1
|
Duyvesteyn HME, Dijokaite-Guraliuc A, Liu C, Supasa P, Kronsteiner B, Jeffery K, Stafford L, Klenerman P, Dunachie SJ, Mongkolsapaya J, Fry EE, Ren J, Stuart DI, Screaton GR. Concerted deletions eliminate a neutralizing supersite in SARS-CoV-2 BA.2.87.1 spike. Structure 2024; 32:1594-1602.e6. [PMID: 39173622 DOI: 10.1016/j.str.2024.07.020] [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] [Received: 05/16/2024] [Revised: 07/01/2024] [Accepted: 07/29/2024] [Indexed: 08/24/2024]
Abstract
BA.2.87.1 represents a major shift in the BA.2 lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is unusual in having two lengthy deletions of polypeptide in the spike (S) protein, one of which removes a beta-strand. Here we investigate its neutralization by a variety of sera from infected and vaccinated individuals and determine its spike (S) ectodomain structure. The BA.2.87.1 receptor binding domain (RBD) is structurally conserved and the RBDs are tightly packed in an "all-down" conformation with a small rotation relative to the trimer axis as compared to the closest previously observed conformation. The N-terminal domain (NTD) maintains a remarkably similar structure overall; however, the rearrangements resulting from the deletions essentially destroy the so-called supersite epitope and eliminate one glycan site, while a mutation creates an additional glycan site, effectively shielding another NTD epitope. BA.2.87.1 is relatively easily neutralized but acquisition of additional mutations in the RBD could increase antibody escape allowing it to become a dominant sub-lineage.
Collapse
Affiliation(s)
- Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Centre for Human Genetics, Oxford, UK
| | - Aiste Dijokaite-Guraliuc
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Piyada Supasa
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Barbara Kronsteiner
- NDM Centre For Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Lizzie Stafford
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Centre for Human Genetics, Oxford, UK.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|
2
|
Banho CA, de Carvalho Marques B, Sacchetto L, Lima AKS, Parra MCP, Lima ARJ, Ribeiro G, Martins AJ, Barros CRDS, Elias MC, Sampaio SC, Slavov SN, Rodrigues ES, Santos EV, Covas DT, Kashima S, Brassaloti RA, Petry B, Clemente LG, Coutinho LL, Assato PA, da Silva da Costa FA, Grotto RMT, Poleti MD, Lesbon JCC, Mattos EC, Fukumasu H, Giovanetti M, Alcantara LCJ, Souza-Neto JA, Rahal P, Araújo JP, Spilki FR, Althouse BM, Vasilakis N, Nogueira ML. Dynamic clade transitions and the influence of vaccination on the spatiotemporal circulation of SARS-CoV-2 variants. NPJ Vaccines 2024; 9:145. [PMID: 39127725 DOI: 10.1038/s41541-024-00933-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 07/17/2024] [Indexed: 08/12/2024] Open
Abstract
Since 2021, the emergence of variants of concern (VOC) has led Brazil to experience record numbers of in COVID-19 cases and deaths. The expanded spread of the SARS-CoV-2 combined with a low vaccination rate has contributed to the emergence of new mutations that may enhance viral fitness, leading to the persistence of the disease. Due to limitations in the real-time genomic monitoring of new variants in some Brazilian states, we aimed to investigate whether genomic surveillance, coupled with epidemiological data and SARS-CoV-2 variants spatiotemporal spread in a smaller region, can reflect the pandemic progression at a national level. Our findings revealed three SARS-CoV-2 variant replacements from 2021 to early 2022, corresponding to the introduction and increase in the frequency of Gamma, Delta, and Omicron variants, as indicated by peaks of the Effective Reproductive Number (Reff). These distinct clade replacements triggered two waves of COVID-19 cases, influenced by the increasing vaccine uptake over time. Our results indicated that the effectiveness of vaccination in preventing new cases during the Delta and Omicron circulations was six and eleven times higher, respectively, than during the period when Gamma was predominant, and it was highly efficient in reducing the number of deaths. Furthermore, we demonstrated that genomic monitoring at a local level can reflect the national trends in the spread and evolution of SARS-CoV-2.
Collapse
Affiliation(s)
- Cecília Artico Banho
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Beatriz de Carvalho Marques
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Lívia Sacchetto
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Ana Karoline Sepedro Lima
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Maisa Carla Pereira Parra
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Alex Ranieri Jeronimo Lima
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Gabriela Ribeiro
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Antonio Jorge Martins
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | | | - Maria Carolina Elias
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Sandra Coccuzzo Sampaio
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Svetoslav Nanev Slavov
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Evandra Strazza Rodrigues
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Elaine Vieira Santos
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Dimas Tadeu Covas
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Simone Kashima
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | - Bruna Petry
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Luan Gaspar Clemente
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Luiz Lehmann Coutinho
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Patricia Akemi Assato
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Felipe Allan da Silva da Costa
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Rejane Maria Tommasini Grotto
- São Paulo State University (UNESP), School of Agricultural Sciences, Botucatu, Brazil
- Molecular Biology Laboratory, Applied Biotechnology Laboratory, Clinical Hospital of the Botucatu Medical School, Botucatu, Brazil
| | - Mirele Daiana Poleti
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Jessika Cristina Chagas Lesbon
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Elisangela Chicaroni Mattos
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Marta Giovanetti
- Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
- Climate Amplified Diseases And Epidemics (CLIMADE), Rio de Janeiro, Brazil
- Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, Selcetta, Italy
| | - Luiz Carlos Junior Alcantara
- Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
- Climate Amplified Diseases And Epidemics (CLIMADE), Rio de Janeiro, Brazil
| | - Jayme A Souza-Neto
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas StateUniversity, Manhattan, KS, USA
| | - Paula Rahal
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista (Unesp), São José do Rio Preto, Brazil
| | - João Pessoa Araújo
- Instituto de Biotecnologia, Universidade Estadual Paulista (Unesp), Botucatu, Brazil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, Brazil
| | - Benjamin M Althouse
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
- Information School, University of Washington, Seattle, WA, USA
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
- Center for Vector-Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil.
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.
| |
Collapse
|
3
|
Mühlemann B, Trimpert J, Walper F, Schmidt ML, Jansen J, Schroeder S, Jeworowski LM, Beheim-Schwarzbach J, Bleicker T, Niemeyer D, Richter A, Adler JM, Vidal RM, Langner C, Vladimirova D, Wilks SH, Smith DJ, Voß M, Paltzow L, Martínez Christophersen C, Rose R, Krumbholz A, Jones TC, Corman VM, Drosten C. Antigenic cartography using variant-specific hamster sera reveals substantial antigenic variation among Omicron subvariants. Proc Natl Acad Sci U S A 2024; 121:e2310917121. [PMID: 39078681 PMCID: PMC11317614 DOI: 10.1073/pnas.2310917121] [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: 07/04/2023] [Accepted: 05/31/2024] [Indexed: 07/31/2024] Open
Abstract
Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) has developed substantial antigenic variability. As the majority of the population now has pre-existing immunity due to infection or vaccination, the use of experimentally generated animal immune sera can be valuable for measuring antigenic differences between virus variants. Here, we immunized Syrian hamsters by two successive infections with one of nine SARS-CoV-2 variants. Their sera were titrated against 16 SARS-CoV-2 variants, and the resulting titers were visualized using antigenic cartography. The antigenic map shows a condensed cluster containing all pre-Omicron variants (D614G, Alpha, Delta, Beta, Mu, and an engineered B.1+E484K variant) and considerably more diversity among a selected panel of Omicron subvariants (BA.1, BA.2, BA.4/BA.5, the BA.5 descendants BF.7 and BQ.1.18, the BA.2.75 descendant BN.1.3.1, the BA.2-derived recombinants XBB.2 and EG.5.1, and the BA.2.86 descendant JN.1). Some Omicron subvariants were as antigenically distinct from each other as the wildtype is from the Omicron BA.1 variant. Compared to titers measured in human sera, titers in hamster sera are of higher magnitude, show less fold change, and result in a more compact antigenic map topology. The results highlight the potential of sera from hamsters for the continued antigenic characterization of SARS-CoV-2.
Collapse
Affiliation(s)
- Barbara Mühlemann
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung), Berlin10117, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Berlin14163, Germany
| | - Felix Walper
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Marie L. Schmidt
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Jenny Jansen
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Simon Schroeder
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Lara M. Jeworowski
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Jörn Beheim-Schwarzbach
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Tobias Bleicker
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Daniela Niemeyer
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Anja Richter
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Julia M. Adler
- Institut für Virologie, Freie Universität Berlin, Berlin14163, Germany
| | | | - Christine Langner
- Institut für Virologie, Freie Universität Berlin, Berlin14163, Germany
| | - Daria Vladimirova
- Institut für Virologie, Freie Universität Berlin, Berlin14163, Germany
| | - Samuel H. Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, CambridgeCB2 3EJ, United Kingdom
| | - Derek J. Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, CambridgeCB2 3EJ, United Kingdom
| | - Mathias Voß
- Institute for Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Kiel24105, Germany
| | - Lea Paltzow
- Labor Dr. Krause und Kollegen Medizinisches Versorgungszentrum GmbH, Kiel24106, Germany
| | | | - Ruben Rose
- Institute for Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Kiel24105, Germany
| | - Andi Krumbholz
- Institute for Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Kiel24105, Germany
- Labor Dr. Krause und Kollegen Medizinisches Versorgungszentrum GmbH, Kiel24106, Germany
| | - Terry C. Jones
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung), Berlin10117, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, CambridgeCB2 3EJ, United Kingdom
| | - Victor M. Corman
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung), Berlin10117, Germany
- Labor Berlin–Charité Vivantes GmbH, Berlin13353, Germany
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung), Berlin10117, Germany
| |
Collapse
|
4
|
Focosi D, Franchini M, Casadevall A, Maggi F. An update on the anti-spike monoclonal antibody pipeline for SARS-CoV-2. Clin Microbiol Infect 2024; 30:999-1006. [PMID: 38663655 DOI: 10.1016/j.cmi.2024.04.012] [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] [Received: 03/08/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND Anti-spike monoclonal antibodies represent one of the most tolerable prophylaxis and therapies for COVID-19 in frail and immunocompromised patients. Unfortunately, viral evolution in Omicron has led all of them to failure. OBJECTIVES We review here the current pipeline of anti-spike mAb's, discussing in detail the most promising candidates. SOURCES We scanned PubMed, ClinicalTrials.gov and manufacturers' press releases for clinical studies on anti-spike monoclonal antibodies. CONTENT We present state-of-art data clinical progress for AstraZeneca's AZD3152, Invivyd's VYD222, Regeneron's REGN-17092 and Aerium Therapeutics' AER-800. IMPLICATIONS The anti-spike monoclonal antibody clinical pipeline is currently limited to few agents (most being single antibodies) with unknown efficacy against the dominant JN.1 sublineage. The field of antibody-based therapies requires boosting by both manufacturers and institutions.
Collapse
Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy.
| | - Massimo Franchini
- Department of Transfusion Medicine and Hematology, Carlo Poma Hospital, Mantua, Italy
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| |
Collapse
|
5
|
Nel I, Ithayakumar A, Blumenthal N, Duneton C, Khourouj VGE, Viala J, Dollfus C, Baudouin V, Guilmin-Crepon S, Theodorou I, Carcelain G. Strategies to determine positive anti-SARS-CoV-2 memory T lymphocyte response during the evolution of an epidemic. J Immunol Methods 2024; 531:113712. [PMID: 38906414 DOI: 10.1016/j.jim.2024.113712] [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] [Received: 12/05/2023] [Revised: 05/22/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
During SARS-CoV-2 pandemic, the assessment of immune protection of people at risk of severe infection was an important goal. The appearance of VOCs (Variant of Concern) highlighted the limits of evaluating immune protection through the humoral response. While the humoral response partly loses its neutralizing activity, the anti-SARS-CoV-2 memory T cell response strongly cross protects against VOCs becoming an indispensable tool to assess immune protection. We compared two techniques available in laboratory to evaluate anti-SARS-CoV-2 memory T cell response in a cohort of infected or vaccinated patients with different levels of risk to develop a severe disease: the ELISpot assay and the T-Cell Lymphocyte Proliferation Assay respectively exploring IFNγ production and cell proliferation. We showed that the ELISpot assay detected more anti-Spike memory T cell response than the Lymphocyte Proliferation Assay. We next observed that the use of two different suppliers as antigenic source in the ELISpot assay did not affect the detection of anti-Spike memory T cell response. Finally, we explored a new approach for defining the positivity threshold, using unsupervised mixed Gaussian modeling, challenging the traditional ROC curve used by the supplier. That will be helpful in endemic situation where it could be difficult to recruit "negative" patients.
Collapse
Affiliation(s)
- Isabelle Nel
- Immunology Department, Robert-Debré Hospital, APHP, Paris, France; University Paris Cité, INSERM U976, France
| | | | | | - Charlotte Duneton
- Immunology Department, Robert-Debré Hospital, APHP, Paris, France; University Paris Cité, INSERM U976, France; Pediatric Nephrology Department, Robert-Debré Hospital, APHP, Paris, France
| | | | - Jérôme Viala
- Department of Pediatric Gastroenterology, Robert-Debré Hospital, APHP, Paris, France
| | - Catherine Dollfus
- Pediatric Hematology and Oncology Department, Trousseau Hospital, APHP, Paris, France
| | - Véronique Baudouin
- Pediatric Nephrology Department, Robert-Debré Hospital, APHP, Paris, France
| | - Sophie Guilmin-Crepon
- Clinical Epidemiology Unit, Inserm CIC-EC 1426, Robert-Debré Hospital, APHP, Paris, France
| | | | - Guislaine Carcelain
- Immunology Department, Robert-Debré Hospital, APHP, Paris, France; University Paris Cité, INSERM U976, France.
| |
Collapse
|
6
|
Salazar VA, Comenge J, Suárez-López R, Burger JA, Sanders RW, Bastús NG, Jaime C, Joseph-Munne J, Puntes V. Gold Nanoparticle Virus-like Particles Presenting SARS-CoV-2 Spike Protein: Synthesis, Biophysical Properties and Immunogenicity in BALB/c Mice. Vaccines (Basel) 2024; 12:829. [PMID: 39203954 PMCID: PMC11359663 DOI: 10.3390/vaccines12080829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 09/03/2024] Open
Abstract
Gold nanoparticles (AuNPs) decorated with antigens have recently emerged as promising tools for vaccine development due to their innate ability to provide stability to antigens and modulate immune responses. In this study, we have engineered deactivated virus-like particles (VLPs) by precisely functionalizing gold cores with coronas comprising the full SARS-CoV-2 spike protein (S). Using BALB/c mice as a model, we investigated the immunogenicity of these S-AuNPs-VLPs. Our results demonstrate that S-AuNPs-VLPs consistently enhanced antigen-specific antibody responses compared to the S protein free in solution. This enhancement included higher binding antibody titers, higher neutralizing capacity of antibodies, and stronger T-cell responses. Compared to the mRNA COVID-19 vaccine, where the S protein is synthesized in situ, S-AuNPs-VLPs induced comparable binding and neutralizing antibody responses, but substantially superior T-cell responses. In conclusion, our study highlights the potential of conjugated AuNPs as an effective antigen-delivery system for protein-based vaccines targeting a broad spectrum of infectious diseases and other emergent viruses.
Collapse
Affiliation(s)
- Vivian A. Salazar
- Vall d’Hebron Institut de Recerca, 08035 Barcelona, Spain; (V.A.S.); (J.C.)
| | - Joan Comenge
- Vall d’Hebron Institut de Recerca, 08035 Barcelona, Spain; (V.A.S.); (J.C.)
- Networking Research Centre for Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Rosa Suárez-López
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; (R.S.-L.); (C.J.)
| | - Judith A. Burger
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, The Netherlands; (J.A.B.); (R.W.S.)
| | - Rogier W. Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, The Netherlands; (J.A.B.); (R.W.S.)
| | - Neus G. Bastús
- Networking Research Centre for Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Instituto de Salud Carlos III, 28029 Madrid, Spain;
- Institut Català de Nanociència i Nanotecnologia (ICN2), CSIC and BIST, Campus Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Carlos Jaime
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; (R.S.-L.); (C.J.)
| | - Joan Joseph-Munne
- Vall d’Hebron Institut de Recerca, 08035 Barcelona, Spain; (V.A.S.); (J.C.)
- Department of Microbiology, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
| | - Victor Puntes
- Vall d’Hebron Institut de Recerca, 08035 Barcelona, Spain; (V.A.S.); (J.C.)
- Networking Research Centre for Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Instituto de Salud Carlos III, 28029 Madrid, Spain;
- Institut Català de Nanociència i Nanotecnologia (ICN2), CSIC and BIST, Campus Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| |
Collapse
|
7
|
Gao Q, Liu S, Zhou Y, Fan J, Ke S, Zhou Y, Fan K, Wang Y, Zhou Y, Xia Z, Deng X. Discovery of meisoindigo derivatives as noncovalent and orally available M pro inhibitors: their therapeutic implications in the treatment of COVID-19. Eur J Med Chem 2024; 273:116498. [PMID: 38762916 DOI: 10.1016/j.ejmech.2024.116498] [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] [Received: 02/16/2024] [Revised: 05/08/2024] [Accepted: 05/11/2024] [Indexed: 05/21/2024]
Abstract
The progressive emergence of SARS-CoV-2 variants has necessitated the urgent exploration of novel therapeutic strategies to combat the COVID-19 pandemic. The SARS-CoV-2 main protease (Mpro) represents an evolutionarily conserved therapeutic target for drug discovery. This study highlights the discovery of meisoindigo (Mei), derived from the traditional Chinese medicine (TCM) Indigo naturalis, as a novel non-covalent and nonpeptidic Mpro inhibitor. Substantial optimizations and structure-activity relationship (SAR) studies, guided by a structure-based drug design approach, led to the identification of several Mei derivatives, including S5-27 and S5-28, exhibiting low micromolar inhibition against SARS-CoV-2 Mpro with high binding affinity. Notably, S5-28 provided significant protection against wild-type SARS-CoV-2 in HeLa-hACE2 cells, with EC50 up to 2.66 μM. Furthermore, it displayed favorable physiochemical properties and remarkable gastrointestinal and metabolic stability, demonstrating its potential as an orally bioavailable drug for anti-COVID-19 therapy. This research presents a promising avenue for the development of new antiviral agents, offering hope in the ongoing battle against COVID-19.
Collapse
Affiliation(s)
- Qingtian Gao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Sixu Liu
- School of Life Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Yuzheng Zhou
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Jinbao Fan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Shufen Ke
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Yuqing Zhou
- School of Life Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Kaiqiang Fan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Yuxuan Wang
- School of Life Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Yingjun Zhou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, 410013, Hunan, China
| | - Zanxian Xia
- School of Life Sciences, Central South University, Changsha, 410013, Hunan, China.
| | - Xu Deng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, 410013, Hunan, China.
| |
Collapse
|
8
|
Yang J, Fan H, Yang A, Wang W, Wan X, Lin F, Yang D, Wu J, Wang K, Li W, Cai Q, You L, Pang D, Lu J, Guo C, Shi J, Sun Y, Li X, Duan K, Shen S, Meng S, Guo J, Wang Z. The Protective Efficacy of a SARS-CoV-2 Vaccine Candidate B.1.351V against Several Variant Challenges in K18-hACE2 Mice. Vaccines (Basel) 2024; 12:742. [PMID: 39066379 PMCID: PMC11281458 DOI: 10.3390/vaccines12070742] [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: 06/20/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
The emergence of SARS-CoV-2 variants of concern (VOCs) with increased transmissibility and partial resistance to neutralization by antibodies has been observed globally. There is an urgent need for an effective vaccine to combat these variants. Our study demonstrated that the B.1.351 variant inactivated vaccine candidate (B.1.351V) generated strong binding and neutralizing antibody responses in BALB/c mice against the B.1.351 virus and other SARS-CoV-2 variants after two doses within 28 days. Immunized K18-hACE2 mice also exhibited elevated levels of live virus-neutralizing antibodies against various SARS-CoV-2 viruses. Following infection with these viruses, K18-hACE2 mice displayed a stable body weight, a high survival rate, minimal virus copies in lung tissue, and no lung damage compared to the control group. These findings indicate that B.1.351V offered protection against infection with multiple SARS-CoV-2 variants in mice, providing insights for the development of a vaccine targeting SARS-CoV-2 VOCs for human use.
Collapse
Affiliation(s)
- Jie Yang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Huifen Fan
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Anna Yang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Wenhui Wang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Xin Wan
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Fengjie Lin
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Dongsheng Yang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Jie Wu
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Kaiwen Wang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Wei Li
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Qian Cai
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Lei You
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Deqin Pang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Jia Lu
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Changfu Guo
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Jinrong Shi
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Yan Sun
- Wuhan Institute for Neuroscience and Neuroengineering, South-Central University for Nationalities, Wuhan 430074, China;
| | - Xinguo Li
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Kai Duan
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Shuo Shen
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Shengli Meng
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Jing Guo
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| | - Zejun Wang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (J.Y.); (H.F.); (A.Y.); (W.W.); (X.W.); (F.L.); (D.Y.); (J.W.); (K.W.); (W.L.); (Q.C.); (L.Y.); (D.P.); (J.L.); (C.G.); (J.S.); (X.L.); (K.D.); (S.S.); (S.M.)
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- National Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430207, China
- Hubei Province Vaccine Technology Innovation Center, Wuhan 430207, China
| |
Collapse
|
9
|
Cai Y, Diallo S, Rosenthal K, Ren K, Flores DJ, Dippel A, Oganesyan V, van Dyk N, Chen X, Cantu E, Choudhary R, Sulikowski M, Adissu H, Chawla B, Kar S, Liu C, Dijokaite-Guraliuc A, Mongkolsapaya J, Rajan S, Loo YM, Beavon R, Webber C, Chang LJ, Thomas S, Clegg L, Zhang H, Screaton GR, Philbin N, Harre M, Selim A, Martinez-Alier N, Uriel A, Cohen TS, Perez JL, Esser MT, Blair W, Francica JR. AZD3152 neutralizes SARS-CoV-2 historical and contemporary variants and is protective in hamsters and well tolerated in adults. Sci Transl Med 2024; 16:eado2817. [PMID: 38924429 DOI: 10.1126/scitranslmed.ado2817] [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: 01/26/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
Abstract
The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in variants that can escape neutralization by therapeutic antibodies. Here, we describe AZD3152, a SARS-CoV-2-neutralizing monoclonal antibody designed to provide improved potency and coverage against emerging variants. AZD3152 binds to the back left shoulder of the SARS-CoV-2 spike protein receptor binding domain and prevents interaction with the human angiotensin-converting enzyme 2 receptor. AZD3152 potently neutralized a broad panel of pseudovirus variants, including the currently dominant Omicron variant JN.1 but has reduced potency against XBB subvariants containing F456L. In vitro studies confirmed F456L resistance and additionally identified T415I and K458E as escape mutations. In a Syrian hamster challenge model, prophylactic administration of AZD3152 protected hamsters from weight loss and inflammation-related lung pathologies and reduced lung viral load. In the phase 1 sentinel safety cohort of the ongoing SUPERNOVA study (ClinicalTrials.gov: NCT05648110), a single 600-mg intramuscular injection of AZD5156 (containing 300 mg each of AZD3152 and cilgavimab) was well tolerated in adults through day 91. Observed serum concentrations of AZD3152 through day 91 were similar to those observed with cilgavimab and consistent with predictions for AZD7442, a SARS-CoV-2-neutralizing antibody combination of cilgavimab and tixagevimab, in a population pharmacokinetic model. On the basis of its pharmacokinetic characteristics, AZD3152 is predicted to provide durable protection against symptomatic coronavirus disease 2019 caused by susceptible SARS-CoV-2 variants, such as JN.1, in humans.
Collapse
MESH Headings
- Animals
- SARS-CoV-2/drug effects
- Humans
- COVID-19/virology
- Antibodies, Neutralizing/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Cricetinae
- COVID-19 Drug Treatment
- Antibodies, Monoclonal, Humanized/pharmacology
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antibodies, Monoclonal, Humanized/pharmacokinetics
- Mesocricetus
- Female
- Male
- Adult
- Antibodies, Viral/immunology
- Mutation/genetics
- Antibodies, Monoclonal
- Angiotensin-Converting Enzyme 2/metabolism
- Viral Load/drug effects
Collapse
Affiliation(s)
- Yingyun Cai
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Seme Diallo
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Kim Rosenthal
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Kuishu Ren
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Daniel J Flores
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Andrew Dippel
- Biologics Engineering, Oncology R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Vaheh Oganesyan
- Biologics Engineering, Oncology R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Nydia van Dyk
- Biologics Engineering, Oncology R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Xiaoru Chen
- Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Erin Cantu
- Imaging and Data Analytics, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Rakesh Choudhary
- Imaging and Data Analytics, AstraZeneca, Gaithersburg, MD 20878, USA
| | | | - Hibret Adissu
- Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | | | | | - Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute, University of Oxford, Oxford OX3 7BN, UK
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Aiste Dijokaite-Guraliuc
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute, University of Oxford, Oxford OX3 7BN, UK
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand, Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Saravanan Rajan
- Biologics Engineering, Oncology R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Yueh-Ming Loo
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Rohini Beavon
- Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 8PA, UK
| | - Chris Webber
- Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 8PA, UK
| | - Lee-Jah Chang
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Steven Thomas
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Lindsay Clegg
- Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Huixia Zhang
- Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute, University of Oxford, Oxford OX3 7BN, UK
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Nora Philbin
- Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 8PA, UK
| | - Mark Harre
- Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 8PA, UK
| | - Abdulhafez Selim
- Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 8PA, UK
| | - Nuria Martinez-Alier
- Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 8PA, UK
| | - Alison Uriel
- Department of Infectious Diseases and Tropical Medicine, North Manchester General Hospital (Manchester University NHS Foundation Trust), Manchester M8 5RB, UK
| | - Taylor S Cohen
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - John L Perez
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Mark T Esser
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Wade Blair
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Joseph R Francica
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| |
Collapse
|
10
|
Gao T, Irie A, Kouwaki T, Oshiumi H. Development of a single-chain variable antibody fragment against a conserved region of the SARS-CoV-2 spike protein. Sci Rep 2024; 14:14419. [PMID: 38909102 PMCID: PMC11193732 DOI: 10.1038/s41598-024-64103-7] [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: 11/24/2023] [Accepted: 06/05/2024] [Indexed: 06/24/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has prolonged the duration of the pandemic because of the continuous emergence of new variant strains. The emergence of these mutant strains makes it difficult to detect the virus with the existing antibodies; thus, the development of novel antibodies that can target both the variants as well as the original strain is necessary. In this study, we generated a high-affinity monoclonal antibody (5G2) against the highly conserved region of the SARS-CoV-2 spike protein to detect the protein variants. Moreover, we generated its single-chain variable antibody fragment (sc5G2). The sc5G2 expressed in mammalian and bacterial cells detected the spike protein of the original SARS-CoV-2 and variant strains. The resulting sc5G2 will be a useful tool to detect the original SARS-CoV-2 and variant strains.
Collapse
Affiliation(s)
- Tingyu Gao
- Department of Immunology, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, 1-1-1, Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Atsushi Irie
- Department of Immunology, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, 1-1-1, Honjo, Chuo-ku, Kumamoto, 860-8556, Japan.
| | - Takahisa Kouwaki
- Department of Immunology, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, 1-1-1, Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Hiroyuki Oshiumi
- Department of Immunology, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, 1-1-1, Honjo, Chuo-ku, Kumamoto, 860-8556, Japan.
| |
Collapse
|
11
|
Maiti AK. Progressive Evolutionary Dynamics of Gene-Specific ω Led to the Emergence of Novel SARS-CoV-2 Strains Having Super-Infectivity and Virulence with Vaccine Neutralization. Int J Mol Sci 2024; 25:6306. [PMID: 38928018 PMCID: PMC11204377 DOI: 10.3390/ijms25126306] [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] [Received: 05/06/2024] [Revised: 05/21/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
An estimation of the proportion of nonsynonymous to synonymous mutation (dn/ds, ω) of the SARS-CoV-2 genome would indicate the evolutionary dynamics necessary to evolve into novel strains with increased infection, virulence, and vaccine neutralization. A temporal estimation of ω of the whole genome, and all twenty-nine SARS-CoV-2 genes of major virulent strains of alpha, delta and omicron demonstrates that the SARS-CoV-2 genome originally emerged (ω ~ 0.04) with a strong purifying selection (ω < 1) and reached (ω ~ 0.85) in omicron towards diversifying selection (ω > 1). A marked increase in the ω occurred in the spike gene from alpha (ω = 0.2) to omicron (ω = 1.97). The ω of the replication machinery genes including RDRP, NSP3, NSP4, NSP7, NSP8, NSP10, NSP13, NSP14, and ORF9 are markedly increased, indicating that these genes/proteins are yet to be evolutionary stabilized and are contributing to the evolution of novel virulent strains. The delta-specific maximum increase in ω in the immunomodulatory genes of NSP8, NSP10, NSP16, ORF4, ORF5, ORF6, ORF7A, and ORF8 compared to alpha or omicron indicates delta-specific vulnerabilities for severe COVID-19 related hospitalization and death. The maximum values of ω are observed for spike (S), NSP4, ORF8 and NSP15, which indicates that the gene-specific temporal estimation of ω identifies specific genes for its super-infectivity and virulency that could be targeted for drug development.
Collapse
Affiliation(s)
- Amit K Maiti
- Department of Genetics and Genomics, Mydnavar, 28475 Greenfield Rd, Southfield, MI 48076, USA
| |
Collapse
|
12
|
Hattab D, Amer MFA, Al-Alami ZM, Bakhtiar A. SARS-CoV-2 journey: from alpha variant to omicron and its sub-variants. Infection 2024; 52:767-786. [PMID: 38554253 PMCID: PMC11143066 DOI: 10.1007/s15010-024-02223-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: 12/27/2023] [Accepted: 02/22/2024] [Indexed: 04/01/2024]
Abstract
The COVID-19 pandemic has affected hundreds of millions of individuals and caused more than six million deaths. The prolonged pandemic duration and the continual inter-individual transmissibility have contributed to the emergence of a wide variety of SARS-CoV-2 variants. Genomic surveillance and phylogenetic studies have shown that substantial mutations in crucial supersites of spike glycoprotein modulate the binding affinity of the evolved SARS-COV-2 lineages to ACE2 receptors and modify the binding of spike protein with neutralizing antibodies. The immunological spike mutations have been associated with differential transmissibility, infectivity, and therapeutic efficacy of the vaccines and the immunological therapies among the new variants. This review highlights the diverse genetic mutations assimilated in various SARS-CoV-2 variants. The implications of the acquired mutations related to viral transmission, infectivity, and COVID-19 severity are discussed. This review also addresses the effectiveness of human neutralizing antibodies induced by SARS-CoV-2 infection or immunization and the therapeutic antibodies against the ascended variants.
Collapse
Affiliation(s)
- Dima Hattab
- School of Pharmacy, The University of Jordan, Queen Rania Street, Amman, Jordan
| | - Mumen F A Amer
- Faculty of Pharmacy, Applied Science Private University, Amman, Jordan
| | - Zina M Al-Alami
- Department of Basic Medical Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Athirah Bakhtiar
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
| |
Collapse
|
13
|
Xue S, Han Y, Wu F, Wang Q. Mutations in the SARS-CoV-2 spike receptor binding domain and their delicate balance between ACE2 affinity and antibody evasion. Protein Cell 2024; 15:403-418. [PMID: 38442025 PMCID: PMC11131022 DOI: 10.1093/procel/pwae007] [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: 11/29/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
Intensive selection pressure constrains the evolutionary trajectory of SARS-CoV-2 genomes and results in various novel variants with distinct mutation profiles. Point mutations, particularly those within the receptor binding domain (RBD) of SARS-CoV-2 spike (S) protein, lead to the functional alteration in both receptor engagement and monoclonal antibody (mAb) recognition. Here, we review the data of the RBD point mutations possessed by major SARS-CoV-2 variants and discuss their individual effects on ACE2 affinity and immune evasion. Many single amino acid substitutions within RBD epitopes crucial for the antibody evasion capacity may conversely weaken ACE2 binding affinity. However, this weakened effect could be largely compensated by specific epistatic mutations, such as N501Y, thus maintaining the overall ACE2 affinity for the spike protein of all major variants. The predominant direction of SARS-CoV-2 evolution lies neither in promoting ACE2 affinity nor evading mAb neutralization but in maintaining a delicate balance between these two dimensions. Together, this review interprets how RBD mutations efficiently resist antibody neutralization and meanwhile how the affinity between ACE2 and spike protein is maintained, emphasizing the significance of comprehensive assessment of spike mutations.
Collapse
Affiliation(s)
- Song Xue
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yuru Han
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Fan Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| |
Collapse
|
14
|
Huang Y, Chen J, Chen S, Huang C, Li B, Li J, Jin Z, Zhang Q, Pan P, Du W, Liu L, Liu Z. Molecular characterization of SARS-CoV-2 nucleocapsid protein. Front Cell Infect Microbiol 2024; 14:1415885. [PMID: 38846351 PMCID: PMC11153676 DOI: 10.3389/fcimb.2024.1415885] [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: 04/11/2024] [Accepted: 05/07/2024] [Indexed: 06/09/2024] Open
Abstract
Corona Virus Disease 2019 (COVID-19) is a highly prevalent and potent infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Until now, the world is still endeavoring to develop new ways to diagnose and treat COVID-19. At present, the clinical prevention and treatment of COVID-19 mainly targets the spike protein on the surface of SRAS-CoV-2. However, with the continuous emergence of SARS-CoV-2 Variants of concern (VOC), targeting the spike protein therapy shows a high degree of limitation. The Nucleocapsid Protein (N protein) of SARS-CoV-2 is highly conserved in virus evolution and is involved in the key process of viral infection and assembly. It is the most expressed viral structural protein after SARS-CoV-2 infection in humans and has high immunogenicity. Therefore, N protein as the key factor of virus infection and replication in basic research and clinical application has great potential research value. This article reviews the research progress on the structure and biological function of SARS-CoV-2 N protein, the diagnosis and drug research of targeting N protein, in order to promote researchers' further understanding of SARS-CoV-2 N protein, and lay a theoretical foundation for the possible outbreak of new and sudden coronavirus infectious diseases in the future.
Collapse
Affiliation(s)
- Yanping Huang
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Junkai Chen
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Siwei Chen
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Congcong Huang
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Bei Li
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Jian Li
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Zhixiong Jin
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Qiwei Zhang
- Central Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Pan Pan
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Weixing Du
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Long Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Zhixin Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| |
Collapse
|
15
|
Liu C, Zhou D, Dijokaite-Guraliuc A, Supasa P, Duyvesteyn HME, Ginn HM, Selvaraj M, Mentzer AJ, Das R, de Silva TI, Ritter TG, Plowright M, Newman TAH, Stafford L, Kronsteiner B, Temperton N, Lui Y, Fellermeyer M, Goulder P, Klenerman P, Dunachie SJ, Barton MI, Kutuzov MA, Dushek O, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity. Cell Rep Med 2024; 5:101553. [PMID: 38723626 PMCID: PMC11148769 DOI: 10.1016/j.xcrm.2024.101553] [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] [Received: 10/06/2023] [Revised: 01/10/2024] [Accepted: 04/11/2024] [Indexed: 05/24/2024]
Abstract
BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible for many infections in 2023. The global spread and plethora of mutations in BA.2.86 has caused concern that it may possess greater immune-evasive potential, leading to a new wave of infection. Here, we examine the ability of BA.2.86 to evade the antibody response to infection using a panel of vaccinated or naturally infected sera and find that it shows marginally less immune evasion than XBB.1.5. We locate BA.2.86 in the antigenic landscape of recent variants and look at its ability to escape panels of potent monoclonal antibodies generated against contemporary SARS-CoV-2 infections. We demonstrate, and provide a structural explanation for, increased affinity of BA.2.86 to ACE2, which may increase transmissibility.
Collapse
Affiliation(s)
- Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daming Zhou
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
| | | | - Piyada Supasa
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
| | - Helen M Ginn
- Centre for Free Electron Laser Science, Hamburg, Germany
| | - Muneeswaran Selvaraj
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Raksha Das
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Thushan I de Silva
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Thomas G Ritter
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Megan Plowright
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | | | - Lizzie Stafford
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Barbara Kronsteiner
- NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and University of Greenwich Chatham Maritime, Kent ME4 4TB, UK
| | - Yuan Lui
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Martin Fellermeyer
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Paul Klenerman
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Michael I Barton
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mikhail A Kutuzov
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Omer Dushek
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK; Sir William Dunn School of Pathology, Oxford, UK.
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|
16
|
Mühlemann B, Wilks SH, Baracco L, Bekliz M, Carreño JM, Corman VM, Davis-Gardner ME, Dejnirattisai W, Diamond MS, Douek DC, Drosten C, Eckerle I, Edara VV, Ellis M, Fouchier RAM, Frieman M, Godbole S, Haagmans B, Halfmann PJ, Henry AR, Jones TC, Katzelnick LC, Kawaoka Y, Kimpel J, Krammer F, Lai L, Liu C, Lusvarghi S, Meyer B, Mongkolsapaya J, Montefiori DC, Mykytyn A, Netzl A, Pollett S, Rössler A, Screaton GR, Shen X, Sigal A, Simon V, Subramanian R, Supasa P, Suthar MS, Türeli S, Wang W, Weiss CD, Smith DJ. Comparative analysis of SARS-CoV-2 neutralization titers reveals consistency between human and animal model serum and across assays. Sci Transl Med 2024; 16:eadl1722. [PMID: 38748773 DOI: 10.1126/scitranslmed.adl1722] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 04/11/2024] [Indexed: 08/31/2024]
Abstract
The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires ongoing monitoring to judge the ability of newly arising variants to escape the immune response. A surveillance system necessitates an understanding of differences in neutralization titers measured in different assays and using human and animal serum samples. We compared 18 datasets generated using human, hamster, and mouse serum and six different neutralization assays. Datasets using animal model serum samples showed higher titer magnitudes than datasets using human serum samples in this comparison. Fold change in neutralization of variants compared to ancestral SARS-CoV-2, immunodominance patterns, and antigenic maps were similar among serum samples and assays. Most assays yielded consistent results, except for differences in fold change in cytopathic effect assays. Hamster serum samples were a consistent surrogate for human first-infection serum samples. These results inform the transition of surveillance of SARS-CoV-2 antigenic variation from dependence on human first-infection serum samples to the utilization of serum samples from animal models.
Collapse
Affiliation(s)
- Barbara Mühlemann
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Samuel H Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Lauren Baracco
- Center for Pathogen Research, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Meriem Bekliz
- Department of Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Centre for Emerging Viral Diseases, University Hospitals of Geneva and University of Geneva, CH-1211, Geneva, Switzerland
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Victor M Corman
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Meredith E Davis-Gardner
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok Noi, Bangkok 10700, Thailand
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Andrew M. and Jane M. Bursky the Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Isabella Eckerle
- Department of Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Centre for Emerging Viral Diseases, University Hospitals of Geneva and University of Geneva, CH-1211, Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, CH-1211 Geneva, Switzerland
| | - Venkata-Viswanadh Edara
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Madison Ellis
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Ron A M Fouchier
- Viroscience Department, Erasmus Medical Center, 3015 Rotterdam, Netherlands
| | - Matthew Frieman
- Center for Pathogen Research, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Sucheta Godbole
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bart Haagmans
- Viroscience Department, Erasmus Medical Center, 3015 Rotterdam, Netherlands
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Terry C Jones
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Leah C Katzelnick
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- 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
| | - Janine Kimpel
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lilin Lai
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7BN, UK
| | - Sabrina Lusvarghi
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Benjamin Meyer
- Centre of Vaccinology, Department of Pathology and Immunology, University of Geneva, CH-1211 Geneva, Switzerland
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7BN, UK
| | - David C Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Anna Mykytyn
- Viroscience Department, Erasmus Medical Center, 3015 Rotterdam, Netherlands
| | - Antonia Netzl
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Simon Pollett
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Annika Rössler
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Xiaoying Shen
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Alex Sigal
- Africa Health Research Institute, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban 4001, South Africa
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rahul Subramanian
- Office of Data Science and Emerging Technologies, Office of Science Management and Operations, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Mehul S Suthar
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Sina Türeli
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Wei Wang
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Carol D Weiss
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| |
Collapse
|
17
|
Yahalom-Ronen Y, Melamed S, Politi B, Erez N, Tamir H, Bar-On L, Ryvkin J, Leshkowitz D, Israeli O, Weiss S, Ben-Shmuel A, Barlev-Gross M, Cherry Mimran L, Achdout H, Paran N, Israely T. Induction of Superior Systemic and Mucosal Protective Immunity to SARS-CoV-2 by Nasal Administration of a VSV-ΔG-Spike Vaccine. Vaccines (Basel) 2024; 12:491. [PMID: 38793742 PMCID: PMC11125831 DOI: 10.3390/vaccines12050491] [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: 03/20/2024] [Revised: 04/21/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
The emergence of rapidly spreading variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) poses a major challenge to vaccines' protective efficacy. Intramuscular (IM) vaccine administration induces short-lived immunity but does not prevent infection and transmission. New vaccination strategies are needed to extend the longevity of vaccine protection, induce mucosal and systemic immunity and prevent viral transmission. The intranasal (IN) administration of the VSV-ΔG-spike vaccine candidate directly to mucosal surfaces yielded superior mucosal and systemic immunity at lower vaccine doses. Compared to IM vaccination in the K18-hACE2 model, IN vaccination preferentially induced mucosal IgA and T-cells, reduced the viral load at the site of infection, and ameliorated disease-associated brain gene expression. IN vaccination was protective even one year after administration. As most of the world population has been vaccinated by IM injection, we demonstrate the potential of a heterologous IM + IN vaccination regimen to induce mucosal immunity while maintaining systemic immunity. Furthermore, the IM + IN regimen prevented virus transmission in a golden Syrian hamster co-caging model. Taken together, we show that IN vaccination with VSV-ΔG-spike, either as a homologous IN + IN regimen or as a boost following IM vaccination, has a favorable potential over IM vaccination in inducing efficient mucosal immunity, long-term protection and preventing virus transmission.
Collapse
Affiliation(s)
- Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Sharon Melamed
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Boaz Politi
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Noam Erez
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Hadas Tamir
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Liat Bar-On
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (L.B.-O.); (O.I.)
| | - Julia Ryvkin
- Bioinformatics Unit, Life Science Core Facilities, Weizmann Institute of Science, Rehovot 52621, Israel; (J.R.); (D.L.)
| | - Dena Leshkowitz
- Bioinformatics Unit, Life Science Core Facilities, Weizmann Institute of Science, Rehovot 52621, Israel; (J.R.); (D.L.)
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (L.B.-O.); (O.I.)
| | - Shay Weiss
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Amir Ben-Shmuel
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Moria Barlev-Gross
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Lilach Cherry Mimran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Hagit Achdout
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Tomer Israely
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| |
Collapse
|
18
|
Nakayama T, Todaka R, Sawada A, Ito T, Fujino M, Haga K, Katayama K. Different immunological responses following immunization with two mRNA vaccines. J Infect Chemother 2024; 30:439-449. [PMID: 38000497 DOI: 10.1016/j.jiac.2023.11.020] [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] [Received: 08/07/2023] [Revised: 10/27/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
INTRODUCTION Immunological responses were investigated following immunization with two mRNA vaccines: BNT162b2 and mRNA-1273. METHODS Neutralizing antibody (NAb) was assayed before, 2-4 weeks after, and 3 and 6 months after the primary immunization, and the same time-points after booster dose with 6- or 8-months interval. Whole-blood culture was stimulated with spike antigen, and cytokine production was assayed. RESULTS NAb was detected after primary immunization, NAb titers began to decrease three months after primary immunization with BNT162b2, lower than those after mRNA-1273, and elevated after booster immunization. The NAb level was 1/2 lower against δ variant, and 1/16 lower against omicron variant in comparison with that against α variant. Cytokine production following immunization with mRNA-1273 was maintained within three months at higher levels of Th1 (TNF-α), Th2 (IL-4 and IL-5), and inflammatory cytokines (IL-6 and IL-17) than that following immunization with BNT162b2, reflecting prominent levels of NAb following immunization with mRNA-1273. Cytokine production decreased six months after primary immunization in both vaccine recipients and was enhanced following booster doses. During the omicron outbreak, medical staff members in the outpatient office experienced asymptomatic infection, with a greater than 4-fold increase in NAb titers against omicron variant even after booster immunization. Asymptomatic infection enhanced the production of Th2 and inflammatory cytokines. CONCLUSION mRNA-1273 induced stronger NAb responses with wide-range cross-reactive antibodies against δ and omicron variants. mRNA-1273 induced higher levels of Th1, Th2, and inflammatory cytokines than BNT162b2 did, reflecting higher levels of NAb against variant strains.
Collapse
Affiliation(s)
- Tetsuo Nakayama
- Laboratory of Viral Infection, Ömura Satoshi Memorial Institute, Tokyo, 108-8641, Japan.
| | - Reiko Todaka
- Laboratory of Viral Infection, Ömura Satoshi Memorial Institute, Tokyo, 108-8641, Japan.
| | - Akihito Sawada
- Laboratory of Viral Infection, Ömura Satoshi Memorial Institute, Tokyo, 108-8641, Japan.
| | - Takashi Ito
- Laboratory of Viral Infection, Ömura Satoshi Memorial Institute, Tokyo, 108-8641, Japan; Department of Pediatrics, Kitasato University Hospital, Sagamihara, Kanagawa, 252-0329, Japan.
| | - Motoko Fujino
- Department of Pediatrics, Saiseikai Central Hospital Tokyo, Tokyo, 108-0073, Japan.
| | - Kei Haga
- Laboratory of Viral Infection, Ömura Satoshi Memorial Institute, Tokyo, 108-8641, Japan.
| | - Kazuhiko Katayama
- Laboratory of Viral Infection, Ömura Satoshi Memorial Institute, Tokyo, 108-8641, Japan.
| |
Collapse
|
19
|
Liu C, Das R, Dijokaite-Guraliuc A, Zhou D, Mentzer AJ, Supasa P, Selvaraj M, Duyvesteyn HME, Ritter TG, Temperton N, Klenerman P, Dunachie SJ, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. Emerging variants develop total escape from potent monoclonal antibodies induced by BA.4/5 infection. Nat Commun 2024; 15:3284. [PMID: 38627386 PMCID: PMC11021415 DOI: 10.1038/s41467-024-47393-3] [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: 11/30/2023] [Accepted: 03/29/2024] [Indexed: 04/19/2024] Open
Abstract
The rapid evolution of SARS-CoV-2 is driven in part by a need to evade the antibody response in the face of high levels of immunity. Here, we isolate spike (S) binding monoclonal antibodies (mAbs) from vaccinees who suffered vaccine break-through infections with Omicron sub lineages BA.4 or BA.5. Twenty eight potent antibodies are isolated and characterised functionally, and in some cases structurally. Since the emergence of BA.4/5, SARS-CoV-2 has continued to accrue mutations in the S protein, to understand this we characterize neutralization of a large panel of variants and demonstrate a steady attrition of neutralization by the panel of BA.4/5 mAbs culminating in total loss of function with recent XBB.1.5.70 variants containing the so-called 'FLip' mutations at positions 455 and 456. Interestingly, activity of some mAbs is regained on the recently reported variant BA.2.86.
Collapse
Affiliation(s)
- Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Raksha Das
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Daming Zhou
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Alexander J Mentzer
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Piyada Supasa
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Muneeswaran Selvaraj
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Thomas G Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich Chatham Maritime, Kent, ME4 4TB, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Neil G Paterson
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK.
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK.
| |
Collapse
|
20
|
Lerdsamran H, Anusorntanawat R, Sangsiriwut K, Sawadpongpan S, Prasertsopon J, Thinpan N, Intalapaporn P, Techasuwanna R, Okada P, Puthavathana P. Higher correlation between neutralizing antibodies and surrogate neutralizing or binding antibodies in COVID-19 patients than vaccine recipients. PLoS One 2024; 19:e0298033. [PMID: 38626137 PMCID: PMC11020499 DOI: 10.1371/journal.pone.0298033] [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: 09/19/2023] [Accepted: 01/17/2024] [Indexed: 04/18/2024] Open
Abstract
This study determined the seropositive rates and levels of antibodies to severe acute respiratory syndrome coronavirus-2 in 50 patients and 108 vaccinees using microneutralization test (MNT), surrogate virus neutralization test (sVNT), chemiluminescent microparticle immunoassay (CMIA), and electrochemiluminescence immunoassay (ECLIA). MNT, as the reference method, employed living clade S and Delta viruses to measure neutralizing (NT) antibodies, while sVNT employed wild type strain and Delta receptor-binding domains (RBD) as the test antigens to measure sVNT antibodies. CMIA and ECLIA employed only one version of RBD to measure the binding antibodies. Our study performed S gene sequencing of the test virus to exclude undesired mutants that might lead to changes in antibody levels in MNT assay. We showed that spike protein amino acid sequences of our Delta virus contained 13 amino acid changes, with 3 related to the reduced neutralization. The MNT assay showed a significant reduction in seropositive rates and antibody levels in the patients' sera when the Delta variant replaced clade S as the test virus. In contrast, the seropositive rates determined by sVNT assay using wild type strain RBD and Delta RBD were non-significantly different, suggesting that sVNT assay could not identify the difference between the antigenicity of wild type RBD and Delta RBD. Furthermore, the correlation between the levels of NT and sVNT antibodies was moderate with the patients' sera but modest with the post-vaccination sera. The seropositive rates in the patients, as determined by CMIA or ECLIA, were not different from the MNT assay using clade S, but not Delta, as the test virus. In all analyses, the correlations between the antibody levels measured by MNT and the other 3 assays were modest to moderate, with the r-values of 0.3500-0.7882.
Collapse
Affiliation(s)
- Hatairat Lerdsamran
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Ratikorn Anusorntanawat
- Chaophraya Yommarat Hospital, Office of the Permanent Secretary, Ministry of Public Health, Suphanburi, Thailand
| | - Kantima Sangsiriwut
- Department of Preventive and Social Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Suteema Sawadpongpan
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Jarunee Prasertsopon
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Nattakarn Thinpan
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Poj Intalapaporn
- Department of Medical Services, Rajavithi Hospital, Ministry of Public Health, Bangkok, Thailand
| | - Ranida Techasuwanna
- Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Pilailuk Okada
- Department of Medical Science, Ministry of Public Health, Nonthaburi, Thailand
| | - Pilaipan Puthavathana
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| |
Collapse
|
21
|
Sarkar A, Ghosh TA, Bandyopadhyay B, Maiti S, Panja AS. Prediction of Prospective Mutational Landscape of SARS-CoV-2 Spike ssRNA and Evolutionary Basis of Its Host Interaction. Mol Biotechnol 2024:10.1007/s12033-024-01146-1. [PMID: 38619800 DOI: 10.1007/s12033-024-01146-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/14/2024] [Indexed: 04/16/2024]
Abstract
Booster doses are crucial against severe COVID-19, as rapid virus mutations and variant emergence prolong the pandemic crisis. The virus's quick evolution, short generation-time, and adaptive changes impact virulence and evolvability, helping predictions about variant of concerns' (VOCs') landscapes. Here, in this study, we used a new computational algorithm, to predict the mutational pattern in SARS-CoV-2 ssRNA, proteomics, structural identification, mutation stability, and functional correlation, as well as immune escape mechanisms. Interestingly, the sequence diversity of SARS Coronavirus-2 has demonstrated a predominance of G- > A and C- > U substitutions. The best validation statistics are explored here in seven homologous models of the expected mutant SARS-CoV-2 spike ssRNA and employed for hACE2 and IgG interactions. The interactome profile of SARS-CoV-2 spike with hACE2 and IgG revealed a strong correlation between phylogeny and divergence time. The systematic adaptation of SARS-CoV-2 spike ssRNA influences infectivity and immune escape. Data suggest higher propensity of Adenine rich sequence promotes MHC system avoidance, preferred by A-rich codons. Phylogenetic data revealed the evolution of SARS-CoV-2 lineages' epidemiology. Our findings may unveil processes governing the genesis of immune-resistant variants, prompting a critical reassessment of the coronavirus mutation rate and exploration of hypotheses beyond mechanical aspects.
Collapse
Affiliation(s)
- Aniket Sarkar
- Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Trijit Arka Ghosh
- Department of Computer Application, Burdwan Institute of Management and Computer Science, The University of Burdwan, Dewandighi, Burdwan, West Bengal, 713102, India
| | - Bidyut Bandyopadhyay
- Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Smarajit Maiti
- Department of Medical Laboratory Technology, Haldia Institute of Health Sciences, ICARE Complex, Haldia, West Bengal, 721657, India
| | - Anindya Sundar Panja
- Post Graduate Department of Biotechnology, Molecular Informatics Laboratory, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal, 721102, India.
| |
Collapse
|
22
|
Grigoryan L, Feng Y, Bellusci L, Lai L, Wali B, Ellis M, Yuan M, Arunachalam PS, Hu M, Kowli S, Gupta S, Maysel-Auslender S, Maecker HT, Samaha H, Rouphael N, Wilson IA, Moreno AC, Suthar MS, Khurana S, Pillet S, Charland N, Ward BJ, Pulendran B. AS03 adjuvant enhances the magnitude, persistence, and clonal breadth of memory B cell responses to a plant-based COVID-19 vaccine in humans. Sci Immunol 2024; 9:eadi8039. [PMID: 38579013 DOI: 10.1126/sciimmunol.adi8039] [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: 05/18/2023] [Accepted: 03/11/2024] [Indexed: 04/07/2024]
Abstract
Vaccine adjuvants increase the breadth of serum antibody responses, but whether this is due to the generation of antigen-specific B cell clones with distinct specificities or the maturation of memory B cell clones that produce broadly cross-reactive antibodies is unknown. Here, we longitudinally analyzed immune responses in healthy adults after two-dose vaccination with either a virus-like particle COVID-19 vaccine (CoVLP), CoVLP adjuvanted with AS03 (CoVLP+AS03), or a messenger RNA vaccination (mRNA-1273). CoVLP+AS03 enhanced the magnitude and durability of circulating antibodies and antigen-specific CD4+ T cell and memory B cell responses. Antigen-specific CD4+ T cells in the CoVLP+AS03 group at day 42 correlated with antigen-specific memory B cells at 6 months. CoVLP+AS03 induced memory B cell responses, which accumulated somatic hypermutations over 6 months, resulting in enhanced neutralization breadth of monoclonal antibodies. Furthermore, the fraction of broadly neutralizing antibodies encoded by memory B cells increased between day 42 and 6 months. These results indicate that AS03 enhances the antigenic breadth of B cell memory at the clonal level and induces progressive maturation of the B cell response.
Collapse
Affiliation(s)
- Lilit Grigoryan
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Yupeng Feng
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | | | - Lilin Lai
- Department of Pediatrics and Department of Microbiology and Immunology, Emory Vaccine Center, Emory National Primate Research Center, Emory School of Medicine, Atlanta, GA 30329, USA
| | - Bushra Wali
- Department of Pediatrics and Department of Microbiology and Immunology, Emory Vaccine Center, Emory National Primate Research Center, Emory School of Medicine, Atlanta, GA 30329, USA
| | - Madison Ellis
- Department of Pediatrics and Department of Microbiology and Immunology, Emory Vaccine Center, Emory National Primate Research Center, Emory School of Medicine, Atlanta, GA 30329, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mengyun Hu
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sangeeta Kowli
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sheena Gupta
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sofia Maysel-Auslender
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Holden T Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Hady Samaha
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nadine Rouphael
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
- Hope Clinic of Emory Vaccine Center, Emory University, Decatur, GA 30030, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alberto C Moreno
- Department of Medicine, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Mehul S Suthar
- Department of Pediatrics and Department of Microbiology and Immunology, Emory Vaccine Center, Emory National Primate Research Center, Emory School of Medicine, Atlanta, GA 30329, USA
| | | | - Stéphane Pillet
- Medicago Inc., Québec, QC G1V 3V9, Canada
- Research Institute of the McGill University Health Center, 1001 Decarie St., Montréal, QC H4A 3J1, Canada
| | | | - Brian J Ward
- Medicago Inc., Québec, QC G1V 3V9, Canada
- Research Institute of the McGill University Health Center, 1001 Decarie St., Montréal, QC H4A 3J1, Canada
| | - Bali Pulendran
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
23
|
Hernández-Bello J, Lorenzo-Leal AC, Muñoz-Valle JF, Morales-Núñez JJ, Díaz-Pérez SA, Hernández-Gutiérrez R, Bach H. Neutralizing antibody responses to the Delta variant of SARS-CoV-2 following vaccination with Ad5-nCoV (CanSino) in the Mexican population. PLoS One 2024; 19:e0299520. [PMID: 38573914 PMCID: PMC10994301 DOI: 10.1371/journal.pone.0299520] [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: 10/02/2023] [Accepted: 02/13/2024] [Indexed: 04/06/2024] Open
Abstract
During the COVID-19 pandemic, the Ad5-nCoV vaccine was applied to the Mexican population before the WHO approved it. In a transversal study, we compare the CanSino vaccine efficacy and a natural SARS-CoV-2 infection in eliciting neutralizing antibodies against the SARS-CoV-2 Delta variant in Guadalajara, Mexico. Participants between 30-60 years were included in the study and classified into three groups: 1) Natural immunity (unvaccinated), 2) Vaccine-induced immunity (vaccinated individuals without a COVID-19 history), and 3) Natural immunity + vaccine-induced immunity. These groups were matched by age and gender. We assessed the ability of individuals' serum to neutralize the Delta variant and compared the results of the different groups using a neutralization test followed by plaque-forming units. Results showed that 39% of individuals' serum with a history of COVID-19 (natural immunity, Group 1) could not neutralize the Delta variant, compared to 33% in vaccinated individuals without COVID-19 (vaccine immunity, Group 2). In contrast, only 7% of vaccinated individuals with a history of COVID-19 (natural + vaccine immunities) could not neutralize the Delta variant. We concluded that the effectiveness of the Ad5-nCoV vaccine to induce neutralizing antibodies against the Delta variant is comparable to that of natural infection (61% vs. 67%). However, in individuals with both forms of immunity (Group 3), it increased to 93%. Based on these results, despite the Ad5-nCoV vaccine originally being designed as a single-dose regimen, it could be recommended that even those who have recovered from COVID-19 should consider vaccination to boost their immunity against this variant.
Collapse
Affiliation(s)
- Jorge Hernández-Bello
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud Universidad de Guadalajara, Guadalajara, Mexico
| | - Ana C. Lorenzo-Leal
- Division of Infectious Diseases, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - José F. Muñoz-Valle
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud Universidad de Guadalajara, Guadalajara, Mexico
| | - José J. Morales-Núñez
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud Universidad de Guadalajara, Guadalajara, Mexico
| | - Saul A. Díaz-Pérez
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud Universidad de Guadalajara, Guadalajara, Mexico
| | | | - Horacio Bach
- Division of Infectious Diseases, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
24
|
Galeota E, Bevilacqua V, Gobbini A, Gruarin P, Bombaci M, Pesce E, Favalli A, Lombardi A, Vincenti F, Ongaro J, Fabbris T, Curti S, Martinovic M, Toccafondi M, Lorenzo M, Critelli A, Clemente F, Crosti M, Sarnicola ML, Martinelli M, La Sala L, Espadas A, Donnici L, Borghi MO, De Feo T, De Francesco R, Prati D, Meroni PL, Notarbartolo S, Geginat J, Gori A, Bandera A, Abrignani S, Grifantini R. Tracking the immune response profiles elicited by the BNT162b2 vaccine in COVID-19 unexperienced and experienced individuals. Clin Immunol 2024; 261:110164. [PMID: 38417765 DOI: 10.1016/j.clim.2024.110164] [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] [Received: 10/02/2023] [Revised: 02/13/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
Multiple vaccines have been approved to control COVID-19 pandemic, with Pfizer/BioNTech (BNT162b2) being widely used. We conducted a longitudinal analysis of the immune response elicited after three doses of the BNT162b2 vaccine in individuals who have previously experienced SARS-CoV-2 infection and in unexperienced ones. We conducted immunological analyses and single-cell transcriptomics of circulating T and B lymphocytes, combined to CITE-seq or LIBRA-seq, and VDJ-seq. We found that antibody levels against SARS-CoV-2 Spike, NTD and RBD from wild-type, delta and omicron VoCs show comparable dynamics in both vaccination groups, with a peak after the second dose, a decline after six months and a restoration after the booster dose. The antibody neutralization activity was maintained, with lower titers against the omicron variant. Spike-specific memory B cell response was sustained over the vaccination schedule. Clonal analysis revealed that Spike-specific B cells were polyclonal, with a partial clone conservation from natural infection to vaccination. Spike-specific T cell responses were oriented towards effector and effector memory phenotypes, with similar trends in unexperienced and experienced individuals. The CD8 T cell compartment showed a higher clonal expansion and persistence than CD4 T cells. The first two vaccinations doses tended to induce new clones rather than promoting expansion of pre-existing clones. However, we identified a fraction of Spike-specific CD8 T cell clones persisting from natural infection that were boosted by vaccination and clones specifically induced by vaccination. Collectively, our observations revealed a moderate effect of the second dose in enhancing the immune responses elicited after the first vaccination. Differently, we found that a third dose was necessary to restore comparable levels of neutralizing antibodies and Spike-specific T and B cell responses in individuals who experienced a natural SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Eugenia Galeota
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Valeria Bevilacqua
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Andrea Gobbini
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Paola Gruarin
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Mauro Bombaci
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Elisa Pesce
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy; Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Andrea Favalli
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy; Ph.D. Program in Translational and Molecular Medicine, Dottorato in Medicina Molecolare e Traslazionale (DIMET), University of Milan-Bicocca, Monza, Italy
| | - Andrea Lombardi
- Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan 20122, Italy; Centre for Multidisciplinary Research in Health Science (MACH), University of Milano, Milan 20122, Italy; Department of Pathophysiology and Transplantation, University of Milan, Milan 20122, Italy
| | - Francesca Vincenti
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Jessica Ongaro
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Tanya Fabbris
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Serena Curti
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Martina Martinovic
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Mirco Toccafondi
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Mariangela Lorenzo
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Angelica Critelli
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Francesca Clemente
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Mariacristina Crosti
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Maria Lucia Sarnicola
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | | | | | - Alejandro Espadas
- Laboratory of Transplant Immunology - North Italy Transplant program (NITp) - Foundation IRCCS Cà Granda Ospedale Maggiore Policlinico of Milan, Italy
| | - Lorena Donnici
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Maria Orietta Borghi
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy; IRCCS Istituto Auxologico Italiano, Immunorheumatology Research Laboratory, Milan, Italy
| | - Tullia De Feo
- Laboratory of Transplant Immunology - North Italy Transplant program (NITp) - Foundation IRCCS Cà Granda Ospedale Maggiore Policlinico of Milan, Italy
| | - Raffaele De Francesco
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy; Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Daniele Prati
- Department of Transfusion Medicine and Hematology, Foundation IRCCS Cà Granda Ospedale Maggiore Policlinico of Milan, Italy
| | - Pier Luigi Meroni
- IRCCS Istituto Auxologico Italiano, Immunorheumatology Research Laboratory, Milan, Italy
| | - Samuele Notarbartolo
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy; Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Jens Geginat
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy; Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Andrea Gori
- Centre for Multidisciplinary Research in Health Science (MACH), University of Milano, Milan 20122, Italy; Infectious Diseases Unit, Ospedale "Luigi Sacco", Milan, Italy
| | - Alessandra Bandera
- Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan 20122, Italy; Centre for Multidisciplinary Research in Health Science (MACH), University of Milano, Milan 20122, Italy; Department of Pathophysiology and Transplantation, University of Milan, Milan 20122, Italy
| | - Sergio Abrignani
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy; Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Renata Grifantini
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy; CheckmAb Srl, Milan, Italy.
| |
Collapse
|
25
|
Zhou D, Supasa P, Liu C, Dijokaite-Guraliuc A, Duyvesteyn HME, Selvaraj M, Mentzer AJ, Das R, Dejnirattisai W, Temperton N, Klenerman P, Dunachie SJ, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. The SARS-CoV-2 neutralizing antibody response to SD1 and its evasion by BA.2.86. Nat Commun 2024; 15:2734. [PMID: 38548763 PMCID: PMC10978878 DOI: 10.1038/s41467-024-46982-6] [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: 12/22/2023] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
Under pressure from neutralising antibodies induced by vaccination or infection the SARS-CoV-2 spike gene has become a hotspot for evolutionary change, leading to the failure of all mAbs developed for clinical use. Most potent antibodies bind to the receptor binding domain which has become heavily mutated. Here we study responses to a conserved epitope in sub-domain-1 (SD1) of spike which have become more prominent because of mutational escape from antibodies directed to the receptor binding domain. Some SD1 reactive mAbs show potent and broad neutralization of SARS-CoV-2 variants. We structurally map the dominant SD1 epitope and provide a mechanism of action by blocking interaction with ACE2. Mutations in SD1 have not been sustained to date, but one, E554K, leads to escape from mAbs. This mutation has now emerged in several sublineages including BA.2.86, reflecting selection pressure on the virus exerted by the increasing prominence of the anti-SD1 response.
Collapse
Affiliation(s)
- Daming Zhou
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Piyada Supasa
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
| | - Muneeswaran Selvaraj
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Raksha Das
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wanwisa Dejnirattisai
- Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-Noi, Bangkok, 10700, Thailand
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich Chatham Maritime, Kent, ME4 4TB, UK
| | - Paul Klenerman
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NDM Centre For Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|
26
|
Ordaya EE, Razonable RR. Emerging anti-spike monoclonal antibodies against SARS-CoV-2. Expert Opin Biol Ther 2024:1-11. [PMID: 38432691 DOI: 10.1080/14712598.2024.2326647] [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: 12/15/2023] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
Abstract
INTRODUCTION Anti-spike monoclonal antibodies (mAbs) were previously authorized for the prevention and treatment of COVID-19 in immunocompromised patients. However, they are no longer authorized in the U.S. due to their lack of neutralizing activity against current circulating SARS-CoV-2 Omicron variants. AREAS COVERED We summarized the available data on emergent mAbs in the early stages of clinical development. Consistent with data on prior mAbs, these novel agents have been well tolerated and demonstrated a good safety profile in early clinical trials. Additionally, many of them have been engineered to ensure prolonged half-life and combined with other mAbs to overcome the potential for emerging resistant mutants. Interestingly, one of these agents has been evaluated using an inhaled route of administration, and another agent is being evaluated for treatment of long COVID. EXPERT OPINION Although the available data of novel mAbs holds promise, we anticipate that these agents will face similar challenges encountered by prior authorized agents, including the continued evolution of SARS-CoV-2 and emergence of new escape mutations. Strategies to potentially mitigate this are discussed. Based on prior successful experience, immunocompromised patients will certainly benefit from the utilization of mAbs for the prevention and treatment of COVID-19; thus, we need to design potential interventions to ensure the sustained activity of these agents.
Collapse
Affiliation(s)
- Eloy E Ordaya
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, MN, USA
| | - Raymund R Razonable
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
27
|
Kumar S, Dasgupta S, Sajadi MM, Snyder GA, DeVico AL, Ray K. Discordant Antigenic Properties of Soluble and Virion SARS-CoV-2 Spike Proteins. Viruses 2024; 16:407. [PMID: 38543772 PMCID: PMC10974403 DOI: 10.3390/v16030407] [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: 01/19/2024] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 04/01/2024] Open
Abstract
Efforts to develop vaccine and immunotherapeutic countermeasures against the COVID-19 pandemic focus on targeting the trimeric spike (S) proteins of SARS-CoV-2. Vaccines and therapeutic design strategies must impart the characteristics of virion S from historical and emerging variants onto practical constructs such as soluble, stabilized trimers. The virus spike is a heterotrimer of two subunits: S1, which includes the receptor binding domain (RBD) that binds the cell surface receptor ACE2, and S2, which mediates membrane fusion. Previous studies suggest that the antigenic, structural, and functional characteristics of virion S may differ from current soluble surrogates. For example, it was reported that certain anti-glycan, HIV-1 neutralizing monoclonal antibodies bind soluble SARS-CoV-2 S but do not neutralize SARS-CoV-2 virions. In this study, we used single-molecule fluorescence correlation spectroscopy (FCS) under physiologically relevant conditions to examine the reactivity of broadly neutralizing and non-neutralizing anti-S human monoclonal antibodies (mAbs) isolated in 2020. Binding efficiency was assessed by FCS with soluble S trimers, pseudoviruses and inactivated wild-type virions representing variants emerging from 2020 to date. Anti-glycan mAbs were tested and compared. We find that both anti-S specific and anti-glycan mAbs exhibit variable but efficient binding to a range of stabilized, soluble trimers. Across mAbs, the efficiencies of soluble S binding were positively correlated with reactivity against inactivated virions but not pseudoviruses. Binding efficiencies with pseudoviruses were generally lower than with soluble S or inactivated virions. Among neutralizing mAbs, potency did not correlate with binding efficiencies on any target. No neutralizing activity was detected with anti-glycan antibodies. Notably, the virion S released from membranes by detergent treatment gained more efficient reactivity with anti-glycan, HIV-neutralizing antibodies but lost reactivity with all anti-S mAbs. Collectively, the FCS binding data suggest that virion surfaces present appreciable amounts of both functional and nonfunctional trimers, with neutralizing anti-S favoring the former structures and non-neutralizing anti-glycan mAbs binding the latter. S released from solubilized virions represents a nonfunctional structure bound by anti-glycan mAbs, while engineered soluble trimers present a composite structure that is broadly reactive with both mAb types. The detection of disparate antigenicity and immunoreactivity profiles in engineered and virion-associated S highlight the value of single-virus analyses in designing future antiviral strategies against SARS-CoV-2.
Collapse
Affiliation(s)
- Sameer Kumar
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Souradip Dasgupta
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Mohammad M. Sajadi
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Division of Clinical Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Greg A. Snyder
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Anthony L. DeVico
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Krishanu Ray
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| |
Collapse
|
28
|
Yu P, Ran J, Yang R, Zhu H, Lu S, Wu Y, Zhao T, Xiong T. Rapid isolation of pan-neutralizing antibodies against Omicron variants from convalescent individuals infected with SARS-CoV-2. Front Immunol 2024; 15:1374913. [PMID: 38510237 PMCID: PMC10950932 DOI: 10.3389/fimmu.2024.1374913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 02/22/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction The emergence of SARS-CoV-2 Omicron subvariants has presented a significant challenge to global health, as these variants show resistance to most antibodies developed early in the pandemic. Therapeutic antibodies with potent efficacy to the Omicron variants are urgently demanded. Methods Utilizing the rapid antibody discovery platform, Berkeley Lights Beacon, we isolated two monoclonal neutralizing antibodies, 2173-A6 and 3462-A4. These antibodies were isolated from individuals who recently recovered from Omicron infections. Results Both antibodies, 2173-A6 and 3462-A4, demonstrated high affinity for the RBD and effectively neutralized pseudoviruses from various Omicron lineages, including BA.4/5, XBB.1.16, XBB.1.5, and EG.5.1. This neutralization was achieved through binding to identical or overlapping epitopes. Discussion The use of the Beacon platform enabled the rapid isolation and identification of effective neutralizing antibodies within less than 10 days. This process significantly accelerates the development of novel therapeutic antibodies, potentially reducing the time required to respond to unknown infectious diseases in the future.
Collapse
Affiliation(s)
- Peng Yu
- Antibody Research Platform, Chongqing International Institute for Immunology, Chongqing, China
| | - Jingping Ran
- Antibody Research Platform, Chongqing International Institute for Immunology, Chongqing, China
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Ruiqi Yang
- Antibody Research Platform, Chongqing International Institute for Immunology, Chongqing, China
| | - Hang Zhu
- Antibody Research Platform, Chongqing International Institute for Immunology, Chongqing, China
| | - Song Lu
- Antibody Research Platform, Chongqing International Institute for Immunology, Chongqing, China
| | - Yuzhang Wu
- Antibody Research Platform, Chongqing International Institute for Immunology, Chongqing, China
| | - Tingting Zhao
- Antibody Research Platform, Chongqing International Institute for Immunology, Chongqing, China
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Tianchen Xiong
- Antibody Research Platform, Chongqing International Institute for Immunology, Chongqing, China
| |
Collapse
|
29
|
Park JS, Jeon J, Um J, Choi YY, Kim MK, Lee KS, Sung HK, Jang HC, Chin B, Kim CK, Oh MD, Lee CS. Magnitude and Duration of Serum Neutralizing Antibody Titers Induced by a Third mRNA COVID-19 Vaccination against Omicron BA.1 in Older Individuals. Infect Chemother 2024; 56:25-36. [PMID: 38014726 PMCID: PMC10990888 DOI: 10.3947/ic.2023.0057] [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: 05/26/2023] [Accepted: 08/21/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant (B.1.1.529) is dominating coronavirus disease 2019 (COVID-19) worldwide. The waning protective effect of available vaccines against the Omicron variant is a critical public health issue. This study aimed to assess the impact of the third COVID-19 vaccination on immunity against the SARS-CoV-2 Omicron BA.1 strain in older individuals. MATERIALS AND METHODS Adults aged ≥60 years who had completed two doses of the homologous COVID-19 vaccine with either BNT162b2 (Pfizer/BioNTech, New York, NY, USA, BNT) or ChAdOx1 nCoV (SK bioscience, Andong-si, Gyeongsangbuk-do, Korea, ChAd) were registered to receive the third vaccination. Participants chose either BNT or mRNA-1273 (Moderna, Norwood, MA, USA, m1273) mRNA vaccine for the third dose and were categorized into four groups: ChAd/ChAd/BNT, ChAd/ChAd/m1273, BNT/BNT/BNT, and BNT/BNT/m1273. Four serum specimens were obtained from each participant at 0, 4, 12, and 24 weeks after the third dose (V1, V2, V3, and V4, respectively). Serum-neutralizing antibody (NAb) activity against BetaCoV/Korea/KCDC03/2020 (NCCP43326, ancestral strain) and B.1.1.529 (NCCP43411, Omicron BA.1 variant) was measured using plaque reduction neutralization tests. A 50% neutralizing dilution (ND50) >10 was considered indicative of protective NAb titers. RESULTS In total, 186 participants were enrolled between November 24, 2021, and June 30, 2022. The respective groups received the third dose at a median (interquartile range [IQR]) of 132 (125 - 191), 123 (122 - 126), 186 (166 - 193), and 182 (175 - 198) days after the second dose. Overall, ND50 was lower at V1 against Omicron BA.1 than against the ancestral strain. NAb titers against the ancestral strain and Omicron BA.1 variant at V2 were increased at least 30-fold (median [IQR], 1235.35 [1021.45 - 2374.65)] and 129.8 [65.3 - 250.7], respectively). ND50 titers against the ancestral strain and Omicron variant did not differ significantly among the four groups (P = 0.57). NAb titers were significantly lower against the Omicron variant than against the ancestral strain at V3 (median [IQR], 36.4 (17.55 - 75.09) vs. 325.9 [276.07 - 686.97]; P = 0.012). NAb titers against Omicron at V4 were 16 times lower than that at V3. Most sera exhibited a protective level (ND50 >10) at V4 (75.0% [24/32], 73.0% [27/37], 73.3% [22/30], and 70.6% [12/17] in the ChAd/ChAd/BNT, ChAd/ChAd/m1273, BNT/BNT/BNT, and BNT/BNT/m1273 groups, respectively), with no significant differences among groups (P = 0.99). CONCLUSION A third COVID-19 mRNA vaccine dose restored waning NAb titers against Omicron BA.1. Our findings support a third-dose vaccination program to prevent the waning of humoral immunity to SARS-CoV-2.
Collapse
Affiliation(s)
- Jun-Sun Park
- Research Institute for Public Healthcare, National Medical Center, Seoul, Korea
| | - Jaehyun Jeon
- Department of Infectious Diseases, National Medical Center, Seoul, Korea
| | - Jihye Um
- Research Institute for Public Healthcare, National Medical Center, Seoul, Korea
| | - Youn Young Choi
- Department of Pediatrics, National Medical Center, Seoul, Korea
| | - Min-Kyung Kim
- Department of Infectious Diseases, National Medical Center, Seoul, Korea
| | - Kyung-Shin Lee
- Research Institute for Public Healthcare, National Medical Center, Seoul, Korea
| | - Ho Kyung Sung
- Research Institute for Public Healthcare, National Medical Center, Seoul, Korea
| | - Hee-Chang Jang
- National Institute of Infectious Diseases, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Korea
| | - BumSik Chin
- Department of Infectious Diseases, National Medical Center, Seoul, Korea
| | - Choon Kwan Kim
- Division of Infectious Diseases, VHS Medical Center, Seoul, Korea
| | - Myung-don Oh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Chang-Seop Lee
- Department of Internal Medicine, Jeonbuk National University Medical School, Jeonju, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| |
Collapse
|
30
|
Zhang Y, Sun J, Zheng J, Li S, Rao H, Dai J, Zhang Z, Wang Y, Liu D, Chen Z, Ran W, Zhu A, Li F, Yan Q, Wang Y, Yu K, Zhang S, Wang D, Tang Y, Liu B, Cheng L, Huo J, Perlman S, Zhao J, Zhao J. Mosaic RBD Nanoparticles Elicit Protective Immunity Against Multiple Human Coronaviruses in Animal Models. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2303366. [PMID: 38105421 PMCID: PMC10916629 DOI: 10.1002/advs.202303366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/27/2023] [Indexed: 12/19/2023]
Abstract
To combat SARS-CoV-2 variants and MERS-CoV, as well as the potential re-emergence of SARS-CoV and spillovers of sarbecoviruses, which pose a significant threat to global public health, vaccines that can confer broad-spectrum protection against betacoronaviruses (β-CoVs) are urgently needed. A mosaic ferritin nanoparticle vaccine is developed that co-displays the spike receptor-binding domains of SARS-CoV, MERS-CoV, and SARS-CoV-2 Wild-type (WT) strain and evaluated its immunogenicity and protective efficacy in mice and nonhuman primates. A low dose of 10 µg administered at a 21-day interval induced a Th1-biased immune response in mice and elicited robust cross-reactive neutralizing antibody responses against a variety of β-CoVs, including a series of SARS-CoV-2 variants. It is also able to effectively protect against challenges of SARS-CoV, MERS-CoV, and SARS-CoV-2 variants in not only young mice but also the more vulnerable mice through induction of long-lived immunity. Together, these results suggest that this mosaic 3-RBD nanoparticle has the potential to be developed as a pan-β-CoV vaccine.
Collapse
Affiliation(s)
- Yanjun Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
| | - Jian Zheng
- Department of Microbiology and ImmunologyUniversity of IowaIowa CityIA52242USA
| | - Suxiang Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
| | - Haiyue Rao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
| | - Jun Dai
- Guangzhou Customs District Technology CenterGuangzhou510700P. R. China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
| | - Donglan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
| | - Zhao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
| | - Wei Ran
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
| | - Fang Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
| | - Qihong Yan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
| | - Yiliang Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
| | - Kuai Yu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
| | - Shengnan Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
| | - Dong Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
| | - Yanhong Tang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
| | - Banghui Liu
- State Key Laboratory of Respiratory DiseaseGuangdong Laboratory of Computational BiomedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou510530P. R. China
| | - Linling Cheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
| | - Jiandong Huo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
- Guangzhou laboratoryBio‐islandGuangzhou510320P. R. China
| | - Stanley Perlman
- Department of Microbiology and ImmunologyUniversity of IowaIowa CityIA52242USA
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
- Guangzhou laboratoryBio‐islandGuangzhou510320P. R. China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510300P. R. China
- Guangzhou laboratoryBio‐islandGuangzhou510320P. R. China
- Institute of Infectious diseaseGuangzhou Eighth People's Hospital of Guangzhou Medical UniversityGuangzhou510060P. R. China
- Institute for HepatologyNational Clinical Research Center for Infectious DiseaseShenzhen Third People's Hospitalthe Second Affiliated HospitalSchool of MedicineSouthern University of Science and TechnologyShenzhen518112P. R. China
- Shanghai Institute for Advanced Immunochemical StudiesSchool of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| |
Collapse
|
31
|
Li L, Zhang J, Sun R, Liu H, Cheng G, Fan F, Wang C, Li A, Liang H, Yu Z, Wang G, Ren Z. Immune Dysregulation in SARS-CoV-2 patients coinfected with Mycobacterium tuberculosis (Mtb) or HIV in China. BMC Public Health 2024; 24:556. [PMID: 38388348 PMCID: PMC10882883 DOI: 10.1186/s12889-024-17905-3] [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: 08/25/2023] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND SARS-CoV-2 infections usually cause immune dysregulation in the human body. Studies of immunological changes resulting from coinfections with Mycobacterium tuberculosis (Mtb) or HIV are limited. METHODS We conducted a retrospective study focusing on patients with COVID-19. A total of 550 patients infected with SARS-CoV-2 were enrolled in our study and categorized into four groups based on the presence of coinfections; 166 Delta-infected patients, among whom 103 patients had no coinfections, 52 who were coinfected with Mtb, 11 who were coinfected with HIV, and 384 Omicron-infected patients. By collecting data on epidemiologic information, laboratory findings, treatments, and clinical outcomes, we analyzed and compared clinical and immunological characteristics. RESULTS Compared with those in the Delta group, the median white blood cell, CD4 + T-cell and B-cell counts were lower in the Mtb group and the HIV group. Except for those in the Omicron group, more than half of the patients in the three groups had abnormal chest CT findings. Among the three groups, there were no significant differences in any of the cytokines. Compared with those in the Delta group, the disease duration and LOS were longer in the Mtb group and the HIV group. For unvaccinated Delta-infected patients, in the Mtb and HIV groups, the number of B cells and CD4 + T cells was lower than that in the Delta group, with no significant difference in the LOS or disease duration. In the Mtb group, three (6%) patients presented with a disease duration greater than four months and had decreased lymphocyte and IL17A counts, possibly due to double infections in the lungs caused by SARS-CoV-2 and M. tuberculosis. CONCLUSIONS We found that SARS-CoV-2 patients coinfected with Mtb or HIV exhibited a longer disease duration and longer LOS, with a decrease in B cells and CD4 + T cells, suggesting that these cells are related to immune function. Changes in cytokine levels suggest that coinfection with Mtb or HIV does not result in dysregulation of the immune response. Importantly, we discovered a chronic course of coinfection involving more than four months of Mtb and SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Lei Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, 450052, Zhengzhou, China
- State Key Laboratory of Antiviral Drugs, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Precision Medicine Center, Gene Hospital of Henan Province, the First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Jianxiang Zhang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, 450052, Zhengzhou, China
- State Key Laboratory of Antiviral Drugs, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Precision Medicine Center, Gene Hospital of Henan Province, the First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Ranran Sun
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, 450052, Zhengzhou, China
- State Key Laboratory of Antiviral Drugs, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Precision Medicine Center, Gene Hospital of Henan Province, the First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Hong Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Genyang Cheng
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Feifei Fan
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Chong Wang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Ang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, 450052, Zhengzhou, China
- State Key Laboratory of Antiviral Drugs, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Precision Medicine Center, Gene Hospital of Henan Province, the First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Hongxia Liang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, 450052, Zhengzhou, China
- State Key Laboratory of Antiviral Drugs, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Precision Medicine Center, Gene Hospital of Henan Province, the First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Zujiang Yu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, 450052, Zhengzhou, China.
- State Key Laboratory of Antiviral Drugs, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
- Precision Medicine Center, Gene Hospital of Henan Province, the First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
| | - Guiqiang Wang
- Department of Infectious Diseases and the Center for Liver Diseases, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, 100034, Beijing, China.
| | - Zhigang Ren
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, 450052, Zhengzhou, China.
- State Key Laboratory of Antiviral Drugs, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
- Precision Medicine Center, Gene Hospital of Henan Province, the First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
| |
Collapse
|
32
|
Han H, Luo RH, Long XY, Wang LQ, Zhu Q, Tang XY, Zhu R, Ma YC, Zheng YT, Zou CG. Transcriptional regulation of SARS-CoV-2 receptor ACE2 by SP1. eLife 2024; 13:e85985. [PMID: 38375778 PMCID: PMC10878691 DOI: 10.7554/elife.85985] [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: 01/05/2023] [Accepted: 01/29/2024] [Indexed: 02/21/2024] Open
Abstract
Angiotensin-converting enzyme 2 (ACE2) is a major cell entry receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The induction of ACE2 expression may serve as a strategy by SARS-CoV-2 to facilitate its propagation. However, the regulatory mechanisms of ACE2 expression after viral infection remain largely unknown. Using 45 different luciferase reporters, the transcription factors SP1 and HNF4α were found to positively and negatively regulate ACE2 expression, respectively, at the transcriptional level in human lung epithelial cells (HPAEpiCs). SARS-CoV-2 infection increased the transcriptional activity of SP1 while inhibiting that of HNF4α. The PI3K/AKT signaling pathway, activated by SARS-CoV-2 infection, served as a crucial regulatory node, inducing ACE2 expression by enhancing SP1 phosphorylation-a marker of its activity-and reducing the nuclear localization of HNF4α. However, colchicine treatment inhibited the PI3K/AKT signaling pathway, thereby suppressing ACE2 expression. In Syrian hamsters (Mesocricetus auratus) infected with SARS-CoV-2, inhibition of SP1 by either mithramycin A or colchicine resulted in reduced viral replication and tissue injury. In summary, our study uncovers a novel function of SP1 in the regulation of ACE2 expression and identifies SP1 as a potential target to reduce SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Hui Han
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Rong-Hua Luo
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bio-Resources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xin-Yan Long
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bio-Resources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Li-Qiong Wang
- Department of Pathology, Yan'an Hospital, Kunming Medical University, Kunming, China
| | - Qian Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Xin-Yue Tang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Rui Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Yi-Cheng Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Yong-Tang Zheng
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bio-Resources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Cheng-Gang Zou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| |
Collapse
|
33
|
Ahmed N, Athavale A, Tripathi AH, Subramaniam A, Upadhyay SK, Pandey AK, Rai RC, Awasthi A. To be remembered: B cell memory response against SARS-CoV-2 and its variants in vaccinated and unvaccinated individuals. Scand J Immunol 2024; 99:e13345. [PMID: 38441373 DOI: 10.1111/sji.13345] [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] [Received: 06/01/2023] [Revised: 10/20/2023] [Accepted: 11/13/2023] [Indexed: 03/07/2024]
Abstract
COVID-19 disease has plagued the world economy and affected the overall well-being and life of most of the people. Natural infection as well as vaccination leads to the development of an immune response against the pathogen. This involves the production of antibodies, which can neutralize the virus during future challenges. In addition, the development of cellular immune memory with memory B and T cells provides long-lasting protection. The longevity of the immune response has been a subject of intensive research in this field. The extent of immunity conferred by different forms of vaccination or natural infections remained debatable for long. Hence, understanding the effectiveness of these responses among different groups of people can assist government organizations in making informed policy decisions. In this article, based on the publicly available data, we have reviewed the memory response generated by some of the vaccines against SARS-CoV-2 and its variants, particularly B cell memory in different groups of individuals.
Collapse
Affiliation(s)
- Nafees Ahmed
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Atharv Athavale
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Ankita H Tripathi
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Adarsh Subramaniam
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Santosh K Upadhyay
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | | | - Ramesh Chandra Rai
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| |
Collapse
|
34
|
Fauziah I, Nugroho HA, Yanthi ND, Tiffarent R, Saputra S. Potential zoonotic spillover at the human-animal interface: A mini-review. Vet World 2024; 17:289-302. [PMID: 38595670 PMCID: PMC11000462 DOI: 10.14202/vetworld.2024.289-302] [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: 10/02/2023] [Accepted: 01/09/2024] [Indexed: 04/11/2024] Open
Abstract
Wildlife markets and wet wildlife markets, a type of human-animal interface, are commonly trading centers for wild-caught and captive-exotic animals as well as their products. These markets provide an ideal environment for spillovers of zoonotic and emerging infectious diseases (EIDs). These conditions may raise serious concerns, particularly in relation to wildlife species that frequently interact with humans and domestic animals. EIDs pose a significant risk to humans, ecosystems, and public health, as demonstrated by the current COVID-19 pandemic, and other previous outbreaks, including the highly pathogenic avian influenza H5N1. Even though it seems appears impossible to eliminate EIDs, we may still be able to minimalize the risks and take several measures to prevent new EIDs originated from animals. The aim of this study was to review several types of human-animal interfaces with a high risk of zoonotic spillover, infectious agents, and animal hosts or reservoirs. Identifying those factors will support the development of interventions and effective disease control in human-animal interface settings.
Collapse
Affiliation(s)
- Ima Fauziah
- Research Center for Applied Microbiology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Jalan Raya Jakarta Bogor Km 46 Cibinong, Bogor, West Java, Indonesia
| | - Herjuno Ari Nugroho
- Research Center for Applied Microbiology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Jalan Raya Jakarta Bogor Km 46 Cibinong, Bogor, West Java, Indonesia
| | - Nova Dilla Yanthi
- Research Center for Applied Microbiology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Jalan Raya Jakarta Bogor Km 46 Cibinong, Bogor, West Java, Indonesia
| | - Rida Tiffarent
- Research Center for Applied Microbiology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Jalan Raya Jakarta Bogor Km 46 Cibinong, Bogor, West Java, Indonesia
| | - Sugiyono Saputra
- Research Center for Applied Microbiology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Jalan Raya Jakarta Bogor Km 46 Cibinong, Bogor, West Java, Indonesia
| |
Collapse
|
35
|
Banho CA, de Carvalho Marques B, Sacchetto L, Sepedro Lima AK, Pereira Parra MC, Jeronimo Lima AR, Ribeiro G, Jorge Martins A, dos Santos Barros CR, Carolina Elias M, Coccuzzo Sampaio S, Nanev Slavov S, Strazza Rodrigues E, Vieira Santos E, Tadeu Covas D, Kashima S, Augusto Brassaloti R, Petry B, Gaspar Clemente L, Lehmann Coutinho L, Akemi Assato P, da Silva da Costa FA, Souza-Neto JA, Maria Tommasini Grotto R, Daiana Poleti M, Cristina Chagas Lesbon J, Chicaroni Mattos E, Fukumasu H, Giovanetti M, Carlos Junior Alcantara L, Rahal P, Pessoa Araújo JF, Althouse BM, Vasilakis N, Lacerda Nogueira M. Dynamic clade transitions and the influence of vaccine rollout on the spatiotemporal circulation of SARS-CoV-2 variants in São Paulo, Brazil. RESEARCH SQUARE 2024:rs.3.rs-3788142. [PMID: 38343798 PMCID: PMC10854302 DOI: 10.21203/rs.3.rs-3788142/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Since 2021, the emergence of variants of concern (VOC) has led Brazil to experience record numbers of in COVID-19 cases and deaths. The expanded spread of the SARS-CoV-2 combined with a low vaccination rate has contributed to the emergence of new mutations that may enhance viral fitness, leading to the persistence of the disease. Due to limitations in the real-time genomic monitoring of new variants in some Brazilian states, we aimed to investigate whether genomic surveillance, coupled with epidemiological data and SARS-CoV-2 variants spatiotemporal spread in a smaller region, can reflect the pandemic progression at a national level. Our findings revealed three SARS-CoV-2 variant replacements from 2021 to early 2022, corresponding to the introduction and increase in the frequency of Gamma, Delta, and Omicron variants, as indicated by peaks of the Effective Reproductive Number (Reff). These distinct clade replacements triggered two waves of COVID-19 cases, influenced by the increasing vaccine uptake over time. Our results indicated that the effectiveness of vaccination in preventing new cases during the Delta and Omicron circulations was six and eleven times higher, respectively, than during the period when Gamma was predominant, and it was highly efficient in reducing the number of deaths. Furthermore, we demonstrated that genomic monitoring at a local level can reflect the national trends in the spread and evolution of SARS-CoV-2.
Collapse
Affiliation(s)
- Cecília Artico Banho
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Beatriz de Carvalho Marques
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Lívia Sacchetto
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Ana Karoline Sepedro Lima
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Maisa Carla Pereira Parra
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Alex Ranieri Jeronimo Lima
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Gabriela Ribeiro
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Antonio Jorge Martins
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | | | - Maria Carolina Elias
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Sandra Coccuzzo Sampaio
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Svetoslav Nanev Slavov
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Evandra Strazza Rodrigues
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Elaine Vieira Santos
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Dimas Tadeu Covas
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Simone Kashima
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | - Bruna Petry
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Luan Gaspar Clemente
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Luiz Lehmann Coutinho
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Patricia Akemi Assato
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Felipe Allan da Silva da Costa
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Jayme A. Souza-Neto
- São Paulo State University (UNESP), School of Agricultural Sciences, Botucatu, Brazil
| | - Rejane Maria Tommasini Grotto
- São Paulo State University (UNESP), School of Agricultural Sciences, Botucatu, Brazil
- Molecular Biology Laboratory, Applied Biotechnology Laboratory, Clinical Hospital of the Botucatu Medical School, Brazil
| | - Mirele Daiana Poleti
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Jessika Cristina Chagas Lesbon
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Elisangela Chicaroni Mattos
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Marta Giovanetti
- Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
- Climate Amplified Diseases And Epidemics (CLIMADE), Brazil, Americas
- Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, Italy
| | - Luiz Carlos Junior Alcantara
- Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
- Climate Amplified Diseases And Epidemics (CLIMADE), Brazil, Americas
| | - Paula Rahal
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista (Unesp), São José do Rio Preto, Brazil
| | - João Fernando Pessoa Araújo
- Instituto de Biotecnologia, Universidade Estadual Paulista (Unesp), Botucatu, Brazil
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, Brazil
| | - Benjamin M. Althouse
- Department of Biology, New Mexico State University, Las Cruces, NM
- Information School, University of Washington, Seattle, WA
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch; Galveston, Texas, United States of America
- Center for Vector-Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
- Department of Pathology, University of Texas Medical Branch; Galveston, Texas, United States of America
| |
Collapse
|
36
|
Panda L, Pradhan A, Subudhi E, Sahoo RK, Nanda B. Ag-loaded BiFeO 3/CuS heterostructured based composite: an efficient photocatalyst for removal of antibiotics and antibacterial activities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:5540-5554. [PMID: 38127232 DOI: 10.1007/s11356-023-31523-3] [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: 07/29/2023] [Accepted: 12/09/2023] [Indexed: 12/23/2023]
Abstract
The performance of advanced materials in environmental applications using green energy is the tremendous interest among researchers. The visible light responsive BiFeO3 (BFO), BiFeO3/CuS (BFOC), and Ag-loaded BiFeO3/CuS (Ag-BFOC) heterostructures have been synthesized by reflux method followed by hydrothermal and wetness impregnation method. These synthesized composites are well characterized through X-ray diffraction, UV diffuse reflectance spectroscopy, scanning electron microscope, and Fourier transfer infrared spectroscopy techniques. Compared with BFO and BFOC, Ag-BFOC exhibits the highest photocatalytic performance towards the degradation of antibiotics ciprofloxacin (76%) within 120-min time and also showed better antibacterial performance towards gram-negative (Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii) bacteria. Moreover, the novelty of the present work is the addition of CuS on the surface of BiFeO3 from heterojunction type II and facilitates the electron-hole channelization at the interfaces between BiFeO3 and CuS. Again, the loading of Ag on BiFeO3/CuS helps in shifting the absorption band towards the red end, is eligible to absorb more sunlight due to surface plasmon resonance effect, improves the separation efficiency of photo-generated charge carriers, and enhances the photocatalytic degradation of ciprofloxacin. The antibacterial property of Ag gives a best result towards antimicrobial activity. The prepared composites have proved their durability and stability by four successive cycles and prove the versatility of the composite.
Collapse
Affiliation(s)
- Lipsa Panda
- Department of Chemistry, Faculty of Engineering and Technology (ITER), Siksha 'O' Anusandhan (Deemed to Be) University, Bhubaneswar, 751030, Odisha, India
| | - Abanti Pradhan
- Department of Chemistry, Faculty of Engineering and Technology (ITER), Siksha 'O' Anusandhan (Deemed to Be) University, Bhubaneswar, 751030, Odisha, India
| | - Enketeswara Subudhi
- Department of Biotechnology, Center of Biotechnology, Siksha 'O' Anusandhan (Deemed to Be) University, Bhubaneswar, 751030, Odisha, India
| | - Rajesh Kumar Sahoo
- Department of Biotechnology, Center of Biotechnology, Siksha 'O' Anusandhan (Deemed to Be) University, Bhubaneswar, 751030, Odisha, India
| | - Binita Nanda
- Department of Chemistry, Faculty of Engineering and Technology (ITER), Siksha 'O' Anusandhan (Deemed to Be) University, Bhubaneswar, 751030, Odisha, India.
| |
Collapse
|
37
|
Alfaleh MA, Alsulaiman RM, Almahboub SA, Nezamuldeen L, Zawawi A, Aljehani ND, Yasir M, Abdulal RH, Alkhaldi R, Helal A, Alamri SS, Malki J, Alhabbab RY, Abujamel TS, Alhakamy NA, Alnami A, Algaissi A, Hassanain M, Hashem AM. ACE2-Fc and DPP4-Fc decoy receptors against SARS-CoV-2 and MERS-CoV variants: a quick therapeutic option for current and future coronaviruses outbreaks. Antib Ther 2024; 7:53-66. [PMID: 38371953 PMCID: PMC10873275 DOI: 10.1093/abt/tbad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 02/20/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and the Middle East respiratory syndrome coronavirus (MERS-CoV) are highly pathogenic human coronaviruses (CoVs). Anti-CoVs mAbs and vaccines may be effective, but the emergence of neutralization escape variants is inevitable. Angiotensin-converting enzyme 2 and dipeptidyl peptidase 4 enzyme are the getaway receptors for SARS-CoV-2 and MERS-CoV, respectively. Thus, we reformatted these receptors as Fc-fusion decoy receptors. Then, we tested them in parallel with anti-SARS-CoV (ab1-IgG) and anti-MERS-CoV (M336-IgG) mAbs against several variants using pseudovirus neutralization assay. The generated Fc-based decoy receptors exhibited a strong inhibitory effect against all pseudotyped CoVs. Results showed that although mAbs can be effective antiviral drugs, they might rapidly lose their efficacy against highly mutated viruses. We suggest that receptor traps can be engineered as Fc-fusion proteins for highly mutating viruses with known entry receptors, for a faster and effective therapeutic response even against virus harboring antibodies escape mutations.
Collapse
Affiliation(s)
- Mohamed A Alfaleh
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Reem M Alsulaiman
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Sarah A Almahboub
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Leena Nezamuldeen
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Ayat Zawawi
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Najwa D Aljehani
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Muhammad Yasir
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Rwaa H Abdulal
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Rami Alkhaldi
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Assala Helal
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Sawsan S Alamri
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Jana Malki
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Rowa Y Alhabbab
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Turki S Abujamel
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Nabil A Alhakamy
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Aisha Alnami
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Abdullah Algaissi
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Mazen Hassanain
- Department of Surgery, Faculty of Medicine, King Saud University, Riyadh 11451, Saudi Arabia
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| |
Collapse
|
38
|
Zhang H, Liu Y, Liu Z. Nanomedicine approaches against SARS-CoV-2 and variants. J Control Release 2024; 365:101-111. [PMID: 37951476 DOI: 10.1016/j.jconrel.2023.11.004] [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] [Received: 07/26/2023] [Revised: 10/27/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023]
Abstract
The world is grappling with the ongoing crisis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), a global pandemic that continues to have a detrimental impact on public health and economies worldwide. The virus's relentless mutation has led to more transmissible, immune-evasive strains, thereby escalating the incidence of reinfection. This underscores the urgent need for highly effective and safe countermeasures against SARS-CoV-2 and its evolving variants. In the current context, nanomedicine presents an innovative and promising alternative to mitigate the impacts of this pandemic wave. It does so by harnessing the structural and functional properties at a nanoscale in a straightforward and adaptable manner. This review emphasizes the most recent progress in the development of nanovaccines, nanodecoys, and nanodisinfectants to tackle SARS-CoV-2 and its variants. Notably, the insights gained and strategies implemented in managing the ongoing pandemic may also offer invaluable guidance for the development of potent nanomedicines to combat future pandemics.
Collapse
Affiliation(s)
- Han Zhang
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China.
| | - Yanbin Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Zhuang Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China.
| |
Collapse
|
39
|
Nahhas AF, Webster TJ. Applications of peptide-functionalized or unfunctionalized selenium nanoparticles for the passivation of SARS-CoV-2 variants and the respiratory syncytial virus (RSV). Colloids Surf B Biointerfaces 2024; 233:113638. [PMID: 37995630 DOI: 10.1016/j.colsurfb.2023.113638] [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] [Received: 06/22/2023] [Revised: 10/24/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023]
Abstract
The SARS-CoV-2 Omicron subvariants BA.4, BA. 5 and XBB are currently causing a COVID resurgence due to their increased spreading and infectivity. These latest subvariants have been shown to be somewhat resistant to the most common vaccines even with the third dose. Moreover, it has been well documented that when patients stop taking some commercial therapies (such as Paxlovid), COVID from these variants may return and may even be more contagious. Herein, we tested unfunctionalized and functionalized selenium (Se) nanoparticles with three novel peptides (NapFFTLUFLTUTEKKKK, NapFFMLUFLMUMEKKKK, and NapFFSAVLQSGFKKKK) previously shown by themselves to passivate the Omicron SARS-CoV-2 BA.4, BA.5 and XBB variants. Se is a natural element in our diet and is well known to boost the immune system, thus, providing a complementary approach to viral infections. NapFFMLUFLMUMEKKKK showed a stronger inhibition ability at 98 % for Omicron BA.4 % and 96 % for Omicron BA.5 after just 15 min in vitro. Two types of Se nanoparticles (those made chemically or biogenically by cells) were tested to passivate the new SARS-CoV-2 XBB variant. Results showed that the combination of any peptide and using either type of Se NP, the Omicron subvariant XBB was inhibited by 100 % after just 15 min in vitro. Interestingly, the use of Se NPs alone outperformed the peptides in terms of XBB passivation. Also, in order to determine a mechanism of action, functionalizing Se nanoparticles with the NapFFSAVLQSGFKKKK peptide showed a high binding ability toward the chemotrypsin-like cysteine protease (SARS CoV-2 3CLpro). Further, as a demonstration of their versatility, these functionalized peptides also passivated the Respiratory Syncytial Virus (RSV). NapFFTLUFLTUTEKKKK and NapFFMLUFLMUMEKKKK showed in silico interactions with the fusion glycoprotein of RSV prompting in vitro RSV pseudo virus testing. Compared to the conventionally precipitated synthetic Se nanoparticles, in vitro results showed that biogenic Se functionalized with the peptides enhanced the inhibition RSV to 100 % after just 15 min of incubation. NapFFTLUFLTUTEKKKK and NapFFMLUFLMUMEKKKK also showed no potential genotoxicity or carcinogenic effects. The peptides showed good gastro-intestinal (GI) tract absorption and bioavailability as predicted using the partition coefficient (QP logPo/w), and high-water solubility as detected by QPlogS. According to these promising results, functionalizing biogenic Se nanoparticles with these novel peptides should be further studied in vivo for the improved diagnosis, prevention, and treatment of SARS-CoV-2, RSV, and other respiratory virus infections.
Collapse
Affiliation(s)
- Alaa F Nahhas
- Biochemistry Department, College of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Thomas J Webster
- Program in Materials Science, UFPI, Teresina, Brazil; School of Engineering, Saveetha University, Chennai, India; School of Health Sciences and Biomedical Engineering, Hebei University of Technology, Tianjin, China
| |
Collapse
|
40
|
Holdenrieder S, Dos Santos Ferreira CE, Izopet J, Theel ES, Wieser A. Clinical and laboratory considerations: determining an antibody-based composite correlate of risk for reinfection with SARS-CoV-2 or severe COVID-19. Front Public Health 2023; 11:1290402. [PMID: 38222091 PMCID: PMC10788057 DOI: 10.3389/fpubh.2023.1290402] [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: 09/07/2023] [Accepted: 11/30/2023] [Indexed: 01/16/2024] Open
Abstract
Much of the global population now has some level of adaptive immunity to SARS-CoV-2 induced by exposure to the virus (natural infection), vaccination, or a combination of both (hybrid immunity). Key questions that subsequently arise relate to the duration and the level of protection an individual might expect based on their infection and vaccination history. A multi-component composite correlate of risk (CoR) could inform individuals and stakeholders about protection and aid decision making. This perspective evaluates the various elements that need to be accommodated in the development of an antibody-based composite CoR for reinfection with SARS-CoV-2 or development of severe COVID-19, including variation in exposure dose, transmission route, viral genetic variation, patient factors, and vaccination status. We provide an overview of antibody dynamics to aid exploration of the specifics of SARS-CoV-2 antibody testing. We further discuss anti-SARS-CoV-2 immunoassays, sample matrices, testing formats, frequency of sampling and the optimal time point for such sampling. While the development of a composite CoR is challenging, we provide our recommendations for each of these key areas and highlight areas that require further work to be undertaken.
Collapse
Affiliation(s)
- Stefan Holdenrieder
- Institute of Laboratory Medicine, German Heart Centre Munich, Technical University Munich, Munich, Germany
| | | | - Jacques Izopet
- Laboratory of Virology, Toulouse University Hospital and INFINITY Toulouse Institute for Infections and Inflammatory Diseases, INSERM UMR 1291 CNRS UMR 5051, University Toulouse III, Toulouse, France
| | - Elitza S. Theel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Centre for Infection Research (DZIF), Munich, Germany
- Faculty of Medicine, Max Von Pettenkofer Institute, LMU Munich, Munich, Germany
- Immunology, Infection and Pandemic Research, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Munich, Germany
| |
Collapse
|
41
|
Freitas MTDS, Sena LOC, Fukutani KF, dos Santos CA, Neto FDCB, Ribeiro JS, dos Reis ES, Balbino VDQ, de Sá Paiva Leitão S, de Aragão Batista MV, Lipscomb MW, de Moura TR. The increase in SARS-CoV-2 lineages during 2020-2022 in a state in the Brazilian Northeast is associated with a number of cases. Front Public Health 2023; 11:1222152. [PMID: 38186707 PMCID: PMC10771345 DOI: 10.3389/fpubh.2023.1222152] [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: 05/13/2023] [Accepted: 11/15/2023] [Indexed: 01/09/2024] Open
Abstract
SARS-CoV-2 has caused a high number of deaths in several countries. In Brazil, there were 37 million confirmed cases of COVID-19 and 700,000 deaths caused by the disease. The population size and heterogeneity of the Brazilian population should be considered in epidemiological surveillance due to the varied tropism of the virus. As such, municipalities and states must be factored in for their unique specificities, such as socioeconomic conditions and population distribution. Here, we investigate the spatiotemporal dispersion of emerging SARS-CoV-2 lineages and their dynamics in each microregion from Sergipe state, northeastern Brazil, in the first 3 years of the pandemic. We analyzed 586 genomes sequenced between March 2020 and November 2022 extracted from the GISAID database. Phylogenetic analyses were carried out for each data set to reconstruct evolutionary history. Finally, the existence of a correlation between the number of lineages and infection cases by SARS-CoV-2 was evaluated. Aracaju, the largest city in northeastern Brazil, had the highest number of samples sequenced. This represented 54.6% (320) of the genomes, and consequently, the largest number of lineages identified. Studies also analyzed the relationship between mean lineage distributions and mean monthly infections, daily cases, daily deaths, and hospitalizations of vaccinated and unvaccinated patients. For this, a correlation matrix was created. Results revealed that the increase in the average number of SARS-CoV-2 variants was related to the average number of SARS-CoV-2 cases in both unvaccinated and vaccinated individuals. Thus, our data indicate that it is necessary to maintain epidemiological surveillance, especially in capital cities, since they have a high rate of circulation of resident and non-resident inhabitants, which contributes to the dynamics of the virus.
Collapse
Affiliation(s)
- Moises Thiago de Souza Freitas
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Brazil
- Parasitic Biology Graduate Program, Federal University of Sergipe, São Cristóvão, Brazil
| | - Ludmila Oliveira Carvalho Sena
- Health Foundation Parreiras Horta, Central Laboratory of Public Health (LACEN/SE), Sergipe State Health Secretariat, Aracaju, Brazil
| | - Kiyoshi Ferreira Fukutani
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Cliomar Alves dos Santos
- Health Foundation Parreiras Horta, Central Laboratory of Public Health (LACEN/SE), Sergipe State Health Secretariat, Aracaju, Brazil
| | | | - Julienne Sousa Ribeiro
- Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão, Brazil
| | | | | | | | | | | | | |
Collapse
|
42
|
Lázaro‐Gorines R, Pérez P, Heras‐Murillo I, Adán‐Barrientos I, Albericio G, Astorgano D, Flores S, Luczkowiak J, Labiod N, Harwood SL, Segura‐Tudela A, Rubio‐Pérez L, Nugraha Y, Shang X, Li Y, Alfonso C, Adipietro KA, Abeyawardhane DL, Navarro R, Compte M, Yu W, MacKerell AD, Sanz L, Weber DJ, Blanco FJ, Esteban M, Pozharski E, Godoy‐Ruiz R, Muñoz IG, Delgado R, Sancho D, García‐Arriaza J, Álvarez‐Vallina L. Dendritic Cell-Mediated Cross-Priming by a Bispecific Neutralizing Antibody Boosts Cytotoxic T Cell Responses and Protects Mice against SARS-CoV-2. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304818. [PMID: 37863812 PMCID: PMC10700188 DOI: 10.1002/advs.202304818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/24/2023] [Indexed: 10/22/2023]
Abstract
Administration of neutralizing antibodies (nAbs) has proved to be effective by providing immediate protection against SARS-CoV-2. However, dual strategies combining virus neutralization and immune response stimulation to enhance specific cytotoxic T cell responses, such as dendritic cell (DC) cross-priming, represent a promising field but have not yet been explored. Here, a broadly nAb, TNT , are first generated by grafting an anti-RBD biparatopic tandem nanobody onto a trimerbody scaffold. Cryo-EM data show that the TNT structure allows simultaneous binding to all six RBD epitopes, demonstrating a high-avidity neutralizing interaction. Then, by C-terminal fusion of an anti-DNGR-1 scFv to TNT , the bispecific trimerbody TNT DNGR-1 is generated to target neutralized virions to type 1 conventional DCs (cDC1s) and promote T cell cross-priming. Therapeutic administration of TNT DNGR-1, but not TNT , protects K18-hACE2 mice from a lethal SARS-CoV-2 infection, boosting virus-specific humoral responses and CD8+ T cell responses. These results further strengthen the central role of interactions with immune cells in the virus-neutralizing antibody activity and demonstrate the therapeutic potential of the Fc-free strategy that can be used advantageously to provide both immediate and long-term protection against SARS-CoV-2 and other viral infections.
Collapse
|
43
|
Chen C, Wang X, Zhang Z. Humoral and cellular immunity against diverse SARS-CoV-2 variants. J Genet Genomics 2023; 50:934-947. [PMID: 37865193 DOI: 10.1016/j.jgg.2023.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/27/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023]
Abstract
Since the outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019, the virus has rapidly spread worldwide. This has led to an unprecedented global pandemic, marked by millions of COVID-19 cases and a significant number of fatalities. Over a relatively short period, several different vaccine platforms are developed and deployed for use globally to curb the pandemic. However, the genome of SARS-CoV-2 continuously undergoes mutation and/or recombination, resulting in the emergence of several variants of concern (VOC). These VOCs can elevate viral transmission and evade the neutralizing antibodies induced by vaccines, leading to reinfections. Understanding the impact of the SARS-CoV-2 genomic mutation on viral pathogenesis and immune escape is crucial for assessing the threat of new variants to public health. This review focuses on the emergence and pathogenesis of VOC, with particular emphasis on their evasion of neutralizing antibodies. Furthermore, the memory B cell, CD4+, and CD8+ T cell memory induced by different COVID-19 vaccines or infections are discussed, along with how these cells recognize VOC. This review summarizes the current knowledge on adaptive immunology regarding SARS-CoV-2 infection and vaccines. Such knowledge may also be applied to vaccine design for other pathogens.
Collapse
Affiliation(s)
- Changxu Chen
- Center for Infectious Disease Research, School of Life Science, Westlake University, Hangzhou, Zhejiang 310001, China
| | - Xin Wang
- Center for Infectious Disease Research, School of Life Science, Westlake University, Hangzhou, Zhejiang 310001, China
| | - Zeli Zhang
- Center for Infectious Disease Research, School of Life Science, Westlake University, Hangzhou, Zhejiang 310001, China.
| |
Collapse
|
44
|
O’Reilly S, Kenny G, Alrawahneh T, Francois N, Gu L, Angeliadis M, de Masson d’Autume V, Garcia Leon A, Feeney ER, Yousif O, Cotter A, de Barra E, Horgan M, Mallon PWG, Gautier V. Development of a novel medium throughput flow-cytometry based micro-neutralisation test for SARS-CoV-2 with applications in clinical vaccine trials and antibody screening. PLoS One 2023; 18:e0294262. [PMID: 38033116 PMCID: PMC10688860 DOI: 10.1371/journal.pone.0294262] [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: 11/16/2022] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Quantifying neutralising capacity of circulating SARS-COV-2 antibodies is critical in evaluating protective humoral immune responses generated post-infection/post-vaccination. Here we describe a novel medium-throughput flow cytometry-based micro-neutralisation test to evaluate Neutralising Antibody (NAb) responses against live SARS-CoV-2 Wild Type and Variants of Concern (VOC) in convalescent/vaccinated populations. Flow Cytometry-Based Micro-Neutralisation Test (Micro-NT) was performed in 96-well plates using clinical isolates WT-B, WT-B.1.177.18 and/or VOCs Beta and Omicron. Plasma samples (All Ireland Infectious Diseases (AIID) Cohort) were serially diluted (8 points, half-log) from 1:20 and pre-incubated with SARS-CoV-2 (1h, 37°C). Virus-plasma mixture were added onto Vero E6 or Vero E6/TMPRSS2 cells for 18h. Percentage infected cells was analysed by automated flow cytometry following trypsinisation, fixation and SARS-CoV-2 Nucleoprotein intracellular staining. Half-maximal Neutralisation Titres (NT50) were determined using non-linear regression. Our assay was compared to Plaque Reduction Neutralisation Test (PRNT) and validated against the First WHO International Standard for anti-SARS-CoV-2 immunoglobulin. Both Micro-NT and PRNT achieved comparable NT50 values. Further validation showed adequate correlation with PRNT using a panel of secondary standards of clinical convalescent and vaccinated plasma samples. We found the assay to be reproducible through measuring both repeatability and intermediate precision. Screening 190 convalescent samples and 11 COVID-19 naive controls (AIID cohort) we demonstrated that Micro-NT has broad dynamic range differentiating NT50s <1/20 to >1/5000. We could also characterise immune-escape VOC Beta and Omicron BA.5, achieving fold-reductions in neutralising capacity similar to those published. Our flow cytometry-based Micro-NT is a robust and reliable assay to quantify NAb titres, and has been selected as an endpoint in clinical trials.
Collapse
Affiliation(s)
- Sophie O’Reilly
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Grace Kenny
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
- Department of Infectious Diseases, St Vincent’s University Hospital, Elm Park, Dublin, Ireland
| | - Tamara Alrawahneh
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Nathan Francois
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Lili Gu
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Matthew Angeliadis
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Valentin de Masson d’Autume
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Alejandro Garcia Leon
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Eoin R. Feeney
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
- Department of Infectious Diseases, St Vincent’s University Hospital, Elm Park, Dublin, Ireland
| | - Obada Yousif
- Endocrinology Department, Wexford General Hospital, Carricklawn, Wexford, Ireland
| | - Aoife Cotter
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
- Department of Infectious Diseases, Mater Misericordiae University Hospital, Eccles St, Dublin, Ireland
| | - Eoghan de Barra
- Department of Infectious Diseases, Beaumont Hospital, Beaumont, Dublin, Ireland
- Department of International Health and Tropical Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Mary Horgan
- Department of Infectious Diseases, Cork University Hospital, Wilton, Cork, Ireland
| | - Patrick W. G. Mallon
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
- Department of Infectious Diseases, St Vincent’s University Hospital, Elm Park, Dublin, Ireland
| | - Virginie Gautier
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Belfield, Dublin 4, Ireland
| |
Collapse
|
45
|
Ismail NF, Rahman AE, Kulkarni D, Zhu F, Wang X, del Carmen Morales G, Srivastava A, Allen KE, Spinardi J, Kyaw MH, Nair H. Incidence and outcome of SARS-CoV-2 reinfection in the pre-Omicron era: A global systematic review and meta-analysis. J Glob Health 2023; 13:06051. [PMID: 37994839 PMCID: PMC10667793 DOI: 10.7189/jogh.13.06051] [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: 11/24/2023] Open
Abstract
Background With the emergence of new variants and sub-lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), reinfections can significantly impact herd immunity, vaccination policies, and decisions on other public health measures. We conducted a systematic review and meta-analysis to synthesise the global evidence on SARS-CoV-2 reinfections in the pre-Omicron era. Methods We searched five global databases (MEDLINE, Embase, CINAHL Plus, Global Health, WHO COVID-19) on 12 May 2022 and 28 July 2023 and three Chinese databases (CNKI, Wanfang, CQvip) on 16 October 2022 for articles reporting incidence and outcomes of SARS-CoV-2 reinfection before the period of Omicron (B.1.1.529) predominance. We assessed risk of bias using Joanna Briggs Institute critical appraisal tools and conducted meta-analyses with random effects models to estimate the proportion of SARS-CoV-2 reinfection among initially infected cases and hospitalisation and mortality proportions among reinfected ones. Results We identified 7593 studies and extracted data from 64 included ones representing 21 countries. The proportion of SARS-CoV-2 reinfection was 1.16% (95% confidence interval (CI) = 1.01-1.33) based on 11 639 247 initially infected cases, with ≥45 days between the two infections. Healthcare providers (2.28%; 95% CI = 1.37-3.40) had a significantly higher risk of reinfection than the general population (1.00%; 95% CI = 0.81-1.20), while young adults aged 18 to 35 years (1.01%; 95% CI = 0.8-1.25) had a higher reinfection burden than other age groups (children <18 years old: 0.57%; 95% CI = 0.39-0.79, older adults aged 36-65 years old: 0.53%; 95% CI = 0.41-0.65, elderly >65 years old: 0.37%; 95% CI = 0.15-0.66). Among the reinfected cases, 8.12% (95% CI = 5.30-11.39) were hospitalised, 1.31% (95% CI = 0.29-2.83) were admitted to the intensive care unit, and 0.71% (95% CI = 0.02-2.01) died. Conclusions Our data suggest a relatively low risk of SARS-CoV-2 reinfection in the pre-Omicron era, but the risk of hospitalisation was relatively high among the reinfected cases. Considering the possibility of underdiagnosis, the reinfection burden may be underestimated. Registration PROSPERO: CRD42023449712.
Collapse
Affiliation(s)
- Nabihah Farhana Ismail
- Centre for Global Health, University of Edinburgh, Edinburgh, United Kingdom
- Communicable Disease Control Unit, Public Health Department, Johor State, Malaysia
| | - Ahmed Ehsanur Rahman
- Centre for Global Health, University of Edinburgh, Edinburgh, United Kingdom
- International Centre for Diarrhoeal Diseases Research, Bangladesh
| | - Durga Kulkarni
- Centre for Global Health, University of Edinburgh, Edinburgh, United Kingdom
| | - Fuyu Zhu
- School of Public Health, Nanjing Medical University, Jiangsu, China
| | - Xin Wang
- Centre for Global Health, University of Edinburgh, Edinburgh, United Kingdom
- School of Public Health, Nanjing Medical University, Jiangsu, China
| | | | - Amit Srivastava
- Pfizer, Vaccines, Emerging Markets
- Orbital Therapeutics, United States of America
| | | | | | | | - Harish Nair
- Centre for Global Health, University of Edinburgh, Edinburgh, United Kingdom
- School of Public Health, Nanjing Medical University, Jiangsu, China
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
46
|
Pezzotti G, Ohgitani E, Fujita Y, Imamura H, Pappone F, Grillo A, Nakashio M, Shin-Ya M, Adachi T, Yamamoto T, Kanamura N, Marin E, Zhu W, Inaba T, Tanino Y, Nukui Y, Higasa K, Yasukochi Y, Okuma K, Mazda O. Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions. ACS Infect Dis 2023; 9:2226-2251. [PMID: 37850869 PMCID: PMC10644350 DOI: 10.1021/acsinfecdis.3c00312] [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: 07/03/2023] [Indexed: 10/19/2023]
Abstract
The latest RNA genomic mutation of SARS-CoV-2 virus, termed the Omicron variant, has generated a stream of highly contagious and antibody-resistant strains, which in turn led to classifying Omicron as a variant of concern. We systematically collected Raman spectra from six Omicron subvariants available in Japan (i.e., BA.1.18, BA.2, BA.4, BA.5, XE, and BA.2.75) and applied machine-learning algorithms to decrypt their structural characteristics at the molecular scale. Unique Raman fingerprints of sulfur-containing amino acid rotamers, RNA purines and pyrimidines, tyrosine phenol ring configurations, and secondary protein structures clearly differentiated the six Omicron subvariants. These spectral characteristics, which were linked to infectiousness, transmissibility, and propensity for immune evasion, revealed evolutionary motifs to be compared with the outputs of genomic studies. The availability of a Raman "metabolomic snapshot", which was then translated into a barcode to enable a prompt subvariant identification, opened the way to rationalize in real-time SARS-CoV-2 activity and variability. As a proof of concept, we applied the Raman barcode procedure to a nasal swab sample retrieved from a SARS-CoV-2 patient and identified its Omicron subvariant by coupling a commercially available magnetic bead technology with our newly developed Raman analyses.
Collapse
Affiliation(s)
- Giuseppe Pezzotti
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
- Department
of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shinmachi, Hirakata, Osaka 573-1010, Japan
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
- Department
of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, 160-0023 Tokyo, Japan
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
- Department
of Molecular Science and Nanosystems, Ca’
Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
- Department
of Applied Science and Technology, Politecnico
di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Eriko Ohgitani
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Yuki Fujita
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Hayata Imamura
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Francesco Pappone
- Department
of Mathematical Science, Politecnico di
Torino, Corso Duca degli
Abruzzi 24, 10129 Torino, Italy
| | - Alfio Grillo
- Department
of Mathematical Science, Politecnico di
Torino, Corso Duca degli
Abruzzi 24, 10129 Torino, Italy
| | - Maiko Nakashio
- Department
of Infection Control & Laboratory Medicine, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Masaharu Shin-Ya
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Tetsuya Adachi
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
- Department
of Microbiology, Kansai Medical University,
School of Medicine, 2-5-1
Shinmachi, Hirakata 573-1010, Osaka Prefecture, Japan
| | - Toshiro Yamamoto
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Narisato Kanamura
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Elia Marin
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Wenliang Zhu
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Tohru Inaba
- Department
of Infection Control & Laboratory Medicine, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Yoko Tanino
- Department of Clinical Laboratory, University
Hospital, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Yoko Nukui
- Department of Clinical Laboratory, University
Hospital, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Koichiro Higasa
- Genome Analysis, Institute of Biomedical
Science, Kansai Medical University, 2-3-1 Shin-machi, Hirakata, Osaka 573-1191, Japan
| | - Yoshiki Yasukochi
- Genome Analysis, Institute of Biomedical
Science, Kansai Medical University, 2-3-1 Shin-machi, Hirakata, Osaka 573-1191, Japan
| | - Kazu Okuma
- Department
of Microbiology, Kansai Medical University,
School of Medicine, 2-5-1
Shinmachi, Hirakata 573-1010, Osaka Prefecture, Japan
| | - Osam Mazda
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| |
Collapse
|
47
|
Meijers M, Ruchnewitz D, Eberhardt J, Łuksza M, Lässig M. Population immunity predicts evolutionary trajectories of SARS-CoV-2. Cell 2023; 186:5151-5164.e13. [PMID: 37875109 PMCID: PMC10964984 DOI: 10.1016/j.cell.2023.09.022] [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: 12/02/2022] [Revised: 08/26/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023]
Abstract
The large-scale evolution of the SARS-CoV-2 virus has been marked by rapid turnover of genetic clades. New variants show intrinsic changes, notably increased transmissibility, and antigenic changes that reduce cross-immunity induced by previous infections or vaccinations. How this functional variation shapes global evolution has remained unclear. Here, we establish a predictive fitness model for SARS-CoV-2 that integrates antigenic and intrinsic selection. The model is informed by tracking of time-resolved sequence data, epidemiological records, and cross-neutralization data of viral variants. Our inference shows that immune pressure, including contributions of vaccinations and previous infections, has become the dominant force driving the recent evolution of SARS-CoV-2. The fitness model can serve continued surveillance in two ways. First, it successfully predicts the short-term evolution of circulating strains and flags emerging variants likely to displace the previously predominant variant. Second, it predicts likely antigenic profiles of successful escape variants prior to their emergence.
Collapse
Affiliation(s)
- Matthijs Meijers
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany
| | - Denis Ruchnewitz
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany
| | - Jan Eberhardt
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany
| | - Marta Łuksza
- Tisch Cancer Institute, Departments of Oncological Sciences and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany.
| |
Collapse
|
48
|
Fernández-González M, Agulló V, García JA, Padilla S, García-Abellán J, de la Rica A, Mascarell P, Masiá M, Gutiérrez F. T-Cell Immunity Against Severe Acute Respiratory Syndrome Coronavirus 2 Measured by an Interferon-γ Release Assay Is Strongly Associated With Patient Outcomes in Vaccinated Persons Hospitalized With Delta or Omicron Variants. J Infect Dis 2023; 228:1240-1252. [PMID: 37418551 DOI: 10.1093/infdis/jiad260] [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] [Received: 03/30/2023] [Revised: 06/08/2023] [Accepted: 07/06/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND We measured T-cell and antibody responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vaccinated patients hospitalized for coronavirus disease 2019 (COVID-19) and explored their potential value to predict outcomes. METHODS This was a prospective, longitudinal study including vaccinated patients hospitalized with Delta and Omicron SARS-CoV-2 variants. TrimericS-IgG antibodies and SARS-CoV-2 T-cell response were measured using a specific quantitative interferon-γ release assay (IGRA). Primary outcome was all-cause 28-day mortality or need for intensive care unit (ICU) admission. Cox models were used to assess associations with outcomes. RESULTS Of 181 individuals, 158 (87.3%) had detectable SARS-CoV-2 antibodies, 92 (50.8%) showed SARS-CoV-2-specific T-cell responses, and 87 (48.1%) had both responses. Patients who died within 28 days or were admitted to ICU were less likely to have both unspecific and specific T-cell responses in IGRA. In adjusted analyses (adjusted hazard ratio [95% confidence interval]), for the entire cohort, having both T-cell and antibody responses at admission (0.16 [.05-.58]) and Omicron variant (0.38 [.17-.87]) reduced the hazard of 28-day mortality or ICU admission, whereas higher Charlson comorbidity index score (1.27 [1.07-1.51]) and lower oxygen saturation to fraction of inspired oxygen ratio (2.36 [1.51-3.67]) increased the risk. CONCLUSIONS Preexisting immunity against SARS-CoV-2 is strongly associated with patient outcomes in vaccinated individuals requiring hospital admission for COVID-19. Persons showing both T-cell and antibody responses have the lowest risk of severe outcomes.
Collapse
Affiliation(s)
- Marta Fernández-González
- Infectious Diseases Unit, Hospital General Universitario de Elche, Elche
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid
| | - Vanesa Agulló
- Infectious Diseases Unit, Hospital General Universitario de Elche, Elche
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid
| | - José Alberto García
- Infectious Diseases Unit, Hospital General Universitario de Elche, Elche
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid
| | - Sergio Padilla
- Infectious Diseases Unit, Hospital General Universitario de Elche, Elche
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid
- Clinical Medicine Department, Universidad Miguel Hernández, San Juan de Alicante
| | - Javier García-Abellán
- Infectious Diseases Unit, Hospital General Universitario de Elche, Elche
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid
- Clinical Medicine Department, Universidad Miguel Hernández, San Juan de Alicante
| | - Alba de la Rica
- Infectious Diseases Unit, Hospital General Universitario de Elche, Elche
- Microbiology Service, Hospital General Universitario de Elche, Elche, Spain
| | - Paula Mascarell
- Infectious Diseases Unit, Hospital General Universitario de Elche, Elche
| | - Mar Masiá
- Infectious Diseases Unit, Hospital General Universitario de Elche, Elche
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid
- Clinical Medicine Department, Universidad Miguel Hernández, San Juan de Alicante
| | - Félix Gutiérrez
- Infectious Diseases Unit, Hospital General Universitario de Elche, Elche
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid
- Clinical Medicine Department, Universidad Miguel Hernández, San Juan de Alicante
| |
Collapse
|
49
|
Tan CW, Zhu F, Chia WN, Young BE, Yeoh AYY, Althaus T, Yung CF, Yap WC, Lim BL, Chen MIC, Zhang J, Mah YY, Voiglio E, Sigal A, Huo J, Xu S, Tan YJ, Lam KP, Lye D, Wang LF. Distinctive serotypes of SARS-related coronaviruses defined by convalescent sera from unvaccinated individuals. HLIFE 2023; 1:26-34. [PMID: 38994526 PMCID: PMC11238253 DOI: 10.1016/j.hlife.2023.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Multiple Omicron sub-lineages have emerged, with Omicron XBB and XBB.1.5 subvariants becoming the dominant variants globally at the time of this study. The key feature of new variants is their ability to escape humoral immunity despite the fact that there are limited genetic changes from their preceding variants. This raises the question of whether Omicron should be regarded as a separate serotype from viruses serologically clustered with the ancestral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Here, we present cross-neutralization data based on a pseudovirus neutralization test using convalescent sera from naïve individuals who had recovered from primary infection by SARS-CoV-1 and SARS-CoV-2 strains/variants including the ancestral virus and variants Beta, Delta, Omicron BA.1, Omicron BA.2 and Omicron BA.5. The results revealed no significant cross-neutralization in any of the three-way testing for SARS-CoV-1, ancestral SARS-CoV-2 and SARS-CoV-2 Omicron subvariants. The data argue for the assignment of three distinct serotypes for the currently known human-infecting SARS-related coronaviruses.
Collapse
Affiliation(s)
- Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Barnaby E. Young
- National Center of Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technology University, Singapore
| | | | - Thomas Althaus
- Centre Scientifique de Monaco, Monaco
- Direction de I’Action Sanitaire de Monaco, Monaco
| | - Chee Fu Yung
- Lee Kong Chian School of Medicine, Nanyang Technology University, Singapore
- Infectious Disease Service, Department of Pediatrics, KK Women’s and Children’s Hospital, Singapore
- Duke-NUS Medical School, Singapore
| | - Wee Chee Yap
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Beng Lee Lim
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Mark I-C Chen
- National Center of Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
| | - Jinyan Zhang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yun Yan Mah
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Eric Voiglio
- Direction de I’Action Sanitaire de Monaco, Monaco
| | - Alex Sigal
- African Health Research Institute, Durban, South Africa
| | - Jianxin Huo
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Shengli Xu
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yee Joo Tan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Infectious Diseases Translational Research Programme, National University of Singapore, Singapore
| | - Kong-Peng Lam
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - David Lye
- National Center of Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technology University, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Singhealth Duke-NUS Global Health Institute, Singapore
| |
Collapse
|
50
|
Pitsillou E, Yu Y, Beh RC, Liang JJ, Hung A, Karagiannis TC. Chronicling the 3-year evolution of the COVID-19 pandemic: analysis of disease management, characteristics of major variants, and impacts on pathogenicity. Clin Exp Med 2023; 23:3277-3298. [PMID: 37615803 DOI: 10.1007/s10238-023-01168-0] [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] [Received: 04/24/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023]
Abstract
Announced on December 31, 2019, the novel coronavirus arising in Wuhan City, Hubei Province resulted in millions of cases and lives lost. Following intense tracking, coronavirus disease 2019 (COVID-19) was declared a pandemic by the World Health Organization (WHO) in 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the cause of COVID-19 and the continuous evolution of the virus has given rise to several variants. In this review, a comprehensive analysis of the response to the pandemic over the first three-year period is provided, focusing on disease management, development of vaccines and therapeutics, and identification of variants. The transmissibility and pathogenicity of SARS-CoV-2 variants including Alpha, Beta, Gamma, Delta, and Omicron are compared. The binding characteristics of the SARS-CoV-2 spike protein to the angiotensin-converting enzyme 2 (ACE2) receptor and reproduction numbers are evaluated. The effects of major variants on disease severity, hospitalisation, and case-fatality rates are outlined. In addition to the spike protein, open reading frames mutations are investigated. We also compare the pathogenicity of SARS-CoV-2 with SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Overall, this study highlights the strengths and weaknesses of the global response to the pandemic, as well as the importance of prevention and preparedness. Monitoring the evolution of SARS-CoV-2 is critical in identifying and potentially predicting the health outcomes of concerning variants as they emerge. The ultimate goal would be a position in which existing vaccines and therapeutics could be adapted to suit new variants in as close to real-time as possible.
Collapse
Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Yiping Yu
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Raymond C Beh
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Julia J Liang
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia.
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| |
Collapse
|