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Maxwell JWC, Stockdale S, Stewart EL, Ashley CL, Smith LJ, Steain M, Triccas JA, Byrne SN, Britton WJ, Ashhurst AS, Payne RJ. Intranasal Self-Adjuvanted Lipopeptide Vaccines Elicit High Antibody Titers and Strong Cellular Responses against SARS-CoV-2. ACS Infect Dis 2024; 10:3419-3429. [PMID: 39196071 DOI: 10.1021/acsinfecdis.4c00544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Despite concerted efforts to tackle the COVID-19 pandemic, the persistent transmission of SARS-CoV-2 demands continued research into novel vaccination strategies to combat the virus. In light of this, intranasally administered peptide vaccines, particularly those conjugated to an immune adjuvant to afford so-called "self-adjuvanted vaccines", remain underexplored. Here, we describe the synthesis and immunological evaluation of self-adjuvanting peptide vaccines derived from epitopes of the spike glycoprotein of SARS-CoV-2 covalently fused to the potent adjuvant, Pam2Cys, that targets toll-like receptor 2 (TLR2). When administered intranasally, these vaccines elicited a strong antigen-specific CD4+ and CD8+ T-cell response in the lungs as well as high titers of IgG and IgA specific to the native spike protein of SARS-CoV-2. Unfortunately, serum and lung fluid from mice immunized with these vaccines failed to inhibit viral entry in spike-expressing pseudovirus assays. Following this, we designed and synthesized fusion vaccines composed of the T-cell epitope discovered in this work, covalently fused to epitopes of the receptor-binding domain of the spike protein reported to be neutralizing. While antibodies elicited against these fusion vaccines were not neutralizing, the T-cell epitope retained its ability to stimulate strong antigen-specific CD4+ lymphocyte responses within the lungs. Given the Spike(883-909) region is still completely conserved in SARS-CoV-2 variants of concern and variants of interest, we envision the self-adjuvanting vaccine platform reported here may inform future vaccine efforts.
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MESH Headings
- Animals
- SARS-CoV-2/immunology
- Administration, Intranasal
- Mice
- COVID-19 Vaccines/immunology
- COVID-19 Vaccines/administration & dosage
- Spike Glycoprotein, Coronavirus/immunology
- COVID-19/prevention & control
- COVID-19/immunology
- Lipopeptides/immunology
- Lipopeptides/administration & dosage
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Adjuvants, Immunologic/administration & dosage
- Adjuvants, Immunologic/pharmacology
- Female
- Humans
- Mice, Inbred BALB C
- Adjuvants, Vaccine/administration & dosage
- Vaccines, Subunit/immunology
- Vaccines, Subunit/administration & dosage
- Immunity, Cellular
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- CD8-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/immunology
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Affiliation(s)
- Joshua W C Maxwell
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Skye Stockdale
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Erica L Stewart
- Sydney Institute for Infectious Diseases and the Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales 2006, Australia
- Tuberculosis Research Program Centenary Institute, The University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Caroline L Ashley
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Institute for Infectious Diseases and the Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Lachlan J Smith
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Institute for Infectious Diseases and the Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Megan Steain
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Institute for Infectious Diseases and the Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales 2006, Australia
| | - James A Triccas
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Institute for Infectious Diseases and the Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Scott N Byrne
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Institute for Infectious Diseases and the Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Warwick J Britton
- Tuberculosis Research Program Centenary Institute, The University of Sydney, Camperdown, New South Wales 2006, Australia
- Department of Clinical Immunology, Royal Prince Alfred Hospital, Camperdown, New South Wales 2050, Australia
| | - Anneliese S Ashhurst
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Institute for Infectious Diseases and the Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales 2006, Australia
- Tuberculosis Research Program Centenary Institute, The University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Richard J Payne
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
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2
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Cohen CA, Leung NHL, Kaewpreedee P, Lee KWK, Jia JZ, Cheung AWL, Cheng SMS, Mori M, Ip DKM, Poon LLM, Peiris JSM, Cowling BJ, Valkenburg SA. Antibody Fc receptor binding and T cell responses to homologous and heterologous immunization with inactivated or mRNA vaccines against SARS-CoV-2. Nat Commun 2024; 15:7358. [PMID: 39191745 PMCID: PMC11350167 DOI: 10.1038/s41467-024-51427-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Whole virion inactivated vaccine CoronaVac (C) and Spike (S) mRNA BNT162b2 (B) vaccines differ greatly in their ability to elicit neutralizing antibodies but have somewhat comparable effectiveness in protecting from severe COVID-19. We conducted further analyses for a randomized trial (Cobovax study, NCT05057169) of third dose homologous and heterologous booster vaccination, i.e. four interventions CC-C, CC-B, BB-C and BB-B. Here, we assess vaccine immunogenicity beyond neutralizing function, including S and non-S antibodies with Fc receptor (FcR) binding, antibody avidity and T cell specificity to 6 months post-vaccination. Ancestral and Omicron S-specific IgG and FcR binding are significantly higher by BNT162b2 booster than CoronaVac, regardless of first doses. Nucleocapsid (N) antibodies are only increased in homologous boosted CoronaVac participants (CC-C). CoronaVac primed participants have lower baseline S-specific CD4+ IFNγ+ cells, but are significantly increased by either CoronaVac or BNT162b2 boosters. Priming vaccine content defined T cell peptide specificity preference, with S-specific T cells dominating B primed groups and non-S structural peptides contributing more in C primed groups, regardless of booster type. S-specific CD4+ T cell responses, N-specific antibodies, and antibody effector functions via Fc receptor binding may contribute to protection and compensate for less potent neutralizing responses in CoronaVac recipients.
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Affiliation(s)
- Carolyn A Cohen
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Nancy H L Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
- Takemi Program in International Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Prathanporn Kaewpreedee
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kelly W K Lee
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Janice Zhirong Jia
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Alan W L Cheung
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Samuel M S Cheng
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Masashi Mori
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Japan
| | - Dennis K M Ip
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Leo L M Poon
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Centre for Immunology and Infection, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - J S Malik Peiris
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Centre for Immunology and Infection, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.
- Department of Microbiology and Immunology, Peter Doherty Institute of Infection and Immunity, The University of Melbourne, Melbourne, Australia.
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3
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Sheetikov SA, Khmelevskaya AA, Zornikova KV, Zvyagin IV, Shomuradova AS, Serdyuk YV, Shakirova NT, Peshkova IO, Titov A, Romaniuk DS, Shagina IA, Chudakov DM, Kiryukhin DO, Shcherbakova OV, Khamaganova EG, Dzutseva V, Afanasiev A, Bogolyubova AV, Efimov GA. Clonal structure and the specificity of vaccine-induced T cell response to SARS-CoV-2 Spike protein. Front Immunol 2024; 15:1369436. [PMID: 38629062 PMCID: PMC11018901 DOI: 10.3389/fimmu.2024.1369436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Adenovirus vaccines, particularly the COVID-19 Ad5-nCoV adenovirus vaccine, have emerged as promising tools in the fight against infectious diseases. In this study, we investigated the structure of the T cell response to the Spike protein of the SARS-CoV-2 virus used in the COVID-19 Ad5-nCoV adenoviral vaccine in a phase 3 clinical trial (NCT04540419). In 69 participants, we collected peripheral blood samples at four time points after vaccination or placebo injection. Sequencing of T cell receptor repertoires from Spike-stimulated T cell cultures at day 14 from 17 vaccinated revealed a more diverse CD4+ T cell repertoire compared to CD8+. Nevertheless, CD8+ clonotypes accounted for more than half of the Spike-specific repertoire. Our longitudinal analysis showed a peak T cell response at day 14, followed by a decline until month 6. Remarkably, multiple T cell clonotypes persisted for at least 6 months after vaccination, as demonstrated by ex vivo stimulation. Examination of CDR3 regions revealed homologous sequences in both CD4+ and CD8+ clonotypes, with major CD8+ clonotypes sharing high similarity with annotated sequences specific for the NYNYLYRLF peptide, suggesting potential immunodominance. In conclusion, our study demonstrates the immunogenicity of the Ad5-nCoV adenoviral vaccine and highlights its ability to induce robust and durable T cell responses. These findings provide valuable insight into the efficacy of the vaccine against COVID-19 and provide critical information for ongoing efforts to control infectious diseases.
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Affiliation(s)
- Saveliy A. Sheetikov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexandra A. Khmelevskaya
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Ksenia V. Zornikova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ivan V. Zvyagin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Alina S. Shomuradova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yana V. Serdyuk
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Naina T. Shakirova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Iuliia O. Peshkova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Aleksei Titov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Dmitrii S. Romaniuk
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Irina A. Shagina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Dmitry M. Chudakov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Dmitry O. Kiryukhin
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Olga V. Shcherbakova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Ekaterina G. Khamaganova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Vitalina Dzutseva
- Novosibirsk State University, Medical School, Novosibirsk, Russia
- NPO Petrovax Pharm LLC, Moscow, Russia
| | | | | | - Grigory A. Efimov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
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4
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Tatsi EB, Filippatos F, Bello T, Syriopoulou V, Michos A. Comparative Study of T-Cell Repertoires after COVID-19 Immunization with Homologous or Heterologous Vaccine Booster. Pathogens 2024; 13:284. [PMID: 38668239 PMCID: PMC11054887 DOI: 10.3390/pathogens13040284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/29/2024] Open
Abstract
Sequencing of the T-cell repertoire is an innovative method to assess the cellular responses after immunization. The purpose of this study was to compare T-cell repertoires after COVID-19 immunization with homologous (HOB) and heterologous (HEB) boosting. The study included 20 participants with a median age of 27.5 (IQR:23) years, who were vaccinated with one dose of the Ad26.COV2.S vaccine and were boosted with either Ad26.COV2.S (n = 10) or BNT162b2 (n = 10) vaccine. Analysis of the T-cell receptor beta locus (TCRβ) sequencing one month after the booster dose identified that the HEB compared to the HOB group exhibited a higher number of both total and COVID-19-related functional T-cell rearrangements [mean of total productive rearrangements (TPRs): 63151.8 (SD ± 18441.5) vs. 34915.4 (SD ± 11121.6), p = 0.001 and COVID-19-TPRs: 522.5 (SD ± 178.0) vs. 298.3 (SD ± 101.1), p = 0.003]. A comparison between the HOB and HEB groups detected no statistically significant differences regarding T-cell Simpson clonality [0.021 (IQR:0.014) vs. 0.019 (IQR:0.007)], richness [8734.5 (IQR:973.3) vs. 8724 (IQR:383.7)] and T-cell fraction [0.19 (IQR:0.08) vs. 0.18 (IQR:0.08)]. HEB also exhibited a substantially elevated humoral immune response one month after the booster dose compared to HOB [median antibody titer (IQR): 10115.0 U/mL (6993.0) vs. 1781.0 U/mL (1314.0), p = 0.001]. T-cell repertoire sequencing indicated that HEB had increased SARS-CoV-2-related T-cell rearrangements, which was in accordance with higher humoral responses and possibly conferring longer protection. Data from the present study indicate that the administration of different COVID-19 vaccines as a booster may provide better protection.
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Affiliation(s)
- Elizabeth-Barbara Tatsi
- Infectious Diseases and Chemotherapy Research Laboratory, First Department of Pediatrics, Medical School, “Aghia Sophia” Children’s Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.-B.T.); (F.F.)
| | - Filippos Filippatos
- Infectious Diseases and Chemotherapy Research Laboratory, First Department of Pediatrics, Medical School, “Aghia Sophia” Children’s Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.-B.T.); (F.F.)
| | - Thomas Bello
- Adaptive Biotechnologies, Seattle 98109, WA, USA;
| | - Vasiliki Syriopoulou
- Infectious Diseases and Chemotherapy Research Laboratory, First Department of Pediatrics, Medical School, “Aghia Sophia” Children’s Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.-B.T.); (F.F.)
| | - Athanasios Michos
- Infectious Diseases and Chemotherapy Research Laboratory, First Department of Pediatrics, Medical School, “Aghia Sophia” Children’s Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.-B.T.); (F.F.)
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5
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Sop J, Traut CC, Dykema AG, Hunt JH, Beckey TP, Basseth CR, Antar AAR, Laeyendecker O, Smith KN, Blankson JN. Bivalent mRNA COVID vaccines elicit predominantly cross-reactive CD4 + T cell clonotypes. Cell Rep Med 2024; 5:101442. [PMID: 38423018 PMCID: PMC10983033 DOI: 10.1016/j.xcrm.2024.101442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/28/2023] [Accepted: 02/03/2024] [Indexed: 03/02/2024]
Abstract
Bivalent COVID vaccines containing mRNA for ancestral and Omicron BA.5 spike proteins do not induce stronger T cell responses to Omicron BA.5 spike proteins than monovalent vaccines that contain only ancestral spike mRNA. The reasons for this finding have not been elucidated. Here, we show that healthy donors (HDs) and people living with HIV (PLWH) on antiretroviral therapy mostly target T cell epitopes that are not affected by BA.5 mutations. We use the functional expansion of specific T cells (FEST) assay to determine the percentage of CD4+ T cells that cross-recognize both spike proteins and those that are monoreactive for each protein. We show a predominance of cross-reactive CD4+ T cells; less than 10% percent of spike-specific CD4+ T cell receptors were BA.5 monoreactive in most HDs and PLWH. Our data suggest that the current bivalent vaccines do not induce robust BA.5-monoreactive T cell responses.
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Affiliation(s)
- Joel Sop
- Department of Medicine, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Caroline C Traut
- Department of Medicine, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Arbor G Dykema
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins Medicine, Baltimore, MD, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Joanne H Hunt
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Baltimore, MD, USA
| | - Tyler P Beckey
- Department of Medicine, Johns Hopkins Medicine, Baltimore, MD, USA
| | | | | | - Oliver Laeyendecker
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Baltimore, MD, USA
| | - Kellie N Smith
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins Medicine, Baltimore, MD, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
| | - Joel N Blankson
- Department of Medicine, Johns Hopkins Medicine, Baltimore, MD, USA.
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6
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Reeves DB, Rigau DN, Romero A, Zhang H, Simonetti FR, Varriale J, Hoh R, Zhang L, Smith KN, Montaner LJ, Rubin LH, Gange SJ, Roan NR, Tien PC, Margolick JB, Peluso MJ, Deeks SG, Schiffer JT, Siliciano JD, Siliciano RF, Antar AAR. Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.13.24302704. [PMID: 38405967 PMCID: PMC10888981 DOI: 10.1101/2024.02.13.24302704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The latent reservoir of HIV persists for decades in people living with HIV (PWH) on antiretroviral therapy (ART). To determine if persistence arises from the natural dynamics of memory CD4+ T cells harboring HIV, we compared the clonal dynamics of HIV proviruses to that of memory CD4+ T cell receptors (TCRβ) from the same PWH and from HIV-seronegative people. We show that clonal dominance of HIV proviruses and antigen-specific CD4+ T cells are similar but that the field's understanding of the persistence of the less clonally dominant reservoir is significantly limited by undersampling. We demonstrate that increasing reservoir clonality over time and differential decay of intact and defective proviruses cannot be explained by mCD4+ T cell kinetics alone. Finally, we develop a stochastic model of TCRβ and proviruses that recapitulates experimental observations and suggests that HIV-specific negative selection mediates approximately 6% of intact and 2% of defective proviral clearance. Thus, HIV persistence is mostly, but not entirely, driven by natural mCD4+ T cell kinetics.
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7
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Ford ES, Mayer-Blackwell K, Jing L, Laing KJ, Sholukh AM, St Germain R, Bossard EL, Xie H, Pulliam TH, Jani S, Selke S, Burrow CJ, McClurkan CL, Wald A, Greninger AL, Holbrook MR, Eaton B, Eudy E, Murphy M, Postnikova E, Robins HS, Elyanow R, Gittelman RM, Ecsedi M, Wilcox E, Chapuis AG, Fiore-Gartland A, Koelle DM. Repeated mRNA vaccination sequentially boosts SARS-CoV-2-specific CD8 + T cells in persons with previous COVID-19. Nat Immunol 2024; 25:166-177. [PMID: 38057617 PMCID: PMC10981451 DOI: 10.1038/s41590-023-01692-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 10/27/2023] [Indexed: 12/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hybrid immunity is more protective than vaccination or previous infection alone. To investigate the kinetics of spike-reactive T (TS) cells from SARS-CoV-2 infection through messenger RNA vaccination in persons with hybrid immunity, we identified the T cell receptor (TCR) sequences of thousands of index TS cells and tracked their frequency in bulk TCRβ repertoires sampled longitudinally from the peripheral blood of persons who had recovered from coronavirus disease 2019 (COVID-19). Vaccinations led to large expansions in memory TS cell clonotypes, most of which were CD8+ T cells, while also eliciting diverse TS cell clonotypes not observed before vaccination. TCR sequence similarity clustering identified public CD8+ and CD4+ TCR motifs associated with spike (S) specificity. Synthesis of longitudinal bulk ex vivo single-chain TCRβ repertoires and paired-chain TCRɑβ sequences from droplet sequencing of TS cells provides a roadmap for the rapid assessment of T cell responses to vaccines and emerging pathogens.
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Affiliation(s)
- Emily S Ford
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kerry J Laing
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Anton M Sholukh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Russell St Germain
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Emily L Bossard
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Thomas H Pulliam
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Saumya Jani
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Stacy Selke
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | | | - Anna Wald
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Michael R Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Brett Eaton
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Elizabeth Eudy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Michael Murphy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Elena Postnikova
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | | | | | - Rachel M Gittelman
- Adaptive Biotechnologies, Seattle, WA, USA
- Guardant Health, Redwood City, CA, USA
| | - Matyas Ecsedi
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Takeda Oncology, Cambridge, MA, USA
| | - Elise Wilcox
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Aude G Chapuis
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, WA, USA.
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA.
- Department of Translational Research, Benaroya Research Institute, Seattle, WA, USA.
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8
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Rakshit S, Babji S, Parthiban C, Madhavan R, Adiga V, J SE, Chetan Kumar N, Ahmed A, Shivalingaiah S, Shashikumar N, V M, Johnson AR, Ramesh N, B RG, Asokan M, Mayor S, Kang G, D'souza G, Dias M, Vyakarnam A. Polyfunctional CD4 T-cells correlating with neutralising antibody is a hallmark of COVISHIELD TM and COVAXIN ® induced immunity in COVID-19 exposed Indians. NPJ Vaccines 2023; 8:134. [PMID: 37709772 PMCID: PMC10502007 DOI: 10.1038/s41541-023-00731-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023] Open
Abstract
Detailed characterisation of immune responses induced by COVID-19 vaccines rolled out in India: COVISHIELDTM (CS) and COVAXIN® (CO) in a pre-exposed population is only recently being discovered. We addressed this issue in subjects who received their primary series of vaccination between November 2021 and January 2022. Both vaccines are capable of strongly boosting Wuhan Spike-specific neutralising antibody, polyfunctional Th1 cytokine producing CD4+ T-cells and single IFN-γ + CD8+ T-cells. Consistent with inherent differences in vaccine platform, the vector-based CS vaccine-induced immunity was of greater magnitude, breadth, targeting Delta and Omicron variants compared to the whole-virion inactivated vaccine CO, with CS vaccinees showing persistent CD8+ T-cells responses until 3 months post primary vaccination. This study provides detailed evidence on the magnitude and quality of CS and CO vaccine induced responses in subjects with pre-existing SARS-CoV-2 immunity in India, thereby mitigating vaccine hesitancy arguments in such a population, which remains a global health challenge.
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Affiliation(s)
- Srabanti Rakshit
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, Karnataka, India
| | - Sudhir Babji
- The Wellcome Trust Research Laboratory, Christian Medical College, Vellore, Tamil Nadu, India
| | - Chaitra Parthiban
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, Karnataka, India
| | - Ramya Madhavan
- The Wellcome Trust Research Laboratory, Christian Medical College, Vellore, Tamil Nadu, India
| | - Vasista Adiga
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, Karnataka, India
- Department of Biotechnology, PES University, Bangalore, Karnataka, India
| | - Sharon Eveline J
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, Karnataka, India
| | - Nirutha Chetan Kumar
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, Karnataka, India
| | - Asma Ahmed
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, Karnataka, India
| | | | - Nandini Shashikumar
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, Karnataka, India
| | - Mamatha V
- St. John's Medical College, Bangalore, Karnataka, India
| | | | - Naveen Ramesh
- St. John's Medical College, Bangalore, Karnataka, India
| | | | | | - Satyajit Mayor
- National Centre for Biological Sciences, Bengaluru, Karnataka, India
| | - Gagandeep Kang
- The Wellcome Trust Research Laboratory, Christian Medical College, Vellore, Tamil Nadu, India
| | - George D'souza
- Department of Pulmonary Medicine, St. John's Medical College, Bangalore, Karnataka, India
| | - Mary Dias
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, Karnataka, India
- St. John's Medical College, Bangalore, Karnataka, India
| | - Annapurna Vyakarnam
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, Karnataka, India.
- Department of Immunobiology, School of Immunology & Microbial Sciences, Faculty of Life Science & Medicine, King's College, London, UK.
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9
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de Greef PC, Lanfermeijer J, Hendriks M, Cevirgel A, Vos M, Borghans JAM, van Baarle D, de Boer RJ. On the feasibility of using TCR sequencing to follow a vaccination response - lessons learned. Front Immunol 2023; 14:1210168. [PMID: 37520553 PMCID: PMC10374308 DOI: 10.3389/fimmu.2023.1210168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
T cells recognize pathogens by their highly specific T-cell receptor (TCR), which can bind small fragments of an antigen presented on the Major Histocompatibility Complex (MHC). Antigens that are provided through vaccination cause specific T cells to respond by expanding and forming specific memory to combat a future infection. Quantification of this T-cell response could improve vaccine monitoring or identify individuals with a reduced ability to respond to a vaccination. In this proof-of-concept study we use longitudinal sequencing of the TCRβ repertoire to quantify the response in the CD4+ memory T-cell pool upon pneumococcal conjugate vaccination. This comes with several challenges owing to the enormous size and diversity of the T-cell pool, the limited frequency of vaccine-specific TCRs in the total repertoire, and the variation in sample size and quality. We defined quantitative requirements to classify T-cell expansions and identified critical parameters that aid in reliable analysis of the data. In the context of pneumococcal conjugate vaccination, we were able to detect robust T-cell expansions in a minority of the donors, which suggests that the T-cell response against the conjugate in the pneumococcal vaccine is small and/or very broad. These results indicate that there is still a long way to go before TCR sequencing can be reliably used as a personal biomarker for vaccine-induced protection. Nevertheless, this study highlights the importance of having multiple samples containing sufficient T-cell numbers, which will support future studies that characterize T-cell responses using longitudinal TCR sequencing.
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Affiliation(s)
- Peter C. de Greef
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | - Josien Lanfermeijer
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Marion Hendriks
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Alper Cevirgel
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Martijn Vos
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - José A. M. Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Debbie van Baarle
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Rob J. de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
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10
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Blankson JN. Bivalent COVID-19 Vaccines: Can the Original Antigenic Sin Be Forgiven? J Infect Dis 2023; 227:1221-1223. [PMID: 37016931 PMCID: PMC10411926 DOI: 10.1093/infdis/jiad073] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 04/06/2023] Open
Affiliation(s)
- Joel N Blankson
- Departments of Medicine and Molecular and Comparative Pathobiology, Johns Hopkins Medicine, Baltimore, Maryland
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11
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Gatti A, Zizzo G, De Paschale M, Tamburello A, Castelnovo L, Faggioli PM, Clerici P, Brando B, Mazzone A. Assessing SARS-CoV-2-specific T-cell reactivity in late convalescents and vaccinees: Comparison and combination of QuantiFERON and activation-induced marker assays, and relation with antibody status. PLoS One 2023; 18:e0285728. [PMID: 37220145 DOI: 10.1371/journal.pone.0285728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/28/2023] [Indexed: 05/25/2023] Open
Abstract
OBJECTIVES Monitoring of SARS-CoV-2 spread and vaccination strategies have relied on antibody (Ab) status as a correlate of protection. We used QuantiFERON™ (QFN) and Activation-Induced Marker (AIM) assays to measure memory T-cell reactivity in unvaccinated individuals with prior documented symptomatic infection (late convalescents) and fully vaccinated asymptomatic donors (vaccinees). METHODS Twenty-two convalescents and 13 vaccinees were enrolled. Serum anti-SARS-CoV-2 S1 and N Abs were measured using chemiluminescent immunoassays. QFN was performed following instructions and interferon-gamma (IFN-γ) measured by ELISA. AIM was performed on aliquots of antigen-stimulated samples from QFN tubes. SARS-CoV-2-specific memory CD4+CD25+CD134+, CD4+CD69+CD137+ and CD8+CD69+CD137+ T-cell frequencies were measured by flow cytometry. RESULTS In convalescents, substantial agreement was observed between QFN and AIM assays. IFN-γ concentrations and AIM+ (CD69+CD137+) CD4+ T-cell frequencies correlated with each other, with Ab levels and AIM+ CD8+ T-cell frequencies, whereas AIM+ (CD25+CD134+) CD4+ T-cell frequencies correlated with age. AIM+ CD4+ T-cell frequencies increased with time since infection, whereas AIM+ CD8+ T-cell expansion was greater after recent reinfection. QFN-reactivity and anti-S1 titers were lower, whereas anti-N titers were higher, and no statistical difference in AIM-reactivity and Ab positivity emerged compared to vaccinees. CONCLUSIONS Albeit on a limited sample size, we confirm that coordinated, cellular and humoral responses are detectable in convalescents up to 2 years after prior infection. Combining QFN with AIM may enhance detection of naturally acquired memory responses and help stratify virus-exposed individuals in T helper 1-type (TH1)-reactive (QFNpos AIMpos Abshigh), non-TH1-reactive (QFNneg AIMpos Abshigh/low), and pauci-reactive (QFNneg AIMneg Abslow).
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Affiliation(s)
- Arianna Gatti
- Laboratory of Haematology, Transfusion Center, Legnano Hospital, ASST Ovest Milanese, via Papa Giovanni Paolo II, Legnano, Milan, Italy
| | - Gaetano Zizzo
- Department of Internal Medicine, Legnano and Cuggiono Hospitals, ASST Ovest Milanese, via Papa Giovanni Paolo II, Legnano, Milan, Italy
| | - Massimo De Paschale
- Unit of Microbiology, Legnano Hospital, ASST Ovest Milanese, via Papa Giovanni Paolo II, Legnano, Milan, Italy
| | - Antonio Tamburello
- Department of Internal Medicine, Legnano and Cuggiono Hospitals, ASST Ovest Milanese, via Papa Giovanni Paolo II, Legnano, Milan, Italy
| | - Laura Castelnovo
- Department of Internal Medicine, Legnano and Cuggiono Hospitals, ASST Ovest Milanese, via Papa Giovanni Paolo II, Legnano, Milan, Italy
| | - Paola Maria Faggioli
- Department of Internal Medicine, Legnano and Cuggiono Hospitals, ASST Ovest Milanese, via Papa Giovanni Paolo II, Legnano, Milan, Italy
| | - Pierangelo Clerici
- Unit of Microbiology, Legnano Hospital, ASST Ovest Milanese, via Papa Giovanni Paolo II, Legnano, Milan, Italy
| | - Bruno Brando
- Laboratory of Haematology, Transfusion Center, Legnano Hospital, ASST Ovest Milanese, via Papa Giovanni Paolo II, Legnano, Milan, Italy
| | - Antonino Mazzone
- Department of Internal Medicine, Legnano and Cuggiono Hospitals, ASST Ovest Milanese, via Papa Giovanni Paolo II, Legnano, Milan, Italy
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12
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Zornikova KV, Sheetikov SA, Rusinov AY, Iskhakov RN, Bogolyubova AV. Architecture of the SARS-CoV-2-specific T cell repertoire. Front Immunol 2023; 14:1070077. [PMID: 37020560 PMCID: PMC10067759 DOI: 10.3389/fimmu.2023.1070077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/08/2023] [Indexed: 03/22/2023] Open
Abstract
The T cell response plays an indispensable role in the early control and successful clearance of SARS-CoV-2 infection. However, several important questions remain about the role of cellular immunity in COVID-19, including the shape and composition of disease-specific T cell repertoires across convalescent patients and vaccinated individuals, and how pre-existing T cell responses to other pathogens—in particular, common cold coronaviruses—impact susceptibility to SARS-CoV-2 infection and the subsequent course of disease. This review focuses on how the repertoire of T cell receptors (TCR) is shaped by natural infection and vaccination over time. We also summarize current knowledge regarding cross-reactive T cell responses and their protective role, and examine the implications of TCR repertoire diversity and cross-reactivity with regard to the design of vaccines that confer broader protection against SARS-CoV-2 variants.
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Affiliation(s)
- Ksenia V. Zornikova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Saveliy A. Sheetikov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander Yu Rusinov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Rustam N. Iskhakov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Apollinariya V. Bogolyubova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- *Correspondence: Apollinariya V. Bogolyubova,
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13
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Paniskaki K, Konik MJ, Anft M, Meister TL, Marheinecke C, Pfaender S, Jäger J, Krawczyk A, Zettler M, Dolff S, Westhoff TH, Rohn H, Stervbo U, Witzke O, Babel N. Superior humoral immunity in vaccinated SARS-CoV-2 convalescence as compared to SARS-COV-2 infection or vaccination. Front Immunol 2022; 13:1031254. [PMID: 36389833 PMCID: PMC9659602 DOI: 10.3389/fimmu.2022.1031254] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/20/2022] [Indexed: 11/24/2023] Open
Abstract
Emerging variants of concern (VOC) raise obstacles in shaping vaccination strategies and ending the pandemic. Vaccinated SARS-CoV-2 convalescence shapes the current immune dynamics. We analyzed the SARS-CoV-2 VOC-specific cellular and humoral response of 57 adults: 42 convalescent mRNA vaccinated patients (C+V+), 8 uninfected mRNA vaccinated (C-V+) and 7 unvaccinated convalescent individuals (C+V-). While C+V+ demonstrated a superior humoral SARS-CoV-2 response against all analyzed VOC (alpha, delta, omicron) compared to C-V+ and C+V-, SARS-CoV-2 reactive CD4+ and CD8+ T cells, which can cross-recognize the alpha, delta and omicron VOC after infection and/or vaccination were observed in all there groups without significant differences between the groups. We observed a preserved cross-reactive C+V+ and C-V+ T cell memory. An inferior humoral response but preserved cross-reactive T cell memory in C+V- compared to C+V+ was observed, as well as an inferior humoral response but preserved cross-reactive T cell memory in C+V- compared to C-V+. Adaptive immunity generated after SARS-CoV-2 infection and vaccination leads to superior humoral immune response against VOC compared to isolated infection or vaccination. Despite the apparent loss of neutralization potential caused by viral evolution, a preserved SARS-CoV-2 reactive T cell response with a robust potential for cross-recognition of the alpha, delta and omicron VOC was detected in all studied cohorts. Our results may have implications on current vaccination strategies.
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Affiliation(s)
- Krystallenia Paniskaki
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Margarethe J. Konik
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Moritz Anft
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Toni L. Meister
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Corinna Marheinecke
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Stephanie Pfaender
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Jasmin Jäger
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Adalbert Krawczyk
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Markus Zettler
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Sebastian Dolff
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Timm H. Westhoff
- Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany
| | - Hana Rohn
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ulrik Stervbo
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Oliver Witzke
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Nina Babel
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
- Berlin Institute of Health at Charité – University Clinic Berlin, BIH Center for Regenerative Therapies (BCRT) Berlin, Berlin, Germany
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14
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Casenaz A, Grosjean S, Aho-Glélé LS, Bour JB, Auvray C, Manoha C. Humoral and cellular immune response after severe acute respiratory syndrome coronavirus 2 messenger ribonucleic acid vaccination in heart transplant recipients: An observational study in France. Front Med (Lausanne) 2022; 9:1027708. [PMID: 36388890 PMCID: PMC9643719 DOI: 10.3389/fmed.2022.1027708] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/05/2022] [Indexed: 07/30/2023] Open
Abstract
INTRODUCTION Heart transplant (HT) recipients have a high risk of developing severe COVID-19. Immunoglobulin G antibodies are considered to provide protective immunity and T-cell activity is thought to confer protection from severe disease. However, data on T-cell response to mRNA vaccination in a context of HT remains limited. METHODS In 96 HT patients, a IFN-γ release assay and an anti-Spike antibody test were used to evaluate the ability of SARS-CoV-2 mRNA vaccines to generate cellular and humoral immune response. Blood samples were collected few weeks to 7 months after vaccination. Multiple fractional polynomial and LASSO regression models were used to define predictors of T-cell response. RESULTS Three to five months after vaccination, three doses of vaccine induced a positive SARS-CoV-2 T-cell response in 47% of recipients and a positive humoral response in 83% of recipients, 11.1% of patients remained negative for both T and B cell responses. Three doses were necessary to reach high IgG response levels (>590 BAU/mL), which were obtained in a third of patients. Immunity was greatly amplified in the group who had three vaccine doses plus COVID-19 infection. CONCLUSION Our study revealed that T and B immunity decreases over time, leading us to suggest the interest of a booster vaccination at 5 months after the third dose. Moreover, a close follow-up of immune response following vaccination is needed to ensure ongoing immune protection. We also found that significant predictors of higher cellular response were infection and active smoking, regardless of immunosuppressive treatment with mycophenolate mofetil (MMF).
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Affiliation(s)
- Alice Casenaz
- Virology Laboratory, Department of Microbiology, Dijon Bourgogne University Hospital, Dijon, France
| | - Sandrine Grosjean
- Department of Anaesthesiology and Critical Care Medicine, Dijon Bourgogne University Hospital, Dijon, France
| | - Ludwig-Serge Aho-Glélé
- Epidemiology and Infection Control Unit, Dijon Bourgogne University Hospital, Dijon, France
| | - Jean-Baptiste Bour
- Virology Laboratory, Department of Microbiology, Dijon Bourgogne University Hospital, Dijon, France
| | - Christelle Auvray
- Virology Laboratory, Department of Microbiology, Dijon Bourgogne University Hospital, Dijon, France
| | - Catherine Manoha
- Virology Laboratory, Department of Microbiology, Dijon Bourgogne University Hospital, Dijon, France
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15
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Ford ES, Mayer-Blackwell K, Jing L, Sholukh AM, St Germain R, Bossard EL, Xie H, Pulliam TH, Jani S, Selke S, Burrow CJ, McClurkan CL, Wald A, Holbrook MR, Eaton B, Eudy E, Murphy M, Postnikova E, Robins HS, Elyanow R, Gittelman RM, Ecsedi M, Wilcox E, Chapuis AG, Fiore-Gartland A, Koelle DM. CD8 + T cell clonotypes from prior SARS-CoV-2 infection predominate during the cellular immune response to mRNA vaccination. RESEARCH SQUARE 2022:rs.3.rs-2146712. [PMID: 36263073 PMCID: PMC9580387 DOI: 10.21203/rs.3.rs-2146712/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Almost three years into the SARS-CoV-2 pandemic, hybrid immunity is highly prevalent worldwide and more protective than vaccination or prior infection alone. Given emerging resistance of variant strains to neutralizing antibodies (nAb), it is likely that T cells contribute to this protection. To understand how sequential SARS-CoV-2 infection and mRNA-vectored SARS-CoV-2 spike (S) vaccines affect T cell clonotype-level expansion kinetics, we identified and cross-referenced TCR sequences from thousands of S-reactive single cells against deeply sequenced peripheral blood TCR repertoires longitudinally collected from persons during COVID-19 convalescence through booster vaccination. Successive vaccinations recalled memory T cells and elicited antigen-specific T cell clonotypes not detected after infection. Vaccine-related recruitment of novel clonotypes and the expansion of S-specific clones were most strongly observed for CD8+ T cells. Severe COVID-19 illness was associated with a more diverse CD4+ T cell response to SARS-CoV-2 both prior to and after mRNA vaccination, suggesting imprinting of CD4+ T cells by severe infection. TCR sequence similarity search algorithms revealed myriad public TCR clusters correlating with human leukocyte antigen (HLA) alleles. Selected TCRs from distinct clusters functionally recognized S in the predicted HLA context, with fine viral peptide requirements differing between TCRs. Most subjects tested had S-specific T cells in the nasal mucosa after a 3rd mRNA vaccine dose. The blood and nasal T cell responses to vaccination revealed by clonal tracking were more heterogeneous than nAb boosts. Analysis of bulk and single cell TCR sequences reveals T cell kinetics and diversity at the clonotype level, without requiring prior knowledge of T cell epitopes or HLA restriction, providing a roadmap for rapid assessment of T cell responses to emerging pathogens.
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