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Prakash S, Dhanushkodi NR, Zayou L, Ibraim IC, Quadiri A, Coulon PG, Tifrea DF, Suzer B, Shaik AM, Chilukuri A, Edwards RA, Singer M, Vahed H, Nesburn AB, Kuppermann BD, Ulmer JB, Gil D, Jones TM, BenMohamed L. Cross-protection induced by highly conserved human B, CD4 +, and CD8 + T-cell epitopes-based vaccine against severe infection, disease, and death caused by multiple SARS-CoV-2 variants of concern. Front Immunol 2024; 15:1328905. [PMID: 38318166 PMCID: PMC10839970 DOI: 10.3389/fimmu.2024.1328905] [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: 10/27/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
Background The coronavirus disease 2019 (COVID-19) pandemic has created one of the largest global health crises in almost a century. Although the current rate of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has decreased significantly, the long-term outlook of COVID-19 remains a serious cause of morbidity and mortality worldwide, with the mortality rate still substantially surpassing even that recorded for influenza viruses. The continued emergence of SARS-CoV-2 variants of concern (VOCs), including multiple heavily mutated Omicron sub-variants, has prolonged the COVID-19 pandemic and underscores the urgent need for a next-generation vaccine that will protect from multiple SARS-CoV-2 VOCs. Methods We designed a multi-epitope-based coronavirus vaccine that incorporated B, CD4+, and CD8+ T- cell epitopes conserved among all known SARS-CoV-2 VOCs and selectively recognized by CD8+ and CD4+ T-cells from asymptomatic COVID-19 patients irrespective of VOC infection. The safety, immunogenicity, and cross-protective immunity of this pan-variant SARS-CoV-2 vaccine were studied against six VOCs using an innovative triple transgenic h-ACE-2-HLA-A2/DR mouse model. Results The pan-variant SARS-CoV-2 vaccine (i) is safe , (ii) induces high frequencies of lung-resident functional CD8+ and CD4+ TEM and TRM cells , and (iii) provides robust protection against morbidity and virus replication. COVID-19-related lung pathology and death were caused by six SARS-CoV-2 VOCs: Alpha (B.1.1.7), Beta (B.1.351), Gamma or P1 (B.1.1.28.1), Delta (lineage B.1.617.2), and Omicron (B.1.1.529). Conclusion A multi-epitope pan-variant SARS-CoV-2 vaccine bearing conserved human B- and T- cell epitopes from structural and non-structural SARS-CoV-2 antigens induced cross-protective immunity that facilitated virus clearance, and reduced morbidity, COVID-19-related lung pathology, and death caused by multiple SARS-CoV-2 VOCs.
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Affiliation(s)
- Swayam Prakash
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Nisha R Dhanushkodi
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Latifa Zayou
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Izabela Coimbra Ibraim
- High Containment Facility, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Afshana Quadiri
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Pierre Gregoire Coulon
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Delia F Tifrea
- Department of Pathology and Laboratory Medicine, School of Medicine, the University of California Irvine, Irvine, CA, United States
| | - Berfin Suzer
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Amin Mohammed Shaik
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Amruth Chilukuri
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Robert A Edwards
- Department of Pathology and Laboratory Medicine, School of Medicine, the University of California Irvine, Irvine, CA, United States
| | - Mahmoud Singer
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Hawa Vahed
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Anthony B Nesburn
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Baruch D Kuppermann
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Jeffrey B Ulmer
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Daniel Gil
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Trevor M Jones
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Lbachir BenMohamed
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
- Division of Infectious Diseases and Hospitalist Program, Department of Medicine, School of Medicine, the University of California Irvine, Irvine, CA, United States
- Institute for Immunology; University of California Irvine, School of Medicine, Irvine, CA, United States
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Prakash S, Dhanushkodi NR, Zayou L, Ibraim IC, Quadiri A, Coulon PG, Tifrea DF, Suzler B, Amin M, Chilukuri A, Edwards RA, Vahed H, Nesburn AB, Kuppermann BD, Ulmer JB, Gil D, Jones TM, BenMohamed L. Cross-Protection Induced by Highly Conserved Human B, CD4 +, and CD8 + T Cell Epitopes-Based Coronavirus Vaccine Against Severe Infection, Disease, and Death Caused by Multiple SARS-CoV-2 Variants of Concern. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.541850. [PMID: 37292861 PMCID: PMC10245830 DOI: 10.1101/2023.05.24.541850] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Background The Coronavirus disease 2019 (COVID-19) pandemic has created one of the largest global health crises in almost a century. Although the current rate of SARS-CoV-2 infections has decreased significantly; the long-term outlook of COVID-19 remains a serious cause of high death worldwide; with the mortality rate still surpassing even the worst mortality rates recorded for the influenza viruses. The continuous emergence of SARS-CoV-2 variants of concern (VOCs), including multiple heavily mutated Omicron sub-variants, have prolonged the COVID-19 pandemic and outlines the urgent need for a next-generation vaccine that will protect from multiple SARS-CoV-2 VOCs. Methods In the present study, we designed a multi-epitope-based Coronavirus vaccine that incorporated B, CD4+, and CD8+ T cell epitopes conserved among all known SARS-CoV-2 VOCs and selectively recognized by CD8+ and CD4+ T-cells from asymptomatic COVID-19 patients irrespective of VOC infection. The safety, immunogenicity, and cross-protective immunity of this pan-Coronavirus vaccine were studied against six VOCs using an innovative triple transgenic h-ACE-2-HLA-A2/DR mouse model. Results The Pan-Coronavirus vaccine: (i) is safe; (ii) induces high frequencies of lung-resident functional CD8+ and CD4+ TEM and TRM cells; and (iii) provides robust protection against virus replication and COVID-19-related lung pathology and death caused by six SARS-CoV-2 VOCs: Alpha (B.1.1.7), Beta (B.1.351), Gamma or P1 (B.1.1.28.1), Delta (lineage B.1.617.2) and Omicron (B.1.1.529). Conclusions A multi-epitope pan-Coronavirus vaccine bearing conserved human B and T cell epitopes from structural and non-structural SARS-CoV-2 antigens induced cross-protective immunity that cleared the virus, and reduced COVID-19-related lung pathology and death caused by multiple SARS-CoV-2 VOCs.
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Affiliation(s)
- Swayam Prakash
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697
| | - Nisha R. Dhanushkodi
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697
| | - Latifa Zayou
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697
| | - Izabela Coimbra Ibraim
- High containment facility, University of California Irvine, School of Medicine, Irvine, CA 92697
| | - Afshana Quadiri
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697
| | - Pierre Gregoire Coulon
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697
| | - Delia F Tifrea
- Department of Pathology and Laboratory Medicine, School of Medicine, the University of California Irvine, Irvine, CA
| | - Berfin Suzler
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697
- Division of Trauma, Burns, Critical Care, and Acute Care Surgery, Department of Surgery, School of Medicine, University of California Irvine, Irvine, CA
| | - Mohamed Amin
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697
| | - Amruth Chilukuri
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697
| | - Robert A Edwards
- Department of Pathology and Laboratory Medicine, School of Medicine, the University of California Irvine, Irvine, CA
| | - Hawa Vahed
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA 92660, USA
| | - Anthony B Nesburn
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697
| | - Baruch D Kuppermann
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697
| | - Jeffrey B. Ulmer
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA 92660, USA
| | - Daniel Gil
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA 92660, USA
| | - Trevor M. Jones
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA 92660, USA
| | - Lbachir BenMohamed
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697
- Division of Infectious Diseases and Hospitalist Program, Department of Medicine, School of Medicine, the University of California Irvine, Irvine, CA
- Institute for Immunology; University of California Irvine, School of Medicine, Irvine, CA 92697
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA 92660, USA
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