2051
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Chen LL, Lu L, Choi CYK, Cai JP, Tsoi HW, Chu AWH, Ip JD, Chan WM, Zhang RR, Zhang X, Tam AR, Lau DPL, To WK, Que TL, Yip CCY, Chan KH, Cheng VCC, Yuen KY, Hung IFN, To KKW. Impact of SARS-CoV-2 variant-associated RBD mutations on the susceptibility to serum antibodies elicited by COVID-19 infection or vaccination. Clin Infect Dis 2021; 74:1623-1630. [PMID: 34309648 DOI: 10.1093/cid/ciab656] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Several SARS-CoV-2 lineages with mutations at the spike protein receptor binding domain (RBD) have reduced susceptibility to antibody neutralization, and have been classified as Variants of Concern (VOCs) or Variants of Interest (VOIs). Here, we systematically compared the neutralization susceptibility and RBD binding of different VOCs/VOIs, including B.1.617.1 (kappa variant) and P.3 (theta variant) which were first detected in India and the Philippines, respectively. METHODS The neutralization susceptibility of the VOCs/VOIs (B.1.351, B.1.617.1 and P.3) and a non-VOC/VOI without RBD mutations (B.1.36.27) to convalescent sera from COVID-19 patients or BNT162b2 vaccinees was determined using a live virus microneutralization (MN) assay. Serum IgG binding to wild type and mutant RBDs were determined using an enzyme immunoassay. RESULTS The geometric mean neutralization titers (GMT) of B.1.351, P.3, and B.1.617.1 were significantly lower than that of B.1.36.27 for COVID-19 patients infected with non-VOCs/VOIs (3.4-5.7-fold lower) or individuals who have received 2 doses of BNT162b2 vaccine (4.4-7.3-fold lower). The GMT of B.1.351 or P.3 were lower than that of B.1.671.1. For the 4 patients infected with B.1.351 or B.1.617.1, the MN titer was highest for their respective lineage. RBD with E484K or E484Q mutation, either alone or in combination with other mutations, showed greatest reduction in serum IgG binding. CONCLUSION P.3 and B.1.617.1 escape serum neutralization induced by natural infection or vaccine. Infection with one variant do not confer cross protection for heterologous lineages. Immunogenicity testing for second generation COVID-19 vaccines should include multiple variant and "non-variant" strains.
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Affiliation(s)
- Lin-Lei Chen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Lu Lu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Charlotte Yee-Ki Choi
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Jian-Piao Cai
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Hoi-Wah Tsoi
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Allen Wing-Ho Chu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Jonathan Daniel Ip
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Wan-Mui Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Ricky Ruiqi Zhang
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Xiaojuan Zhang
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Anthony Raymond Tam
- Department of Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Daphne Pui-Ling Lau
- Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Wing-Kin To
- Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Tak-Lun Que
- Department of Pathology, Tuen Mun Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Cyril Chik-Yan Yip
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Kwok-Hung Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Vincent Chi-Chung Cheng
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Ivan Fan-Ngai Hung
- Department of Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Kelvin Kai-Wang To
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People's Republic of China
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2052
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Imai N, Hogan AB, Williams L, Cori A, Mangal TD, Winskill P, Whittles LK, Watson OJ, Knock ES, Baguelin M, Perez-Guzman PN, Gaythorpe KA, Sonabend R, Ghani AC, Ferguson NM. Interpreting estimates of coronavirus disease 2019 (COVID-19) vaccine efficacy and effectiveness to inform simulation studies of vaccine impact: a systematic review. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.16992.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background: The multiple efficacious vaccines authorised for emergency use worldwide represent the first preventative intervention against coronavirus disease 2019 (COVID-19) that does not rely on social distancing measures. The speed at which data are emerging and the heterogeneities in study design, target populations, and implementation make it challenging to interpret and assess the likely impact of vaccine campaigns on local epidemics. We reviewed available vaccine efficacy and effectiveness studies to generate working estimates that can be used to parameterise simulation studies of vaccine impact. Methods: We searched MEDLINE, the World Health Organization’s Institutional Repository for Information Sharing, medRxiv, and vaccine manufacturer websites for studies that evaluated the emerging data on COVID-19 vaccine efficacy and effectiveness. Studies providing an estimate of the efficacy or effectiveness of a COVID-19 vaccine using disaggregated data against SARS-CoV-2 infection, symptomatic disease, severe disease, death, or transmission were included. We extracted information on study population, variants of concern (VOC), vaccine platform, dose schedule, study endpoints, and measures of impact. We applied an evidence synthesis approach to capture a range of plausible and consistent parameters for vaccine efficacy and effectiveness that can be used to inform and explore a variety of vaccination strategies as the COVID-19 pandemic evolves. Results: Of the 602 articles and reports identified, 53 were included in the analysis. The availability of vaccine efficacy and effectiveness estimates varied by vaccine and were limited for VOCs. Estimates for non-primary endpoints such as effectiveness against infection and onward transmission were sparse. Synthesised estimates were relatively consistent for the same vaccine platform for wild-type, but was more variable for VOCs. Conclusions: Assessment of efficacy and effectiveness of COVID-19 vaccines is complex. Simulation studies must acknowledge and capture the uncertainty in vaccine effectiveness to robustly explore and inform vaccination policies and policy around the lifting of non-pharmaceutical interventions.
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2053
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Nguyen D, Simmonds P, Steenhuis M, Wouters E, Desmecht D, Garigliany M, Romano M, Barbezange C, Maes P, Van Holm B, Mendoza J, Oyonarte S, Fomsgaard A, Lassaunière R, Zusinaite E, Resman Rus K, Avšič-Županc T, Reimerink JH, Brouwer F, Hoogerwerf M, Reusken CB, Grodeland G, Le Cam S, Gallian P, Amroun A, Brisbarre N, Martinaud C, Leparc Goffart I, Schrezenmeier H, Feys HB, van der Schoot CE, Harvala H. SARS-CoV-2 neutralising antibody testing in Europe: towards harmonisation of neutralising antibody titres for better use of convalescent plasma and comparability of trial data. ACTA ACUST UNITED AC 2021; 26. [PMID: 34240697 PMCID: PMC8268650 DOI: 10.2807/1560-7917.es.2021.26.27.2100568] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We compared the performance of SARS-CoV-2 neutralising antibody testing between 12 European laboratories involved in convalescent plasma trials. Raw titres differed almost 100-fold differences between laboratories when blind-testing 15 plasma samples. Calibration of titres in relation to the reference reagent and standard curve obtained by testing a dilution series reduced the inter-laboratory variability ca 10-fold. The harmonisation of neutralising antibody quantification is a vital step towards determining the protective and therapeutic levels of neutralising antibodies.
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Affiliation(s)
- Dung Nguyen
- University of Oxford, Oxford, United Kingdom
| | | | - Maurice Steenhuis
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, Amsterdam, Netherlands
| | - Elise Wouters
- Transfusion Research Centre, Belgian Red Cross-Flanders, Ghent, Belgium
| | - Daniel Desmecht
- Department of Pathology, Faculty of Veterinary Medicine, Liège University, Liège, Belgium
| | - Mutien Garigliany
- Department of Pathology, Faculty of Veterinary Medicine, Liège University, Liège, Belgium
| | - Marta Romano
- Immune Response service, Sciensano, Brussels, Belgium
| | | | - Piet Maes
- KU Leuven, Rega Institute, Clinical and Epidemiological Virology, Leuven, Belgium
| | - Bram Van Holm
- KU Leuven, Rega Institute, Clinical and Epidemiological Virology, Leuven, Belgium
| | | | - Salvador Oyonarte
- Andalusian Network of Transfusion Medicine, Tissues and Cells, Sevilla, Spain
| | - Anders Fomsgaard
- Virus and Microbiological Special Diagnostics, Statens Serum Institute, Copenhagen, Denmark
| | - Ria Lassaunière
- Virus and Microbiological Special Diagnostics, Statens Serum Institute, Copenhagen, Denmark
| | - Eva Zusinaite
- Tartu University Institute of Technology, Tartu, Estonia
| | | | | | - Johan Hj Reimerink
- Centre for Infectious Disease Control, WHO COVID-19 Reference Laboratory, RIVML, Bilthoven, the Netherlands
| | - Fiona Brouwer
- Centre for Infectious Disease Control, WHO COVID-19 Reference Laboratory, RIVML, Bilthoven, the Netherlands
| | - Marieke Hoogerwerf
- Centre for Infectious Disease Control, WHO COVID-19 Reference Laboratory, RIVML, Bilthoven, the Netherlands
| | - Chantal Bem Reusken
- Centre for Infectious Disease Control, WHO COVID-19 Reference Laboratory, RIVML, Bilthoven, the Netherlands
| | - Gunnveig Grodeland
- Dep. of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Sophie Le Cam
- Etablissement Français du Sang, La Plaine Saint Denis, France
| | - Pierre Gallian
- Etablissement Français du Sang, La Plaine Saint Denis, France.,Unité des Virus Émergents (Aix-Marseille University - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Abdennour Amroun
- Unité des Virus Émergents (Aix-Marseille University - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Nadège Brisbarre
- Unité des Virus Émergents (Aix-Marseille University - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France.,Etablissement français du Sang Provence Alpes Côte d'Azur et Corse, Marseille, France
| | | | | | - Hubert Schrezenmeier
- Department of Transfusion Medicine, Ulm University, Ulm, Germany.,Institute for Clinical Transfusion Medicine and Immunogenetics, German Red Cross Blood Transfusion Service Baden-Wurttemberg - Hessen and University Hospital Ulm, Ulm, Germany
| | - Hendrik B Feys
- Transfusion Research Centre, Belgian Red Cross-Flanders, Ghent, Belgium
| | - C Ellen van der Schoot
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, Amsterdam, Netherlands
| | - Heli Harvala
- Microbiology Services, NHS Blood and Transplant, Colindale, United Kingdom.,University College of London, London, United Kingdom
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2054
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Farinholt T, Doddapaneni H, Qin X, Menon V, Meng Q, Metcalf G, Chao H, Gingras MC, Farinholt P, Agrawal C, Muzny DM, Piedra PA, Gibbs RA, Petrosino J. Transmission event of SARS-CoV-2 Delta variant reveals multiple vaccine breakthrough infections. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.06.28.21258780. [PMID: 34268529 PMCID: PMC8282118 DOI: 10.1101/2021.06.28.21258780] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Importance Vaccine breakthrough by an emergent SARS-CoV-2 variant poses a great risk to global public health. Objective To determine the SARS-CoV-2 variant responsible for 6 cases of vaccine breakthrough. Design Nasopharyngeal swabs from suspected vaccine breakthrough cases were tested for SARS-CoV-2 by qPCR for Wuhan-Hu1 and Alpha variant. Positive samples were then sequenced by Swift Normalase Amplicon Panels to determine the causal variant. Setting Transmission event occurred at events surrounding a wedding outside of Houston, TX. Two patients from India, likely transmitted the Delta variant to other guests. Participants Following a positive SARS-CoV-2 qPCR test at a third-party site, six fully vaccinated patients were investigated. Three males and three females ranged from 53 to 69 years old. One patient suffered from diabetes while three others were classified as overweight. No significant other comorbidities were identified. None of the patients had a history of failed vaccination.
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Affiliation(s)
- Timothy Farinholt
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Harsha Doddapaneni
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Xiang Qin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Vipin Menon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Qingchang Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ginger Metcalf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Hsu Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Marie-Claude Gingras
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Paige Farinholt
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Charu Agrawal
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Pedro A Piedra
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Joseph Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
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2055
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Martínez-Flores D, Zepeda-Cervantes J, Cruz-Reséndiz A, Aguirre-Sampieri S, Sampieri A, Vaca L. SARS-CoV-2 Vaccines Based on the Spike Glycoprotein and Implications of New Viral Variants. Front Immunol 2021; 12:701501. [PMID: 34322129 PMCID: PMC8311925 DOI: 10.3389/fimmu.2021.701501] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022] Open
Abstract
Coronavirus 19 Disease (COVID-19) originating in the province of Wuhan, China in 2019, is caused by the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), whose infection in humans causes mild or severe clinical manifestations that mainly affect the respiratory system. So far, the COVID-19 has caused more than 2 million deaths worldwide. SARS-CoV-2 contains the Spike (S) glycoprotein on its surface, which is the main target for current vaccine development because antibodies directed against this protein can neutralize the infection. Companies and academic institutions have developed vaccines based on the S glycoprotein, as well as its antigenic domains and epitopes, which have been proven effective in generating neutralizing antibodies. However, the emergence of new SARS-CoV-2 variants could affect the effectiveness of vaccines. Here, we review the different types of vaccines designed and developed against SARS-CoV-2, placing emphasis on whether they are based on the complete S glycoprotein, its antigenic domains such as the receptor-binding domain (RBD) or short epitopes within the S glycoprotein. We also review and discuss the possible effectiveness of these vaccines against emerging SARS-CoV-2 variants.
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Affiliation(s)
- Daniel Martínez-Flores
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jesús Zepeda-Cervantes
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Adolfo Cruz-Reséndiz
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sergio Aguirre-Sampieri
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alicia Sampieri
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis Vaca
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
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2056
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Koopman JS, Simon CP, Getz WM, Salter R. Modeling the population effects of escape mutations in SARS-CoV-2 to guide vaccination strategies. Epidemics 2021; 36:100484. [PMID: 34375814 PMCID: PMC8274275 DOI: 10.1016/j.epidem.2021.100484] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 06/16/2021] [Accepted: 07/12/2021] [Indexed: 11/18/2022] Open
Abstract
SARS-Cov-2 escape mutations (EM) have been detected and are spreading. Vaccines may need adjustment to respond to these or future mutations. We designed a population level model integrating both waning immunity and EM. We also designed a set of criteria for elaborating and fitting this model to cross-neutralization and other data with a goal of minimizing vaccine decision errors. We formulated four related models. These differ regarding which strains can drift to escape immunity in the host when that immunity was elicited by different strains. Across changing waning and escape mutation parameter values, these model variations led to patterns where: 1) EM are rare in the first epidemic, 2) rebound outbreaks after the first outbreak are accelerated by increasing waning and by increasing drifting, 3) the long term endemic level of infection is determined mostly by waning rates with small effects of the drifting parameter, 4) EM caused loss of vaccine effectiveness, and under some conditions: vaccines induced EM that caused higher levels of infection with vaccines than without them. The differences and similarities across the four models suggest paths for developing models specifying the epitopes where EM act. This model provides a base on which to construct epitope specific evolutionary models using new high-throughput assay data from population samples to guide vaccine decisions.
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Affiliation(s)
| | | | - Wayne M Getz
- University of California, Berkeley, United States; Numerus
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2057
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Muecksch F, Wise H, Templeton K, Batchelor B, Squires M, McCance K, Jarvis L, Malloy K, Furrie E, Richardson C, MacGuire J, Godber I, Burns A, Mavin S, Zhang F, Schmidt F, Bieniasz P, Jenks S, Hatziioannou T. Longitudinal variation in SARS-CoV-2 antibody levels and emergence of viral variants: implications for the ability of serological assays to predict immunity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.07.02.21259939. [PMID: 34268524 PMCID: PMC8282113 DOI: 10.1101/2021.07.02.21259939] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Serological assays are being deployed to monitor antibody responses in SARS-CoV-2 convalescents and vaccine recipients. There is a need to determine whether such assays can predict immunity, as antibody levels wane and viral variants emerge. METHODS We measured antibodies in a cohort of SARS-CoV-2 infected patients using several high-throughput serological tests and functional neutralization assays. The effects of time and spike protein sequence variation on the performance and predictive value of the various assays was assessed. FINDINGS Neutralizing antibody titers decreased over the first few months post-infection but stabilized thereafter, at about 30% of the level observed shortly after infection. Serological assays commonly used to measure antibodies against SARS-CoV-2 displayed a range of sensitivities that declined to varying extents over time. Quantitative measurements generated by serological assays based on the spike protein were better at predicting neutralizing antibody titers than assays based on nucleocapsid, but performance was variable and manufacturer positivity thresholds were not able to predict the presence or absence of detectable neutralizing activity. Even though there was some deterioration in correlation between serological measurements and functional neutralization activity, some assays maintained an ability to predict neutralizing titers, even against variants of concern. INTERPRETATION The ability of high throughput serological assays to predict neutralizing antibody titers is likely crucial for evaluation of immunity at the population scale. These data will facilitate the selection of the most suitable assays as surrogates of functional neutralizing activity and suggest that such measurements may have utility in clinical practice.
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Affiliation(s)
- Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10065
| | - Helen Wise
- Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA
| | - Kate Templeton
- Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA
| | - Becky Batchelor
- Western General Hospital, Crewe Road South, Edinburgh, EH4 2XU
| | - Maria Squires
- Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA
| | - Kirsty McCance
- Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA
| | - Lisa Jarvis
- SNBTS Microbiology Reference Laboratory, The Jack Copland Centre, 52 Research Avenue North, Heriot Watt Research Park, Edinburgh, EH14 4AP
| | - Kristen Malloy
- SNBTS Microbiology Reference Laboratory, The Jack Copland Centre, 52 Research Avenue North, Heriot Watt Research Park, Edinburgh, EH14 4AP
| | - Elizabeth Furrie
- Ninewells Hospital and Medical School, NHS Tayside, Dundee, DD1 9SY
| | | | | | - Ian Godber
- Queen Elizabeth University Hospital, Govan Road, Glasgow, G51 4TF
| | - Alana Burns
- Queen Elizabeth University Hospital, Govan Road, Glasgow, G51 4TF
| | - Sally Mavin
- Scottish Microbiology Reference Laboratory, NHS Highland, Inverness, IV2 3UJ
| | - Fengwen Zhang
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10065
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10065
| | - Paul Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10065
- Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York NY 10065
| | - Sara Jenks
- Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA
| | - Theodora Hatziioannou
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10065
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2058
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Widera M, Wilhelm A, Hoehl S, Pallas C, Kohmer N, Wolf T, Rabenau HF, Corman VM, Drosten C, Vehreschild MJGT, Goetsch U, Gottschalk R, Ciesek S. Limited neutralization of authentic SARS-CoV-2 variants carrying E484K in vitro. J Infect Dis 2021; 224:1109-1114. [PMID: 34223909 PMCID: PMC8344430 DOI: 10.1093/infdis/jiab355] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/02/2021] [Indexed: 12/14/2022] Open
Abstract
Whether monoclonal antibodies are able to neutralise SARS-CoV-2 variants of concern has been investigated using pseudoviruses. In this study we show that bamlanivimab, casirivimab, and imdevimab efficiently neutralise authentic SARS-CoV-2 including variant B.1.1.7 (Alpha) but variants B.1.351 (Beta) and P.2 (Zeta) were resistant against bamlanivimab and partially to casirivimab.
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Affiliation(s)
- Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Alexander Wilhelm
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sebastian Hoehl
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Christiane Pallas
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Niko Kohmer
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Timo Wolf
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Germany.,University Center for Infectious Diseases (UCI), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Holger F Rabenau
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,German Center for Infection Research, DZIF, Braunschweig, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,German Center for Infection Research, DZIF, Braunschweig, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Germany.,University Center for Infectious Diseases (UCI), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Udo Goetsch
- Public Health Department of the City of Frankfurt am Main, Frankfurt am Main, Germany
| | - Rene Gottschalk
- Public Health Department of the City of Frankfurt am Main, Frankfurt am Main, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany.,German Center for Infection Research, DZIF, Braunschweig, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine and Pharmacology, Frankfurt am Main, Germany
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2059
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Redhead MA, Owen CD, Brewitz L, Collette AH, Lukacik P, Strain-Damerell C, Robinson SW, Collins PM, Schäfer P, Swindells M, Radoux CJ, Hopkins IN, Fearon D, Douangamath A, von Delft F, Malla TR, Vangeel L, Vercruysse T, Thibaut J, Leyssen P, Nguyen TT, Hull M, Tumber A, Hallett DJ, Schofield CJ, Stuart DI, Hopkins AL, Walsh MA. Bispecific repurposed medicines targeting the viral and immunological arms of COVID-19. Sci Rep 2021; 11:13208. [PMID: 34168183 PMCID: PMC8225628 DOI: 10.1038/s41598-021-92416-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/10/2021] [Indexed: 12/15/2022] Open
Abstract
Effective agents to treat coronavirus infection are urgently required, not only to treat COVID-19, but to prepare for future outbreaks. Repurposed anti-virals such as remdesivir and human anti-inflammatories such as barcitinib have received emergency approval but their overall benefits remain unclear. Vaccines are the most promising prospect for COVID-19, but will need to be redeveloped for any future coronavirus outbreak. Protecting against future outbreaks requires the identification of targets that are conserved between coronavirus strains and amenable to drug discovery. Two such targets are the main protease (Mpro) and the papain-like protease (PLpro) which are essential for the coronavirus replication cycle. We describe the discovery of two non-antiviral therapeutic agents, the caspase-1 inhibitor SDZ 224015 and Tarloxotinib that target Mpro and PLpro, respectively. These were identified through extensive experimental screens of the drug repurposing ReFRAME library of 12,000 therapeutic agents. The caspase-1 inhibitor SDZ 224015, was found to be a potent irreversible inhibitor of Mpro (IC50 30 nM) while Tarloxotinib, a clinical stage epidermal growth factor receptor inhibitor, is a sub micromolar inhibitor of PLpro (IC50 300 nM, Ki 200 nM) and is the first reported PLpro inhibitor with drug-like properties. SDZ 224015 and Tarloxotinib have both undergone safety evaluation in humans and hence are candidates for COVID-19 clinical evaluation.
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Affiliation(s)
- Martin A Redhead
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK.
| | - C David Owen
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Lennart Brewitz
- Department of Chemistry, Chemistry Research Laboratory,, The Ineos Oxford Institute for Antimicrobial Research, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Amelia H Collette
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Petra Lukacik
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Claire Strain-Damerell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Sean W Robinson
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Patrick M Collins
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Philipp Schäfer
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Mark Swindells
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Chris J Radoux
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | | | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Tika R Malla
- Department of Chemistry, Chemistry Research Laboratory,, The Ineos Oxford Institute for Antimicrobial Research, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Laura Vangeel
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000, Leuven, Belgium
| | - Thomas Vercruysse
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000, Leuven, Belgium
| | - Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000, Leuven, Belgium
| | - Pieter Leyssen
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000, Leuven, Belgium
| | - Tu-Trinh Nguyen
- Calibr, Scripps Research, 11119 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Mitchell Hull
- Calibr, Scripps Research, 11119 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Anthony Tumber
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - David J Hallett
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Christopher J Schofield
- Department of Chemistry, Chemistry Research Laboratory,, The Ineos Oxford Institute for Antimicrobial Research, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - David I Stuart
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, OX4 2JY, UK
| | - Andrew L Hopkins
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Martin A Walsh
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK.
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2060
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2061
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Dupont L, Snell LB, Graham C, Seow J, Merrick B, Lechmere T, Hallett SR, Charalampous T, Alcolea-Medina A, Huettner I, Maguire TJA, Acors S, Almeida N, Cox D, Dickenson RE, Galao RP, Jimenez-Guardeño JM, Kouphou N, Lista MJ, Pickering S, Ortega-Prieto AM, Wilson H, Winstone H, Fairhead C, Su J, Nebbia G, Batra R, Neil S, Shankar-Hari M, Edgeworth JD, Malim MH, Doores KJ. Antibody longevity and cross-neutralizing activity following SARS-CoV-2 wave 1 and B.1.1.7 infections. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.06.07.21258351. [PMID: 34127977 PMCID: PMC8202432 DOI: 10.1101/2021.06.07.21258351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
As SARS-CoV-2 variants continue to emerge globally, a major challenge for COVID-19 vaccination is the generation of a durable antibody response with cross-neutralizing activity against both current and newly emerging viral variants. Cross-neutralizing activity against major variants of concern (B.1.1.7, P.1 and B.1.351) has been observed following vaccination, albeit at a reduced potency, but whether vaccines based on the Spike glycoprotein of these viral variants will produce a superior cross-neutralizing antibody response has not been fully investigated. Here, we used sera from individuals infected in wave 1 in the UK to study the long-term cross-neutralization up to 10 months post onset of symptoms (POS), as well as sera from individuals infected with the B.1.1.7 variant to compare cross-neutralizing activity profiles. We show that neutralizing antibodies with cross-neutralizing activity can be detected from wave 1 up to 10 months POS. Although neutralization of B.1.1.7 and B.1.351 is lower, the difference in neutralization potency decreases at later timepoints suggesting continued antibody maturation and improved tolerance to Spike mutations. Interestingly, we found that B.1.1.7 infection also generates a cross-neutralizing antibody response, which, although still less potent against B.1.351, can neutralize parental wave 1 virus to a similar degree as B.1.1.7. These findings have implications for the optimization of vaccines that protect against newly emerging viral variants.
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Affiliation(s)
- Liane Dupont
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Luke B Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Blair Merrick
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Thomas Lechmere
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Sadie R Hallett
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Themoula Charalampous
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Adela Alcolea-Medina
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Thomas J A Maguire
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Sam Acors
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Nathalia Almeida
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Daniel Cox
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Ruth E Dickenson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Rui Pedro Galao
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jose M Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Neophytos Kouphou
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Marie Jose Lista
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Ana Maria Ortega-Prieto
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Harry Wilson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Helena Winstone
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Cassandra Fairhead
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Jia Su
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Stuart Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Manu Shankar-Hari
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jonathan D Edgeworth
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
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2062
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Gu R, Mao T, Lu Q, Tianjiao Su T, Wang J. Myeloid dysregulation and therapeutic intervention in COVID-19. Semin Immunol 2021; 55:101524. [PMID: 34823995 PMCID: PMC8576142 DOI: 10.1016/j.smim.2021.101524] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 11/01/2021] [Accepted: 11/05/2021] [Indexed: 12/15/2022]
Abstract
The dysregulation of myeloid cell responses is increasingly demonstrated to be a major mechanism of pathogenesis for COVID-19. The pathological cellular and cytokine signatures associated with this disease point to a critical role of a hyperactivated innate immune response in driving pathology. Unique immunopathological features of COVID-19 include myeloid-cell dominant inflammation and cytokine release syndrome (CRS) alongside lymphopenia and acute respiratory distress syndrome (ARDS), all of which correlate with severe disease. Studies suggest a range of causes mediating myeloid hyperactivation, such as aberrant innate sensing, asynchronized immune cellular responses, as well as direct viral protein/host interactions. These include the recent identification of new myeloid cell receptors that bind SARS-CoV-2, which drive myeloid cell hyperinflammatory responses independently of lung epithelial cell infection via the canonical receptor, angiotensin-converting enzyme 2 (ACE2). The spectrum and nature of myeloid cell dysregulation in COVID-19 also differs from, at least to some extent, what is observed in other infectious diseases involving myeloid cell activation. While much of the therapeutic effort has focused on preventative measures with vaccines or neutralizing antibodies that block viral infection, recent clinical trials have also targeted myeloid cells and the associated cytokines as a means to resolve CRS and severe disease, with promising but thus far modest effects. In this review, we critically examine potential mechanisms driving myeloid cell dysregulation, leading to immunopathology and severe disease, and discuss potential therapeutic strategies targeting myeloid cells as a new paradigm for COVID-19 treatment.
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Affiliation(s)
- Runxia Gu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Tianyang Mao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Qiao Lu
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, 10016, USA
| | - Tina Tianjiao Su
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06520, USA.
| | - Jun Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, 10016, USA.
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2063
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Mengist HM, Kombe Kombe AJ, Mekonnen D, Abebaw A, Getachew M, Jin T. Mutations of SARS-CoV-2 spike protein: Implications on immune evasion and vaccine-induced immunity. Semin Immunol 2021; 55:101533. [PMID: 34836774 PMCID: PMC8604694 DOI: 10.1016/j.smim.2021.101533] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/09/2021] [Accepted: 11/16/2021] [Indexed: 02/04/2023]
Abstract
Responsible for more than 4.9 million deaths so far, COVID-19, caused by SARS-CoV-2, is instigating devastating effects on the global health care system whose impacts could be longer for the years to come. Acquiring a comprehensive knowledge of host-virus interaction is critical for designing effective vaccines and/or drugs. Understanding the evolution of the virus and the impact of genetic variability on host immune evasion and vaccine efficacy is helpful to design novel strategies to minimize the effects of the emerging variants of concern (VOC). Most vaccines under development and/or in current use target the spike protein owning to its unique function of host receptor binding, relatively conserved nature, potent immunogenicity in inducing neutralizing antibodies, and being a good target of T cell responses. However, emerging SARS-CoV-2 strains are exhibiting variability on the spike protein which could affect the efficacy of vaccines and antibody-based therapies in addition to enhancing viral immune evasion mechanisms. Currently, the degree to which mutations on the spike protein affect immunity and vaccination, and the ability of the current vaccines to confer protection against the emerging variants attracts much attention. This review discusses the implications of SARS-CoV-2 spike protein mutations on immune evasion and vaccine-induced immunity and forward directions which could contribute to future studies focusing on designing effective vaccines and/or immunotherapies to consider viral evolution. Combining vaccines derived from different regions of the spike protein that boost both the humoral and cellular wings of adaptive immunity could be the best options to cope with the emerging VOC.
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Affiliation(s)
- Hylemariam Mihiretie Mengist
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Arnaud John Kombe Kombe
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, Anhui, 230027, China
| | - Daniel Mekonnen
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, Anhui, 230027, China
| | - Abtie Abebaw
- Department of Medical Laboratory Science, College of Health Science, Debre Markos University, Debre Markos, 269, Ethiopia
| | - Melese Getachew
- Department of Clinical Pharmacy, College of Health Science, Debre Markos University, Debre Markos, 269, Ethiopia
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China; Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, Anhui, 230027, China; CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Science, Shanghai, 200031, China.
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2064
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Vaishya R, Sibal A, Singh SK, Malani A, Das S. Emergence of COVID-19 variants among ChAdOx1 nCoV-19 (recombinant) vaccine recipients. Indian J Med Res 2021; 153:559-561. [PMID: 34528522 PMCID: PMC8555616 DOI: 10.4103/ijmr.ijmr_2061_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Raju Vaishya
- Depatment of Orthopaedic Surgery, Apollo Hospital Group, New Delhi 110 076, India
| | - Anupam Sibal
- Group Medical Director, Apollo Hospital Group, New Delhi 110 076, India
| | - Sujeet Kumar Singh
- Epidermiology Division, National Centre for Disease Control, Shamnath Marg, Delhi 110 054, India
| | - Arpita Malani
- Depatment of Orthopaedic Surgery, Apollo Hospital Group, New Delhi 110 076, India
| | - Shreya Das
- Depatment of Orthopaedic Surgery, Apollo Hospital Group, New Delhi 110 076, India
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2065
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) harbor mutations in the spike (S) glycoprotein that confer more efficient transmission and dampen the efficacy of COVID-19 vaccines and antibody therapies. S mediates virus entry and is the primary target for antibody responses, with structural studies of soluble S variants revealing an increased propensity toward conformations accessible to the human angiotensin-converting enzyme 2 (hACE2) receptor. However, real-time observations of conformational dynamics that govern the structural equilibriums of the S variants have been lacking. Here, we report single-molecule Förster resonance energy transfer (smFRET) studies of critical mutations observed in VOCs, including D614G and E484K, in the context of virus particles. Investigated variants predominately occupied more open hACE2-accessible conformations, agreeing with previous structures of soluble trimers. Additionally, these S variants exhibited slower transitions in hACE2-accessible/bound states. Our finding of increased S kinetic stability in the open conformation provides a new perspective on SARS-CoV-2 adaptation to the human population. IMPORTANCE SARS-CoV-2 surface S glycoprotein-the target of antibodies and vaccines-is responsible for binding to the cellular receptor hACE2. The interactions between S and hACE2 trigger structural rearrangements of S from closed to open conformations prerequisite for virus entry. Under the selection pressure imposed by adaptation to the human host and increasing vaccinations and convalescent patients, SARS-CoV-2 is evolving and has adopted numerous mutations on S variants. These promote virus spreading and immune evasion, partially by increasing the propensity of S to adopt receptor-binding competent open conformations. Here, we determined a time dimension, using smFRET to delineate the temporal prevalence of distinct structures of S in the context of virus particles. We present the first experimental evidence of decelerated transition dynamics from the open state, revealing increased stability of S open conformations to be part of the SARS-CoV-2 adaption strategies.
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2066
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Jacob Machado D, White RA, Kofsky J, Janies DA. Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2021; 1:e60. [PMID: 36168505 PMCID: PMC9495640 DOI: 10.1017/ash.2021.222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 04/19/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic was one of the significant causes of death worldwide in 2020. The disease is caused by severe acute coronavirus syndrome (SARS) coronavirus 2 (SARS-CoV-2), an RNA virus of the subfamily Orthocoronavirinae related to 2 other clinically relevant coronaviruses, SARS-CoV and MERS-CoV. Like other coronaviruses and several other viruses, SARS-CoV-2 originated in bats. However, unlike other coronaviruses, SARS-CoV-2 resulted in a devastating pandemic. The SARS-CoV-2 pandemic rages on due to viral evolution that leads to more transmissible and immune evasive variants. Technology such as genomic sequencing has driven the shift from syndromic to molecular epidemiology and promises better understanding of variants. The COVID-19 pandemic has exposed critical impediments that must be addressed to develop the science of pandemics. Much of the progress is being applied in the developed world. However, barriers to the use of molecular epidemiology in low- and middle-income countries (LMICs) remain, including lack of logistics for equipment and reagents and lack of training in analysis. We review the molecular epidemiology literature to understand its origins from the SARS epidemic (2002-2003) through influenza events and the current COVID-19 pandemic. We advocate for improved genomic surveillance of SARS-CoV and understanding the pathogen diversity in potential zoonotic hosts. This work will require training in phylogenetic and high-performance computing to improve analyses of the origin and spread of pathogens. The overarching goals are to understand and abate zoonosis risk through interdisciplinary collaboration and lowering logistical barriers.
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Affiliation(s)
- Denis Jacob Machado
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
- Author for correspondence: Denis Jacob Machado, PhD, Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, BINF 224, Charlotte, NC28223. E-mail:
| | - Richard Allen White
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
- University of North Carolina at Charlotte, North Carolina Research Campus (NCRC), Kannapolis, North Carolina
| | - Janice Kofsky
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
| | - Daniel A. Janies
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
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2067
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Khan N, Kumar N, Geiger JD. Possible therapeutic targets for SARS-CoV-2 infection and COVID-19. JOURNAL OF ALLERGY AND INFECTIOUS DISEASES 2021; 2:75-83. [PMID: 37564275 PMCID: PMC10414779 DOI: 10.46439/allergy.2.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
SARS-CoV-2 infection causes COVID-19, which has emerged as a health emergency worldwide. SARS-CoV-2 infects cells by binding to ACE2 receptors and enters into the cytoplasm following its escape from endolysosomes. Once in the cytoplasm, the virus replicates and eventually causes various pathological conditions including acute respiratory distress syndrome (ARDS) that is caused by pro-inflammatory cytokine storms. Thus, endolysosomes and cytokine storms are important therapeutic targets to suppress SARS-CoV-2 infection and COVID-19. Here, we discuss therapeutic targets of SARS-CoV-2 infection and available drugs that could be helpful in the suppression of the SARS-CoV-2 infection and pathological condition COVID-19. The urgency of the COVID-19 pandemic precludes the development of new drugs and increased focus on drug repurposing might provide the quickest way to finding effective medicines.
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Affiliation(s)
- Nabab Khan
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203, USA
| | - Nirmal Kumar
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203, USA
| | - Jonathan D. Geiger
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203, USA
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2068
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Deb B, Vilvadrinath R, Goel S. COVID-19 variants that escape vaccine immunity: Global and Indian context-are more vaccines needed? J Biosci 2021; 46:112. [PMID: 34857677 PMCID: PMC8633907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/28/2021] [Indexed: 04/05/2024]
Abstract
The COVID-19 pandemic that emerged around December 2019 claimed millions of lives. For vaccine development, S protein on viral envelope that binds to ACE2 receptor on cells for entry was identified as vaccine candidate. S protein consists of Receptor Binding Motif (RBM) in the S1 subunit followed by the S2 subunit with an intermediate furin cleavage site. A stabilized version of S protein with 2 proline residues was used as antigen. Overall, most vaccines exhibited efficacy between 80 and 95%. However, being a RNA virus that is prone to mutations along with selection pressure on S protein and frequent use of convalescent plasma led to evolution of variants. These variants are responsible for multiple waves of infection observed globally. In our review, we discuss current data on vaccines and its efficacy in neutralizing SARS-CoV-2 from Wuhan and its variants. Further, our docked mutations observed in variants on the ACE2-S complex cryo-EM structure show that mostly the S1 domain is under selection pressure where major mutations occur in the N terminal domain (NTD), RBM and junction near S1-S2 subunit. Therefore, this review would be a reference for development of new candidate antigen(s) with better efficacy against variants.
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Affiliation(s)
- Bijayeeta Deb
- Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
| | - Ramya Vilvadrinath
- Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
| | - Suchi Goel
- Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
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2069
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Yang H, Rao Z. Structural biology of SARS-CoV-2 and implications for therapeutic development. Nat Rev Microbiol 2021; 19:685-700. [PMID: 34535791 PMCID: PMC8447893 DOI: 10.1038/s41579-021-00630-8] [Citation(s) in RCA: 228] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 02/04/2023]
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an unprecedented global health crisis. However, therapeutic options for treatment are still very limited. The development of drugs that target vital proteins in the viral life cycle is a feasible approach for treating COVID-19. Belonging to the subfamily Orthocoronavirinae with the largest RNA genome, SARS-CoV-2 encodes a total of 29 proteins. These non-structural, structural and accessory proteins participate in entry into host cells, genome replication and transcription, and viral assembly and release. SARS-CoV-2 proteins can individually perform essential physiological roles, be components of the viral replication machinery or interact with numerous host cellular factors. In this Review, we delineate the structural features of SARS-CoV-2 from the whole viral particle to the individual viral proteins and discuss their functions as well as their potential as targets for therapeutic interventions.
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Affiliation(s)
- Haitao Yang
- grid.440637.20000 0004 4657 8879Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zihe Rao
- grid.440637.20000 0004 4657 8879Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China ,grid.12527.330000 0001 0662 3178Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China ,grid.216938.70000 0000 9878 7032State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin, China ,grid.9227.e0000000119573309National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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2070
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Mukherjee S, Ray SK. The Newfangled Upsurge of Double Mutant SARS-CoV-2 Virus in 2021-Current Scenario and Inspecting Ahead. RECENT ADVANCES IN ANTI-INFECTIVE DRUG DISCOVERY 2021; 16:175-178. [PMID: 34819015 DOI: 10.2174/2772434416666211124150255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/11/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Sukhes Mukherjee
- Department of Biochemistry, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh-462020,India
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