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Yu T, Xing J, Zhuang X, Tian M. Evaluation of broad-spectrum protection by novel mRNA vaccines against SARS-CoV-2 variants (Delta, Omicron-BA.5, XBB-EG.5) in the golden hamster model. Virol J 2025; 22:159. [PMID: 40410742 PMCID: PMC12102927 DOI: 10.1186/s12985-025-02787-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2025] [Accepted: 05/10/2025] [Indexed: 05/25/2025] Open
Abstract
BACKGROUND The SARS-CoV-2 virus has continuously evolved, with new variants like Delta, Omicron-BA.5, and XBB-EG.5 posing challenges to vaccine efficacy. mRNA vaccines have emerged as a promising tool due to their rapid development and adaptability. This study evaluates the protective efficacy of six novel mRNA vaccine candidates against these variants using a golden hamster model. METHODS Six mRNA vaccines were designed, targeting the spike (S) and nucleocapsid (N) proteins of SARS-CoV-2. The vaccines were tested on golden hamsters, which were immunized and then challenged with Delta, Omicron-BA.5, and XBB-EG.5 variants. Key outcomes measured included body weight, viral RNA loads in various tissues, cytokine levels, and lung tissue pathology. RESULTS Hamsters vaccinated with the novel mRNA vaccines showed reduced weight loss, lower viral RNA loads in throat swabs and lung tissues, and reduced levels of pro-inflammatory cytokines compared to control groups. Additionally, vaccinated animals exhibited significantly less lung damage as evidenced by both histological and immunofluorescence analyses, especially in groups vaccinated with RBD-Fe, RE-N, and COVID-19 epitope formulations. CONCLUSIONS These mRNA vaccines demonstrated broad protective efficacy against multiple SARS-CoV-2 variants. They elicited immune responses, reduced viral RNA loads, and mitigated inflammatory and pathological damage, highlighting their potential in combating rapidly evolving SARS-CoV-2 variants.
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MESH Headings
- Animals
- SARS-CoV-2/immunology
- SARS-CoV-2/genetics
- COVID-19/prevention & control
- COVID-19/immunology
- COVID-19/virology
- COVID-19 Vaccines/immunology
- COVID-19 Vaccines/administration & dosage
- Mesocricetus
- Cricetinae
- Disease Models, Animal
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Lung/pathology
- Lung/virology
- Viral Load
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- mRNA Vaccines/immunology
- Cytokines
- Coronavirus Nucleocapsid Proteins/immunology
- Coronavirus Nucleocapsid Proteins/genetics
- Vaccines, Synthetic/immunology
- RNA, Viral
- Female
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- RNA, Messenger/immunology
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Affiliation(s)
- Tong Yu
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Changchun Veterinary Research Institute, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Chinese Academy of Agricultural Sciences, Changchun, China
| | - JunHong Xing
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China.
- College of Veterinary Medicine, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China.
| | - XinYu Zhuang
- Changchun Veterinary Research Institute, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Chinese Academy of Agricultural Sciences, Changchun, China.
| | - MingYao Tian
- Changchun Veterinary Research Institute, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Chinese Academy of Agricultural Sciences, Changchun, China.
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2
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Jagne YJ, Jobe D, Darboe A, Danso M, Barratt N, Gomez M, Wenlock R, Jarju S, Sylva EL, Touray AF, Toure F, Kumado M, Saso A, Zafred D, Nicklin M, Sayers J, Hornsby H, Lindsey B, Sesay AK, Temperton N, Kucharski A, Hodgson D, de Silva T, Kampmann B. Compartmentalised mucosal and blood immunity to SARS-CoV-2 is associated with high seroprevalence before the Delta wave in Africa. COMMUNICATIONS MEDICINE 2025; 5:178. [PMID: 40379979 DOI: 10.1038/s43856-025-00902-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 05/09/2025] [Indexed: 05/19/2025] Open
Abstract
BACKGROUND The reported number of SARS-CoV-2 cases and deaths are lower in Africa compared to many high-income countries. However, in African cohorts, detailed characterisation of SARS-CoV-2 mucosal and T cell immunity are limited. We assessed the SARS-CoV-2-specific immune landscape in The Gambia during the presence of the pre-Delta variant in July 2021. METHODS A cross-sectional assessment of SARS-CoV-2 immunity in 349 unvaccinated individuals from 52 Gambian households was performed between March-June 2021. SARS-CoV-2 spike (S) and nucleocapsid (N) specific binding antibodies were measured by ELISA, variant-specific serum neutralizing-antibodies (NAb) by viral pseudotype assays and nasal fluid IgA by mesoscale discovery assay. SARS-CoV-2 T-cell responses were evaluated using ELISpot assay. RESULTS We show that adjusted anti-Spike antibody seroprevalence is 56.7% (95% confidence interval (CI) 49.0-64.0), with lower rates in children <5 years (26.2%, 13.9-43.8) and 5-17 years (46.4%, 36.2-56.7) compared to adults 18-49 years (78.4%, 68.8-85.8). Among spike-seropositive individuals, NAb titres are highest against Alpha variant (median IC50 110), with 27% showing pre-existing Delta variant titres >1:50. T-cell responses are higher in spike-seropositive individuals, although 34% of spike-seronegative individuals show responses to at least one antigen pool. We observe strong correlations within SARS-CoV-2 T-cell, mucosal IgA, and serum NAb responses. CONCLUSIONS High SARS-CoV-2 seroprevalence in The-Gambia induce mucosal and blood immunity, reducing Delta and Omicron impact. Children are relatively protected from infection. T-cell responses in seronegative individuals may indicate either pre-pandemic cross-reactivity or individuals with a T-cell dominated response to SARS-CoV-2 infection with absent or poor humoral responses.
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Affiliation(s)
- Ya Jankey Jagne
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia.
| | - Dawda Jobe
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Alansana Darboe
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Madikoi Danso
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Natalie Barratt
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK
| | - Marie Gomez
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Rhys Wenlock
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Sheikh Jarju
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Ellen Lena Sylva
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Aji Fatou Touray
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Fatoumata Toure
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Michelle Kumado
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Anja Saso
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Domen Zafred
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Martin Nicklin
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Jon Sayers
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Hailey Hornsby
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK
| | - Benjamin Lindsey
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK
| | - Abdul Karim Sesay
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Canterbury, UK
| | - Adam Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - David Hodgson
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Thushan de Silva
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia.
- Charité Centre for Global Health; Charité Universitätsmedizin, Berlin, Germany.
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Kuroda M, Halfmann PJ, Uraki R, Yamayoshi S, Kim T, Armbrust TA, Spyra S, Dahn R, Babujee L, Kawaoka Y. SARS-CoV-2 virus lacking the envelope and membrane open-reading frames as a vaccine platform. Nat Commun 2025; 16:4453. [PMID: 40360482 PMCID: PMC12075476 DOI: 10.1038/s41467-025-59533-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 04/25/2025] [Indexed: 05/15/2025] Open
Abstract
To address the need for broadly protective SARS-CoV-2 vaccines, we developed an attenuated a SARS-CoV-2 vaccine virus that lacks the open reading frames of two viral structural proteins: the envelope (E) and membrane (M) proteins. This vaccine virus (ΔEM) replicates in a cell line stably expressing E and M but not in wild-type cells. Vaccination with ΔEM elicits a CD8 T-cell response against the viral spike and nucleocapsid proteins. Two vaccinations with ΔEM provide better protection of the lower respiratory tissues than a single dose against the Delta and Omicron XBB variants in hamsters. Moreover, ΔEM is effective as a booster in hamsters previously vaccinated with an mRNA-based vaccine, providing higher levels of protection in both respiratory tissues compared to the mRNA vaccine booster. Collectively, our data demonstrate the feasibility of a SARS-CoV-2 ΔEM vaccine candidate virus as a vaccine platform.
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Affiliation(s)
- Makoto Kuroda
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA.
| | - Ryuta Uraki
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo, 162-8655, Japan
| | - Seiya Yamayoshi
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo, 162-8655, Japan
- International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, 162-8655, Japan
| | - Taksoo Kim
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Tammy A Armbrust
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Sam Spyra
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Randall Dahn
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Lavanya Babujee
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA.
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan.
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo, 162-8655, Japan.
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Browne DJ, Crooks P, Smith C, Doolan DL. Differential reactivity of SARS-CoV-2 S-protein T-cell epitopes in vaccinated versus naturally infected individuals. Clin Transl Immunology 2025; 14:e70031. [PMID: 40342296 PMCID: PMC12056234 DOI: 10.1002/cti2.70031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2024] [Revised: 02/20/2025] [Accepted: 03/18/2025] [Indexed: 05/11/2025] Open
Abstract
Objectives Vaccine-induced protective immunity against SARS-CoV-2 has proved difficult to sustain. Robust T-cell responses are thought to play an important role, but T-cell responses against the SARS-CoV-2 spike protein (S-protein), the core vaccine antigen, following vaccination or natural infection are incompletely understood. Methods Herein, the reactivity of 170 putative SARS-CoV-2 S-protein CD8+ and CD4+ T-cell peptide epitopes in the same individuals prior to vaccination, after COVID-19 vaccination, and again following subsequent natural infection was assayed using a high-throughput reverse transcription-quantitative PCR (HTS-RT-qPCR) assay. Results The profile of immunoreactive SARS-CoV-2 S-protein epitopes differed between vaccination and natural infection. Vaccine-induced immunoreactive epitopes were localised primarily into two extra-domanial regions. In contrast, epitopes recognised following natural infection were spread across the antigen. Furthermore, T-cell epitopes in naïve individuals were primarily recognised in association with HLA-A, while natural infection shifted epitope associations towards HLA-B, particularly the B7 supertype. Conclusion This study provides insight into T-cell responses against the SARS-CoV-2 S-protein following vaccination and subsequent natural infection.
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Affiliation(s)
- Daniel J Browne
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and MedicineJames Cook UniversityCairnsQLDAustralia
| | - Pauline Crooks
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Department of ImmunologyQIMR Berghofer Medical Research InstituteBrisbaneQLDAustralia
| | - Corey Smith
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Department of ImmunologyQIMR Berghofer Medical Research InstituteBrisbaneQLDAustralia
- Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Denise L Doolan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and MedicineJames Cook UniversityCairnsQLDAustralia
- Institute for Molecular BioscienceThe University of QueenslandSt LuciaQLDAustralia
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5
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Chang CM, Wu CJ, Shkurnikov M, Guo CL, Huang WC, Tonevitsky A, Chang WC. Characterization of binding affinity changes of SARS-CoV-2 omicron variant peptides to population-specific HLA. J Biomed Sci 2025; 32:44. [PMID: 40301887 PMCID: PMC12039199 DOI: 10.1186/s12929-025-01139-5] [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: 02/03/2025] [Accepted: 04/01/2025] [Indexed: 05/01/2025] Open
Abstract
BACKGROUND The evolution of SARS-CoV-2, particularly through new variants, presents significant global health challenges due to their potential for immune evasion and reduced vaccine effectiveness. This study aims to investigate the impact of mutations in the Spike protein of Omicron EG.5 and XBB.1.16 variants on the binding affinities of viral peptides to common human leukocyte antigen (HLA) class I and II alleles across Taiwanese, British, and Russian populations. Understanding these interactions is crucial for elucidating differences in immune responses and disease severity among diverse populations. METHODS We updated the T-CoV portal to incorporate and analyze EG.5 and XBB.1.16 variants. Binding affinities between mutated Spike protein peptides and HLA class I and II alleles were predicted and compared across the three populations. Statistical analyses, including chi-squared tests, were conducted to assess the significance of binding affinity differences across the three populations and between HLA classes. RESULTS Our findings revealed that mutations in the Spike protein had a more pronounced effect on HLA class II binding affinities than on HLA class I. While binding affinity profiles for HLA class I were largely consistent across populations, significant population-specific variations were observed for HLA class II alleles. Specifically, the British population exhibited lower proportions of tightly binding mutated peptides compared to the Taiwanese and Russian populations. Furthermore, substantial differences were identified in the binding affinity changes of mutated Spike peptides for HLA class II across Taiwanese, British, and Russian populations, as well as between the Omicron EG.5 and XBB.1.16 variants. Subsequent analyses revealed significant differences in the conservation and evolutionary trajectories of binding affinities between mutated Spike peptides and common HLA class II alleles, both between the EG.5 and XBB.1.16 variants and across the three populations for the XBB.1.16 variant. CONCLUSIONS In summary, Spike protein mutations in SARS-CoV-2 variants significantly influence immune responses by altering HLA-peptide interactions, with pronounced population-specific effects on HLA class II alleles. These findings underscore the critical role of HLA class II diversity in shaping immune responses and susceptibility to COVID-19. Integrating population-specific HLA profiles into vaccine development and public health strategies is essential for improving interventions against evolving SARS-CoV-2 variants.
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Affiliation(s)
- Che-Mai Chang
- Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Chang-Jiun Wu
- Department of Pharmaceutical Sciences, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Maxim Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Chin-Lin Guo
- Institute of Physics, Academia Sinica, Taipei, Taiwan
| | - Wan-Chen Huang
- Single-Molecule Biology Core Lab, Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Art Photonics GmbH, Berlin, Germany
| | - Wei-Chiao Chang
- Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, No. 250, Wu-Xing St, Taipei, 11031, Taiwan.
- Department of Medical Education and Research, Integrative Research Center for Critical Care, Taipei Medical University, Wan-Fang Hospital, Taipei, Taiwan.
- Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
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Saha A, Ghosh Roy S, Dwivedi R, Tripathi P, Kumar K, Nambiar SM, Pathak R. Beyond the Pandemic Era: Recent Advances and Efficacy of SARS-CoV-2 Vaccines Against Emerging Variants of Concern. Vaccines (Basel) 2025; 13:424. [PMID: 40333293 PMCID: PMC12031379 DOI: 10.3390/vaccines13040424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2025] [Revised: 04/10/2025] [Accepted: 04/14/2025] [Indexed: 05/09/2025] Open
Abstract
Vaccination has been instrumental in curbing the transmission of SARS-CoV-2 and mitigating the severity of clinical manifestations associated with COVID-19. Numerous COVID-19 vaccines have been developed to this effect, including BioNTech-Pfizer and Moderna's mRNA vaccines, as well as adenovirus vector-based vaccines such as Oxford-AstraZeneca. However, the emergence of new variants and subvariants of SARS-CoV-2, characterized by enhanced transmissibility and immune evasion, poses significant challenges to the efficacy of current vaccination strategies. In this review, we aim to comprehensively outline the landscape of emerging SARS-CoV-2 variants of concern (VOCs) and sub-lineages that have recently surfaced in the post-pandemic years. We assess the effectiveness of existing vaccines, including their booster doses, against these emerging variants and subvariants, such as BA.2-derived sub-lineages, XBB sub-lineages, and BA.2.86 (Pirola). Furthermore, we discuss the latest advancements in vaccine technology, including multivalent and pan-coronavirus approaches, along with the development of several next-generation coronavirus vaccines, such as exosome-based, virus-like particle (VLP), mucosal, and nanomaterial-based vaccines. Finally, we highlight the key challenges and critical areas for future research to address the evolving threat of SARS-CoV-2 subvariants and to develop strategies for combating the emergence of new viral threats, thereby improving preparedness for future pandemics.
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Affiliation(s)
- Ankita Saha
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA;
| | - Sounak Ghosh Roy
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Naval Medical Research Command, Silver Spring, MD 20910, USA;
| | - Richa Dwivedi
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN 37208, USA;
| | - Prajna Tripathi
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA;
| | - Kamal Kumar
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA;
| | - Shashank Manohar Nambiar
- Division of Hepatology, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA;
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Rajiv Pathak
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
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Karl V, Hofmann M, Thimme R. Role of antiviral CD8+ T cell immunity to SARS-CoV-2 infection and vaccination. J Virol 2025; 99:e0135024. [PMID: 40029063 PMCID: PMC11998524 DOI: 10.1128/jvi.01350-24] [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] [Indexed: 03/05/2025] Open
Abstract
The COVID-19 pandemic has greatly enhanced our understanding of CD8+ T cell immunity and their role in natural infection and vaccine-induced protection. Rapid and early SARS-CoV-2-specific CD8+ T cell responses have been associated with efficient viral clearance and mild disease. Virus-specific CD8+ T cell responses can compensate for waning, morbidity-related, and iatrogenic reduction of humoral immunity. After infection or vaccination, SARS-CoV-2-specific memory CD8+ T cells are formed, which mount an efficient recall response in the event of breakthrough infection and help to protect from severe disease. Due to their breadth and ability to target mainly highly conserved epitopes, SARS-CoV-2-specific CD8+ T cells are also able to cross-recognize epitopes of viral variants, thus maintaining immunity even after the emergence of viral evolution. In some cases, however, CD8+ T cells may contribute to the pathogenesis of severe COVID-19. In particular, delayed and uncontrolled, e.g., nonspecific and hyperactivated, cytotoxic CD8+ T cell responses have been linked to poor COVID-19 outcomes. In this minireview, we summarize the tremendous knowledge about CD8+ T cell responses to SARS-CoV-2 infection and COVID-19 vaccination that has been gained over the past 5 years, while also highlighting the critical knowledge gaps that remain.
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Affiliation(s)
- Vivien Karl
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Maike Hofmann
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Robert Thimme
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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8
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Case JB, Jain S, Suthar MS, Diamond MS. SARS-CoV-2: The Interplay Between Evolution and Host Immunity. Annu Rev Immunol 2025; 43:29-55. [PMID: 39705164 DOI: 10.1146/annurev-immunol-083122-043054] [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: 12/22/2024]
Abstract
The persistence of SARS-CoV-2 infections at a global level reflects the repeated emergence of variant strains encoding unique constellations of mutations. These variants have been generated principally because of a dynamic host immune landscape, the countermeasures deployed to combat disease, and selection for enhanced infection of the upper airway and respiratory transmission. The resulting viral diversity creates a challenge for vaccination efforts to maintain efficacy, especially regarding humoral aspects of protection. Here, we review our understanding of how SARS-CoV-2 has evolved during the pandemic, the immune mechanisms that confer protection, and the impact viral evolution has had on transmissibility and adaptive immunity elicited by natural infection and/or vaccination. Evidence suggests that SARS-CoV-2 evolution initially selected variants with increased transmissibility but currently is driven by immune escape. The virus likely will continue to drift to maintain fitness until countermeasures capable of disrupting transmission cycles become widely available.
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Affiliation(s)
- James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA;
| | - Shilpi Jain
- Emory Vaccine Center, Emory National Primate Research Center, Atlanta, Georgia, USA
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Mehul S Suthar
- Emory Vaccine Center, Emory National Primate Research Center, Atlanta, Georgia, USA
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Michael S Diamond
- Department of Pathology & Immunology; Department of Molecular Microbiology; and Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA;
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de Munter L, Meeraus W, Dwivedi A, Mitratza M, Wyndham-Thomas C, Carty L, Ouwens M, Hartig-Merkel W, Drikite L, Rebry G, Casas I, Mira-Iglesias A, Icardi G, Otero-Romero S, Baumgartner S, Martin C, Holemans X, ten Kate GL, Bollaerts K, Taylor S. Effectiveness of the AZD1222 vaccine against COVID-19 hospitalization in Europe: final results from the COVIDRIVE test-negative case-control study. Eur J Public Health 2025; 35:373-378. [PMID: 39836896 PMCID: PMC11967879 DOI: 10.1093/eurpub/ckae219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2025] Open
Abstract
Marketing authorization holders of vaccines typically need to report brand-specific vaccine effectiveness (VE) to the regulatory authorities as part of their regulatory obligations. COVIDRIVE (now id. DRIVE) is a European public-private partnership for respiratory pathogen surveillance and studies of brand-specific VE with long-term follow-up. We report the final VE results from a two-dose primary series AZD1222 (ChAdOx1 nCoV-19) vaccine schedule in ≥18-year-old individuals not receiving boosters. Patients (N = 1,333) hospitalized with severe acute respiratory infection at 14 hospitals in Austria, Belgium, Italy, and Spain were included in the test-negative case-control study in 2021-2023. Absolute VE was calculated using generalized additive model (GAM), generalized estimating equation (GEE), and spline-based area under the curve (AUC, measuring VE up to 6 months after the last dose of AZD1222). Overall VE (against coronavirus disease 2019 [COVID-19] hospitalization) of an AZD1222 primary series was estimated as 65% using GEE (95% confidence interval [CI]: 52.9-74.5), and 69% using GAM (95% CI: 50.1-80.9) over the 22-month study period (comparator group: unvaccinated patients). The AUC of the spline-based VE estimate was 74.1% (95% CI: 60.0-88.3). VE against hospitalization in study participants who received their second AZD1222 dose 2 months or less before hospitalization was 86% using GEE (95% CI: 77.8-91.4), 93% using GAM (95% CI: 67.2-98.6). During this study period, where mainly the severe acute respiratory syndrome coronavirus 2 Omicron variant was circulating, a two-dose primary series AZD1222 vaccination conferred protection against COVID-19 hospitalization up to at least 6 months after the last dose.
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Affiliation(s)
| | - Wilhelmine Meeraus
- Medical Evidence, Vaccines & Immune Therapies, BioPharmaceuticals Medical, AstraZeneca, Cambridge, United Kingdom
| | | | | | | | - Lucy Carty
- Medical and Payor Statistics, BioPharmaceuticals Medical, AstraZeneca, Cambridge, United Kingdom
| | - Mario Ouwens
- Medical and Payor Statistics, BioPharmaceuticals Medical, AstraZeneca, Mölndal, Sweden
| | | | - Laura Drikite
- P95 Epidemiology and Pharmacovigilance, Leuven, Belgium
| | - Griet Rebry
- P95 Epidemiology and Pharmacovigilance, Leuven, Belgium
| | - Irma Casas
- Preventive Medicine Department, Germans Trias i Pujol University Hospital, Badalona, Spain
- Autonomous University of Barcelona, Bellaterra, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Ainara Mira-Iglesias
- Vaccine Research Department, Fundación para el Fomento de la Investigación Sanitaria y Biomédica (FISABIO) de la Comunitat Valenciana, Salud Pública, Valencia, Spain
- Biomedical Research Consortium of Epidemiology and Public Health (CIBER-ESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Giancarlo Icardi
- Interuniversity Research Centre on Influenza and Other Transmissible Infections (CIRI-IT), Genoa, Italy
- Department of Health Sciences, University of Genoa, Genoa, Italy
| | - Susana Otero-Romero
- Servicio de Medicina Preventiva y Epidemiología, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Campus Hospitalari, Barcelona, Spain
| | - Sebastian Baumgartner
- Fourth Medical Department with Infectious Diseases and Tropical Medicine, Klinik Favoriten/Kaiser-Franz-Josef Hospital, Vienna, Austria
| | - Charlotte Martin
- Infectious Diseases Department, Centre Hospitalier Universitaire Saint-Pierre, Brussels, Belgium
| | - Xavier Holemans
- Infectious Diseases Department, Grand Hôpital de Charleroi, Charleroi, Belgium
| | - Gerrit Luit ten Kate
- General Internal Medicine, Infectious Diseases & Tropical Medicine, University Hospital Antwerp, Edegem, Belgium
| | | | - Sylvia Taylor
- Medical Evidence, Vaccines & Immune Therapies, BioPharmaceuticals Medical, AstraZeneca, Cambridge, United Kingdom
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10
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Yuan L, Stoddard M, Sarkar S, van Egeren D, Mangalaganesh S, Nolan RP, Rogers MS, Hather G, White LF, Chakravarty A. The Impact of Vaccination Frequency on COVID-19 Public Health Outcomes: A Model-Based Analysis. Vaccines (Basel) 2025; 13:368. [PMID: 40333247 PMCID: PMC12031506 DOI: 10.3390/vaccines13040368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2024] [Revised: 03/16/2025] [Accepted: 03/27/2025] [Indexed: 05/09/2025] Open
Abstract
Background: While the rapid deployment of SARS-CoV-2 vaccines had a significant impact on the ongoing COVID-19 pandemic, rapid viral immune evasion and waning neutralizing antibody titers have degraded vaccine efficacy. Nevertheless, vaccine manufacturers and public health authorities have a number of options at their disposal to maximize the benefits of vaccination. In particular, the effect of booster schedules on vaccine performance bears further study. Methods: To better understand the effect of booster schedules on vaccine performance, we used an agent-based modeling framework and a population pharmacokinetic model to simulate the impact of boosting frequency on the durability of vaccine protection against infection and severe acute disease. Results: Our work suggests that repeated dosing at frequent intervals (three or more times a year) may offset the degradation of vaccine efficacy, preserving the utility of vaccines in managing the ongoing pandemic. Conclusions: Given the practical significance of potential improvements in vaccine utility, clinical research to better understand the effects of repeated vaccination would be highly impactful. These findings are particularly relevant as public health authorities worldwide have reduced the frequency of boosters to once a year or less.
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Affiliation(s)
- Lin Yuan
- Fractal Therapeutics, Lexington, MA 02420, USA; (L.Y.); (M.S.)
| | | | - Sharanya Sarkar
- Department of Microbiology and Immunology, Dartmouth College, Hanover, NH 03755, USA;
| | - Debra van Egeren
- Department of Oncology, School of Medicine, Stanford University, Stanford, CA 94305, USA;
| | - Shruthi Mangalaganesh
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC 3800, Australia;
| | | | - Michael S. Rogers
- Department of Surgery, Harvard Medical School, Boston, MA 02114, USA;
- Vascular Biology Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Greg Hather
- Sage Therapeutics, Cambridge, MA 02142, USA;
| | - Laura F. White
- School of Public Health, Boston University, Boston, MA 02118, USA;
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11
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Marques-Ferreira G, Lourenço AA, Campi-Azevedo AC, Clarindo FA, Bernardes AFL, Lamounier LO, Guimaraes NR, Adelino TER, de Melo Iani FC, Santos DA, Magalhães VCR, da Mata CPSM, Reis EVDS, Moraes TDFS, Gomes-de-Pontes L, da Fonseca FG, Teixeira-Carvalho A, Menegueti MG, Auxiliadora-Martins M, Amaral PHR, Pérez JCG, Martins-Filho OA, Coelho-Dos-Reis JG. Unique signatures of airway and systemic immunity in severe COVID-19 patients infected with alpha to Omicron SARS-CoV-2 variants of concern. Inflamm Res 2025; 74:57. [PMID: 40153054 DOI: 10.1007/s00011-025-02018-3] [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: 10/31/2024] [Revised: 02/21/2025] [Accepted: 02/25/2025] [Indexed: 03/30/2025] Open
Abstract
In this study, systemic and localized immunity induced by SARS-CoV-2 variants of concern or interest (VOC/VOI) was investigated. For that, serum and tracheal aspirate soluble chemokines, pro-inflammatory/regulatory cytokines, and growth factors were measured in severe COVID-19 patients under mechanical ventilation upon infection with different SARS-CoV-2 variants, namely Alpha, Gamma, Zeta, Delta and Omicron. Increased levels of soluble mediators were observed in serum from severe COVID-19 patients regardless of the variant. In tracheal aspirate samples, the patients infected with the Gamma, Zeta, Delta, and Omicron variants exhibited reduced levels of inflammatory cytokines when compared to those infected with the Alpha variant. The trend of lower cytokine levels was also observed in the serum of patients across these variants, except for the Delta variant. By using network analysis and cytokine storm signatures, the data confirmed that severe COVID-19 induced by different variants have a completely divergent pattern of connectivity in serum samples as well as tracheal aspirates. Patients infected with variants at later time points in the pandemic such as Omicron exhibited networks of weak central architecture in serum samples as compared to tracheal aspirates, with lower number of neighborhood connections and clusters of pro-inflammatory and regulatory cytokines. By and large, this study points out to important systemic and local divergences and to loss of airway localized immunity in severe COVID-19 patients infected with SARS-CoV-2 variants, which brings insight into understanding host responses and viral escape vis-à-vis the virus mutations and evolution.
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Affiliation(s)
- Geovane Marques-Ferreira
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627- Pampulha, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Alice Aparecida Lourenço
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627- Pampulha, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | | | - Felipe Alves Clarindo
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627- Pampulha, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - André Felipe Leal Bernardes
- Laboratório Central de Saúde Pública de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Ludmila Oliveira Lamounier
- Laboratório Central de Saúde Pública de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Natalia Rocha Guimaraes
- Laboratório Central de Saúde Pública de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Talita Emile Ribeiro Adelino
- Laboratório Central de Saúde Pública de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Felipe Campos de Melo Iani
- Laboratório Central de Saúde Pública de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Daniel Assis Santos
- Laboratório de Micologia, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vanessa Caroline Randi Magalhães
- Laboratório de Micologia, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Camila Pacheco Silveira Martins da Mata
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627- Pampulha, Belo Horizonte, Minas Gerais, 31270-901, Brazil
- Hospital Risoleta Tolentino Neves, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Erik Vinicius de Sousa Reis
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627- Pampulha, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Thaís de Fátima Silva Moraes
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627- Pampulha, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Letícia Gomes-de-Pontes
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627- Pampulha, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Flávio Guimarães da Fonseca
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627- Pampulha, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | | | - Mayra Gonçalves Menegueti
- Departamento de Enfermagem Geral e Especializada, Escola de Enfermagem de Ribeirão Preto da Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Maria Auxiliadora-Martins
- Divisão de Medicina Intensiva, Departamento de Cirurgia e Anatomia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Juan Carlos González Pérez
- Departamento de Física, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Jordana Grazziela Coelho-Dos-Reis
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627- Pampulha, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
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12
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Mackay M, Wagner CA, Pinckney A, Cohen JA, Wallace ZS, Khosroshahi A, Sparks JA, Lord S, Saxena A, Caricchio R, Kim AH, Kamen DL, Koumpouras F, Askanase AD, Smith K, Guthridge JM, Pardo G, Mao-Draayer Y, Macwana S, McCarthy S, Sherman MA, Hamrah SD, Veri M, Walker S, York K, Tedeschi S, Wang J, Dziubla G, Castro M, Carroll R, Narpala S, Lin BC, Serebryannyy L, McDermott A, Barry WT, Goldmuntz E, McNamara J, Payne AS, Bar-Or A, Khanna D, James JA. Prospective SARS-CoV-2 Booster Vaccination in Immunosuppressant-Treated Systemic Autoimmune Disease Patients in a Randomized Controlled Trial. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2025.03.25.25324558. [PMID: 40196267 PMCID: PMC11974989 DOI: 10.1101/2025.03.25.25324558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
Abstract
Background Autoimmune disease patients on immunosuppressants exhibit reduced humoral responses to primary COVID-19 vaccination. Booster vaccine responses and the effects of holding immunosuppression around vaccination are less studied. We evaluated the efficacy and safety of additional vaccination in mycophenolate mofetil/mycophenolic acid (MMF/MPA)-, methotrexate (MTX)-, and B cell-depleting therapy (BCDT)-treated autoimmune disease patients, including the impact of withholding MMF/MPA and MTX. Methods In this open-label, multicenter, randomized trial, 22 MMF/MPA-, 26 MTX-, and 93 BCDT-treated autoimmune disease patients with negative or suboptimal antibody responses to initial COVID-19 vaccines (BNT162b2, mRNA-1273, or AD26.COV2.S) received a homologous booster. MMF/MPA and MTX participants were randomized (1:1) to continue or withhold treatment around vaccination. The primary outcome was the change in anti-Wuhan-Hu-1 receptor-binding domain (RBD) concentrations at 4 weeks post-additional vaccination. Secondary outcomes included adverse events, COVID-19 infections, and autoimmune disease activity through 48 weeks. Results Additional vaccination increased anti-RBD concentrations in MMF/MPA and MTX patients, irrespective of whether immunosuppression was continued or withheld. BCDT-treated patients also demonstrated increased anti-RBD concentrations, albeit lower than MMF/MPA- and MTX-treated cohorts. COVID-19 infections occurred in 30-46% of participants, were predominantly mild, and included only two non-fatal hospitalizations. Additional vaccination was well-tolerated, with low frequencies of severe disease flares and adverse events. Conclusion Additional COVID-19 vaccination is effective and safe in immunosuppressant-treated autoimmune disease patients, regardless of whether MMF/MPA or MTX is withheld. Trial Registration. ClinicalTrials.gov (NCT#05000216).
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13
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Liu J, Wu Y, Gao GF. A Structural Voyage Toward the Landscape of Humoral and Cellular Immune Escapes of SARS-CoV-2. Immunol Rev 2025; 330:e70000. [PMID: 39907512 DOI: 10.1111/imr.70000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2024] [Accepted: 01/08/2025] [Indexed: 02/06/2025]
Abstract
The genome-based surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the past nearly 5 years since its emergence has refreshed our understanding of virus evolution, especially on convergent co-evolution with the host. SARS-CoV-2 evolution has been characterized by the emergence of sets of mutations that affect the functional properties of the virus by altering its infectivity, virulence, transmissibility, and interactions with host immunity. This poses a huge challenge to global prevention and control measures based on drug treatment and vaccine application. As one of the key evasion strategies in response to the immune profile of the human population, there are overwhelming amounts of evidence for the reduced antibody neutralization of SARS-CoV-2 variants. Additionally, data also suggest that the levels of CD4+ and CD8+ T-cell responses against variants or sub-variants decrease in the populations, although non-negligible cross-T-cell responses are maintained. Herein, from the perspectives of structural immunology, we outline the characteristics and mechanisms of the T cell and antibody responses to SARS-CoV and its variants/sub-variants. The molecular bases for the impact of the immune escaping variants on the interaction of the epitopes with the key receptors in adaptive immunity, that is, major histocompatibility complex (MHC), T-cell receptor (TCR), and antibody are summarized and discussed, the knowledge of which will widen our understanding of this pandemic-threatening virus and assist the preparedness for Pathogen X in the future.
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Affiliation(s)
- Jun Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yan Wu
- Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - George F Gao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- The D. H. Chen School of Universal Health, Zhejiang University, Hangzhou, China
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14
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Cao J, Gan M, Zhang Z, Lin X, Ouyang Q, Fu H, Xu X, Wang Z, Li X, Wang Y, Cai H, Lei Q, Liu L, Wang H, Fan X. A Hidden Guardian: The Stability and Spectrum of Antibody-Dependent Cell-Mediated Cytotoxicity in COVID-19 Response in Chinese Adults. Vaccines (Basel) 2025; 13:262. [PMID: 40266151 PMCID: PMC11945335 DOI: 10.3390/vaccines13030262] [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: 01/23/2025] [Revised: 02/20/2025] [Accepted: 02/26/2025] [Indexed: 04/24/2025] Open
Abstract
OBJECTIVES Identifying immune-protective biomarkers is crucial for the effective management and mitigation of current and future COVID-19 outbreaks, particularly in preventing or counteracting the immune evasion exhibited by the Omicron variants. The emergence of SARS-CoV-2 variants, especially those within the Omicron lineage, has highlighted their capacity to evade neutralizing antibodies, emphasizing the need to understand the role of antibody-dependent cell-mediated cytotoxicity (ADCC) in combating these infections. METHODS This study, conducted in Qichun City, Hubei province, from December 2021 to March 2023, involved 50 healthy Chinese adults who had received two doses of inactivated vaccines and had subsequently experienced mild infections with the Omicron BA.5 variant. Blood samples from these 50 healthy Chinese adults were collected at six distinct time points: at baseline and at the 1st, 3rd, 6th, and 9th months following the third dose of the inactivated vaccine, as well as 3 months post-breakthrough infection. Their sera were analyzed to assess ADCC and neutralization effects. RESULTS The results indicated that the antibodies elicited by the inactivated SARS-CoV-2 vaccine targeted the spike protein, exhibiting both pre-existing neutralizing and ADCC activities against Omicron variants BA.5 and XBB.1.5. Notably, the ADCC activity demonstrated greater stability compared to that of the neutralizing effects, persisting for at least 15 months post-vaccination, and could be augmented by additional vaccine doses and breakthrough infections. The ADCC effect associated with hybrid immunity effectively targets a spectrum of prospective Omicron variants, including BA.2.86, CH.1.1, EG.5.1, and JN.1. CONCLUSIONS In light of its stability and broad-spectrum efficacy, we recommend the use of the ADCC effect as a biomarker for assessing protective immunity and guiding the development of vaccines and monoclonal antibodies.
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Affiliation(s)
- Jinge Cao
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan 430030, China; (J.C.); (M.G.); (X.L.); (Q.O.); (H.F.); (X.X.)
| | - Mengze Gan
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan 430030, China; (J.C.); (M.G.); (X.L.); (Q.O.); (H.F.); (X.X.)
| | - Zhihao Zhang
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Huazhong University of Science and Technology, Wuhan 430030, China; (Z.Z.); (Z.W.); (X.L.); (Y.W.); (H.C.); (L.L.)
| | - Xiaosong Lin
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan 430030, China; (J.C.); (M.G.); (X.L.); (Q.O.); (H.F.); (X.X.)
| | - Qi Ouyang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan 430030, China; (J.C.); (M.G.); (X.L.); (Q.O.); (H.F.); (X.X.)
| | - Hui Fu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan 430030, China; (J.C.); (M.G.); (X.L.); (Q.O.); (H.F.); (X.X.)
| | - Xinyue Xu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan 430030, China; (J.C.); (M.G.); (X.L.); (Q.O.); (H.F.); (X.X.)
| | - Zhen Wang
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Huazhong University of Science and Technology, Wuhan 430030, China; (Z.Z.); (Z.W.); (X.L.); (Y.W.); (H.C.); (L.L.)
| | - Xinlian Li
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Huazhong University of Science and Technology, Wuhan 430030, China; (Z.Z.); (Z.W.); (X.L.); (Y.W.); (H.C.); (L.L.)
| | - Yaxin Wang
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Huazhong University of Science and Technology, Wuhan 430030, China; (Z.Z.); (Z.W.); (X.L.); (Y.W.); (H.C.); (L.L.)
| | - Hao Cai
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Huazhong University of Science and Technology, Wuhan 430030, China; (Z.Z.); (Z.W.); (X.L.); (Y.W.); (H.C.); (L.L.)
| | - Qing Lei
- Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China;
| | - Li Liu
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Huazhong University of Science and Technology, Wuhan 430030, China; (Z.Z.); (Z.W.); (X.L.); (Y.W.); (H.C.); (L.L.)
| | - Hao Wang
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Huazhong University of Science and Technology, Wuhan 430030, China; (Z.Z.); (Z.W.); (X.L.); (Y.W.); (H.C.); (L.L.)
| | - Xionglin Fan
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan 430030, China; (J.C.); (M.G.); (X.L.); (Q.O.); (H.F.); (X.X.)
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15
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Qin D, Phung Q, Wu P, Yin Z, Tam S, Tran P, ElSohly AM, Gober J, Hu Z, Zhou Z, Cohen S, He D, Bainbridge TW, Kemball CC, Zarzar J, Sreedhara A, Stephens N, Decalf J, Moussion C, Ye Z, Balazs M, Li Y. A single point mutation on FLT3L-Fc protein increases the risk of immunogenicity. Front Immunol 2025; 16:1519452. [PMID: 40018031 PMCID: PMC11865242 DOI: 10.3389/fimmu.2025.1519452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Accepted: 01/07/2025] [Indexed: 03/01/2025] Open
Abstract
Introduction As a crucial asset for human health and modern medicine, an increasing number of biotherapeutics are entering the clinic. However, due to their complexity, these drugs have a higher potential to be immunogenic, leading to the generation of anti-drug antibodies (ADAs). Clinically significant ADAs have an impact on pharmacokinetics (PK), pharmacodynamics (PD), effectiveness, and/or safety. Thus, it is crucial to understand, manage and minimize the immunogenicity potential during drug development, ideally starting from the molecule design stage. Methods In this study, we utilized various immunogenicity risk assessment methods, including in silico prediction, dendritic cell internalization, MHC-associated peptide proteomics, in vitro HLA peptide binding, and in vitro T cell proliferation, to assess the immunogenicity risk of FLT3L-Fc variants. Results We identified a single point mutation in the human FLT3L-Fc protein that introduced highly immunogenic T cell epitopes, leading to the induction of T cell responses and thereby increasing the immunogenicity risk in clinical settings. Consequently, the variant with this point mutation was removed from further consideration as a clinical candidate. Discussion This finding underscores the necessity for careful evaluation of mutations during the engineering of protein therapeutics. The integration of multiple immunogenicity risk assessment tools offers critical insights for informed decision-making in candidate sequence design and therapeutic lead selection.
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Affiliation(s)
- Dan Qin
- Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, United States
| | - Qui Phung
- Proteomic and Genomic Technologies, Genentech Inc., South San Francisco, CA, United States
| | - Patrick Wu
- BioAnalytical Sciences, Genentech Inc., South San Francisco, CA, United States
| | - Zhaojun Yin
- BioAnalytical Sciences, Genentech Inc., South San Francisco, CA, United States
| | - Sien Tam
- Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, United States
| | - Peter Tran
- BioAnalytical Sciences, Genentech Inc., South San Francisco, CA, United States
| | - Adel M. ElSohly
- Protein Chemistry, Genentech Inc., South San Francisco, CA, United States
| | - Joshua Gober
- Protein Chemistry, Genentech Inc., South San Francisco, CA, United States
| | - Zicheng Hu
- BioAnalytical Sciences, Genentech Inc., South San Francisco, CA, United States
| | - Zhenru Zhou
- Proteomic and Genomic Technologies, Genentech Inc., South San Francisco, CA, United States
| | - Sivan Cohen
- BioAnalytical Sciences, Genentech Inc., South San Francisco, CA, United States
| | - Dongping He
- Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, United States
| | | | - Christopher C. Kemball
- Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, United States
| | - Jonathan Zarzar
- Pharmaceutical Development, Genentech Inc., South San Francisco, CA, United States
| | - Alavattam Sreedhara
- Pharmaceutical Development, Genentech Inc., South San Francisco, CA, United States
| | - Nicole Stephens
- Analytical Development & Quality Control, Genentech Inc., South San Francisco, CA, United States
| | - Jérémie Decalf
- Cancer Immunology, Genentech Inc., South San Francisco, CA, United States
| | - Christine Moussion
- Cancer Immunology, Genentech Inc., South San Francisco, CA, United States
| | - Zhengmao Ye
- Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, United States
| | - Mercedesz Balazs
- Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, United States
| | - Yinyin Li
- Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, United States
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16
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Sidney J, Kim AR, de Vries RD, Peters B, Meade PS, Krammer F, Grifoni A, Sette A. Targets of influenza human T-cell response are mostly conserved in H5N1. mBio 2025; 16:e0347924. [PMID: 39714185 PMCID: PMC11796400 DOI: 10.1128/mbio.03479-24] [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: 11/19/2024] [Accepted: 12/05/2024] [Indexed: 12/24/2024] Open
Abstract
Frequent recent spillovers of subtype H5N1 clade 2.3.4.4b highly pathogenic avian influenza (HPAI) virus into poultry and mammals, especially dairy cattle, including several human cases, increased concerns over a possible future pandemic. Here, we performed an analysis of epitope data curated in the Immune Epitope Database (IEDB). We found that the patterns of immunodominance of seasonal influenza viruses circulating in humans and H5N1 are similar. We further conclude that a significant fraction of the T-cell epitopes is conserved at a level associated with cross-reactivity between avian and seasonal sequences, and we further experimentally demonstrate extensive cross-reactivity in the most dominant T-cell epitopes curated in the IEDB. Based on these observations, and the overall similarity of the neuraminidase (NA) N1 subtype encoded in both HPAI and seasonal H1N1 influenza virus as well as cross-reactive group 1 HA stalk-reactive antibodies, we expect that a degree of pre-existing immunity is present in the general human population that could blunt the severity of human H5N1 infections.IMPORTANCEInfluenza A viruses (IAVs) cause pandemics that can result in millions of deaths. The highly pathogenic avian influenza (HPAI) virus of the H5N1 subtype is presently among the top viruses of pandemic concern, according to the WHO and the National Institute of Allergy and Infectious Diseases (NIAID). Previous exposure by infection and/or vaccination to a given IAV subtype or clade influences immune responses to a different subtype or clade. Analysis of human CD4 and CD8 T-cell epitope conservation between HPAI H5N1 and seasonal IAV sequences revealed levels of identity and conservation conducive to T cell cross-reactivity, suggesting that pre-existing T cell immune memory should, to a large extent, cross-recognize avian influenza viruses. This observation was experimentally verified by testing responses from human T cells to non-avian IAV and their HPAI H5N1 counterparts. Accordingly, should a more widespread HPAI H5N1 outbreak occur, we hypothesize that cross-reactive T-cell responses might be able to limit disease severity.
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Affiliation(s)
- John Sidney
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, California, USA
| | - A-Reum Kim
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, California, USA
| | - Rory D. de Vries
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Bjoern Peters
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, California, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, California, USA
| | - Philip S. Meade
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Ignaz Semmelweis Institute, Interuniversity Institute for Infection Research, Medical University of Vienna, Vienna, Austria
| | - Alba Grifoni
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, California, USA
| | - Alessandro Sette
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, California, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, California, USA
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17
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Li B, Jiang AY, Raji I, Atyeo C, Raimondo TM, Gordon AGR, Rhym LH, Samad T, MacIsaac C, Witten J, Mughal H, Chicz TM, Xu Y, McNamara RP, Bhatia S, Alter G, Langer R, Anderson DG. Enhancing the immunogenicity of lipid-nanoparticle mRNA vaccines by adjuvanting the ionizable lipid and the mRNA. Nat Biomed Eng 2025; 9:167-184. [PMID: 37679571 DOI: 10.1038/s41551-023-01082-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 07/27/2023] [Indexed: 09/09/2023]
Abstract
To elicit optimal immune responses, messenger RNA vaccines require intracellular delivery of the mRNA and the careful use of adjuvants. Here we report a multiply adjuvanted mRNA vaccine consisting of lipid nanoparticles encapsulating an mRNA-encoded antigen, optimized for efficient mRNA delivery and for the enhanced activation of innate and adaptive responses. We optimized the vaccine by screening a library of 480 biodegradable ionizable lipids with headgroups adjuvanted with cyclic amines and by adjuvanting the mRNA-encoded antigen by fusing it with a natural adjuvant derived from the C3 complement protein. In mice, intramuscular or intranasal administration of nanoparticles with the lead ionizable lipid and with mRNA encoding for the fusion protein (either the spike protein or the receptor-binding domain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)) increased the titres of antibodies against SARS-CoV-2 tenfold with respect to the vaccine encoding for the unadjuvanted antigen. Multiply adjuvanted mRNA vaccines may improve the efficacy, safety and ease of administration of mRNA-based immunization.
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MESH Headings
- Animals
- Mice
- Nanoparticles/chemistry
- SARS-CoV-2/immunology
- SARS-CoV-2/genetics
- RNA, Messenger/immunology
- RNA, Messenger/genetics
- RNA, Messenger/administration & dosage
- COVID-19 Vaccines/immunology
- COVID-19 Vaccines/administration & dosage
- COVID-19/prevention & control
- COVID-19/immunology
- Lipids/chemistry
- Adjuvants, Immunologic
- Female
- mRNA Vaccines/immunology
- Antibodies, Viral/immunology
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Humans
- Mice, Inbred BALB C
- Immunogenicity, Vaccine
- Adjuvants, Vaccine
- Liposomes
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Affiliation(s)
- Bowen Li
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Allen Yujie Jiang
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Idris Raji
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Division of Medical Sciences, Harvard University, Boston, MA, USA
| | - Theresa M Raimondo
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Akiva G R Gordon
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luke H Rhym
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tahoura Samad
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Corina MacIsaac
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jacob Witten
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Haseeb Mughal
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Taras M Chicz
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Yue Xu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Ryan P McNamara
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Sangeeta Bhatia
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Wyss Institute at Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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18
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Tian J, Shang B, Zhang J, Guo Y, Li M, Hu Y, Bai D, She J, Han Y, Guo P, Huang M, Wang Y, Liu M, Zhang J, Ye B, Guo Y, Yang M, Lin Y, Zhang T, Sun X, Yuan X, Zhang D, Xu Z, Chai Y, Qi J, Liu K, Tan S, Zhao Y, Zhou J, Song R, Gao GF, Liu J. T cell immune evasion by SARS-CoV-2 JN.1 escapees targeting two cytotoxic T cell epitope hotspots. Nat Immunol 2025; 26:265-278. [PMID: 39875585 DOI: 10.1038/s41590-024-02051-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Accepted: 12/03/2024] [Indexed: 01/30/2025]
Abstract
Although antibody escape is observed in emerging severe acute respiratory syndrome coronavirus 2 variants, T cell escape, especially after the global circulation of BA.2.86/JN.1, is unexplored. Here we demonstrate that T cell evasion exists in epitope hotspots spanning BA.2.86/JN.1 mutations. The newly emerging Q229K at this conserved nucleocapsid protein site impairs HLA-A2 epitope hotspot recognition. The association between HLA-A24 convalescents and T cell immune escape points to the spike (S) protein epitope S448-456NYNYLYRLF, with multiple mutations from Delta to JN.1, including L452Q, L452R, F456L, N450D and L452W, and N450D, L452W and L455S. A cliff drop of immune responses was observed for S448-456NYNYRYRLF (Delta/BA.5.2) and S448-456NYDYWYRSF (JN.1), but with immune preservation of S448-456NYDYWYRLF (BA.2.86). Structural analyses showed that hydrophobicity exposure determines the pronounced escape of L452R and L455S mutants, which was further confirmed by T cell receptor binding. This study highlights the characteristics and molecular mechanisms of the T cell immune escape for JN.1 and provides new insights into understanding the dominant circulation of variants, from the viewpoint of cytotoxic T cell evasion.
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Affiliation(s)
- Jinmin Tian
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bingli Shang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jianing Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuanyuan Guo
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Min Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuechao Hu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dan Bai
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, China
| | - Junying She
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yang Han
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, China
| | - Peipei Guo
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Mengkun Huang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, China
| | - Yalan Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Maoshun Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jie Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
| | - Beiwei Ye
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yaxin Guo
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mengjie Yang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Ying Lin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ting Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, China
| | - Xin Sun
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiaoju Yuan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Danni Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ziqian Xu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Shuguang Tan
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yingze Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing, China.
| | - Jikun Zhou
- The Fifth Hospital of Shijiazhuang, Shijiazhuang, China.
| | - Rui Song
- Beijing Ditan Hospital, Capital Medical University, Beijing, China.
| | - George F Gao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, China.
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
- The D. H. Chen School of Universal Health, Zhejiang University, Hangzhou, China.
| | - Jun Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing, China.
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19
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Patel RS, Duque D, Bavananthasivam J, Hewitt M, Sandhu JK, Kumar R, Tran A, Agrawal B. Mixed lipopeptide-based mucosal vaccine candidate induces cross-variant immunity and protects against SARS-CoV-2 infection in hamsters. Immunohorizons 2025; 9:vlae011. [PMID: 39849995 PMCID: PMC11841972 DOI: 10.1093/immhor/vlae011] [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: 11/07/2024] [Accepted: 11/14/2024] [Indexed: 01/25/2025] Open
Abstract
The global dissemination of SARS-CoV-2 led to a worldwide pandemic in March 2020. Even after the official downgrading of the COVID-19 pandemic, infection with SARS-CoV-2 variants continues. The rapid development and deployment of SARS-CoV-2 vaccines helped to mitigate the pandemic to a great extent. However, the current vaccines are suboptimal; they elicit incomplete and short-lived protection and are ineffective against evolving virus variants. Updating the spike antigen according to the prevailing variant and repeated boosters is not the long-term solution. We have designed a lipopeptide-based, mucosal, pan-coronavirus vaccine candidate, derived from highly conserved and/or functional regions of the SARS-CoV-2 spike, nucleocapsid, and membrane proteins. Our studies demonstrate that the designed lipopeptides (LPMix) induced both cellular and humoral (mucosal and systemic) immune responses upon intranasal immunization in mice. Furthermore, the antibodies bound to the wild-type and mutated S proteins of SARS-CoV-2 variants of concern, including Alpha, Beta, Delta and Omicron, and also led to efficient neutralization in a surrogate viral neutralization assay. Our sequence alignment and 3-dimensional molecular modeling studies demonstrated that spike-derived epitopes, P1 and P2, are sequentially and/or structurally conserved among the SARS-CoV-2 variants. The addition of a novel mucosal adjuvant, heat-killed Caulobacter crescentus, to the lipopeptide vaccine significantly bolstered mucosal antibody responses. Finally, the lipopeptide-based intranasal vaccine demonstrated significant improvement in lung pathologies in a hamster model of SARS-CoV-2 infection. These studies are fundamentally important and open new avenues in the investigation of an innovative, broadly protective intranasal vaccine platform for SARS-CoV-2 and its variants.
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Affiliation(s)
- Raj S Patel
- Department of Surgery, Faculty of Medicine and Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB, Canada
| | - Diana Duque
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Jegarubee Bavananthasivam
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Melissa Hewitt
- Preclinical Imaging, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Jagdeep K Sandhu
- Preclinical Imaging, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | | | - Anh Tran
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Babita Agrawal
- Department of Surgery, Faculty of Medicine and Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB, Canada
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20
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Liu J, Wang L, Kurtesi A, Budylowski P, Potts KG, Menon H, Tan Y, Samaan P, Liu X, Wang Y, Hu Q, Samson R, Qi F, Evseev D, John C, Ellestad KK, Fan Y, Budiman F, Tohan ER, Udayakumar S, Yang J, Marcusson EG, Gingras AC, Mahoney DJ, Ostrowski MA, Martin-Orozco N. A bivalent COVID-19 mRNA vaccine elicited broad immune responses and protection against Omicron subvariants infection. NPJ Vaccines 2025; 10:4. [PMID: 39788981 PMCID: PMC11718203 DOI: 10.1038/s41541-025-01062-8] [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: 04/04/2024] [Accepted: 01/02/2025] [Indexed: 01/12/2025] Open
Abstract
Continuously emerging SARS-CoV-2 Omicron subvariants pose a threat thwarting the effectiveness of approved COVID-19 vaccines. Especially, the protection breadth and degree of these vaccines against antigenically distant Omicron subvariants is unclear. Here, we report the immunogenicity and efficacy of a bivalent mRNA vaccine, PTX-COVID19-M1.2 (M1.2), which encodes native spike proteins from Wuhan-Hu-1 (D614G) and Omicron BA.2.12.1, in mouse and hamster models. Both primary series and booster vaccination using M1.2 elicited potent and broad nAbs against Wuhan-Hu-1 (D614G) and some Omicron subvariants. Strong spike-specific T cell responses against Wuhan-Hu-1 and Omicron subvariants, including JN.1, were also induced. Vaccination with M1.2 protected animals from Wuhan-Hu-1 and multiple Omicron subvariants challenges. Interestingly, protection against XBB.1.5 lung infection did not correlate with nAb levels. These results indicate that M1.2 generated a broadly protective immune response against antigenically distant Omicron subvariants, and spike-specific T cells probably contributed to the breadth of the protection.
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Affiliation(s)
- Jun Liu
- Providence Therapeutics Holdings, Inc., Calgary, Canada.
| | - Li Wang
- Everest Medicines, Shanghai, China
| | - Alexandra Kurtesi
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, Canada
| | - Patrick Budylowski
- Department of Medicine, University of Toronto, Toronto, Canada
- Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Kyle G Potts
- Riddell Center for Cancer Immunotherapy, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Molecular Biology and Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Haritha Menon
- Providence Therapeutics Holdings, Inc., Calgary, Canada
| | - Yilin Tan
- Providence Therapeutics Holdings, Inc., Calgary, Canada
| | - Philip Samaan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | | | | | - Queenie Hu
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, Canada
| | - Reuben Samson
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, Canada
| | - Freda Qi
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, Canada
| | - Danyel Evseev
- Riddell Center for Cancer Immunotherapy, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Molecular Biology and Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Cini John
- Riddell Center for Cancer Immunotherapy, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Molecular Biology and Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Kristofor K Ellestad
- Riddell Center for Cancer Immunotherapy, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Molecular Biology and Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Yue Fan
- Everest Medicines, Shanghai, China
| | - Frans Budiman
- Department of Medicine, University of Toronto, Toronto, Canada
| | | | - Suji Udayakumar
- Department of Medicine, University of Toronto, Toronto, Canada
| | | | | | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, Canada
| | - Douglas J Mahoney
- Riddell Center for Cancer Immunotherapy, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Molecular Biology and Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Mario A Ostrowski
- Department of Medicine, University of Toronto, Toronto, Canada.
- Institute of Medical Science, University of Toronto, Toronto, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.
- Department of Immunology, University of Toronto, Toronto, Canada.
- Keenan Research Centre for Biomedical Science of St. Michael's Hospital, Unity Health Toronto, Toronto, Canada.
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21
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da Silva Antunes R, Fajardo-Rosas V, Yu ED, Gálvez RI, Abawi A, Alexandar Escarrega E, Martínez-Pérez A, Johansson E, Goodwin B, Frazier A, Dan JM, Crotty S, Seumois G, Weiskopf D, Vijayanand P, Sette A. Evolution of SARS-CoV-2 T cell responses as a function of multiple COVID-19 boosters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.08.631842. [PMID: 39829792 PMCID: PMC11741356 DOI: 10.1101/2025.01.08.631842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
The long-term effects of repeated COVID-19 vaccinations on adaptive immunity remain incompletely understood. Here, we conducted a comprehensive three-year longitudinal study examining T cell and antibody responses in 78 vaccinated individuals without reported symptomatic infections. We observed distinct dynamics in Spike-specific humoral and cellular immune responses across multiple vaccine doses. While antibody titers incrementally increased and stabilized with each booster, T cell responses rapidly plateaued, maintaining remarkable stability across CD4+ and CD8+ subsets. Notably, approximately 30% of participants showed CD4+ T cell reactivity to non-Spike antigens, consistent with asymptomatic infections. Single-cell RNA sequencing revealed a diverse landscape of Spike-specific T cell phenotypes, with no evidence of increased exhaustion or significant functional impairment. However, qualitative changes were observed in individuals with evidence of asymptomatic infection, exhibiting unique immunological characteristics, including increased frequencies of Th17-like CD4+ T cells and GZMKhi/IFNR CD8+ T cell subsets. Remarkably, repeated vaccinations in this group were associated with a progressive increase in regulatory T cells, potentially indicating a balanced immune response that may mitigate immunopathology. By regularly stimulating T cell memory, boosters contribute to a stable and enhanced immune response, which may provide better protection against symptomatic infections.
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Affiliation(s)
- Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- These authors contributed equally
| | - Vicente Fajardo-Rosas
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Bioinformatics and Systems Biology Graduate Program; University of California, San Diego, La Jolla, CA 92093, USA
- These authors contributed equally
| | - Esther Dawen Yu
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Rosa Isela Gálvez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Adam Abawi
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - E. Alexandar Escarrega
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Amparo Martínez-Pérez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Emil Johansson
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Benjamin Goodwin
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Jennifer M. Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Grégory Seumois
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Pandurangan Vijayanand
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
- Senior authorship
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
- Senior authorship
- Lead contact
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22
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Sheehan J, Trauth AJ, Hagensee ME, Ramsay AJ. Characterization of Vaccine-Enhanced Humoral Immune Responses Against Emergent SARS-CoV-2 Variants in a Convalescent Cohort. Pathogens 2025; 14:44. [PMID: 39861005 PMCID: PMC11768806 DOI: 10.3390/pathogens14010044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Revised: 01/03/2025] [Accepted: 01/05/2025] [Indexed: 01/27/2025] Open
Abstract
Vaccination of COVID-19-convalescent individuals may generate 'hybrid' immunity of enhanced magnitude, durability, and cross-reactive breadth. Our primary goal was to characterize hybrid antibody (Ab) responses in a patient cohort infected with ancestral Wuhan-Hu-1 virus and vaccinated between 6 and 10 months later with the Wuhan-Hu-1-based BNT162b2 mRNA vaccine. We were particularly interested in determining the efficacy of neutralizing Ab responses against subsequently emergent SARS-CoV-2 variants. Sera collected at 3-monthly intervals over a period of 12 months were analyzed by ELISA for SARS-CoV-2 RBD-specific Ab responses, and also for neutralizing Ab activity using pseudovirus-based neutralization assays. We found that convalescent RBD-reactive IgG and IgA Ab responses did not decline significantly through 9 months post-diagnosis. These responses improved significantly following vaccination and remained elevated through at least 12-months. SARS-CoV-2 neutralizing Ab activity was detected in convalescent sera through 9 months post-diagnosis, although it trended downwards from 3 months. Neutralizing Ab activity against the Wuhan-Hu-1 strain was significantly improved by vaccination, to levels that persisted through the end of the study. However, sera collected from vaccinated convalescent subjects also had significant neutralization activity against Delta B.1.617.2 and Omicron variants that persisted for at least 2-3 months, unlike sera from unvaccinated convalescent controls. Thus, vaccination of Wuhan-Hu-1-convalescent individuals with the BNT162b2 vaccine improved and sustained protective neutralizing Ab activity against SARS-CoV-2, including cross-reactive neutralizing activity against variants that emerged months later.
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Affiliation(s)
- Jared Sheehan
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA;
| | - Amber J. Trauth
- Stanley S. Scott Cancer, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA;
| | - Michael E. Hagensee
- Department of Internal Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA;
| | - Alistair J. Ramsay
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA;
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23
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Mambelli F, de Araujo ACVSC, Farias JP, de Andrade KQ, Ferreira LCS, Minoprio P, Leite LCC, Oliveira SC. An Update on Anti-COVID-19 Vaccines and the Challenges to Protect Against New SARS-CoV-2 Variants. Pathogens 2025; 14:23. [PMID: 39860984 PMCID: PMC11768231 DOI: 10.3390/pathogens14010023] [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: 10/04/2024] [Revised: 12/11/2024] [Accepted: 12/20/2024] [Indexed: 01/27/2025] Open
Abstract
The COVID-19 pandemic has posed a significant threat to global health systems, with extensive impacts across many sectors of society. The pandemic has been responsible for millions of deaths worldwide since its first identification in late 2019. Several actions have been taken to prevent the disease, including the unprecedented fast development and global vaccination campaigns, which were pivotal in reducing symptoms and deaths. Given the impact of the pandemic, the continuous changes of the virus, and present vaccine technologies, this review analyzes how, so far, we have met the challenge posed by the emergence of new variants and discusses how next-generation pan-coronavirus vaccines, with enhanced longevity and breadth of immune responses, may be tackled with alternative administration routes and antigen delivery platforms. By addressing these critical aspects, this review aims to contribute to the ongoing efforts to achieve long-term control of COVID-19, stimulating the discussion and work on next-generation vaccines capable of facing future waves of infection.
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Affiliation(s)
- Fábio Mambelli
- Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, Brazil; (F.M.); (A.C.V.S.C.d.A.); (K.Q.d.A.)
- Institut Pasteur de São Paulo, São Paulo 05508-020, Brazil; (L.C.S.F.); (P.M.)
| | - Ana Carolina V. S. C. de Araujo
- Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, Brazil; (F.M.); (A.C.V.S.C.d.A.); (K.Q.d.A.)
| | - Jéssica P. Farias
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, Brazil;
| | - Kivia Q. de Andrade
- Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, Brazil; (F.M.); (A.C.V.S.C.d.A.); (K.Q.d.A.)
| | - Luis C. S. Ferreira
- Institut Pasteur de São Paulo, São Paulo 05508-020, Brazil; (L.C.S.F.); (P.M.)
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, Brazil;
| | - Paola Minoprio
- Institut Pasteur de São Paulo, São Paulo 05508-020, Brazil; (L.C.S.F.); (P.M.)
| | - Luciana C. C. Leite
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo 05503-900, Brazil;
| | - Sergio C. Oliveira
- Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, Brazil; (F.M.); (A.C.V.S.C.d.A.); (K.Q.d.A.)
- Institut Pasteur de São Paulo, São Paulo 05508-020, Brazil; (L.C.S.F.); (P.M.)
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24
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Yang Y, Miller H, Byazrova MG, Cndotti F, Benlagha K, Camara NOS, Shi J, Forsman H, Lee P, Yang L, Filatov A, Zhai Z, Liu C. The characterization of CD8 + T-cell responses in COVID-19. Emerg Microbes Infect 2024; 13:2287118. [PMID: 37990907 PMCID: PMC10786432 DOI: 10.1080/22221751.2023.2287118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/19/2023] [Indexed: 11/23/2023]
Abstract
This review gives an overview of the protective role of CD8+ T cells in SARS-CoV-2 infection. The cross-reactive responses intermediated by CD8+ T cells in unexposed cohorts are described. Additionally, the relevance of resident CD8+ T cells in the upper and lower airway during infection and CD8+ T-cell responses following vaccination are discussed, including recent worrisome breakthrough infections and variants of concerns (VOCs). Lastly, we explain the correlation between CD8+ T cells and COVID-19 severity. This review aids in a deeper comprehension of the association between CD8+ T cells and SARS-CoV-2 and broadens a vision for future exploration.
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Affiliation(s)
- Yuanting Yang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, Hubei, People’s Republic of China
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Heather Miller
- Cytek Biosciences, R&D Clinical Reagents, Fremont, CA, USA
| | - Maria G. Byazrova
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, Russia
| | - Fabio Cndotti
- Division of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Kamel Benlagha
- Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Niels Olsen Saraiva Camara
- Laboratory of Human Immunology, Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Junming Shi
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, Hubei, People’s Republic of China
| | - Huamei Forsman
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Pamela Lee
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Lu Yang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, Hubei, People’s Republic of China
| | - Alexander Filatov
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, Russia
| | - Zhimin Zhai
- Department of Hematology, The Second Hospital of Anhui Medical University, Hefei, People’s Republic of China
| | - Chaohong Liu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, Hubei, People’s Republic of China
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25
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Shimizu J, Sasaki T, Ong GH, Koketsu R, Samune Y, Nakayama EE, Nagamoto T, Yamamoto Y, Miyazaki K, Shioda T. IFN-γ derived from activated human CD4 + T cells inhibits the replication of SARS-CoV-2 depending on cell-type and viral strain. Sci Rep 2024; 14:26660. [PMID: 39496837 PMCID: PMC11535250 DOI: 10.1038/s41598-024-77969-4] [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: 08/03/2024] [Accepted: 10/28/2024] [Indexed: 11/06/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and vaccination elicit both T cell and B cell immune responses in immunocompetent individuals. However, the mechanisms underlying the antiviral effects mediated by CD4+ T cells are not fully understood. In this study, we analyzed the culture supernatant (SN) from polyclonally stimulated human CD4+ T cells as a model for soluble mediators derived from SARS-CoV-2-stimulated CD4+ T cells. Interestingly, this SN inhibited SARS-CoV-2 propagation in a viral strain- and host cell type-dependent manner. The original wild-type showed the highest susceptibility, whereas the Delta variant exhibited resistance in the human monocyte cell line. In addition, antibody-dependent enhancement (ADE) of infection with the original strain was also abolished in the presence of the SN. The findings showed that the inhibitory effect on viral propagation by the SN was mostly attributed to interferon-γ (IFN-γ) that was present in the SN. These results highlight the potential role of IFN-γ as an anti-SARS-CoV-2 mediator derived from CD4+ T cells, and suggest that we need to understand the SARS-CoV-2 strain-dependent sensitivity to IFN-γ in controlling clinical outcomes. In addition, characterization of new SARS-CoV-2 variants in terms of IFN-γ-sensitivity will have important implications for selecting therapeutic strategies.
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Affiliation(s)
- Jun Shimizu
- MiCAN Technologies Inc., KKVP 1-36, Goryo-Ohara, Nishikyo-Ku, Kyoto, 615-8245, Japan
| | - Tadahiro Sasaki
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, 3-1, Yamada-Oka, Suita, Osaka, 565-0871, Japan
| | - Guang Han Ong
- MiCAN Technologies Inc., KKVP 1-36, Goryo-Ohara, Nishikyo-Ku, Kyoto, 615-8245, Japan
| | - Ritsuko Koketsu
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, 3-1, Yamada-Oka, Suita, Osaka, 565-0871, Japan
| | - Yoshihiro Samune
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, 3-1, Yamada-Oka, Suita, Osaka, 565-0871, Japan
| | - Emi E Nakayama
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, 3-1, Yamada-Oka, Suita, Osaka, 565-0871, Japan
| | - Tetsuharu Nagamoto
- HiLung Inc., Innovation Hub Kyoto, 46-29, Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto, 606-8304, Japan
| | - Yuki Yamamoto
- HiLung Inc., Innovation Hub Kyoto, 46-29, Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto, 606-8304, Japan
| | - Kazuo Miyazaki
- MiCAN Technologies Inc., KKVP 1-36, Goryo-Ohara, Nishikyo-Ku, Kyoto, 615-8245, Japan.
| | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, 3-1, Yamada-Oka, Suita, Osaka, 565-0871, Japan.
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26
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Sharma S, Roy D, Cherian S. In-silico evaluation of the T-cell based immune response against SARS-CoV-2 omicron variants. Sci Rep 2024; 14:25413. [PMID: 39455652 PMCID: PMC11511884 DOI: 10.1038/s41598-024-75658-w] [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: 01/29/2024] [Accepted: 10/07/2024] [Indexed: 10/28/2024] Open
Abstract
During of COVID-19 pandemic, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has continuously evolved, resulting in the emergence of several new variants of concerns (VOCs) with numerous mutations. These VOCs dominate in various regions due to increased transmissibility and antibody evasion, potentially reducing vaccine effectiveness. Nonetheless, it remains uncertain whether the recent SARS-CoV-2 VOCs have the ability to circumvent the T cell immunity elicited by either COVID-19 vaccination or natural infection. To address this, we conducted in-silico analysis to examine the impact of VOC-specific mutations at the epitope level and T cell cross-reactivity with the ancestral SARS-CoV-2. According to the in-silico investigation, T cell responses triggered by immunization or prior infections still recognize the variants in spite of mutations. These variants are expected to either maintain their dominant epitope HLA patterns or bind with new HLAs, unlike the epitopes of the ancestral strain. Our findings indicate that a significant proportion of immuno-dominant CD8 + and CD4 + epitopes are conserved across all the variants, implying that existing vaccines might maintain efficacy against new variations. However, further in-vitro and in-vivo studies are needed to validate the in-silico results and fully elucidate immune sensitivities to VOCs.
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Affiliation(s)
- Shivangi Sharma
- Bioinformatics and Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, 411001, India
| | - Diya Roy
- Bioinformatics and Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, 411001, India
| | - Sarah Cherian
- Bioinformatics and Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, 411001, India.
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27
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Perdiguero B, Álvarez E, Marcos-Villar L, Sin L, López-Bravo M, Valverde JR, Sorzano CÓS, Falqui M, Coloma R, Esteban M, Guerra S, Gómez CE. B and T Cell Bi-Cistronic Multiepitopic Vaccine Induces Broad Immunogenicity and Provides Protection Against SARS-CoV-2. Vaccines (Basel) 2024; 12:1213. [PMID: 39591118 PMCID: PMC11598604 DOI: 10.3390/vaccines12111213] [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: 09/18/2024] [Revised: 10/18/2024] [Accepted: 10/22/2024] [Indexed: 11/28/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic, caused by SARS-CoV-2, has highlighted the need for vaccines targeting both neutralizing antibodies (NAbs) and long-lasting cross-reactive T cells covering multiple viral proteins to provide broad and durable protection against emerging variants. METHODS To address this, here we developed two vaccine candidates, namely (i) DNA-CoV2-TMEP, expressing the multiepitopic CoV2-TMEP protein containing immunodominant and conserved T cell regions from SARS-CoV-2 structural proteins, and (ii) MVA-CoV2-B2AT, encoding a bi-cistronic multiepitopic construct that combines conserved B and T cell overlapping regions from SARS-CoV-2 structural proteins. RESULTS Both candidates were assessed in vitro and in vivo demonstrating their ability to induce robust immune responses. In C57BL/6 mice, DNA-CoV2-TMEP enhanced the recruitment of innate immune cells and stimulated SARS-CoV-2-specific polyfunctional T cells targeting multiple viral proteins. MVA-CoV2-B2AT elicited NAbs against various SARS-CoV-2 variants of concern (VoCs) and reduced viral replication and viral yields against the Beta variant in susceptible K18-hACE2 mice. The combination of MVA-CoV2-B2AT with a mutated ISG15 form as an adjuvant further increased the magnitude, breadth and polyfunctional profile of the response. CONCLUSION These findings underscore the potential of these multiepitopic proteins when expressed from DNA or MVA vectors to provide protection against SARS-CoV-2 and its variants, supporting their further development as next-generation COVID-19 vaccines.
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Affiliation(s)
- Beatriz Perdiguero
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; (E.Á.); (L.M.-V.); (M.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain;
| | - Enrique Álvarez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; (E.Á.); (L.M.-V.); (M.E.)
| | - Laura Marcos-Villar
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; (E.Á.); (L.M.-V.); (M.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain;
| | - Laura Sin
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain;
| | - María López-Bravo
- Department of Microbial Biotechnology, CNB-CSIC, 28049 Madrid, Spain;
| | | | | | - Michela Falqui
- Department of Preventive Medicine, Public Health and Microbiology, Faculty of Medicine, Universidad Autónoma de Madrid, 28029 Madrid, Spain; (M.F.); (R.C.); (S.G.)
| | - Rocío Coloma
- Department of Preventive Medicine, Public Health and Microbiology, Faculty of Medicine, Universidad Autónoma de Madrid, 28029 Madrid, Spain; (M.F.); (R.C.); (S.G.)
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; (E.Á.); (L.M.-V.); (M.E.)
| | - Susana Guerra
- Department of Preventive Medicine, Public Health and Microbiology, Faculty of Medicine, Universidad Autónoma de Madrid, 28029 Madrid, Spain; (M.F.); (R.C.); (S.G.)
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carmen Elena Gómez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; (E.Á.); (L.M.-V.); (M.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain;
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Im KI, Kim N, Lee J, Oh UH, Lee HW, Lee DG, Min GJ, Lee R, Lee J, Kim S, Cho SG. SARS-CoV-2-Specific T-Cell as a Potent Therapeutic Strategy against Immune Evasion of Emerging COVID-19 Variants. Int J Mol Sci 2024; 25:10512. [PMID: 39408840 PMCID: PMC11477143 DOI: 10.3390/ijms251910512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Revised: 09/24/2024] [Accepted: 09/26/2024] [Indexed: 10/20/2024] Open
Abstract
Despite advances in vaccination and therapies for coronavirus disease, challenges remain due to reduced antibody longevity and the emergence of virulent variants like Omicron (BA.1) and its subvariants (BA.1.1, BA.2, BA.3, and BA.5). This study explored the potential of adoptive immunotherapy and harnessing the protective abilities using virus-specific T cells (VSTs). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) VSTs were generated by stimulating donor-derived peripheral blood mononuclear cells with spike, nucleocapsid, and membrane protein peptide mixtures. Phenotypic characterization, including T-cell receptor (TCR) vβ and pentamer analyses, was performed on the ex vivo-expanded cells. We infected human leukocyte antigen (HLA)-partially matched human Calu-3 cells with various authentic SARS-CoV-2 strains in a Biosafety Level 3 facility and co-cultured them with VSTs. VSTs exhibited a diverse TCR vβ repertoire, confirming their ability to target a broad range of SARS-CoV-2 antigens from both the ancestral and mutant strains, including Omicron BA.1 and BA.5. These ex vivo-expanded cells exhibited robust cytotoxicity and low alloreactivity against HLA-partially matched SARS-CoV-2-infected cells. Their cytotoxic effects were consistent across variants, targeting conserved spike and nucleocapsid epitopes. Our findings suggest that third-party partial HLA-matching VSTs could counter immune-escape mechanisms posed by emerging variants of concern.
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Affiliation(s)
- Keon-Il Im
- Institute for Translational Research and Molecular Imaging, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (K.-I.I.); (N.K.); (J.L.); (G.-J.M.)
- Research and Development Division, LucasBio Co., Ltd., Seoul 06591, Republic of Korea; (U.-H.O.); (H.-W.L.)
| | - Nayoun Kim
- Institute for Translational Research and Molecular Imaging, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (K.-I.I.); (N.K.); (J.L.); (G.-J.M.)
- Research and Development Division, LucasBio Co., Ltd., Seoul 06591, Republic of Korea; (U.-H.O.); (H.-W.L.)
| | - Junseok Lee
- Institute for Translational Research and Molecular Imaging, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (K.-I.I.); (N.K.); (J.L.); (G.-J.M.)
| | - Ui-Hyeon Oh
- Research and Development Division, LucasBio Co., Ltd., Seoul 06591, Republic of Korea; (U.-H.O.); (H.-W.L.)
| | - Hye-Won Lee
- Research and Development Division, LucasBio Co., Ltd., Seoul 06591, Republic of Korea; (U.-H.O.); (H.-W.L.)
| | - Dong-Gun Lee
- Division of Infectious Diseases, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (D.-G.L.); (R.L.)
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Gi-June Min
- Institute for Translational Research and Molecular Imaging, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (K.-I.I.); (N.K.); (J.L.); (G.-J.M.)
- Department of Hematology, Seoul St. Mary’s Hematology Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Raeseok Lee
- Division of Infectious Diseases, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (D.-G.L.); (R.L.)
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Jinah Lee
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam 13488, Republic of Korea; (J.L.); (S.K.)
| | - Seungtaek Kim
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam 13488, Republic of Korea; (J.L.); (S.K.)
| | - Seok-Goo Cho
- Institute for Translational Research and Molecular Imaging, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (K.-I.I.); (N.K.); (J.L.); (G.-J.M.)
- Research and Development Division, LucasBio Co., Ltd., Seoul 06591, Republic of Korea; (U.-H.O.); (H.-W.L.)
- Department of Hematology, Seoul St. Mary’s Hematology Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
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García-Pérez J, Borobia AM, Pérez-Olmeda M, Portolés A, Castaño L, Campins-Artí M, Bertrán MJ, Bermejo M, Arribas JR, López A, Ascaso-Del-Rio A, Arana-Arri E, Fuentes Camps I, Vilella A, Cascajero A, García-Morales MT, Castillo de la Osa M, Pérez Ingidua C, Lora D, Jiménez-Santana P, Pino-Rosa S, Gómez de la Cámara A, De La Torre-Tarazona E, Calonge E, Cruces R, Belda-Iniesta C, Alcamí J, Frías J, Carcas AJ, Díez-Fuertes F. Immunogenicity of a third dose with mRNA-vaccines in the ChAdOx1-S/BNT162b2 vaccination regimen against SARS-CoV-2 variants. iScience 2024; 27:110728. [PMID: 39286494 PMCID: PMC11404211 DOI: 10.1016/j.isci.2024.110728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/28/2024] [Accepted: 08/09/2024] [Indexed: 09/19/2024] Open
Abstract
CombiVacS study has demonstrated a strong immune response of the heterologous ChAdOx1-S/BNT162b2 vaccine combination. The primary outcomes of the study were to assess the humoral immune response against SARS-CoV-2, 28 days after a third dose of a mRNA vaccine, in subjects that received a previous prime-boost scheme with ChAdOx1-S/BNT162b2. Secondary outcomes extended the study to 3 and 6 months. The third vaccine dose of mRNA-1273 in naive participants previously vaccinated with ChAdOx1-S/BNT162b2 regimen reached higher neutralizing antibodies titers against the variants of concern Delta and BA.1 lineage of Omicron compared with those receiving a third dose of BNT162b2 at day 28. These differences between BNT162b2 and mRNA-1273 arms were observed against the ancestral variant G614 at day 90. Suboptimal neutralizing response was observed against BQ.1.1, XBB.1.5/XBB.1.9, and JN.1 in a relevant proportion of individuals 180 days after the third dose, even after asymptomatic Omicron breakthrough infections. EudraCT (2021-001978-37); ClinicalTrials.gov (NCT04860739).
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Affiliation(s)
- Javier García-Pérez
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
| | - Alberto M Borobia
- Servicio de Farmacología Clínica, Hospital Universitario La Paz, Departamento de Farmacología y Terapéutica, Facultad de Medicina, Universidad Autónoma de Madrid, IdiPAZ, 28046 Madrid, Spain
- Servicio de Medicina Interna, Departamento de Medicina, Facultad de Medicina, Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, 28046 Madrid, Spain
| | - Mayte Pérez-Olmeda
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
- Laboratorio de Serología, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
| | - Antonio Portolés
- Servicio de Farmacología Clínica, Hospital Clínico San Carlos, IdISSC, 28040 Madrid, Spain
- Departamento de Farmacología y Toxicología, Facultad de Medicina, Universidad Complutense de Madrid (UCM), 28040 Madrid, Spain
| | - Luis Castaño
- Cruces University Hospital, Bio-Bizkaia, UPV/EHU, CIBERDEM/CIBERER, Endo-ERN, Barakaldo, 48903 Vizcaya, Spain
| | - Magdalena Campins-Artí
- Servicio de Medicina Preventiva y Epidemiología, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - María Jesús Bertrán
- Servicio de Medicina Preventiva y Epidemiología, Hospital Clínic de Barcelona, 08036 Barcelona, Spain
| | - Mercedes Bermejo
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
| | - José Ramón Arribas
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
- Servicio de Medicina Interna, Departamento de Medicina, Facultad de Medicina, Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, 28046 Madrid, Spain
| | - Andrea López
- Laboratorio de Serología, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
| | - Ana Ascaso-Del-Rio
- Servicio de Farmacología Clínica, Hospital Clínico San Carlos, IdISSC, 28040 Madrid, Spain
| | - Eunate Arana-Arri
- Cruces University Hospital, Bio-Bizkaia, UPV/EHU, CIBERDEM/CIBERER, Endo-ERN, Barakaldo, 48903 Vizcaya, Spain
| | - Inmaculada Fuentes Camps
- Unidad de Soporte a la Investigación Clínica, Vall d'Hebron Institut de Recerca, Servicio de Farmacología Clínica, Hospital Universitari Vall d'Hebron, 08035 Barcelona, Spain
| | - Anna Vilella
- Servicio de Medicina Preventiva y Epidemiología, Hospital Clínic de Barcelona, 08036 Barcelona, Spain
| | - Almudena Cascajero
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
| | | | - María Castillo de la Osa
- Laboratorio de Serología, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
| | - Carla Pérez Ingidua
- Servicio de Farmacología Clínica, Hospital Clínico San Carlos, IdISSC, 28040 Madrid, Spain
| | - David Lora
- Spanish Clinical Research Network - SCReN - ISCIII, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Universitario 12 de octubre, 28041 Madrid, Spain
- Facultad de Estudios Estadísticos, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Paloma Jiménez-Santana
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
| | - Silvia Pino-Rosa
- Laboratorio de Serología, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
| | - Agustín Gómez de la Cámara
- Instituto de Investigación Sanitaria del Hospital Universitario 12 de octubre, 28041 Madrid, Spain
- Facultad de Estudios Estadísticos, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Erick De La Torre-Tarazona
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
| | - Esther Calonge
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
- Laboratorio de Serología, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
| | - Raquel Cruces
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
| | | | - José Alcamí
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
| | - Jesús Frías
- Servicio de Farmacología Clínica, Hospital Universitario La Paz, Departamento de Farmacología y Terapéutica, Facultad de Medicina, Universidad Autónoma de Madrid, IdiPAZ, 28046 Madrid, Spain
| | - Antonio J Carcas
- Servicio de Farmacología Clínica, Hospital Universitario La Paz, Departamento de Farmacología y Terapéutica, Facultad de Medicina, Universidad Autónoma de Madrid, IdiPAZ, 28046 Madrid, Spain
| | - Francisco Díez-Fuertes
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Majadahonda, 28222 Madrid, Spain
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30
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Tsagkli P, Geropeppa M, Papadatou I, Spoulou V. Hybrid Immunity against SARS-CoV-2 Variants: A Narrative Review of the Literature. Vaccines (Basel) 2024; 12:1051. [PMID: 39340081 PMCID: PMC11436074 DOI: 10.3390/vaccines12091051] [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: 08/11/2024] [Revised: 09/04/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024] Open
Abstract
The emergence of SARS-CoV-2 led to a global health crisis and the burden of the disease continues to persist. The rapid development and emergency authorization of various vaccines, including mRNA-based vaccines, played a pivotal role in mitigating severe illness and mortality. However, rapid viral mutations, leading to several variants of concern, challenged vaccine effectiveness, particularly concerning immune evasion. Research on immunity, both from natural infection and vaccination, revealed that while neutralizing antibodies provide protection against infection, their effect is short-lived. The primary defense against severe COVID-19 is derived from the cellular immune response. Hybrid immunity, developed from a combination of natural infection and vaccination, offers enhanced protection, with convalescent vaccinated individuals showing significantly higher levels of neutralizing antibodies. As SARS-CoV-2 continues to evolve, understanding the durability and breadth of hybrid immunity becomes crucial. This narrative review examines the latest data on humoral and cellular immunity from both natural infection and vaccination, discussing how hybrid immunity could inform and optimize future vaccination strategies in the ongoing battle against COVID-19 and in fear of a new pandemic.
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Affiliation(s)
- Panagiota Tsagkli
- Immunobiology and Vaccinology Research Laboratory and Infectious Diseases Department "MAKKA", First Department of Paediatrics, "Aghia Sophia" Children's Hospital, Athens Medical School, 11527 Athens, Greece
| | - Maria Geropeppa
- Immunobiology and Vaccinology Research Laboratory and Infectious Diseases Department "MAKKA", First Department of Paediatrics, "Aghia Sophia" Children's Hospital, Athens Medical School, 11527 Athens, Greece
| | - Ioanna Papadatou
- Immunobiology and Vaccinology Research Laboratory and Infectious Diseases Department "MAKKA", First Department of Paediatrics, "Aghia Sophia" Children's Hospital, Athens Medical School, 11527 Athens, Greece
| | - Vana Spoulou
- Immunobiology and Vaccinology Research Laboratory and Infectious Diseases Department "MAKKA", First Department of Paediatrics, "Aghia Sophia" Children's Hospital, Athens Medical School, 11527 Athens, Greece
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Yao D, Patel RS, Lam A, Glover Q, Srinivasan C, Herchen A, Ritchie B, Agrawal B. Antibody Responses in SARS-CoV-2-Exposed and/or Vaccinated Individuals Target Conserved Epitopes from Multiple CoV-2 Antigens. Int J Mol Sci 2024; 25:9814. [PMID: 39337303 PMCID: PMC11432605 DOI: 10.3390/ijms25189814] [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: 08/28/2024] [Revised: 09/06/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
There is a need to investigate novel strategies in order to create an effective, broadly protective vaccine for current and future severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks. The currently available vaccines demonstrate compromised efficacy against emerging SARS-CoV-2 variants of concern (VOCs), short-lived immunity, and susceptibility to immune imprinting due to frequent boosting practices. In this study, we examined the specificity of cross-reactive IgG antibody responses in mRNA-vaccinated, AstraZeneca-vaccinated, and unvaccinated donors to identify potentially conserved, cross-reactive epitopes to target in order to create a broadly protective SARS-CoV-2 vaccine. Our study provides evidence for cross-reactive IgG antibodies specific to eight different spike (S) variants. Furthermore, the specificities of these cross-variant IgG antibody titers were associated to some extent with spike S1- and S2-subunit-derived epitopes P1 and P2, respectively. In addition, nucleocapsid (N)- and membrane (M)-specific IgG antibody titers correlated with N- and M-derived epitopes conserved across beta-CoVs, P3-7. This study reveals conserved epitopes of viral antigens, targeted by natural and/or vaccine-induced human immunity, for future designs of next-generation COVID-19 vaccines.
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Affiliation(s)
- David Yao
- Department of Surgery, Faculty of Medicine and Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada; (D.Y.); (R.S.P.); (A.L.)
| | - Raj S. Patel
- Department of Surgery, Faculty of Medicine and Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada; (D.Y.); (R.S.P.); (A.L.)
| | - Adrien Lam
- Department of Surgery, Faculty of Medicine and Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada; (D.Y.); (R.S.P.); (A.L.)
| | - Quarshie Glover
- Department of Medicine, Faculty of Medicine and Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada; (Q.G.); (C.S.); (A.H.); (B.R.)
| | - Cindy Srinivasan
- Department of Medicine, Faculty of Medicine and Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada; (Q.G.); (C.S.); (A.H.); (B.R.)
| | - Alex Herchen
- Department of Medicine, Faculty of Medicine and Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada; (Q.G.); (C.S.); (A.H.); (B.R.)
| | - Bruce Ritchie
- Department of Medicine, Faculty of Medicine and Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada; (Q.G.); (C.S.); (A.H.); (B.R.)
| | - Babita Agrawal
- Department of Surgery, Faculty of Medicine and Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada; (D.Y.); (R.S.P.); (A.L.)
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McMahon WC, Kwatra G, Izu A, Jones SA, Mbele NJ, Jafta N, Lala R, Shalekoff S, Tiemessen CT, Madhi SA, Nunes MC. T-cell responses to ancestral SARS-CoV-2 and Omicron variant among unvaccinated pregnant and postpartum women living with and without HIV in South Africa. Sci Rep 2024; 14:20348. [PMID: 39223211 PMCID: PMC11369237 DOI: 10.1038/s41598-024-70725-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
SARS-CoV-2 cell-mediated immunity remains understudied during pregnancy in unvaccinated Black African women living with HIV (WLWH) from low- and middle-income countries. We investigated SARS-CoV-2-specific T-cell responses 1 month following infection in 24 HIV-uninfected women and 15 WLWH at any stage during pregnancy or postpartum. The full-length spike (FLS) glycoprotein and nucleocapsid (N) protein of wild-type (WT) SARS-CoV-2, as well as mutated spike protein regions found in the Omicron variant (B.1.1.529) were targeted by flow cytometry. WT-specific CD4+ and CD8+ T cells elicited similar FLS- and N-specific responses in HIV-uninfected women and WLWH. SARS-CoV-2-specific T-lymphocytes were predominantly TNF-α monofunctional in pregnant and postpartum women living with and without HIV, with fever cells producing either IFN-γ or IL-2. Furthermore, T-cell responses were unaffected by Omicron-specific spike mutations as similar responses between Omicron and the ancestral virus were detected for CD4+ and CD8+ T cells. Our results collectively demonstrate comparable T-cell responses between WLWH on antiretroviral therapy and HIV-uninfected pregnant and postpartum women who were naïve to Covid-19 vaccination. Additionally, we show that T cells from women infected with the ancestral virus, Beta variant (B.1.351), or Delta variant (B.1.617.2) can cross-recognize Omicron, suggesting an overall preservation of T-cell immunity.
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Affiliation(s)
- William C McMahon
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- South African Research Chair Initiative in Vaccine Preventable Diseases, Department of Science and Innovation/National Research Foundation, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gaurav Kwatra
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH, USA.
- Department of Clinical Microbiology, Christian Medical College, Vellore, India.
| | - Alane Izu
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- African Leadership in Vaccinology Expertise, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephanie A Jones
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nkululeko J Mbele
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nwabisa Jafta
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Rushil Lala
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sharon Shalekoff
- A Division of the National Health Laboratory Service, Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline T Tiemessen
- A Division of the National Health Laboratory Service, Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- African Leadership in Vaccinology Expertise, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- South African Research Chair Initiative in Vaccine Preventable Diseases, Department of Science and Innovation/National Research Foundation, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Center of Excellence in Respiratory Pathogens, Hospices Civils de Lyon, and Centre International de Recherche en Infectiologie, Inserm U1111, CNRS UMR5308, ENS de Lyon, Université Claude Bernard Lyon 1, Lyon, France
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Serdyuk YV, Zornikova KV, Dianov DV, Ivanova NO, Davydova VD, Fefelova EI, Nenasheva TA, Sheetikov SA, Bogolyubova AV. T-Cell Receptors Cross-Reactive to Coronaviral Epitopes Homologous to the SPR Peptide. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:1631-1642. [PMID: 39418521 DOI: 10.1134/s0006297924090098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/26/2024] [Accepted: 08/09/2024] [Indexed: 10/19/2024]
Abstract
The COVID-19 pandemic caused by the rapid spread of the novel coronavirus SARS-CoV-2, has promoted an interest in studying the T-cell immune response. It was found that the polyclonal and cross-reactive T-cell response against seasonal coronaviruses and other SARS-CoV-2 strains reduced disease severity. We investigated the immunodominant T-cell epitope SPRWYFYYYL from the nucleocapsid protein of SARS-CoV-2. The immune response to this epitope is characterized by the formation of highly homologous (convergent) receptors that have been found in the T-cell receptor (TCR) repertoires of different individuals. This epitope belongs to a group of highly conserved peptides that are rarely mutated in novel SARS-CoV-2 strains and are homologous to the epitopes of seasonal coronaviruses. It has been suggested that the cross-reactive response to homologous peptides contributes to the reduction of COVID-19 severity. However, some investigators have questioned this hypothesis, suggesting that the low affinity of the cross-reactive receptors reduces the strength of the immune response. The aim of this study was to evaluate the effect of amino acid substitutions in the SPR epitope on its binding affinity to specific TCRs. For this, we performed antigen-dependent cellular expansions were performed using samples from four COVID-19-transfected donors and sequenced their TCR repertoires. The resulting SPR-specific repertoire of β-chains in TCRs had a greater sequence diversity than the repertoire of α-chains. However, the TCR repertoires of all four donors contained public receptors, three of which were cloned and used to generate the Jurkat E6-1 TPR cell line. Only one of these receptors was activated by the SPR peptide and recognized with the same affinity by its mutant homologue LPRWYFYYY from seasonal coronaviruses. This indicates that the presence of the mutation did not affect the strength of the immune response, which may explain why the cross-reactive response to the SPR epitope is so frequent and contributes positively to COVID-19 infection.
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Affiliation(s)
- Yana V Serdyuk
- National Medical Research Center for Hematology, Ministry of Health of the Russian Federation, Moscow, 125167, Russia
| | - Ksenia V Zornikova
- National Medical Research Center for Hematology, Ministry of Health of the Russian Federation, Moscow, 125167, Russia
| | - Dmitry V Dianov
- National Medical Research Center for Hematology, Ministry of Health of the Russian Federation, Moscow, 125167, Russia
| | - Nataliia O Ivanova
- National Medical Research Center for Hematology, Ministry of Health of the Russian Federation, Moscow, 125167, Russia
| | - Vassa D Davydova
- National Medical Research Center for Hematology, Ministry of Health of the Russian Federation, Moscow, 125167, Russia
| | - Ekaterina I Fefelova
- National Medical Research Center for Hematology, Ministry of Health of the Russian Federation, Moscow, 125167, Russia
| | - Tatiana A Nenasheva
- National Medical Research Center for Hematology, Ministry of Health of the Russian Federation, Moscow, 125167, Russia
| | - Saveliy A Sheetikov
- National Medical Research Center for Hematology, Ministry of Health of the Russian Federation, Moscow, 125167, Russia
| | - Apollinariya V Bogolyubova
- National Medical Research Center for Hematology, Ministry of Health of the Russian Federation, Moscow, 125167, Russia.
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Liu X, Ng WH, Zusinaite E, Freitas J, Taylor A, Yerragunta V, Aavula SM, Gorriparthi S, Ponsekaran S, Bonda RL, Mani P, Nimmagadda SV, Wang S, Lello LS, Zaid A, Dua U, Taft-Benz SA, Anderson E, Baxter VK, Sarkar S, Ling ZL, Ashhurst TM, Cheng SMS, Pattnaik P, Kanakasapapathy AK, Baric RS, Burt FJ, Peiris M, Heise MT, King NJC, Merits A, Lingala R, Mahalingam S. A single-dose intranasal live-attenuated codon deoptimized vaccine provides broad protection against SARS-CoV-2 and its variants. Nat Commun 2024; 15:7225. [PMID: 39187479 PMCID: PMC11347628 DOI: 10.1038/s41467-024-51535-y] [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: 05/06/2024] [Accepted: 08/07/2024] [Indexed: 08/28/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) continues its significant health and economic impact globally. Despite the success of spike-protein vaccines in preventing severe disease, long-lasting protection against emerging variants and the prevention of breakthrough infections and transmission remain elusive. We generate an intranasal live-attenuated SARS-CoV-2 vaccine, CDO-7N-1, using codon deoptimization. CDO-7N-1 shows highly attenuated replication and minimal or no lung pathology in vivo over multiple passages. It induces robust mucosal and systemic neutralizing antibody and T-cell subset responses, in mice (female K18-hACE2 and male HFH4-hACE2 mice), hamsters, and macaques triggered by a single immunization. Mice and hamsters vaccinated with CDO-7N-1 are protected from challenge with wild-type (WT) SARS-CoV-2 and other variants of concern. Serum from vaccinated animals neutralizes WT SARS-CoV-2, variants of concern (beta and delta), variants of interest (omicron XBB.1.5) and SARS-CoV-1. Antibody responses are sustained and enhanced by repeated immunization or infection with WT SARS-CoV-2. Immunity against all SARS-CoV-2 proteins by CDO-7N-1 should improve efficacy against future SARS-CoV-2 variants.
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Affiliation(s)
- Xiang Liu
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia
- Global Virus Network (GVN) Centre of Excellence in Arboviruses, Griffith University, Gold Coast, QLD, Australia
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, QLD, Australia
| | - Wern Hann Ng
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia
- Global Virus Network (GVN) Centre of Excellence in Arboviruses, Griffith University, Gold Coast, QLD, Australia
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, QLD, Australia
| | - Eva Zusinaite
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
| | - Joseph Freitas
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia
- Global Virus Network (GVN) Centre of Excellence in Arboviruses, Griffith University, Gold Coast, QLD, Australia
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, QLD, Australia
| | - Adam Taylor
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia
- Global Virus Network (GVN) Centre of Excellence in Arboviruses, Griffith University, Gold Coast, QLD, Australia
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, QLD, Australia
| | - Venugopal Yerragunta
- Indian Immunologicals Ltd (IIL), Rakshapuram, Gachibowli Post, Hyderabad, 500032, Telangana, India
| | - Shukra Madhaha Aavula
- Indian Immunologicals Ltd (IIL), Rakshapuram, Gachibowli Post, Hyderabad, 500032, Telangana, India
| | - Sambaiah Gorriparthi
- Indian Immunologicals Ltd (IIL), Rakshapuram, Gachibowli Post, Hyderabad, 500032, Telangana, India
| | - Santhakumar Ponsekaran
- Indian Immunologicals Ltd (IIL), Rakshapuram, Gachibowli Post, Hyderabad, 500032, Telangana, India
| | - Rama Lakshmi Bonda
- Indian Immunologicals Ltd (IIL), Rakshapuram, Gachibowli Post, Hyderabad, 500032, Telangana, India
| | - Priyanka Mani
- Indian Immunologicals Ltd (IIL), Rakshapuram, Gachibowli Post, Hyderabad, 500032, Telangana, India
| | - Sridevi V Nimmagadda
- Indian Immunologicals Ltd (IIL), Rakshapuram, Gachibowli Post, Hyderabad, 500032, Telangana, India
| | - Sainan Wang
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
| | | | - Ali Zaid
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia
- Global Virus Network (GVN) Centre of Excellence in Arboviruses, Griffith University, Gold Coast, QLD, Australia
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, QLD, Australia
| | - Ujjwal Dua
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia
- Griffith Enterprise, Griffith University, Brisbane, QLD, Australia
| | - Sharon A Taft-Benz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elizabeth Anderson
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Victoria K Baxter
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sanjay Sarkar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zheng L Ling
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Thomas M Ashhurst
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Cytometry Core Research Facility, The University of Sydney and Centenary Institute, Sydney, NSW, Australia
| | - Samuel M S Cheng
- School of Public Health, The University of Hong Kong, Special Administrative Region of Hong Kong, Hong Kong, China
| | - Priyabrata Pattnaik
- Indian Immunologicals Ltd (IIL), Rakshapuram, Gachibowli Post, Hyderabad, 500032, Telangana, India
| | | | - Ralph S Baric
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Felicity J Burt
- Division of Virology, National Health Laboratory Service and Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Malik Peiris
- School of Public Health, The University of Hong Kong, Special Administrative Region of Hong Kong, Hong Kong, China
- HKU-Pasteur Research Pole, The University of Hong Kong, Special Administrative Region of Hong Kong, Hong Kong, China
| | - Mark T Heise
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholas J C King
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
- Viral Immunopathology Laboratory, The Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Nano, The University of Sydney, Sydney, NSW 2006, Australia
| | - Andres Merits
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
| | - Rajendra Lingala
- Indian Immunologicals Ltd (IIL), Rakshapuram, Gachibowli Post, Hyderabad, 500032, Telangana, India
| | - Suresh Mahalingam
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia.
- Global Virus Network (GVN) Centre of Excellence in Arboviruses, Griffith University, Gold Coast, QLD, Australia.
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, QLD, Australia.
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Leno-Duran E, Serrano-Conde E, Salas-Rodríguez A, Salcedo-Bellido I, Barrios-Rodríguez R, Fuentes A, Viñuela L, García F, Requena P. Evaluation of inflammatory biomarkers and their association with anti-SARS-CoV-2 antibody titers in healthcare workers vaccinated with BNT162B2. Front Immunol 2024; 15:1447317. [PMID: 39247198 PMCID: PMC11377239 DOI: 10.3389/fimmu.2024.1447317] [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: 06/11/2024] [Accepted: 07/31/2024] [Indexed: 09/10/2024] Open
Abstract
Introduction Vaccine-induced immunity against COVID-19 generates antibody and lymphocyte responses. However, variability in antibody titers has been observed after vaccination, and the determinants of a better response should be studied. The main objective of this investigation was to analyze the inflammatory biomarker response induced in healthcare workers vaccinated with BNT162b2, and its association with anti-Spike (a SARS-CoV-2 antigen) antibodies measured throughout a 1-year follow-up. Methods Anti-spike antibodies and 92 biomarkers were analyzed in serum, along with socio-demographic and clinical variables collected by interview or exploration. Results In our study, four biomarkers (ADA, IL-17C, CCL25 and CD8α) increased their expression after the first vaccine dose; and 8 others (uPA, IL-18R1, EN-RAGE, CASP-8, MCP-2, TNFβ, CD5 and CXCL10) decreased their expression. Age, body mass index (BMI), smoking, alcohol consumption, and prevalent diseases were associated with some of these biomarkers. Furthermore, higher baseline levels of T-cell surface glycoprotein CD6 and hepatocyte growth factor (HGF) were associated with lower mean antibody titers at follow-up, while levels of monocyte chemotactic protein 2 (MCP-2) had a positive association with antibody levels. Age and BMI were positively related to baseline levels of MCP-2 (β=0.02, 95%CI 0.00-0.04, p=0.036) and HGF (β=0.03, 95%CI 0.00-0.06, p=0.039), respectively. Conclusion Our findings indicate that primary BNT162b2 vaccination had a positive effect on the levels of several biomarkers related to T cell function, and a negative one on some others related to cancer or inflammatory processes. In addition, a higher level of MCP-2 and lower levels of HGF and CD6 were found to be associated with higher anti-Spike antibody titer following vaccination.
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Affiliation(s)
- Ester Leno-Duran
- Universidad de Granada, Departamento de Obstetricia y Ginecología, Granada, Spain
| | - Esther Serrano-Conde
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
| | - Ana Salas-Rodríguez
- Universidad de Granada, Departamento de Medicina Preventiva y Salud Pública, Granada, Spain
| | - Inmaculada Salcedo-Bellido
- Universidad de Granada, Departamento de Medicina Preventiva y Salud Pública, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Rocío Barrios-Rodríguez
- Universidad de Granada, Departamento de Medicina Preventiva y Salud Pública, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Ana Fuentes
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Laura Viñuela
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Federico García
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Pilar Requena
- Universidad de Granada, Departamento de Medicina Preventiva y Salud Pública, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
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Koolaparambil Mukesh R, Yinda CK, Munster VJ, van Doremalen N. Beyond COVID-19: the promise of next-generation coronavirus vaccines. NPJ VIRUSES 2024; 2:39. [PMID: 40295763 PMCID: PMC11721646 DOI: 10.1038/s44298-024-00043-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/26/2024] [Indexed: 04/30/2025]
Abstract
Coronaviruses (CoVs) have caused three global outbreaks: severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) in 2003, Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, and SARS-CoV-2 in 2019, with significant mortality and morbidity. The impact of coronavirus disease 2019 (COVID-19) raised serious concerns about the global preparedness for a pandemic. Furthermore, the changing antigenic landscape of SARS-CoV-2 led to new variants with increased transmissibility and immune evasion. Thus, the development of broad-spectrum vaccines against current and future emerging variants of CoVs will be an essential tool in pandemic preparedness. Distinct phylogenetic features within CoVs complicate and limit the process of generating a pan-CoV vaccine capable of targeting the entire Coronaviridae family. In this review, we aim to provide a detailed overview of the features of CoVs, their phylogeny, current vaccines against various CoVs, the efforts in developing broad-spectrum coronavirus vaccines, and the future.
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Affiliation(s)
| | - Claude K Yinda
- Laboratory of Virology, Division of Intramural Research, National Institutes of Health, Hamilton, MT, USA
| | - Vincent J Munster
- Laboratory of Virology, Division of Intramural Research, National Institutes of Health, Hamilton, MT, USA
| | - Neeltje van Doremalen
- Laboratory of Virology, Division of Intramural Research, National Institutes of Health, Hamilton, MT, USA.
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37
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De Biasi S, Ciobanu AL, Santacroce E, Lo Tartaro D, Degliesposti G, D’Angerio M, Leccese M, Cardi M, Trenti T, Cuccorese M, Gibellini L, Ferraro D, Cossarizza A. SARS-CoV-2 Vaccination Responses in Anti-CD20-Treated Progressive Multiple Sclerosis Patients Show Immunosenescence in Antigen-Specific B and T Cells. Vaccines (Basel) 2024; 12:924. [PMID: 39204047 PMCID: PMC11360119 DOI: 10.3390/vaccines12080924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/08/2024] [Accepted: 08/09/2024] [Indexed: 09/03/2024] Open
Abstract
Clinical, pathological, and imaging evidence in multiple sclerosis (MS) shows that inflammation starts early and progresses with age. B cells play a central role in this process, contributing to cytokine production, defective regulatory functions, and abnormal immunoglobulin production, even in the central nervous system. Anti-CD20 (aCD20) therapies, which deplete CD20+ B cells, are largely used in the treatment of both relapsing remitting (RR) and progressive (PR) forms of MS. Although effective against MS symptoms and lesions detectable by magnetic resonance imaging, aCD20 therapies can reduce the immune response to COVID-19 vaccination. By using high-parameter flow cytometry, we examined the antigen-specific (Ag+) immune response six months post-third COVID-19 mRNA vaccination in MS patients with RR and PR forms on aCD20 therapy. Despite lower Ag+ B cell responses and lower levels of anti-SARS-CoV2, both total and neutralizing antibodies, RR and PR patients developed strong Ag+ T cell responses. We observed similar percentages and numbers of Ag+ CD4+ T cells and a high proportion of Ag+ CD8+ T cells, with slight differences in T cell phenotype and functionality; this, however, suggested the presence of differences in immune responses driven by age and disease severity.
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Affiliation(s)
- Sara De Biasi
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy (A.C.)
| | - Alin Liviu Ciobanu
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy (A.C.)
| | - Elena Santacroce
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy (A.C.)
| | - Domenico Lo Tartaro
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy (A.C.)
| | - Gianluca Degliesposti
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy (A.C.)
| | - Miriam D’Angerio
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy (A.C.)
| | - Maristella Leccese
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy (A.C.)
| | - Martina Cardi
- AOU Policlinico di Modena, Neurology Unit, Department of Biomedical, Metabolic and Neuroscience, University of Modena and Reggio Emilia, 41124 Modena, Italy
| | - Tommaso Trenti
- AOU Policlinico di Modena, Diagnostic Hematology and Clinical Genomics, Department of Laboratory Medicine and Pathology, 41124 Modena, Italy
| | - Michela Cuccorese
- AOU Policlinico di Modena, Diagnostic Hematology and Clinical Genomics, Department of Laboratory Medicine and Pathology, 41124 Modena, Italy
| | - Lara Gibellini
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy (A.C.)
| | - Diana Ferraro
- AOU Policlinico di Modena, Neurology Unit, Department of Biomedical, Metabolic and Neuroscience, University of Modena and Reggio Emilia, 41124 Modena, Italy
| | - Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy (A.C.)
- National Institute for Cardiovascular Research, 40126 Bologna, Italy
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38
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Nicolai E, Tomassetti F, Pignalosa S, Redi S, Marino M, Basile U, Ciotti M. The Evolution of Serological Assays during Two Years of the COVID-19 Pandemic: From an Easy-to-Use Screening Tool for Identifying Current Infections to Laboratory Algorithms for Discovering Immune Protection and Optimizing Vaccine Administration. COVID 2024; 4:1272-1290. [DOI: 10.3390/covid4080091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2025]
Abstract
The emergence of COVID-19 has evolved into a global pandemic, causing an unprecedented public health crisis marked by unprecedented levels of morbidity never seen in the recent past. Considerable research efforts have been made in the scientific community to establish an optimal method to identify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and to understand the induced immune response. This review examined the development of serological tests during the COVID-19 pandemic, considering the factors affecting sensitivity and specificity, which are key to promote an efficient vaccination strategy for public health. The market has witnessed the introduction of various serological tests for the detection of SARS-CoV-2, such as the chemiluminescence immunoassay (CLIA), which emerged as a powerful and rapid tool to monitor the antibody response before and after vaccination or infection. Therefore, developing serological tests by studying antibody trends and persistence is essential for creating long-term strategies. Our analysis underscores the multifaceted applications of serological tests in pandemic management with a focus on the critical insights they provide into antibody dynamics that help in managing the ongoing pandemic and shaping future public health initiatives, providing a basis for optimizing the future response to viral threats.
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Affiliation(s)
- Eleonora Nicolai
- Department of Experimental Medicine, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy
| | - Flaminia Tomassetti
- Department of Experimental Medicine, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy
| | - Stefano Pignalosa
- Department of Clinical Pathology, Santa Maria Goretti Hospital, A.U.S.L. Latina, 04100 Latina, Italy
| | - Serena Redi
- Department of Clinical Pathology, Santa Maria Goretti Hospital, A.U.S.L. Latina, 04100 Latina, Italy
| | - Mariapaola Marino
- Dipartimento di Medicina e Chirurgia Traslazionale, Sezione di Patologia Generale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Fondazione Policlinico Universitario “A. Gemelli” I.R.C.C.S., 00168 Rome, Italy
| | - Umberto Basile
- Department of Clinical Pathology, Santa Maria Goretti Hospital, A.U.S.L. Latina, 04100 Latina, Italy
| | - Marco Ciotti
- Department of Laboratory Medicine, Virology Unit, Tor Vergata University Hospital, Viale Oxford 81, 00133 Rome, Italy
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Kister I, Curtin R, Piquet AL, Borko T, Pei J, Banbury BL, Bacon TE, Kim A, Tuen M, Velmurugu Y, Nyovanie S, Selva S, Samanovic MI, Mulligan MJ, Patskovsky Y, Priest J, Cabatingan M, Winger RC, Krogsgaard M, Silverman GJ. Longitudinal study of immunity to SARS-CoV2 in ocrelizumab-treated MS patients up to 2 years after COVID-19 vaccination. Ann Clin Transl Neurol 2024; 11:1750-1764. [PMID: 38713096 PMCID: PMC11251481 DOI: 10.1002/acn3.52081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/04/2024] [Accepted: 04/06/2024] [Indexed: 05/08/2024] Open
Abstract
OBJECTIVES (1) To plot the trajectory of humoral and cellular immune responses to the primary (two-dose) COVID-19 mRNA series and the third/booster dose in B-cell-depleted multiple sclerosis (MS) patients up to 2 years post-vaccination; (2) to identify predictors of immune responses to vaccination; and (3) to assess the impact of intercurrent COVID-19 infections on SARS CoV-2-specific immunity. METHODS Sixty ocrelizumab-treated MS patients were enrolled from NYU (New York) and University of Colorado (Anschutz) MS Centers. Samples were collected pre-vaccination, and then 4, 12, 24, and 48 weeks post-primary series, and 4, 12, 24, and 48 weeks post-booster. Binding anti-Spike antibody responses were assessed with multiplex bead-based immunoassay (MBI) and electrochemiluminescence (Elecsys®, Roche Diagnostics), and neutralizing antibody responses with live-virus immunofluorescence-based microneutralization assay. Spike-specific cellular responses were assessed with IFNγ/IL-2 ELISpot (Invitrogen) and, in a subset, by sequencing complementarity determining regions (CDR)-3 within T-cell receptors (Adaptive Biotechnologies). A linear mixed-effect model was used to compare antibody and cytokine levels across time points. Multivariate analyses identified predictors of immune responses. RESULTS The primary vaccination induced an 11- to 208-fold increase in binding and neutralizing antibody levels and a 3- to 4-fold increase in IFNγ/IL-2 responses, followed by a modest decline in antibody but not cytokine responses. Booster dose induced a further 3- to 5-fold increase in binding antibodies and 4- to 5-fold increase in IFNγ/IL-2, which were maintained for up to 1 year. Infections had a variable impact on immunity. INTERPRETATION Humoral and cellular benefits of COVID-19 vaccination in B-cell-depleted MS patients were sustained for up to 2 years when booster doses were administered.
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MESH Headings
- Humans
- COVID-19/immunology
- COVID-19/prevention & control
- Male
- Female
- Middle Aged
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antibodies, Monoclonal, Humanized/pharmacology
- Antibodies, Monoclonal, Humanized/administration & dosage
- Adult
- COVID-19 Vaccines/immunology
- COVID-19 Vaccines/administration & dosage
- Longitudinal Studies
- SARS-CoV-2/immunology
- Multiple Sclerosis/immunology
- Multiple Sclerosis/drug therapy
- Antibodies, Viral/blood
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Immunity, Cellular/drug effects
- Vaccination
- Immunity, Humoral/drug effects
- Immunity, Humoral/immunology
- BNT162 Vaccine/administration & dosage
- BNT162 Vaccine/immunology
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Affiliation(s)
- Ilya Kister
- NYU Multiple Sclerosis Comprehensive Care Center, Department of NeurologyNew York University Grossman School of MedicineNew YorkNew YorkUSA
| | - Ryan Curtin
- Laura and Isaac Perlmutter Cancer Center and Department of PathologyNYU Grossman School of MedicineNew YorkNew YorkUSA
| | - Amanda L. Piquet
- Rocky Mountain MS CenterUniversity of Colorado School of MedicineAuroraColoradoUSA
| | - Tyler Borko
- Rocky Mountain MS CenterUniversity of Colorado School of MedicineAuroraColoradoUSA
| | - Jinglan Pei
- Genentech, Inc.South San FranciscoCaliforniaUSA
| | | | - Tamar E. Bacon
- NYU Multiple Sclerosis Comprehensive Care Center, Department of NeurologyNew York University Grossman School of MedicineNew YorkNew YorkUSA
| | - Angie Kim
- NYU Multiple Sclerosis Comprehensive Care Center, Department of NeurologyNew York University Grossman School of MedicineNew YorkNew YorkUSA
| | - Michael Tuen
- NYU Langone Vaccine Center and Department of MedicineNYU Grossman School of MedicineNew YorkNew YorkUSA
| | - Yogambigai Velmurugu
- Laura and Isaac Perlmutter Cancer Center and Department of PathologyNYU Grossman School of MedicineNew YorkNew YorkUSA
| | - Samantha Nyovanie
- Laura and Isaac Perlmutter Cancer Center and Department of PathologyNYU Grossman School of MedicineNew YorkNew YorkUSA
| | - Sean Selva
- Rocky Mountain MS CenterUniversity of Colorado School of MedicineAuroraColoradoUSA
| | - Marie I. Samanovic
- NYU Langone Vaccine Center and Department of MedicineNYU Grossman School of MedicineNew YorkNew YorkUSA
| | - Mark J. Mulligan
- NYU Langone Vaccine Center and Department of MedicineNYU Grossman School of MedicineNew YorkNew YorkUSA
| | - Yury Patskovsky
- Laura and Isaac Perlmutter Cancer Center and Department of PathologyNYU Grossman School of MedicineNew YorkNew YorkUSA
| | | | | | | | - Michelle Krogsgaard
- Laura and Isaac Perlmutter Cancer Center and Department of PathologyNYU Grossman School of MedicineNew YorkNew YorkUSA
| | - Gregg J. Silverman
- Division of Rheumatology, Department of MedicineNYU Grossman School of MedicineNew YorkNew YorkUSA
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Fan X, Song JW, Cao WJ, Zhou MJ, Yang T, Wang J, Meng FP, Shi M, Zhang C, Wang FS. T-Cell Epitope Mapping of SARS-CoV-2 Reveals Coordinated IFN-γ Production and Clonal Expansion of T Cells Facilitates Recovery from COVID-19. Viruses 2024; 16:1006. [PMID: 39066169 PMCID: PMC11281491 DOI: 10.3390/v16071006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/01/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND T-cell responses can be protective or detrimental during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection; however, the underlying mechanism is poorly understood. METHODS In this study, we screened 144 15-mer peptides spanning the SARS-CoV-2 spike, nucleocapsid (NP), M, ORF8, ORF10, and ORF3a proteins and 39 reported SARS-CoV-1 peptides in peripheral blood mononuclear cells (PBMCs) from nine laboratory-confirmed coronavirus disease 2019 (COVID-19) patients (five moderate and four severe cases) and nine healthy donors (HDs) collected before the COVID-19 pandemic. T-cell responses were monitored by IFN-γ and IL-17A production using ELISA, and the positive samples were sequenced for the T cell receptor (TCR) β chain. The positive T-cell responses to individual SARS-CoV-2 peptides were validated by flow cytometry. RESULTS COVID-19 patients with moderate disease produced more IFN-γ than HDs and patients with severe disease (moderate vs. HDs, p < 0.0001; moderate vs. severe, p < 0.0001) but less IL-17A than those with severe disease (p < 0.0001). A positive correlation was observed between IFN-γ production and T-cell clonal expansion in patients with moderate COVID-19 (r = 0.3370, p = 0.0214) but not in those with severe COVID-19 (r = -0.1700, p = 0.2480). Using flow cytometry, we identified that a conserved peptide of the M protein (Peptide-120, P120) was a dominant epitope recognized by CD8+ T cells in patients with moderate disease. CONCLUSION Coordinated IFN-γ production and clonal expansion of SARS-CoV-2-specific T cells are associated with disease resolution in COVID-19. Our findings contribute to a better understanding of T-cell-mediated immunity in COVID-19 and may inform future strategies for managing and preventing severe outcomes of SARS-CoV-2 infection.
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Affiliation(s)
- Xing Fan
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
| | - Jin-Wen Song
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
- Medical School of Chinese PLA, Beijing 100853, China
| | - Wen-Jing Cao
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Ming-Ju Zhou
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
| | - Tao Yang
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
| | - Jing Wang
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
| | - Fan-Ping Meng
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
| | - Ming Shi
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
| | - Chao Zhang
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
| | - Fu-Sheng Wang
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
- Medical School of Chinese PLA, Beijing 100853, China
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Richards KA, Changrob S, Thomas PG, Wilson PC, Sant AJ. Lack of memory recall in human CD4 T cells elicited by the first encounter with SARS-CoV-2. iScience 2024; 27:109992. [PMID: 38868209 PMCID: PMC11166706 DOI: 10.1016/j.isci.2024.109992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/11/2024] [Accepted: 05/13/2024] [Indexed: 06/14/2024] Open
Abstract
The studies reported here focus on the impact of pre-existing CD4 T cell immunity on the first encounter with SARS-CoV-2. They leverage PBMC samples from plasma donors collected after a first SARS-CoV-2 infection, prior to vaccine availability and compared to samples collected prior to the emergence of SARS-CoV-2. Analysis of CD4 T cell specificity across the entire SARS-CoV-2 proteome revealed that the recognition of SARS-CoV-2-derived epitopes by CD4 memory cells prior to the pandemic are enriched for reactivity toward non-structural proteins conserved across endemic CoV strains. However, CD4 T cells after primary infection with SARS-CoV-2 focus on epitopes from structural proteins. We observed little evidence for preferential recall to epitopes conserved between SARS-CoV-2 and seasonal CoV, a finding confirmed through use of selectively curated conserved and SARS-unique peptides. Our data suggest that SARS-CoV-2 CD4 T cells elicited by the first infection are primarily established from the naive CD4 T cell pool.
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Affiliation(s)
- Katherine A. Richards
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Siriruk Changrob
- Drukier Institute for Children’s Health, Department of Pediatrics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Paul G. Thomas
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Patrick C. Wilson
- Drukier Institute for Children’s Health, Department of Pediatrics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andrea J. Sant
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
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Cheng YL, Chang SS, Chao CH, Chen PT, Lin YL, Syu GD, Lee NY, Chen PL, Ko WC, Ho TS. Optimizing SARS-CoV-2 vaccine responses in kidney transplant recipients: an urgent need. Microbiol Spectr 2024; 12:e0000424. [PMID: 38747636 PMCID: PMC11237705 DOI: 10.1128/spectrum.00004-24] [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: 01/02/2024] [Accepted: 04/18/2024] [Indexed: 06/06/2024] Open
Abstract
Kidney transplant recipients (KTRs) have been identified as a population at increased risk for severe SARS-CoV-2 infection outcomes. This study focused on understanding the immune response of KTRs post-vaccination, specifically examining both serological and cellular responses to the SARS-CoV-2 vaccine. Thirteen individuals, including seven KTRs and six healthy donors, were evaluated for antibody levels and T cell responses post-vaccination. The study revealed that KTRs had significantly lower serological responses, including reduced anti-receptor binding domain (RBD) binding antibodies and neutralizing antibodies against the Wuhan, Delta, and Omicron BA.2 strains. Additionally, KTRs demonstrated weaker CD8 T cell cytotoxic responses and lower Th1 cytokine secretion, particularly IFN-γ, after stimulation with variant spike peptide pools. These findings highlight the compromised immunity in KTRs post-vaccination and underscore the need for tailored strategies to bolster immune responses in this vulnerable group. Further investigations are warranted into the mechanisms underlying reduced vaccine efficacy in KTRs and potential therapeutic interventions. IMPORTANCE Some studies have revealed that KTRs had lower serological response against SARS-CoV-2 than healthy people. Nevertheless, limited studies investigate the cellular response against SARS-CoV-2 in KTRs receiving SARS-CoV-2 vaccines. Here, we found that KTRs have lower serological and cellular responses. Moreover, we found that KTRs had a significantly lower IFN-γ secretion than healthy individuals when their PBMCs were stimulated with SARS-CoV-2 spike peptide pools. Thus, our findings suggested that additional strategies are needed to enhance KTR immunity triggered by the vaccine.
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Affiliation(s)
- Yi-Ling Cheng
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shen-Shin Chang
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chiao-Hsuan Chao
- Department of Medical Laboratory and Regenerative Medicine, MacKay Medical College, New Taipei, Taiwan
| | - Po-Ta Chen
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Lan Lin
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Guan-Da Syu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, Tainan, Taiwan
| | - Nan-Yao Lee
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Lin Chen
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tzong-Shiann Ho
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Pediatrics, National Cheng Kung University Hospital Dou-Liou Branch, College of Medicine, National Cheng Kung University, Yunlin, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
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Kim GJ, Elnaggar JH, Varnado M, Feehan AK, Tauzier D, Rose R, Lamers SL, Sevalia M, Nicholas N, Gravois E, Fort D, Crabtree JS, Miele L. A bioinformatic analysis of T-cell epitope diversity in SARS-CoV-2 variants: association with COVID-19 clinical severity in the United States population. Front Immunol 2024; 15:1357731. [PMID: 38784379 PMCID: PMC11112498 DOI: 10.3389/fimmu.2024.1357731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/05/2024] [Indexed: 05/25/2024] Open
Abstract
Long-term immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires the identification of T-cell epitopes affecting host immunogenicity. In this computational study, we explored the CD8+ epitope diversity estimated in 27 of the most common HLA-A and HLA-B alleles, representing most of the United States population. Analysis of 16 SARS-CoV-2 variants [B.1, Alpha (B.1.1.7), five Delta (AY.100, AY.25, AY.3, AY.3.1, AY.44), and nine Omicron (BA.1, BA.1.1, BA.2, BA.4, BA.5, BQ.1, BQ.1.1, XBB.1, XBB.1.5)] in analyzed MHC class I alleles revealed that SARS-CoV-2 CD8+ epitope conservation was estimated at 87.6%-96.5% in spike (S), 92.5%-99.6% in membrane (M), and 94.6%-99% in nucleocapsid (N). As the virus mutated, an increasing proportion of S epitopes experienced reduced predicted binding affinity: 70% of Omicron BQ.1-XBB.1.5 S epitopes experienced decreased predicted binding, as compared with ~3% and ~15% in the earlier strains Delta AY.100-AY.44 and Omicron BA.1-BA.5, respectively. Additionally, we identified several novel candidate HLA alleles that may be more susceptible to severe disease, notably HLA-A*32:01, HLA-A*26:01, and HLA-B*53:01, and relatively protected from disease, such as HLA-A*31:01, HLA-B*40:01, HLA-B*44:03, and HLA-B*57:01. Our findings support the hypothesis that viral genetic variation affecting CD8 T-cell epitope immunogenicity contributes to determining the clinical severity of acute COVID-19. Achieving long-term COVID-19 immunity will require an understanding of the relationship between T cells, SARS-CoV-2 variants, and host MHC class I genetics. This project is one of the first to explore the SARS-CoV-2 CD8+ epitope diversity that putatively impacts much of the United States population.
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Affiliation(s)
- Grace J. Kim
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Jacob H. Elnaggar
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
- Department of Microbiology, Immunology, and Parasitology, Lousiana State University Health Sciences Center (LSUHSC), New Orleans, LA, United States
| | - Mallory Varnado
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Amy K. Feehan
- Research and Development, Oschner Medical Center, New Orleans, LA, United States
| | - Darlene Tauzier
- Department of Pathology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Rebecca Rose
- Research and Development, BioInfoExperts, LLC, Thibodaux, LA, United States
| | - Susanna L. Lamers
- Research and Development, BioInfoExperts, LLC, Thibodaux, LA, United States
| | - Maya Sevalia
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Najah Nicholas
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Elizabeth Gravois
- Department of Pathology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Daniel Fort
- Research and Development, Oschner Medical Center, New Orleans, LA, United States
| | - Judy S. Crabtree
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Lucio Miele
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
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Brummelman J, Suárez-Hernández S, de Rond L, Bogaard-van Maurik M, Molenaar P, van Wijlen E, Oomen D, Beckers L, Rots NY, van Beek J, Nicolaie MA, van Els CACM, Boer MC, Kaaijk P, Buisman AM, de Wit J. Distinct T cell responsiveness to different COVID-19 vaccines and cross-reactivity to SARS-CoV-2 variants with age and CMV status. Front Immunol 2024; 15:1392477. [PMID: 38774878 PMCID: PMC11106399 DOI: 10.3389/fimmu.2024.1392477] [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: 02/27/2024] [Accepted: 04/09/2024] [Indexed: 05/24/2024] Open
Abstract
Introduction Accumulating evidence indicates the importance of T cell immunity in vaccination-induced protection against severe COVID-19 disease, especially against SARS-CoV-2 Variants-of-Concern (VOCs) that more readily escape from recognition by neutralizing antibodies. However, there is limited knowledge on the T cell responses across different age groups and the impact of CMV status after primary and booster vaccination with different vaccine combinations. Moreover, it remains unclear whether age has an effect on the ability of T cells to cross-react against VOCs. Methods Therefore, we interrogated the Spike-specific T cell responses in healthy adults of the Dutch population across different ages, whom received different vaccine types for the primary series and/or booster vaccination, using IFNɣ ELISpot. Cells were stimulated with overlapping peptide pools of the ancestral Spike protein and different VOCs. Results Robust Spike-specific T cell responses were detected in the vast majority of participants upon the primary vaccination series, regardless of the vaccine type (i.e. BNT162b2, mRNA-1273, ChAdOx1 nCoV-19, or Ad26.COV2.S). Clearly, in the 70+ age group, responses were overall lower and showed more variation compared to younger age groups. Only in CMV-seropositive older adults (>70y) there was a significant inverse relation of age with T cell responses. Although T cell responses increased in all age groups after booster vaccination, Spike-specific T cell frequencies remained lower in the 70+ age group. Regardless of age or CMV status, primary mRNA-1273 vaccination followed by BNT162b2 booster vaccination showed limited booster effect compared to the BNT162b2/BNT162b2 or BNT162b2/mRNA-1273 primary-booster regimen. A modest reduction in cross-reactivity to the Alpha, Delta and Omicron BA.1, but not the Beta or Gamma variant, was observed after primary vaccination. Discussion Together, this study shows that age, CMV status, but also the primary-booster vaccination regimen influence the height of the vaccination-induced Spike-specific T cell response, but did not impact the VOC cross-reactivity.
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Affiliation(s)
- Jolanda Brummelman
- Center for Infectious Disease Control, Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Sara Suárez-Hernández
- Center for Infectious Disease Control, Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Lia de Rond
- Center for Infectious Disease Control, Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Marjan Bogaard-van Maurik
- Center for Infectious Disease Control, Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Petra Molenaar
- Center for Infectious Disease Control, Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Emma van Wijlen
- Center for Infectious Disease Control, Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Debbie Oomen
- Center for Infectious Disease Control, Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Lisa Beckers
- Center for Infectious Disease Control, Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Nynke Y. Rots
- Center for Infectious Disease Control, Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Josine van Beek
- Center for Infectious Disease Control, Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Mioara A. Nicolaie
- Center for Infectious Disease Control, Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Cécile A. C. M. van Els
- Center for Infectious Disease Control, Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Mardi C. Boer
- Center for Infectious Disease Control, Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Patricia Kaaijk
- Center for Infectious Disease Control, Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Anne-Marie Buisman
- Center for Infectious Disease Control, Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Jelle de Wit
- Center for Infectious Disease Control, Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
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45
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Hou Q, Jiang J, Na K, Zhang X, Liu D, Jing Q, Yan C, Han Y. Potential therapeutic targets for COVID-19 complicated with pulmonary hypertension: a bioinformatics and early validation study. Sci Rep 2024; 14:9294. [PMID: 38653779 DOI: 10.1038/s41598-024-60113-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/18/2024] [Indexed: 04/25/2024] Open
Abstract
Coronavirus disease (COVID-19) and pulmonary hypertension (PH) are closely correlated. However, the mechanism is still poorly understood. In this article, we analyzed the molecular action network driving the emergence of this event. Two datasets (GSE113439 and GSE147507) from the GEO database were used for the identification of differentially expressed genes (DEGs).Common DEGs were selected by VennDiagram and their enrichment in biological pathways was analyzed. Candidate gene biomarkers were selected using three different machine-learning algorithms (SVM-RFE, LASSO, RF).The diagnostic efficacy of these foundational genes was validated using independent datasets. Eventually, we validated molecular docking and medication prediction. We found 62 common DEGs, including several ones that could be enriched for Immune Response and Inflammation. Two DEGs (SELE and CCL20) could be identified by machine-learning algorithms. They performed well in diagnostic tests on independent datasets. In particular, we observed an upregulation of functions associated with the adaptive immune response, the leukocyte-lymphocyte-driven immunological response, and the proinflammatory response. Moreover, by ssGSEA, natural killer T cells, activated dendritic cells, activated CD4 T cells, neutrophils, and plasmacytoid dendritic cells were correlated with COVID-19 and PH, with SELE and CCL20 showing the strongest correlation with dendritic cells. Potential therapeutic compounds like FENRETI-NIDE, AFLATOXIN B1 and 1-nitropyrene were predicted. Further molecular docking and molecular dynamics simulations showed that 1-nitropyrene had the most stable binding with SELE and CCL20.The findings indicated that SELE and CCL20 were identified as novel diagnostic biomarkers for COVID-19 complicated with PH, and the target of these two key genes, FENRETI-NIDE and 1-nitropyrene, was predicted to be a potential therapeutic target, thus providing new insights into the prediction and treatment of COVID-19 complicated with PH in clinical practice.
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Affiliation(s)
- Qingbin Hou
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, China
| | - Jinping Jiang
- Department of Cardiology, Shengjing Hospital Affiliated to China Medical University, Shenyang, China
| | - Kun Na
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, China
| | - Xiaolin Zhang
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, China
| | - Dan Liu
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, China
| | - Quanmin Jing
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, China
| | - Chenghui Yan
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, China.
| | - Yaling Han
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, China.
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Montmaneix-Engels F, Dimeglio C, Staes L, Da Silva I, Porcheron M, Jougla I, Hérin F, Izopet J. Study of the cellular and humoral immune responses to SARS-CoV-2 vaccination. Heliyon 2024; 10:e29116. [PMID: 38601689 PMCID: PMC11004869 DOI: 10.1016/j.heliyon.2024.e29116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/12/2024] Open
Abstract
Our understanding of cellular immunity in response to COVID-19 infection or vaccination is limited because of less commonly used techniques. We investigated both the cellular and humoral immune responses before and after the administration of a third dose of the SARS-CoV-2 vaccine among a group of healthcare workers. Cellular immunity was evaluated using the VIDAS interferon-gamma (IFNγ) RUO test, which enables automated measurement of IFNγ levels after stimulating peripheral blood lymphocytes. Booster doses significantly enhanced both cellular and humoral immunity. Concerning cellular response, the booster dose increased the percentage of positive IFNγ release assay (IGRA) results but no difference in IFNγ release was found. The cellular response was not associated with protection against SARS-CoV-2 infection. Interestingly, vaccinated and infected healthcare workers exhibited the highest levels of anti-spike and neutralizing antibodies. In conclusion, the IGRA is a simple method for measuring cellular immune responses after vaccination. However, its usefulness as a complement to the study of humoral responses is yet to be demonstrated in future research.
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Affiliation(s)
- Faustine Montmaneix-Engels
- INSERM UMR1291-CNRS UMR5051-University Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, 31300, Toulouse, France
- Toulouse III Paul Sabatier University, 31062, Toulouse, France
| | - Chloé Dimeglio
- INSERM UMR1291-CNRS UMR5051-University Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, 31300, Toulouse, France
- CHU Toulouse, Purpan Hospital, Virology Laboratory, 31300, Toulouse, France
| | - Laeticia Staes
- CHU Toulouse, Purpan Hospital, Virology Laboratory, 31300, Toulouse, France
| | - Isabelle Da Silva
- CHU Toulouse, Purpan Hospital, Virology Laboratory, 31300, Toulouse, France
| | - Marion Porcheron
- CHU Toulouse, Purpan Hospital, Virology Laboratory, 31300, Toulouse, France
| | - Isabelle Jougla
- Occupational Diseases Department, Toulouse University Hospital, 31000, Toulouse, France
| | - Fabrice Hérin
- Occupational Diseases Department, Toulouse University Hospital, 31000, Toulouse, France
- UMR1295, Joint Research Unit INSERM- University Toulouse III Paul Sabatier, Centre for Epidemiology and Research in Population Health Unit (CERPOP), 31000, Toulouse, France
| | - Jacques Izopet
- INSERM UMR1291-CNRS UMR5051-University Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, 31300, Toulouse, France
- Toulouse III Paul Sabatier University, 31062, Toulouse, France
- CHU Toulouse, Purpan Hospital, Virology Laboratory, 31300, Toulouse, France
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47
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Kristensen NP, Dionisio E, Bentzen AK, Tamhane T, Kemming JS, Nos G, Voss LF, Hansen UK, Lauer GM, Hadrup SR. Simultaneous analysis of pMHC binding and reactivity unveils virus-specific CD8 T cell immunity to a concise epitope set. SCIENCE ADVANCES 2024; 10:eadm8951. [PMID: 38608022 PMCID: PMC11014448 DOI: 10.1126/sciadv.adm8951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/12/2024] [Indexed: 04/14/2024]
Abstract
CD8 T cells provide immunity to virus infection through recognition of epitopes presented by peptide major histocompatibility complexes (pMHCs). To establish a concise panel of widely recognized T cell epitopes from common viruses, we combined analysis of TCR down-regulation upon stimulation with epitope-specific enumeration based on barcode-labeled pMHC multimers. We assess CD8 T cell binding and reactivity for 929 previously reported epitopes in the context of 1 of 25 HLA alleles representing 29 viruses. The prevalence and magnitude of CD8 T cell responses were evaluated in 48 donors and reported along with 137 frequently recognized virus epitopes, many of which were underrepresented in the public domain. Eighty-four percent of epitope-specific CD8 T cell populations demonstrated reactivity to peptide stimulation, which was associated with effector and long-term memory phenotypes. Conversely, nonreactive T cell populations were associated primarily with naive phenotypes. Our analysis provides a reference map of epitopes for characterizing CD8 T cell responses toward common human virus infections.
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Affiliation(s)
- Nikolaj Pagh Kristensen
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Edoardo Dionisio
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Amalie Kai Bentzen
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Tripti Tamhane
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Janine Sophie Kemming
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Grigorii Nos
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Lasse Frank Voss
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Ulla Kring Hansen
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Georg Michael Lauer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Sine Reker Hadrup
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
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48
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Nhu LNT, Chambers M, Chantratita N, Cheah PY, Day NP, Dejnirattisai W, Dunachie SJ, Grifoni A, Hamers RL, Hill J, Jones EY, Klenerman P, Mongkolsapaya J, Screaton G, Sette A, Stuart DI, Tan CW, Thwaites G, Thanh VD, Wang LF, Tan LV, SEACOVARIANTS Consortium. Southeast Asia initiative to combat SARS-CoV-2 variants (SEACOVARIANTS) consortium. Wellcome Open Res 2024; 9:181. [PMID: 39022321 PMCID: PMC11252647 DOI: 10.12688/wellcomeopenres.20742.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2024] [Indexed: 07/20/2024] Open
Abstract
A strong and effective COVID-19 and future pandemic responses rely on global efforts to carry out surveillance of infections and emerging SARS-CoV-2 variants and to act accordingly in real time. Many countries in Southeast Asia lack capacity to determine the potential threat of new variants, or other emerging infections. Funded by Wellcome, the Southeast Asia initiative to combat SARS-CoV-2 variants (SEACOVARIANTS) consortium aims to develop and apply a multidisciplinary research platform in Southeast Asia (SEA) for rapid assessment of the biological significance of SARS-CoV-2 variants, thereby informing coordinated local, regional and global responses to the COVID-19 pandemic. Our proposal is delivered by the Vietnam and Thailand Wellcome Africa Asia Programmes, bringing together a multidisciplinary team in Indonesia, Thailand and Vietnam with partners in Singapore, the UK and the USA. Herein we outline five work packages to deliver strengthened regional scientific capacity that can be rapidly deployed for future outbreak responses.
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Affiliation(s)
| | - Mary Chambers
- Oxford University Clinical Research Unit, Ho Chi Minh city, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Phaik Yeong Cheah
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nicholas P.J. Day
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Wanwisa Dejnirattisai
- Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Susanna J. Dunachie
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | - Alba Grifoni
- La Jolla Institute for Immunology, San Diego, California, USA
| | - Raph L. Hamers
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
- Oxford University Clinical Research Unit Indonesia, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Jennifer Hill
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | - E. Yvonne Jones
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | - Paul Klenerman
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | - Juthathip Mongkolsapaya
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, England, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | - Gavin Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, England, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | | | - David I. Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | - Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh city, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | - Vu Duy Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh city, Vietnam
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Le Van Tan
- Oxford University Clinical Research Unit, Ho Chi Minh city, Vietnam
| | - SEACOVARIANTS Consortium
- Oxford University Clinical Research Unit, Ho Chi Minh city, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
- La Jolla Institute for Immunology, San Diego, California, USA
- Oxford University Clinical Research Unit Indonesia, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, England, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
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Caldera F, Rolak S, Farraye FA, Necela BM, Cogen D, Zona EE, Schell TL, Ramirez OR, Almasry M, Chun K, Hayney MS, Knutson KL. Higher and Sustained Cell-Mediated Immune Responses After 3 Doses of mRNA COVID-19 Vaccine in Patients With Inflammatory Bowel Disease on Anti-Tumor Necrosis Factor Therapy. Clin Transl Gastroenterol 2024; 15:e00688. [PMID: 38349178 PMCID: PMC11042770 DOI: 10.14309/ctg.0000000000000688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/19/2024] [Indexed: 04/26/2024] Open
Abstract
INTRODUCTION Studies suggest that the generation of durable T-cell immunity following coronavirus disease 2019 (COVID-19) vaccination protects against severe disease. The aim of this study was to measure cell-mediated immune response (CMIR) 1-2 months and 6 months after a third dose of a COVID-19 mRNA vaccine. METHODS This prospective study (HumoRal and CellULar initial and Sustained immunogenicity in patients with inflammatory bowel disease [IBD]) evaluated CMIR at 28-65 days (t 1 ) after dose 2, 28-65 days (t 2 ) (n = 183) and 6 months (±45 days) (t 3 ) (n = 167) after a third dose of an mRNA COVID-19 vaccine. A small cohort had blood sample available 28-65 days (t 4 ) (n = 55) after a fourth dose. Primary outcomes were CMIR at (t 2 ) and (t 3 ). Secondary outcomes included the effect of immunosuppressing IBD medications on CMIR and response at (t 4 ). RESULTS All patients had measurable CMIR at all time points. CMIR increased at t 2 compared with that at t 1 (median 1,467 responding cells per million (interquartile range [IQR] 410-5,971) vs 313 (94-960) P < 0.001). There was no significant waning in t 2 vs t 3 or significant boosting at t 4 . Those on anti-tumor necrosis factor monotherapy had a higher CMIR compared with those not on this therapy at t 2 (4,132 [IQR 1,136-8,795] vs 869 [IQR 343-3,221] P < 0.001) and t 3 (2,843 [IQR 596-6,459] vs 654 [IQR 143-2,067] P < 0.001). In univariable analysis, anti-tumor necrosis factor monotherapy was associated with a higher CMIR at t 2 ( P < 0.001) and t 3 ( P < 0.001) and confirmed in a multivariable model ( P < 0.001). DISCUSSION A third dose of a COVID-19 vaccine boosts CMIR, and the response is sustained in patients with IBD.
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Affiliation(s)
- Freddy Caldera
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin, USA
| | - Stacey Rolak
- Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Francis A. Farraye
- Inflammatory Bowel Disease Center, Department of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, Florida, USA
| | - Brian M. Necela
- Department of Immunology, Mayo Clinic, Jacksonville, Florida, USA
| | - Davitte Cogen
- Department of Immunology, Mayo Clinic, Jacksonville, Florida, USA
| | - Emily E. Zona
- University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Trevor L. Schell
- Department of Internal Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Oscar Ramirez Ramirez
- Department of Internal Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Mazen Almasry
- Department of Internal Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Kelly Chun
- LabCorp, R&D and Specialty Medicine, Calabasas, CA, USA
| | - Mary S. Hayney
- School of Pharmacy, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin, USA
| | - Keith L. Knutson
- Department of Immunology, Mayo Clinic, Jacksonville, Florida, USA
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50
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Qian J, Zhang S, Wang F, Li J, Zhang J. What makes SARS-CoV-2 unique? Focusing on the spike protein. Cell Biol Int 2024; 48:404-430. [PMID: 38263600 DOI: 10.1002/cbin.12130] [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: 10/09/2023] [Revised: 12/25/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) seriously threatens public health and safety. Genetic variants determine the expression of SARS-CoV-2 structural proteins, which are associated with enhanced transmissibility, enhanced virulence, and immune escape. Vaccination is encouraged as a public health intervention, and different types of vaccines are used worldwide. However, new variants continue to emerge, especially the Omicron complex, and the neutralizing antibody responses are diminished significantly. In this review, we outlined the uniqueness of SARS-CoV-2 from three perspectives. First, we described the detailed structure of the spike (S) protein, which is highly susceptible to mutations and contributes to the distinct infection cycle of the virus. Second, we systematically summarized the immunoglobulin G epitopes of SARS-CoV-2 and highlighted the central role of the nonconserved regions of the S protein in adaptive immune escape. Third, we provided an overview of the vaccines targeting the S protein and discussed the impact of the nonconserved regions on vaccine effectiveness. The characterization and identification of the structure and genomic organization of SARS-CoV-2 will help elucidate its mechanisms of viral mutation and infection and provide a basis for the selection of optimal treatments. The leaps in advancements regarding improved diagnosis, targeted vaccines and therapeutic remedies provide sound evidence showing that scientific understanding, research, and technology evolved at the pace of the pandemic.
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Affiliation(s)
- Jingbo Qian
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Shichang Zhang
- Department of Clinical Laboratory Medicine, Shenzhen Hospital of Southern Medical University, Shenzhen, China
| | - Fang Wang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiexin Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
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