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Adair A, Tan LL, Feng J, Girkin J, Bryant N, Wang M, Mordant F, Chan LJ, Bartlett NW, Subbarao K, Pymm P, Tham WH. Human coronavirus OC43 nanobody neutralizes virus and protects mice from infection. J Virol 2024; 98:e0053124. [PMID: 38709106 PMCID: PMC11237593 DOI: 10.1128/jvi.00531-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 05/07/2024] Open
Abstract
Human coronavirus (hCoV) OC43 is endemic to global populations and usually causes asymptomatic or mild upper respiratory tract illness. Here, we demonstrate the neutralization efficacy of isolated nanobodies from alpacas immunized with the S1B and S1C domain of the hCoV-OC43 spike glycoprotein. A total of 40 nanobodies bound to recombinant OC43 protein with affinities ranging from 1 to 149 nM. Two nanobodies WNb 293 and WNb 294 neutralized virus at 0.21 and 1.79 nM, respectively. Intranasal and intraperitoneal delivery of WNb 293 fused to an Fc domain significantly reduced nasal viral load in a mouse model of hCoV-OC43 infection. Using X-ray crystallography, we observed that WNb 293 bound to an epitope on the OC43 S1B domain, distal from the sialoglycan-binding site involved in host cell entry. This result suggests that neutralization mechanism of this nanobody does not involve disruption of glycan binding. Our work provides characterization of nanobodies against hCoV-OC43 that blocks virus entry and reduces viral loads in vivo and may contribute to future nanobody-based therapies for hCoV-OC43 infections. IMPORTANCE The pandemic potential presented by coronaviruses has been demonstrated by the ongoing COVID-19 pandemic and previous epidemics caused by severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus. Outside of these major pathogenic coronaviruses, there are four endemic coronaviruses that infect humans: hCoV-OC43, hCoV-229E, hCoV-HKU1, and hCoV-NL63. We identified a collection of nanobodies against human coronavirus OC43 (hCoV-OC43) and found that two high-affinity nanobodies potently neutralized hCoV-OC43 at low nanomolar concentrations. Prophylactic administration of one neutralizing nanobody reduced viral loads in mice infected with hCoV-OC43, showing the potential for nanobody-based therapies for hCoV-OC43 infections.
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Affiliation(s)
- Amy Adair
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Li Lynn Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Jackson Feng
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jason Girkin
- />College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Infection Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Nathan Bryant
- />College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Infection Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Mingyang Wang
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Francesca Mordant
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Li-Jin Chan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nathan W. Bartlett
- />College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Infection Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Phillip Pymm
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Wai-Hong Tham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
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Lytton SD, Ghosh AK, Bulbul RH, Nasifa T, Mamunur R, Meier C, Landt O, Kaiser M. The severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) omicron sub-variants in Bangladesh cause mild COVID-19 and associate with similar antibody responses irrespective of natural infection or vaccination history. Heliyon 2024; 10:e31011. [PMID: 38770337 PMCID: PMC11103536 DOI: 10.1016/j.heliyon.2024.e31011] [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: 09/16/2023] [Revised: 05/09/2024] [Accepted: 05/09/2024] [Indexed: 05/22/2024] Open
Abstract
Objective Genomic surveillance and seroprevalence of severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) in Bangladesh is paramount for COVID-19 pandemic preparedness yet lagging the high-income countries due to limited resources. Methods SARS-CoV-2 variants, COVID-19 symptoms, and serology were prospectively evaluated in a cross-sectional study of Bangladeshi adults testing RT-PCR positive in 2021 and 2022. Results SARS CoV-2 Omicron variants of asymptomatic or mild COVID-19 in 2022 replaced Delta variant infections requiring hospitalization and oxygen support. The omicron XBB became predominant in July 2022 and associated with cough, headache or body ache and loss of smell; 47 of 68 (69 %), 30 of 68 (44 %) and 27 of 68 (40 %) respectively at higher frequency than BA.1/BA.2; 16 of 88 (18 %), 13 of 88 (15 %) and 0 of 88 (0 %) p < 0.01, p < 0.01 and p < 0.0001. Linear regression analysis reveals no associations between the number of previous infections and the number of symptoms, r = -0.084, p = 0.68. The anti-nucleoprotein (N)-protein IgG post COVID-19 and anti-Spike (S) protein IgG post-COVID-19 vaccination were similar between BA.2, BA.4/BA.5 and XBB and significantly lower than the levels in delta variant infections (p < 0.001). Conclusions Omicron XBB subvariants emerged in Bangladesh two months prior to previous reports and include unique patterns of S-protein mutations not assigned in PANGO lineage. The SARS CoV-2 omicron break-through infections persist in the presence of sustained antibody responses and vaccinations, underscoring the importance of molecular surveillance in low-income countries.
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Affiliation(s)
| | - Asish Kumar Ghosh
- Department of Virology, Dhaka Medical College Hospital, Dhaka, 1000, Bangladesh
| | | | - Tasnim Nasifa
- National Institute of Laboratory Medicine and Referral Center, Sher E-Bangla Nagar, Dhaka, 1207, Bangladesh
| | - Rashid Mamunur
- Bangladesh Institute Tropical Infectious Disease (BITID), Fouzderhat, Chittagong, 4317, Bangladesh
| | - Christian Meier
- TIB Molbiol GmbH, Eresburgstraße 22-23, 12103, Berlin, Germany
| | - Olfert Landt
- TIB Molbiol GmbH, Eresburgstraße 22-23, 12103, Berlin, Germany
| | - Marco Kaiser
- TIB Molbiol GmbH, Eresburgstraße 22-23, 12103, Berlin, Germany
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3
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Liu C, Zhou D, Dijokaite-Guraliuc A, Supasa P, Duyvesteyn HME, Ginn HM, Selvaraj M, Mentzer AJ, Das R, de Silva TI, Ritter TG, Plowright M, Newman TAH, Stafford L, Kronsteiner B, Temperton N, Lui Y, Fellermeyer M, Goulder P, Klenerman P, Dunachie SJ, Barton MI, Kutuzov MA, Dushek O, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity. Cell Rep Med 2024; 5:101553. [PMID: 38723626 PMCID: PMC11148769 DOI: 10.1016/j.xcrm.2024.101553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/10/2024] [Accepted: 04/11/2024] [Indexed: 05/24/2024]
Abstract
BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible for many infections in 2023. The global spread and plethora of mutations in BA.2.86 has caused concern that it may possess greater immune-evasive potential, leading to a new wave of infection. Here, we examine the ability of BA.2.86 to evade the antibody response to infection using a panel of vaccinated or naturally infected sera and find that it shows marginally less immune evasion than XBB.1.5. We locate BA.2.86 in the antigenic landscape of recent variants and look at its ability to escape panels of potent monoclonal antibodies generated against contemporary SARS-CoV-2 infections. We demonstrate, and provide a structural explanation for, increased affinity of BA.2.86 to ACE2, which may increase transmissibility.
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Affiliation(s)
- Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daming Zhou
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
| | | | - Piyada Supasa
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
| | - Helen M Ginn
- Centre for Free Electron Laser Science, Hamburg, Germany
| | - Muneeswaran Selvaraj
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Raksha Das
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Thushan I de Silva
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Thomas G Ritter
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Megan Plowright
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | | | - Lizzie Stafford
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Barbara Kronsteiner
- NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and University of Greenwich Chatham Maritime, Kent ME4 4TB, UK
| | - Yuan Lui
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Martin Fellermeyer
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Paul Klenerman
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Michael I Barton
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mikhail A Kutuzov
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Omer Dushek
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK; Sir William Dunn School of Pathology, Oxford, UK.
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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4
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Wu Y, Jin R, Chang Y, Liu M. A high-fidelity DNAzyme-assisted CRISPR/Cas13a system with single-nucleotide resolved specificity. Chem Sci 2024; 15:6934-6942. [PMID: 38725495 PMCID: PMC11077575 DOI: 10.1039/d4sc01501k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/01/2024] [Indexed: 05/12/2024] Open
Abstract
A CRISPR/Cas system represents an innovative tool for developing a new-generation biosensing and diagnostic strategy. However, the off-target issue (i.e., mistaken cleavage of nucleic acid targets and reporters) remains a great challenge for its practical applications. We hypothesize that this issue can be overcome by taking advantage of the site-specific cleavage ability of RNA-cleaving DNAzymes. To test this idea, we propose a DNAzyme Operation Enhances the Specificity of CRISPR/Cas13a strategy (termed DOES-CRISPR) to overcome the problem of relatively poor specificity that is typical of the traditional CRISPR/Cas13a system. The key to the design is that the partial hybridization of the CRISPR RNA (crRNA) with the cleavage fragment of off-target RNA was not able to activate the collateral cleavage activity of Cas13a. We showed that DOES-CRISPR can significantly improve the specificity of traditional CRISPR/Cas13a-based molecular detection by up to ∼43-fold. The broad utility of the strategy is illustrated through engineering three different systems for the detection of microRNAs (miR-17 and let-7e), CYP2C19*17 gene, SARS-Cov-2 variants (Gamma, Delta, and Omicron) and Omicron subtypes (BQ.1 and XBB.1) with single-nucleotide resolved specificity. Finally, clinical evaluation of this assay using 10 patient blood samples demonstrated a clinical sensitivity of 100% and specificity of 100% for genotyping CYP2C19*17, and analyzing 20 throat swab samples provided a diagnostic sensitivity of 95% and specificity of 100% for Omicron detection, and a clinical sensitivity of 92% and specificity of 100% for XBB.1 detection.
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Affiliation(s)
- Yunping Wu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
| | - Ruigang Jin
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
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5
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Focosi D, Franchini M, Casadevall A, Maggi F. An update on the anti-spike monoclonal antibody pipeline for SARS-CoV-2. Clin Microbiol Infect 2024:S1198-743X(24)00207-6. [PMID: 38663655 DOI: 10.1016/j.cmi.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND Anti-spike monoclonal antibodies represent one of the most tolerable prophylaxis and therapies for COVID-19 in frail and immunocompromised patients. Unfortunately, viral evolution in Omicron has led all of them to failure. OBJECTIVES We review here the current pipeline of anti-spike mAb's, discussing in detail the most promising candidates. SOURCES We scanned PubMed, ClinicalTrials.gov and manufacturers' press releases for clinical studies on anti-spike monoclonal antibodies. CONTENT We present state-of-art data clinical progress for AstraZeneca's AZD3152, Invivyd's VYD222, Regeneron's REGN-17092 and Aerium Therapeutics' AER-800. IMPLICATIONS The anti-spike monoclonal antibody clinical pipeline is currently limited to few agents (most being single antibodies) with unknown efficacy against the dominant JN.1 sublineage. The field of antibody-based therapies requires boosting by both manufacturers and institutions.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy.
| | - Massimo Franchini
- Department of Transfusion Medicine and Hematology, Carlo Poma Hospital, Mantua, Italy
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
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6
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Liu C, Das R, Dijokaite-Guraliuc A, Zhou D, Mentzer AJ, Supasa P, Selvaraj M, Duyvesteyn HME, Ritter TG, Temperton N, Klenerman P, Dunachie SJ, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. Emerging variants develop total escape from potent monoclonal antibodies induced by BA.4/5 infection. Nat Commun 2024; 15:3284. [PMID: 38627386 PMCID: PMC11021415 DOI: 10.1038/s41467-024-47393-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/29/2024] [Indexed: 04/19/2024] Open
Abstract
The rapid evolution of SARS-CoV-2 is driven in part by a need to evade the antibody response in the face of high levels of immunity. Here, we isolate spike (S) binding monoclonal antibodies (mAbs) from vaccinees who suffered vaccine break-through infections with Omicron sub lineages BA.4 or BA.5. Twenty eight potent antibodies are isolated and characterised functionally, and in some cases structurally. Since the emergence of BA.4/5, SARS-CoV-2 has continued to accrue mutations in the S protein, to understand this we characterize neutralization of a large panel of variants and demonstrate a steady attrition of neutralization by the panel of BA.4/5 mAbs culminating in total loss of function with recent XBB.1.5.70 variants containing the so-called 'FLip' mutations at positions 455 and 456. Interestingly, activity of some mAbs is regained on the recently reported variant BA.2.86.
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Affiliation(s)
- Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Raksha Das
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Daming Zhou
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Alexander J Mentzer
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Piyada Supasa
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Muneeswaran Selvaraj
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Thomas G Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich Chatham Maritime, Kent, ME4 4TB, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Neil G Paterson
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK.
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK.
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7
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Halvorson T, Ivison S, Huang Q, Ladua G, Yotis DM, Mannar D, Subramaniam S, Ferreira VH, Kumar D, Belga S, Levings MK. SARS-CoV-2 Variants Omicron BA.4/5 and XBB.1.5 Significantly Escape T Cell Recognition in Solid-organ Transplant Recipients Vaccinated Against the Ancestral Strain. Transplantation 2024; 108:e49-e62. [PMID: 38012843 DOI: 10.1097/tp.0000000000004873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
BACKGROUND Immune-suppressed solid-organ transplant recipients (SOTRs) display impaired humoral responses to COVID-19 vaccination, but T cell responses are incompletely understood. SARS-CoV-2 variants Omicron BA.4/5 (BA.4/5) and XBB.1.5 escape neutralization by antibodies induced by vaccination or infection with earlier strains, but T cell recognition of these lineages in SOTRs is unclear. METHODS We characterized Spike-specific T cell responses to ancestral SARS-CoV-2 and BA.4/5 peptides in 42 kidney, liver, and lung transplant recipients throughout a 3- or 4-dose ancestral Spike mRNA vaccination schedule. As the XBB.1.5 variant emerged during the study, we tested vaccine-induced T cell responses in 10 additional participants using recombinant XBB.1.5 Spike protein. Using an optimized activation-induced marker assay, we quantified circulating Spike-specific CD4 + and CD8 + T cells based on antigen-stimulated expression of CD134, CD69, CD25, CD137, and/or CD107a. RESULTS Vaccination strongly induced SARS-CoV-2-specific T cells, including BA.4/5- and XBB.1.5-reactive T cells, which remained detectable over time and further increased following a fourth dose. However, responses to BA.4/5 (1.34- to 1.67-fold lower) XBB.1.5 (2.0- to 18-fold lower) were significantly reduced in magnitude compared with ancestral strain responses. CD4 + responses correlated with anti-receptor-binding domain antibodies and predicted subsequent antibody responses in seronegative individuals. Lung transplant recipients receiving prednisone and older adults displayed weaker responses. CONCLUSIONS Ancestral strain vaccination stimulates BA.4/5 and XBB.1.5-cross-reactive T cells in SOTRs, but at lower magnitudes. Antigen-specific T cells can predict future antibody responses. Our data support monitoring both humoral and cellular immunity in SOTRs to track COVID-19 vaccine immunogenicity against emerging variants.
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Affiliation(s)
- Torin Halvorson
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Sabine Ivison
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Qing Huang
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Gale Ladua
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- Infection and Immunity Research Centre, Vancouver Coastal Health Research Institute, Vancouver, BC, Canada
| | - Demitra M Yotis
- Canadian Donation and Transplantation Research Program, Edmonton, AB, Canada
| | - Dhiraj Mannar
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Victor H Ferreira
- Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Deepali Kumar
- Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Sara Belga
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- Infection and Immunity Research Centre, Vancouver Coastal Health Research Institute, Vancouver, BC, Canada
| | - Megan K Levings
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
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8
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Zhou D, Supasa P, Liu C, Dijokaite-Guraliuc A, Duyvesteyn HME, Selvaraj M, Mentzer AJ, Das R, Dejnirattisai W, Temperton N, Klenerman P, Dunachie SJ, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. The SARS-CoV-2 neutralizing antibody response to SD1 and its evasion by BA.2.86. Nat Commun 2024; 15:2734. [PMID: 38548763 PMCID: PMC10978878 DOI: 10.1038/s41467-024-46982-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
Under pressure from neutralising antibodies induced by vaccination or infection the SARS-CoV-2 spike gene has become a hotspot for evolutionary change, leading to the failure of all mAbs developed for clinical use. Most potent antibodies bind to the receptor binding domain which has become heavily mutated. Here we study responses to a conserved epitope in sub-domain-1 (SD1) of spike which have become more prominent because of mutational escape from antibodies directed to the receptor binding domain. Some SD1 reactive mAbs show potent and broad neutralization of SARS-CoV-2 variants. We structurally map the dominant SD1 epitope and provide a mechanism of action by blocking interaction with ACE2. Mutations in SD1 have not been sustained to date, but one, E554K, leads to escape from mAbs. This mutation has now emerged in several sublineages including BA.2.86, reflecting selection pressure on the virus exerted by the increasing prominence of the anti-SD1 response.
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Affiliation(s)
- Daming Zhou
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Piyada Supasa
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
| | - Muneeswaran Selvaraj
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Raksha Das
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wanwisa Dejnirattisai
- Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-Noi, Bangkok, 10700, Thailand
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich Chatham Maritime, Kent, ME4 4TB, UK
| | - Paul Klenerman
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NDM Centre For Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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9
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Arantes I, Gomes M, Ito K, Sarafim S, Gräf T, Miyajima F, Khouri R, de Carvalho FC, de Almeida WAF, Siqueira MM, Resende PC, Naveca FG, Bello G. Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023. Microbiol Spectr 2024; 12:e0383123. [PMID: 38315011 PMCID: PMC10913747 DOI: 10.1128/spectrum.03831-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/27/2023] [Indexed: 02/07/2024] Open
Abstract
The SARS-CoV-2 XBB is a group of highly immune-evasive lineages of the Omicron variant of concern that emerged by recombining BA.2-descendent lineages and spread worldwide during 2023. In this study, we combine SARS-CoV-2 genomic data (n = 11,065 sequences) with epidemiological data of severe acute respiratory infection (SARI) cases collected in Brazil between October 2022 and July 2023 to reconstruct the space-time dynamics and epidemiologic impact of XBB dissemination in the country. Our analyses revealed that the introduction and local emergence of lineages carrying convergent mutations within the Spike protein, especially F486P, F456L, and L455F, propelled the spread of XBB* lineages in Brazil. The average relative instantaneous reproduction numbers of XBB* + F486P, XBB* + F486P + F456L, and XBB* + F486P + F456L + L455F lineages in Brazil were estimated to be 1.24, 1.33, and 1.48 higher than that of other co-circulating lineages (mainly BQ.1*/BE*), respectively. Despite such a growth advantage, the dissemination of these XBB* lineages had a reduced impact on Brazil's epidemiological scenario concerning previous Omicron subvariants. The peak number of SARI cases from SARS-CoV-2 during the XBB wave was approximately 90%, 80%, and 70% lower than that observed during the previous BA.1*, BA.5*, and BQ.1* waves, respectively. These findings revealed the emergence of multiple XBB lineages with progressively increasing growth advantage, yet with relatively limited epidemiological impact in Brazil throughout 2023. The XBB* + F486P + F456L + L455F lineages stand out for their heightened transmissibility, warranting close monitoring in the months ahead. IMPORTANCE Brazil was one the most affected countries by the SARS-CoV-2 pandemic, with more than 700,000 deaths by mid-2023. This study reconstructs the dissemination of the virus in the country in the first half of 2023, a period characterized by the dissemination of descendants of XBB.1, a recombinant of Omicron BA.2 lineages evolved in late 2022. The analysis supports that XBB dissemination was marked by the continuous emergence of indigenous lineages bearing similar mutations in key sites of their Spike protein, a process followed by continuous increments in transmissibility, and without repercussions in the incidence of severe cases. Thus, the results suggest that the epidemiological impact of the spread of a SARS-CoV-2 variant is influenced by an intricate interplay of factors that extend beyond the virus's transmissibility alone. The study also underlines the need for SARS-CoV-2 genomic surveillance that allows the monitoring of its ever-shifting composition.
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Affiliation(s)
- Ighor Arantes
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Marcelo Gomes
- Grupo de Métodos Analíticos em Vigilância Epidemiológica, Fiocruz, Rio de Janeiro, Brazil
| | - Kimihito Ito
- International Institute for Zoonosis Control, Hokkaido University, Hokkaido, Japan
| | - Sharbilla Sarafim
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Tiago Gräf
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fiocruz, Curitiba, Brazil
| | | | | | - Felipe Cotrim de Carvalho
- Departamento do Programa Nacional de Imunizações, Coordenação-Geral de Vigilância das doenças imunopreveníveis, Secretaria de Vigilância em saúde e ambiente, Brasília, Brazil
| | - Walquiria Aparecida Ferreira de Almeida
- Departamento do Programa Nacional de Imunizações, Coordenação-Geral de Vigilância das doenças imunopreveníveis, Secretaria de Vigilância em saúde e ambiente, Brasília, Brazil
| | - Marilda Mendonça Siqueira
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Felipe Gomes Naveca
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Núcleo de Vigilância de Vírus Emergentes, Reemergentes ou Negligenciados, Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Gonzalo Bello
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - COVID-19 Fiocruz Genomic Surveillance Network
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Grupo de Métodos Analíticos em Vigilância Epidemiológica, Fiocruz, Rio de Janeiro, Brazil
- International Institute for Zoonosis Control, Hokkaido University, Hokkaido, Japan
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fiocruz, Curitiba, Brazil
- Fiocruz, Fortaleza, Brazil
- Instituto Gonçalo Moniz, Fiocruz, Salvador, Brazil
- Departamento do Programa Nacional de Imunizações, Coordenação-Geral de Vigilância das doenças imunopreveníveis, Secretaria de Vigilância em saúde e ambiente, Brasília, Brazil
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Núcleo de Vigilância de Vírus Emergentes, Reemergentes ou Negligenciados, Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
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10
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Babu TM, Shen X, McClelland RS, Wang Z, Selke S, Wilkens C, Hauge KA, McClurkan CL, Goecker E, Laing KJ, Koelle DM, Greninger AL, Nussenzweig MC, Montefiori DC, Corey L, Wald A. Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Subvariant Neutralization Following a Primary Vaccine Series of NVX-CoV2373 and BNT162b2 Monovalent Booster Vaccine. Open Forum Infect Dis 2024; 11:ofad673. [PMID: 38379566 PMCID: PMC10878050 DOI: 10.1093/ofid/ofad673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 12/20/2023] [Indexed: 02/22/2024] Open
Abstract
We evaluated the immunologic response to a novel vaccine regimen that included 2 doses of NVX-CoV2373 (Novavax) followed by 1 dose of BNT162b2 (Pfizer-BioNTech) monovalent booster vaccine. A durable neutralizing antibody response to Omicron BA.4/BA.5 and BA.1 variants was observed at month 6 after the booster, while immune escape was noted for the XBB.1.5 variant.
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Affiliation(s)
- Tara M Babu
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Xiaoying Shen
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - R Scott McClelland
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Washington, Seattle, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Stacy Selke
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Chloe Wilkens
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Kirsten A Hauge
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Christopher L McClurkan
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Erin Goecker
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Kerry J Laing
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - David M Koelle
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Washington, Seattle, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Benaroya Research Institute, Seattle, Washington, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Lawrence Corey
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Anna Wald
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
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11
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Wang Y, Yan A, Song D, Duan M, Dong C, Chen J, Jiang Z, Gao Y, Rao M, Feng J, Zhang Z, Qi R, Ma X, Liu H, Yu B, Wang Q, Zong M, Jiao J, Xing P, Pan R, Li D, Xiao J, Sun J, Li Y, Zhang L, Shen Z, Sun B, Zhao Y, Zhang L, Dai J, Zhao J, Wang L, Dou C, Liu Z, Zhao J. Identification of a highly conserved neutralizing epitope within the RBD region of diverse SARS-CoV-2 variants. Nat Commun 2024; 15:842. [PMID: 38287016 PMCID: PMC10825162 DOI: 10.1038/s41467-024-45050-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 01/11/2024] [Indexed: 01/31/2024] Open
Abstract
The constant emergence of SARS-CoV-2 variants continues to impair the efficacy of existing neutralizing antibodies, especially XBB.1.5 and EG.5, which showed exceptional immune evasion properties. Here, we identify a highly conserved neutralizing epitope targeted by a broad-spectrum neutralizing antibody BA7535, which demonstrates high neutralization potency against not only previous variants, such as Alpha, Beta, Gamma, Delta and Omicron BA.1-BA.5, but also more recently emerged Omicron subvariants, including BF.7, CH.1.1, XBB.1, XBB.1.5, XBB.1.9.1, EG.5. Structural analysis of the Omicron Spike trimer with BA7535-Fab using cryo-EM indicates that BA7535 recognizes a highly conserved cryptic receptor-binding domain (RBD) epitope, avoiding most of the mutational hot spots in RBD. Furthermore, structural simulation based on the interaction of BA7535-Fab/RBD complexes dissects the broadly neutralizing effect of BA7535 against latest variants. Therapeutic and prophylactic treatment with BA7535 alone or in combination with BA7208 protected female mice from the circulating Omicron BA.5 and XBB.1 variant infection, suggesting the highly conserved neutralizing epitope serves as a potential target for developing highly potent therapeutic antibodies and vaccines.
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Affiliation(s)
- Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Clinical Laboratory Medicine Department, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - An Yan
- Cryo-electron Microscopy Center, Southern University of Science and Technology, Shenzhen, China
| | - Deyong Song
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Maoqin Duan
- Division of Monoclonal Antibodies, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Chuangchuang Dong
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Jiantao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zihe Jiang
- Cryo-electron Microscopy Center, Southern University of Science and Technology, Shenzhen, China
| | - Yuanzhu Gao
- Cryo-electron Microscopy Center, Southern University of Science and Technology, Shenzhen, China
| | - Muding Rao
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Jianxia Feng
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ruxi Qi
- Cryo-electron Microscopy Center, Southern University of Science and Technology, Shenzhen, China
| | - Xiaomin Ma
- Cryo-electron Microscopy Center, Southern University of Science and Technology, Shenzhen, China
| | - Hong Liu
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Beibei Yu
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Qiaoping Wang
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Mengqi Zong
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Jie Jiao
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Pingping Xing
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Rongrong Pan
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Dan Li
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Juxue Xiao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Junbo Sun
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Ying Li
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Linfeng Zhang
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Zhenduo Shen
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Baiping Sun
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Yanyan Zhao
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Lu Zhang
- Health and Quarantine Laboratory, Guangzhou Customs District Technology Centre, Guangzhou, China
| | - Jun Dai
- Health and Quarantine Laboratory, Guangzhou Customs District Technology Centre, Guangzhou, China
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lan Wang
- Division of Monoclonal Antibodies, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China.
| | - Changlin Dou
- Antibody Research and Development Center, Shandong Boan Biotechnology Co., Ltd., Yantai, China.
| | - Zheng Liu
- Cryo-electron Microscopy Center, Southern University of Science and Technology, Shenzhen, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou National Laboratory, Bio-Island, Guangzhou, China.
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
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12
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Jian F, Feng L, Yang S, Yu Y, Wang L, Song W, Yisimayi A, Chen X, Xu Y, Wang P, Yu L, Wang J, Liu L, Niu X, Wang J, Xiao T, An R, Wang Y, Gu Q, Shao F, Jin R, Shen Z, Wang Y, Wang X, Cao Y. Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 synergistically enhances antibody evasion and ACE2 binding. PLoS Pathog 2023; 19:e1011868. [PMID: 38117863 PMCID: PMC10766189 DOI: 10.1371/journal.ppat.1011868] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/04/2024] [Accepted: 11/28/2023] [Indexed: 12/22/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) XBB lineages have achieved dominance worldwide and keep on evolving. Convergent evolution of XBB lineages on the receptor-binding domain (RBD) L455F and F456L is observed, resulting in variants with substantial growth advantages, such as EG.5, FL.1.5.1, XBB.1.5.70, and HK.3. Here, we show that neutralizing antibody (NAb) evasion drives the convergent evolution of F456L, while the epistatic shift caused by F456L enables the subsequent convergence of L455F through ACE2 binding enhancement and further immune evasion. L455F and F456L evade RBD-targeting Class 1 public NAbs, reducing the neutralization efficacy of XBB breakthrough infection (BTI) and reinfection convalescent plasma. Importantly, L455F single substitution significantly dampens receptor binding; however, the combination of L455F and F456L forms an adjacent residue flipping, which leads to enhanced NAbs resistance and ACE2 binding affinity. The perturbed receptor-binding mode leads to the exceptional ACE2 binding and NAb evasion, as revealed by structural analyses. Our results indicate the evolution flexibility contributed by epistasis cannot be underestimated, and the evolution potential of SARS-CoV-2 RBD remains high.
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Affiliation(s)
- Fanchong Jian
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, People’s Republic of China
- Changping Laboratory, Beijing, People’s Republic of China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, People’s Republic of China
| | - Leilei Feng
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Sijie Yang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, People’s Republic of China
- Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Yuanling Yu
- Changping Laboratory, Beijing, People’s Republic of China
| | - Lei Wang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Weiliang Song
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, People’s Republic of China
- Changping Laboratory, Beijing, People’s Republic of China
- School of Life Sciences, Peking University, Beijing, People’s Republic of China
| | - Ayijiang Yisimayi
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, People’s Republic of China
- Changping Laboratory, Beijing, People’s Republic of China
- School of Life Sciences, Peking University, Beijing, People’s Republic of China
| | - Xiaosu Chen
- Institute for Immunology, College of Life Sciences, Nankai University, Tianjin, People’s Republic of China
| | - Yanli Xu
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Peng Wang
- Changping Laboratory, Beijing, People’s Republic of China
| | - Lingling Yu
- Changping Laboratory, Beijing, People’s Republic of China
| | - Jing Wang
- Changping Laboratory, Beijing, People’s Republic of China
| | - Lu Liu
- Changping Laboratory, Beijing, People’s Republic of China
| | - Xiao Niu
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, People’s Republic of China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, People’s Republic of China
| | - Jing Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, People’s Republic of China
- Changping Laboratory, Beijing, People’s Republic of China
- School of Life Sciences, Peking University, Beijing, People’s Republic of China
| | - Tianhe Xiao
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, People’s Republic of China
- Joint Graduate Program of Peking-Tsinghua-NIBS, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People’s Republic of China
| | - Ran An
- Changping Laboratory, Beijing, People’s Republic of China
| | - Yao Wang
- Changping Laboratory, Beijing, People’s Republic of China
| | - Qingqing Gu
- Changping Laboratory, Beijing, People’s Republic of China
| | - Fei Shao
- Changping Laboratory, Beijing, People’s Republic of China
| | - Ronghua Jin
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Zhongyang Shen
- Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, People’s Republic of China
| | - Youchun Wang
- Changping Laboratory, Beijing, People’s Republic of China
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, People’s Republic of China
| | - Xiangxi Wang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yunlong Cao
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, People’s Republic of China
- Changping Laboratory, Beijing, People’s Republic of China
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13
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Roemer C, Sheward DJ, Hisner R, Gueli F, Sakaguchi H, Frohberg N, Schoenmakers J, Sato K, O'Toole Á, Rambaut A, Pybus OG, Ruis C, Murrell B, Peacock TP. SARS-CoV-2 evolution in the Omicron era. Nat Microbiol 2023; 8:1952-1959. [PMID: 37845314 DOI: 10.1038/s41564-023-01504-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 09/13/2023] [Indexed: 10/18/2023]
Abstract
Since SARS-CoV-2 BA.5 (Omicron) emerged and spread in 2022, Omicron lineages have markedly diversified. Here we review the evolutionary trajectories and processes that underpin the emergence of these lineages, and identify the most prevalent sublineages. We discuss the potential origins of second-generation BA.2 lineages. Simple and complex recombination, antigenic drift and convergent evolution have enabled SARS-CoV-2 to accumulate mutations that alter its antigenicity. We also discuss the potential evolutionary trajectories of SARS-CoV-2 in the future.
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Affiliation(s)
- Cornelius Roemer
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ryan Hisner
- University of Cape Town, Rondebosch, South Africa
| | | | | | | | | | - Kenta Sato
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Áine O'Toole
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, London, UK
| | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK.
- The Pirbright Institute, Woking, UK.
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14
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Chrysostomou AC, Vrancken B, Haralambous C, Alexandrou M, Gregoriou I, Ioannides M, Ioannou C, Kalakouta O, Karagiannis C, Marcou M, Masia C, Mendris M, Papastergiou P, Patsalis PC, Pieridou D, Shammas C, Stylianou DC, Zinieri B, Lemey P, Network TCOMESSAR, Kostrikis LG. Unraveling the Dynamics of Omicron (BA.1, BA.2, and BA.5) Waves and Emergence of the Deltacton Variant: Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus (Oct 2021-Oct 2022). Viruses 2023; 15:1933. [PMID: 37766339 PMCID: PMC10535466 DOI: 10.3390/v15091933] [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: 08/31/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Commencing in December 2019 with the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), three years of the coronavirus disease 2019 (COVID-19) pandemic have transpired. The virus has consistently demonstrated a tendency for evolutionary adaptation, resulting in mutations that impact both immune evasion and transmissibility. This ongoing process has led to successive waves of infections. This study offers a comprehensive assessment spanning genetic, phylogenetic, phylodynamic, and phylogeographic dimensions, focused on the trajectory of the SARS-CoV-2 epidemic in Cyprus. Based on a dataset comprising 4700 viral genomic sequences obtained from affected individuals between October 2021 and October 2022, our analysis is presented. Over this timeframe, a total of 167 distinct lineages and sublineages emerged, including variants such as Delta and Omicron (1, 2, and 5). Notably, during the fifth wave of infections, Omicron subvariants 1 and 2 gained prominence, followed by the ascendancy of Omicron 5 in the subsequent sixth wave. Additionally, during the fifth wave (December 2021-January 2022), a unique set of Delta sequences with genetic mutations associated with Omicron variant 1, dubbed "Deltacron", was identified. The emergence of this phenomenon initially evoked skepticism, characterized by concerns primarily centered around contamination or coinfection as plausible etiological contributors. These hypotheses were predominantly disseminated through unsubstantiated assertions within the realms of social and mass media, lacking concurrent scientific evidence to validate their claims. Nevertheless, the exhaustive molecular analyses presented in this study have demonstrated that such occurrences would likely lead to a frameshift mutation-a genetic aberration conspicuously absent in our provided sequences. This substantiates the accuracy of our initial assertion while refuting contamination or coinfection as potential etiologies. Comparable observations on a global scale dispelled doubt, eventually leading to the recognition of Delta-Omicron variants by the scientific community and their subsequent monitoring by the World Health Organization (WHO). As our investigation delved deeper into the intricate dynamics of the SARS-CoV-2 epidemic in Cyprus, a discernible pattern emerged, highlighting the major role of international connections in shaping the virus's local trajectory. Notably, the United States and the United Kingdom were the central conduits governing the entry and exit of the virus to and from Cyprus. Moreover, notable migratory routes included nations such as Greece, South Korea, France, Germany, Brazil, Spain, Australia, Denmark, Sweden, and Italy. These empirical findings underscore that the spread of SARS-CoV-2 within Cyprus was markedly influenced by the influx of new, highly transmissible variants, triggering successive waves of infection. This investigation elucidates the emergence of new waves of infection subsequent to the advent of highly contagious and transmissible viral variants, notably characterized by an abundance of mutations localized within the spike protein. Notably, this discovery decisively contradicts the hitherto hypothesis of seasonal fluctuations in the virus's epidemiological dynamics. This study emphasizes the importance of meticulously examining molecular genetics alongside virus migration patterns within a specific region. Past experiences also emphasize the substantial evolutionary potential of viruses such as SARS-CoV-2, underscoring the need for sustained vigilance. However, as the pandemic's dynamics continue to evolve, a balanced approach between caution and resilience becomes paramount. This ethos encourages an approach founded on informed prudence and self-preservation, guided by public health authorities, rather than enduring apprehension. Such an approach empowers societies to adapt and progress, fostering a poised confidence rooted in well-founded adaptation.
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Affiliation(s)
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Christos Haralambous
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus
| | - Maria Alexandrou
- Microbiology Department, Larnaca General Hospital, 6301 Larnaca, Cyprus
| | - Ioanna Gregoriou
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus
| | | | - Costakis Ioannou
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, 5310 Paralimni, Cyprus
| | - Olga Kalakouta
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus
| | | | - Markella Marcou
- Department of Microbiology, Archbishop Makarios III Hospital, 2012 Nicosia, Cyprus
| | - Christina Masia
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, 5310 Paralimni, Cyprus
| | - Michail Mendris
- Microbiology Department, Limassol General Hospital, 4131 Limassol, Cyprus
| | | | - Philippos C. Patsalis
- Medicover Genetics, 2409 Nicosia, Cyprus
- Medical School, University of Nicosia, 2417 Nicosia, Cyprus
| | - Despo Pieridou
- Microbiology Department, Nicosia General Hospital, 2029 Nicosia, Cyprus
| | - Christos Shammas
- S.C.I.N.A. Bioanalysis Sciomedical Centre Ltd., 4040 Limassol, Cyprus
| | - Dora C. Stylianou
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
| | - Barbara Zinieri
- Microbiology Department, Paphos General Hospital, Achepans, 8026 Paphos, Cyprus
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | | | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60-68 Phaneromenis Street, 1011 Nicosia, Cyprus
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15
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Zhou D, Ren J, Fry EE, Stuart DI. Broadly neutralizing antibodies against COVID-19. Curr Opin Virol 2023; 61:101332. [PMID: 37285620 PMCID: PMC10301462 DOI: 10.1016/j.coviro.2023.101332] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/26/2023] [Accepted: 05/02/2023] [Indexed: 06/09/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has led to hundreds of millions of infections and millions of deaths, however, human monoclonal antibodies (mAbs) can be an effective treatment. Since SARS-CoV-2 emerged, a variety of strains have acquired increasing numbers of mutations to gain increased transmissibility and escape from the immune response. Most reported neutralizing human mAbs, including all approved therapeutic ones, have been knocked down or out by these mutations. Broadly neutralizing mAbs are therefore of great value, to treat current and possible future variants. Here, we review four types of neutralizing mAbs against the spike protein with broad potency against previously and currently circulating variants. These mAbs target the receptor-binding domain, the subdomain 1, the stem helix, or the fusion peptide. Understanding how these mAbs retain potency in the face of mutational change could guide future development of therapeutic antibodies and vaccines.
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Affiliation(s)
- Daming Zhou
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK; Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7FZ, UK.
| | - Jingshan Ren
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK
| | - Elizabeth E Fry
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK
| | - David I Stuart
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK; Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7FZ, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK; Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
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