, Tokunaga K. Differential anti-APOBEC3G activity of HIV-1 Vif proteins derived from different subtypes. J Biol Chem 2010; 285:35350-8. [PMID: 20833716 DOI: 10.1074/jbc.m110.173286] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Antiretroviral cytidine deaminase APOBEC3G, which is abundantly expressed in peripheral blood lymphocytes and macrophages, strongly protects these cells against HIV-1 infection. The HIV-1 Vif protein overcomes this antiviral effect by enhancing proteasome-mediated APOBEC3G degradation and is key for maintaining viral infectivity. The 579-bp-long vif gene displays high genetic diversity among HIV-1 subtypes. Therefore, it is intriguing to address whether Vif proteins derived from different subtypes differ in their viral defense activity against APOBEC3G. Expression plasmids encoding Vif proteins derived from subtypes A, B, C, CRF01_AE, and CRF02_AG isolates were created, and their anti-APOBEC3G activities were compared. Viruses produced from cells expressing APOBEC3G and Vif proteins from different subtypes showed relatively different viral infectivities. Notably, subtype C-derived Vif proteins tested had the highest activity against APOBEC3G that was ascribed to its increased binding activity, for which the N-terminal domain of the Vif protein sequences was responsible. These results suggest that the biological differences of Vif proteins belonging to different subtypes might affect viral fitness and quasispecies in vivo.
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Affiliation(s)
- Yukie Iwabu
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
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26
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Cuevas M, Fernández-García A, Pinilla M, García-Álvarez V, Thomson M, Delgado E, González-Galeano M, Miralles C, Serrano-Bengoechea E, Ojea de Castro R, López-Álvarez M, Lezáun M, Sánchez-García A, Sánchez-Martínez M, Muñoz-Nieto M, Pérez-Álvarez L. Short communication: Biological and genetic characterization of HIV type 1 subtype B and nonsubtype B transmitted viruses: usefulness for vaccine candidate assessment. AIDS Res Hum Retroviruses 2010; 26:1019-25. [PMID: 20707647 DOI: 10.1089/aid.2010.0018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Due to the extraordinary degree of genetic diversity of HIV-1 and the structural complexity of its envelope glycoproteins, designing an effective vaccine is difficult, requiring the development of viral reagents to assess vaccine-elicited neutralizing antibodies. The aim of this study was to improve on our previously developed panel of HIV-1 strains of different genetic forms, focusing on strains from acute and recently acquired infections as the most representative of the transmitted viruses. HIV-1 primary isolates were expanded in peripheral blood mononuclear cells. Viral stocks of 40 ml each were produced. Syncytium-inducing (SI) phenotype, coreceptor use, and TCID(50)/ml were determined. Near full-length HIV-1 genomes were amplified by RT-nested PCR in four overlapping segments. Phylogenetic analyses were performed with neighbor-joining trees and bootscanning. Forty-four HIV-1 strains were included in the panel. Twenty-four (54.1%) strains were from early infections (16 acute and 8 recent); of them, 21 (87%) were sexually transmitted. NSI/R5 phenotype was detected in 37 (84.1%) viruses and SI/R5,X4 in another 7 (15.9%). TCID(50)/ml ranged between 10(4) and 10(6.6). Twelve different genetic forms constituted this panel: subtypes A1, B, C, F1, and G; circulating recombinant forms CRF02_AG, CRF14_BG, and CRF24_BG; and unique recombinant forms CRF02_AG/A3, BF1, CRF12_BF/B, and DF1G. In conclusion, in this study, we report the development of a comprehensive and well-characterized panel of HIV-1 isolates for assessing neutralization in HIV vaccine research. This panel is available for distribution through the Programme EVA Centre for AIDS Reagents, National Institute for Biological Standard and Control (NIBSC).
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Affiliation(s)
- M.T. Cuevas
- HIV Biology and Variability Department, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - A. Fernández-García
- HIV Biology and Variability Department, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - M. Pinilla
- HIV Biology and Variability Department, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - V. García-Álvarez
- HIV Biology and Variability Department, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - M. Thomson
- HIV Biology and Variability Department, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - E. Delgado
- HIV Biology and Variability Department, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - M. González-Galeano
- HIV Biology and Variability Department, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - C. Miralles
- Complejo Hospitalario Universitario Xeral Cies de Vigo, Pontevedra, Galicia, Spain
| | | | | | | | - M.J. Lezáun
- Hospital Txagorritxu, Vitoria, Álava, País Vasco, Spain
| | - A.M. Sánchez-García
- HIV Biology and Variability Department, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - M. Sánchez-Martínez
- HIV Biology and Variability Department, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - M. Muñoz-Nieto
- HIV Biology and Variability Department, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - L. Pérez-Álvarez
- HIV Biology and Variability Department, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Zhang H, Tully DC, Zhang T, Moriyama H, Thompson J, Wood C. Molecular determinants of HIV-1 subtype C coreceptor transition from R5 to R5X4. Virology 2010; 407:68-79. [PMID: 20797755 DOI: 10.1016/j.virol.2010.07.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/01/2010] [Accepted: 07/28/2010] [Indexed: 11/18/2022]
Abstract
The molecular mechanism(s) underlying transition from CCR5 to CXCR4 usage of subtype C viruses remain largely unknown. We previously identified a subtype C HIV-1 infected child whose virus demonstrated CXCR4 usage along with CCR5 upon longitudinal follow-up. Here we delineated the molecular determinants of Env involved in expanded coreceptor usage. Residue changes in three positions of Env V3 domain are critical for the dual tropic phenotype. These include: substitution of arginine at position 11, MG or LG insertion between positions 13 and 14, and substitution of threonine at the position immediately downstream of the GPGQ crown. Introducing these mutations into V3 region of a heterologous R5 virus also conferred dual tropism. Molecular modeling of V3 revealed a possible structural basis for the dual tropic phenotype. Determining what defines a subtype C X4 virus will lead to a better understanding of subtype C HIV-1 pathogenesis, and will provide important information relevant to anti-retroviral therapy.
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Affiliation(s)
- Hong Zhang
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900, USA
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Low frequency of CXCR4-using viruses in patients at the time of primary non-subtype-B HIV-1 infection. J Clin Microbiol 2010; 48:3487-91. [PMID: 20686090 DOI: 10.1128/jcm.00704-10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We used genotypic and phenotypic assays to estimate the frequency of X4/DM viruses in 131 patients infected with non-subtype-B viruses at the time of primary HIV-1 infection (PHI). All patients were enrolled in the French PRIMO Cohort from 1996 to 2007. Most strains belonged to CRF02_AG (51.1%) and subtype A (14.5%). Sixteen viruses (12.2%) were classified as CXCR4 tropic ("X4 strains") by the combined criteria of amino acids 11 and 25 of the V3 loop (11/25) and net charge rules and/or the SVMgeno2pheno(10%) algorithm: 6 strains by the combined genotypic rule, 7 by the SVMgeno2pheno(10%) algorithm, and 3, clustering in subtype D, by both algorithms. However, only one strain (0.8%), belonging to subtype A, was defined as a dual-tropic (DM) virus by the phenotypic assay. The 67 CRF02_AG strains included 2 classified as X4 strains by the combined genotypic rule (3%) and 2 others classified as X4 strains by SVMgeno2pheno(10%) (3%), but none of these 4 strains was an X4 or DM strain according to the phenotypic assay. These results suggest that the cellular virus reservoir was established with X4 strains in very few non-subtype-B-infected patients at the time of PHI. Genotypic predictions can overestimate the proportion of non-subtype-B X4 viruses at PHI.
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Restriction of HIV-1 genotypes in breast milk does not account for the population transmission genetic bottleneck that occurs following transmission. PLoS One 2010; 5:e10213. [PMID: 20422033 PMCID: PMC2857876 DOI: 10.1371/journal.pone.0010213] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 03/17/2010] [Indexed: 12/27/2022] Open
Abstract
Background Breast milk transmission of HIV-1 remains a major route of pediatric infection. Defining the characteristics of viral variants to which breastfeeding infants are exposed is important for understanding the genetic bottleneck that occurs in the majority of mother-to-child transmissions. The blood-milk epithelial barrier markedly restricts the quantity of HIV-1 in breast milk, even in the absence of antiretroviral drugs. The basis of this restriction and the genetic relationship between breast milk and blood variants are not well established. Methodology/Principal Findings We compared 356 HIV-1 subtype C gp160 envelope (env) gene sequences from the plasma and breast milk of 13 breastfeeding women. A trend towards lower viral population diversity and divergence in breast milk was observed, potentially indicative of clonal expansion within the breast. No differences in potential N-linked glycosylation site numbers or in gp160 variable loop amino acid lengths were identified. Genetic compartmentalization was evident in only one out of six subjects in whom contemporaneously obtained samples were studied. However, in samples that were collected 10 or more days apart, six of seven subjects were classified as having compartmentalized viral populations, highlighting the necessity of contemporaneous sampling for genetic compartmentalization studies. We found evidence of CXCR4 co-receptor using viruses in breast milk and blood in nine out of the thirteen subjects, but no evidence of preferential localization of these variants in either tissue. Conclusions/Significance Despite marked restriction of HIV-1 quantities in milk, our data indicate intermixing of virus between blood and breast milk. Thus, we found no evidence that a restriction in viral genotype diversity in breast milk accounts for the genetic bottleneck observed following transmission. In addition, our results highlight the rapidity of HIV-1 env evolution and the importance of sample timing in analyses of gene flow.
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Campbell GR, Loret EP, Spector SA. HIV-1 clade B Tat, but not clade C Tat, increases X4 HIV-1 entry into resting but not activated CD4+ T cells. J Biol Chem 2010; 285:1681-91. [PMID: 19917610 PMCID: PMC2804326 DOI: 10.1074/jbc.m109.049957] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 11/13/2009] [Indexed: 11/06/2022] Open
Abstract
CXCR4-using human immunodeficiency virus, type 1 (HIV-1) variants emerge late in the course of infection in >40% of individuals infected with clade B HIV-1 but are described less commonly with clade C isolates. Tat is secreted by HIV-1-infected cells where it acts on both uninfected bystander cells and infected cells. In this study, we show that clade B Tat, but not clade C Tat, increases CXCR4 surface expression on resting CD4+ T cells through a CCR2b-dependent mechanism that does not involve de novo protein synthesis. The expression of plectin, a cytolinker protein that plays an important role as a scaffolding platform for proteins involved in cellular signaling including CXCR4 signaling and trafficking, was found to be significantly increased following B Tat but not C Tat treatment. Knockdown of plectin using RNA interference showed that plectin is essential for the B Tat-induced translocation of CXCR4 to the surface of resting CD4+ T cells. The increased surface CXCR4 expression following B Tat treatment led to increased function of CXCR4 including increased chemoattraction toward CXCR4-using-gp120. Moreover, increased CXCR4 surface expression rendered resting CD4+ T cells more permissive to X4 but not R5 HIV-1 infection. However, neither B Tat nor C Tat was able to up-regulate surface expression of CXCR4 on activated CD4+ T cells, and both proteins inhibited the infection of activated CD4+ T cells with X4 but not R5 HIV-1. Thus, B Tat, but not C Tat, has the capacity to render resting, but not activated, CD4+ T cells more susceptible to X4 HIV-1 infection.
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Affiliation(s)
- Grant R. Campbell
- From the Department of Pediatrics, Division of Infectious Diseases, University of California San Diego, La Jolla, California 92093-0672
| | - Erwann P. Loret
- INSERM U911, Faculté de Pharmacie, Université de la Méditerranée, 13385 Marseille Cedex 5, France
| | - Stephen A. Spector
- From the Department of Pediatrics, Division of Infectious Diseases, University of California San Diego, La Jolla, California 92093-0672
- Rady Children's Hospital, San Diego, California 92123, and
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31
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Singh A, Page T, Moore PL, Allgaier RL, Hiramen K, Coovadia HM, Walker BD, Morris L, Ndung’u T. Functional and genetic analysis of coreceptor usage by dualtropic HIV-1 subtype C isolates. Virology 2009; 393:56-67. [PMID: 19695656 PMCID: PMC3492694 DOI: 10.1016/j.virol.2009.07.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2009] [Revised: 05/19/2009] [Accepted: 07/15/2009] [Indexed: 11/25/2022]
Abstract
It is widely documented that a complete switch from the predominant CCR5 (R5) to CXCR4 (X4) phenotype is less common for HIV-1 subtype C (HIV-1C) compared to other major subtypes. We investigated whether dualtropic HIV-1C isolates represented dualtropic, mixed R5 and X4 clones or both. Thirty of 35 functional HIV-1 env clones generated by bulk PCR amplification from peripheral blood mononuclear cells (PBMCs) infected with seven dualtropic HIV-1C isolates utilized CXCR4 exclusively. Five of 35 clones displayed dualtropism. Endpoint dilution of one isolate did not yield a substantial proportion of R5-monotropic env clones. Sequence-based predictive algorithms showed that env sequences from PBMCs, CXCR4 or CCR5-expressing cell lines were indistinguishable and all possessed X4/dualtropic characteristics. We describe HIV-1C CXCR4-tropic env sequence features. Our results suggest a dramatic loss of CCR5 monotropism as dualtropism emerges in HIV-1C which has important implications for the use of coreceptor antagonists in therapeutic strategies for this subtype.
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MESH Headings
- Amino Acid Sequence
- Cells, Cultured
- Cluster Analysis
- DNA, Viral/chemistry
- DNA, Viral/genetics
- HIV-1/classification
- HIV-1/genetics
- HIV-1/physiology
- Humans
- Leukocytes, Mononuclear/virology
- Molecular Sequence Data
- Phylogeny
- Polymerase Chain Reaction/methods
- Receptors, CCR5/analysis
- Receptors, CXCR5/analysis
- Receptors, HIV/analysis
- Receptors, HIV/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology
- Virus Internalization
- env Gene Products, Human Immunodeficiency Virus/genetics
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Affiliation(s)
- Ashika Singh
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
| | - Taryn Page
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
| | - Penny L. Moore
- AIDS Virus Research Unit, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
| | - Rachel L. Allgaier
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
- Ragon Institute of MGH, MIT and Harvard, Charlestown, MA, USA
| | - Keshni Hiramen
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
| | - Hoosen M. Coovadia
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
- Department of Paediatrics and Child Heath, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
| | - Bruce D. Walker
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
- Ragon Institute of MGH, MIT and Harvard, Charlestown, MA, USA
| | - Lynn Morris
- AIDS Virus Research Unit, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
| | - Thumbi Ndung’u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
- Ragon Institute of MGH, MIT and Harvard, Charlestown, MA, USA
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32
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Heterosexual transmission of human immunodeficiency virus type 1 subtype C: Macrophage tropism, alternative coreceptor use, and the molecular anatomy of CCR5 utilization. J Virol 2009; 83:8208-20. [PMID: 19515785 DOI: 10.1128/jvi.00296-09] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Human immunodeficiency virus type 1 transmission selects for virus variants with genetic characteristics distinct from those of donor quasispecies, but the biological factors favoring their transmission or establishment in new hosts are poorly understood. We compared primary target cell tropisms and entry coreceptor utilizations of donor and recipient subtype C Envs obtained near the time of acute infection from Zambian heterosexual transmission pairs. Both donor and recipient Envs demonstrated only modest macrophage tropism, and there was no overall difference between groups in macrophage or CD4 T-cell infection efficiency. Several individual pairs showed donor/recipient differences in primary cell infection, but these were not consistent between pairs. Envs had surprisingly broad uses of GPR15, CXCR6, and APJ, but little or no use of CCR2b, CCR3, CCR8, GPR1, and CXCR4. Donors overall used GPR15 better than did recipients. However, while several individual pairs showed donor/recipient differences for GPR15 and/or other coreceptors, the direction of the differences was inconsistent, and several pairs had unique alternative coreceptor patterns that were conserved across the transmission barrier. CCR5/CCR2b chimeras revealed that recipients as a group were more sensitive than were donors to replacement of the CCR5 extracellular loops with corresponding regions of CCR2b, but significant differences in this direction were not consistent within pairs. These data show that sexual transmission does not select for enhanced macrophage tropism, nor for preferential use of any alternative coreceptor. Recipient Envs are somewhat more constrained than are donors in flexibility of CCR5 use, but this pattern is not universal for all pairs, indicating that it is not an absolute requirement.
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33
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Impact of HIV-1 viral subtype on CD4+ T-cell decline and clinical outcomes in antiretroviral naive patients receiving universal healthcare. AIDS 2009; 23:731-7. [PMID: 19279446 DOI: 10.1097/qad.0b013e328326f77f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The influence of viral subtype on the natural history of HIV is unclear and confounded by socioeconomic and host factors that vary between groups harboring different clades. We compared Canadians (clade B), with recent immigrants from Haiti (clade B) and sub-Saharan Africa (clades non-B) to determine whether there were differences in disease progression attributable to viral subtype. METHODS We conducted a retrospective cohort study in a universal healthcare setting between 1996 and 2007. The rate of CD4+ T-lymphocyte decline prior to initiation of antiretroviral therapy was determined in all participants with at least two CD4+ T-lymphocyte measures using mixed linear regression models. Time to first AIDS-defining illness was compared using adjusted Cox proportional hazards models. RESULTS Two hundred and eighty-nine Canadians, 44 Haitians, and 123 Africans were studied for a median of 260 days (2 days-11 years). Africans and Haitians were demographically and clinically similar. However, the adjusted slope of square root CD4+ T-lymphocyte decline was significantly lower in Africans [-0.04/year; 95% confidence interval (CI) = -0.08 to -0.003] compared with Canadians (-0.07/year; 95% CI = -0.11 to -0.03; P = 0.02), and Haitians (-0.10/year; 95% CI = -0.12 to -0.07; P = 0.001). Africans were also less likely to develop AIDS. CONCLUSION Despite having similar demographic, socioeconomic, and nutritional status to Haitians, Africans infected with non-B clade HIV had slower rates of disease progression compared with both Haitians and Canadians, with both groups being infected by the clade B virus. Our findings suggest that viral subtype may be an important predictor of HIV natural history in a developed medical setting.
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Lynch RM, Shen T, Gnanakaran S, Derdeyn CA. Appreciating HIV type 1 diversity: subtype differences in Env. AIDS Res Hum Retroviruses 2009; 25:237-48. [PMID: 19327047 DOI: 10.1089/aid.2008.0219] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) group M is responsible for the current AIDS pandemic and exhibits exceedingly high levels of viral genetic diversity around the world, necessitating categorization of viruses into distinct lineages, or subtypes. These subtypes can differ by around 35% in the envelope (Env) glycoproteins of the virus, which are displayed on the surface of the virion and are targets for both neutralizing antibody and cell-mediated immune responses. This diversity reflects the remarkable ability of the virus to adapt to selective pressures, the bulk of which is applied by the host immune response, and represents a serious obstacle for developing an effective vaccine with broad coverage. Thus, it is important to understand the underlying biological consequences of intersubtype diversity. Recent studies have revealed that some of the HIV-1 subtypes exhibit phenotypic differences stemming from subtle changes in Env structure, particularly within the highly immunogenic V3 domain, which participates directly in viral entry. This review will therefore explore current research that describes subtype differences in Env at the genetic and phenotypic level, focusing in particular on V3, and highlighting recent discoveries about the unique features of subtype C Env, which is the most globally prevalent subtype.
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Affiliation(s)
- Rebecca M. Lynch
- Immunology and Molecular Pathogenesis Program, Emory University, Atlanta, Georgia 30329
| | - Tongye Shen
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - S. Gnanakaran
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Cynthia A. Derdeyn
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia 30329
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329
- Emory Vaccine Center, Emory University, Atlanta, Georgia 30329
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35
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Soares MA. Drug resistance differences among HIV types and subtypes: a growing problem. ACTA ACUST UNITED AC 2008. [DOI: 10.2217/17469600.2.6.579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Although HIV-1 subtype B accounts for only 10% of worldwide HIV infections, almost all knowledge regarding antiretroviral (ARV) drug development and viral resistance is based on this subtype. More recently, an increasing body of evidence suggests that distinct HIV genetic variants possess different biological properties, including susceptibility and response to ARVs. In this review, we will summarize recent in vitro and in vivo studies reporting such differences. In general terms, infections with most HIV variants respond well to ARVs, but minor differences in susceptibility, in the emergence and selection of subtype-specific drug resistance mutations and in the acquisition of similar mutations over the period of ARV exposure have been reported. Such differences impact on drugresistance interpretation algorithms, which are mostly based on inference from sequence information. Despite the differences observed, clinical response to ARV therapy among subjects infected with distinct HIV variants is effective, and the dissemination of ARV access in developing countries where non-B subtypes prevail should not be delayed.
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Affiliation(s)
- Marcelo A Soares
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Divisão de Genética, Instituto Nacional de Câncer CCS, Bloco A, sala A2–120, Cidade Universitária, Ilha do Fundão, 21949-570, Rio de Janeiro, Brazil
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36
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Evolution of proviral gp120 over the first year of HIV-1 subtype C infection. Virology 2008; 383:47-59. [PMID: 18973914 DOI: 10.1016/j.virol.2008.09.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2008] [Revised: 07/14/2008] [Accepted: 09/11/2008] [Indexed: 11/21/2022]
Abstract
The evolution of proviral gp120 during the first year after seroconversion in HIV-1 subtype C infection was addressed in a case series of eight subjects. Multiple viral variants were found in two out of eight cases. Slow rate of viral RNA decline and high early viral RNA set point were associated with a higher level of proviral diversity from 0 to 200 days after seroconversion. Proviral divergence from MRCA over the same period also differed between subjects with slow and fast decline of viral RNA, suggesting that evolution of proviral gp120 early in infection may be linked to the level of viral RNA replication. Changes in the length of variable loops were minimal, and length reduction was more common than length increase. Potential N-linked glycosylation sites ranged +/-one site, showing common fluctuations in the V4 and V5 loops. These results highlight the role of proviral gp120 diversity and diversification in the pathogenesis of acute HIV-1 subtype C infection.
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37
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Michler K, Connell BJ, Venter WD, Stevens WS, Capovilla A, Papathanasopoulos MA. Genotypic characterization and comparison of full-length envelope glycoproteins from South African HIV type 1 subtype C primary isolates that utilize CCR5 and/or CXCR4. AIDS Res Hum Retroviruses 2008; 24:743-51. [PMID: 18507530 DOI: 10.1089/aid.2007.0304] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
CCR5 has preferentially been used by all circulating HIV-1 subtype C viruses for cell entry. Recently, we reported the highest proportion of CXCR4-utilizing primary isolates among a cohort of 20 South African AIDS patients. This study describes and compares the Env genotypic characteristics from these 20 HIV-1 subtype C (and unique CD recombinant) primary isolates. Fourteen primary isolates utilized CCR5, four (including the CD recombinant) used CXCR4, and two were dual tropic. Extensive analysis and comparison of important structural motifs such as the N-linked glycosylation sites, signal sequences, CD4-binding sites, variable loops, cleavage sites, known neutralizing antibody and small molecule inhibitor binding sites confirmed that other than the expected differences in the V3 loop, no sequence motifs distinguished between R5 and X4 tropism. Further correlation of the env genotype to functionally relevant motifs is necessary to elucidate the relationship between biologically and immunologically relevant sites and aid vaccine and novel drug design.
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Affiliation(s)
- Katherine Michler
- HIV Pathogenesis Research Laboratory, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, Parktown, Johannesburg, 2193, South Africa
| | - Bridgette J. Connell
- HIV Pathogenesis Research Laboratory, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, Parktown, Johannesburg, 2193, South Africa
| | - Willem D.F. Venter
- Reproductive Health and HIV Research Unit, University of the Witwatersrand Medical School, Parktown, Johannesburg, 2193, South Africa
| | - Wendy S. Stevens
- HIV Pathogenesis Research Laboratory, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, Parktown, Johannesburg, 2193, South Africa
| | - Alexio Capovilla
- HIV Pathogenesis Research Laboratory, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, Parktown, Johannesburg, 2193, South Africa
| | - Maria A. Papathanasopoulos
- HIV Pathogenesis Research Laboratory, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, Parktown, Johannesburg, 2193, South Africa
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Abstract
This study investigated the genotype and phenotype of HIV-1 isolates of 20 South African AIDS patients. We found the highest percentage of CXCR4 usage among primary isolates, in which 30% efficiently utilized CXCR4 and exhibited the syncytium-inducing phenotype. Phylogenetic analysis of env confirmed that 19 of the 20 were subtype C, and syncytium-inducing viruses had genetic changes in the V3 loop, characteristic of CXCR4 usage. Results imply that the frequency of CXCR4-utilizing subtype C is increasing with time.
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Clade-specific differences in neurotoxicity of human immunodeficiency virus-1 B and C Tat of human neurons: significance of dicysteine C30C31 motif. Ann Neurol 2008; 63:366-76. [DOI: 10.1002/ana.21292] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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40
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Evaluation of eight different bioinformatics tools to predict viral tropism in different human immunodeficiency virus type 1 subtypes. J Clin Microbiol 2008; 46:887-91. [PMID: 18199789 DOI: 10.1128/jcm.01611-07] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) tropism can be assessed using phenotypic assays, but this is quite laborious, expensive, and time-consuming and can be made only in sophisticated laboratories. More accessible albeit reliable tools for testing of HIV-1 tropism are needed in view of the prompt introduction of CCR5 antagonists in clinical practice. Bioinformatics tools based on V3 sequences might help to predict HIV-1 tropism; however, most of these methods have been designed by taking only genetic information derived from HIV-1 subtype B into consideration. The aim of this study was to evaluate the performances of several genotypic tools to predict HIV-1 tropism in non-B subtypes, as data on this issue are scarce. Plasma samples were tested using a new phenotypic tropism assay (Phenoscript-tropism; Eurofins), and results were compared with estimates of coreceptor usage using eight different genotypic predictor softwares (Support Vector Machine [SVM], C4.5, C4.5 with positions 8 to 12 only, PART, Charge Rule, geno2pheno coreceptor, Position-Specific Scoring Matrix X4R5 [PSSM(X4R5)], and PSSM(sinsi)). A total of 150 samples were tested, with 115 belonging to patients infected with non-B subtypes and 35 drawn from subtype B-infected patients, which were taken as controls. When non-B subtypes were tested, the concordances between the results obtained using the phenotypic assay and distinct genotypic tools were as follows: 78.8% for SVM, 77.5% for C4.5, 82.5% for C4.5 with positions 8 to 12 only, 82.5% for PART, 82.5% for Charge Rule, 82.5% for PSSM(X4R5), 83.8% for PSSM(sinsi), and 71.3% for geno2pheno. When clade B viruses were tested, the best concordances were seen for PSSM(X4R5) (91.4%), PSSM(sinsi) (88.6%), and geno2pheno (88.6%). The sensitivity for detecting X4 variants was lower for non-B than for B viruses, especially in the case of PSSM(sinsi) (38.4% versus 100%, respectively), SVM(wetcat) (46% versus 100%, respectively), and PART (30% versus 90%, respectively). In summary, while inferences of HIV-1 coreceptor usage using genotypic tools seem to be reliable for clade B viruses, their performances are poor for non-B subtypes, in which they particularly fail to detect X4 variants.
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