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Smyth M, Khamina K, Popa A, Gudipati V, Agerer B, Lercher A, Kosack L, Endler L, Baazim H, Viczenczova C, Huppa JB, Bergthaler A. Characterization of CD8 T Cell-Mediated Mutations in the Immunodominant Epitope GP33-41 of Lymphocytic Choriomeningitis Virus. Front Immunol 2021; 12:638485. [PMID: 34194424 PMCID: PMC8236698 DOI: 10.3389/fimmu.2021.638485] [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: 12/06/2020] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Cytotoxic T lymphocytes (CTLs) represent key immune effectors of the host response against chronic viruses, due to their cytotoxic response to virus-infected cells. In response to this selection pressure, viruses may accumulate escape mutations that evade CTL-mediated control. To study the emergence of CTL escape mutations, we employed the murine chronic infection model of lymphocytic choriomeningitis virus (LCMV). We developed an amplicon-based next-generation sequencing pipeline to detect low frequency mutations in the viral genome and identified non-synonymous mutations in the immunodominant LCMV CTL epitope, GP33-41, in infected wildtype mice. Infected Rag2-deficient mice lacking CTLs did not contain such viral mutations. By using transgenic mice with T cell receptors specific to GP33-41, we characterized the emergence of viral mutations in this epitope under varying selection pressure. We investigated the two most abundant viral mutations by employing reverse genetically engineered viral mutants encoding the respective mutations. These experiments provided evidence that these mutations prevent activation and expansion of epitope-specific CD8 T cells. Our findings on the mutational dynamics of CTL escape mutations in a widely-studied viral infection model contributes to our understanding of how chronic viruses interact with their host and evade the immune response. This may guide the development of future treatments and vaccines against chronic infections.
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Affiliation(s)
- Mark Smyth
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kseniya Khamina
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexandra Popa
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Venugopal Gudipati
- Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Benedikt Agerer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexander Lercher
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lindsay Kosack
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lukas Endler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Hatoon Baazim
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Csilla Viczenczova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Johannes B Huppa
- Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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Ayala VI, Trivett MT, Barsov EV, Jain S, Piatak M, Trubey CM, Alvord WG, Chertova E, Roser JD, Smedley J, Komin A, Keele BF, Ohlen C, Ott DE. Adoptive Transfer of Engineered Rhesus Simian Immunodeficiency Virus-Specific CD8+ T Cells Reduces the Number of Transmitted/Founder Viruses Established in Rhesus Macaques. J Virol 2016; 90:9942-9952. [PMID: 27558423 PMCID: PMC5068542 DOI: 10.1128/jvi.01522-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 08/18/2016] [Indexed: 01/16/2023] Open
Abstract
AIDS virus infections are rarely controlled by cell-mediated immunity, in part due to viral immune evasion and immunodeficiency resulting from CD4+ T-cell infection. One likely aspect of this failure is that antiviral cellular immune responses are either absent or present at low levels during the initial establishment of infection. To test whether an extensive, timely, and effective response could reduce the establishment of infection from a high-dose inoculum, we adoptively transferred large numbers of T cells that were molecularly engineered with anti-simian immunodeficiency virus (anti-SIV) activity into rhesus macaques 3 days following an intrarectal SIV inoculation. To measure in vivo antiviral activity, we assessed the number of viruses transmitted using SIVmac239X, a molecularly tagged viral stock containing 10 genotypic variants, at a dose calculated to transmit 12 founder viruses. Single-genome sequencing of plasma virus revealed that the two animals receiving T cells expressing SIV-specific T-cell receptors (TCRs) had significantly fewer viral genotypes than the two control animals receiving non-SIV-specific T cells (means of 4.0 versus 7.5 transmitted viral genotypes; P = 0.044). Accounting for the likelihood of transmission of multiple viruses of a particular genotype, the calculated means of the total number of founder viruses transmitted were 4.5 and 14.5 in the experimental and control groups, respectively (P = 0.021). Thus, a large antiviral T-cell response timed with virus exposure can limit viral transmission. The presence of strong, preexisting T-cell responses, including those induced by vaccines, might help prevent the establishment of infection at the lower-exposure doses in humans that typically transmit only a single virus. IMPORTANCE The establishment of AIDS virus infection in an individual is essentially a race between the spreading virus and host immune defenses. Cell-mediated immune responses induced by infection or vaccination are important contributors in limiting viral replication. However, in human immunodeficiency virus (HIV)/SIV infection, the virus usually wins the race, irreversibly crippling the immune system before an effective cellular immune response is developed and active. We found that providing an accelerated response by adoptively transferring large numbers of antiviral T cells shortly after a high-dose mucosal inoculation, while not preventing infection altogether, limited the number of individual viruses transmitted. Thus, the presence of strong, preexisting T-cell responses, including those induced by vaccines, might prevent infection in humans, where the virus exposure is considerably lower.
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Affiliation(s)
- Victor I Ayala
- AIDS and Cancer Virus Program and Laboratory Animal Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Matthew T Trivett
- AIDS and Cancer Virus Program and Laboratory Animal Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Eugene V Barsov
- AIDS and Cancer Virus Program and Laboratory Animal Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Sumiti Jain
- AIDS and Cancer Virus Program and Laboratory Animal Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Michael Piatak
- AIDS and Cancer Virus Program and Laboratory Animal Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Charles M Trubey
- AIDS and Cancer Virus Program and Laboratory Animal Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - W Gregory Alvord
- DMS Applied Information & Management Sciences, Frederick National Laboratory for Cancer Research, Maryland, USA
| | - Elena Chertova
- AIDS and Cancer Virus Program and Laboratory Animal Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - James D Roser
- AIDS and Cancer Virus Program and Laboratory Animal Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jeremy Smedley
- AIDS and Cancer Virus Program and Laboratory Animal Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Alexander Komin
- AIDS and Cancer Virus Program and Laboratory Animal Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program and Laboratory Animal Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Claes Ohlen
- AIDS and Cancer Virus Program and Laboratory Animal Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - David E Ott
- AIDS and Cancer Virus Program and Laboratory Animal Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
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van Dorp CH, van Boven M, de Boer RJ. Immuno-epidemiological modeling of HIV-1 predicts high heritability of the set-point virus load, while selection for CTL escape dominates virulence evolution. PLoS Comput Biol 2014; 10:e1003899. [PMID: 25522184 PMCID: PMC4270429 DOI: 10.1371/journal.pcbi.1003899] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 09/07/2014] [Indexed: 02/07/2023] Open
Abstract
It has been suggested that HIV-1 has evolved its set-point virus load to be optimized for transmission. Previous epidemiological models and studies into the heritability of set-point virus load confirm that this mode of adaptation within the human population is feasible. However, during the many cycles of replication between infection of a host and transmission to the next host, HIV-1 is under selection for escape from immune responses, and not transmission. Here we investigate with computational and mathematical models how these two levels of selection, within-host and between-host, are intertwined. We find that when the rate of immune escape is comparable to what has been observed in patients, immune selection within hosts is dominant over selection for transmission. Surprisingly, we do find high values for set-point virus load heritability, and argue that high heritability estimates can be caused by the 'footprints' left by differing hosts' immune systems on the virus.
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Affiliation(s)
- Christiaan H. van Dorp
- Theoretical Biology and Bioinformatics, Universiteit Utrecht, Utrecht, The Netherlands
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- * E-mail:
| | - Michiel van Boven
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Rob J. de Boer
- Theoretical Biology and Bioinformatics, Universiteit Utrecht, Utrecht, The Netherlands
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Trivalent live attenuated influenza-simian immunodeficiency virus vaccines: efficacy and evolution of cytotoxic T lymphocyte escape in macaques. J Virol 2013; 87:4146-60. [PMID: 23345519 DOI: 10.1128/jvi.02645-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There is an urgent need for a human immunodeficiency virus (HIV) vaccine that induces robust mucosal immunity. CD8(+) cytotoxic T lymphocytes (CTLs) apply substantial antiviral pressure, but CTLs to individual epitopes select for immune escape variants in both HIV in humans and SIV in macaques. Inducing multiple simian immunodeficiency virus (SIV)-specific CTLs may assist in controlling viremia. We vaccinated 10 Mane-A1*08401(+) female pigtail macaques with recombinant influenza viruses expressing three Mane-A1*08401-restricted SIV-specific CTL epitopes and subsequently challenged the animals, along with five controls, intravaginally with SIV(mac251). Seroconversion to the influenza virus vector resulted and small, but detectable, SIV-specific CTL responses were induced. There was a boost in CTL responses after challenge but no protection from high-level viremia or CD4 depletion was observed. All three CTL epitopes underwent a coordinated pattern of immune escape during early SIV infection. CTL escape was more rapid in the vaccinees than in the controls at the more dominant CTL epitopes. Although CTL escape can incur a "fitness" cost to the virus, a putative compensatory mutation 20 amino acids upstream from an immunodominant Gag CTL epitope also evolved soon after the primary CTL escape mutation. We conclude that vaccines based only on CTL epitopes will likely be undermined by rapid evolution of both CTL escape and compensatory mutations. More potent and possibly broader immune responses may be required to protect pigtail macaques from SIV.
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Preferential CTL targeting of Gag is associated with relative viral control in long-term surviving HIV-1 infected former plasma donors from China. Cell Res 2012; 22:903-14. [PMID: 22290423 DOI: 10.1038/cr.2012.19] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
It is generally believed that CD8(+) cytotoxic T lymphocytes (CTLs) play a critical role in limiting the replication of human immunodeficiency virus type 1 (HIV-1) and in determining the outcome of the infection, and this effect may partly depend on which HIV product is preferentially targeted. To address the correlation between HIV-1-specific CTL responses and virus replication in a cohort of former plasma donors (FPDs), 143 antiretroviral therapy naive FPDs infected with HIV-1 clade B' strains were assessed for HIV-1-specific CTL responses with an IFN-γ Elispot assay at single peptide level by using overlapping peptides (OLPs) covering the whole consensus clade B proteome. By using a Spearman's rank correlation analysis, we found that the proportion of Gag-specific CTL responses among the total virus-specific CTL activity was inversely correlated with viral loads while being positively correlated to CD4 counts, as opposed to Pol- and Env-specific responses that were associated with increased viral loads and decreased CD4 counts. In addition, Vpr-specifc CTL responses showed a similar protective effect with Gag responses, but with a much lower frequency of recognition. Significantly, we also observed an association between HLA-A*30/B*13/Cw*06 haplotype and lower viral loads that was probably due to restricted Gag-specific CTL responses. Thus, our data demonstrate the prominent role of Gag-specific CTL responses in disease control. The advantage of HLA-A*30/B*13/Cw*06 haplotype in viral control may be associated with the contribution of Gag-specific CTL responses in the studied individuals.
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6
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Immune escape from HIV-specific antibody-dependent cellular cytotoxicity (ADCC) pressure. Proc Natl Acad Sci U S A 2011; 108:7505-10. [PMID: 21502492 DOI: 10.1073/pnas.1016048108] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Effective immunity to HIV is poorly understood. In particular, a role for antibody-dependent cellular cytotoxicity (ADCC) in controlling HIV is controversial. We hypothesized that significant pressure from HIV-specific ADCC would result in immune-escape variants. A series of ADCC epitopes in HIV-infected subjects to specific consensus strain HIV peptides were mapped using a flow cytometric assay for natural killer cell activation. We then compared the ADCC responses to the same peptide epitope derived from the concurrent HIV sequence(s) expressed in circulating virus. In 9 of 13 epitopes studied, ADCC antibodies were unable to recognize the concurrent HIV sequence. Our studies suggest ADCC responses apply significant immune pressure on the virus. This result has implications for the induction of ADCC responses by HIV vaccines.
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Balamurali M, Petravic J, Loh L, Alcantara S, Kent SJ, Davenport MP. Does cytolysis by CD8+ T cells drive immune escape in HIV infection? THE JOURNAL OF IMMUNOLOGY 2010; 185:5093-101. [PMID: 20881189 DOI: 10.4049/jimmunol.1002204] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CD8(+) "cytotoxic" T cells are important for the immune control of HIV and the closely related simian models SIV and chimeric simian-human immunodeficiency virus (SHIV), although the mechanisms of this control are unclear. One effect of CD8(+) T cell-mediated recognition of virus-infected cells is the rapid selection of escape mutant (EM) virus that is not recognized. To investigate the mechanisms of virus-specific CD8(+) T cell control during immune escape in vivo, we used a real-time PCR assay to study the dynamics of immune escape in early SHIV infection of pigtail macaques. For immune escape mediated by cytolysis, we would expect that the death rate of wild type (WT) infected cells should be faster than that of EM-infected cells. In addition, escape should be fastest during periods when the total viral load is declining. However, we find that there is no significant difference in the rate of decay of WT virus compared with EM virus. Further, immune escape is often fastest during periods of viral growth, rather than viral decline. These dynamics are consistent with an epitope-specific, MHC class I-restricted, noncytolytic mechanism of CD8(+) T cell control of SHIV that specifically inhibits the growth of WT virus in vivo.
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Affiliation(s)
- Mehala Balamurali
- Centre for Vascular Research, University of New South Wales, Sydney, New South Wales, Australia
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Vaccination reduces simian-human immunodeficiency virus sequence reversion through enhanced viral control. J Virol 2010; 84:12782-9. [PMID: 20881040 DOI: 10.1128/jvi.01193-10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It has been suggested that vaccination prior to infection may direct the mutational evolution of human immunodeficiency virus type 1 (HIV-1) to a less fit virus, resulting in an attenuated course of disease. The present study was initiated to explore whether prior immunization might prevent the reversion of the virus to the wild-type form. Mamu-A*01 monkeys were vaccinated to generate a cytotoxic T-lymphocyte response to the immunodominant Gag p11C epitope and were then challenged with a cloned pathogenic CXCR4-tropic simian-human immunodeficiency virus (SHIV) expressing a mutant Gag p11C sequence (Δp11C SHIV). The epitopic and extraepitopic compensatory mutations introduced into gag of Δp11C SHIV resulted in attenuated replicative capacity and eventual reversions to the wild-type Gag p11C sequence in naïve rhesus monkeys. However, in vaccinated rhesus monkeys, no reversions of the challenge virus were observed, an effect that may have been a consequence of significantly decreased viral replication rather than a redirection of the mutational evolution of the virus. These findings highlight the multifactorial pressures that affect the evolution of primate immunodeficiency viruses.
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9
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Minang JT, Trivett MT, Bolton DL, Trubey CM, Estes JD, Li Y, Smedley J, Pung R, Rosati M, Jalah R, Pavlakis GN, Felber BK, Piatak M, Roederer M, Lifson JD, Ott DE, Ohlen C. Distribution, persistence, and efficacy of adoptively transferred central and effector memory-derived autologous simian immunodeficiency virus-specific CD8+ T cell clones in rhesus macaques during acute infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2010; 184:315-26. [PMID: 19949091 PMCID: PMC2797560 DOI: 10.4049/jimmunol.0902410] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Plasma viremia decreases coincident with the appearance of virus-specific CD8(+) T cells during acute HIV or SIV infection. This finding, along with demonstrations of viral mutational escape from CD8(+) T cell responses and transient increase in plasma viremia after depletion of CD8(+) T cells in SIV-infected monkeys strongly suggest a role for CD8(+) T cells in controlling HIV/SIV. However, direct quantitative or qualitative correlates between CD8(+) T cell activity and virus control have not been established. To directly assess the impact of large numbers of virus-specific CD8(+) T cells present at time of SIV infection, we transferred in vitro expanded autologous central and effector memory-derived Gag CM9-, Nef YY9-, and Vif WY8-specific CD8(+) T cell clones to acutely infected rhesus macaques. The cells persisted in PBMCs between 4 and 9 d, but were not detected in gut-associated lymphoid tissue or lymph nodes. Interestingly, a high frequency of the infused cells localized to the lungs, where they persisted at high frequency for >6 wk. Although persisting cells in the lungs were Ag reactive, there was no measurable effect on virus load. Sequencing of virus from the animal receiving Nef YY9-specific CD8(+) T cells demonstrated an escape mutation in this epitope <3 wk postinfection, consistent with immune selection pressure by the infused cells. These studies establish methods for adoptive transfer of autologous SIV-specific CD8(+) T cells for evaluating immune control during acute infection and demonstrate that infused cells retain function and persist for at least 2 mo in specific tissues.
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Affiliation(s)
- Jacob T. Minang
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
| | - Matthew T. Trivett
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
| | - Diane L. Bolton
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892
| | - Charles M. Trubey
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
| | - Jacob D. Estes
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
| | - Yuan Li
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
| | - Jeremy Smedley
- Laboratory Animal Science Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
| | - Rhonda Pung
- Laboratory Animal Science Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
| | - Margherita Rosati
- Human Retrovirus Section, NCI-Frederick, Frederick, Maryland 21702, USA
| | - Rashmi Jalah
- Human Retrovirus Pathogenesis Section, NCI-Frederick, Frederick, Maryland 21702, USA
| | | | - Barbara K. Felber
- Human Retrovirus Pathogenesis Section, NCI-Frederick, Frederick, Maryland 21702, USA
| | - Michael Piatak
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
| | - David E. Ott
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
| | - Claes Ohlen
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
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10
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Payne RP, Matthews PC, Prado JG, Goulder PJR. HLA-mediated control of HIV and HIV adaptation to HLA. ADVANCES IN PARASITOLOGY 2009; 68:1-20. [PMID: 19289188 DOI: 10.1016/s0065-308x(08)00601-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The human immunodeficiency virus (HIV) epidemic provides a rare opportunity to examine in detail the initial stages of a host-pathogen co-evolutionary struggle in humans. The genes encoding the human leukocyte antigen (HLA) class I molecules have a critical influence in the success or failure of the immune response against HIV. The particular HLA class I molecules expressed by each individual defines the type of cytotoxic T-lymphocyte (CTL) response that is made against the virus. This chapter describes the role of HLA class I and the CTL response in controlling HIV replication, and discusses the extent to which HIV has already adapted to those HLA class I molecules and CTL responses that are most effective in viral suppression. It is evident that viral mutations that enable HIV to evade the CTL response are indeed already accumulating in populations where the selecting HLA molecules are highly prevalent, indicating the dynamic and shifting nature of the evolutionary interplay between HIV and human populations.
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Affiliation(s)
- Rebecca P Payne
- Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
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11
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Balancing reversion of cytotoxic T-lymphocyte and neutralizing antibody escape mutations within human immunodeficiency virus type 1 Env upon transmission. J Virol 2009; 83:8986-92. [PMID: 19515763 DOI: 10.1128/jvi.00599-09] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) envelope protein (Env) is subject to both neutralizing antibody (NAb) and CD8 T-cell (cytotoxic T-lymphocyte [CTL]) immune pressure. We studied the reversion of the Env CTL escape mutant virus to the wild type and the relationship between the reversion of CTL mutations with N-linked glycosylation site (NLGS)-driven NAb escape in pigtailed macaques. Env CTL mutations either did not revert to the wild type or only transiently reverted 5 to 7 weeks after infection. The CTL escape mutant reversion was coincident, for the same viral clones, with the loss of NLGS mutations. At one site studied, both CTL and NLGS mutations were needed to confer NAb escape. We conclude that CTL and NAb escape within Env can be tightly linked, suggesting opportunities to induce effective multicomponent anti-Env immunity.
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12
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Evaluation of recombinant influenza virus-simian immunodeficiency virus vaccines in macaques. J Virol 2009; 83:7619-28. [PMID: 19439474 DOI: 10.1128/jvi.00470-09] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There is an urgent need for human immunodeficiency virus (HIV) vaccines that induce robust mucosal immunity. Influenza A viruses (both H1N1 and H3N2) were engineered to express simian immunodeficiency virus (SIV) CD8 T-cell epitopes and evaluated following administration to the respiratory tracts of 11 pigtail macaques. Influenza virus was readily detected from respiratory tract secretions, although the infections were asymptomatic. Animals seroconverted to influenza virus and generated CD8 and CD4 T-cell responses to influenza virus proteins. SIV-specific CD8 T-cell responses bearing the mucosal homing marker beta7 integrin were induced by vaccination of naïve animals. Further, SIV-specific CD8 T-cell responses could be boosted by recombinant influenza virus-SIV vaccination of animals with already-established SIV infection. Sequential vaccination with influenza virus-SIV recombinants of different subtypes (H1N1 followed by H3N2 or vice versa) produced only a limited boost in immunity, probably reflecting T-cell immunity to conserved internal proteins of influenza A virus. SIV challenge of macaques vaccinated with an influenza virus expressing a single SIV CD8 T cell resulted in a large anamnestic recall CD8 T-cell response, but immune escape rapidly ensued and there was no impact on chronic SIV viremia. Although our results suggest that influenza virus-HIV vaccines hold promise for the induction of mucosal immunity to HIV, broader antigen cover will be needed to limit cytotoxic T-lymphocyte escape.
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13
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Loh L, Reece JC, Fernandez CS, Alcantara S, Center R, Howard J, Purcell DFJ, Balamurali M, Petravic J, Davenport MP, Kent SJ. Complexity of the inoculum determines the rate of reversion of SIV Gag CD8 T cell mutant virus and outcome of infection. PLoS Pathog 2009; 5:e1000378. [PMID: 19360124 PMCID: PMC2660429 DOI: 10.1371/journal.ppat.1000378] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Accepted: 03/12/2009] [Indexed: 11/19/2022] Open
Abstract
Escape mutant (EM) virus that evades CD8+ T cell recognition is frequently observed following infection with HIV-1 or SIV. This EM virus is often less replicatively “fit” compared to wild-type (WT) virus, as demonstrated by reversion to WT upon transmission of HIV to a naïve host and the association of EM virus with lower viral load in vivo in HIV-1 infection. The rate and timing of reversion is, however, highly variable. We quantified reversion to WT of a series of SIV and SHIV viruses containing minor amounts of WT virus in pigtail macaques using a sensitive PCR assay. Infection with mixes of EM and WT virus containing ≥10% WT virus results in immediate and rapid outgrowth of WT virus at SIV Gag CD8 T cell epitopes within 7 days of infection of pigtail macaques with SHIV or SIV. In contrast, infection with biologically passaged SHIVmn229 viruses with much smaller proportions of WT sequence, or a molecular clone of pure EM SIVmac239, demonstrated a delayed or slow pattern of reversion. WT virus was not detectable until ≥8 days after inoculation and took ≥8 weeks to become the dominant quasispecies. A delayed pattern of reversion was associated with significantly lower viral loads. The diversity of the infecting inoculum determines the timing of reversion to WT virus, which in turn predicts the outcome of infection. The delay in reversion of fitness-reducing CD8 T cell escape mutations in some scenarios suggests opportunities to reduce the pathogenicity of HIV during very early infection. Understanding how to contain HIV replication by the immune system is a key goal of vaccine strategies. HIV frequently mutates to avoid immune recognition, but this may come at a “fitness cost”, weakening the virus. When HIV is transmitted to a new host, the mutations often revert back to wild-type, allowing the virus to regain a fitter state. We found that when multiple HIV-like viruses are transmitted to monkeys, containing both mutant and wild-type, reversion to wild-type is very rapid and the fitter virus results in higher viral levels. In contrast, when only escape mutant virus initiates the infection, reversion to wild-type is delayed to later during early infection, and lower levels of virus result. Our results suggest that the composition of the infecting virus plays a role in determining the outcome of HIV infections. Strategies to maintain weakened virus strains during the early HIV infection may help the host control virus replication.
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Affiliation(s)
- Liyen Loh
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Jeanette C. Reece
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Caroline S. Fernandez
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Sheilajen Alcantara
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Robert Center
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Jane Howard
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Damian F. J. Purcell
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Mehala Balamurali
- Center for Vascular Research, University of New South Wales, Sydney, Australia
| | - Janka Petravic
- Center for Vascular Research, University of New South Wales, Sydney, Australia
| | - Miles P. Davenport
- Center for Vascular Research, University of New South Wales, Sydney, Australia
| | - Stephen J. Kent
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
- * E-mail:
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14
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Rollman E, Mason RD, Lin J, Brooks AG, Kent SJ. Protection afforded by live attenuated SIV is associated with rapid killing kinetics of CTLs. J Med Primatol 2009; 37 Suppl 2:24-32. [PMID: 19187428 DOI: 10.1111/j.1600-0684.2008.00326.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND Live attenuated SIV vaccines are highly efficacious, but how they mediate protection is poorly understood. A feature of the effectiveness of live attenuated vaccines is their ability to control high dose challenge viruses early, without a large peak of acute viraemia. We hypothesized that long-lived antigen exposure from live attenuated SIV may result in CD8+ cytotoxic T lymphocytes persistently capable of rapidly cytolytic potential. METHODS We employed a kinetic degranulation assay to study multiple tetramer+ SIV-specific CTL specificities before and after the SIV(mac251) challenge of pigtail macaques inoculated with a live attenuated SIV. RESULTS Live attenuated SIV-vaccinated animals rapidly controlled a subsequent challenge, with minimal viraemia after exposure. For over 9 months after the initial vaccination with live attenuated SIV we could detect both Gag- and Tat-specific CTLs that maintained a long-term capacity to rapidly degranulate (CD107a expression) and release granzyme B within 30 minutes of antigen exposure. This rapid cytolytic phenotype was maintained throughout the early period after challenge, despite the absence of a marked enhancement in CTL frequencies. CONCLUSIONS Our results suggest that highly functional CTLs may contribute to the remarkable efficacy of live attenuated SIV vaccines. Studying the killing kinetics of CTLs induced by other, safer, HIV vaccines could facilitate a better understanding of the requirements for an effective HIV vaccine.
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Affiliation(s)
- Erik Rollman
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Vic., Australia
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15
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Peut V, Kent SJ. Substantial envelope-specific CD8 T-cell immunity fails to control SIV disease. Virology 2008; 384:21-7. [PMID: 19091370 DOI: 10.1016/j.virol.2008.11.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 10/30/2008] [Accepted: 11/10/2008] [Indexed: 10/21/2022]
Abstract
It is unknown which HIV proteins to target by vaccination in order to generate the most effective CD8 T-cell immunity. We recently immunized SIV(mac251)-infected pigtail macaques with Gag peptides or a cocktail of peptides spanning all SIV proteins, including SIV Env. High-level SIV Env-specific CD8 T-cell responses were generated and 7 novel Env-specific CD8 T-cell epitopes in 10 animals were mapped. Env-specific CD8 T-cell responses were significantly inferior to Gag-specific responses, and no better than unvaccinated control animals, in the control of SIV replication and prevention of disease. Escape mutations emerged within several Env-specific CTL epitopes, suggesting at least some pressure imparted by the Env CTL responses, but this did not correlate with significantly reduced SIV replication. We conclude Env-specific CTL may not be the most effective response to induce by vaccination.
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Affiliation(s)
- Viv Peut
- Department of Microbiology and Immunology, University of Melbourne, Parkville Victoria, Australia
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16
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De Rose R, Mason RD, Loh L, Peut V, Smith MZ, Fernandez CS, Alcantara S, Amarasena T, Reece J, Seddiki N, Kelleher AD, Zaunders J, Kent SJ. Safety, immunogenicity and efficacy of peptide-pulsed cellular immunotherapy in macaques. J Med Primatol 2008; 37 Suppl 2:69-78. [PMID: 19187433 DOI: 10.1111/j.1600-0684.2008.00329.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Robert De Rose
- Department of Microbiology and Immunology, University of Melbourne, Australia
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17
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Mason RD, Rose RD, Seddiki N, Kelleher AD, Kent SJ. Low pre-infection levels and loss of central memory CD4+ T cells may predict rapid progression in SIV-infected pigtail macaques. Virology 2008; 381:11-5. [PMID: 18835006 DOI: 10.1016/j.virol.2008.08.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 08/15/2008] [Accepted: 08/30/2008] [Indexed: 11/25/2022]
Abstract
CD4+ T lymphocyte subsets are targeted to different degrees by SIV infection. We studied central memory, effector memory, naïve, and regulatory T cell levels longitudinally in 11 SIV(mac251)-infected pigtail macaques. Depletion of CD28+CD95+ central memory CD4+ T cells, but not other populations, correlated with both SIV viral load and disease progression. A low pre-infection level of central memory CD4+ T cells was also predictive of rapid disease progression. If confirmed in larger studies, our results suggest stratifying macaques for baseline central memory CD4+ T cells would be useful in defining both the pathogenesis of SIV disease and SIV vaccine efficacy.
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Affiliation(s)
- Rosemarie D Mason
- Department of Microbiology and Immunology, University of Melbourne, 3010 Australia
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18
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Goulder PJR, Watkins DI. Impact of MHC class I diversity on immune control of immunodeficiency virus replication. Nat Rev Immunol 2008; 8:619-30. [PMID: 18617886 PMCID: PMC2963026 DOI: 10.1038/nri2357] [Citation(s) in RCA: 370] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The recent failure of the T-cell-based HIV vaccine trial led by Merck & Co., Inc. prompts the urgent need to refocus on the question of which T-cell responses are required to control HIV replication. The well-described association between the expression of particular MHC class I molecules and successful containment of HIV or, in the macaque model, SIV replication provide a valuable starting point from which to evaluate more precisely what might constitute effective CD8(+) T-cell responses. Here, we review recent studies of T-cell-mediated control of HIV and SIV infection, and offer insight for the design of a successful T-cell-based HIV vaccine in the future.
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Affiliation(s)
- Philip J R Goulder
- Department of Paediatrics, Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK.
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19
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Smith MZ, Asher TE, Venturi V, Davenport MP, Douek DC, Price DA, Kent SJ. Limited maintenance of vaccine-induced simian immunodeficiency virus-specific CD8 T-cell receptor clonotypes after virus challenge. J Virol 2008; 82:7357-68. [PMID: 18508897 PMCID: PMC2493343 DOI: 10.1128/jvi.00607-08] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 05/16/2008] [Indexed: 11/20/2022] Open
Abstract
T-cell receptors (TCRs) govern the specificity, efficacy, and cross-reactivity of CD8 T cells. Here, we studied CD8 T-cell clonotypes from Mane-A*10(+) pigtail macaques responding to the simian immunodeficiency virus (SIV) Gag KP9 epitope in a setting of vaccination and subsequent viral challenge. We observed a diverse TCR repertoire after DNA, recombinant poxvirus, and live attenuated virus vaccination, with none of 59 vaccine-induced KP9-specific TCRs being identical between macaques. The KP9-specific TCR repertoires remained diverse after SIV or simian-human immunodeficiency virus challenge but, remarkably, exhibited substantially different clonotypic compositions compared to the corresponding populations prechallenge. Within serial samples from individual pigtail macaques, only a small subset (33.9%) of TCRs induced by vaccination were maintained or expanded after challenge. Most (66.1%) of the TCRs induced by vaccination were not detectable after challenge. Our results suggest that some CD8 T cells induced by vaccination are more efficient than others at responding to a viral challenge. These findings have implications for future AIDS virus vaccine studies, which should consider the "fitness" of vaccine-induced T cells in order to generate robust responses in the face of virus exposure.
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Affiliation(s)
- Miranda Z Smith
- Department of Microbiology and Immunology, University of Melbourne, Melbourne 3010, Australia
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20
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Loh L, Kent SJ. Quantification of simian immunodeficiency virus cytotoxic T lymphocyte escape mutant viruses. AIDS Res Hum Retroviruses 2008; 24:1067-72. [PMID: 18620496 DOI: 10.1089/aid.2007.0309] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Escape from cytotoxic T-lymphocyte (CTL) pressure is common in HIV-1 infection of humans and simian immunodeficiency virus (SIV) infections of macaques. CTL escape typically incurs a fitness cost as reversion back to wild-type can occur upon transmission. We utilized sequence-specific primers and DNA probes with real-time polymerase chain reaction (PCR) to sensitively and specifically track wild-type and escape mutant viremia at the Mane-A*17-restricted SIV Gag(371379) epitope AF9 in pigtail macaques. The generation of minor escape mutant populations is detected by the real-time PCR 2 weeks earlier than observed using standard sequencing techniques. We passaged the AF9 CTL escape mutant virus into two naïve Mane-A*17-negative pigtail macaques and showed that reversion to wild-type was rapid during acute infection and then slowed considerably at later stages of the infection. These data help refine our understanding of how CTL escape mutant viruses evolve.
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Affiliation(s)
- Liyen Loh
- Department of Microbiology and Immunology, University of Melbourne, 3010, Australia
| | - Stephen J. Kent
- Department of Microbiology and Immunology, University of Melbourne, 3010, Australia
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21
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Rollman E, Turner SJ, Kedzierska K, Kent SJ. Anti-SIV cytolytic molecules in pigtail macaques. AIDS Res Hum Retroviruses 2008; 24:1127-31. [PMID: 18665802 DOI: 10.1089/aid.2008.0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Release of granzymes and perforin from the cytolytic granules of SIV-specific CD8 T cells is a critically important effector mechanism facilitating the elimination of SIV-infected cells. We sequenced granzyme A, B, and K and perforin in pigtail macaques and defined polymorphisms between humans, rhesus macaques, and pigtail macaques. The pigtail macaque sequences were similar to the corresponding rhesus sequences at the mRNA and protein level and (0.4-1.1% sequence differences) but substantially different from human sequences (3.8-8.1% sequence differences). We used this sequence information to develop multiplex PCR assays to detect these genes. We also successfully studied the release of perforin and granzyme B from deregulating SIV-specific CD8 T cells by flow cytometry. These sequences and tools enable further study of the cytolytic control of SIV in pigtail macaques.
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Affiliation(s)
- Erik Rollman
- Department of Microbiology and Immunology, University of Melbourne, Melbourne 3010, Australia
| | - Stephen J. Turner
- Department of Microbiology and Immunology, University of Melbourne, Melbourne 3010, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, Melbourne 3010, Australia
| | - Stephen J. Kent
- Department of Microbiology and Immunology, University of Melbourne, Melbourne 3010, Australia
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22
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Biesinger T, Kimata JT. HIV-1 Transmission, Replication Fitness and Disease Progression. Virology (Auckl) 2008; 2008:49-63. [PMID: 20354593 PMCID: PMC2846839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023] Open
Abstract
Upon transmission, human immunodeficiency virus type 1 (HIV-1) establishes infection of the lymphatic reservoir, leading to profound depletion of the memory CD4(+) T cell population, despite the induction of the adaptive immune response. The rapid evolution and association of viral variants having distinct characteristics with different stages of infection, the level of viral burden, and rate of disease progression suggest a role for viral variants in this process. Here, we review the literature on HIV-1 variants and disease and discuss the importance of viral fitness for transmission and disease.
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Affiliation(s)
| | - Jason T. Kimata
- Corresponding Author: Department of Molecular Virology and Microbiology, BCM385, Room 811D, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA, Tel: 713-798-4536, FAX: 713-798-4435,
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23
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Biesinger T, Kimata JT. HIV-1 Transmission, Replication Fitness and Disease Progression. Virology (Auckl) 2008. [DOI: 10.4137/vrt.s860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Upon transmission, human immunodeficiency virus type 1 (HIV-1) establishes infection of the lymphatic reservoir, leading to profound depletion of the memory CD4+ T cell population despite the induction of the adaptive immune response. The rapid evolution and association of viral variants having distinct characteristics during different stages of infection, the level of viral burden, and rate of disease progression suggest a role for viral variants in this process. Here, we review the literature on HIV-1 variants and disease and discuss the importance of viral fitness for transmission and disease.
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Affiliation(s)
- Tasha Biesinger
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030. U.S.A
| | - Jason T. Kimata
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030. U.S.A
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24
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Pérez CL, Larsen MV, Gustafsson R, Norström MM, Atlas A, Nixon DF, Nielsen M, Lund O, Karlsson AC. Broadly immunogenic HLA class I supertype-restricted elite CTL epitopes recognized in a diverse population infected with different HIV-1 subtypes. THE JOURNAL OF IMMUNOLOGY 2008; 180:5092-100. [PMID: 18354235 DOI: 10.4049/jimmunol.180.7.5092] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The genetic variations of the HIV-1 virus and its human host constitute major obstacles for obtaining potent HIV-1-specific CTL responses in individuals of diverse ethnic backgrounds infected with different HIV-1 variants. In this study, we developed and used a novel algorithm to select 184 predicted epitopes representing seven different HLA class I supertypes that together constitute a broad coverage of the different HIV-1 strains as well as the human HLA alleles. Of the tested 184 HLA class I-restricted epitopes, 114 were recognized by at least one study subject, and 45 were novel epitopes, not previously described in the HIV-1 immunology database. In addition, we identified 21 "elite" epitopes that induced CTL responses in at least 4 of the 31 patients. A majority (27 of 31) of the study population recognized one or more of these highly immunogenic epitopes. We also found a limited set of 9 epitopes that together induced HIV-1-specific CTL responses in all HIV-1-responsive patients in this study. Our results have important implications for the validation of potent CTL responses and show that the goal for a vaccine candidate in inducing broadly reactive CTL immune responses is attainable.
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Affiliation(s)
- Carina L Pérez
- Department of Microbiology, Cell Biology, and Tumor Biology, Karolinska Institutet, and The Swedish Institute of Infectious Disease Control, Stockholm, Sweden
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25
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CD4+ target cell availability determines the dynamics of immune escape and reversion in vivo. J Virol 2008; 82:4091-101. [PMID: 18272587 DOI: 10.1128/jvi.02552-07] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Infections with human immunodeficiency virus (HIV) and the closely related monkey viruses simian-human immunodeficiency virus (SHIV) and simian immunodeficiency virus (SIV) are characterized by progressive waves of immune responses, followed by viral mutation and "immune escape." However, escape mutation usually leads to lower replicative fitness, and in the absence of immune pressure, an escape mutant (EM) virus "reverts" to the wild-type phenotype. Analysis of the dynamics of immune escape and reversion has suggested it is a mechanism for identifying the immunogens best capable of controlling viremia. We have analyzed and modeled data of the dynamics of wild-type (WT) and EM viruses during SHIV infection of macaques. Modeling suggests that the dynamics of reversion and immune escape should be determined by the availability of target cells for infection. Consistent with this suggestion, we find that the rate of reversion of cytotoxic T-lymphocyte (CTL) EM virus strongly correlates with the number of CD4(+) T cells available for infection. This phenomenon also affects the rate of immune escape, since this rate is determined by the balance of CTL killing and the WT fitness advantage. This analysis predicts that the optimal timing for the selection of immune escape variants will be immediately after the peak of viremia and that the development of escape variants at later times will lead to slower selection. This has important implications for comparative studies of immune escape and reversion in different infections and for identifying epitopes with high fitness cost for use as vaccine targets.
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26
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Kent SJ, De Rose R, Mokhonov VV, Mokhonova EI, Fernandez CS, Alcantara S, Rollman E, Mason RD, Loh L, Peut V, Reece JC, Wang XJ, Wilson KM, Suhrbier A, Khromykh A. Evaluation of recombinant Kunjin replicon SIV vaccines for protective efficacy in macaques. Virology 2008; 374:528-34. [PMID: 18272194 DOI: 10.1016/j.virol.2008.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 01/02/2008] [Accepted: 01/05/2008] [Indexed: 01/03/2023]
Abstract
Persistent gag-specific T cell immunity would be a useful component of an effective HIV vaccine. The Flavivirus Kunjin replicon was previously engineered to persistently express HIV gag and was shown to induce protective responses in mice. We evaluated Kunjin replicon virus-like-particles expressing SIVgag-pol in pigtail macaques. Kunjin-specific antibodies were induced, but no SIV-specific T cell immunity were detected. Following SIVmac251 challenge, there was no difference in SIV viremia or retention of CD4 T cells between Kunjin-SIVgag-pol vaccine immunized animals and controls. An amnestic SIV gag-specific CD8 T cell response associated with control of viremia was observed in 1 of 6 immunized animals. Refinements of this vector system and optimization of the immunization doses, routes, and schedules are required prior to clinical trials.
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Affiliation(s)
- Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne, 3010, Australia.
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27
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Loh L, Petravic J, Batten CJ, Davenport MP, Kent SJ. Vaccination and timing influence SIV immune escape viral dynamics in vivo. PLoS Pathog 2008; 4:e12. [PMID: 18225952 PMCID: PMC2323283 DOI: 10.1371/journal.ppat.0040012] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Accepted: 12/10/2007] [Indexed: 11/30/2022] Open
Abstract
CD8+ cytotoxic T lymphocytes (CTL) can be effective at controlling HIV-1 in humans and SIV in macaques, but their utility is partly offset by mutational escape. The kinetics of CTL escape and reversion of escape mutant viruses upon transmission to MHC-mismatched hosts can help us understand CTL-mediated viral control and the fitness cost extracted by immune escape mutation. Traditional methods for following CTL escape and reversion are, however, insensitive to minor viral quasispecies. We developed sensitive quantitative real-time PCR assays to track the viral load of SIV Gag164–172 KP9 wild-type (WT) and escape mutant (EM) variants in pigtail macaques. Rapid outgrowth of EM virus occurs during the first few weeks of infection. However, the rate of escape plateaued soon after, revealing a prolonged persistence of WT viremia not detectable by standard cloning and sequencing methods. The rate of escape of KP9 correlated with levels of vaccine-primed KP9-specific CD8+ T cells present at that time. Similarly, when non-KP9 responder (lacking the restricting Mane-A*10 allele) macaques were infected with SHIVmn229 stock containing a mixture of EM and WT virus, rapid reversion to WT was observed over the first 2 weeks following infection. However, the rate of reversion to WT slowed dramatically over the first month of infection. The serial quantitation of escape mutant viruses evolving during SIV infection shows that rapid dynamics of immune escape and reversion can be observed in early infection, particularly when CD8 T cells are primed by vaccination. However, these early rapid rates of escape and reversion are transient and followed by a significant slowing in these rates later during infection, highlighting that the rate of escape is significantly influenced by the timing of its occurrence. Immune escape from AIDS virus–specific cellular immunity is common. The driving forces behind how quickly cellular immunity forces escape are poorly understood. We developed a novel assay for a common immune escape variant of SIV in macaques. This allowed us to sensitively track the rates of immune escape even when levels of escape mutant or wild-type virus were low. We found that prior immunization of macaques resulted in very rapid immune escape during acute infection. However, when escape starts to occur later, during chronic infection, the rate of immune escape is much more gradual. Thus, both prior vaccination and timing influence the rates of immune escape and provide a fuller picture of the effectiveness of T cell immunity to HIV.
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Affiliation(s)
- Liyen Loh
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Janka Petravic
- Centre for Vascular Research, University of New South Wales, Sydney, New South Wales, Australia
| | - C. Jane Batten
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Miles P Davenport
- Centre for Vascular Research, University of New South Wales, Sydney, New South Wales, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
- * To whom correspondence should be addressed. E-mail:
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28
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Analysis of the evolutionary forces in an immunodominant CD8 epitope in hepatitis C virus at a population level. J Virol 2008; 82:3438-51. [PMID: 18216107 PMCID: PMC2268453 DOI: 10.1128/jvi.01700-07] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Failure of the adaptive immune response to control infection with the hepatitis C virus (HCV) can result from mutational escape in targeted T-cell epitopes. Recent studies suggest that T-cell immune pressure is an important factor in the evolution of the nonstructural proteins in HCV. The aim of this study was to characterize the forces that contribute to viral evolution in an HLA-A*01-restricted epitope in HCV NS3. This epitope represents a potentially attractive target for vaccination strategies since it is conserved across all genotypes. In our cohort of subjects with chronic HCV infection (genotype 1b or 3a), it is a frequently recognized CD8 epitope in HLA-A*01-positive subjects. Viral sequence data reveal that an escape variant is the dominant residue in both genotypes. The predominant Y1444F substitution seemingly impairs binding to the HLA-A*01 molecule, which may have an important impact on the ability to prime a functional CD8 response upon infection. Interestingly, a case of evolution toward the prototype sequence was observed during chronic infection, possibly because the helicase activity of the protein containing the Y1444F substitution is reduced compared to the prototype sequence. Comparison of HCV sequences from Asia and Europe suggests that the frequency of the HLA-A*01 allele in a population may influence the frequency of the escape variant in circulating strains. These data suggest a complex interaction of multiple forces shaping the evolution of HCV in which immune pressure both within the individual and also at the population level in addition to functional constraints are important contributing factors.
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29
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Rollman E, Smith MZ, Brooks AG, Purcell DFJ, Zuber B, Ramshaw IA, Kent SJ. Killing kinetics of simian immunodeficiency virus-specific CD8+ T cells: implications for HIV vaccine strategies. THE JOURNAL OF IMMUNOLOGY 2007; 179:4571-9. [PMID: 17878354 DOI: 10.4049/jimmunol.179.7.4571] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Both the magnitude and function of vaccine-induced HIV-specific CD8+ CTLs are likely to be important in the outcome of infection. We hypothesized that rapid cytolysis by CTLs may facilitate control of viral challenge. Release kinetics of the cytolytic effector molecules granzyme B and perforin, as well as the expression of the degranulation marker CD107a and IFN-gamma were simultaneously studied in SIV Gag(164-172) KP9-specific CD8+ T cells from Mane-A*10+ pigtail macaques. Macaques were vaccinated with either prime-boost poxvirus vector vaccines or live-attenuated SIV vaccines. Prime-boost vaccination induced Gag-specific CTLs capable of only slow (after 3 h) production of IFN-gamma and with limited (<5%) degranulation and granzyme B release. Vaccination with live-attenuated SIV resulted in a rapid cytolytic profile of SIV-specific CTLs with rapid (<0.5 h) and robust (>50% of tetramer-positive CD8+ T cells) degranulation and granzyme B release. The cytolytic phenotype following live-attenuated SIV vaccinations were similar to that associated with the partial resolution of viremia following SIV(mac251) challenge of prime-boost-vaccinated macaques, albeit with less IFN-gamma expression. High proportions of KP9-specific T cells expressed the costimulatory molecule CD28 when they exhibited a rapid cytolytic phenotype. The delayed cytolytic phenotype exhibited by standard vector-based vaccine-induced CTLs may limit the ability of T cell-based HIV vaccines to rapidly control acute infection following a pathogenic lentiviral exposure.
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Affiliation(s)
- Erik Rollman
- Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
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30
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Abstract
Human immunodeficiency virus (HIV)-specific CD8 T lymphocytes are important for the control of viremia, but the relative utility of responses to the various HIV proteins is controversial. Immune responses that force escape mutations that exact a significant fitness cost from the mutating virus would help slow progression to AIDS. The HIV envelope (Env) protein is subject to both humoral and cellular immune responses, suggesting that multiple rounds of mutation are needed to facilitate viral escape. The Gag protein, however, has recently been shown to elicit a more effective CD8 T-cell immune response in humans. We studied 30 pigtail macaques for their CD8 T-lymphocyte responses to HIV-1 Env and simian immunodeficiency virus (SIV) Gag following prime/boost vaccination and intrarectal challenge with simian-human immunodeficiency virus SHIV(mn229). Eight CD8 Env-specific T-cell epitopes were identified and mapped in 10 animals. Animals that generated Env-specific CD8 T-cell responses had equivalent viral loads and only a modest advantage in retention of peripheral CD4 T lymphocytes compared to those animals without responses to Env. This contrasts with animals that generated CD8 T-cell responses to SIV Gag in the same trial, demonstrating superior control of viral load and a larger advantage in retention of peripheral CD4 T cells than Gag nonresponders. Mutational escape was common in Env but, in contrast to mutations in Gag, did not result in the rapid emergence of dominant escape motifs, suggesting modest selective pressure from Env-specific T cells. These results suggest that Env may have limited utility as a CD8 T-cell immunogen.
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Affiliation(s)
- Viv Peut
- Department of Microbiology and Immunology, University of Melbourne, Parkville 3010, Australia
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31
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Crawford H, Prado JG, Leslie A, Hué S, Honeyborne I, Reddy S, van der Stok M, Mncube Z, Brander C, Rousseau C, Mullins JI, Kaslow R, Goepfert P, Allen S, Hunter E, Mulenga J, Kiepiela P, Walker BD, Goulder PJR. Compensatory mutation partially restores fitness and delays reversion of escape mutation within the immunodominant HLA-B*5703-restricted Gag epitope in chronic human immunodeficiency virus type 1 infection. J Virol 2007; 81:8346-51. [PMID: 17507468 PMCID: PMC1951305 DOI: 10.1128/jvi.00465-07] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HLA-B*5703 is associated with effective immune control in human immunodeficiency virus type 1 (HIV-1) infection. Here we describe an escape mutation within the immunodominant HLA-B*5703-restricted epitope in chronic HIV-1 infection, KAFSPEVIPMF (Gag 162-172), and demonstrate that this mutation reduces viral replicative capacity. Reversion of this mutation following transmission to HLA-B*5703-negative recipients was delayed by the compensatory mutation S165N within the same epitope. These data may help explain the observed association between HLA-B*5703 and long-term control of viremia.
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Affiliation(s)
- Hayley Crawford
- Department of Pediatrics, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Rd., Oxford OX1 3SY, United Kingdom
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