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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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Yasugi M, Nakagama Y, Kaku N, Nitahara Y, Hatanaka N, Yamasaki S, Kido Y. Characteristics of epitope dominance pattern and cross-variant neutralisation in 16 SARS-CoV-2 mRNA vaccine sera. Vaccine 2023; 41:6248-6254. [PMID: 37673717 DOI: 10.1016/j.vaccine.2023.08.076] [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: 05/22/2023] [Revised: 08/09/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023]
Abstract
SARS-CoV-2 serological studies suggest that individual serum antibody repertoires can affect neutralisation breadth. Herein, we asked whether a BNT162b2 vaccine-induced epitope dominance pattern (i.e., predominant viral structural domain targeted by serum antibodies for virus neutralisation) affects cross-variant neutralisation. When a neutralisation assay against the ancestral strain was carried out using 16 vaccine sera preabsorbed with a recombinant receptor-binding domain (RBD) or an N-terminal domain (NTD) protein, three and 13 sera, respectively, showed lower neutralisation under NTD and RBD protein-preabsorbed conditions than under the other protein-preabsorbed conditions. This suggests that the NTD was responsible for virus neutralisation in three sera, whereas the other 13 sera elicited RBD-dominant neutralisation. The results also suggest the presence of infectivity-enhancing antibodies in four out of the 13 RBD-dominant sera. A neutralisation assay using SARS-CoV-2 variants revealed that NTD-dominant sera showed significantly reduced neutralising activity against the B.1.617.2 variant, whereas RBD-dominant sera retained neutralising activity even in the presence of infectivity-enhancing antibodies. Taken together, these results suggest the followings: (i) epitope dominance patterns are divided into at least two types: NTD-dominant and RBD-dominant; (ii) NTD-dominant sera have less potential to neutralise the B.1.617.2 variant than RBD-dominant sera; and (iii) infectivity-enhancing antibodies play a limited role in cross-variant neutralisation against the five variants tested.
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Affiliation(s)
- Mayo Yasugi
- Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan; Asian Health Science Research Institute, Osaka Metropolitan University, Izumisano, Osaka, Japan; Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan.
| | - Yu Nakagama
- Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan; Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Natsuko Kaku
- Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Yuko Nitahara
- Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Noritoshi Hatanaka
- Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan; Asian Health Science Research Institute, Osaka Metropolitan University, Izumisano, Osaka, Japan; Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
| | - Shinji Yamasaki
- Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan; Asian Health Science Research Institute, Osaka Metropolitan University, Izumisano, Osaka, Japan; Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
| | - Yasutoshi Kido
- Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan; Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
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Azulay A, Cohen-Lavi L, Friedman LM, McGargill MA, Hertz T. Mapping antibody footprints using binding profiles. CELL REPORTS METHODS 2023; 3:100566. [PMID: 37671022 PMCID: PMC10475849 DOI: 10.1016/j.crmeth.2023.100566] [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: 02/21/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023]
Abstract
The increasing use of monoclonal antibodies (mAbs) in biology and medicine necessitates efficient methods for characterizing their binding epitopes. Here, we developed a high-throughput antibody footprinting method based on binding profiles. We used an antigen microarray to profile 23 human anti-influenza hemagglutinin (HA) mAbs using HA proteins of 43 human influenza strains isolated between 1918 and 2018. We showed that the mAb's binding profile can be used to characterize its influenza subtype specificity, binding region, and binding site. We present mAb-Patch-an epitope prediction method that is based on a mAb's binding profile and the 3D structure of its antigen. mAb-Patch was evaluated using four mAbs with known solved mAb-HA structures. mAb-Patch identifies over 67% of the true epitope when considering only 50-60 positions along the antigen. Our work provides proof of concept for utilizing antibody binding profiles to screen large panels of mAbs and to down-select antibodies for further functional studies.
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Affiliation(s)
- Asaf Azulay
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute of Biotechnology in the Negev, Beer-Sheva, Israel
| | - Liel Cohen-Lavi
- National Institute of Biotechnology in the Negev, Beer-Sheva, Israel
- Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Lilach M. Friedman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute of Biotechnology in the Negev, Beer-Sheva, Israel
| | - Maureen A. McGargill
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Tomer Hertz
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute of Biotechnology in the Negev, Beer-Sheva, Israel
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Research Center, Seattle, WA, USA
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Oliveira JR, Ruiz CMR, Machado RRG, Magawa JY, Daher IP, Urbanski AH, Schmitz GJH, Arcuri HA, Ferreira MA, Sasahara GL, de Medeiros GX, Júnior RCVS, Durigon EL, Boscardin SB, Rosa DS, Schechtman D, Nakaya HI, Cunha-Neto E, Gadermaier G, Kalil J, Coelho V, Santos KS. Immunodominant antibody responses directed to SARS-CoV-2 hotspot mutation sites and risk of immune escape. Front Immunol 2023; 13:1010105. [PMID: 36685521 PMCID: PMC9849925 DOI: 10.3389/fimmu.2022.1010105] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/13/2022] [Indexed: 01/07/2023] Open
Abstract
Introduction Considering the likely need for the development of novel effective vaccines adapted to emerging relevant CoV-2 variants, the increasing knowledge of epitope recognition profile among convalescents and afterwards vaccinated with identification of immunodominant regions may provide important information. Methods We used an RBD peptide microarray to identify IgG and IgA binding regions in serum of 71 COVID-19 convalescents and 18 vaccinated individuals. Results We found a set of immunodominant RBD antibody epitopes, each recognized by more than 30% of the tested cohort, that differ among the two different groups and are within conserved regions among betacoronavirus. Of those, only one peptide, P44 (S415-429), recognized by 68% of convalescents, presented IgG and IgA antibody reactivity that positively correlated with nAb titers, suggesting that this is a relevant RBD region and a potential target of IgG/IgA neutralizing activity. Discussion This peptide is localized within the area of contact with ACE-2 and harbors the mutation hotspot site K417 present in gamma (K417T), beta (K417N), and omicron (K417N) variants of concern. The epitope profile of vaccinated individuals differed from convalescents, with a more diverse repertoire of immunodominant peptides, recognized by more than 30% of the cohort. Noteworthy, immunodominant regions of recognition by vaccinated coincide with mutation sites at Omicron BA.1, an important variant emerging after massive vaccination. Together, our data show that immune pressure induced by dominant antibody responses may favor hotspot mutation sites and the selection of variants capable of evading humoral response.
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Affiliation(s)
- Jamille Ramos Oliveira
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Laboratório de Imunologia, LIM19, Instituto do Coração (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP) São Paulo da Universidade de São Paulo, São Paulo, Brazil
- Instituto de Investigação em Imunologia–Instituto Nacional de Ciências e Tecnologia – instituto de investigação em imunologia - Instituto Nacional de Ciências e Tecnologia (iii-INCT), São Paulo, Brazil
| | - Cesar Manuel Remuzgo Ruiz
- Laboratório de Imunologia, LIM19, Instituto do Coração (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP) São Paulo da Universidade de São Paulo, São Paulo, Brazil
| | | | - Jhosiene Yukari Magawa
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Laboratório de Imunologia, LIM19, Instituto do Coração (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP) São Paulo da Universidade de São Paulo, São Paulo, Brazil
- Instituto de Investigação em Imunologia–Instituto Nacional de Ciências e Tecnologia – instituto de investigação em imunologia - Instituto Nacional de Ciências e Tecnologia (iii-INCT), São Paulo, Brazil
| | - Isabela Pazotti Daher
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Laboratório de Imunologia, LIM19, Instituto do Coração (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP) São Paulo da Universidade de São Paulo, São Paulo, Brazil
- Instituto de Investigação em Imunologia–Instituto Nacional de Ciências e Tecnologia – instituto de investigação em imunologia - Instituto Nacional de Ciências e Tecnologia (iii-INCT), São Paulo, Brazil
| | - Alysson Henrique Urbanski
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Gabriela Justamante Händel Schmitz
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Laboratório de Imunologia, LIM19, Instituto do Coração (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP) São Paulo da Universidade de São Paulo, São Paulo, Brazil
| | - Helen Andrade Arcuri
- Centro de Estudos de Insetos Sociais, Departamento de Biologia, Instituto de Biociências de Rio Claro, Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Marcelo Alves Ferreira
- Laboratório de Biologia Celular, Laboratório de Investigação Médica 59 (LIM59), Departamento de Patologia, Faculdade de Medicina Faculdade de Medicina da Universidade de São Paulo (FMUSP), Universidade de São Paulo, São Paulo, Brazil
| | - Greyce Luri Sasahara
- Laboratório de Imunologia, LIM19, Instituto do Coração (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP) São Paulo da Universidade de São Paulo, São Paulo, Brazil
| | - Giuliana Xavier de Medeiros
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Roberto Carlos Vieira Silva Júnior
- Laboratório de Imunologia, LIM19, Instituto do Coração (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP) São Paulo da Universidade de São Paulo, São Paulo, Brazil
| | - Edison Luiz Durigon
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
- Plataforma Científica Pasteur-USP, São Paulo, SP, Brazil
| | - Silvia Beatriz Boscardin
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Daniela Santoro Rosa
- Laboratório de Imunologia, LIM19, Instituto do Coração (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP) São Paulo da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo (UNIFESP/EPM, São Paulo, SP, Brazil
| | - Deborah Schechtman
- Departamento de Bioquímica, instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Helder I. Nakaya
- Plataforma Científica Pasteur-USP, São Paulo, SP, Brazil
- Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Edecio Cunha-Neto
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Laboratório de Imunologia, LIM19, Instituto do Coração (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP) São Paulo da Universidade de São Paulo, São Paulo, Brazil
- Instituto de Investigação em Imunologia–Instituto Nacional de Ciências e Tecnologia – instituto de investigação em imunologia - Instituto Nacional de Ciências e Tecnologia (iii-INCT), São Paulo, Brazil
| | - Gabriele Gadermaier
- Department of Biosciences and Medical Biology, Paris Lodron University Salzburg, Salzburg, Brazil
| | - Jorge Kalil
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Laboratório de Imunologia, LIM19, Instituto do Coração (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP) São Paulo da Universidade de São Paulo, São Paulo, Brazil
- Instituto de Investigação em Imunologia–Instituto Nacional de Ciências e Tecnologia – instituto de investigação em imunologia - Instituto Nacional de Ciências e Tecnologia (iii-INCT), São Paulo, Brazil
| | - Verônica Coelho
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Laboratório de Imunologia, LIM19, Instituto do Coração (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP) São Paulo da Universidade de São Paulo, São Paulo, Brazil
- Instituto de Investigação em Imunologia–Instituto Nacional de Ciências e Tecnologia – instituto de investigação em imunologia - Instituto Nacional de Ciências e Tecnologia (iii-INCT), São Paulo, Brazil
| | - Keity Souza Santos
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Laboratório de Imunologia, LIM19, Instituto do Coração (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP) São Paulo da Universidade de São Paulo, São Paulo, Brazil
- Instituto de Investigação em Imunologia–Instituto Nacional de Ciências e Tecnologia – instituto de investigação em imunologia - Instituto Nacional de Ciências e Tecnologia (iii-INCT), São Paulo, Brazil
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5
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Nakagama S, Nakagama Y, Komase Y, Kudo M, Imai T, Tshibangu-Kabamba E, Nitahara Y, Kaku N, Kido Y. Age-adjusted impact of prior COVID-19 on SARS-CoV-2 mRNA vaccine response. Front Immunol 2023; 14:1087473. [PMID: 36742291 PMCID: PMC9892832 DOI: 10.3389/fimmu.2023.1087473] [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: 11/04/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
More people with a history of prior infection are receiving SARS-CoV-2 vaccines. Understanding the level of protection granted by 'hybrid immunity', the combined response of infection- and vaccine-induced immunity, may impact vaccination strategies through tailored dosing. A total of 36 infected ('prior infection') and 33 SARS-CoV-2 'naïve' individuals participated. Participants provided sera six months after completing a round of BNT162b2 vaccination, to be processed for anti-spike antibody measurements and the receptor binding domain-ACE2 binding inhibition assays. The relationships between antibody titer, groups and age were explored. Anti-spike antibody titers at 6 months post-vaccination were significantly higher, reaching 13- to 17-fold, in the 'prior infection' group. Semi-log regression models showed that participants with 'prior infection' demonstrated higher antibody titer compared with the 'naïve' even after adjusting for age. The enhancement in antibody titer attributable to positive infection history increased from 8.9- to 9.4- fold at age 30 to 19- to 32-fold at age 60. Sera from the 'prior infection' group showed higher inhibition capacity against all six analyzed strains, including the Omicron variant. Prior COVID-19 led to establishing enhanced humoral immunity at 6 months after vaccination. Antibody fold-difference attributed to positive COVID-19 history increased with age, possibly because older individuals are prone to symptomatic infection accompanied by potentiated immune responses. While still pending any modifications of dosing recommendations (i.e. reduced doses for individuals with prior infection), our observation adds to the series of real-world data demonstrating the enhanced and more durable immune response evoked by booster vaccinations following prior infection.
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Affiliation(s)
- Sachie Nakagama
- Department of Virology & Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan.,Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Yu Nakagama
- Department of Virology & Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan.,Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Yuko Komase
- Department of Respiratory Internal Medicine, St. Marianna University, Yokohama Seibu Hospital, Yokohama, Japan
| | - Masaharu Kudo
- Department of Medical Statistics, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Takumi Imai
- Department of Medical Statistics, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Evariste Tshibangu-Kabamba
- Department of Virology & Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan.,Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Yuko Nitahara
- Department of Virology & Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan.,Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Natsuko Kaku
- Department of Virology & Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan.,Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Yasutoshi Kido
- Department of Virology & Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan.,Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
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6
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Abstract
We performed an annotation of 35 mutations in the spike protein of the SARS-CoV-2 Omicron variant. Our analysis of the mutations indicates that Omicron has gained prominent immune evasion and potential for enhanced transmissibility. Previous modeling study has revealed that continued evolution in both immune evasion and enhanced transmissibility by SARS-CoV-2 would compromise vaccines as tools for the pandemic control. To combat the future variants of SARS-CoV-2, the world needs novel antiviral drugs that are effective at curb viral spreading without introducing additional selective pressure towards resistant variants.
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Affiliation(s)
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
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7
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Bajoria S, Kaur K, Kumru OS, Van Slyke G, Doering J, Novak H, Rodriguez Aponte SA, Dalvie NC, Naranjo CA, Johnston RS, Silverman JM, Kleanthous H, Love JC, Mantis NJ, Joshi SB, Volkin DB. Antigen-adjuvant interactions, stability, and immunogenicity profiles of a SARS-CoV-2 receptor-binding domain (RBD) antigen formulated with aluminum salt and CpG adjuvants. Hum Vaccin Immunother 2022; 18:2079346. [PMID: 35666264 PMCID: PMC9621007 DOI: 10.1080/21645515.2022.2079346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/16/2022] [Indexed: 02/07/2023] Open
Abstract
Low-cost, refrigerator-stable COVID-19 vaccines will facilitate global access and improve vaccine coverage in low- and middle-income countries. To this end, subunit-based approaches targeting the receptor-binding domain (RBD) of SARS-CoV-2 Spike protein remain attractive. Antibodies against RBD neutralize SARS-CoV-2 by blocking viral attachment to the host cell receptor, ACE2. Here, a yeast-produced recombinant RBD antigen (RBD-L452K-F490W or RBD-J) was formulated with various combinations of aluminum-salt (Alhydrogel®, AH; AdjuPhos®, AP) and CpG 1018 adjuvants. We assessed the effect of antigen-adjuvant interactions on the stability and mouse immunogenicity of various RBD-J preparations. While RBD-J was 50% adsorbed to AH and <15% to AP, addition of CpG resulted in complete AH binding, yet no improvement in AP adsorption. ACE2 competition ELISA analyses of formulated RBD-J stored at varying temperatures (4, 25, 37°C) revealed that RBD-J was destabilized by AH, an effect exacerbated by CpG. DSC studies demonstrated that aluminum-salt and CpG adjuvants decrease the conformational stability of RBD-J and suggest a direct CpG-RBD-J interaction. Although AH+CpG-adjuvanted RBD-J was the least stable in vitro, the formulation was most potent at eliciting SARS-CoV-2 pseudovirus neutralizing antibodies in mice. In contrast, RBD-J formulated with AP+CpG showed minimal antigen-adjuvant interactions, a better stability profile, but suboptimal immune responses. Interestingly, the loss of in vivo potency associated with heat-stressed RBD-J formulated with AH+CpG after one dose was abrogated by a booster. Our findings highlight the importance of elucidating the key interrelationships between antigen-adjuvant interactions, storage stability, and in vivo performance to enable successful formulation development of stable and efficacious subunit vaccines.
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Affiliation(s)
- Sakshi Bajoria
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Kawaljit Kaur
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Ozan S. Kumru
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Greta Van Slyke
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Jennifer Doering
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Hayley Novak
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Sergio A. Rodriguez Aponte
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Neil C. Dalvie
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Christopher A. Naranjo
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ryan S. Johnston
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - J. Christopher Love
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Nicholas J. Mantis
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Sangeeta B. Joshi
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - David B. Volkin
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
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8
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Nakashima K, Ishida M, Matsui H, Yoshida C, Nagai T, Shiraga M, Nakaoka H, Otsuka Y, Nakagama Y, Kaku N, Nitahara Y, Kido Y, Hirota Y. Immunogenicity and safety of COVID-19 vaccine in lung cancer patients receiving anticancer treatment: A prospective multicenter cohort study. Hum Vaccin Immunother 2022; 18:2140549. [PMID: 36369871 DOI: 10.1080/21645515.2022.2140549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
This study assessed the immunogenicity and safety of the BNT162b2 mRNA vaccine in lung cancer patients receiving anticancer treatment. We enrolled lung cancer patients receiving anticancer treatment and non-cancer patients; all participants were fully vaccinated with the BNT162b2 vaccine. Blood samples were collected before the first and second vaccinations and 4 ± 1 weeks after the second vaccination. Anti-severe respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein S1 subunit receptor-binding domain antibody titers were measured using the Architect SARS-CoV-2 IgG II Quant and Elecsys Anti-SARS-CoV-2 S assays. Fifty-five lung cancer patients and 38 non-cancer patients were included in the immunogenicity analysis. Lung cancer patients showed significant increase in the geometric mean antibody concentration, which was significantly lower than that in the non-cancer patients after the first (30 vs. 121 AU/mL, p < .001 on Architect; 4.0 vs 1.2 U/mL, p < .001 on Elecsys) and second vaccinations (1632 vs. 3472 AU/mL, p = .005 on Architect; 213 vs 573 A/mL, p = .002 on Elecsys). The adjusted odds ratio (aOR) for seroprotection was significantly lower (p < .05) in lung cancer patients than that in non-cancer patients. Analysis of the anticancer treatment types showed that the aOR for seroprotection was significantly lower (p < .05) in lung cancer patients receiving cytotoxic agents. They showed no increase in adverse reactions. BNT162b2 vaccination in lung cancer patients undergoing anticancer treatment significantly increased (p < .05) antibody titers and showed acceptable safety. Immunogenicity in these patients could be inadequate compared with that in non-cancer patients.
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Affiliation(s)
- Kei Nakashima
- Department of Pulmonology, Kameda Medical Center, Kamogawa, Chiba, Japan
| | | | - Hiroki Matsui
- Clinical Research Support Office, Kameda Medical Center, Kamogawa, Chiba, Japan
| | - Chihiro Yoshida
- Department of Pulmonology, Kameda Medical Center, Kamogawa, Chiba, Japan
| | - Tatsuya Nagai
- Department of Pulmonology, Kameda Medical Center, Kamogawa, Chiba, Japan
| | - Minoru Shiraga
- Department of Pulmonology, Chikamori Hospital, Kochi, Japan
| | | | - Yoshihito Otsuka
- Department of Laboratory medicine, Kameda Medical Center, Kamogawa, Chiba, Japan
| | - Yu Nakagama
- Department of Virology & Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Natsuko Kaku
- Department of Virology & Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Yuko Nitahara
- Department of Virology & Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Yasutoshi Kido
- Department of Virology & Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Yoshio Hirota
- Clinical Epidemiology Research Center, SOUSEIKAI Medical Group (Medical Co. LTA), Fukuoka, Japan
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9
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Matsuura T, Fukushima W, Nakagama Y, Kido Y, Kase T, Kondo K, Kaku N, Matsumoto K, Suita A, Komiya E, Mukai E, Nitahara Y, Konishi A, Kasamatsu A, Nakagami-Yamaguchi E, Ohfuji S, Kaneko Y, Kaneko A, Kakeya H, Hirota Y. Kinetics of anti-SARS-CoV-2 antibody titer in healthy adults up to 6 months after BNT162b2 vaccination measured by two immunoassays: A prospective cohort study in Japan. Vaccine 2022; 40:5631-5640. [PMID: 36028457 PMCID: PMC9376311 DOI: 10.1016/j.vaccine.2022.08.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/03/2022] [Accepted: 08/10/2022] [Indexed: 01/07/2023]
Abstract
Background Although several assays are used to measure anti-receptor-binding domain (RBD) antibodies induced after severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) vaccination, the assays are not fully comparable in practice. This study evaluated the immunogenicity of the BNT162b2 mRNA vaccine in healthy adults using two immunoassays. Methods This prospective cohort study included SARS-CoV-2-naïve adults, predominantly healthcare workers, aged 20–64 years, who received two BNT162b2 vaccine doses between March and May 2021. Blood samples were collected before the first vaccination (S0), before the second vaccination (S1), 4 weeks after the second vaccination (S2), and 6 months after the second vaccination (S3). anti-RBD antibodies were measured using the Architect SARS-CoV-2 IgG II Quant (Abbott Laboratory) and Elecsys anti-SARS-CoV-2 S (Roche Diagnostics) assays. Results Among the 385 participants, the geometric mean antibody titers (GMTs) on the Architect assay (AU/mL) were 7.5, 693, 7007, and 1030 for S0, S1, S2, and S3, respectively. The corresponding GMTs on the Elecsys assay (U/mL) were 0.40, 24, 928, and 659, respectively. The GMT ratio (S3/S2) was 0.15 on the Architect and 0.71 on the Elecsys assay. The correlation between antibody titers measured with the two assays were strong at all time points after vaccination (Spearman's correlation coefficient: 0.74 to 0.86, P < 0.01 for all). GMT was significantly lower in the older age group after vaccination (P < 0.01), with no significant differences according to sex. Seroprotection (≥5458 AU/mL on the Architect assay and ≥ 753 U/mL on the Elecsys) at each time point was 0 %, 1 %, 67 %, and 1 % on the Architect assay and 0 %, 1 %, 62 %, and 43 % on the Elecsys, respectively. Conclusions Two BNT162b2 vaccine doses resulted in adequate anti-RBD antibody response, which varied by age. As the two assays showed different kinetics, the results of single immunoassays should be interpreted with caution.
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Affiliation(s)
- Tomoka Matsuura
- Department of Public Health, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan; Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka Metropolitan University, Japan.
| | - Wakaba Fukushima
- Department of Public Health, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan; Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka Metropolitan University, Japan
| | - Yu Nakagama
- Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka Metropolitan University, Japan; Department of Virology and Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Japan
| | - Yasutoshi Kido
- Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka Metropolitan University, Japan; Department of Virology and Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Japan
| | - Tetsuo Kase
- Department of Public Health, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan; Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka Metropolitan University, Japan
| | - Kyoko Kondo
- Management Bureau, Osaka Metropolitan University Hospital, Japan
| | - Natsuko Kaku
- Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka Metropolitan University, Japan; Department of Virology and Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Japan
| | - Kazuhiro Matsumoto
- Department of Public Health, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Asae Suita
- Department of Public Health, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Eriko Komiya
- Department of Orthopedic Surgery, Graduate School of Medicine, Osaka Metropolitan University, Japan
| | - Emiko Mukai
- Department of Public Health, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Yuko Nitahara
- Department of Virology and Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Japan
| | - Ayako Konishi
- Department of Public Health, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Ayane Kasamatsu
- Department of Public Health, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Etsuko Nakagami-Yamaguchi
- Department of Medical Quality and Safety Science, Graduate School of Medicine, Osaka Metropolitan University, Japan
| | - Satoko Ohfuji
- Department of Public Health, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan; Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka Metropolitan University, Japan
| | - Yukihiro Kaneko
- Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka Metropolitan University, Japan; Department of Bacteriology, Graduate School of Medicine, Osaka Metropolitan University, Japan
| | - Akira Kaneko
- Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka Metropolitan University, Japan; Department of Virology and Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Japan
| | - Hiroshi Kakeya
- Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka Metropolitan University, Japan; Department of Infection Control Science, Graduate School of Medicine, Osaka Metropolitan University, Japan
| | - Yoshio Hirota
- Clinical Epidemiology Research Center, SOUSEIKAI Medical Group (Medical Co. LTA), Fukuoka, Japan
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10
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Abd El-Baky N, Amara AAAF. Depending on Epitope Profile of COVID-19 mRNA Vaccine Recipients: Are They More Efficient Against the Arising Viral Variants? An Opinion Article. Front Med (Lausanne) 2022; 9:903876. [PMID: 35795625 PMCID: PMC9251123 DOI: 10.3389/fmed.2022.903876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/01/2022] [Indexed: 12/02/2022] Open
Affiliation(s)
- Nawal Abd El-Baky
- Department of Protein Research, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), Alexandria, Egypt
| | - Amro Abd Al Fattah Amara
- Department of Protein Research, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), Alexandria, Egypt
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11
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Bugatti A, Filippini F, Bardelli M, Zani A, Chiodelli P, Messali S, Caruso A, Caccuri F. SARS-CoV-2 Infects Human ACE2-Negative Endothelial Cells through an αvβ3 Integrin-Mediated Endocytosis Even in the Presence of Vaccine-Elicited Neutralizing Antibodies. Viruses 2022; 14:v14040705. [PMID: 35458435 PMCID: PMC9032829 DOI: 10.3390/v14040705] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/15/2022] [Accepted: 03/23/2022] [Indexed: 02/06/2023] Open
Abstract
Integrins represent a gateway of entry for many viruses and the Arg-Gly-Asp (RGD) motif is the smallest sequence necessary for proteins to bind integrins. All Severe Acute Respiratory Syndrome Virus type 2 (SARS-CoV-2) lineages own an RGD motif (aa 403–405) in their receptor binding domain (RBD). We recently showed that SARS-CoV-2 gains access into primary human lung microvascular endothelial cells (HL-mECs) lacking Angiotensin-converting enzyme 2 (ACE2) expression through this conserved RGD motif. Following its entry, SARS-CoV-2 remodels cell phenotype and promotes angiogenesis in the absence of productive viral replication. Here, we highlight the αvβ3 integrin as the main molecule responsible for SARS-CoV-2 infection of HL-mECs via a clathrin-dependent endocytosis. Indeed, pretreatment of virus with αvβ3 integrin or pretreatment of cells with a monoclonal antibody against αvβ3 integrin was found to inhibit SARS-CoV-2 entry into HL-mECs. Surprisingly, the anti-Spike antibodies evoked by vaccination were neither able to impair Spike/integrin interaction nor to prevent SARS-CoV-2 entry into HL-mECs. Our data highlight the RGD motif in the Spike protein as a functional constraint aimed to maintain the interaction of the viral envelope with integrins. At the same time, our evidences call for the need of intervention strategies aimed to neutralize the SARS-CoV-2 integrin-mediated infection of ACE2-negative cells in the vaccine era.
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Affiliation(s)
- Antonella Bugatti
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.F.); (M.B.); (A.Z.); (S.M.); (A.C.)
| | - Federica Filippini
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.F.); (M.B.); (A.Z.); (S.M.); (A.C.)
| | - Marta Bardelli
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.F.); (M.B.); (A.Z.); (S.M.); (A.C.)
| | - Alberto Zani
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.F.); (M.B.); (A.Z.); (S.M.); (A.C.)
| | - Paola Chiodelli
- Section of General Pathology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy;
| | - Serena Messali
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.F.); (M.B.); (A.Z.); (S.M.); (A.C.)
| | - Arnaldo Caruso
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.F.); (M.B.); (A.Z.); (S.M.); (A.C.)
| | - Francesca Caccuri
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.F.); (M.B.); (A.Z.); (S.M.); (A.C.)
- Correspondence:
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