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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.
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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
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2
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Bellusci L, Grubbs G, Sait S, Herbst KW, Salazar JC, Khurana S. Evolution of the Antigenic Landscape in Children and Young Adults with COVID-19 and MIS-C. Vaccines (Basel) 2024; 12:638. [PMID: 38932367 PMCID: PMC11209438 DOI: 10.3390/vaccines12060638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
There is minimal knowledge regarding the durability of neutralization capacity and level of binding antibody generated against the highly transmissible circulating Omicron subvariants following SARS-CoV-2 infection in children with acute COVID-19 and those diagnosed with multisystem inflammatory syndrome in children (MIS-C) in the absence of vaccination. In this study, SARS-CoV-2 neutralization titers against the ancestral strain (WA1) and Omicron sublineages were evaluated in unvaccinated children admitted for COVID-19 (n = 32) and MIS-C (n = 32) at the time of hospitalization (baseline) and at six to eight weeks post-discharge (follow-up) between 1 April 2020, and 1 September 2022. In addition, antibody binding to the spike receptor binding domain (RBD) from WA1, BA.1, BA.2.75, and BA.4/BA.5 was determined using surface plasmon resonance (SPR). At baseline, the children with MIS-C demonstrated two-fold to three-fold higher binding and neutralizing antibodies against ancestral WA1 compared to those with COVID-19. Importantly, in children with COVID-19, the virus neutralization titers against the Omicron subvariants at six to eight weeks post-discharge reached the same level as those with MIS-C had at baseline but were higher than titers at 6-8 weeks post-discharge for MIS-C cases. Cross-neutralization capacity against recently emerged Omicron BQ.1, BQ.1.1, and XBB.1 variants was very low in children with either COVID-19 or MIS-C at all time points. These findings about post-infection immunity in children with either COVID-19 or MIS-C suggest the need for vaccinations in children with prior COVID-19 or MIS-C to provide effective protection from emerging and circulating SARS-CoV-2 variants.
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Affiliation(s)
- Lorenza Bellusci
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD 20871, USA
| | - Gabrielle Grubbs
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD 20871, USA
| | - Shaimaa Sait
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD 20871, USA
| | - Katherine W. Herbst
- Division of Pediatric Infectious Diseases, Connecticut Children’s, Hartford, CT 06106, USA; (K.W.H.); (J.C.S.)
| | - Juan C. Salazar
- Division of Pediatric Infectious Diseases, Connecticut Children’s, Hartford, CT 06106, USA; (K.W.H.); (J.C.S.)
- Departments of Pediatrics and Immunology, School of Medicine, University of Connecticut, Farmington, CT 06030, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD 20871, USA
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Schulte B, Richter E, Büning A, Baum M, Breuer A, Zorn J, König J, Geiger M, Eschbach-Bludau M, Heuser J, Zölzer D, Korencak M, Hollstein R, Beins E, Emmert D, Aldabbagh S, Eis-Hübinger AM, Streeck H. A longitudinal study on SARS-CoV-2 seroconversion, reinfection and neutralisation spanning several variant waves and vaccination campaigns, Heinsberg, Germany, April 2020 to November 2022. Euro Surveill 2024; 29:2300659. [PMID: 38940003 PMCID: PMC11212458 DOI: 10.2807/1560-7917.es.2024.29.26.2300659] [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: 11/21/2023] [Accepted: 03/19/2024] [Indexed: 06/29/2024] Open
Abstract
BackgroundSince its emergence in December 2019, over 700 million people worldwide have been infected with SARS-CoV-2 up to May 2024. While early rollout of mRNA vaccines against COVID-19 has saved many lives, there was increasing immune escape of new virus variants. Longitudinal monitoring of population-wide SARS-CoV-2 antibody responses from regular sample collection irrespective of symptoms provides representative data on infection and seroconversion/seroreversion rates.AimTo examine adaptive and cellular immune responses of a German SARS-CoV-2 outbreak cohort through several waves of infection with different virus variants.MethodsUtilising a 31-month longitudinal seroepidemiological study (n = 1,446; mean age: 50 years, range: 2-103) initiated during the first SARS-CoV-2 superspreading event (February 2020) in Heinsberg, Germany, we analysed acute infection, seroconversion and virus neutralisation at five follow-up visits between October 2020 and November 2022; cellular and cross-protective immunity against SARS-CoV-2 Omicron variants were also examined.ResultsSARS-CoV-2 spike (S)-specific IgAs decreased shortly after infection, while IgGs remained stable. Both increased significantly after vaccination. We predict an 18-month half-life of S IgGs upon infection. Nucleocapsid (N)-specific responses declined over 12 months post-infection but increased (p < 0.0001) during Omicron. Frequencies of SARS-CoV-2-specific TNF-alpha+/IFN-gamma+ CD4+ T-cells declined over 12 months after infection (p < 0.01). SARS-CoV-2 S antibodies and neutralisation titres were highest in triple-vaccinated participants infected between April 2021 and November 2022 compared with infections between April 2020 and January 2021. Cross neutralisation against Omicron BQ.1.18 and XBB.1.5 was very low in all groups.ConclusionInfection and/or vaccination did not provide the population with cross-protection against Omicron variants.
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Affiliation(s)
- Bianca Schulte
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
- Institute of Virology, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Enrico Richter
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
- Institute of Virology, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Antonia Büning
- Institute of Virology, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Maximilian Baum
- Institute of Virology, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Annika Breuer
- Institute of Virology, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Jasmin Zorn
- Institute of Virology, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Julia König
- Institute of Virology, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Melanie Geiger
- Institute of Virology, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | | | - Johanna Heuser
- Institute of Virology, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Dominik Zölzer
- Institute of Virology, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Marek Korencak
- Institute of Virology, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Ronja Hollstein
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Eva Beins
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Dorian Emmert
- Institute of Virology, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Souhaib Aldabbagh
- Institute of Virology, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | | | - Hendrik Streeck
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
- Institute of Virology, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
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4
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Rössler A, Netzl A, Knabl L, Wilks SH, Mühlemann B, Türeli S, Mykytyn A, von Laer D, Haagmans BL, Smith DJ, Kimpel J. Direct comparison of SARS-CoV-2 variant specific neutralizing antibodies in human and hamster sera. NPJ Vaccines 2024; 9:85. [PMID: 38762525 PMCID: PMC11102554 DOI: 10.1038/s41541-024-00888-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/07/2024] [Indexed: 05/20/2024] Open
Abstract
Antigenic characterization of newly emerging SARS-CoV-2 variants is important to assess their immune escape and judge the need for future vaccine updates. To bridge data obtained from animal sera with human sera, we analyzed neutralizing antibody titers in human and hamster single infection sera in a highly controlled setting using the same authentic virus neutralization assay performed in one laboratory. Using a Bayesian framework, we found that titer fold changes in hamster sera corresponded well to human sera and that hamster sera generally exhibited higher reactivity.
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Affiliation(s)
- Annika Rössler
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Antonia Netzl
- University of Cambridge, Centre for Pathogen Evolution, Department of Zoology, Cambridge, UK
| | - Ludwig Knabl
- Tyrolpath Obrist Brunhuber GmbH, Hauptplatz 4, 6511, Zams, Austria
| | - Samuel H Wilks
- University of Cambridge, Centre for Pathogen Evolution, Department of Zoology, Cambridge, UK
| | - Barbara Mühlemann
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Ins+titute of Health, 10117, Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117, Berlin, Germany
| | - Sina Türeli
- University of Cambridge, Centre for Pathogen Evolution, Department of Zoology, Cambridge, UK
| | - Anna Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Dorothee von Laer
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria
| | - Bart L Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Derek J Smith
- University of Cambridge, Centre for Pathogen Evolution, Department of Zoology, Cambridge, UK.
| | - Janine Kimpel
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria.
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5
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Astakhova EA, Morozov AA, Vavilova JD, Filatov AV. Antigenic Cartography of SARS-CoV-2. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:862-871. [PMID: 38880647 DOI: 10.1134/s0006297924050079] [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: 11/07/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 06/18/2024]
Abstract
Antigenic cartography is a tool for interpreting and visualizing antigenic differences between virus variants based on virus neutralization data. This approach has been successfully used in the selection of influenza vaccine seed strains. With the emergence of SARS-CoV-2 variants escaping vaccine-induced antibody response, adjusting COVID-19 vaccines has become essential. This review provides information on the antigenic differences between SARS-CoV-2 variants revealed by antigenic cartography and explores a potential of antigenic cartography-based methods (e.g., building antibody landscapes and neutralization breadth gain plots) for the quantitative assessment of the breadth of the antibody response. Understanding the antigenic differences of SARS-CoV-2 and the possibilities of the formed humoral immunity aids in the prompt modification of preventative vaccines against COVID-19.
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Affiliation(s)
- Ekaterina A Astakhova
- National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, 115522, Russia.
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Alexey A Morozov
- National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, 115522, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Julia D Vavilova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexander V Filatov
- National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, 115522, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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6
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Luo S, Xiong D, Tang B, Liu B, Zhao X, Duan L. Evaluating mAbs binding abilities to Omicron subvariant RBDs: implications for selecting effective mAb therapies. Phys Chem Chem Phys 2024; 26:11414-11428. [PMID: 38591159 DOI: 10.1039/d3cp05893j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
The ongoing evolution of the Omicron lineage of SARS-CoV-2 has led to the emergence of subvariants that pose challenges to antibody neutralization. Understanding the binding dynamics between the receptor-binding domains (RBD) of these subvariants spike and monoclonal antibodies (mAbs) is pivotal for elucidating the mechanisms of immune escape and for advancing the development of therapeutic antibodies. This study focused on the RBD regions of Omicron subvariants BA.2, BA.5, BF.7, and XBB.1.5, employing molecular dynamics simulations to unravel their binding mechanisms with a panel of six mAbs, and subsequently analyzing the origins of immune escape from energetic and structural perspectives. Our results indicated that the antibody LY-COV1404 maintained binding affinities across all studied systems, suggesting the resilience of certain antibodies against variant-induced immune escape, as seen with the mAb 1D1-Fab. The newly identified mAb 002-S21F2 showed a similar efficacy profile to LY-COV1404, though with a slightly reduced binding to BF.7. In parallel, mAb REGN-10933 emerged as a potential therapeutic candidate against BF.7 and XBB.1.5, reflecting the importance of identifying variant-specific antibody interactions, akin to the binding optimization observed in BA.4/5 and XBB.1.5. And key residues that facilitate RBD-mAb binding were identified (T345, L441, K444, V445, and T500), alongside residues that hinder protein-protein interactions (D420, L455, K440, and S446). Particularly noteworthy was the inhibited binding of V445 and R509 with mAbs in the presence of mAb 002-S21F2, suggesting a mechanism for immune escape, especially through the reduction of V445 hydrophobicity. These findings enhance our comprehension of the binding interactions between mAbs and RBDs, contributing to the understanding of immune escape mechanisms. They also lay the groundwork for the design and optimization of antiviral drugs and have significant implications for the development of treatments against current and future coronaviruses.
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Affiliation(s)
- Song Luo
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Danyang Xiong
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Bolin Tang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Bangyu Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Xiaoyu Zhao
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
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Springer DN, Daller S, Knappik M, Prüger K, Hartl S, Breyer-Kohansal R, Puchhammer-Stöckl E, Aberle JH, Weseslindtner L, Breyer MK. A Multivariant Surrogate Virus Neutralization Test Demonstrates Distinct SARS-CoV-2-Specific Antibody Responses in People Living with HIV after a Fourth Monovalent mRNA Vaccination or an Omicron Breakthrough Infection. Diagnostics (Basel) 2024; 14:822. [PMID: 38667468 PMCID: PMC11049121 DOI: 10.3390/diagnostics14080822] [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: 02/23/2024] [Revised: 03/30/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
While neutralizing antibodies (nAbs) induced by monovalent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccinations are primarily directed against the wildtype (WT), subsequent exposure to the Omicron variants may increase the breadth of the antibodies' cross-neutralizing activity. Here, we analyzed the impact of an Omicron breakthrough infection (BTI) or a fourth monovalent mRNA vaccination on nAb profiles in people living with human immunodeficiency virus (PLWH). Using a multivariant surrogate virus neutralization test (sVNT), we quantified nAbs in 36 three-times vaccinated PLWH, of whom 9 acquired a serologically confirmed Omicron BTI, 8 received a fourth vaccine dose, and 19 were neither infected nor additionally vaccinated. While nAbs against WT and Delta increased after the BTI and a fourth vaccination, a significant increase against BA.1, BA.2, and BA.5 was only observed after the BTI. However, there was no significant difference in nAb concentrations between the samples obtained after the BTI and fourth vaccination. In contrast, nAb levels were significantly lower in PLWH, who were neither infected nor additionally vaccinated after three vaccinations. Thus, our study demonstrates the suitability of a multivariant sVNT to assess hybrid humoral immunity after Omicron BTIs in PLWH vaccinated against SARS-CoV-2.
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Affiliation(s)
- David Niklas Springer
- Center for Virology, Medical University of Vienna, 1090 Vienna, Austria; (D.N.S.); (K.P.); (E.P.-S.); (J.H.A.)
| | - Simon Daller
- Department of Respiratory and Pulmonary Diseases, Vienna Healthcare Group, Clinic Penzing, 1140 Vienna, Austria; (S.D.); (M.K.); (S.H.); (R.B.-K.); (M.K.B.)
| | - Michael Knappik
- Department of Respiratory and Pulmonary Diseases, Vienna Healthcare Group, Clinic Penzing, 1140 Vienna, Austria; (S.D.); (M.K.); (S.H.); (R.B.-K.); (M.K.B.)
| | - Katja Prüger
- Center for Virology, Medical University of Vienna, 1090 Vienna, Austria; (D.N.S.); (K.P.); (E.P.-S.); (J.H.A.)
| | - Sylvia Hartl
- Department of Respiratory and Pulmonary Diseases, Vienna Healthcare Group, Clinic Penzing, 1140 Vienna, Austria; (S.D.); (M.K.); (S.H.); (R.B.-K.); (M.K.B.)
- Ludwig Boltzmann Institute for Lung Health, 1140 Vienna, Austria
- Faculty of Medicine, Sigmund Freud University, 1020 Vienna, Austria
| | - Robab Breyer-Kohansal
- Department of Respiratory and Pulmonary Diseases, Vienna Healthcare Group, Clinic Penzing, 1140 Vienna, Austria; (S.D.); (M.K.); (S.H.); (R.B.-K.); (M.K.B.)
- Ludwig Boltzmann Institute for Lung Health, 1140 Vienna, Austria
| | - Elisabeth Puchhammer-Stöckl
- Center for Virology, Medical University of Vienna, 1090 Vienna, Austria; (D.N.S.); (K.P.); (E.P.-S.); (J.H.A.)
| | - Judith Helene Aberle
- Center for Virology, Medical University of Vienna, 1090 Vienna, Austria; (D.N.S.); (K.P.); (E.P.-S.); (J.H.A.)
| | - Lukas Weseslindtner
- Center for Virology, Medical University of Vienna, 1090 Vienna, Austria; (D.N.S.); (K.P.); (E.P.-S.); (J.H.A.)
| | - Marie Kathrin Breyer
- Department of Respiratory and Pulmonary Diseases, Vienna Healthcare Group, Clinic Penzing, 1140 Vienna, Austria; (S.D.); (M.K.); (S.H.); (R.B.-K.); (M.K.B.)
- Ludwig Boltzmann Institute for Lung Health, 1140 Vienna, Austria
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8
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Wang W, Bhushan GL, Paz S, Stauft CB, Selvaraj P, Goguet E, Bishop-Lilly KA, Subramanian R, Vassell R, Lusvarghi S, Cong Y, Agan B, Richard SA, Epsi NJ, Fries A, Fung CK, Conte MA, Holbrook MR, Wang TT, Burgess TH, Mitre E, Pollett SD, Katzelnick LC, Weiss CD. Antigenic cartography using hamster sera identifies SARS-CoV-2 JN.1 evasion seen in human XBB.1.5 booster sera. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.05.588359. [PMID: 38712124 PMCID: PMC11071293 DOI: 10.1101/2024.04.05.588359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Antigenic assessments of SARS-CoV-2 variants inform decisions to update COVID-19 vaccines. Primary infection sera are often used for assessments, but such sera are rare due to population immunity from SARS-CoV-2 infections and COVID-19 vaccinations. Here, we show that neutralization titers and breadth of matched human and hamster pre-Omicron variant primary infection sera correlate well and generate similar antigenic maps. The hamster antigenic map shows modest antigenic drift among XBB sub-lineage variants, with JN.1 and BA.4/BA.5 variants within the XBB cluster, but with five to six-fold antigenic differences between these variants and XBB.1.5. Compared to sera following only ancestral or bivalent COVID-19 vaccinations, or with post-vaccination infections, XBB.1.5 booster sera had the broadest neutralization against XBB sub-lineage variants, although a five-fold titer difference was still observed between JN.1 and XBB.1.5 variants. These findings suggest that antibody coverage of antigenically divergent JN.1 could be improved with a matched vaccine antigen.
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Affiliation(s)
- Wei Wang
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Gitanjali L. Bhushan
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephanie Paz
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Charles B. Stauft
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Prabhu Selvaraj
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Emilie Goguet
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, Maryland, USA
| | - Kimberly A. Bishop-Lilly
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, Maryland, 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, Maryland, USA
| | - Russell Vassell
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Sabrina Lusvarghi
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Yu Cong
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Ft. Detrick, Frederick, Maryland, USA
| | - Brian Agan
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Stephanie A. Richard
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Nusrat J. Epsi
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Anthony Fries
- US Air Force School of Aerospace Medicine, Dayton, Ohio, USA
| | - Christian K. Fung
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Matthew A. Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Michael R. Holbrook
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Ft. Detrick, Frederick, Maryland, USA
| | - Tony T. Wang
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Timothy H. Burgess
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Edward Mitre
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Simon D. Pollett
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Leah C. Katzelnick
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Carol D. Weiss
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
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9
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Jung SM, Loo SL, Howerton E, Contamin L, Smith CP, Carcelén EC, Yan K, Bents SJ, Levander J, Espino J, Lemaitre JC, Sato K, McKee CD, Hill AL, Chinazzi M, Davis JT, Mu K, Vespignani A, Rosenstrom ET, Rodriguez-Cartes SA, Ivy JS, Mayorga ME, Swann JL, España G, Cavany S, Moore SM, Perkins TA, Chen S, Paul R, Janies D, Thill JC, Srivastava A, Aawar MA, Bi K, Bandekar SR, Bouchnita A, Fox SJ, Meyers LA, Porebski P, Venkatramanan S, Adiga A, Hurt B, Klahn B, Outten J, Chen J, Mortveit H, Wilson A, Hoops S, Bhattacharya P, Machi D, Vullikanti A, Lewis B, Marathe M, Hochheiser H, Runge MC, Shea K, Truelove S, Viboud C, Lessler J. Potential impact of annual vaccination with reformulated COVID-19 vaccines: Lessons from the US COVID-19 scenario modeling hub. PLoS Med 2024; 21:e1004387. [PMID: 38630802 PMCID: PMC11062554 DOI: 10.1371/journal.pmed.1004387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 05/01/2024] [Accepted: 03/27/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Coronavirus Disease 2019 (COVID-19) continues to cause significant hospitalizations and deaths in the United States. Its continued burden and the impact of annually reformulated vaccines remain unclear. Here, we present projections of COVID-19 hospitalizations and deaths in the United States for the next 2 years under 2 plausible assumptions about immune escape (20% per year and 50% per year) and 3 possible CDC recommendations for the use of annually reformulated vaccines (no recommendation, vaccination for those aged 65 years and over, vaccination for all eligible age groups based on FDA approval). METHODS AND FINDINGS The COVID-19 Scenario Modeling Hub solicited projections of COVID-19 hospitalization and deaths between April 15, 2023 and April 15, 2025 under 6 scenarios representing the intersection of considered levels of immune escape and vaccination. Annually reformulated vaccines are assumed to be 65% effective against symptomatic infection with strains circulating on June 15 of each year and to become available on September 1. Age- and state-specific coverage in recommended groups was assumed to match that seen for the first (fall 2021) COVID-19 booster. State and national projections from 8 modeling teams were ensembled to produce projections for each scenario and expected reductions in disease outcomes due to vaccination over the projection period. From April 15, 2023 to April 15, 2025, COVID-19 is projected to cause annual epidemics peaking November to January. In the most pessimistic scenario (high immune escape, no vaccination recommendation), we project 2.1 million (90% projection interval (PI) [1,438,000, 4,270,000]) hospitalizations and 209,000 (90% PI [139,000, 461,000]) deaths, exceeding pre-pandemic mortality of influenza and pneumonia. In high immune escape scenarios, vaccination of those aged 65+ results in 230,000 (95% confidence interval (CI) [104,000, 355,000]) fewer hospitalizations and 33,000 (95% CI [12,000, 54,000]) fewer deaths, while vaccination of all eligible individuals results in 431,000 (95% CI: 264,000-598,000) fewer hospitalizations and 49,000 (95% CI [29,000, 69,000]) fewer deaths. CONCLUSIONS COVID-19 is projected to be a significant public health threat over the coming 2 years. Broad vaccination has the potential to substantially reduce the burden of this disease, saving tens of thousands of lives each year.
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Affiliation(s)
- Sung-mok Jung
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sara L. Loo
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Emily Howerton
- The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Lucie Contamin
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Claire P. Smith
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Erica C. Carcelén
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Katie Yan
- The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Samantha J. Bents
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John Levander
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jessi Espino
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Joseph C. Lemaitre
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Koji Sato
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Clifton D. McKee
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Alison L. Hill
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Matteo Chinazzi
- Northeastern University, Boston, Massachusetts, United States of America
| | - Jessica T. Davis
- Northeastern University, Boston, Massachusetts, United States of America
| | - Kunpeng Mu
- Northeastern University, Boston, Massachusetts, United States of America
| | | | - Erik T. Rosenstrom
- North Carolina State University, Raleigh, North Carolina, United States of America
| | | | - Julie S. Ivy
- North Carolina State University, Raleigh, North Carolina, United States of America
| | - Maria E. Mayorga
- North Carolina State University, Raleigh, North Carolina, United States of America
| | - Julie L. Swann
- North Carolina State University, Raleigh, North Carolina, United States of America
| | - Guido España
- University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Sean Cavany
- University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Sean M. Moore
- University of Notre Dame, Notre Dame, Indiana, United States of America
| | - T. Alex Perkins
- University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Shi Chen
- University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Rajib Paul
- University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Daniel Janies
- University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Jean-Claude Thill
- University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Ajitesh Srivastava
- University of Southern California, Los Angeles, California, United States of America
| | - Majd Al Aawar
- University of Southern California, Los Angeles, California, United States of America
| | - Kaiming Bi
- University of Texas at Austin, Austin, Texas, United States of America
| | | | - Anass Bouchnita
- University of Texas at El Paso, El Paso, Texas, United States of America
| | - Spencer J. Fox
- University of Georgia, Athens, Georgia, United States of America
| | | | | | | | - Aniruddha Adiga
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Benjamin Hurt
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Brian Klahn
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Joseph Outten
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Jiangzhuo Chen
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Henning Mortveit
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Amanda Wilson
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Stefan Hoops
- University of Virginia, Charlottesville, Virginia, United States of America
| | | | - Dustin Machi
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Anil Vullikanti
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Bryan Lewis
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Madhav Marathe
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Harry Hochheiser
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michael C. Runge
- U.S. Geological Survey, Laurel, Maryland, United States of America
| | - Katriona Shea
- The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Shaun Truelove
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Justin Lessler
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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10
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Karim F, Riou C, Bernstein M, Jule Z, Lustig G, van Graan S, Keeton RS, Upton JL, Ganga Y, Khan K, Reedoy K, Mazibuko M, Govender K, Thambu K, Ngcobo N, Venter E, Makhado Z, Hanekom W, von Gottberg A, Hoque M, Karim QA, Abdool Karim SS, Manickchund N, Magula N, Gosnell BI, Lessells RJ, Moore PL, Burgers WA, de Oliveira T, Moosa MYS, Sigal A. Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation. Nat Commun 2024; 15:2360. [PMID: 38491050 PMCID: PMC10943233 DOI: 10.1038/s41467-024-46673-2] [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: 08/10/2023] [Accepted: 02/27/2024] [Indexed: 03/18/2024] Open
Abstract
SARS-CoV-2 clearance requires adaptive immunity but the contribution of neutralizing antibodies and T cells in different immune states is unclear. Here we ask which adaptive immune responses associate with clearance of long-term SARS-CoV-2 infection in HIV-mediated immunosuppression after suppressive antiretroviral therapy (ART) initiation. We assembled a cohort of SARS-CoV-2 infected people in South Africa (n = 994) including participants with advanced HIV disease characterized by immunosuppression due to T cell depletion. Fifty-four percent of participants with advanced HIV disease had prolonged SARS-CoV-2 infection (>1 month). In the five vaccinated participants with advanced HIV disease tested, SARS-CoV-2 clearance associates with emergence of neutralizing antibodies but not SARS-CoV-2 specific CD8 T cells, while CD4 T cell responses were not determined due to low cell numbers. Further, complete HIV suppression is not required for clearance, although it is necessary for an effective vaccine response. Persistent SARS-CoV-2 infection led to SARS-CoV-2 evolution, including virus with extensive neutralization escape in a Delta variant infected participant. The results provide evidence that neutralizing antibodies are required for SARS-CoV-2 clearance in HIV-mediated immunosuppression recovery, and that suppressive ART is necessary to curtail evolution of co-infecting pathogens to reduce individual health consequences as well as public health risk linked with generation of escape mutants.
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Affiliation(s)
- Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | | | - Zesuliwe Jule
- Africa Health Research Institute, Durban, South Africa
| | - Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Strauss van Graan
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Roanne S Keeton
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | | | - Yashica Ganga
- Africa Health Research Institute, Durban, South Africa
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kajal Reedoy
- Africa Health Research Institute, Durban, South Africa
| | | | | | | | | | - Elizabeth Venter
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Zanele Makhado
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Willem Hanekom
- Africa Health Research Institute, Durban, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Monjurul Hoque
- KwaDabeka Community Health Centre, KwaDabeka, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nithendra Manickchund
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nombulelo Magula
- Department of Internal Medicine, Nelson R. Mandela School of Medicine, University of Kwa-Zulu Natal, Durban, South Africa
| | - Bernadett I Gosnell
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard J Lessells
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Penny L Moore
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Tulio de Oliveira
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa.
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa.
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11
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Choi MJ, Hyun H, Heo JY, Seo YB, Noh JY, Cheong HJ, Kim WJ, Kim HJ, Choi JY, Lee YJ, Chung EJ, Kim SH, Jeong H, Kim B, Song JY. Longitudinal immune kinetics of COVID-19 booster versus primary series vaccination: Insight into the annual vaccination strategy. Heliyon 2024; 10:e27211. [PMID: 38468934 PMCID: PMC10926122 DOI: 10.1016/j.heliyon.2024.e27211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
Background Data on the durability of booster dose immunity of COVID-19 vaccines are relatively limited. Methods Immunogenicity was evaluated for up to 9-12 months after the third dose of vaccination in 94 healthy adults. Results Following the third dose, the anti-spike immunoglobulin G (IgG) antibody response against the wild-type was boosted markedly, which decreased gradually over time. However, even 9-12 months after the booster dose, both the median and geometric mean of anti-spike IgG antibody levels were higher than those measured 4 weeks after the second dose. Breakthrough infection during the Omicron-dominant period boosted neutralizing antibody titers against Omicron sublineages (BA.1 and BA.5) and the ancestral strain. T-cell immune response was efficiently induced and maintained during the study period. Conclusions mRNA vaccine booster dose elicited durable humoral immunity for up to 1 year after the third dose and T-cell immunity was sustained during the study period, supporting an annual COVID-19 vaccination strategy.
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Affiliation(s)
- Min Joo Choi
- Department of Internal Medicine, International St. Mary's Hospital, Catholic Kwandong University College of Medicine, Incheon, Republic of Korea
| | - Hakjun Hyun
- Department of Infectious Diseases, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Jung Yeon Heo
- Department of Infectious Diseases, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Yu Bin Seo
- Division of Infectious Disease, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Ji Yun Noh
- Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
- Vaccine Innovation Center - Korea University College of Medicine, Seoul, Republic of Korea
| | - Hee Jin Cheong
- Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
- Vaccine Innovation Center - Korea University College of Medicine, Seoul, Republic of Korea
| | - Woo Joo Kim
- Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
- Vaccine Innovation Center - Korea University College of Medicine, Seoul, Republic of Korea
| | - Hwa Jung Kim
- Department of Clinical Epidemiology and Biostatistics, ASAN Medical Center, Ulsan University College of Medicine, Seoul, Republic of Korea
| | - Ju-yeon Choi
- Division of Vaccine Clinical Research, Center for Vaccine Research, National Institute of Infectious Diseases, Cheongju, Republic of Korea
| | - Young Jae Lee
- Division of Vaccine Clinical Research, Center for Vaccine Research, National Institute of Infectious Diseases, Cheongju, Republic of Korea
| | - Eun Joo Chung
- Division of Vaccine Clinical Research, Center for Vaccine Research, National Institute of Infectious Diseases, Cheongju, Republic of Korea
| | - Su-Hwan Kim
- Division of Vaccine Clinical Research, Center for Vaccine Research, National Institute of Infectious Diseases, Cheongju, Republic of Korea
| | - Hyeonji Jeong
- Division of Vaccine Clinical Research, Center for Vaccine Research, National Institute of Infectious Diseases, Cheongju, Republic of Korea
| | - Byoungguk Kim
- Division of Vaccine Clinical Research, Center for Vaccine Research, National Institute of Infectious Diseases, Cheongju, Republic of Korea
| | - Joon Young Song
- Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
- Vaccine Innovation Center - Korea University College of Medicine, Seoul, Republic of Korea
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12
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Rössler A, Knabl L, Netzl A, Bante D, Borena W, von Laer D, Smith DJ, Kimpel J. Durability of Cross-Neutralizing Antibodies 5.5 Months After Bivalent Coronavirus Disease 2019 Vaccine Booster. J Infect Dis 2024; 229:644-647. [PMID: 38016020 PMCID: PMC10938204 DOI: 10.1093/infdis/jiad472] [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: 09/11/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 11/30/2023] Open
Abstract
We analyzed neutralizing antibodies in samples from ancestral + BA.1 and ancestral + BA.4/5 boosted individuals, collected around 5.5 months after booster. Titers of neutralizing antibodies generally decreased compared to a time point early after the bivalent booster immunization. This was more pronounced for individuals without infection history and for recently emerged Omicron variants.
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Affiliation(s)
- Annika Rössler
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Austria
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Antonia Netzl
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, United Kingdom
| | - David Bante
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Austria
| | - Wegene Borena
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Austria
| | - Dorothee von Laer
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Austria
| | - Derek J Smith
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, United Kingdom
| | - Janine Kimpel
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Austria
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13
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Halfmann PJ, Loeffler K, Duffy A, Kuroda M, Yang JE, Wright ER, Kawaoka Y, Kane RS. Broad protection against clade 1 sarbecoviruses after a single immunization with cocktail spike-protein-nanoparticle vaccine. Nat Commun 2024; 15:1284. [PMID: 38346966 PMCID: PMC10861510 DOI: 10.1038/s41467-024-45495-6] [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: 06/20/2023] [Accepted: 01/25/2024] [Indexed: 02/15/2024] Open
Abstract
The 2002 SARS outbreak, the 2019 emergence of COVID-19, and the continuing evolution of immune-evading SARS-CoV-2 variants together highlight the need for a broadly protective vaccine against ACE2-utilizing sarbecoviruses. While updated variant-matched formulations are a step in the right direction, protection needs to extend beyond SARS-CoV-2 and its variants to include SARS-like viruses. Here, we introduce bivalent and trivalent vaccine formulations using our spike protein nanoparticle platform that completely protect female hamsters against BA.5 and XBB.1 challenges with no detectable virus in the lungs. The trivalent cocktails elicit highly neutralizing responses against all tested Omicron variants and the bat sarbecoviruses SHC014 and WIV1. Finally, our 614D/SHC014/XBB trivalent spike formulation completely protects human ACE2-transgenic female hamsters against challenges with WIV1 and SHC014 with no detectable virus in the lungs. Collectively, these results illustrate that our trivalent protein-nanoparticle cocktail can provide broad protection against SARS-CoV-2-like and SARS-CoV-1-like sarbecoviruses.
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Affiliation(s)
- Peter J Halfmann
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Kathryn Loeffler
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Augustine Duffy
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Makoto Kuroda
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, Cryo-EM Research Center, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, Midwest Center for Cryo-Electron Tomography, University of Wisconsin, Madison, WI, 53706, USA
| | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, Cryo-EM Research Center, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, Midwest Center for Cryo-Electron Tomography, University of Wisconsin, Madison, WI, 53706, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA.
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan.
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo, 162-8655, Japan.
| | - Ravi S Kane
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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14
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Belongia EA, Petrie JG, Feldstein LR, Guan L, Halfmann PJ, King JP, Neumann G, Pattinson D, Rolfes MA, McLean HQ, Kawaoka Y. Neutralizing Immunity Against Antigenically Advanced Omicron BA.5 in Children After SARS-CoV-2 Infection. J Pediatric Infect Dis Soc 2024; 13:100-104. [PMID: 38142128 DOI: 10.1093/jpids/piad109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Abstract
We assessed serum neutralization of Omicron BA.5 in children following SARS-CoV-2 infection during the Delta or Omicron BA.1/BA.2 variant period. Convalescent BA.5 titers were higher following infections during the Omicron BA.1/BA.2 vs Delta variant period, and in vaccinated vs unvaccinated children. Titers against BA.5 did not differ by age group.
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Affiliation(s)
- Edward A Belongia
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Joshua G Petrie
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Leora R Feldstein
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lizheng Guan
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Peter J Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Jennifer P King
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Gabriele Neumann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - David Pattinson
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Melissa A Rolfes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Huong Q McLean
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
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15
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Springer DN, Höltl E, Prüger K, Puchhammer-Stöckl E, Aberle JH, Stiasny K, Weseslindtner L. Measuring Variant-Specific Neutralizing Antibody Profiles after Bivalent SARS-CoV-2 Vaccinations Using a Multivariant Surrogate Virus Neutralization Microarray. Vaccines (Basel) 2024; 12:94. [PMID: 38250907 PMCID: PMC10818493 DOI: 10.3390/vaccines12010094] [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: 12/04/2023] [Revised: 01/03/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024] Open
Abstract
The capability of antibodies to neutralize different SARS-CoV-2 variants varies among individuals depending on the previous exposure to wild-type or Omicron-specific immunogens by mono- or bivalent vaccinations or infections. Such profiles of neutralizing antibodies (nAbs) usually have to be assessed via laborious live-virus neutralization tests (NTs). We therefore analyzed whether a novel multivariant surrogate-virus neutralization test (sVNT) (adapted from a commercial microarray) that quantifies the antibody-mediated inhibition between the receptor angiotensin-converting enzyme 2 (ACE2) and variant-specific receptor-binding domains (RBDs) can assess the neutralizing activity against the SARS-CoV-2 wild-type, and Delta Omicron BA.1, BA.2, and BA.5 subvariants after a booster with Omicron-adapted bivalent vaccines in a manner similar to live-virus NTs. Indeed, by using the live-virus NTs as a reference, we found a significant correlation between the variant-specific NT titers and levels of ACE2-RBD binding inhibition (p < 0.0001, r ≤ 0.78 respectively). Furthermore, the sVNTs identified higher inhibition values against BA.5 and BA.1 in individuals vaccinated with Omicron-adapted vaccines than in those with monovalent wild-type vaccines. Our data thus demonstrate the ability of sVNTs to detect variant-specific nAbs following a booster with bivalent vaccines.
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Affiliation(s)
- David Niklas Springer
- Center for Virology, Medical University of Vienna, A-1090 Vienna, Austria (K.P.); (E.P.-S.); (J.H.A.)
| | - Eva Höltl
- Center for Public Health, Medical University of Vienna, A-1090 Vienna, Austria;
| | - Katja Prüger
- Center for Virology, Medical University of Vienna, A-1090 Vienna, Austria (K.P.); (E.P.-S.); (J.H.A.)
| | | | - Judith Helene Aberle
- Center for Virology, Medical University of Vienna, A-1090 Vienna, Austria (K.P.); (E.P.-S.); (J.H.A.)
| | - Karin Stiasny
- Center for Virology, Medical University of Vienna, A-1090 Vienna, Austria (K.P.); (E.P.-S.); (J.H.A.)
| | - Lukas Weseslindtner
- Center for Virology, Medical University of Vienna, A-1090 Vienna, Austria (K.P.); (E.P.-S.); (J.H.A.)
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16
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Li L, Xie Z, Li Y, Luo M, Zhang L, Feng C, Tang G, Huang H, Hou R, Xu Y, Jia S, Shi J, Fan Q, Gan Q, Yu N, Hu F, Li Y, Lan Y, Tang X, Li F, Deng X. Immune response and severity of Omicron BA.5 reinfection among individuals previously infected with different SARS-CoV-2 variants. Front Cell Infect Microbiol 2023; 13:1277880. [PMID: 38188634 PMCID: PMC10766752 DOI: 10.3389/fcimb.2023.1277880] [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: 08/15/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction COVID-19 continues to spread worldwide, with an increasing number of individuals experiencing reinfection after recovering from their primary infection. However, the nature and progression of this infection remain poorly understood. We aimed to investigate the immune response, severity and outcomes of Omicron BA.5 reinfection among individuals previously infected with different SARS-CoV-2 variants. Methods We enrolled 432 COVID-19 cases who had experienced prior infection with the ancestral SARS-CoV-2 virus, Delta variant or Omicron BA.2 variant between January 2020 and May 2022 in Guangzhou, China. All cases underwent follow-up from March to April, 2023 through telephone questionnaires and clinical visits. Nasal lavage fluid and peripheral blood were collected to assess anti-RBD IgA, anti-RBD IgG and virus-specific IFN-γ secreting T cells. Results Our study shows that 73.1%, 56.7% and 12.5% of individuals with a prior infection of the ancestral virus, Delta or Omicron BA.2 variant experienced reinfection with the BA.5 variant, respectively. Fever, cough and sore throat were the most common symptoms of BA.5 reinfection, with most improving within one week and none progressing to a critical condition. Compared with individuals without reinfection, reinfected patients with a prior Delta infection exhibited elevated levels of nasal anti-RBD IgA, serum anti-RBD IgG and IFN-γ secreting T cells, whereas there was no noticeable change in reinfected individuals with a prior BA.2 infection. Conclusion These results suggest that BA.5 reinfection is common but severe outcomes are relatively rare. Reinfection with a novel SARS-CoV-2 variant different from the prior infection may induce a more robust immune protection, which should be taken into account during vaccine development.
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Affiliation(s)
- Lu Li
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Zhiwei Xie
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Youxia Li
- Department of Critical Care Medicine, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Minhan Luo
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Lieguang Zhang
- Department of Radiology, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Chengqian Feng
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Guofang Tang
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Huang Huang
- Department of Critical Care Medicine, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Ruitian Hou
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yujuan Xu
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Shijie Jia
- Department of Traditional Chinese Medicine, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jingrong Shi
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qinghong Fan
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qingxin Gan
- Department of Radiology, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Na Yu
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Fengyu Hu
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Bio-Island, Guangzhou, China
| | - Yueping Li
- Department of Infectious Critical Care Medicine, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yun Lan
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiaoping Tang
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Bio-Island, Guangzhou, China
| | - Feng Li
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Bio-Island, Guangzhou, China
| | - Xilong Deng
- Department of Critical Care Medicine, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
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17
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Bianco A, Bortolami A, Miccolupo A, Sottili R, Ghergo P, Castellana S, Del Sambro L, Capozzi L, Pagliari M, Bonfante F, Ridolfi D, Bulzacchelli C, Giannico A, Parisi A. SARS-CoV-2 in Animal Companions: A Serosurvey in Three Regions of Southern Italy. Life (Basel) 2023; 13:2354. [PMID: 38137955 PMCID: PMC10745004 DOI: 10.3390/life13122354] [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: 09/19/2023] [Revised: 11/06/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Several animal species have been found to be susceptible to SARS-CoV-2 infection. The occurrence of infection in dogs and cats living in close contact with owners deserves particular attention from public health authorities in a One Health approach. In this study, we conducted serological screening to identify SARS-CoV-2 exposure in the sera from dogs and cats in three regions of southern Italy sampled during the years 2021 and 2022. We collected 100 serum samples in 2021 (89 from dogs and 11 from cats) and 640 in 2022 (577 from dogs and 63 from cats). Overall, the ELISA positivity rate was found to be 2.7% (20/740), with higher seroprevalence in dogs. Serum neutralization tests confirmed positivity only in two samples collected from dogs, and the assays, performed with serologically distinct SARS-CoV-2 variants, showed variant-specific positivity. This paper shows that monitoring SARS-CoV-2 exposure in animals might be affected by the viral antigenic evolution, which requires continuous updates to the serological tests used. Serological surveys are useful in understanding the true extent of exposure occurring in specific animal populations, not suffering the same limitations as molecular tests, and could help in identifying the infecting virus if tests able to characterize the immune response are used. The use of variant-specific validated serological methods should always be considered in serosurvey studies in order to determine the real impact of emerging variants on animal populations and its implications for veterinary and human health, as well as to identify potential reservoirs of the virus and its evolutionary changes.
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Affiliation(s)
- Angelica Bianco
- Istituto Zooprofilattico Sperimentale della Puglia e Basilicata, Via Manfredonia n. 20, 71121 Foggia, Italy; (A.B.); (S.C.); (L.D.S.); (L.C.); (D.R.); (C.B.); (A.G.); (A.P.)
| | - Alessio Bortolami
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35020 Legnaro, Italy; (A.B.); (M.P.); (F.B.)
| | - Angela Miccolupo
- Istituto Zooprofilattico Sperimentale della Puglia e Basilicata, Via Manfredonia n. 20, 71121 Foggia, Italy; (A.B.); (S.C.); (L.D.S.); (L.C.); (D.R.); (C.B.); (A.G.); (A.P.)
| | - Roldano Sottili
- ACV Triggiano Laboratorio di Analisi Cliniche Veterinarie, Via Suor Marcella Arosio 8, 70019 Triggiano, Italy; (R.S.)
| | - Paola Ghergo
- ACV Triggiano Laboratorio di Analisi Cliniche Veterinarie, Via Suor Marcella Arosio 8, 70019 Triggiano, Italy; (R.S.)
| | - Stefano Castellana
- Istituto Zooprofilattico Sperimentale della Puglia e Basilicata, Via Manfredonia n. 20, 71121 Foggia, Italy; (A.B.); (S.C.); (L.D.S.); (L.C.); (D.R.); (C.B.); (A.G.); (A.P.)
| | - Laura Del Sambro
- Istituto Zooprofilattico Sperimentale della Puglia e Basilicata, Via Manfredonia n. 20, 71121 Foggia, Italy; (A.B.); (S.C.); (L.D.S.); (L.C.); (D.R.); (C.B.); (A.G.); (A.P.)
| | - Loredana Capozzi
- Istituto Zooprofilattico Sperimentale della Puglia e Basilicata, Via Manfredonia n. 20, 71121 Foggia, Italy; (A.B.); (S.C.); (L.D.S.); (L.C.); (D.R.); (C.B.); (A.G.); (A.P.)
| | - Matteo Pagliari
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35020 Legnaro, Italy; (A.B.); (M.P.); (F.B.)
| | - Francesco Bonfante
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35020 Legnaro, Italy; (A.B.); (M.P.); (F.B.)
| | - Donato Ridolfi
- Istituto Zooprofilattico Sperimentale della Puglia e Basilicata, Via Manfredonia n. 20, 71121 Foggia, Italy; (A.B.); (S.C.); (L.D.S.); (L.C.); (D.R.); (C.B.); (A.G.); (A.P.)
| | - Carmela Bulzacchelli
- Istituto Zooprofilattico Sperimentale della Puglia e Basilicata, Via Manfredonia n. 20, 71121 Foggia, Italy; (A.B.); (S.C.); (L.D.S.); (L.C.); (D.R.); (C.B.); (A.G.); (A.P.)
| | - Anna Giannico
- Istituto Zooprofilattico Sperimentale della Puglia e Basilicata, Via Manfredonia n. 20, 71121 Foggia, Italy; (A.B.); (S.C.); (L.D.S.); (L.C.); (D.R.); (C.B.); (A.G.); (A.P.)
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e Basilicata, Via Manfredonia n. 20, 71121 Foggia, Italy; (A.B.); (S.C.); (L.D.S.); (L.C.); (D.R.); (C.B.); (A.G.); (A.P.)
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18
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Bellusci L, Grubbs G, Sait S, Yonker LM, Randolph AG, Novak T, Kobayashi T, Khurana S. Neutralization of SARS-CoV-2 Omicron BQ.1, BQ.1.1 and XBB.1 variants following SARS-CoV-2 infection or vaccination in children. Nat Commun 2023; 14:7952. [PMID: 38040697 PMCID: PMC10692185 DOI: 10.1038/s41467-023-43152-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: 03/10/2023] [Accepted: 10/31/2023] [Indexed: 12/03/2023] Open
Abstract
Emergence of highly transmissible Omicron subvariants led to increased SARS-CoV-2 infection and disease in children. However, minimal knowledge exists regarding the neutralization capacity against circulating Omicron BA.4/BA.5, BA.2.75, BQ.1, BQ.1.1 and XBB.1 subvariants following SARS-CoV-2 vaccination in children versus during acute or convalescent COVID-19, or versus multisystem inflammatory syndrome (MIS-C). Here, we evaluate virus-neutralizing capacity against SARS-CoV-2 variants in 151 age-stratified children ( <5, 5-11, 12-21 years old) hospitalized with acute severe COVID-19 or MIS-C or convalescent mild (outpatient) infection compared with 62 age-stratified vaccinated children. An age-associated effect on neutralizing antibodies is observed against SARS-CoV-2 following acute COVID-19 or vaccination. The primary series BNT162b2 mRNA vaccinated adolescents show higher vaccine-homologous WA-1 neutralizing titers compared with <12 years vaccinated children. Post-infection antibodies did not neutralize BQ.1, BQ.1.1 and XBB.1 subvariants. In contrast, monovalent mRNA vaccination induces more cross-neutralizing antibodies in young children <5 years against BQ.1, BQ.1.1 and XBB.1 variants compared with ≥5 years old children. Our study demonstrates that in children, infection and monovalent vaccination-induced neutralization activity is low against BQ.1, BQ.1.1 and XBB.1 variants. These findings suggest a need for improved SARS-CoV-2 vaccines to induce durable, more cross-reactive neutralizing antibodies to provide effective protection against emerging variants in children.
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Affiliation(s)
- Lorenza Bellusci
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, 20993, USA
| | - Gabrielle Grubbs
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, 20993, USA
| | - Shaimaa Sait
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, 20993, USA
| | - Lael M Yonker
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital for Children, Harvard Medical School, Boston, MA, 02114, USA
| | - Adrienne G Randolph
- Department of Anesthesia, Harvard Medical School, Boston, MA, USA
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Tanya Novak
- Department of Anesthesia, Harvard Medical School, Boston, MA, USA
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Takuma Kobayashi
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, 20993, USA.
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19
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Baerends EAM, Reekie J, Andreasen SR, Stærke NB, Raben D, Nielsen H, Petersen KT, Johansen IS, Lindvig SO, Madsen LW, Wiese L, Iversen MB, Benfield T, Iversen KK, Larsen FD, Andersen SD, Juhl AK, Dietz LL, Hvidt AK, Ostrowski SR, Krause TG, Østergaard L, Søgaard OS, Lundgren J, Tolstrup M. Omicron Variant-Specific Serological Imprinting Following BA.1 or BA.4/5 Bivalent Vaccination and Previous SARS-CoV-2 Infection: A Cohort Study. Clin Infect Dis 2023; 77:1511-1520. [PMID: 37392436 PMCID: PMC10686961 DOI: 10.1093/cid/ciad402] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/10/2023] [Accepted: 06/27/2023] [Indexed: 07/03/2023] Open
Abstract
BACKGROUND Continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outpaces monovalent vaccine cross-protection to new viral variants. Consequently, bivalent coronavirus disease 2019 (COVID-19) vaccines including Omicron antigens were developed. The contrasting immunogenicity of the bivalent vaccines and the impact of prior antigenic exposure on new immune imprinting remains to be clarified. METHODS In the large prospective ENFORCE cohort, we quantified spike-specific antibodies to 5 Omicron variants (BA.1 to BA.5) before and after BA.1 or BA.4/5 bivalent booster vaccination to compare Omicron variant-specific antibody inductions. We evaluated the impact of previous infection and characterized the dominant antibody responses. RESULTS Prior to the bivalent fourth vaccine, all participants (N = 1697) had high levels of Omicron-specific antibodies. Antibody levels were significantly higher in individuals with a previous polymerase chain reaction positive (PCR+) infection, particularly for BA.2-specific antibodies (geometric mean ratio [GMR] 6.79, 95% confidence interval [CI] 6.05-7.62). Antibody levels were further significantly boosted in all individuals by receiving either of the bivalent vaccines, but greater fold inductions to all Omicron variants were observed in individuals with no prior infection. The BA.1 bivalent vaccine generated a dominant response toward BA.1 (adjusted GMR 1.31, 95% CI 1.09-1.57) and BA.3 (1.32, 1.09-1.59) antigens in individuals with no prior infection, whereas the BA.4/5 bivalent vaccine generated a dominant response toward BA.2 (0.87, 0.76-0.98), BA.4 (0.85, 0.75-0.97), and BA.5 (0.87, 0.76-0.99) antigens in individuals with a prior infection. CONCLUSIONS Vaccination and previous infection leave a clear serological imprint that is focused on the variant-specific antigen. Importantly, both bivalent vaccines induce high levels of Omicron variant-specific antibodies, suggesting broad cross-protection of Omicron variants.
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Affiliation(s)
- Eva A M Baerends
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Joanne Reekie
- Center of Excellence for Health, Immunity and Infections, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Signe R Andreasen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Nina B Stærke
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Dorthe Raben
- Center of Excellence for Health, Immunity and Infections, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Nielsen
- Department of Infectious Diseases, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Kristine T Petersen
- Department of Infectious Diseases, Aalborg University Hospital, Aalborg, Denmark
| | - Isik S Johansen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Susan O Lindvig
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Lone W Madsen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Lothar Wiese
- Department of Medicine, Zealand University Hospital, Roskilde, Denmark
| | - Mette B Iversen
- Department of Medicine, Zealand University Hospital, Roskilde, Denmark
| | - Thomas Benfield
- Department of Infectious Diseases, Copenhagen University Hospital—Amager and Hvidovre, Hvidovre, Denmark
- Departments of Clinical Medicine and Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Kasper K Iversen
- Departments of Clinical Medicine and Public Health, University of Copenhagen, Copenhagen, Denmark
- Department of Cardiology and Emergency Medicine, Herlev Hospital, Herlev, Denmark
| | - Fredrikke D Larsen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Sidsel D Andersen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Anna K Juhl
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Lisa L Dietz
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Astrid K Hvidt
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Sisse R Ostrowski
- Department of Clinical Immunology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Tyra G Krause
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Lars Østergaard
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Ole S Søgaard
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jens Lundgren
- Center of Excellence for Health, Immunity and Infections, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Departments of Clinical Medicine and Public Health, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital—Rigshospitalet, Copenhagen, Denmark
| | - Martin Tolstrup
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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20
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Jung SM, Loo SL, Howerton E, Contamin L, Smith CP, Carcelén EC, Yan K, Bents SJ, Levander J, Espino J, Lemaitre JC, Sato K, McKee CD, Hill AL, Chinazzi M, Davis JT, Mu K, Vespignani A, Rosenstrom ET, Rodriguez-Cartes SA, Ivy JS, Mayorga ME, Swann JL, España G, Cavany S, Moore SM, Perkins A, Chen S, Paul R, Janies D, Thill JC, Srivastava A, Al Aawar M, Bi K, Bandekar SR, Bouchnita A, Fox SJ, Meyers LA, Porebski P, Venkatramanan S, Adiga A, Hurt B, Klahn B, Outten J, Chen J, Mortveit H, Wilson A, Hoops S, Bhattacharya P, Machi D, Vullikanti A, Lewis B, Marathe M, Hochheiser H, Runge MC, Shea K, Truelove S, Viboud C, Lessler J. Potential impact of annual vaccination with reformulated COVID-19 vaccines: lessons from the U.S. COVID-19 Scenario Modeling Hub. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.26.23297581. [PMID: 37961207 PMCID: PMC10635209 DOI: 10.1101/2023.10.26.23297581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Importance COVID-19 continues to cause significant hospitalizations and deaths in the United States. Its continued burden and the impact of annually reformulated vaccines remain unclear. Objective To project COVID-19 hospitalizations and deaths from April 2023-April 2025 under two plausible assumptions about immune escape (20% per year and 50% per year) and three possible CDC recommendations for the use of annually reformulated vaccines (no vaccine recommendation, vaccination for those aged 65+, vaccination for all eligible groups). Design The COVID-19 Scenario Modeling Hub solicited projections of COVID-19 hospitalization and deaths between April 15, 2023-April 15, 2025 under six scenarios representing the intersection of considered levels of immune escape and vaccination. State and national projections from eight modeling teams were ensembled to produce projections for each scenario. Setting The entire United States. Participants None. Exposure Annually reformulated vaccines assumed to be 65% effective against strains circulating on June 15 of each year and to become available on September 1. Age and state specific coverage in recommended groups was assumed to match that seen for the first (fall 2021) COVID-19 booster. Main outcomes and measures Ensemble estimates of weekly and cumulative COVID-19 hospitalizations and deaths. Expected relative and absolute reductions in hospitalizations and deaths due to vaccination over the projection period. Results From April 15, 2023-April 15, 2025, COVID-19 is projected to cause annual epidemics peaking November-January. In the most pessimistic scenario (high immune escape, no vaccination recommendation), we project 2.1 million (90% PI: 1,438,000-4,270,000) hospitalizations and 209,000 (90% PI: 139,000-461,000) deaths, exceeding pre-pandemic mortality of influenza and pneumonia. In high immune escape scenarios, vaccination of those aged 65+ results in 230,000 (95% CI: 104,000-355,000) fewer hospitalizations and 33,000 (95% CI: 12,000-54,000) fewer deaths, while vaccination of all eligible individuals results in 431,000 (95% CI: 264,000-598,000) fewer hospitalizations and 49,000 (95% CI: 29,000-69,000) fewer deaths. Conclusion and Relevance COVID-19 is projected to be a significant public health threat over the coming two years. Broad vaccination has the potential to substantially reduce the burden of this disease.
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Affiliation(s)
- Sung-mok Jung
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Sara L. Loo
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Emily Howerton
- The Pennsylvania State University, State College, Pennsylvania
| | | | - Claire P. Smith
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Erica C. Carcelén
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Katie Yan
- The Pennsylvania State University, State College, Pennsylvania
| | - Samantha J. Bents
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | | | - Jessi Espino
- University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Joseph C. Lemaitre
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Koji Sato
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Clif D. McKee
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Alison L. Hill
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | | | - Kunpeng Mu
- University of Massachusetts Amherst, Amherst, Massachusetts
| | | | | | | | - Julie S. Ivy
- North Carolina State University, Raleigh, North Carolina
| | | | - Julie L. Swann
- North Carolina State University, Raleigh, North Carolina
| | | | - Sean Cavany
- University of Notre Dame, Notre Dame, Indiana
| | | | | | - Shi Chen
- University of North Carolina at Charlotte, Charlotte, North Carolina
| | - Rajib Paul
- University of North Carolina at Charlotte, Charlotte, North Carolina
| | - Daniel Janies
- University of North Carolina at Charlotte, Charlotte, North Carolina
| | - Jean-Claude Thill
- University of North Carolina at Charlotte, Charlotte, North Carolina
| | | | - Majd Al Aawar
- University of Southern California, Los Angeles, California
| | - Kaiming Bi
- University of Texas at Austin, Austin, Texas
| | | | | | | | | | | | | | | | | | - Brian Klahn
- University of Virginia, Charlottesville, Virginia
| | | | | | | | | | - Stefan Hoops
- University of Virginia, Charlottesville, Virginia
| | | | - Dustin Machi
- University of Virginia, Charlottesville, Virginia
| | | | - Bryan Lewis
- University of Virginia, Charlottesville, Virginia
| | | | | | | | - Katriona Shea
- The Pennsylvania State University, State College, Pennsylvania
| | - Shaun Truelove
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | - Justin Lessler
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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21
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Zhou J, Sukhova K, Peacock TP, McKay PF, Brown JC, Frise R, Baillon L, Moshe M, Kugathasan R, Shattock RJ, Barclay WS. Omicron breakthrough infections in vaccinated or previously infected hamsters. Proc Natl Acad Sci U S A 2023; 120:e2308655120. [PMID: 37903249 PMCID: PMC10636328 DOI: 10.1073/pnas.2308655120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/17/2023] [Indexed: 11/01/2023] Open
Abstract
The ongoing SARS-CoV-2 epidemic was marked by the repeated emergence and replacement of "variants" with genetic and phenotypic distance from the ancestral strains, the most recent examples being viruses of the Omicron lineage. Here, we describe a hamster direct contact exposure challenge model to assess protection against reinfection conferred by either vaccination or prior infection. We found that two doses of self-amplifying RNA vaccine based on the ancestral Spike ameliorated weight loss following Delta infection and decreased viral loads but had minimal effect on Omicron BA.1 infection. Prior vaccination followed by Delta or BA.1 breakthrough infections led to a high degree of cross-reactivity to all tested variants, suggesting that repeated exposure to antigenically distinct Spikes, via infection and/or vaccination drives a cross-reactive immune response. Prior infection with ancestral or Alpha variant was partially protective against BA.1 infection, whereas all animals previously infected with Delta and exposed to BA.1 became reinfected, although they shed less virus than BA.1-infected naive hamsters. Hamsters reinfected with BA.1 after prior Delta infection emitted infectious virus into the air, indicating that they could be responsible for onwards airborne transmission. We further tested whether prior infection with BA.1 protected from reinfection with Delta or later Omicron sublineages BA.2, BA.4, or BA.5. BA.1 was protective against BA.2 but not against Delta, BA.4, or BA.5 reinfection. These findings suggest that cohorts whose only immune experience of COVID-19 is Omicron BA.1 infection may be vulnerable to future circulation of reemerged Delta-like derivatives, as well as emerging Omicron sublineages.
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Affiliation(s)
- Jie Zhou
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Ksenia Sukhova
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Thomas P. Peacock
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Paul F. McKay
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Jonathan C. Brown
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Rebecca Frise
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Laury Baillon
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Maya Moshe
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Ruthiran Kugathasan
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Robin J. Shattock
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
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22
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Santos da Silva E, Servais JY, Kohnen M, Arendt V, Staub T, Krüger R, Fagherazzi G, Wilmes P, Hübschen JM, Ollert M, Perez-Bercoff D, Seguin-Devaux C. Validation of a SARS-CoV-2 Surrogate Neutralization Test Detecting Neutralizing Antibodies against the Major Variants of Concern. Int J Mol Sci 2023; 24:14965. [PMID: 37834413 PMCID: PMC10573711 DOI: 10.3390/ijms241914965] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
SARS-CoV-2 infection and/or vaccination elicit a broad range of neutralizing antibody responses against the different variants of concern (VOC). We established a new variant-adapted surrogate virus neutralization test (sVNT) and assessed the neutralization activity against the ancestral B.1 (WT) and VOC Delta, Omicron BA.1, BA.2, and BA.5. Analytical performances were compared against the respective VOC to the reference virus neutralization test (VNT) and two CE-IVD labeled kits using three different cohorts collected during the COVID-19 waves. Correlation analyses showed moderate to strong correlation for Omicron sub-variants (Spearman's r = 0.7081 for BA.1, r = 0.7205 for BA.2, and r = 0.6042 for BA.5), and for WT (r = 0.8458) and Delta-sVNT (r = 0.8158), respectively. Comparison of the WT-sVNT performance with two CE-IVD kits, the "Icosagen SARS-CoV-2 Neutralizing Antibody ELISA kit" and the "Genscript cPass, kit" revealed an overall good correlation ranging from 0.8673 to -0.8773 and a midway profile between both commercial kits with 87.76% sensitivity and 90.48% clinical specificity. The BA.2-sVNT performance was similar to the BA.2 Genscript test. Finally, a correlation analysis revealed a strong association (r = 0.8583) between BA.5-sVNT and VNT sVNT using a double-vaccinated cohort (n = 100) and an Omicron-breakthrough infection cohort (n = 91). In conclusion, the sVNT allows for the efficient prediction of immune protection against the various VOCs.
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Affiliation(s)
- Eveline Santos da Silva
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (J.M.H.); (M.O.); (D.P.-B.)
| | - Jean-Yves Servais
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (J.M.H.); (M.O.); (D.P.-B.)
| | - Michel Kohnen
- National Service of Infectious Diseases, Centre Hospitalier de Luxembourg, 4 Rue Ernest Barblé, L-1210 Luxembourg, Luxembourg; (M.K.); (V.A.); (T.S.)
| | - Vic Arendt
- National Service of Infectious Diseases, Centre Hospitalier de Luxembourg, 4 Rue Ernest Barblé, L-1210 Luxembourg, Luxembourg; (M.K.); (V.A.); (T.S.)
| | - Therese Staub
- National Service of Infectious Diseases, Centre Hospitalier de Luxembourg, 4 Rue Ernest Barblé, L-1210 Luxembourg, Luxembourg; (M.K.); (V.A.); (T.S.)
| | | | | | - Rejko Krüger
- Transversal Translational Medicine, Luxembourg Institute of Health; Centre Hospitalier de Luxembourg, 4 rue Ernest Barblé, L-1210 Luxembourg, Luxembourg;
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Guy Fagherazzi
- Department of Precision Health, Luxembourg Institute of Health, 1AB Rue Thomas Edison, L-1445 Strassen, Luxembourg;
| | - Paul Wilmes
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, 7 Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg;
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Judith M. Hübschen
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (J.M.H.); (M.O.); (D.P.-B.)
| | - Markus Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (J.M.H.); (M.O.); (D.P.-B.)
| | - Danielle Perez-Bercoff
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (J.M.H.); (M.O.); (D.P.-B.)
| | - Carole Seguin-Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (J.M.H.); (M.O.); (D.P.-B.)
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23
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Wilks SH, Mühlemann B, Shen X, Türeli S, LeGresley EB, Netzl A, Caniza MA, Chacaltana-Huarcaya JN, Corman VM, Daniell X, Datto MB, Dawood FS, Denny TN, Drosten C, Fouchier RAM, Garcia PJ, Halfmann PJ, Jassem A, Jeworowski LM, Jones TC, Kawaoka Y, Krammer F, McDanal C, Pajon R, Simon V, Stockwell MS, Tang H, van Bakel H, Veguilla V, Webby R, Montefiori DC, Smith DJ. Mapping SARS-CoV-2 antigenic relationships and serological responses. Science 2023; 382:eadj0070. [PMID: 37797027 DOI: 10.1126/science.adj0070] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/23/2023] [Indexed: 10/07/2023]
Abstract
During the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, multiple variants escaping preexisting immunity emerged, causing reinfections of previously exposed individuals. Here, we used antigenic cartography to analyze patterns of cross-reactivity among 21 variants and 15 groups of human sera obtained after primary infection with 10 different variants or after messenger RNA (mRNA)-1273 or mRNA-1273.351 vaccination. We found antigenic differences among pre-Omicron variants caused by substitutions at spike-protein positions 417, 452, 484, and 501. Quantifying changes in response breadth over time and with additional vaccine doses, our results show the largest increase between 4 weeks and >3 months after a second dose. We found changes in immunodominance of different spike regions, depending on the variant an individual was first exposed to, with implications for variant risk assessment and vaccine-strain selection.
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Affiliation(s)
- Samuel H Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - 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
| | - Xiaoying Shen
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sina Türeli
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Eric B LeGresley
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Antonia Netzl
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Miguela A Caniza
- Department of Global Pediatric Medicine, Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 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
| | - Xiaoju Daniell
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Michael B Datto
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | | | - Thomas N Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 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
| | | | - Patricia J Garcia
- School of Public Health, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Science, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Agatha Jassem
- BC Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Lara M Jeworowski
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Terry C Jones
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
- 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
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Science, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo, Japan
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charlene McDanal
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | | | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa S Stockwell
- Division of Child and Adolescent Health, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, and Department of Population and Family Health, Mailman School of Public Health, New York, NY, USA
| | - Haili Tang
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vic Veguilla
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Richard Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David C Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
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24
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Vinzón SE, Lopez MV, Cafferata EGA, Soto AS, Berguer PM, Vazquez L, Nusblat L, Pontoriero AV, Belotti EM, Salvetti NR, Viale DL, Vilardo AE, Avaro MM, Benedetti E, Russo ML, Dattero ME, Carobene M, Sánchez-Lamas M, Afonso J, Heitrich M, Cristófalo AE, Otero LH, Baumeister EG, Ortega HH, Edelstein A, Podhajcer OL. Cross-protection and cross-neutralization capacity of ancestral and VOC-matched SARS-CoV-2 adenoviral vector-based vaccines. NPJ Vaccines 2023; 8:149. [PMID: 37794010 PMCID: PMC10550992 DOI: 10.1038/s41541-023-00737-4] [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: 11/16/2022] [Accepted: 09/15/2023] [Indexed: 10/06/2023] Open
Abstract
COVID-19 vaccines were originally designed based on the ancestral Spike protein, but immune escape of emergent Variants of Concern (VOC) jeopardized their efficacy, warranting variant-proof vaccines. Here, we used preclinical rodent models to establish the cross-protective and cross-neutralizing capacity of adenoviral-vectored vaccines expressing VOC-matched Spike. CoroVaxG.3-D.FR, matched to Delta Plus Spike, displayed the highest levels of nAb to the matched VOC and mismatched variants. Cross-protection against viral infection in aged K18-hACE2 mice showed dramatic differences among the different vaccines. While Delta-targeted vaccines fully protected mice from a challenge with Gamma, a Gamma-based vaccine offered only partial protection to Delta challenge. Administration of CorovaxG.3-D.FR in a prime/boost regimen showed that a booster was able to increase the neutralizing capacity of the sera against all variants and fully protect aged K18-hACE2 mice against Omicron BA.1, as a BA.1-targeted vaccine did. The neutralizing capacity of the sera diminished in all cases against Omicron BA.2 and BA.5. Altogether, the data demonstrate that a booster with a vaccine based on an antigenically distant variant, such as Delta or BA.1, has the potential to protect from a wider range of SARS-CoV-2 lineages, although careful surveillance of breakthrough infections will help to evaluate combination vaccines targeting antigenically divergent variants yet to emerge.
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Affiliation(s)
- Sabrina E Vinzón
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - María V Lopez
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Eduardo G A Cafferata
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Ariadna S Soto
- Laboratorio de Microbiología e Inmunología Molecular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Paula M Berguer
- Laboratorio de Microbiología e Inmunología Molecular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Luciana Vazquez
- Unidad Operativa Centro de Contención Biológica, ANLIS Dr. Carlos G. Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Leonora Nusblat
- Unidad Operativa Centro de Contención Biológica, ANLIS Dr. Carlos G. Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Andrea V Pontoriero
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Eduardo M Belotti
- Centro de Medicina Comparada, ICiVet-Litoral, Universidad Nacional del Litoral-CONICET; Esperanza, Santa Fe, 3080, Argentina
| | - Natalia R Salvetti
- Centro de Medicina Comparada, ICiVet-Litoral, Universidad Nacional del Litoral-CONICET; Esperanza, Santa Fe, 3080, Argentina
| | - Diego L Viale
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Ariel E Vilardo
- Unidad Operativa Centro de Contención Biológica, ANLIS Dr. Carlos G. Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Martin M Avaro
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Estefanía Benedetti
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Mara L Russo
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - María E Dattero
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Mauricio Carobene
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Buenos Aires, Argentina
| | | | - Jimena Afonso
- Area de Bioterio, Fundación Instituto Leloir; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Mauro Heitrich
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Alejandro E Cristófalo
- Centro de Re-diseño e Ingeniería de Proteínas (CRIP), Universidad Nacional de San Martín, San Martin, Buenos Aires, 1650, Argentina
| | - Lisandro H Otero
- Centro de Re-diseño e Ingeniería de Proteínas (CRIP), Universidad Nacional de San Martín, San Martin, Buenos Aires, 1650, Argentina
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Instituto de Biotecnología Ambiental y Salud, CONICET, Universidad Nacional de Río Cuarto, Córdoba, X5804BYA, Argentina
| | - Elsa G Baumeister
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Hugo H Ortega
- Centro de Medicina Comparada, ICiVet-Litoral, Universidad Nacional del Litoral-CONICET; Esperanza, Santa Fe, 3080, Argentina
| | - Alexis Edelstein
- Unidad Operativa Centro de Contención Biológica, ANLIS Dr. Carlos G. Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Osvaldo L Podhajcer
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina.
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25
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Mykytyn AZ, Fouchier RA, Haagmans BL. Antigenic evolution of SARS coronavirus 2. Curr Opin Virol 2023; 62:101349. [PMID: 37647851 DOI: 10.1016/j.coviro.2023.101349] [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: 05/10/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 09/01/2023]
Abstract
SARS coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, emerged in China in December 2019. Vaccines developed were very effective initially, however, the virus has shown remarkable evolution with multiple variants spreading globally over the last three years. Nowadays, newly emerging Omicron lineages are gaining substitutions at a fast rate, resulting in escape from neutralization by antibodies that target the Spike protein. Tools to map the impact of substitutions on the further antigenic evolution of SARS-CoV-2, such as antigenic cartography, may be helpful to update SARS-CoV-2 vaccines. In this review, we focus on the antigenic evolution of SARS-CoV-2, highlighting the impact of Spike protein substitutions individually and in combination on immune escape.
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Affiliation(s)
- Anna Z Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Ron Am Fouchier
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Bart L Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands.
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26
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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 M, Türeli S, Wang W, Weiss CD, Smith DJ. Comparative Analysis of SARS-CoV-2 Antigenicity across Assays and in Human and Animal Model Sera. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559689. [PMID: 37808679 PMCID: PMC10557678 DOI: 10.1101/2023.09.27.559689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The antigenic evolution of SARS-CoV-2 requires ongoing monitoring to judge the immune escape of newly arising variants. A surveillance system necessitates an understanding of differences in neutralization titers measured in different assays and using human and animal sera. We compared 18 datasets generated using human, hamster, and mouse sera, and six different neutralization assays. Titer magnitude was lowest in human, intermediate in hamster, and highest in mouse sera. Fold change, immunodominance patterns and antigenic maps were similar among sera. Most assays yielded similar results, except for differences in fold change in cytopathic effect assays. Not enough data was available for conclusively judging mouse sera, but hamster sera were a consistent surrogate for human first-infection sera.
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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, Switzerland
- Centre for Emerging Viral Diseases, University Hospitals of Geneva and University of Geneva, Switzerland
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 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, 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, Bangkoknoi, Bangkok 10700, Thailand
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Andrew M. and Jane M. Bursky the Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 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, Switzerland
- Centre for Emerging Viral Diseases, University Hospitals of Geneva and University of Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Venkata-Viswanadh Edara
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Madison Ellis
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Ron A M Fouchier
- Viroscience Department, Erasmus Medical Center, 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, USA
| | - Bart Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 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, USA
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo 162-8655, Japan
| | - 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, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lilin Lai
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA, 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, UK
| | - Sabrina Lusvarghi
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Benjamin Meyer
- Centre of Vaccinology, Department of Pathology and Immunology, University of Geneva, 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, UK
| | - David C Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Anna Mykytyn
- Viroscience Department, Erasmus Medical Center, 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, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, 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, UK
| | - Xiaoying Shen
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 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, USA
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Mehul Suthar
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA, 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, U.S. 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, U.S. 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
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27
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Andre M, Lau LS, Pokharel MD, Ramelow J, Owens F, Souchak J, Akkaoui J, Ales E, Brown H, Shil R, Nazaire V, Manevski M, Paul NP, Esteban-Lopez M, Ceyhan Y, El-Hage N. From Alpha to Omicron: How Different Variants of Concern of the SARS-Coronavirus-2 Impacted the World. BIOLOGY 2023; 12:1267. [PMID: 37759666 PMCID: PMC10525159 DOI: 10.3390/biology12091267] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/07/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023]
Abstract
SARS-CoV-2, the virus that causes COVID-19, is prone to mutations and the generation of genetic variants. Since its first outbreak in 2019, SARS-CoV-2 has continually evolved, resulting in the emergence of several lineages and variants of concern (VOC) that have gained more efficient transmission, severity, and immune evasion properties. The World Health Organization has given these variants names according to the letters of the Greek Alphabet, starting with the Alpha (B.1.1.7) variant, which emerged in 2020, followed by the Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529) variants. This review explores the genetic variation among different VOCs of SARS-CoV-2 and how the emergence of variants made a global impact on the pandemic.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Nazira El-Hage
- Herbert Wertheim College of Medicine, Biomedical Sciences Program Florida International University, Miami, FL 33199, USA; (M.A.); (L.-S.L.); (M.D.P.); (J.R.); (F.O.); (J.S.); (J.A.); (E.A.); (H.B.); (R.S.); (V.N.); (M.M.); (N.P.P.); (M.E.-L.); (Y.C.)
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28
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Suntronwong N, Kanokudom S, Assawakosri S, Vichaiwattana P, Klinfueng S, Phowatthanasathian H, Chansaenroj J, Srimuan D, Thatsanathorn T, Duangchinda T, Chantima W, Pakchotanon P, Sudhinaraset N, Wanlapakorn N, Poovorawan Y. Neutralizing antibodies against Omicron BA.5 among children with infection alone, vaccination alone, and hybrid immunity. Int J Infect Dis 2023; 134:18-22. [PMID: 37207716 DOI: 10.1016/j.ijid.2023.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/25/2023] [Accepted: 05/04/2023] [Indexed: 05/21/2023] Open
Abstract
OBJECTIVES To assess the binding antibody response and strength of neutralization against Omicron BA.5 in serum samples from children with different antigen exposures (infection/vaccination) and hybrid immunity. METHODS This study recruited children aged 5-7 years. All samples were tested for anti-nucleocapsid immunoglobulin (Ig)G, anti-receptor binding domain (RBD) IgG, and total anti-RBD Ig. Neutralizing antibodies (nAbs) against Omicron BA.5 were determined using a focus reduction neutralization test. RESULTS A total of 196 serum samples from unvaccinated children with infection (n = 57), vaccination alone (n = 71), and hybrid immunity (n = 68). Our results showed that 90% of the samples from children with hybrid immunity, 62.2% from two-dose vaccination, and 48% from Omicron infection alone had detectable nAbs against Omicron BA.5. The highest neutralizing titer was observed in infection plus two-dose vaccination, which reached 6.3-fold increase, whereas nAb titers in two-dose vaccination was comparable to Omicron-infected sera. However, sera from pre-Omicron infection and single-dose vaccination failed to neutralize Omicron BA.5; although, the total anti-RBD Ig were comparable with Omicron-infected sera. CONCLUSION This result highlights that hybrid immunity provided cross-reactive antibodies to neutralize Omicron BA.5 compared with either vaccination or infection alone. The finding emphasizes the importance of vaccination in unvaccinated children who are infected with pre-Omicron or Omicron variants.
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Affiliation(s)
- Nungruthai Suntronwong
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sitthichai Kanokudom
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; Center of Excellence in Osteoarthritis and Musculoskeleton, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok 10330, Thailand
| | - Suvichada Assawakosri
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; Center of Excellence in Osteoarthritis and Musculoskeleton, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok 10330, Thailand
| | - Preeyaporn Vichaiwattana
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sirapa Klinfueng
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Harit Phowatthanasathian
- Chulalongkorn University International Medical Program (CU-MEDi), Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jira Chansaenroj
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Donchida Srimuan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thaksaporn Thatsanathorn
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thaneeya Duangchinda
- Molecular Biology of Dengue and Flaviviruses Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Warangkana Chantima
- Division of Dengue Hemorrhagic Fever Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Pattarakul Pakchotanon
- Molecular Biology of Dengue and Flaviviruses Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Natthinee Sudhinaraset
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nasamon Wanlapakorn
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; The Royal Society of Thailand (FRS(T)), Sanam Sueapa, Dusit, Bangkok 10330, Thailand.
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29
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Branche AR, Rouphael NG, Diemert DJ, Falsey AR, Losada C, Baden LR, Frey SE, Whitaker JA, Little SJ, Anderson EJ, Walter EB, Novak RM, Rupp R, Jackson LA, Babu TM, Kottkamp AC, Luetkemeyer AF, Immergluck LC, Presti RM, Bäcker M, Winokur PL, Mahgoub SM, Goepfert PA, Fusco DN, Malkin E, Bethony JM, Walsh EE, Graciaa DS, Samaha H, Sherman AC, Walsh SR, Abate G, Oikonomopoulou Z, El Sahly HM, Martin TCS, Kamidani S, Smith MJ, Ladner BG, Porterfield L, Dunstan M, Wald A, Davis T, Atmar RL, Mulligan MJ, Lyke KE, Posavad CM, Meagher MA, Stephens DS, Neuzil KM, Abebe K, Hill H, Albert J, Telu K, Mu J, Lewis TC, Giebeig LA, Eaton A, Netzl A, Wilks SH, Türeli S, Makhene M, Crandon S, Montefiori DC, Makowski M, Smith DJ, Nayak SU, Roberts PC, Beigel JH. Comparison of bivalent and monovalent SARS-CoV-2 variant vaccines: the phase 2 randomized open-label COVAIL trial. Nat Med 2023; 29:2334-2346. [PMID: 37640860 PMCID: PMC10504073 DOI: 10.1038/s41591-023-02503-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/17/2023] [Indexed: 08/31/2023]
Abstract
Vaccine protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection wanes over time, requiring updated boosters. In a phase 2, open-label, randomized clinical trial with sequentially enrolled stages at 22 US sites, we assessed safety and immunogenicity of a second boost with monovalent or bivalent variant vaccines from mRNA and protein-based platforms targeting wild-type, Beta, Delta and Omicron BA.1 spike antigens. The primary outcome was pseudovirus neutralization titers at 50% inhibitory dilution (ID50 titers) with 95% confidence intervals against different SARS-CoV-2 strains. The secondary outcome assessed safety by solicited local and systemic adverse events (AEs), unsolicited AEs, serious AEs and AEs of special interest. Boosting with prototype/wild-type vaccines produced numerically lower ID50 titers than any variant-containing vaccine against all variants. Conversely, boosting with a variant vaccine excluding prototype was not associated with decreased neutralization against D614G. Omicron BA.1 or Beta monovalent vaccines were nearly equivalent to Omicron BA.1 + prototype or Beta + prototype bivalent vaccines for neutralization of Beta, Omicron BA.1 and Omicron BA.4/5, although they were lower for contemporaneous Omicron subvariants. Safety was similar across arms and stages and comparable to previous reports. Our study shows that updated vaccines targeting Beta or Omicron BA.1 provide broadly crossprotective neutralizing antibody responses against diverse SARS-CoV-2 variants without sacrificing immunity to the ancestral strain. ClinicalTrials.gov registration: NCT05289037 .
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Affiliation(s)
- Angela R Branche
- Department of Medicine, Division of Infectious Diseases, University of Rochester, Rochester, NY, USA.
| | | | - David J Diemert
- George Washington Vaccine Research Unit, George Washington University, Washington D.C., WA, USA
| | - Ann R Falsey
- Department of Medicine, Division of Infectious Diseases, University of Rochester, Rochester, NY, USA
| | | | - Lindsey R Baden
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sharon E Frey
- Center for Vaccine Development, Saint Louis University, St. Louis, MO, USA
| | - Jennifer A Whitaker
- Departments of Molecular Virology and Microbiology and Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Susan J Little
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Evan J Anderson
- Center for Childhood Infections and Vaccines (CCIV) of Children's Healthcare of Atlanta and Emory University Department of Pediatrics, Atlanta, GA, USA
| | - Emmanuel B Walter
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Richard M Novak
- Project WISH, University of Illinois at Chicago, Chicago, IL, USA
| | - Richard Rupp
- University of Texas Medical Branch, Galveston, TX, USA
| | - Lisa A Jackson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Tara M Babu
- Departments of Medicine, Epidemiology and Laboratory Medicine and Pathology, University of Washington, Vaccines and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Angelica C Kottkamp
- NYU VTEU Manhattan Research Clinic, NYU Grossman School of Medicine, New York, NY, USA
| | - Anne F Luetkemeyer
- Zuckerberg San Francisco General, University of California San Francisco, San Francisco, CA, USA
| | - Lilly C Immergluck
- Department of Microbiology, Biochemistry and Immunology, and Clinical Research Center, Morehouse School of Medicine, Atlanta, GA, USA
| | - Rachel M Presti
- Washington University School of Medicine, St. Louis, MO, USA
| | - Martín Bäcker
- NYU VTEU Long Island Research Clinic, NYU Long Island School of Medicine, Mineola, NY, USA
| | | | - Siham M Mahgoub
- Howard University College of Medicine, Howard University Hospital, Washington D.C., WA, USA
| | - Paul A Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Elissa Malkin
- George Washington Vaccine Research Unit, George Washington University, Washington D.C., WA, USA
| | - Jeffrey M Bethony
- George Washington Vaccine Research Unit, George Washington University, Washington D.C., WA, USA
| | - Edward E Walsh
- Department of Medicine, Division of Infectious Diseases, University of Rochester, Rochester, NY, USA
| | | | - Hady Samaha
- Hope Clinic, Emory University, Decatur, GA, USA
| | - Amy C Sherman
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephen R Walsh
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Getahun Abate
- Center for Vaccine Development, Saint Louis University, St. Louis, MO, USA
| | | | - Hana M El Sahly
- Departments of Molecular Virology and Microbiology and Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Thomas C S Martin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Satoshi Kamidani
- Center for Childhood Infections and Vaccines (CCIV) of Children's Healthcare of Atlanta and Emory University Department of Pediatrics, Atlanta, GA, USA
| | - Michael J Smith
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | | | - Maya Dunstan
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Anna Wald
- Departments of Medicine, Epidemiology and Laboratory Medicine and Pathology, University of Washington, Vaccines and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Tamia Davis
- NYU VTEU Manhattan Research Clinic, NYU Grossman School of Medicine, New York, NY, USA
| | - Robert L Atmar
- Departments of Molecular Virology and Microbiology and Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Mark J Mulligan
- NYU VTEU Manhattan Research Clinic, NYU Grossman School of Medicine, New York, NY, USA
| | - Kirsten E Lyke
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine Baltimore, Baltimore, MD, USA
| | - Christine M Posavad
- IDCRC Laboratory Operations Unit, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Megan A Meagher
- IDCRC Laboratory Operations Unit, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David S Stephens
- Department of Medicine and Woodruff Health Sciences Center, Emory University, Atlanta, GA, USA
| | - Kathleen M Neuzil
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine Baltimore, Baltimore, MD, USA
| | | | - Heather Hill
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Jim Albert
- The Emmes Company, LLC, Rockville, MD, USA
| | | | - Jinjian Mu
- The Emmes Company, LLC, Rockville, MD, USA
| | - Teri C Lewis
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lisa A Giebeig
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amanda Eaton
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Antonia Netzl
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Samuel H Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Sina Türeli
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Mamodikoe Makhene
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sonja Crandon
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | | | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Seema U Nayak
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Paul C Roberts
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John H Beigel
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Rössler A, Netzl A, Knabl L, Bante D, Wilks SH, Borena W, von Laer D, Smith DJ, Kimpel J. Characterizing SARS-CoV-2 neutralization profiles after bivalent boosting using antigenic cartography. Nat Commun 2023; 14:5224. [PMID: 37633965 PMCID: PMC10460376 DOI: 10.1038/s41467-023-41049-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/21/2023] [Indexed: 08/28/2023] Open
Abstract
Since emergence of the initial SARS-CoV-2 BA.1, BA.2 and BA.5 variants, Omicron has diversified substantially. Antigenic characterization of these new variants is important to analyze their potential immune escape from population immunity and implications for future vaccine composition. Here, we describe an antigenic map based on human single-exposure sera and live-virus isolates that includes a broad selection of recently emerged Omicron variants such as BA.2.75, BF.7, BQ, XBB and XBF variants. Recent Omicron variants clustered around BA.1 and BA.5 with some variants further extending the antigenic space. Based on this antigenic map we constructed antibody landscapes to describe neutralization profiles after booster immunization with bivalent mRNA vaccines based on ancestral virus and either BA.1 or BA.4/5. Immune escape of BA.2.75, BQ, XBB and XBF variants was also evident in bivalently boosted individuals, however, cross-neutralization was improved for those with hybrid immunity. Our results indicate that future vaccine updates are needed to induce cross-neutralizing antibodies against currently circulating variants.
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Affiliation(s)
- Annika Rössler
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria
| | - Antonia Netzl
- University of Cambridge, Centre for Pathogen Evolution, Department of Zoology, Cambridge, UK
| | - Ludwig Knabl
- Tyrolpath Obrist Brunhuber GmbH, Hauptplatz 4, 6511, Zams, Austria
| | - David Bante
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria
| | - Samuel H Wilks
- University of Cambridge, Centre for Pathogen Evolution, Department of Zoology, Cambridge, UK
| | - Wegene Borena
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria
| | - Dorothee von Laer
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria
| | - Derek J Smith
- University of Cambridge, Centre for Pathogen Evolution, Department of Zoology, Cambridge, UK.
| | - Janine Kimpel
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria.
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31
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Lin YCJ, Evans DH, Robbins NF, Orjuela G, Abe KT, Rathod B, Colwill K, Gingras AC, Tuite A, Yi QL, O’Brien SF, Drews SJ. Diminished Neutralization Capacity of SARS-CoV-2 Omicron BA.1 in Donor Plasma Collected from January to March 2021. Microbiol Spectr 2023; 11:e0525622. [PMID: 37289096 PMCID: PMC10434250 DOI: 10.1128/spectrum.05256-22] [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: 12/21/2022] [Accepted: 05/25/2023] [Indexed: 06/09/2023] Open
Abstract
The 50% plaque reduction neutralization assay (PRNT50) has been previously used to assess the neutralization capacity of donor plasma against wild-type and variant of concern (VOC) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Emerging data suggest that plasma with an anti-SARS-CoV-2 level of ≥2 × 104 binding antibody units/mL (BAU/mL) protects against SARS-CoV-2 Omicron BA.1 infection. Specimens were collected using a cross-sectional random sampling approach. For PRNT50 studies, 63 previously analyzed specimens by PRNT50 versus SARS-CoV-2 wild-type, Alpha, Beta, Gamma, and Delta were analyzed by PRNT50 versus Omicron BA.1. The 63 specimens plus 4,390 specimens (randomly sampled regardless of serological evidence of infection) were also tested using the Abbott SARS-CoV-2 IgG II Quant assay (anti-spike [S]; Abbott, Chicago, IL, USA; Abbott Quant assay). In the vaccinated group, the percentages of specimens with any measurable PRNT50 versus wild-type or VOC were wild type (21/25 [84%]), Alpha (19/25 [76%]), Beta (18/25 [72%]), Gamma (13/25 [52%]), Delta (19/25 [76%]), and Omicron BA.1 (9/25 [36%]). In the unvaccinated group, the percentages of specimens with any measurable PRNT50 versus wild type or VOC were wild-type SARS-CoV-2 (16/39 [41%]), Alpha (16/39 [41%]), Beta (10/39 [26%]), Gamma (9/39 [23%]), Delta (16/39 [41%]), and Omicron BA.1 (0/39) (Fisher's exact tests, vaccinated versus unvaccinated for each variant, P < 0.05). None of the 4,453 specimens tested by the Abbott Quant assay had a binding capacity of ≥2 × 104 BAU/mL. Vaccinated donors were more likely than unvaccinated donors to neutralize Omicron when assessed by a PRNT50 assay. IMPORTANCE SARS-CoV-2 Omicron emergence occurred in Canada during the period from November 2021 to January 2022. This study assessed the ability of donor plasma collected earlier (January to March 2021) to generate any neutralizing capacity against Omicron BA.1 SARS-CoV-2. Vaccinated individuals, regardless of infection status, were more likely to neutralize Omicron BA.1 than unvaccinated individuals. This study then used a semiquantitative binding antibody assay to screen a larger number of specimens (4,453) for individual specimens that might have high-titer neutralizing capacity against Omicron BA.1. None of the 4,453 specimens tested by the semiquantitative SARS-CoV-2 assay had a binding capacity suggestive of a high-titer neutralizing capacity against Omicron BA.1. These data do not imply that Canadians lacked immunity to Omicron BA.1 during the study period. Immunity to SARS-CoV-2 is complex, and there is still no wide consensus on correlation of protection to SARS-CoV-2.
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Affiliation(s)
- Yi-Chan J. Lin
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada
| | - David H. Evans
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada
| | | | | | - Kento T. Abe
- Lunenfeld-Tanenbaum Research Institute at Mt. Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Bhavisha Rathod
- Lunenfeld-Tanenbaum Research Institute at Mt. Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Karen Colwill
- Lunenfeld-Tanenbaum Research Institute at Mt. Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute at Mt. Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ashleigh Tuite
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Qi-Long Yi
- Epidemiology and Surveillance, Canadian Blood Services, Ottawa, Ontario, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Sheila F. O’Brien
- Epidemiology and Surveillance, Canadian Blood Services, Ottawa, Ontario, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Steven J. Drews
- Canadian Blood Services, Microbiology, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
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32
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Verkhivker G, Alshahrani M, Gupta G, Xiao S, Tao P. Probing conformational landscapes of binding and allostery in the SARS-CoV-2 omicron variant complexes using microsecond atomistic simulations and perturbation-based profiling approaches: hidden role of omicron mutations as modulators of allosteric signaling and epistatic relationships. Phys Chem Chem Phys 2023; 25:21245-21266. [PMID: 37548589 PMCID: PMC10536792 DOI: 10.1039/d3cp02042h] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
In this study, we systematically examine the conformational dynamics, binding and allosteric communications in the Omicron BA.1, BA.2, BA.3 and BA.4/BA.5 spike protein complexes with the ACE2 host receptor using molecular dynamics simulations and perturbation-based network profiling approaches. Microsecond atomistic simulations provided a detailed characterization of the conformational landscapes and revealed the increased thermodynamic stabilization of the BA.2 variant which can be contrasted with the BA.4/BA.5 variants inducing a significant mobility of the complexes. Using the dynamics-based mutational scanning of spike residues, we identified structural stability and binding affinity hotspots in the Omicron complexes. Perturbation response scanning and network-based mutational profiling approaches probed the effect of the Omicron mutations on allosteric interactions and communications in the complexes. The results of this analysis revealed specific roles of Omicron mutations as conformationally plastic and evolutionary adaptable modulators of binding and allostery which are coupled to the major regulatory positions through interaction networks. Through perturbation network scanning of allosteric residue potentials in the Omicron variant complexes performed in the background of the original strain, we characterized regions of epistatic couplings that are centered around the binding affinity hotspots N501Y and Q498R. Our results dissected the vital role of these epistatic centers in regulating protein stability, efficient ACE2 binding and allostery which allows for accumulation of multiple Omicron immune escape mutations at other sites. Through integrative computational approaches, this study provides a systematic analysis of the effects of Omicron mutations on thermodynamics, binding and allosteric signaling in the complexes with ACE2 receptor.
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Affiliation(s)
- Gennady Verkhivker
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA.
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
| | - Grace Gupta
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
| | - Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75275, USA.
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75275, USA.
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33
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Hu YF, Yuen TTT, Gong HR, Hu B, Hu JC, Lin XS, Rong L, Zhou CL, Chen LL, Wang X, Lei C, Yau T, Hung IFN, To KKW, Yuen KY, Zhang BZ, Chu H, Huang JD. Rational design of a booster vaccine against COVID-19 based on antigenic distance. Cell Host Microbe 2023; 31:1301-1316.e8. [PMID: 37527659 DOI: 10.1016/j.chom.2023.07.004] [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: 01/11/2023] [Revised: 06/03/2023] [Accepted: 07/07/2023] [Indexed: 08/03/2023]
Abstract
Current COVID-19 vaccines are highly effective against symptomatic disease, but repeated booster doses using vaccines based on the ancestral strain offer limited additional protection against SARS-CoV-2 variants of concern (VOCs). To address this, we used antigenic distance to in silico select optimized booster vaccine seed strains effective against both current and future VOCs. Our model suggests that a SARS-CoV-1-based booster vaccine has the potential to cover a broader range of VOCs. Candidate vaccines including the spike protein from ancestral SARS-CoV-2, Delta, Omicron (BA.1), SARS-CoV-1, or MERS-CoV were experimentally evaluated in mice following two doses of the BNT162b2 vaccine. The SARS-CoV-1-based booster vaccine outperformed other candidates in terms of neutralizing antibody breadth and duration, as well as protective activity against Omicron (BA.2) challenge. This study suggests a unique strategy for selecting booster vaccines based on antigenic distance, which may be useful in designing future booster vaccines as new SARS-CoV-2 variants emerge.
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Affiliation(s)
- Ye-Fan Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 3/F, Laboratory Block, 21 Sassoon Road, Hong Kong, China; Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, 4/F Professional Block, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China; BayVax Biotech Limited, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong, China
| | - Terrence Tsz-Tai Yuen
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, 19/F Block T, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China
| | - Hua-Rui Gong
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen 518055, China; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 3/F, Laboratory Block, 21 Sassoon Road, Hong Kong, China
| | - Bingjie Hu
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, 19/F Block T, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China
| | - Jing-Chu Hu
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen 518055, China; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 3/F, Laboratory Block, 21 Sassoon Road, Hong Kong, China
| | - Xuan-Sheng Lin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 3/F, Laboratory Block, 21 Sassoon Road, Hong Kong, China
| | - Li Rong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 3/F, Laboratory Block, 21 Sassoon Road, Hong Kong, China
| | - Coco Luyao Zhou
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 3/F, Laboratory Block, 21 Sassoon Road, Hong Kong, China
| | - Lin-Lei Chen
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, 19/F Block T, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China
| | - Xiaolei Wang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 3/F, Laboratory Block, 21 Sassoon Road, Hong Kong, China
| | - Chaobi Lei
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen 518055, China
| | - Thomas Yau
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, 4/F Professional Block, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China
| | - Ivan Fan-Ngai Hung
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, 4/F Professional Block, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China
| | - Kelvin Kai-Wang To
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, 19/F Block T, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China
| | - Kwok-Yung Yuen
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, 19/F Block T, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China
| | - Bao-Zhong Zhang
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen 518055, China; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 3/F, Laboratory Block, 21 Sassoon Road, Hong Kong, China.
| | - Hin Chu
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, 19/F Block T, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China.
| | - Jian-Dong Huang
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen 518055, China; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 3/F, Laboratory Block, 21 Sassoon Road, Hong Kong, China; Clinical Oncology Center, Shenzhen Key Laboratory for Cancer Metastasis and Personalized Therapy, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, China; Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen University, Guangzhou 510120, China.
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34
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Springer DN, Traugott M, Reuberger E, Kothbauer KB, Borsodi C, Nägeli M, Oelschlägel T, Kelani H, Lammel O, Deutsch J, Puchhammer-Stöckl E, Höltl E, Aberle JH, Stiasny K, Weseslindtner L. A Multivariant Surrogate Neutralization Assay Identifies Variant-Specific Neutralizing Antibody Profiles in Primary SARS-CoV-2 Omicron Infection. Diagnostics (Basel) 2023; 13:2278. [PMID: 37443672 DOI: 10.3390/diagnostics13132278] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Primary infection with the Omicron variant of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) can be serologically identified with distinct profiles of neutralizing antibodies (nAbs), as indicated by high titers against the Omicron variant and low titers against the ancestral wild-type (WT). Here, we evaluated whether a novel surrogate virus neutralization assay (sVNT) that simultaneously quantifies the binding inhibition of angiotensin-converting enzyme 2 (ACE2) to the proteins of the WT- and Omicron-specific receptor-binding domains (RBDs) can identify nAb profiles after primary Omicron infection with accuracy similar to that of variant-specific live-virus neutralization tests (NTs). Therefore, we comparatively tested 205 samples from individuals after primary infection with the Omicron variant and the WT, and vaccinated subjects with or without Omicron breakthrough infections. Indeed, variant-specific RBD-ACE2 binding inhibition levels significantly correlated with respective NT titers (p < 0.0001, Spearman's r = 0.92 and r = 0.80 for WT and Omicron, respectively). In addition, samples from individuals after primary Omicron infection were securely identified with the sVNT according to their distinctive nAb profiles (area under the curve = 0.99; sensitivity: 97.2%; specificity: 97.84%). Thus, when laborious live-virus NTs are not feasible, the novel sVNT we evaluated in this study may serve as an acceptable substitute for the serological identification of individuals with primary Omicron infection.
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Affiliation(s)
| | - Marianna Traugott
- 4th Medical Department, Clinic Favoriten, Kaiser-Franz-Josef Hospital, 1100 Vienna, Austria
| | | | | | - Christian Borsodi
- Center for Virology, Medical University of Vienna, 1090 Vienna, Austria
| | - Michelle Nägeli
- 4th Medical Department, Clinic Favoriten, Kaiser-Franz-Josef Hospital, 1100 Vienna, Austria
| | - Theresa Oelschlägel
- 4th Medical Department, Clinic Favoriten, Kaiser-Franz-Josef Hospital, 1100 Vienna, Austria
| | - Hasan Kelani
- 4th Medical Department, Clinic Favoriten, Kaiser-Franz-Josef Hospital, 1100 Vienna, Austria
| | - Oliver Lammel
- Independent Researcher, 8972 Ramsau am Dachstein, Austria
| | | | | | - Eva Höltl
- Center for Public Health, Medical University of Vienna, 1090 Vienna, Austria
| | | | - Karin Stiasny
- Center for Virology, Medical University of Vienna, 1090 Vienna, Austria
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35
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Halfmann PJ, Loeffler K, Duffy A, Kuroda M, Kawaoka Y, Kane RS. Broad Protection Against Clade 1 Sarbecoviruses After a Single Immunization with Cocktail Spike-Protein-Nanoparticle Vaccine. RESEARCH SQUARE 2023:rs.3.rs-3088907. [PMID: 37461652 PMCID: PMC10350183 DOI: 10.21203/rs.3.rs-3088907/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The 2002 SARS outbreak, the 2019 emergence of COVID-19, and the continuing evolution of immune-evading SARS-CoV-2 variants together highlight the need for a broadly protective vaccine against ACE2-utilizing sarbecoviruses. While updated variant-matched formulations such as Pfizer-BioNTech's bivalent vaccine are a step in the right direction, protection needs to extend beyond SARS-CoV-2 and its variants to include SARS-like viruses. Here, we introduce bivalent and trivalent vaccine formulations using our spike protein nanoparticle platform that completely protected hamsters against BA.5 and XBB.1 challenges with no detectable virus in the lungs. The trivalent cocktails elicited highly neutralizing responses against all tested Omicron variants and the bat sarbecoviruses SHC014 and WIV1. Finally, our 614D/SHC014/XBB trivalent spike formulation completely protected human ACE2-transgenic hamsters against challenges with WIV1 and SHC014 with no detectable virus in the lungs. Collectively, these results illustrate that our trivalent protein-nanoparticle cocktail can provide broad protection against SARS-CoV-2-like and SARS-CoV-1-like sarbecoviruses.
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Affiliation(s)
- Peter J. Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Kathryn Loeffler
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Augustine Duffy
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Makoto Kuroda
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo 162-8655, Japan
| | - Ravi S. Kane
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
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36
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Astakhova EA, Morozov AA, Byazrova MG, Sukhova MM, Mikhailov AA, Minnegalieva AR, Gorchakov AA, Filatov AV. Antigenic Cartography Indicates That the Omicron BA.1 and BA.4/BA.5 Variants Remain Antigenically Distant to Ancestral SARS-CoV-2 after Sputnik V Vaccination Followed by Homologous (Sputnik V) or Heterologous (Comirnaty) Revaccination. Int J Mol Sci 2023; 24:10493. [PMID: 37445671 PMCID: PMC10341525 DOI: 10.3390/ijms241310493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
The rapid emergence of evasive SARS-CoV-2 variants is an ongoing challenge for COVID-19 vaccinology. Traditional virus neutralization tests provide detailed datasets of neutralization titers against the viral variants. Such datasets are difficult to interpret and do not immediately inform of the sufficiency of the breadth of the antibody response. Some of these issues could be tackled using the antigenic cartography approach. In this study, we created antigenic maps using neutralization titers of sera from donors who received the Sputnik V booster vaccine after primary Sputnik V vaccination and compared them with the antigenic maps based on serum neutralization titers of Comirnaty-boosted donors. A traditional analysis of neutralization titers against the WT (wild-type), Alpha, Beta, Delta, Omicron BA.1, and BA.4/BA.5 variants showed a significant booster humoral response after both homologous (Sputnik V) and heterologous (Comirnaty) revaccinations against all of the studied viral variants. However, despite this, a more in-depth analysis using antigenic cartography revealed that Omicron variants remain antigenically distant from the WT, which is indicative of the formation of insufficient levels of cross-neutralizing antibodies. The implications of these findings may be significant when developing a new vaccine regimen.
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Affiliation(s)
- Ekaterina A. Astakhova
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, 115522 Moscow, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Alexey A. Morozov
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, 115522 Moscow, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Maria G. Byazrova
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, 115522 Moscow, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Ministry of Science and Higher Education of Russia, RUDN University, 117198 Moscow, Russia
| | - Maria M. Sukhova
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, 115522 Moscow, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Artem A. Mikhailov
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, 115522 Moscow, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Aygul R. Minnegalieva
- Laboratory of Synthetic and Evolutionary Biology, Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan
| | - Andrey A. Gorchakov
- Laboratory of Immunogenetics, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alexander V. Filatov
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, 115522 Moscow, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
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37
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Chenchula S, Amerneni KC, Ghanta MK, Padmavathi R, Chandra MB, Adusumilli MB, Chavan M, Mudda S, Gupta R, Lakhawat B. Clinical virology and effect of Covid-19 vaccination and monoclonal antibodies against highly infectious SARS- CoV-2 omicron sub variant BF.7 (BA.5.2.1.7): A systematic review. Virology 2023; 584:38-43. [PMID: 37229914 DOI: 10.1016/j.virol.2023.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 05/27/2023]
Abstract
Over time, the SARS-CoV-2 virus has acquired several genetic mutations, particularly on the receptor-binding domain (RBD) spike glycoprotein. The Omicron variant is highly infectious, with enhanced immune escape activity, and has given rise to various sub-lineages due to mutations. However, there has been a sudden increase in COVID-19 reports of the Omicron subvariant BF.7 (BA.2.75.2), which has the highest number of reported cases, accounting for 76.2% of all cases worldwide. Hence, the present systematic review aimed to understand the viral mutations and factors associated with the increase in the reports of COVID-19 cases and to assess the effectiveness of vaccines and mAbs against the novel Omicron variant BF.7. The R346T mutation on the spike glycoprotein RBD might be associated with increased infection rates, severity, and resistance to vaccines and mAbs. Booster doses of COVID-19 vaccination with bivalent mRNA booster vaccine shots are effective in curtailing infections and decreasing the severity and mortality by enhancing the neutralizing antibodies (Abs) against the emerging Omicron subvariants of SARS-CoV-2, including BF.7 and future VOCs.
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Affiliation(s)
- Santenna Chenchula
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Bhopal, Madhya Pradesh, India.
| | | | - Mohan Krishna Ghanta
- Department of Pharmacology, MVJ Medical College and Research Hospital, Bangalore, Karnataka, India.
| | - R Padmavathi
- SVS Medical College and Hospital, Telangana, India.
| | | | | | - Madhavrao Chavan
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Mangalagiri, Andhra Pradesh, India.
| | - Sofia Mudda
- All India Institute of Medical Sciences, Bhopal, India.
| | - Rupesh Gupta
- Department of Internal Medicine, Government Medical College, Shahdol, Madhya Pradesh, India.
| | - Bhawna Lakhawat
- Department of Pharmacology, All India Institute of Medical Sciences, Bhopal, India.
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Punnoy P, Siripongpreda T, Pisitkun T, Rodthongkum N, Potiyaraj P. Alternative platform for COVID-19 diagnosis based on AuNP-modified lab-on-paper. Analyst 2023. [PMID: 37194362 DOI: 10.1039/d3an00595j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
COVID-19 has caused global health problems, and so rapid diagnosis is crucial to slow spread of the disease. Herein, a novel lab-on-paper screening method for SARS-CoV-2 Omicron BA.2 variant was developed using a gold nanoparticle-based colorimetric biosensor along with sensitive detection of SARS-CoV-2 antigen using laser desorption ionization-mass spectrometry (LDI-MS). As a result of antigen-antibody interaction, in the presence of SARS-CoV-2 antigen the gold nanoparticles undergo aggregation and change color from red to light purple, allowing for rapid determination of SARS-CoV-2 antigen with the naked eye. Furthermore, the lab-on-paper method can be directly applied as a substrate for sensitive quantitation of SARS-CoV-2 antigen in saliva using LDI-MS without the use of a conventional organic matrix and sample preparation. LDI-MS offers early diagnosis with high sensitivity, rapidity without sample preparation and lower cost per test compared with reverse transcriptase-PCR, which is crucial for preventing mortality in patients with underlying conditions. This method showed linearity over 0.01-1 μg mL-1 covering the cut-off value of 0.048 μg mL-1 for COVID-19 detection in human saliva. Moreover, a colorimetric sensor for urea was also fabricated in-parallel, for prediction of COVID-19 severity in patients with chronic kidney disease. The color change upon increasing urea concentration directly reflected kidney damage, which is related to increasing risk of mortality among patients with COVID-19. Hence, this platform might be a potential device for non-invasive diagnosis of SARS-CoV-2 Omicron BA.2 variant, which is the variant of most concern because it is transmitted more rapidly than the original SARS-CoV-2 virus and the Delta variant.
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Affiliation(s)
- Pornchanok Punnoy
- Department of Materials Science, Faculty of Science, Chulalongkorn University, Soi Chula12, Phayathai Road, Pathumwan, Bangkok 10330, Thailand.
| | - Tatiya Siripongpreda
- Nanoscience and Technology Interdisciplinary Program, Chulalongkorn University, Phayathai Road, Wangmai, Patumwan, Bangkok 10330, Thailand
| | - Trairak Pisitkun
- Chulalongkorn University Systems Biology, Faculty of Medicine, Chulalongkorn University, Patumwan, Bangkok 10330, Thailand
| | - Nadnudda Rodthongkum
- Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula12, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
- Center of Excellence in Responsive Wearable Materials, Chulalongkorn University, Thailand
| | - Pranut Potiyaraj
- Department of Materials Science, Faculty of Science, Chulalongkorn University, Soi Chula12, Phayathai Road, Pathumwan, Bangkok 10330, Thailand.
- Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula12, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
- Center of Excellence in Responsive Wearable Materials, Chulalongkorn University, Thailand
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39
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Branche A, Rouphael N, Diemert D, Falsey A, Losada C, Baden LR, Frey S, Whitaker J, Little S, Anderson E, Walter E, Novak R, Rupp R, Jackson L, Babu T, Kottkamp A, Luetkemeyer A, Immergluck L, Presti R, Backer M, Winokur P, Mahgoub S, Goepfert P, Fusco D, Malkin E, Bethony J, Walsh E, Graciaa D, Samaha H, Sherman A, Walsh S, Abate G, Oikonomopoulou Z, El Sahly H, Martin T, Kamidani S, Smith M, Ladner B, Porterfield L, Dunstan M, Wald A, Davis T, Atmar R, Mulligan M, Lyke K, Posavad C, Meagher M, Stephens D, Neuzil K, Abebe K, Hill H, Albert J, Telu K, Mu J, Lewis T, Giebeig L, Eaton A, Netzl A, Wilks S, Tureli S, Makhene M, Crandon S, Montefiori D, Makowski M, Smith D, Nayak S, Roberts P, Beigel J. Bivalent and Monovalent SARS-CoV-2 Variant Vaccine Boosters Improve coverage of the known Antigenic Landscape: Results of the COVID-19 Variant Immunologic Landscape (COVAIL) Trial. RESEARCH SQUARE 2023:rs.3.rs-2653179. [PMID: 37205592 PMCID: PMC10187423 DOI: 10.21203/rs.3.rs-2653179/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Vaccine protection against COVID-19 wanes over time and has been impacted by the emergence of new variants with increasing escape of neutralization. The COVID-19 Variant Immunologic Landscape (COVAIL) randomized clinical trial (clinicaltrials.gov NCT05289037) compares the breadth, magnitude and durability of antibody responses induced by a second COVID-19 vaccine boost with mRNA (Moderna mRNA-1273 and Pfizer-BioNTech BNT162b2), or adjuvanted recombinant protein (Sanofi CoV2 preS DTM-AS03) monovalent or bivalent vaccine candidates targeting ancestral and variant SARS-CoV-2 spike antigens (Beta, Delta and Omicron BA.1). We found that boosting with a variant strain is not associated with loss in neutralization against the ancestral strain. However, while variant vaccines compared to the prototype/wildtype vaccines demonstrated higher neutralizing activity against Omicron BA.1 and BA.4/5 subvariants for up to 3 months after vaccination, neutralizing activity was lower for more recent Omicron subvariants. Our study, incorporating both antigenic distances and serologic landscapes, can provide a framework for objectively guiding decisions for future vaccine updates.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Susan Little
- Department of Medicine, University of California, San Diego, CA 92903
| | | | | | | | | | - Lisa Jackson
- Kaiser Permanente Washington Health Research Institute
| | | | | | | | | | | | | | | | | | - Paul Goepfert
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham
| | | | | | | | | | - Daniel Graciaa
- Department of Medicine, Emory University School of Medicine
| | | | | | | | | | | | | | | | - Satoshi Kamidani
- Center for Childhood Infections and Vaccines (CCIV) of Children's Healthcare of Atlanta and Emory University Department of Pediatrics
| | | | | | | | | | | | | | | | | | - Kirsten Lyke
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine
| | - Christine Posavad
- Department of Laboratory Medicine and Pathology, University of Washington
| | | | | | | | | | | | | | | | | | - Teri Lewis
- 29. Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research
| | - Lisa Giebeig
- 29. Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research
| | | | | | - Sam Wilks
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge
| | | | - Mamodikoe Makhene
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH)
| | - Sonja Crandon
- Division of Microbiology and Infectious Diseases, NIAID, NIH
| | | | | | | | - Seema Nayak
- Division of Microbiology and Infectious Diseases, NIAID, NIH
| | - Paul Roberts
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH)
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40
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Verkhivker G, Alshahrani M, Gupta G, Xiao S, Tao P. Probing Conformational Landscapes of Binding and Allostery in the SARS-CoV-2 Omicron Variant Complexes Using Microsecond Atomistic Simulations and Perturbation-Based Profiling Approaches: Hidden Role of Omicron Mutations as Modulators of Allosteric Signaling and Epistatic Relationships. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539337. [PMID: 37205479 PMCID: PMC10187228 DOI: 10.1101/2023.05.03.539337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In this study, we systematically examine the conformational dynamics, binding and allosteric communications in the Omicron BA.1, BA.2, BA.3 and BA.4/BA.5 complexes with the ACE2 host receptor using molecular dynamics simulations and perturbation-based network profiling approaches. Microsecond atomistic simulations provided a detailed characterization of the conformational landscapes and revealed the increased thermodynamic stabilization of the BA.2 variant which is contrasted with the BA.4/BA.5 variants inducing a significant mobility of the complexes. Using ensemble-based mutational scanning of binding interactions, we identified binding affinity and structural stability hotspots in the Omicron complexes. Perturbation response scanning and network-based mutational profiling approaches probed the effect of the Omicron variants on allosteric communications. The results of this analysis revealed specific roles of Omicron mutations as "plastic and evolutionary adaptable" modulators of binding and allostery which are coupled to the major regulatory positions through interaction networks. Through perturbation network scanning of allosteric residue potentials in the Omicron variant complexes, which is performed in the background of the original strain, we identified that the key Omicron binding affinity hotspots N501Y and Q498R could mediate allosteric interactions and epistatic couplings. Our results suggested that the synergistic role of these hotspots in controlling stability, binding and allostery can enable for compensatory balance of fitness tradeoffs with conformationally and evolutionary adaptable immune-escape Omicron mutations. Through integrative computational approaches, this study provides a systematic analysis of the effects of Omicron mutations on thermodynamics, binding and allosteric signaling in the complexes with ACE2 receptor. The findings support a mechanism in which Omicron mutations can evolve to balance thermodynamic stability and conformational adaptability in order to ensure proper tradeoff between stability, binding and immune escape.
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Grant R, Sacks JA, Abraham P, Chunsuttiwat S, Cohen C, Figueroa JP, Fleming T, Fine P, Goldblatt D, Hasegawa H, MacIntrye CR, Memish ZA, Miller E, Nishioka S, Sall AA, Sow S, Tomori O, Wang Y, Van Kerkhove MD, Wambo MA, Cohen HA, Mesfin S, Otieno JR, Subissi L, Briand S, Wentworth DE, Subbarao K. When to update COVID-19 vaccine composition. Nat Med 2023; 29:776-780. [PMID: 36807683 DOI: 10.1038/s41591-023-02220-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- Rebecca Grant
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Jilian A Sacks
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Priya Abraham
- Indian Council of Medical Research - National Institute of Virology, Pune, India
| | | | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Thomas Fleming
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Paul Fine
- London School of Hygiene and Tropical Medicine, London, UK
| | - David Goldblatt
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Hideki Hasegawa
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - C Raina MacIntrye
- Biosecurity Program, The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Ziad A Memish
- Research and Innovation Centre, King Saud Medical City, Ministry of Health and College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Elizabeth Miller
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | | | | | - Samba Sow
- Centre for Vaccine Development, Ministry of Health, Bamako, Mali
| | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria
| | - Youchun Wang
- Institute for Biological Product Control, National Institutes for Food and Drug Control, Beijing, China
| | - Maria D Van Kerkhove
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Marie-Ange Wambo
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Homa Attar Cohen
- Department of Acute Response Coordination, World Health Organization, Geneva, Switzerland
| | - Samuel Mesfin
- Department of Acute Response Coordination, World Health Organization, Geneva, Switzerland
| | - James R Otieno
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Lorenzo Subissi
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Sylvie Briand
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland.
| | - David E Wentworth
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kanta Subbarao
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
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42
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Moore KA, Leighton T, Ostrowsky JT, Anderson CJ, Danila RN, Ulrich AK, Lackritz EM, Mehr AJ, Baric RS, Baylor NW, Gellin BG, Gordon JL, Krammer F, Perlman S, Rees HV, Saville M, Weller CL, Osterholm MT. A research and development (R&D) roadmap for broadly protective coronavirus vaccines: A pandemic preparedness strategy. Vaccine 2023; 41:2101-2112. [PMID: 36870874 PMCID: PMC9941884 DOI: 10.1016/j.vaccine.2023.02.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/23/2023]
Abstract
Broadly protective coronavirus vaccines are an important tool for protecting against future SARS-CoV-2 variants and could play a critical role in mitigating the impact of future outbreaks or pandemics caused by novel coronaviruses. The Coronavirus Vaccines Research and Development (R&D) Roadmap (CVR) is aimed at promoting the development of such vaccines. The CVR, funded by the Bill & Melinda Gates Foundation and The Rockefeller Foundation, was generated through a collaborative and iterative process, which was led by the Center for Infectious Disease Research and Policy (CIDRAP) at the University of Minnesota and involved 50 international subject matter experts and recognized leaders in the field. This report summarizes the major issues and areas of research outlined in the CVR and identifies high-priority milestones. The CVR covers a 6-year timeframe and is organized into five topic areas: virology, immunology, vaccinology, animal and human infection models, and policy and finance. Included in each topic area are key barriers, gaps, strategic goals, milestones, and additional R&D priorities. The roadmap includes 20 goals and 86 R&D milestones, 26 of which are ranked as high priority. By identifying key issues, and milestones for addressing them, the CVR provides a framework to guide funding and research campaigns that promote the development of broadly protective coronavirus vaccines.
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Affiliation(s)
- Kristine A Moore
- Center for Infectious Disease Research and Policy, University of Minnesota, Minneapolis, Minnesota, USA; Center for Infectious Disease Research and Policy, C315 Mayo Memorial Building, MMC 263, 420 Delaware Street, SE, Minneapolis, Minnesota 55455, USA.
| | - Tabitha Leighton
- Center for Infectious Disease Research and Policy, University of Minnesota, Minneapolis, Minnesota, USA
| | - Julia T Ostrowsky
- Center for Infectious Disease Research and Policy, University of Minnesota, Minneapolis, Minnesota, USA
| | - Cory J Anderson
- Center for Infectious Disease Research and Policy, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Angela K Ulrich
- Center for Infectious Disease Research and Policy, University of Minnesota, Minneapolis, Minnesota, USA
| | - Eve M Lackritz
- Center for Infectious Disease Research and Policy, University of Minnesota, Minneapolis, Minnesota, USA
| | - Angela J Mehr
- Center for Infectious Disease Research and Policy, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ralph S Baric
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | - Jennifer L Gordon
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Florian Krammer
- Department of Microbiology, Department of Pathology, Molecular and Cell-Based Medicine, and Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | | | - Helen V Rees
- Wits RHI, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Melanie Saville
- Coalition for Epidemic Preparedness Innovations, London, United Kingdom
| | | | - Michael T Osterholm
- Center for Infectious Disease Research and Policy, University of Minnesota, Minneapolis, Minnesota, USA
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43
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Wang W, Lusvarghi S, Subramanian R, Epsi NJ, Wang R, Goguet E, Fries AC, Echegaray F, Vassell R, Coggins SA, Richard SA, Lindholm DA, Mende K, Ewers EC, Larson DT, Colombo RE, Colombo CJ, Joseph JO, Rozman JS, Smith A, Lalani T, Berjohn CM, Maves RC, Jones MU, Mody R, Huprikar N, Livezey J, Saunders D, Hollis-Perry M, Wang G, Ganesan A, Simons MP, Broder CC, Tribble DR, Laing ED, Agan BK, Burgess TH, Mitre E, Pollett SD, Katzelnick LC, Weiss CD. Antigenic cartography of well-characterized human sera shows SARS-CoV-2 neutralization differences based on infection and vaccination history. Cell Host Microbe 2022; 30:1745-1758.e7. [PMID: 36356586 PMCID: PMC9584854 DOI: 10.1016/j.chom.2022.10.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/31/2022] [Accepted: 10/18/2022] [Indexed: 01/26/2023]
Abstract
The rapid emergence of SARS-CoV-2 variants challenges vaccination strategies. Here, we collected 201 serum samples from persons with a single infection or multiple vaccine exposures, or both. We measured their neutralization titers against 15 natural variants and 7 variants with engineered spike mutations and analyzed antigenic diversity. Antigenic maps of primary infection sera showed that Omicron sublineages BA.2, BA.4/BA.5, and BA.2.12.1 are distinct from BA.1 and more similar to Beta/Gamma/Mu variants. Three mRNA COVID-19 vaccinations increased neutralization of BA.1 more than BA.4/BA.5 or BA.2.12.1. BA.1 post-vaccination infection elicited higher neutralization titers to all variants than three vaccinations alone, although with less neutralization to BA.2.12.1 and BA.4/BA.5. Those with BA.1 infection after two or three vaccinations had similar neutralization titer magnitude and antigenic recognition. Accounting for antigenic differences among variants when interpreting neutralization titers can aid the understanding of complex patterns in humoral immunity that informs the selection of future COVID-19 vaccine strains.
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Affiliation(s)
- Wei Wang
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Sabrina Lusvarghi
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 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, USA
| | - Nusrat J Epsi
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Richard Wang
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Emilie Goguet
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA; Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Anthony C Fries
- U.S. Air Force School of Aerospace Medicine, Wright-Patterson Air Force Base, Fairborn, OH, USA
| | - Fernando Echegaray
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Russell Vassell
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Si'Ana A Coggins
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA; Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Stephanie A Richard
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - David A Lindholm
- Brooke Army Medical Center, Joint Base San Antonio-Fort Sam Houston, San Antonio, TX, USA; Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Katrin Mende
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Evan C Ewers
- Fort Belvoir Community Hospital, Fort Belvoir, VA, USA
| | | | - Rhonda E Colombo
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA; Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Madigan Army Medical Center, Tacoma, WA, USA
| | - Christopher J Colombo
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Madigan Army Medical Center, Tacoma, WA, USA
| | - Janet O Joseph
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Julia S Rozman
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Alfred Smith
- Naval Medical Center Portsmouth, Portsmouth, VA, USA
| | - Tahaniyat Lalani
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA; Naval Medical Center Portsmouth, Portsmouth, VA, USA
| | - Catherine M Berjohn
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Naval Medical Center San Diego, San Diego, CA, USA
| | - Ryan C Maves
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Section of Infectious Diseases, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | | | - Rupal Mody
- William Beaumont Army Medical Center, El Paso, TX, USA
| | - Nikhil Huprikar
- Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Jeffrey Livezey
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - David Saunders
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Monique Hollis-Perry
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, MD, USA
| | - Gregory Wang
- General Dynamics Information Technology, Falls Church, VA, USA
| | - Anuradha Ganesan
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA; Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Mark P Simons
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - David R Tribble
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Eric D Laing
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Brian K Agan
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Timothy H Burgess
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Edward Mitre
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Simon D Pollett
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA.
| | - 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, USA.
| | - Carol D Weiss
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA.
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44
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Kimura I, Yamasoba D, Tamura T, Nao N, Suzuki T, Oda Y, Mitoma S, Ito J, Nasser H, Zahradnik J, Uriu K, Fujita S, Kosugi Y, Wang L, Tsuda M, Kishimoto M, Ito H, Suzuki R, Shimizu R, Begum MM, Yoshimatsu K, Kimura KT, Sasaki J, Sasaki-Tabata K, Yamamoto Y, Nagamoto T, Kanamune J, Kobiyama K, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Shirakawa K, Takaori-Kondo A, Kuramochi J, Schreiber G, Ishii KJ, Hashiguchi T, Ikeda T, Saito A, Fukuhara T, Tanaka S, Matsuno K, Sato K. Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5. Cell 2022; 185:3992-4007.e16. [PMID: 36198317 PMCID: PMC9472642 DOI: 10.1016/j.cell.2022.09.018] [Citation(s) in RCA: 144] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/20/2022] [Accepted: 09/06/2022] [Indexed: 01/26/2023]
Abstract
After the global spread of the SARS-CoV-2 Omicron BA.2, some BA.2 subvariants, including BA.2.9.1, BA.2.11, BA.2.12.1, BA.4, and BA.5, emerged in multiple countries. Our statistical analysis showed that the effective reproduction numbers of these BA.2 subvariants are greater than that of the original BA.2. Neutralization experiments revealed that the immunity induced by BA.1/2 infections is less effective against BA.4/5. Cell culture experiments showed that BA.2.12.1 and BA.4/5 replicate more efficiently in human alveolar epithelial cells than BA.2, and particularly, BA.4/5 is more fusogenic than BA.2. We further provided the structure of the BA.4/5 spike receptor-binding domain that binds to human ACE2 and considered how the substitutions in the BA.4/5 spike play roles in ACE2 binding and immune evasion. Moreover, experiments using hamsters suggested that BA.4/5 is more pathogenic than BA.2. Our multiscale investigations suggest that the risk of BA.2 subvariants, particularly BA.4/5, to global health is greater than that of original BA.2.
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Affiliation(s)
- Izumi Kimura
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Daichi Yamasoba
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Faculty of Medicine, Kobe University, Kobe, Japan
| | - Tomokazu Tamura
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Naganori Nao
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Tateki Suzuki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Shuya Mitoma
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan; Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shigeru Fujita
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yusuke Kosugi
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Mai Kishimoto
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hayato Ito
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Mst Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | | | - Kanako Terakado Kimura
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Jiei Sasaki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kaori Sasaki-Tabata
- Department of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | | | | | | | - Kouji Kobiyama
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jin Kuramochi
- Interpark Kuramochi Clinic, Utsunomiya, Japan; Department of Global Health Promotion, Tokyo Medical and Dental University, Tokyo, Japan
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ken J Ishii
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan; Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan.
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan.
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
| | - Keita Matsuno
- One Health Research Center, Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan; Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Japan.
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