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Heide J, Schulte S, Kohsar M, Brehm TT, Herrmann M, Karsten H, Marget M, Peine S, Johansson AM, Sette A, Lütgehetmann M, Kwok WW, Sidney J, Schulze zur Wiesch J. Broadly directed SARS-CoV-2-specific CD4+ T cell response includes frequently detected peptide specificities within the membrane and nucleoprotein in patients with acute and resolved COVID-19. PLoS Pathog 2021; 17:e1009842. [PMID: 34529740 PMCID: PMC8445433 DOI: 10.1371/journal.ppat.1009842] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/27/2021] [Indexed: 01/21/2023] Open
Abstract
The aim of this study was to define the breadth and specificity of dominant SARS-CoV-2-specific T cell epitopes using a comprehensive set of 135 overlapping 15-mer peptides covering the SARS-CoV-2 envelope (E), membrane (M) and nucleoprotein (N) in a cohort of 34 individuals with acute (n = 10) and resolved (n = 24) COVID-19. Following short-term virus-specific in vitro cultivation, the single peptide-specific CD4+ T cell response of each patient was screened using enzyme linked immuno spot assay (ELISpot) and confirmed by single-peptide intracellular cytokine staining (ICS) for interferon-γ (IFN-γ) production. 97% (n = 33) of patients elicited one or more N, M or E-specific CD4+ T cell responses and each patient targeted on average 21.7 (range 0-79) peptide specificities. Overall, we identified 10 N, M or E-specific peptides that showed a response frequency of more than 36% and five of them showed high binding affinity to multiple HLA class II binders in subsequent in vitro HLA binding assays. Three peptides elicited CD4+ T cell responses in more than 55% of all patients, namely Mem_P30 (aa146-160), Mem_P36 (aa176-190), both located within the M protein, and Ncl_P18 (aa86-100) located within the N protein. These peptides were further defined in terms of length and HLA restriction. Based on this epitope and restriction data we developed a novel DRB*11 tetramer (Mem_aa145-164) and examined the ex vivo phenotype of SARS-CoV-2-specific CD4+ T cells in one patient. This detailed characterization of single T cell peptide responses demonstrates that SARS-CoV-2 infection universally primes a broad T cell response directed against multiple specificities located within the N, M and E structural protein.
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Affiliation(s)
- Janna Heide
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center, Hamburg-Eppendorf, Germany
- German Center for Infection Research (DZIF), Partner Site, Hamburg-Lübeck-Borstel-Riems, Germany
| | - Sophia Schulte
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center, Hamburg-Eppendorf, Germany
| | - Matin Kohsar
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center, Hamburg-Eppendorf, Germany
| | - Thomas Theo Brehm
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center, Hamburg-Eppendorf, Germany
- German Center for Infection Research (DZIF), Partner Site, Hamburg-Lübeck-Borstel-Riems, Germany
| | - Marissa Herrmann
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center, Hamburg-Eppendorf, Germany
- German Center for Infection Research (DZIF), Partner Site, Hamburg-Lübeck-Borstel-Riems, Germany
| | - Hendrik Karsten
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center, Hamburg-Eppendorf, Germany
| | - Matthias Marget
- Department of Transfusion Medicine, University Medical Center, Hamburg-Eppendorf, Germany
| | - Sven Peine
- Department of Transfusion Medicine, University Medical Center, Hamburg-Eppendorf, Germany
| | - Alexandra M. Johansson
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States of America
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, California, United States of America
| | - Marc Lütgehetmann
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center, Hamburg-Eppendorf, Germany
| | - William W. Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States of America
| | - John Sidney
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, California, United States of America
| | - Julian Schulze zur Wiesch
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center, Hamburg-Eppendorf, Germany
- German Center for Infection Research (DZIF), Partner Site, Hamburg-Lübeck-Borstel-Riems, Germany
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Heide J, Wildner NH, Ackermann C, Wittner M, Marget M, Sette A, Sidney J, Jacobs T, Schulze Zur Wiesch J. Detection of EXP1-Specific CD4+ T Cell Responses Directed Against a Broad Range of Epitopes Including Two Promiscuous MHC Class II Binders During Acute Plasmodium falciparum Malaria. Front Immunol 2020; 10:3037. [PMID: 32038611 PMCID: PMC6993587 DOI: 10.3389/fimmu.2019.03037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 12/11/2019] [Indexed: 01/02/2023] Open
Abstract
Background: T cells are thought to play a major role in conferring immunity against malaria. This study aimed to comprehensively define the breadth and specificity of the Plasmodium falciparum (P. falciparum)-specific CD4+ T cell response directed against the exported protein 1 (EXP1) in a cohort of patients diagnosed with acute malaria. Methods: Peripheral blood mononuclear cells of 44 patients acutely infected with P. falciparum, and of one patient infected with P. vivax, were stimulated and cultured in vitro with an overlapping set of 31 P. falciparum-specific 13-17-mer peptides covering the entire EXP1 sequence. EXP1-specific T cell responses were analyzed by ELISPOT and intracellular cytokine staining for interferon-γ production after re-stimulation with individual peptides. For further characterization of the epitopes, in silico and in vitro human leukocyte antigen (HLA) binding studies and fine mapping assays were performed. Results: We detected one or more EXP1-specific CD4+ T cell responses (mean: 1.09, range 0–5) in 47% (21/45) of our patients. Responses were directed against 15 of the 31 EXP1 peptides. Peptides EXP1-P13 (aa60-74) and P15 (aa70-85) were detected by 18% (n = 8) and 27% (n = 12) of the 45 patients screened. The optimal length, as well as the corresponding most likely HLA-restriction, of each of these two peptides was assessed. Interestingly, we also identified one CD4+ T cell response against peptide EXP1-P15 in a patient who was infected with P. vivax but not falciparum. Conclusions: This first detailed characterization of novel EXP1-specific T cell epitopes provides important information for future analysis with major histocompatibility complex-multimer technology as well as for immunomonitoring and vaccine design.
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Affiliation(s)
- Janna Heide
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Nils H Wildner
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christin Ackermann
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Melanie Wittner
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Matthias Marget
- Department of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States.,Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Thomas Jacobs
- Protozoa Immunology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Julian Schulze Zur Wiesch
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
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Xu X, Zhang Y, Li Q. Characteristics of herpes simplex virus infection and pathogenesis suggest a strategy for vaccine development. Rev Med Virol 2019; 29:e2054. [PMID: 31197909 PMCID: PMC6771534 DOI: 10.1002/rmv.2054] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/03/2019] [Accepted: 04/27/2019] [Indexed: 12/15/2022]
Abstract
Herpes simplex virus (HSV) can cause oral or genital ulcerative lesions and even encephalitis in various age groups with high infection rates. More seriously, HSV may lead to a wide range of recurrent diseases throughout a lifetime. No vaccines against HSV are currently available. The accumulated clinical research data for HSV vaccines reveal that the effects of HSV interacting with the host, especially the host immune system, may be important for the development of HSV vaccines. HSV vaccine development remains a major challenge. Thus, we focus on the research data regarding the interactions of HSV and host immune cells, including dendritic cells (DCs), innate lymphoid cells (ILCs), macrophages, and natural killer (NK) cells, and the related signal transduction pathways involved in immune evasion and cytokine production. The aim is to explore possible strategies to develop new effective HSV vaccines.
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Affiliation(s)
- Xingli Xu
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Institute of Medical Biology, Chinese Academy of Medical SciencesPeking Union Medical CollegeKunmingChina
| | - Ying Zhang
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Institute of Medical Biology, Chinese Academy of Medical SciencesPeking Union Medical CollegeKunmingChina
| | - Qihan Li
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Institute of Medical Biology, Chinese Academy of Medical SciencesPeking Union Medical CollegeKunmingChina
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Asian Elephant T Cell Responses to Elephant Endotheliotropic Herpesvirus. J Virol 2018; 92:JVI.01951-17. [PMID: 29263271 PMCID: PMC5827410 DOI: 10.1128/jvi.01951-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 12/14/2017] [Indexed: 12/20/2022] Open
Abstract
Elephant endotheliotropic herpesvirus (EEHV) can cause lethal hemorrhagic disease in juvenile Asian elephants, an endangered species. One hypothesis to explain this vulnerability of some juvenile elephants is that they fail to mount an effective T cell response to the virus. To our knowledge, there have been no studies of Asian elephant T cell responses to EEHV. To address this deficiency, we validated the gamma interferon (IFN-γ) enzyme-linked immunospot assay for tracking antigen-directed T cell activity by monitoring rabies-specific responses in vaccinated elephants. In addition, we generated monoclonal antibodies to Asian elephant CD4 and CD8 to facilitate phenotypic T cell profiling. Using these tools, we screened healthy elephants with a history of EEHV infection for reactivity against nine EEHV proteins whose counterparts in other herpesviruses are known to induce T cell responses in their natural hosts. We identified glycoprotein B (gB) and the putative regulatory protein E40 as the most immunogenic T cell targets (IFN-γ responses in five of seven elephants), followed by the major capsid protein (IFN-γ responses in three of seven elephants). We also observed that IFN-γ responses were largely from CD4+ T cells. We detected no activity against the predicted major immediate early (E44) and large tegument (E34) proteins, both immunodominant T cell targets in humans latently infected with cytomegalovirus. These studies identified EEHV-specific T cells in Asian elephants for the first time, lending insight into the T cell priming that might be required to protect against EEHV disease, and will guide the design of effective vaccine strategies. IMPORTANCE Endangered Asian elephants are facing many threats, including lethal hemorrhagic disease from elephant endotheliotropic herpesvirus (EEHV). EEHV usually establishes chronic, benign infections in mature Asian elephants but can be lethal to juvenile elephants in captivity and the wild. It is the leading cause of death in captive Asian elephants in North America and Europe. Despite the availability of sensitive tests and protocols for treating EEHV-associated illness, these measures are not always effective. The best line of defense would be a preventative vaccine. We interrogated normal healthy elephants previously infected with EEHV for T cell responses to nine EEHV proteins predicted to induce cellular immune responses. Three proteins elicited IFN-γ responses, suggesting their potential usefulness as vaccine candidates. Our work is the first to describe T cell responses to a member of the proposed fourth subfamily of mammalian herpesviruses, the Deltaherpesvirinae, within a host species in the clade Afrotheria. An EEHV vaccine would greatly contribute to the health care of Asian and African elephants that are also susceptible to this disease.
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Kuo T, Wang C, Badakhshan T, Chilukuri S, BenMohamed L. The challenges and opportunities for the development of a T-cell epitope-based herpes simplex vaccine. Vaccine 2014; 32:6733-45. [PMID: 25446827 DOI: 10.1016/j.vaccine.2014.10.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/26/2014] [Accepted: 10/01/2014] [Indexed: 01/29/2023]
Abstract
Herpes simplex virus type 1 and type 2 (HSV-1 & HSV-2) infections have been prevalent since the ancient Greek times. To this day, they still affect a staggering number of over a billion individuals worldwide. HSV-1 infections are predominant than HSV-2 infections and cause potentially blinding ocular herpes, oro-facial herpes and encephalitis. HSV-2 infections cause painful genital herpes, encephalitis, and death in newborns. While prophylactic and therapeutic HSV vaccines remain urgently needed for centuries, their development has been difficult. During the most recent National Institute of Health (NIH) workshop titled "Next Generation Herpes Simplex Virus Vaccines: The Challenges and Opportunities", basic researchers, funding agencies, and pharmaceutical representatives gathered: (i) to assess the status of herpes vaccine research; and (ii) to identify the gaps and propose alternative approaches in developing a safe and efficient herpes vaccine. One "common denominator" among previously failed clinical herpes vaccine trials is that they either used a whole virus or a whole viral protein, which contain both "pathogenic symptomatic" and "protective asymptomatic" antigens and epitopes. In this report, we continue to advocate developing "asymptomatic" epitope-based sub-unit vaccine strategies that selectively incorporate "protective asymptomatic" epitopes which: (i) are exclusively recognized by effector memory CD4(+) and CD8(+) T cells (TEM cells) from "naturally" protected seropositive asymptomatic individuals; and (ii) protect human leukocyte antigen (HLA) transgenic animal models of ocular and genital herpes. We review the role of animal models in herpes vaccine development and discuss their current status, challenges, and prospects.
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Affiliation(s)
- Tiffany Kuo
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697-4375, USA
| | - Christine Wang
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697-4375, USA
| | - Tina Badakhshan
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697-4375, USA
| | - Sravya Chilukuri
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697-4375, USA
| | - Lbachir BenMohamed
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697-4375, USA; Department of Molecular Biology & Biochemistry, University of California Irvine, School of Medicine, Irvine, CA 92697, USA; Institute for Immunology, University of California Irvine, School of Medicine, Irvine, CA 92697, USA.
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Coppo MJC, Hartley CA, Devlin JM. Immune responses to infectious laryngotracheitis virus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 41:454-462. [PMID: 23567343 DOI: 10.1016/j.dci.2013.03.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 03/28/2013] [Accepted: 03/28/2013] [Indexed: 06/02/2023]
Abstract
Infectious laryngotracheitis (ILT) is an upper respiratory tract disease in chickens caused by infectious laryngotracheitis virus (ILTV), an alphaherpesvirus. Despite the extensive use of attenuated, and more recently recombinant, vaccines for the control of this disease, ILT continues to affect the intensive poultry industries worldwide. Innate and cell-mediated, rather than humoral immune responses, have been identified as responsible for protection against disease. This review examines the current understandings in innate and adaptive immune responses towards ILTV, as well as the role of ILTV glycoprotein G in modulating the host immune response towards infection. Protective immunity induced by ILT vaccines is also examined. The increasing availability of tools and reagents for the characterisation of avian innate and cell-mediated immune responses are expected to further our understanding of immunity against ILTV and drive the development of new generation vaccines towards enhanced control of this disease.
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Affiliation(s)
- Mauricio J C Coppo
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary Science, The University of Melbourne, Victoria, Australia
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Freer G, Rindi L. Intracellular cytokine detection by fluorescence-activated flow cytometry: basic principles and recent advances. Methods 2013; 61:30-8. [PMID: 23583887 DOI: 10.1016/j.ymeth.2013.03.035] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 03/26/2013] [Accepted: 03/31/2013] [Indexed: 01/24/2023] Open
Abstract
Intracellular cytokine staining is a flow cytometric technique consisting of culturing stimulated cytokine-producing cells in the presence of a protein secretion inhibitor, followed by fixation, permeabilization and staining of intracellular cytokines and cell markers (surface or cytoplasmic) with fluorescent antibodies. Up to 18 different colors can be detected by modern flow cytometers, making it the only immunological technique allowing simultaneous determination of antigen-specific T cell function and phenotype. In addition, cell proliferation and viability can be also measured. For this reason, it is probably the most popular method to measure antigenicity during vaccine trials and in the study of infectious diseases, along with ELISPOT. In this review, we will summarize its features, provide the protocol used by most laboratories and review its most recent applications.
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Affiliation(s)
- Giulia Freer
- Department of Experimental Pathology, University of Pisa, Via San Zeno, I-56127 Pisa, Italy.
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Ramachandran H, Laux J, Moldovan I, Caspell R, Lehmann PV, Subbramanian RA. Optimal thawing of cryopreserved peripheral blood mononuclear cells for use in high-throughput human immune monitoring studies. Cells 2012; 1:313-24. [PMID: 24710478 PMCID: PMC3901099 DOI: 10.3390/cells1030313] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 06/29/2012] [Accepted: 07/03/2012] [Indexed: 11/20/2022] Open
Abstract
Cryopreserved peripheral blood mononuclear cells (PBMC) constitute an important component of immune monitoring studies as they allow for efficient batch- testing of samples as well as for the validation and extension of original studies in the future. In this study, we systematically test the permutations of PBMC thawing practices commonly employed in the field and identify conditions that are high and low risk for the viability of PBMC and their functionality in downstream ELISPOT assays. The study identifies the addition of ice-chilled washing media to thawed cells at the same temperature as being a high risk practice, as it yields significantly lower viability and functionality of recovered PBMC when compared to warming the cryovials to 37 °C and adding a warm washing medium. We found thawed PBMC in cryovials could be kept up to 30 minutes at 37 °C in the presence of DMSO before commencement of washing, which surprisingly identifies exposure to DMSO as a low risk step during the thawing process. This latter finding is of considerable practical relevance since it permits batch-thawing of PBMC in high-throughput immune monitoring environments.
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Affiliation(s)
| | - Jessica Laux
- Cellular Technology Limited, Shaker Heights, OH 44122, USA.
| | - Ioana Moldovan
- Cellular Technology Limited, Shaker Heights, OH 44122, USA.
| | | | - Paul V Lehmann
- Cellular Technology Limited, Shaker Heights, OH 44122, USA.
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Laing KJ, Dong L, Sidney J, Sette A, Koelle DM. Immunology in the Clinic Review Series; focus on host responses: T cell responses to herpes simplex viruses. Clin Exp Immunol 2012; 167:47-58. [PMID: 22132884 PMCID: PMC3248086 DOI: 10.1111/j.1365-2249.2011.04502.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2011] [Indexed: 01/04/2023] Open
Abstract
Herpes virus infections are chronic and co-exist with acquired immune responses that generally prevent severe damage to the host, while allowing periodic shedding of virus and maintenance of its transmission in the community. Herpes simplex viruses type 1 and 2 (HSV-1, HSV-2) are typical in this regard and are representative of the viral subfamily Alphaherpesvirinae, which has a tropism for neuronal and epithelial cells. This review will emphasize recent progress in decoding the physiologically important CD8(+) and CD4(+) T cell responses to HSV in humans. The expanding data set is discussed in the context of the search for an effective HSV vaccine as therapy for existing infections and to prevent new infections.
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Affiliation(s)
- K J Laing
- Department of Medicine, University of Washington, Seattle, WA, USA
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