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Heeregrave EJ, Thomas J, van Capel TM, de Jong EC, Pollakis G, Paxton WA. Glycan dependent phenotype differences of HIV-1 generated from macrophage versus CD4 + T helper cell populations. Front Immunol 2023; 14:1107349. [PMID: 37415979 PMCID: PMC10320205 DOI: 10.3389/fimmu.2023.1107349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 06/06/2023] [Indexed: 07/08/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) is able to infect a variety of cell types with differences in entry efficiency and replication kinetics determined by the host cell type or the viral phenotype. The phenotype of the virus produced from these various cell types, including infectivity, co-receptor usage and neutralisation sensitivity, may also be affected by the characteristics of the producing cell. This can be due to incorporation of variant cell-specific molecules or differences in post-translational modifications of the gp41/120 envelope. In this study we produced genetically identical virus strains from macrophages, CD4-enriched lymphocytes as well as Th1 and Th2 CD4+ cell lines and compared each different virus stock for their infectivity in various cell types and sensitivity to neutralisation. In order to study the effect of the producer host cell on the virus phenotype, virus stocks were normalised on infectivity and were sequenced to confirm env gene homogeneity. Virus production by Th1 or Th2 cells did not compromise infectivity of the variant cell types tested. We observed no difference in sensitivity to co-receptor blocking agents upon viral passage through Th1 and Th2 CD4+ cell lineages nor did this affect DC-SIGN-mediated viral capture as measured in a transfer assay to CD4+ lymphocytes. Virus produced by macrophages was comparably sensitive to CC-chemokine inhibition as was virus generated from the array of CD4+ lymphocytes. We identified that virus produced from macrophages was fourteen times more resistant to 2G12 neutralisation than virus produced from CD4+ lymphocytes. Macrophage-produced dual-tropic (R5/X4) virus was six times more efficiently transmitted to CD4+ cells than lymphocyte-derived HIV-1 (p<0.0001) after DCSIGN capture. These results provide further insights to what extent the host cell influences viral phenotype and thereby various aspects of HIV-1 pathogenesis but suggest that viruses generated from Th1 versus Th2 cells are consistent in phenotype.
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Affiliation(s)
- Edwin J. Heeregrave
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Toni M. van Capel
- Department of Experimental Immunology, University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Esther C. de Jong
- Department of Experimental Immunology, University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Georgios Pollakis
- Department of Experimental Immunology, University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - William A. Paxton
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Clinical Infection, Microbiology and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
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MAVS Genetic Variation Is Associated with Decreased HIV-1 Replication In Vitro and Reduced CD4 + T Cell Infection in HIV-1-Infected Individuals. Viruses 2020; 12:v12070764. [PMID: 32708557 PMCID: PMC7412276 DOI: 10.3390/v12070764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 02/07/2023] Open
Abstract
The mitochondrial antiviral protein MAVS is a key player in the induction of antiviral responses; however, human immunodeficiency virus 1 (HIV-1) is able to suppress these responses. Two linked single nucleotide polymorphisms (SNPs) in the MAVS gene render MAVS insensitive to HIV-1-dependent suppression, and have been shown to be associated with a lower viral load at set point and delayed increase of viral load during disease progression. Here, we studied the underlying mechanisms involved in the control of viral replication in individuals homozygous for this MAVS genotype. We observed that individuals with the MAVS minor genotype had more stable total CD4+ T cell counts during a 7-year follow up and had lower cell-associated proviral DNA loads. Genetic variation in MAVS did not affect immune activation levels; however, a significantly lower percentage of naïve CD4+ but not CD8+ T cells was observed in the MAVS minor genotype. In vitro HIV-1 infection of peripheral blood mononuclear cells (PBMCs) from healthy donors with the MAVS minor genotype resulted in decreased viral replication. Although the precise underlying mechanism remains unclear, our data suggest that the protective effect of the MAVS minor genotype may be exerted by the initiation of local innate responses affecting viral replication and CD4+ T cell susceptibility.
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Abstract
PURPOSE OF REVIEW The major target groups for an HIV vaccine include breastfeeding infants and adolescents. Differential immune maturity in these age groups may significantly impact vaccine efficacy, and should be taken into account when developing vaccines. Here we review these differences, with an emphasis on the immune response to vaccines for HIV and other pathogens. Recommendations for potential adaptation of current HIV vaccines are also made. RECENT FINDINGS An effective neonatal vaccine needs to be immunogenic in the presence of maternal antibody, and must induce cytotoxic T-lymphocyte responses, neutralizing antibody responses, both systemic and mucosal. There is renewed hope in the possibility of stimulating neutralizing antibodies with HIV vaccination. DNA vaccines are promising for neonates, but will need appropriate boosting. Certain adjuvants and vector delivery systems are more suitable for neonates. Adolescents may have stronger immune responses to HIV vaccines than adults, and will also require induction of mucosal neutralizing humoral and cellular immunity. SUMMARY Some current HIV vaccine strategies may need adaptation for neonates and suitable product development should be accelerated. Vaccines could induce better responses in adolescents and therefore should not be discarded prematurely. Development of vaccines that have potential for these age groups is an urgent global priority.
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Wang W, Qiu C, Qiu C, Wang Y, Zhang X, Xu J. Development of skewed functionality of HIV-1-specific cytotoxic CD8(+) T cells from primary to early chronic phase of HIV infection. PLoS One 2012; 7:e44983. [PMID: 23028721 PMCID: PMC3441698 DOI: 10.1371/journal.pone.0044983] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 08/15/2012] [Indexed: 11/18/2022] Open
Abstract
In recent years, the prevalence of HIV-1 infection has been rapidly increasing among men who have sex with men (MSM). However, it remains unknown how the host immune system responds to the infection in this population. We assessed the quantity of HIV-specific CD8+ T-cell responses by using Elispot assay and their functionalities by measuring 5 CD8+ T-cell evaluations (IL-2, MIP-1β, CD107a, TNF-α, IFN-γ) with flow cytometry assays among 18 primarily and 37 early chronically HIV-infected MSM. Our results demonstrated that subjects at early chronic phase developed HIV-specific CD8+ T-cell responses with higher magnitudes and more diversified functionalities in comparison with those at primary infection. However, populations with IL-2+ CD107a+ or in combination with other functionality failed to develop in parallel. The multifunctional but not monofunctional HIV-specific CD8+ T cells were associated with higher CD4+ T -cell counts and lower viral loads. These data revealed that prolonged infection from primary to early chronic infection could selectively increase the functionalities of HIV-specific CD8+ T cells in HIV-infected MSM population, the failure to develop IL-2 and cytotoxic functionalities in parallel may explain why the increased HIV-specific CD8+ T cells were unable to enhance the containment of HIV-1 replication at the early chronic stage.
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Affiliation(s)
- Wanhai Wang
- Shanghai Public Health Clinical Center, the Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai, China
| | - Chenli Qiu
- Shanghai Public Health Clinical Center, the Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai, China
| | - Chao Qiu
- Shanghai Public Health Clinical Center, the Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai, China
| | - Ying Wang
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center, the Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai, China
- State Key Laboratory for Infectious Disease Prevention and Control, China CDC, Beijing, China
- * E-mail: (JX); (XZ)
| | - Jianqing Xu
- Shanghai Public Health Clinical Center, the Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai, China
- State Key Laboratory for Infectious Disease Prevention and Control, China CDC, Beijing, China
- * E-mail: (JX); (XZ)
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5
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Cytotoxic T-lymphocyte escape mutations identified by HLA association favor those which escape and revert rapidly. J Virol 2012; 86:8568-80. [PMID: 22674992 DOI: 10.1128/jvi.07020-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Identifying human immunodeficiency virus (HIV) immune escape mutations has implications for understanding the impact of host immunity on pathogen evolution and guiding the choice of vaccine antigens. One means of identifying cytotoxic-T-lymphocyte (CTL) escape mutations is to search for statistical associations between mutations and host human leukocyte antigen (HLA) class I alleles at the population level. The impact of evolutionary rates on the strength of such associations is not well defined. Here, we address this topic using a mathematical model of within-host evolution and between-host transmission of CTL escape mutants that predicts the prevalence of escape mutants at the population level. We ask how the rates at which an escape mutation emerges in a host who bears the restricting HLA and reverts when transmitted to a host who does not bear the HLA affect the strength of an association. We consider the impact of these factors when using a standard statistical method to test for an association and when using an adaptation of that method that corrects for phylogenetic relationships. We show that with both methods, the average sample size required to identify an escape mutation is smaller if the mutation escapes and reverts quickly. Thus, escape mutations identified as HLA associated systematically favor those that escape and revert rapidly. We also present expressions that can be used to infer escape and reversion rates from cross-sectional escape prevalence data.
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Novitsky V, Wang R, Baca J, Margolin L, McLane MF, Moyo S, van Widenfelt E, Makhema J, Essex M. Evolutionary gamut of in vivo Gag substitutions during early HIV-1 subtype C infection. Virology 2011; 421:119-28. [PMID: 22014506 DOI: 10.1016/j.virol.2011.09.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/18/2011] [Accepted: 09/21/2011] [Indexed: 01/03/2023]
Abstract
Two analyses of HIV-1 subtype C Gag quasispecies were performed in a prospective cohort of 42 acutely and recently infected individuals by SGA on viral RNA/proviral DNA templates. First, in vivo Gag substitutions were assessed in relation to the HIV-1C consensus sequence, which revealed that 29.3% of detected amino acid substitutions can be classified as reversions to subtype consensus, 61.3% as forward substitutions from subtype consensus, and 9.3% as polymorphisms not associated with the subtype consensus sequence. Second, the proportion, dynamics, and relationships within individual pools of viral quasispecies were analyzed. Among reverse substitutions, 16.1% were minor, 11.0% transient, 13.6% dominant, and 59.2% fixed. In contrast, 31.6% of forward substitutions were minor, 59.3% transient, 3.8% dominant, and 5.3% fixed. The distinct patterns in the spectrum and dynamics of reverse and forward Gag substitutions suggest that these differences should be considered in HIV-1 evolutionary studies and analyses of viral mutational pathways.
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Affiliation(s)
- Vladimir Novitsky
- Harvard School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, United States
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Kadolsky UD, Asquith B. Quantifying the impact of human immunodeficiency virus-1 escape from cytotoxic T-lymphocytes. PLoS Comput Biol 2010; 6:e1000981. [PMID: 21079675 PMCID: PMC2973816 DOI: 10.1371/journal.pcbi.1000981] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Accepted: 09/28/2010] [Indexed: 11/20/2022] Open
Abstract
HIV-1 escape from the cytotoxic T-lymphocyte (CTL) response leads to a weakening of viral control and is likely to be detrimental to the patient. To date, the impact of escape on viral load and CD4+ T cell count has not been quantified, primarily because of sparse longitudinal data and the difficulty of separating cause and effect in cross-sectional studies. We use two independent methods to quantify the impact of HIV-1 escape from CTLs in chronic infection: mathematical modelling of escape and statistical analysis of a cross-sectional cohort. Mathematical modelling revealed a modest increase in log viral load of 0.051 copies ml−1 per escape event. Analysis of the cross-sectional cohort revealed a significant positive association between viral load and the number of “escape events”, after correcting for length of infection and rate of replication. We estimate that a single CTL escape event leads to a viral load increase of 0.11 log copies ml−1 (95% confidence interval: 0.040–0.18), consistent with the predictions from the mathematical modelling. Overall, the number of escape events could only account for approximately 6% of the viral load variation in the cohort. Our findings indicate that although the loss of the CTL response for a single epitope results in a highly statistically significant increase in viral load, the biological impact is modest. We suggest that this small increase in viral load is explained by the small growth advantage of the variant relative to the wildtype virus. Escape from CTLs had a measurable, but unexpectedly low, impact on viral load in chronic infection. HIV, like many viruses, has evolved multiple strategies to evade immune surveillance. One of these strategies is the evolution of escape mutations which reduce the ability of the immune response to kill HIV-infected cells. But does HIV escape matter? Some believe that the accumulation of escape mutations leads to AIDS; many more believe escape is likely to be highly detrimental to human health. Yet, to date, it has not been possible to measure the impact of escape. We developed two independent methods to quantify the impact of escape on HIV viral load. Both methods showed that escape does lead to a detectable increase in viral load, but is unlikely to have a major impact on patient health as the increase is small. Indeed, only 6% of between-individual variation in viral load could be attributed to HIV escape. This work suggests that the current research focus on escape in chronic HIV infection might be out of proportion to its importance with other factors playing a more significant role in determining viral load.
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Affiliation(s)
- Ulrich D Kadolsky
- Department of Immunology, Division of Medicine, Imperial College London, London, United Kingdom.
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Biru T, Lennemann T, Stürmer M, Stephan C, Nisius G, Cinatl J, Staszewski S, Gürtler LG. Human immunodeficiency virus type-1 group M quasispecies evolution: diversity and divergence in patients co-infected with active tuberculosis. Med Microbiol Immunol 2010; 199:323-32. [PMID: 20697741 DOI: 10.1007/s00430-010-0167-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Indexed: 10/19/2022]
Abstract
The evolution of intra-host human immunodeficiency virus type 1 (HIV-1) quasispecies prior and after treating active tuberculosis (TB) with chemotherapy in HIV-1/TB patients was assessed. Two time points HIV-1 quasispecies were evaluated by comparing HIV-1-infected patients with active tuberculosis (HIV-1/TB) and HIV-1-infected patients without tuberculosis (HIV-1/non-TB). Plasma samples were obtained from the Frankfurt HIV cohort, and HIV-1 RNA was isolated. C2V5 env was amplified by PCR and molecular cloning was performed. Eight to twenty-five clones were sequenced from each patient. Various phylogenetic analyses were performed. We found a significant increase in diversity and divergence in HIV-1/TB compared to the HIV-1/non-TB. For HIV-1/TB, the average rate of evolution of C2V5 env was higher than previous reports (2.4 × 10(-4) substitution/site/day). Two groups of HIV-1/TB were observed based on the rate of HIV-1 evolution and coreceptor usage: A fast evolving R5-tropic dominating group and a relatively slowly evolving X4 group. The results demonstrated that active TB has an impact on HIV-1 viral diversity and divergence over time. The influence of active TB on longitudinal evolution of HIV-1 may be predominant for R5 viruses.
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Affiliation(s)
- T Biru
- Institute for Medical Virology, Hospital of Johann Wolfgang Goethe University, Frankfurt am Main, Germany.
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Kopycinski J, Osman M, Griffiths PD, Emery VC. Sequence flexibility of the immunodominant HLA A*0201 restricted ppUL83 CD8 T-cell epitope of human cytomegalovirus. J Med Virol 2010; 82:94-103. [DOI: 10.1002/jmv.21668] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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10
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Heeregrave EJ, Geels MJ, Brenchley JM, Baan E, Ambrozak DR, van der Sluis RM, Bennemeer R, Douek DC, Goudsmit J, Pollakis G, Koup RA, Paxton WA. Lack of in vivo compartmentalization among HIV-1 infected naïve and memory CD4+ T cell subsets. Virology 2009; 393:24-32. [PMID: 19698967 PMCID: PMC2753733 DOI: 10.1016/j.virol.2009.07.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 06/29/2009] [Accepted: 07/13/2009] [Indexed: 11/28/2022]
Abstract
Viral compartmentalization between naïve and memory CD4(+) T cell subsets has been described, but only for individuals who were receiving antiretroviral therapy (ART). We present here an extensive analysis of the viral quasispecies residing in the naïve, central and effector memory CD4(+) T cell subsets in a number of therapy naïve individuals and representing an array of HIV-1 subtypes. We longitudinally analyzed subset-specific infection and evolution in a subtype B infected individual who switches from CCR5 to dual CCR5/CXCR4 coreceptor usage. We show that the central memory subset, the predominantly infected subset, harbors a more diverse viral population compared to the others. Through sequence analysis of the env C2V3 region we demonstrate a lack of viral compartmentalization among all subsets. Upon coreceptor switch we observe a pronounced increase in the infection level of the naïve population. Our findings emphasize the importance of all CD4(+) T cell subsets to viral evolution.
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Affiliation(s)
- Edwin J. Heeregrave
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | - Mark J. Geels
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | - Jason M. Brenchley
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, USA
| | - Elly Baan
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | - David R. Ambrozak
- Immunology Laboratory, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, USA
| | - Renee M. van der Sluis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | - Rune Bennemeer
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | - Daniel C. Douek
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, USA
| | | | - Georgios Pollakis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | - Richard A. Koup
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, USA
| | - William A. Paxton
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
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Abstract
The CTL response plays a central part in deciding the outcome of viral infections. Evidence from host and viral genetics, gene expression microarrays and assays of T-cell phenotype and function indicate that individual differences in the efficiency of the virus-specific CTL response strongly determine the outcome of infection with the human retroviruses HTLV-1 and HIV-1. It is now believed that differences in anti-viral CTL efficiency or "quality" at the single-cell level are critical in determining the efficacy of the host response to viruses. However, it is difficult to identify and quantify the reasons for this apparent individual variation in CTL efficiency, because of the chronic course of infection and the dynamical complexity of the equilibrium that is established between the virus and the host immune response. Specifically, it is unclear whether the observed variations among infected hosts, i.e. in the frequency, phenotype and function or quality of T cells, are the causes or effects - or both - of the variation in the efficiency of virus control.
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Reduced viral replication capacity of human immunodeficiency virus type 1 subtype C caused by cytotoxic-T-lymphocyte escape mutations in HLA-B57 epitopes of capsid protein. J Virol 2008; 83:2460-8. [PMID: 19109381 DOI: 10.1128/jvi.01970-08] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cytotoxic-T-lymphocyte (CTL) escape mutations in human immunodeficiency viruses encode amino acid substitutions in positions that disrupt CTL targeting, thereby increasing virus survival and conferring a relative fitness benefit. However, it is now clear that CTL escape mutations can also confer a fitness cost, and there is increasing evidence to suggest that in some cases, e.g., escape from HLA-B*57/B*5801-restricted responses, the costs to the escape virus may affect the clinical course of infection. To quantify the magnitude of the costs of HLA-B*57/B*5801 escape, a highly sensitive dual-infection assay that uses synonymous nucleotide sequence tags to quantify viral relative replication capacity (RRC) was developed. We then asked whether such CTL escape mutations had an impact equivalent to that seen for a benchmark mutation, the M184V antiretroviral drug resistance mutation of reverse transcriptase (RRC(V184) = 0.86). To answer the question, the RRCs were quantified for escape mutations in three immunodominant HLA-B*57/B*5801 epitopes in capsid: A146P in IW9 (RRC(P146) = 0.91), A163G in KF11 (RRC(G163) = 0.89), and T242N in TW10 (RRC(N242) = 0.86). Individually, the impact of the escape mutations on RRC was comparable to that of M184V, while coexpression of the mutations resulted in substantial further reductions, with the maximum impact observed for the triple mutant (RRC(P146-G163-N242) = 0.62). By comparison to M184V, the magnitude of the reductions in RRC caused by the escape mutations, particularly when coexpressed, suggests that the costs of escape are sufficient to affect in vivo viral dynamics and may thus play a role in the protective effect associated with HLA-B*57/B*5801.
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Asquith B. The evolutionary selective advantage of HIV-1 escape variants and the contribution of escape to the HLA-associated risk of AIDS progression. PLoS One 2008; 3:e3486. [PMID: 18941529 PMCID: PMC2567026 DOI: 10.1371/journal.pone.0003486] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Accepted: 10/01/2008] [Indexed: 11/19/2022] Open
Abstract
HIV-1 escape from surveillance by cytotoxic T lymphocytes (CTL) is thought to cause at least transient weakening of immune control. However, the CTL response is highly adaptable and the long-term consequences of viral escape are not fully understood. The objective of this study was to address the question “to what extent does HIV-1 escape from CTL contribute to HLA-associated AIDS progression?” We combined an analysis of 21 escape events in longitudinally-studied HIV-1 infected people with a population-level analysis of the functional CTL response in 150 subjects (by IFNg ELISpot) and an analysis of the HIV-1 sequence database to quantify the contribution of escape to the HLA-associated rate of AIDS progression. We found that CTL responses restricted by protective HLA class I alleles, which are associated with slow progression to AIDS, recognised epitopes where escape variants had a weak evolutionary selective advantage (P = 0.008) and occurred infrequently (P = 0.017). Epitopes presented by protective HLA class I alleles were more likely to elicit a CTL response (P = 0.001) and less likely to contain sequence variation (P = 0.006). A third of between-individual variation in HLA-associated disease risk was predicted by the selective advantage of escape variants: a doubling in the evolutionary selective advantage was associated with a decrease in the AIDS-free period of 1.2 yrs. These results contribute to our understanding of what makes a CTL response protective and why some individuals progress to AIDS more rapidly than others.
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Affiliation(s)
- Becca Asquith
- Department of Immunology, Imperial College London, London, United Kingdom.
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14
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Dilernia DA, Jones L, Rodriguez S, Turk G, Rubio AE, Pampuro S, Gomez-Carrillo M, Bautista C, Deluchi G, Benetucci J, Lasala MB, Lourtau L, Losso MH, Perez H, Cahn P, Salomón H. HLA-driven convergence of HIV-1 viral subtypes B and F toward the adaptation to immune responses in human populations. PLoS One 2008; 3:e3429. [PMID: 18941505 PMCID: PMC2565011 DOI: 10.1371/journal.pone.0003429] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Accepted: 09/10/2008] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Cytotoxic T-Lymphocyte (CTL) response drives the evolution of HIV-1 at a host-level by selecting HLA-restricted escape mutations. Dissecting the dynamics of these escape mutations at a population-level would help to understand how HLA-mediated selection drives the evolution of HIV-1. METHODOLOGY/PRINCIPAL FINDINGS We undertook a study of the dynamics of HIV-1 CTL-escape mutations by analyzing through statistical approaches and phylogenetic methods the viral gene gag sequenced in plasma samples collected between the years 1987 and 2006 from 302 drug-naïve HIV-positive patients. By applying logistic regression models and after performing correction for multiple test, we identified 22 potential CTL-escape mutations (p-value<0.05; q-value<0.2); 10 of these associations were confirmed in samples biologically independent by a Bayesian Markov Chain Monte-Carlo method. Analyzing their prevalence back in time we found that escape mutations that are the consensus residue in samples collected after 2003 have actually significantly increased in time in one of either B or F subtype until becoming the most frequent residue, while dominating the other viral subtype. Their estimated prevalence in the viral subtype they did not dominate was lower than 30% for the majority of samples collected at the end of the 80's. In addition, when screening the entire viral region, we found that the 75% of positions significantly changing in time (p<0.05) were located within known CTL epitopes. CONCLUSIONS Across HIV Gag protein, the rise of polymorphisms from independent origin during the last twenty years of epidemic in our setting was related to an association with an HLA allele. The fact that these mutations accumulated in one of either B or F subtypes have also dominated the other subtype shows how this selection might be causing a convergence of viral subtypes to variants which are more likely to evade the immune response of the population where they circulate.
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Affiliation(s)
- Dario Alberto Dilernia
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Leandro Jones
- Estación de fotobiología “Playa Unión”, Rawson, Chubut, Argentina
| | - Sabrina Rodriguez
- Instituto de Virologia, Centro de Investigación en Ciencias Veterinarias y Agronómicas, INTA-Castelar, Castelar, Buenos Aires, Argentina
| | - Gabriela Turk
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Andrea E. Rubio
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Sandra Pampuro
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Manuel Gomez-Carrillo
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Christian Bautista
- Instituto de Medicina Tropical “Daniel A. Carrión”, Universidad Nacional Mayor San Marcos, Lima, Peru
| | - Gabriel Deluchi
- Departamento de Enfermedades Infecciosas, Hospital de Enfermedades Infecciosas “Francisco Javier Muñiz”, Capital Federal, Buenos Aires, Argentina
| | - Jorge Benetucci
- Departamento de Enfermedades Infecciosas, Hospital de Enfermedades Infecciosas “Francisco Javier Muñiz”, Capital Federal, Buenos Aires, Argentina
| | - María Beatriz Lasala
- División de Infectología, Hospital de Clínicas “José de San Martín”, Capital Federal, Buenos Aires, Argentina
| | - Leonardo Lourtau
- Servicio de Inmunocomprometidos, Hospital General de Agudos “Jose Maria Ramos Mejia”, Capital Federal, Buenos Aires, Argentina
| | - Marcelo Horacio Losso
- Servicio de Inmunocomprometidos, Hospital General de Agudos “Jose Maria Ramos Mejia”, Capital Federal, Buenos Aires, Argentina
| | - Héctor Perez
- Unidad de Enfermedades Infecciosas, Hospital General de Agudos “Juan A. Fernandez”, Capital Federal, Buenos Aires, Argentina
| | - Pedro Cahn
- Unidad de Enfermedades Infecciosas, Hospital General de Agudos “Juan A. Fernandez”, Capital Federal, Buenos Aires, Argentina
- Fundación Huesped, Capital Federal, Buenos Aires, Argentina
| | - Horacio Salomón
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
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Structural and functional constraints limit options for cytotoxic T-lymphocyte escape in the immunodominant HLA-B27-restricted epitope in human immunodeficiency virus type 1 capsid. J Virol 2008; 82:5594-605. [PMID: 18385228 DOI: 10.1128/jvi.02356-07] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Control of human immunodeficiency virus type 1 (HIV-1) by HLA-B27-positive subjects has been linked to an immunodominant CD8(+) cytotoxic T-lymphocyte (CTL) response targeting the conserved KK10 epitope (KRWIILGLNK(263-272)) in p24/Gag. Viral escape in KK10 typically occurs through development of an R(264)K substitution in conjunction with the upstream compensatory mutation S(173)A, and the difficulty of the virus to escape from the immune response against the KK10 epitope until late in infection has been associated with slower clinical progression. Rare alternative escape mutations at R(264) have been observed, but factors dictating the preferential selection of R(264)K remain unclear. Here we illustrate that while all observed R(264) mutations (K, G, Q, and T) reduced peptide binding to HLA-B27 and impaired viral replication, the replicative defects of the alternative mutants were actually less pronounced than those for R(264)K. Importantly, however, none of these mutants replicated as well as an R(264)K variant containing the compensatory mutation S(173)A. In assessing the combined effects of viral replication and CTL escape using an in vitro coculture assay, we further observed that the compensated R(264)K mutant also displayed the highest replication capacity in the presence of KK10-specific CTLs. Comparisons of codon usage for the respective variants indicated that generation of the R(264)K mutation may also be favored due to a G-to-A bias in nucleotide substitutions during HIV-1 replication. Together, these data suggest that the preference for R(264)K is due primarily to the ability of the S(173)A-compensated virus to replicate better than alternative variants in the presence of CTLs, suggesting that viral fitness is a key contributor for the selection of immune escape variants.
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Daucher M, Price DA, Brenchley JM, Lamoreaux L, Metcalf JA, Rehm C, Nies-Kraske E, Urban E, Yoder C, Rock D, Gumkowski J, Betts MR, Dybul MR, Douek DC. Virological outcome after structured interruption of antiretroviral therapy for human immunodeficiency virus infection is associated with the functional profile of virus-specific CD8+ T cells. J Virol 2008; 82:4102-14. [PMID: 18234797 PMCID: PMC2292997 DOI: 10.1128/jvi.02212-07] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Accepted: 01/19/2008] [Indexed: 12/11/2022] Open
Abstract
A clear understanding of the antiviral effects of CD8(+) T cells in the context of chronic human immunodeficiency virus (HIV) infection is critical for the development of prophylactic vaccines and therapeutics designed to support T-cell-mediated immunity. However, defining the potential correlates of effective CD8(+) T-cell immunity has proven difficult; notably, comprehensive analyses have demonstrated that the size and shape of the CD8(+) T-cell response are not necessarily indicative of efficacy determined by measures of plasma viral load. Here, we conducted a detailed quantitative and qualitative analysis of CD8(+) T-cell responses to autologous virus in a cohort of six HIV-infected individuals with a history of structured interruption of antiretroviral therapy (ART) (SIT). The magnitude and breadth of the HIV-specific response did not, by themselves, explain the changes observed in plasma virus levels after the cessation of ART. Furthermore, mutational escape from targeted epitopes could not account for the differential virological outcomes in this cohort. However, the functionality of HIV-specific CD8(+) T-cell populations upon antigen encounter, determined by the simultaneous and independent measurement of five CD8(+) T-cell functions (degranulation and gamma interferon, macrophage inflammatory protein 1beta, tumor necrosis factor alpha, and interleukin-2 levels) reflected the emergent level of plasma virus, with multiple functions being elicited in those individuals with lower levels of viremia after SIT. These data show that the quality of the HIV-specific CD8(+) T-cell response, rather than the quantity, is associated with the dynamics of viral replication in the absence of ART and suggest that the effects of SIT can be assessed by measuring the functional profile of HIV-specific CD8(+) T cells.
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Affiliation(s)
- Marybeth Daucher
- National Institute of Allergy and Infectious Diseases, Bldg. 10/Rm. 11B13, Bethesda, MD 20892, USA.
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18
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Alimonti JB, Kimani J, Matu L, Wachihi C, Kaul R, Plummer FA, Fowke KR. Characterization of CD8 T-cell responses in HIV-1-exposed seronegative commercial sex workers from Nairobi, Kenya. Immunol Cell Biol 2006; 84:482-5. [PMID: 16942489 DOI: 10.1111/j.1440-1711.2006.01455.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CD8+ T-lymphocyte responses are crucial to the control of HIV-1; therefore, studying the CD8+ immune response in a naturally resistant population could provide valuable insights into an effective anti-HIV response in healthy uninfected individuals. Approximately 5-10% of the women in the Pumwani Commercial Sex Worker cohort in Nairobi, Kenya, have been highly exposed to HIV-1 yet remain HIV-IgG-seronegative and HIV-PCR negative (HIV(ES)). As IFN-gamma production correlates to cytotoxic function, the CD8+ T-lymphocyte IFN-gamma response to HIV p24 peptides was compared in HIV(ES) and HIV-infected (HIV+) individuals. Almost 40% of the HIV(ES) had a CD8+ IFN-gamma+ response that was five times lower in magnitude than that of the HIV+ group. The breadth of the response in HIV(ES) was very narrow and focused primarily on one peptide that is similar to the protective KK10 peptide. In the HIV+ group, low peripheral CD4+ counts negatively influenced the number of CD8+ cells producing IFN-gamma, which may undermine the ability to control HIV. Overall, many of the HIV(ES) women possess a HIV-1 p24-specific CD8+ IFN-gamma response, providing evidence to the specificity needed for an effective HIV vaccine.
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Affiliation(s)
- Judie B Alimonti
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
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Li B, Gladden AD, Altfeld M, Kaldor JM, Cooper DA, Kelleher AD, Allen TM. Rapid reversion of sequence polymorphisms dominates early human immunodeficiency virus type 1 evolution. J Virol 2006; 81:193-201. [PMID: 17065207 PMCID: PMC1797245 DOI: 10.1128/jvi.01231-06] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The error-prone replication of human immunodeficiency virus type 1 (HIV-1) enables it to continuously evade host CD8+ T-cell responses. The observed transmission, and potential accumulation, of CD8+ T-cell escape mutations in the population may suggest a gradual adaptation of HIV-1 to immune pressures. Recent reports, however, have highlighted the propensity of some escape mutations to revert upon transmission to a new host in order to restore efficient replication capacity. To more specifically address the role of reversions in early HIV-1 evolution, we examined sequence polymorphisms arising across the HIV-1 genome in seven subjects followed longitudinally 1 year from primary infection. As expected, numerous nonsynonymous mutations were associated with described CD8+ T-cell epitopes, supporting a prominent role for cellular immune responses in driving early HIV-1 evolution. Strikingly, however, a substantial proportion of substitutions (42%) reverted toward the clade B consensus sequence, with nearly one-quarter of them located within defined CD8 epitopes not restricted by the contemporary host's HLA. More importantly, these reversions arose significantly faster than forward mutations, with the most rapidly reverting mutations preferentially arising within structurally conserved residues. These data suggest that many transmitted mutations likely incur a fitness cost that is recovered through retrieval of an optimal, or ancestral, form of the virus. The propensity of mutations to revert may limit the accumulation of immune pressure-driven mutations in the population, thus preserving critical CD8+ T-cell epitopes as vaccine targets, and argue against an unremitting adaptation of HIV-1 to host immune pressures.
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Affiliation(s)
- Bin Li
- Partners AIDS Research Center, MGH-East, CNY 6616, 149 13th Street, Charlestown, MA 02129, USA
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