1
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Khairnar K, Tomar SS. COVID-19 genome surveillance: A geographical landscape and mutational mapping of SARS-CoV-2 variants in central India over two years. Virus Res 2024; 344:199365. [PMID: 38527669 PMCID: PMC10998191 DOI: 10.1016/j.virusres.2024.199365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 03/27/2024]
Abstract
Reading the viral genome through whole genome sequencing (WGS) enables the detection of changes in the viral genome. The rapid changes in the SARS-CoV-2 viral genome may cause immune escape leading to an increase in the pathogenicity or infectivity. Monitoring mutations through genomic surveillance helps understand the amino acid changes resulting from the mutation. These amino acid changes, especially in the spike glycoprotein, may have implications on the pathogenicity of the virus by rendering it immune-escape. The region of Vidarbha in Maharashtra represents 31.6 % of the state's total area. It holds 21.3 % of the total population. In total, 7457 SARS-CoV-2 positive samples belonging to 16 Indian States were included in the study, out of which 3002 samples passed the sequencing quality control criteria. The metadata of 7457 SARS-CoV-2 positive samples included in the study was sourced from the Integrated Health Information Platform (IHIP). The metadata of 3002 sequenced samples, including the FASTA sequence, was submitted to the Global Initiative on Sharing Avian Influenza Data (GISAID) and the Indian biological data centre (IBDC). This study identified 104 different SARS-CoV-2 pango-lineages classified into 19 clades. We have also analysed the mutation profiles of the variants found in the study, which showed eight mutations of interest, including L18F, K417N, K417T, L452R, S477N, N501Y, P681H, P681R, and mutation of concern E484K in the spike glycoprotein region. The study was from November 2020 to December 2022, making this study the most comprehensive genomic surveillance of SARS-CoV-2 conducted for the region.
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Affiliation(s)
- Krishna Khairnar
- Environmental Epidemiology & Pandemic Management (EE&PM), Council of Scientific and Industrial Research-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, India.
| | - Siddharth Singh Tomar
- Environmental Epidemiology & Pandemic Management (EE&PM), Council of Scientific and Industrial Research-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, India
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2
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Maiti AK. Therapeutic Challenges in COVID-19. Curr Mol Med 2024; 24:14-25. [PMID: 36567277 DOI: 10.2174/1566524023666221222162641] [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: 09/02/2022] [Revised: 10/18/2022] [Accepted: 11/10/2022] [Indexed: 12/27/2022]
Abstract
SARS-CoV2 is a novel respiratory coronavirus and, understanding its molecular mechanism is a prerequisite to developing effective treatment for COVID-19. This RNA genome-carrying virus has a protein coat with spikes (S) that attaches to the ACE2 receptor at the cell surface of human cells. Several repurposed drugs are used to treat COVID-19 patients that are proven to be largely unsuccessful or have limited success in reducing mortalities. Several vaccines are in use to reduce the viral load to prevent developing symptoms. Major challenges to their efficacy include the inability of antibody molecules to enter cells but remain effective in the bloodstream to kill the virus. The efficacy of vaccines also depends on their neutralizing ability to constantly evolve new virus strains due to novel mutations and evolutionary survival dynamics. Taken together, SARS-CoV2 antibody vaccines may not be very effective and other approaches based on genetic, genomic, and protein interactome could be fruitful to identify therapeutic targets to reduce disease-related mortalities.
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Affiliation(s)
- Amit K Maiti
- Department of Genetics and Genomics, Mydnavar, 28475 Greenfield Rd, Southfield MI 48076, USA
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3
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Rouet R, Henry JY, Johansen MD, Sobti M, Balachandran H, Langley DB, Walker GJ, Lenthall H, Jackson J, Ubiparipovic S, Mazigi O, Schofield P, Burnett DL, Brown SHJ, Martinello M, Hudson B, Gilroy N, Post JJ, Kelleher A, Jäck HM, Goodnow CC, Turville SG, Rawlinson WD, Bull RA, Stewart AG, Hansbro PM, Christ D. Broadly neutralizing SARS-CoV-2 antibodies through epitope-based selection from convalescent patients. Nat Commun 2023; 14:687. [PMID: 36755042 PMCID: PMC9907207 DOI: 10.1038/s41467-023-36295-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 01/25/2023] [Indexed: 02/10/2023] Open
Abstract
Emerging variants of concern (VOCs) are threatening to limit the effectiveness of SARS-CoV-2 monoclonal antibodies and vaccines currently used in clinical practice; broadly neutralizing antibodies and strategies for their identification are therefore urgently required. Here we demonstrate that broadly neutralizing antibodies can be isolated from peripheral blood mononuclear cells of convalescent patients using SARS-CoV-2 receptor binding domains carrying epitope-specific mutations. This is exemplified by two human antibodies, GAR05, binding to epitope class 1, and GAR12, binding to a new epitope class 6 (located between class 3 and 5). Both antibodies broadly neutralize VOCs, exceeding the potency of the clinical monoclonal sotrovimab (S309) by orders of magnitude. They also provide prophylactic and therapeutic in vivo protection of female hACE2 mice against viral challenge. Our results indicate that exposure to SARS-CoV-2 induces antibodies that maintain broad neutralization against emerging VOCs using two unique strategies: either by targeting the divergent class 1 epitope in a manner resistant to VOCs (ACE2 mimicry, as illustrated by GAR05 and mAbs P2C-1F11/S2K14); or alternatively, by targeting rare and highly conserved epitopes, such as the new class 6 epitope identified here (as illustrated by GAR12). Our results provide guidance for next generation monoclonal antibody development and vaccine design.
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Affiliation(s)
- Romain Rouet
- Garvan Institute of Medical Research, Sydney, NSW, Australia.
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia.
| | - Jake Y Henry
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Matt D Johansen
- Center for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia
| | - Meghna Sobti
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | - Harikrishnan Balachandran
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia
- Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - David B Langley
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Gregory J Walker
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia
- Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
- Prince of Wales Hospital, Sydney, NSW, Australia
| | - Helen Lenthall
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Jennifer Jackson
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Stephanie Ubiparipovic
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Ohan Mazigi
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Deborah L Burnett
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Simon H J Brown
- Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Marianne Martinello
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia
- Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | | | | | | | - Anthony Kelleher
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia
- Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Friedrich-Alexander University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen-Nürnberg, Germany
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Stuart G Turville
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia
- Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - William D Rawlinson
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia
- Prince of Wales Hospital, Sydney, NSW, Australia
| | - Rowena A Bull
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia
- Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Alastair G Stewart
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | | | - Daniel Christ
- Garvan Institute of Medical Research, Sydney, NSW, Australia.
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia.
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4
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Novakovsky G, Dexter N, Libbrecht MW, Wasserman WW, Mostafavi S. Obtaining genetics insights from deep learning via explainable artificial intelligence. Nat Rev Genet 2023; 24:125-137. [PMID: 36192604 DOI: 10.1038/s41576-022-00532-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2022] [Indexed: 01/24/2023]
Abstract
Artificial intelligence (AI) models based on deep learning now represent the state of the art for making functional predictions in genomics research. However, the underlying basis on which predictive models make such predictions is often unknown. For genomics researchers, this missing explanatory information would frequently be of greater value than the predictions themselves, as it can enable new insights into genetic processes. We review progress in the emerging area of explainable AI (xAI), a field with the potential to empower life science researchers to gain mechanistic insights into complex deep learning models. We discuss and categorize approaches for model interpretation, including an intuitive understanding of how each approach works and their underlying assumptions and limitations in the context of typical high-throughput biological datasets.
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Affiliation(s)
- Gherman Novakovsky
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Bioinformatics Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nick Dexter
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada.,School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Maxwell W Libbrecht
- School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada.
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Sara Mostafavi
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA. .,Canadian Institute for Advanced Research, Toronto, Ontario, Canada.
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5
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Shishido AA, Barnes AH, Narayanan S, Chua JV. COVID-19 Vaccines-All You Want to Know. Semin Respir Crit Care Med 2023; 44:143-172. [PMID: 36646092 DOI: 10.1055/s-0042-1759779] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) pandemic has led to an unprecedented public health crisis. The collective global response has led to production of multiple safe and effective vaccines utilizing novel platforms to combat the virus that have propelled the field of vaccinology forward. Significant challenges to universal vaccine effectiveness remain, including immune evasion by SARS-CoV-2 variants, waning of immune response, inadequate knowledge of correlates of protection, and dosing in special populations. This review serves as a detailed evaluation of the development of the current SARS-CoV-2 vaccines, their effectiveness, and challenges to their deployment as a preventive tool.
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Affiliation(s)
- Akira A Shishido
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland.,Division of Infectious Diseases, Virginia Commonwealth University, Richmond, Virginia
| | - Ashley H Barnes
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Shivakumar Narayanan
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Joel V Chua
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
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6
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Kumar N, Kaushik R, Zhang KYJ, Uversky VN, Sahu U, Sood R, Bhatia S. A novel consensus-based computational pipeline for screening of antibody therapeutics for efficacy against SARS-CoV-2 variants of concern including Omicron variant. Proteins 2023; 91:798-806. [PMID: 36629264 DOI: 10.1002/prot.26467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 11/11/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
Multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to evolve carrying flexible amino acid substitutions in the spike protein's receptor binding domain (RBD). These substitutions modify the binding of the SARS-CoV-2 to human angiotensin-converting enzyme 2 (hACE2) receptor and have been implicated in altered host fitness, transmissibility, and efficacy against antibody therapeutics and vaccines. Reliably predicting the binding strength of SARS-CoV-2 variants RBD to hACE2 receptor and neutralizing antibodies (NAbs) can help assessing their fitness, and rapid deployment of effective antibody therapeutics, respectively. Here, we introduced a two-step computational framework with 3-fold validation that first identified dissociation constant as a reliable predictor of binding affinity in hetero- dimeric and trimeric protein complexes. The second step implements dissociation constant as descriptor of the binding strengths of SARS-CoV-2 variants RBD to hACE2 and NAbs. Then, we examined several variants of concerns (VOCs) such as Alpha, Beta, Gamma, Delta, and Omicron and demonstrated that these VOCs RBD bind to the hACE2 with enhanced affinity. Furthermore, the binding affinity of Omicron variant's RBD was reduced with majority of the RBD-directed NAbs, which is highly consistent with the experimental neutralization data. By studying the atomic contacts between RBD and NAbs, we revealed the molecular footprints of four NAbs (GH-12, P2B-1A1, Asarnow_3D11, and C118)-that may likely neutralize the recently emerged Omicron variant-facilitating enhanced binding affinity. Finally, our findings suggest a computational pathway that could aid researchers identify a range of current NAbs that may be effective against emerging SARS-CoV-2 variants.
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Affiliation(s)
- Naveen Kumar
- Zoonotic Diseases Group, ICAR-National Institute of High Security Animal Diseases, Bhopal, India
| | - Rahul Kaushik
- Biotechnology Research Center, Technology Innovation Institute, Abu Dhabi, UAE.,Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center 'Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences', Pushchino, Russia
| | - Upasana Sahu
- Zoonotic Diseases Group, ICAR-National Institute of High Security Animal Diseases, Bhopal, India
| | - Richa Sood
- Zoonotic Diseases Group, ICAR-National Institute of High Security Animal Diseases, Bhopal, India
| | - Sandeep Bhatia
- Zoonotic Diseases Group, ICAR-National Institute of High Security Animal Diseases, Bhopal, India
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7
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Bender Ignacio RA, Wohl DA, Arends R, Pilla Reddy V, Mu Y, Javan AC, Hughes MD, Eron JJ, Currier JS, Smith D, Chew KW, Gibbs M, Fletcher CV. Comparative Pharmacokinetics of Tixagevimab/Cilgavimab (AZD7442) Administered Intravenously Versus Intramuscularly in Symptomatic SARS-CoV-2 Infection. Clin Pharmacol Ther 2022; 112:1207-1213. [PMID: 35797235 PMCID: PMC9349574 DOI: 10.1002/cpt.2706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/28/2022] [Indexed: 01/31/2023]
Abstract
AZD7442 (Evusheld) is a combination of two human anti-severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) monoclonal antibodies (mAbs), tixagevimab (AZD8895) and cilgavimab (AZD1061). Route of administration is an important consideration to improve treatment access. We assessed pharmacokinetics (PKs) of AZD7442 absorption following 600 mg administered intramuscularly (i.m.) in the thigh compared with 300 mg intravenously (i.v.) in ambulatory adults with symptomatic COVID-19. PK analysis included 84 of 110 participants randomized to receive i.m. AZD7442 and 16 of 61 randomized to receive i.v. AZD7442. Serum was collected prior to AZD7442 administration and at 24 hours and 3, 7, and 14 days later. PK parameters were calculated using noncompartmental methods. Following 600 mg i.m., the geometric mean maximum concentration (Cmax ) was 38.19 μg/mL (range: 17.30-60.80) and 37.33 μg/mL (range: 14.90-58.90) for tixagevimab and cilgavimab, respectively. Median observed time to maximum concentration (Tmax ) was 7.1 and 7.0 days for tixagevimab and cilgavimab, respectively. Serum concentrations after i.m. dosing were similar to the i.v. dose (27-29 μg/mL each component) at 3 days. The area under the concentration-time curve (AUC)0-7d geometric mean ratio was 0.9 for i.m. vs. i.v. Participants with higher weight or body mass index were more likely to have lower concentrations with either route. Women appeared to have higher interparticipant variability in concentrations compared with men. The concentrations of tixagevimab and cilgavimab after administration i.m. to the thigh were similar to those achieved with i.v. after 3 days from dosing. Exposure in the i.m. group was 90% of i.v. over 7 days. Administration to the thigh can be considered to provide consistent mAb exposure and improve access.
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Affiliation(s)
- Rachel A Bender Ignacio
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - David A Wohl
- Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Rosalin Arends
- Clinical Pharmacology and Quantitative Pharmacology, Vaccines & Immunotherapies, Neuroscience and Clinical Immunogenicity, AstraZeneca, Cambridge, UK
| | - Venkatesh Pilla Reddy
- Clinical Pharmacology and Quantitative Pharmacology, Vaccines & Immunotherapies, Neuroscience and Clinical Immunogenicity, AstraZeneca, Cambridge, UK
| | - Ying Mu
- UNMC Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Arzhang Cyrus Javan
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael D Hughes
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Joseph J Eron
- Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Judith S Currier
- Division of Infectious Diseases, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, USA
| | - Davey Smith
- Division of Infectious Diseases and Global Public Health, University of California - San Diego, San Diego, California, USA
| | - Kara W Chew
- Division of Infectious Diseases, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, USA
| | - Michael Gibbs
- Clinical Pharmacology and Quantitative Pharmacology, Vaccines & Immunotherapies, Neuroscience and Clinical Immunogenicity, AstraZeneca, Cambridge, UK
| | - Courtney V Fletcher
- UNMC Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska, USA
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Takaoka Y, Sugano A, Morinaga Y, Ohta M, Miura K, Kataguchi H, Kumaoka M, Kimura S, Maniwa Y. Prediction of infectivity of SARS-CoV2: Mathematical model with analysis of docking simulation for spike proteins and angiotensin-converting enzyme 2. MICROBIAL RISK ANALYSIS 2022; 22:100227. [PMID: 35756961 PMCID: PMC9212987 DOI: 10.1016/j.mran.2022.100227] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/15/2022] [Accepted: 06/15/2022] [Indexed: 05/13/2023]
Abstract
Objectives Variants of a coronavirus (SARS-CoV-2) have been spreading in a global pandemic. Improved understanding of the infectivity of future new variants is important so that effective countermeasures against them can be quickly undertaken. In our research reported here, we aimed to predict the infectivity of SARS-CoV-2 by using a mathematical model with molecular simulation analysis, and we used phylogenetic analysis to determine the evolutionary distance of the spike protein gene (S gene) of SARS-CoV-2. Methods We subjected the six variants and the wild type of spike protein and human angiotensin-converting enzyme 2 (ACE2) to molecular docking simulation analyses to understand the binding affinity of spike protein and ACE2. We then utilized regression analysis of the correlation coefficient of the mathematical model and the infectivity of SARS-CoV-2 to predict infectivity. Results The evolutionary distance of the S gene correlated with the infectivity of SARS-CoV-2 variants. The calculated biding affinity for the mathematical model obtained with results of molecular docking simulation also correlated with the infectivity of SARS-CoV-2 variants. These results suggest that the data from the docking simulation for the receptor binding domain of variant spike proteins and human ACE2 were valuable for prediction of SARS-CoV-2 infectivity. Conclusion We developed a mathematical model for prediction of SARS-CoV-2 variant infectivity by using binding affinity obtained via molecular docking and the evolutionary distance of the S gene.
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Affiliation(s)
- Yutaka Takaoka
- Department of Computational Drug Design and Mathematical Medicine, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
- Data Science Center for Medicine and Hospital Management, Toyama University Hospital, Toyama 930-0194, Japan
- Center for Advanced Antibody Drug Development, University of Toyama, Toyama 930-0194, Japan
- Department of Medical Systems, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
- Life Science Institute, Kobe Tokiwa University, Kobe, Hyogo 653-0838, Japan
| | - Aki Sugano
- Department of Medical Systems, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
- Center for Clinical Research, Toyama University Hospital, Toyama 930-0194, Japan
| | - Yoshitomo Morinaga
- Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Mika Ohta
- Department of Computational Drug Design and Mathematical Medicine, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
- Data Science Center for Medicine and Hospital Management, Toyama University Hospital, Toyama 930-0194, Japan
- Department of Medical Systems, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
- Life Science Institute, Kobe Tokiwa University, Kobe, Hyogo 653-0838, Japan
| | - Kenji Miura
- Data Science Center for Medicine and Hospital Management, Toyama University Hospital, Toyama 930-0194, Japan
| | - Haruyuki Kataguchi
- Department of Computational Drug Design and Mathematical Medicine, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
- Data Science Center for Medicine and Hospital Management, Toyama University Hospital, Toyama 930-0194, Japan
| | - Minoru Kumaoka
- Data Science Center for Medicine and Hospital Management, Toyama University Hospital, Toyama 930-0194, Japan
- Department of Medical Systems, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
| | - Shigemi Kimura
- Department of Medical Systems, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
| | - Yoshimasa Maniwa
- Department of Medical Systems, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
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9
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Misasi J, Wei RR, Wang L, Pegu A, Wei CJ, Oloniniyi OK, Zhou T, Moliva JI, Zhao B, Choe M, Yang ES, Zhang Y, Boruszczak M, Chen M, Leung K, Li J, Yang ZY, Andersen H, Carlton K, Godbole S, Harris DR, Henry AR, Ivleva VB, Lei P, Liu C, Longobardi L, Merriam JS, Nase D, Olia AS, Pessaint L, Porto M, Shi W, Wolff JJ, Douek DC, Suthar MS, Gall J, Koup RA, Kwong PD, Mascola JR, Nabel GJ, Sullivan NJ. A multispecific antibody prevents immune escape and confers pan-SARS-CoV-2 neutralization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.07.29.502029. [PMID: 35982683 PMCID: PMC9387125 DOI: 10.1101/2022.07.29.502029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Despite effective countermeasures, SARS-CoV-2 persists worldwide due to its ability to diversify and evade human immunity1. This evasion stems from amino-acid substitutions, particularly in the receptor-binding domain of the spike, that confer resistance to vaccines and antibodies 2-16. To constrain viral escape through resistance mutations, we combined antibody variable regions that recognize different receptor binding domain (RBD) sites17,18 into multispecific antibodies. Here, we describe multispecific antibodies, including a trispecific that prevented virus escape >3000-fold more potently than the most effective clinical antibody or mixtures of the parental antibodies. Despite being generated before the evolution of Omicron, this trispecific antibody potently neutralized all previous variants of concern and major Omicron variants, including the most recent BA.4/BA.5 strains at nanomolar concentrations. Negative stain electron microscopy revealed that synergistic neutralization was achieved by engaging different epitopes in specific orientations that facilitated inter-spike binding. An optimized trispecific antibody also protected Syrian hamsters against Omicron variants BA.1, BA.2 and BA.5, each of which uses different amino acid substitutions to mediate escape from therapeutic antibodies. Such multispecific antibodies decrease the likelihood of SARS-CoV-2 escape, simplify treatment, and maximize coverage, providing a strategy for universal antibody therapies that could help eliminate pandemic spread for this and other pathogens.
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Affiliation(s)
- John Misasi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ronnie R. Wei
- Modex Therapeutics Inc., an OPKO Health Company, Natick, MA 01760, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Chih-Jen Wei
- Modex Therapeutics Inc., an OPKO Health Company, Natick, MA 01760, USA
| | - Olamide K. Oloniniyi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Juan I. Moliva
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bingchun Zhao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Misook Choe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marika Boruszczak
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwan Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Juan Li
- Modex Therapeutics Inc., an OPKO Health Company, Natick, MA 01760, USA
| | - Zhi-Yong Yang
- Modex Therapeutics Inc., an OPKO Health Company, Natick, MA 01760, USA
| | | | - Kevin Carlton
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sucheta Godbole
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Darcy R. Harris
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy R. Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vera B. Ivleva
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paula Lei
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cuiping Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lindsay Longobardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonah S. Merriam
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Adam S. Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeremy J. Wolff
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mehul S. Suthar
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jason Gall
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard A. Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gary J. Nabel
- Modex Therapeutics Inc., an OPKO Health Company, Natick, MA 01760, USA
| | - Nancy J. Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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10
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Li ZL, Buck M. Computational analysis of interior mutations of SARS-CoV-2 Spike protein suggest a balance of protein stability and S2: S1 separation propensity. Comput Struct Biotechnol J 2022; 20:6078-6086. [PMID: 36373151 PMCID: PMC9638846 DOI: 10.1016/j.csbj.2022.10.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
SARS-CoV-2 variants often include surface mutations in the Spike protein that are important for viruses to recognize host receptors and evade antibody neutralization. The Spike protein also has mutations in the interior of the protein likely to affect the Spike protein S1 - S2 subunit's separation propensity, the most important of which is the D614G mutation. Remarkably, the Omicron variant contains a large number of internal mutations at the S2: S1 interface, which have not been investigated yet. In this study, we examined the effects of such interfacial mutations on the S2: S1 and subunit domain interactions and on the subunit's dissociation process. We found that the interaction with S2 is mainly contributed by the three encapsulation domains, named INT, ED1 and ED2 of S1, which are sandwiched between the S1 RBD and N-terminal NTD domain. We found that D614 is the strongest contributor for the S2: S1 interaction which is greatly weakened by the D614G mutation. Surprisingly, we found that, mutations T547K, H655Y, N764K, N856K, N969K, L981F in the Omicron variant largely enhance the S2: ED1 interaction, partially compensating the loss of S2: ED2 interaction due to the D614G mutation. Lastly, these results, together with biological considerations, allow us to suggest that in addition to the binding strength of between the RBD and ACE2, the stability of the Spike protein and the propensity of Spike protein S2: S1 separation are critical factors which likely exist in a balance for a particular infectivity and pathogenicity of the virus.
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Affiliation(s)
- Zhen-lu Li
- School of Life Science, Tianjin University, Tianjin 300072, China
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Pharmacology, Department of Neurosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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11
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Chen Z, Zhang P, Matsuoka Y, Tsybovsky Y, West K, Santos C, Boyd LF, Nguyen H, Pomerenke A, Stephens T, Olia AS, Zhang B, De Giorgi V, Holbrook MR, Gross R, Postnikova E, Garza NL, Johnson RF, Margulies DH, Kwong PD, Alter HJ, Buchholz UJ, Lusso P, Farci P. Potent monoclonal antibodies neutralize Omicron sublineages and other SARS-CoV-2 variants. Cell Rep 2022; 41:111528. [PMID: 36302375 PMCID: PMC9554601 DOI: 10.1016/j.celrep.2022.111528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/29/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
The emergence and global spread of the SARS-CoV-2 Omicron variants, which carry an unprecedented number of mutations, raise serious concerns due to the reduced efficacy of current vaccines and resistance to therapeutic antibodies. Here, we report the generation and characterization of two potent human monoclonal antibodies, NA8 and NE12, against the receptor-binding domain of the SARS-CoV-2 spike protein. NA8 interacts with a highly conserved region and has a breadth of neutralization with picomolar potency against the Beta variant and the Omicron BA.1 and BA.2 sublineages and nanomolar potency against BA.2.12.1 and BA.4. Combination of NA8 and NE12 retains potent neutralizing activity against the major SARS-CoV-2 variants of concern. Cryo-EM analysis provides the structural basis for the broad and complementary neutralizing activity of these two antibodies. We confirm the in vivo protective and therapeutic efficacies of NA8 and NE12 in the hamster model. These results show that broad and potent human antibodies can overcome the continuous immune escape of evolving SARS-CoV-2 variants.
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Affiliation(s)
- Zhaochun Chen
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Peng Zhang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yumiko Matsuoka
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yaroslav Tsybovsky
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kamille West
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Celia Santos
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lisa F Boyd
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hanh Nguyen
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Anna Pomerenke
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tyler Stephens
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Valeria De Giorgi
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Michael R Holbrook
- National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, National Institutes of Health, Frederick, MD, USA
| | - Robin Gross
- National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, National Institutes of Health, Frederick, MD, USA
| | - Elena Postnikova
- National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, National Institutes of Health, Frederick, MD, USA
| | - Nicole L Garza
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Reed F Johnson
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David H Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Harvey J Alter
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Ursula J Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Paolo Lusso
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Patrizia Farci
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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12
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Lam JH, Shivhare D, Chia TW, Chew SL, Sinsinbar G, Aw TY, Wong S, Venkataraman S, Lim FWI, Vandepapeliere P, Nallani M. Artificial Cell Membrane Polymersome-Based Intranasal Beta Spike Formulation as a Second Generation Covid-19 Vaccine. ACS NANO 2022; 16:16757-16775. [PMID: 36223228 PMCID: PMC9578649 DOI: 10.1021/acsnano.2c06350] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/06/2022] [Indexed: 05/25/2023]
Abstract
Current parenteral coronavirus disease 2019 (Covid-19) vaccines inadequately protect against infection of the upper respiratory tract. Additionally, antibodies generated by wild type (WT) spike-based vaccines poorly neutralize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. To address the need for a second-generation vaccine, we have initiated a preclinical program to produce and evaluate a potential candidate. Our vaccine consists of recombinant Beta spike protein coadministered with synthetic CpG adjuvant. Both components are encapsulated within artificial cell membrane (ACM) polymersomes, synthetic nanovesicles efficiently internalized by antigen presenting cells, including dendritic cells, enabling targeted delivery of cargo for enhanced immune responses. ACM vaccine is immunogenic in C57BL/6 mice and Golden Syrian hamsters, evoking high serum IgG and neutralizing responses. Compared to an ACM-WT spike vaccine that generates predominantly WT-neutralizing antibodies, the ACM-Beta spike vaccine induces antibodies that neutralize WT and Beta viruses equally. Intramuscular (IM)-immunized hamsters are strongly protected from weight loss and other clinical symptoms after the Beta challenge but show delayed viral clearance in the upper airway. With intranasal (IN) immunization, however, neutralizing antibodies are generated in the upper airway concomitant with rapid and potent reduction of viral load. Moreover, antibodies are cross-neutralizing and show good activity against Omicron. Safety is evaluated in New Zealand white rabbits in a repeated dose toxicological study under Good Laboratory Practice (GLP) conditions. Three doses, IM or IN, at two-week intervals do not induce an adverse effect or systemic toxicity. Cumulatively, these results support the application for a Phase 1 clinical trial of ACM-polymersome-based Covid-19 vaccine (ClinicalTrials.gov identifier: NCT05385991).
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Affiliation(s)
- Jian Hang Lam
- ACM Biolabs Pte Ltd., 71
Nanyang Drive, #02M-02, NTU Innovation Center, 638075, Singapore
| | - Devendra Shivhare
- ACM Biolabs Pte Ltd., 71
Nanyang Drive, #02M-02, NTU Innovation Center, 638075, Singapore
| | - Teck Wan Chia
- ACM Biolabs Pte Ltd., 71
Nanyang Drive, #02M-02, NTU Innovation Center, 638075, Singapore
| | - Suet Li Chew
- ACM Biolabs Pte Ltd., 71
Nanyang Drive, #02M-02, NTU Innovation Center, 638075, Singapore
| | - Gaurav Sinsinbar
- ACM Biolabs Pte Ltd., 71
Nanyang Drive, #02M-02, NTU Innovation Center, 638075, Singapore
| | - Ting Yan Aw
- ACM Biolabs Pte Ltd., 71
Nanyang Drive, #02M-02, NTU Innovation Center, 638075, Singapore
| | - Siamy Wong
- ACM Biolabs Pte Ltd., 71
Nanyang Drive, #02M-02, NTU Innovation Center, 638075, Singapore
| | - Shrinivas Venkataraman
- ACM Biolabs Pte Ltd., 71
Nanyang Drive, #02M-02, NTU Innovation Center, 638075, Singapore
| | - Francesca Wei Inng Lim
- Department of Hematology, Singapore General
Hospital, Outram Road, Block 7, Level 2, 169608,
Singapore
| | | | - Madhavan Nallani
- ACM Biolabs Pte Ltd., 71
Nanyang Drive, #02M-02, NTU Innovation Center, 638075, Singapore
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13
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Freire-Neto FP, Teixeira DG, da Cunha DCS, Morais IC, Tavares CPM, Gurgel GP, Medeiros SDN, dos Santos DC, Sales ADO, Jeronimo SMB. SARS-CoV-2 reinfections with BA.1 (Omicron) variant among fully vaccinated individuals in northeastern Brazil. PLoS Negl Trop Dis 2022; 16:e0010337. [PMID: 36191040 PMCID: PMC9560550 DOI: 10.1371/journal.pntd.0010337] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/13/2022] [Accepted: 08/31/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in Rio Grande do Norte, northeastern Brazil, was diagnosed on March 12, 2020; thereafter, multiple surges of infection occurred, similar to what was seen elsewhere. These surges were mostly due to SARS-CoV-2 mutations leading to emergence of variants of concern (VoC). The introduction of new VoCs in a population previously exposed to SARS-CoV-2 or after vaccination has been a challenge to understanding the kinetics of the protective immune response against this virus. The aim of this study was to investigate the outbreak of SARS-CoV-2 reinfections observed in mid-January 2022 in Rio Grande do Norte state, Brazil. It describes the clinical and genomic characteristics of nine cases of reinfection that occurred coincident with the introduction of the omicron variant. METHODOLOGY/PRINCIPAL FINDINGS Of a total of 172,965 individuals with upper respiratory symptoms tested for SARS-CoV-2, between March 2020 through mid-February 2022, 58,097 tested positive. Of those, 444 had documented a second SARS-CoV-2 infection and nine reinfection cases were selected for sequencing. Genomic analysis revealed that virus lineages diverged between primary infections and the reinfections, with the latter caused by the Omicron (BA.1) variant among individuals fully vaccinated against SARS-CoV-2. CONCLUSIONS/SIGNIFICANCE Our findings suggest that the Omicron variant is able to evade both natural and vaccine-induced immunity, since all nine cases had prior natural infection and, in addition, were fully vaccinated, emphasizing the need to develop effective blocking vaccines.
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Affiliation(s)
- Francisco P. Freire-Neto
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
- Departmento de Bioquímica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
- Getúlio Sales Diagnósticos, Natal, Rio Grande do Norte, Brazil
| | - Diego G. Teixeira
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Dayse C. S. da Cunha
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Ingryd C. Morais
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Celisa P. M. Tavares
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | | | - David C. dos Santos
- Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | - Selma M. B. Jeronimo
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
- Departmento de Bioquímica, Centro de Biociências, Universidade Federal do Rio Grande Norte, Natal, Rio Grande do Norte, Brazil
- Instituto Nacional de Ciência e Tecnologia de Doenças Tropicais, Natal, Rio Grande do Norte, Brazil
- * E-mail:
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14
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Freire-Neto FP, Teixeira DG, da Cunha DCS, Morais IC, Tavares CPM, Gurgel GP, Medeiros SDN, Santos DCD, Sales ADO, Jeronimo SMB. SARS-CoV-2 reinfections with BA.1 (Omicron) variant among fully vaccinated individuals in northeastern Brazil. PLoS Negl Trop Dis 2022; 16:e0010337. [PMID: 36191040 DOI: 10.1101/2022.04.08.22272726] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/13/2022] [Accepted: 08/31/2022] [Indexed: 05/23/2023] Open
Abstract
BACKGROUND The first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in Rio Grande do Norte, northeastern Brazil, was diagnosed on March 12, 2020; thereafter, multiple surges of infection occurred, similar to what was seen elsewhere. These surges were mostly due to SARS-CoV-2 mutations leading to emergence of variants of concern (VoC). The introduction of new VoCs in a population previously exposed to SARS-CoV-2 or after vaccination has been a challenge to understanding the kinetics of the protective immune response against this virus. The aim of this study was to investigate the outbreak of SARS-CoV-2 reinfections observed in mid-January 2022 in Rio Grande do Norte state, Brazil. It describes the clinical and genomic characteristics of nine cases of reinfection that occurred coincident with the introduction of the omicron variant. METHODOLOGY/PRINCIPAL FINDINGS Of a total of 172,965 individuals with upper respiratory symptoms tested for SARS-CoV-2, between March 2020 through mid-February 2022, 58,097 tested positive. Of those, 444 had documented a second SARS-CoV-2 infection and nine reinfection cases were selected for sequencing. Genomic analysis revealed that virus lineages diverged between primary infections and the reinfections, with the latter caused by the Omicron (BA.1) variant among individuals fully vaccinated against SARS-CoV-2. CONCLUSIONS/SIGNIFICANCE Our findings suggest that the Omicron variant is able to evade both natural and vaccine-induced immunity, since all nine cases had prior natural infection and, in addition, were fully vaccinated, emphasizing the need to develop effective blocking vaccines.
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Affiliation(s)
- Francisco P Freire-Neto
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
- Departmento de Bioquímica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
- Getúlio Sales Diagnósticos, Natal, Rio Grande do Norte, Brazil
| | - Diego G Teixeira
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Dayse C S da Cunha
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Ingryd C Morais
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Celisa P M Tavares
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | | | - David C Dos Santos
- Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | - Selma M B Jeronimo
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
- Departmento de Bioquímica, Centro de Biociências, Universidade Federal do Rio Grande Norte, Natal, Rio Grande do Norte, Brazil
- Instituto Nacional de Ciência e Tecnologia de Doenças Tropicais, Natal, Rio Grande do Norte, Brazil
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15
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Ku Z, Xie X, Lin J, Gao P, Wu B, El Sahili A, Su H, Liu Y, Ye X, Tan EY, Li X, Fan X, Goh BC, Xiong W, Boyd H, Muruato AE, Deng H, Xia H, Zou J, Kalveram BK, Menachery VD, Zhang N, Lescar J, Shi PY, An Z. Engineering SARS-CoV-2 specific cocktail antibodies into a bispecific format improves neutralizing potency and breadth. Nat Commun 2022; 13:5552. [PMID: 36138032 PMCID: PMC9499943 DOI: 10.1038/s41467-022-33284-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 09/12/2022] [Indexed: 01/20/2023] Open
Abstract
One major limitation of neutralizing antibody-based COVID-19 therapy is the requirement of costly cocktails to reduce emergence of antibody resistance. Here we engineer two bispecific antibodies (bsAbs) using distinct designs and compared them with parental antibodies and their cocktail. Single molecules of both bsAbs block the two epitopes targeted by parental antibodies on the receptor-binding domain (RBD). However, bsAb with the IgG-(scFv)2 design (14-H-06) but not the CrossMAb design (14-crs-06) shows increased antigen-binding and virus-neutralizing activities against multiple SARS-CoV-2 variants as well as increased breadth of neutralizing activity compared to the cocktail. X-ray crystallography and cryo-EM reveal distinct binding models for individual cocktail antibodies, and computational simulations suggest higher inter-spike crosslinking potentials by 14-H-06 than 14-crs-06. In mouse models of infections by SARS-CoV-2 and multiple variants, 14-H-06 exhibits higher or equivalent therapeutic efficacy than the cocktail. Rationally engineered bsAbs represent a cost-effective alternative to antibody cocktails and a promising strategy to improve potency and breadth.
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Affiliation(s)
- Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Infectious Disease Research, Science of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, Institute for Human Infection and Immunity, Sealy Institute for Vaccine Sciences, Sealy Center for Structural Biology & Molecular Biophysics, Department of Pharmacology & Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jianqing Lin
- NTU Institute of Structural Biology and School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Peng Gao
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Bin Wu
- NTU Institute of Structural Biology and School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Abbas El Sahili
- NTU Institute of Structural Biology and School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Hang Su
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, Institute for Human Infection and Immunity, Sealy Institute for Vaccine Sciences, Sealy Center for Structural Biology & Molecular Biophysics, Department of Pharmacology & Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xiaohua Ye
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Infectious Disease Research, Science of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Eddie Yongjun Tan
- NTU Institute of Structural Biology and School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xin Li
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Xuejun Fan
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Boon Chong Goh
- NTU Institute of Structural Biology and School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore, Singapore
| | - Wei Xiong
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hannah Boyd
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Antonio E Muruato
- Department of Biochemistry and Molecular Biology, Institute for Human Infection and Immunity, Sealy Institute for Vaccine Sciences, Sealy Center for Structural Biology & Molecular Biophysics, Department of Pharmacology & Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hui Deng
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, Institute for Human Infection and Immunity, Sealy Institute for Vaccine Sciences, Sealy Center for Structural Biology & Molecular Biophysics, Department of Pharmacology & Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, Institute for Human Infection and Immunity, Sealy Institute for Vaccine Sciences, Sealy Center for Structural Biology & Molecular Biophysics, Department of Pharmacology & Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Birte K Kalveram
- Department of Biochemistry and Molecular Biology, Institute for Human Infection and Immunity, Sealy Institute for Vaccine Sciences, Sealy Center for Structural Biology & Molecular Biophysics, Department of Pharmacology & Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D Menachery
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Julien Lescar
- NTU Institute of Structural Biology and School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, Institute for Human Infection and Immunity, Sealy Institute for Vaccine Sciences, Sealy Center for Structural Biology & Molecular Biophysics, Department of Pharmacology & Toxicology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA.
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16
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Murari TB, Fonseca LMDS, Pereira HBDB, Nascimento Filho AS, Saba H, Scorza FA, G. de Almeida AC, Maciel ELN, Mendes JFF, Rocha Filho TM, David JR, Badaró R, Machado BAS, Moret MA. Retrospective Cohort Study of COVID-19 in Patients of the Brazilian Public Health System with SARS-CoV-2 Omicron Variant Infection. Vaccines (Basel) 2022; 10:1504. [PMID: 36146584 PMCID: PMC9500832 DOI: 10.3390/vaccines10091504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/03/2022] [Accepted: 09/04/2022] [Indexed: 12/02/2022] Open
Abstract
Several vaccines against COVID-19 are now available, based on different techniques and made by different laboratories spread around the world. With the roll out of the vaccination process in an advanced stage in many countries, the reduced risk of hospitalization due to the Omicron variant relative to the Delta variant infection, despite the higher transmission risk of Omicron, may lead to a misinterpretation of the results, as infection by Omicron is associated with a significant reduction in severe outcomes and shorter hospitalization time than the Delta variant. We compared the in-hospital mortality due to the Omicron (Jan-Mar 2022) with Gamma (Jan 2021) and Delta (Oct-Dec 2021) variants of patients in the Brazilian public health system. This study also discusses the decrease in booster vaccine effectiveness in patients hospitalized due to the Omicron variant compared with the Delta variant. Without a remodeling of vaccines for new variants, booster doses may be necessary with a shorter time interval.
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Affiliation(s)
- Thiago B. Murari
- Modelagem Computacional, University Center SENAI/CIMATEC, Salvador 41650-010, BA, Brazil
| | - Larissa Moraes dos Santos Fonseca
- Modelagem Computacional, University Center SENAI/CIMATEC, Salvador 41650-010, BA, Brazil
- SENAI Institute of Innovation (ISI) in Health Advanced Systems, University Center SENAI/CIMATEC, Salvador 41650-010, BA, Brazil
| | - Hernane B. de B. Pereira
- Modelagem Computacional, University Center SENAI/CIMATEC, Salvador 41650-010, BA, Brazil
- Departamento de Ciências Exatas e da Terra, Universidade do Estado da Bahia, Salvador 41150-000, BA, Brazil
| | | | - Hugo Saba
- Modelagem Computacional, University Center SENAI/CIMATEC, Salvador 41650-010, BA, Brazil
- Departamento de Ciências Exatas e da Terra, Universidade do Estado da Bahia, Salvador 41150-000, BA, Brazil
| | - Fulvio A. Scorza
- Disciplina de Neurociência, Escola Paulista de Medicina, Universidade Federal de São Paulo (EPM/UNIFESP), São Paulo 04021-001, SP, Brazil
| | - Antônio-Carlos G. de Almeida
- Departamento de Engenharia de Biossistemas, Universidade Federal de São João del-Rei (UFSJ), São João del-Rei 36307-352, MG, Brazil
| | - Ethel L. N. Maciel
- Laboratório de Epidemiologia, Universidade Federal do Espírito Santo, Vitória 29075-910, ES, Brazil
| | - José F. F. Mendes
- Departamento de Física and I3N, Universidade de Aveiro, 3880 Aveiro, Portugal
| | - Tarcísio M. Rocha Filho
- International Center for Condensed Matter Physics and Instituto de Física, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | - John R. David
- Faculty of Public Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Immunology and Infectious Diseases, Harvard Medical School, Boston, MA 02115, USA
| | - Roberto Badaró
- Modelagem Computacional, University Center SENAI/CIMATEC, Salvador 41650-010, BA, Brazil
- SENAI Institute of Innovation (ISI) in Health Advanced Systems, University Center SENAI/CIMATEC, Salvador 41650-010, BA, Brazil
| | - Bruna Aparecida Souza Machado
- Modelagem Computacional, University Center SENAI/CIMATEC, Salvador 41650-010, BA, Brazil
- SENAI Institute of Innovation (ISI) in Health Advanced Systems, University Center SENAI/CIMATEC, Salvador 41650-010, BA, Brazil
| | - Marcelo A. Moret
- Modelagem Computacional, University Center SENAI/CIMATEC, Salvador 41650-010, BA, Brazil
- Departamento de Ciências Exatas e da Terra, Universidade do Estado da Bahia, Salvador 41150-000, BA, Brazil
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17
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da Silva SJR, do Nascimento JCF, Germano Mendes RP, Guarines KM, Targino Alves da Silva C, da Silva PG, de Magalhães JJF, Vigar JRJ, Silva-Júnior A, Kohl A, Pardee K, Pena L. Two Years into the COVID-19 Pandemic: Lessons Learned. ACS Infect Dis 2022; 8:1758-1814. [PMID: 35940589 PMCID: PMC9380879 DOI: 10.1021/acsinfecdis.2c00204] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and virulent human-infecting coronavirus that emerged in late December 2019 in Wuhan, China, causing a respiratory disease called coronavirus disease 2019 (COVID-19), which has massively impacted global public health and caused widespread disruption to daily life. The crisis caused by COVID-19 has mobilized scientists and public health authorities across the world to rapidly improve our knowledge about this devastating disease, shedding light on its management and control, and spawned the development of new countermeasures. Here we provide an overview of the state of the art of knowledge gained in the last 2 years about the virus and COVID-19, including its origin and natural reservoir hosts, viral etiology, epidemiology, modes of transmission, clinical manifestations, pathophysiology, diagnosis, treatment, prevention, emerging variants, and vaccines, highlighting important differences from previously known highly pathogenic coronaviruses. We also discuss selected key discoveries from each topic and underline the gaps of knowledge for future investigations.
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Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Jessica Catarine Frutuoso do Nascimento
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Renata Pessôa Germano Mendes
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Klarissa Miranda Guarines
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Caroline Targino Alves da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Poliana Gomes da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Jurandy Júnior Ferraz de Magalhães
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Virology, Pernambuco State Central Laboratory (LACEN/PE), 52171-011 Recife, Pernambuco, Brazil.,University of Pernambuco (UPE), Serra Talhada Campus, 56909-335 Serra Talhada, Pernambuco, Brazil.,Public Health Laboratory of the XI Regional Health, 56912-160 Serra Talhada, Pernambuco, Brazil
| | - Justin R J Vigar
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Abelardo Silva-Júnior
- Institute of Biological and Health Sciences, Federal University of Alagoas (UFAL), 57072-900 Maceió, Alagoas, Brazil
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
| | - Keith Pardee
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada.,Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
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18
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Tsui WNT, Hamill V, Noll L, Lu N, Porter EP, Harbidge D, Cox E, Richardson C, Gray M, Sebhatu T, Goerl K, Brown S, Hanzlicek G, Retallick J, Bai J. Molecular detection of SARS-CoV-2 and differentiation of Omicron and Delta variant strains. Transbound Emerg Dis 2022; 69:e1618-e1631. [PMID: 35218683 PMCID: PMC9115370 DOI: 10.1111/tbed.14497] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/04/2022]
Abstract
The SARS-CoV-2 virus is the causative agent of COVID-19 and has undergone continuous mutations throughout the pandemic. The more transmissible Omicron variant has quickly spread and is replacing the Delta variant as the most prevalent strain globally, including in the United States. A new molecular assay that can detect and differentiate both the Delta and Omicron variants was developed. A collection of 660,035 SARS-CoV-2 full- or near-full genomes, including 169,454 Delta variant and 24,202 Omicron variant strains, were used for primer and probe designs. In silico data analysis predicted an assay coverage of >99% of all strains, including >99% of the Delta and >99% of Omicron strains. The Omicron variant differential test was designed based on the Δ31-33 aa deletion in the N-gene, which is present in the original B.1.1.529 main genotype, BA.1, as well as in BA.2 and BA.3 subtypes. Therefore, the assay should detect the majority of all Omicron variant strains. Standard curves generated with human clinical samples indicated that the PCR amplification efficiencies were 104%, 90.7% and 90.4% for the Omicron, Delta, and non-Delta/non-Omicron wild-type genotypes, respectively. Correlation coefficients of the standard curves were all >0.99. The detection limit of the assay was 14.3, 32.0, and 21.5 copies per PCR reaction for Omicron, Delta, and wild-type genotypes, respectively. The assay was designed to specifically detect SAR-CoV-2 strains. Selected samples with Omicron, Delta and wild-type genotypes identified by the RT-qPCR assay were also confirmed by sequencing. The assay did not detect any animal coronavirus-positive samples that were tested. Human nasal swab samples that previously tested positive (n = 182) or negative (n = 42) for SARS-CoV-2 by the ThermoFisher TaqPath COVID-19 Combo Kit, produced the same result with the new assay. Among positive samples, 55.5% (101/182), 23.1% (42/182), and 21.4% (39/182) were identified as Omicron, Delta, and non-Omicron/non-Delta wild-type genotypes, respectively.
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Affiliation(s)
- Wai Ning Tiffany Tsui
- Kansas State Veterinary Diagnostic LaboratoryKansas State UniversityManhattanKansasUSA
| | - Vaughn Hamill
- Kansas State Veterinary Diagnostic LaboratoryKansas State UniversityManhattanKansasUSA
| | - Lance Noll
- Kansas State Veterinary Diagnostic LaboratoryKansas State UniversityManhattanKansasUSA
- Department of Diagnostic Medicine/PathobiologyKansas State UniversityManhattanKansasUSA
| | - Nanyan Lu
- Kansas State Veterinary Diagnostic LaboratoryKansas State UniversityManhattanKansasUSA
- Division of BiologyKansas State UniversityManhattanKansasUSA
| | | | - Donald Harbidge
- Kansas State Veterinary Diagnostic LaboratoryKansas State UniversityManhattanKansasUSA
| | - Emily Cox
- Kansas State Veterinary Diagnostic LaboratoryKansas State UniversityManhattanKansasUSA
| | - Claire Richardson
- Kansas State Veterinary Diagnostic LaboratoryKansas State UniversityManhattanKansasUSA
| | - Mark Gray
- Kansas State Veterinary Diagnostic LaboratoryKansas State UniversityManhattanKansasUSA
| | - Tesfaalem Sebhatu
- Kansas State Veterinary Diagnostic LaboratoryKansas State UniversityManhattanKansasUSA
| | - Kyle Goerl
- Lafene Health CenterKansas State UniversityManhattanKansasUSA
| | - Susan Brown
- Division of BiologyKansas State UniversityManhattanKansasUSA
| | - Gregg Hanzlicek
- Kansas State Veterinary Diagnostic LaboratoryKansas State UniversityManhattanKansasUSA
- Department of Diagnostic Medicine/PathobiologyKansas State UniversityManhattanKansasUSA
| | - Jamie Retallick
- Kansas State Veterinary Diagnostic LaboratoryKansas State UniversityManhattanKansasUSA
- Department of Diagnostic Medicine/PathobiologyKansas State UniversityManhattanKansasUSA
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic LaboratoryKansas State UniversityManhattanKansasUSA
- Department of Diagnostic Medicine/PathobiologyKansas State UniversityManhattanKansasUSA
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19
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Omicron SARS-CoV-2 variant: An observational study from a hospital in Southern India. ACTA MEDICA MARTINIANA 2022. [DOI: 10.2478/acm-2022-0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Introduction
The Omicron variant rapidly outpaced Delta with documented community transmission in most countries and has led to an upsurge in cases in most regions. Since its initial detection from a specimen collected on November 8th 2021, Omicron amounted to 74.0% of the genome sequenced in South Africa and more than 99.0% in rest of the world.
Objectives
1. To describe the socio-demographic and clinical profile of Omicron cases treated at our tertiary care institution. 2. To assess the factors associated with the vaccination status of such Omicron cases.
Methods
This observational study was conducted at a 500 bedded hospital in southern India from 15th of December 2021 to 5th of February 2022. Of the 333 COVID-19 patients who were registered with Reverse Transcription-Polymerase Chain Reaction (RT-PCR) positive result along with S Gene Target Failure (SGTF), 203 patients were included and were interviewed using a pre-designed semi-structured questionnaire. With prior approval from the Institutional Ethics Committee (IEC) data was collected and statistically analyzed with descriptive statistics and inferential statistics using SPSS software trial version 28.0 and OpenEpi software. At 95% confidence level, a P value of < 0.05 was considered as statistically significant.
Results
Of the 203 cases studied, majority 149 (73.4%) were symptomatic, of which almost 114 (76.5%) had fever, 72 (48.3%) had cough and 29 (19.5%) had myalgia. 193 (95.1%) cases were categorized as mild, 8 (3.9%) as moderate and 2 (1.0%) as severe cases of COVID-19 with SGTF. Only 10 (4.9%) patients received supplementary oxygen support. Almost 158 patients (77.8%) were vaccinated against COVID-19 of which 106 (67%) were vaccinated with Covishield vaccine followed by 50 (31.7%) of them with Covaxin. 126 (79.7%) patients were completely vaccinated with two doses of any COVID-19 vaccine and 32 (20.3%) were partially vaccinated with a single dose of any COVID-19 vaccine. Among those who required supplemental oxygen (n = 10), the proportion of those vaccinated (40.0%) was lower com pared to those who were unvaccinated (60.0%). This association was statistically significant (P = 0.003, OR = 0.169, 95% CI of OR = 0.045, 0.628). Among the completely vaccinated subjects (n = 125), there was a statistically significant difference in mean (95% CI) interval between the last dose of vaccine taken and date of RT-PCR positivity with SGTF (P < 0.001). It was 186 (162, 210) days for Covaxin and was 131 (114, 148) days for Covishield vaccine.
Conclusion
Omicron (SGTF) cases manifests mostly as mild cases with symptoms like fever, cough, myalgia and majority were independent of oxygen supplementation and had good prognosis. Omicron infection was delayed over six months among completely vaccinated subjects especially those who were vaccinated with Covaxin.
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20
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Bekliz M, Adea K, Vetter P, Eberhardt CS, Hosszu-Fellous K, Vu DL, Puhach O, Essaidi-Laziosi M, Waldvogel-Abramowski S, Stephan C, L'Huillier AG, Siegrist CA, Didierlaurent AM, Kaiser L, Meyer B, Eckerle I. Neutralization capacity of antibodies elicited through homologous or heterologous infection or vaccination against SARS-CoV-2 VOCs. Nat Commun 2022; 13:3840. [PMID: 35787633 PMCID: PMC9253337 DOI: 10.1038/s41467-022-31556-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/22/2022] [Indexed: 12/30/2022] Open
Abstract
Emerging SARS-CoV-2 variants raise questions about escape from previous immunity. As the population immunity to SARS-CoV-2 has become more complex due to prior infections with different variants, vaccinations or the combination of both, understanding the antigenic relationship between variants is needed. Here, we have assessed neutralizing capacity of 120 blood specimens from convalescent individuals infected with ancestral SARS-CoV-2, Alpha, Beta, Gamma or Delta, double vaccinated individuals and patients after breakthrough infections with Delta or Omicron-BA.1. Neutralization against seven authentic SARS-CoV-2 isolates (B.1, Alpha, Beta, Gamma, Delta, Zeta and Omicron-BA.1) determined by plaque-reduction neutralization assay allowed us to map the antigenic relationship of SARS-CoV-2 variants. Highest neutralization titers were observed against the homologous variant. Antigenic cartography identified Zeta and Omicron-BA.1 as separate antigenic clusters. Substantial immune escape in vaccinated individuals was detected for Omicron-BA.1 but not Zeta. Combined infection/vaccination derived immunity results in less Omicron-BA.1 immune escape. Last, breakthrough infections with Omicron-BA.1 lead to broadly neutralizing sera.
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Affiliation(s)
- Meriem Bekliz
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Kenneth Adea
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Pauline Vetter
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Christiane S Eberhardt
- Center for Vaccinology and Neonatal Immunology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- Division of General Pediatrics, Department of Woman, Child and Adolescent Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Center for Vaccinology, Geneva University Hospitals, Geneva, Switzerland
| | - Krisztina Hosszu-Fellous
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Diem-Lan Vu
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Olha Puhach
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Manel Essaidi-Laziosi
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | | | - Caroline Stephan
- Transfusion Unit, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Arnaud G L'Huillier
- Pediatric Infectious Diseases Unit, Department of Women, Child and Adolescent Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Claire-Anne Siegrist
- Center for Vaccinology and Neonatal Immunology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Arnaud M Didierlaurent
- Center for Vaccinology and Neonatal Immunology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Laurent Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Benjamin Meyer
- Center for Vaccinology and Neonatal Immunology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland.
| | - Isabella Eckerle
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland.
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland.
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21
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Celik I, Abdellattif MH, Tallei TE. An Insight Based on Computational Analysis of the Interaction between the Receptor-Binding Domain of the Omicron Variants and Human Angiotensin-Converting Enzyme 2. BIOLOGY 2022; 11:biology11050797. [PMID: 35625526 PMCID: PMC9171583 DOI: 10.3390/biology11050797] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 12/13/2022]
Abstract
Simple Summary The Omicron variant has recently been divided into BA.1, BA.2, and BA.3 subvariants. In the present study, we focused on comparing the interaction between the receptor-binding domain (RBD) of BA.1 and BA.2 spike proteins with human angiotensin-converting enzyme 2 (hACE2) using a computational approach. The RBD BA.2 was modeled after the BA.1. The results from molecular docking and molecular dynamics studies showed that RBD BA.2 has a higher and more stable affinity for hACE2 compared to RBD BA.1. Abstract Concerns have been raised about the high number of mutations in the spike protein of the new emergence of the highly transmissible Omicron variant (B.1.1529 lineage) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This variant’s extraordinary ability to evade antibodies would significantly impair the current vaccination program. This present study aimed to computationally analyze the interaction between the receptor-binding domain (RBD) in the spike protein of Omicron variants and human angiotensin-converting enzyme 2 (hACE2). The docking results indicated that Omicron BA.2 has exceptionally strong interactions with hACE2 in comparison to Omicron BA.1, Delta, and wild-type, as indicated by various parameters such as salt bridge, hydrogen bond, and non-bonded interactions. The results of the molecular dynamics simulation study corroborate these findings, indicating that Omicron BA.2 has a strong and stable interaction with hACE2. This study provides insight into the development of an effective intervention against this variant.
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Affiliation(s)
- Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey;
| | - Magda H. Abdellattif
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia
- Correspondence: ; Tel.: +62-811-4314-880
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22
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Li C, Guo Y, Fang Z, Zhang H, Zhang Y, Chen K. Analysis of the Protective Efficacy of Approved COVID-19 Vaccines Against Various Mutants. Front Immunol 2022; 13:804945. [PMID: 35572594 PMCID: PMC9095899 DOI: 10.3389/fimmu.2022.804945] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 04/04/2022] [Indexed: 11/30/2022] Open
Abstract
The outbreak of COVID-19 (caused by SARS-CoV-2) has posed a significant threat to global public health security because of its high pathogenicity and infectivity. To date, the pathogenic mechanism of this novel coronavirus (SARS-CoV-2) is still unclear, and there is no effective treatment. As one of the most effective strategies to prevent viral infection, vaccines have become a research hotspot. Based on the current understanding of SARS-CoV-2, the research and development of its vaccines cover almost all forms of current vaccine research, including inactivated vaccines, recombinant protein vaccines, viral vector vaccines, and nucleic acid vaccines. Moreover, with the spread of the new mutant virus, it is necessary to evaluate the protection rate of previous administered vaccines. This article reviews the candidate targets, vaccine types, research and development status, progress of SARS-CoV-2 vaccines, and the effectiveness of neutralizing antibodies against SARS-CoV-2 mutants (B.1.1.7, B.1.351, P.1, B.1.617.2, and B.1.1.529) induced by these vaccines, to provide a reference for follow-up research and prevention.
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Affiliation(s)
- Chaonan Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Yikai Guo
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Zhongbiao Fang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Haiyan Zhang
- Zhejiang Shuren College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yanjun Zhang
- Department of Virus Inspection, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Keda Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
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23
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Cantoni D, Mayora-Neto M, Thakur N, Elrefaey AME, Newman J, Vishwanath S, Nadesalingam A, Chan A, Smith P, Castillo-Olivares J, Baxendale H, Charleston B, Heeney J, Bailey D, Temperton N. Pseudotyped Bat Coronavirus RaTG13 is efficiently neutralised by convalescent sera from SARS-CoV-2 infected patients. Commun Biol 2022; 5:409. [PMID: 35505237 PMCID: PMC9065041 DOI: 10.1038/s42003-022-03325-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/28/2022] [Indexed: 12/24/2022] Open
Abstract
RaTG13 is a close relative of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, sharing 96% sequence similarity at the genome-wide level. The spike receptor binding domain (RBD) of RaTG13 contains a number of amino acid substitutions when compared to SARS-CoV-2, likely impacting affinity for the ACE2 receptor. Antigenic differences between the viruses are less well understood, especially whether RaTG13 spike can be efficiently neutralised by antibodies generated from infection with, or vaccination against, SARS-CoV-2. Using RaTG13 and SARS-CoV-2 pseudotypes we compared neutralisation using convalescent sera from previously infected patients or vaccinated healthcare workers. Surprisingly, our results revealed that RaTG13 was more efficiently neutralised than SARS-CoV-2. In addition, neutralisation assays using spike mutants harbouring single and combinatorial amino acid substitutions within the RBD demonstrated that both spike proteins can tolerate multiple changes without dramatically reducing neutralisation. Moreover, introducing the 484 K mutation into RaTG13 resulted in increased neutralisation, in contrast to the same mutation in SARS-CoV-2 (E484K). This is despite E484K having a well-documented role in immune evasion in variants of concern (VOC) such as B.1.351 (Beta). These results indicate that the future spill-over of RaTG13 and/or related sarbecoviruses could be mitigated using current SARS-CoV-2-based vaccination strategies.
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Affiliation(s)
- Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent & Greenwich, Chatham, UK
| | - Martin Mayora-Neto
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent & Greenwich, Chatham, UK
| | - Nazia Thakur
- The Pirbright Institute, Guildford, Surrey, GU24 0NF, UK
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Joseph Newman
- The Pirbright Institute, Guildford, Surrey, GU24 0NF, UK
| | - Sneha Vishwanath
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Andrew Chan
- DIOSynVax, University of Cambridge, Madingley Road, CB3-0ES, Cambridge, UK
| | - Peter Smith
- DIOSynVax, University of Cambridge, Madingley Road, CB3-0ES, Cambridge, UK
| | | | | | | | - Jonathan Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- DIOSynVax, University of Cambridge, Madingley Road, CB3-0ES, Cambridge, UK
| | - Dalan Bailey
- The Pirbright Institute, Guildford, Surrey, GU24 0NF, UK.
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent & Greenwich, Chatham, UK.
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24
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van der Straten K, van Gils MJ, de Taeye SW, de Bree GJ. Optimization of Anti-SARS-CoV-2 Neutralizing Antibody Therapies: Roadmap to Improve Clinical Effectiveness and Implementation. FRONTIERS IN MEDICAL TECHNOLOGY 2022; 4:867982. [PMID: 35419561 PMCID: PMC8996231 DOI: 10.3389/fmedt.2022.867982] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/07/2022] [Indexed: 12/11/2022] Open
Abstract
One of the major breakthroughs to combat the current Coronavirus Disease 2019 (COVID-19) pandemic has been the development of highly effective vaccines against the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Still, alternatives are needed for individuals who are at high risk of developing severe COVID-19 and are not protected by vaccination. Monoclonal antibodies against the spike protein of SARS-CoV-2 have been shown to be effective as prophylaxis and treatment against COVID-19. However, the emergence of variants of concern (VOCs) challenges the efficacy of antibody therapies. This review describes the neutralization resistance of the clinically-approved monoclonal antibody therapies against the Alpha (B.1.1.7), Beta (B.1.351), Gamma (P1), Delta (B.1.617.2), and the Omicron (B.1.1.529) variants. To guide the development of monoclonal antibody therapies and to anticipate on the continuous evolution of SARS-CoV-2, we highlight different strategies to broaden the antibody activity by targeting more conserved epitopes and/or simultaneously targeting multiple sites of vulnerability of the virus. This review further describes the contribution of antibody Fc effector functions to optimize the antibody efficacy. In addition, the main route of SARS-CoV-2 antibody administration is currently intravenously and dictates a monthly injection when used as prophylactic. Therefore, we discusses the concept of long-acting antibodies (LAABs) and non-intravenously routes of antibody administration in order to broaden the clinical applicability of antibody therapies.
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Affiliation(s)
- Karlijn van der Straten
- Department of Medical Microbiology and Infection Prevention, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Internal Medicine, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Marit J. van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Steven W. de Taeye
- Department of Medical Microbiology and Infection Prevention, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Godelieve J. de Bree
- Department of Internal Medicine, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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25
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Loo YM, McTamney PM, Arends RH, Abram ME, Aksyuk AA, Diallo S, Flores DJ, Kelly EJ, Ren K, Roque R, Rosenthal K, Streicher K, Tuffy KM, Bond NJ, Cornwell O, Bouquet J, Cheng LI, Dunyak J, Huang Y, Rosenbaum AI, Pilla Reddy V, Andersen H, Carnahan RH, Crowe JE, Kuehne AI, Herbert AS, Dye JM, Bright H, Kallewaard NL, Pangalos MN, Esser MT. The SARS-CoV-2 monoclonal antibody combination, AZD7442, is protective in nonhuman primates and has an extended half-life in humans. Sci Transl Med 2022; 14:eabl8124. [PMID: 35076282 PMCID: PMC8939769 DOI: 10.1126/scitranslmed.abl8124] [Citation(s) in RCA: 132] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 01/18/2022] [Indexed: 12/14/2022]
Abstract
Despite the success of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines, there remains a need for more prevention and treatment options for individuals remaining at risk of coronavirus disease 2019 (COVID-19). Monoclonal antibodies (mAbs) against the viral spike protein have potential to both prevent and treat COVID-19 and reduce the risk of severe disease and death. Here, we describe AZD7442, a combination of two mAbs, AZD8895 (tixagevimab) and AZD1061 (cilgavimab), that simultaneously bind to distinct, nonoverlapping epitopes on the spike protein receptor binding domain to neutralize SARS-CoV-2. Initially isolated from individuals with prior SARS-CoV-2 infection, the two mAbs were designed to extend their half-lives and reduce effector functions. The AZD7442 mAbs individually prevent the spike protein from binding to angiotensin-converting enzyme 2 receptor, blocking virus cell entry, and neutralize all tested SARS-CoV-2 variants of concern. In a nonhuman primate model of SARS-CoV-2 infection, prophylactic AZD7442 administration prevented infection, whereas therapeutic administration accelerated virus clearance from the lung. In an ongoing phase 1 study in healthy participants (NCT04507256), a 300-mg intramuscular injection of AZD7442 provided SARS-CoV-2 serum geometric mean neutralizing titers greater than 10-fold above those of convalescent serum for at least 3 months, which remained threefold above those of convalescent serum at 9 months after AZD7442 administration. About 1 to 2% of serum AZD7442 was detected in nasal mucosa, a site of SARS-CoV-2 infection. Extrapolation of the time course of serum AZD7442 concentration suggests AZD7442 may provide up to 12 months of protection and benefit individuals at high-risk of COVID-19.
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Affiliation(s)
- Yueh-Ming Loo
- Virology and Vaccine Discovery, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Patrick M McTamney
- Virology and Vaccine Discovery, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Rosalinda H Arends
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Michael E Abram
- Translational Medicine, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Anastasia A Aksyuk
- Translational Medicine, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Seme Diallo
- Virology and Vaccine Discovery, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Daniel J Flores
- Virology and Vaccine Discovery, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Elizabeth J Kelly
- Translational Medicine, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Kuishu Ren
- Virology and Vaccine Discovery, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Richard Roque
- Virology and Vaccine Discovery, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Kim Rosenthal
- Virology and Vaccine Discovery, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Katie Streicher
- Translational Medicine, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Kevin M Tuffy
- Translational Medicine, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Nicholas J Bond
- Analytical Sciences, BioPharmaceuticals R&D, AstraZeneca, Granta Park, Cambridge CB21 6GH, UK
| | - Owen Cornwell
- Analytical Sciences, BioPharmaceuticals R&D, AstraZeneca, Granta Park, Cambridge CB21 6GH, UK
| | - Jerome Bouquet
- Integrated Bioanalysis, Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, San Francisco, CA 94080, USA
| | - Lily I Cheng
- Oncology Safety Pathology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - James Dunyak
- Clinical Pharmacology and Pharmacometrics, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Yue Huang
- Integrated Bioanalysis, Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, San Francisco, CA 94080, USA
| | - Anton I Rosenbaum
- Integrated Bioanalysis, Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, San Francisco, CA 94080, USA
| | - Venkatesh Pilla Reddy
- Clinical Pharmacology and Pharmacometrics, BioPharmaceuticals R&D, AstraZeneca, Granta Park, Cambridge CB21 6GH, UK
| | | | - Robert H Carnahan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James E Crowe
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN 37232, USA
| | | | | | - John M Dye
- USAMRIID, Fort Detrick, MD 21702-5011, USA
| | - Helen Bright
- Virology and Vaccine Discovery, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Nicole L Kallewaard
- Virology and Vaccine Discovery, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | | | - Mark T Esser
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
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26
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Warwicker J. The Physical Basis for pH Sensitivity in Biomolecular Structure and Function, With Application to the Spike Protein of SARS-CoV-2. Front Mol Biosci 2022; 9:834011. [PMID: 35252354 PMCID: PMC8894873 DOI: 10.3389/fmolb.2022.834011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/19/2022] [Indexed: 11/24/2022] Open
Abstract
Since pH sensitivity has a fundamental role in biology, much effort has been committed to establishing physical models to rationalize and predict pH dependence from molecular structures. Two of the key challenges are to accurately calculate ionizable group solvation and hydration and then to apply this modeling to all conformations relevant to the process in question. Explicit solvent methods coupled to molecular dynamics simulation are increasingly complementing lower resolution implicit solvent techniques, but equally, the scale of biological data acquisition leaves a role for high-throughput modeling. Additionally, determination of ranges of structures for a system allows sampling of key stages in solvation. In a review of the area, it is emphasized that pH sensors in biology beyond the most obvious candidate (histidine side chain, with an unshifted pK a near neutral pH) should be considered; that modeling can benefit from other concepts in bioinformatics, in particular modulation of interactions and function in families of homologs; and that it can also be beneficial to incorporate as many experimental structures as possible, to mitigate against small variations in conformation and to analyze larger, functional, conformational changes. These aspects are then demonstrated with new work on the spike protein of SARS-CoV-2, looking at the pH dependence of variants, including prediction of a change in the balance of locked, closed, and open forms at neutral pH for the Omicron variant spike protein.
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Affiliation(s)
- Jim Warwicker
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
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27
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Ku Z, Xie X, Lin J, Gao P, El Sahili A, Su H, Liu Y, Ye X, Li X, Fan X, Goh BC, Xiong W, Boyd H, Muruato AE, Deng H, Xia H, Jing Z, Kalveram BK, Menachery VD, Zhang N, Lescar J, Shi PY, An Z. Engineering SARS-CoV-2 cocktail antibodies into a bispecific format improves neutralizing potency and breadth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022. [PMID: 35132410 PMCID: PMC8820655 DOI: 10.1101/2022.02.01.478504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
One major limitation of neutralizing antibody-based COVID-19 therapy is the requirement of costly cocktails to reduce antibody resistance. We engineered two bispecific antibodies (bsAbs) using distinct designs and compared them with parental antibodies and their cocktail. Single molecules of both bsAbs block the two epitopes targeted by parental antibodies on the receptor-binding domain (RBD). However, bsAb with the IgG-(scFv)2 design (14-H-06) but not the CrossMAb design (14-crs-06) increases antigen-binding and virus-neutralizing activities and spectrum against multiple SARS-CoV-2 variants including the Omicron, than the cocktail. X-ray crystallography and computational simulations reveal distinct neutralizing mechanisms for individual cocktail antibodies and suggest higher inter-spike crosslinking potentials by 14-H-06 than 14-crs-06. In mouse models of infections by SARS-CoV-2 and the Beta, Gamma, and Delta variants, 14-H-06 exhibits higher or equivalent therapeutic efficacy than the cocktail. Rationally engineered bsAbs represent a cost-effective alternative to antibody cocktails and a promising strategy to improve potency and breadth.
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28
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Katchkovsky S, Chatterjee B, Abramovitch-Dahan CV, Papo N, Levaot N. Competitive blocking of LRP4-sclerostin binding interface strongly promotes bone anabolic functions. Cell Mol Life Sci 2022; 79:113. [PMID: 35099616 PMCID: PMC11073160 DOI: 10.1007/s00018-022-04127-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/16/2021] [Accepted: 01/03/2022] [Indexed: 01/07/2023]
Abstract
Induction of bone formation by Wnt ligands is inhibited when sclerostin (Scl), an osteocyte-produced antagonist, binds to its receptors, the low-density lipoprotein receptor-related proteins 5 or 6 (LRP5/6). Recently, it was shown that enhanced inhibition is achieved by Scl binding to the co-receptor LRP4. However, it is not clear if the binding of Scl to LRP4 facilitates Scl binding to LRP5/6 or inhibits the Wnt pathway in an LRP5/6-independent manner. Here, using the yeast display system, we demonstrate that Scl exhibits a stronger binding affinity for LRP4 than for LRP6. Moreover, we found stronger Scl binding to LRP6 in the presence of LRP4. We further show that a Scl mutant (SclN93A), which tightly binds LRP4 but not LRP6, does not inhibit the Wnt pathway on its own. We demonstrate that SclN93A competes with Scl for a common binding site on LRP4 and antagonizes Scl inhibition of the Wnt signaling pathway in osteoblasts in vitro. Finally, we demonstrate that 2 weeks of bi-weekly subcutaneous injections of SclN93A fused to the fragment crystallizable (Fc) domain of immunoglobulin (SclN93AFc), which retains the antagonistic activity of the mutant, significantly increases bone formation rate and enhances trabecular volumetric bone fraction, trabecular number, and bone length in developing mice. Our data show that LRP4 serves as an anchor that facilitates Scl-LRP6 binding and that inhibition of the Wnt pathway by Scl depends on its prior binding to LRP4. We further provide evidence that compounds that inhibit Scl-LRP4 interactions offer a potential strategy to promote anabolic bone functions.
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Affiliation(s)
- Svetlana Katchkovsky
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Biplab Chatterjee
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Chen-Viki Abramovitch-Dahan
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Niv Papo
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel.
| | - Noam Levaot
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel.
- Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel.
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29
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Parra-Lucares A, Segura P, Rojas V, Pumarino C, Saint-Pierre G, Toro L. Emergence of SARS-CoV-2 Variants in the World: How Could This Happen? Life (Basel) 2022; 12:194. [PMID: 35207482 PMCID: PMC8879166 DOI: 10.3390/life12020194] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic has had a significant global impact, with more than 280,000,000 people infected and 5,400,000 deaths. The use of personal protective equipment and the anti-SARS-CoV-2 vaccination campaigns have reduced infection and death rates worldwide. However, a recent increase in infection rates has been observed associated with the appearance of SARS-CoV-2 variants, including the more recently described lineage B.1.617.2 (Delta variant) and lineage B.1.1.529/BA.1 (Omicron variant). These new variants put the effectiveness of international vaccination at risk, with the appearance of new outbreaks of COVID-19 throughout the world. This emergence of new variants has been due to multiple predisposing factors, including molecular characteristics of the virus, geographic and environmental conditions, and the impact of social determinants of health that favor the genetic diversification of SARS-CoV-2. We present a literature review on the most recent information available on the emergence of new variants of SARS-CoV-2 in the world. We analyzed the biological, geographical, and sociocultural factors that favor the development of these variants. Finally, we evaluate the surveillance strategies for the early detection of new variants and prevent their distribution outside these regions.
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Affiliation(s)
- Alfredo Parra-Lucares
- Division of Critical Care Medicine, Department of Medicine, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile; (A.P.-L.); (V.R.)
| | - Paula Segura
- Department of Anatomic Pathology, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile;
| | - Verónica Rojas
- Division of Critical Care Medicine, Department of Medicine, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile; (A.P.-L.); (V.R.)
- Centro de Investigación Clínica Avanzada, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile
| | - Catalina Pumarino
- School of Medicine, Faculty of Medicine, Universidad de Chile, 8380456 Santiago, Chile;
| | - Gustavo Saint-Pierre
- Microbiology Unit, Clinical Laboratory, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile;
| | - Luis Toro
- Centro de Investigación Clínica Avanzada, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile
- Division of Nephrology, Department of Medicine, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile
- Critical Care Unit, Clínica Las Condes, 7591047 Santiago, Chile
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30
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Shah M, Woo HG. Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. Front Immunol 2022; 12:830527. [PMID: 35140714 PMCID: PMC8819067 DOI: 10.3389/fimmu.2021.830527] [Citation(s) in RCA: 130] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/31/2021] [Indexed: 12/29/2022] Open
Abstract
The new SARS-CoV-2 variant of concern “Omicron” was recently spotted in South Africa and spread quickly around the world due to its enhanced transmissibility. The variant became conspicuous as it harbors more than 30 mutations in the Spike protein with 15 mutations in the receptor-binding domain (RBD) alone, potentially dampening the potency of therapeutic antibodies and enhancing the ACE2 binding. More worrying, Omicron infections have been reported in vaccinees in South Africa and Hong Kong, and that post-vaccination sera poorly neutralize the new variant. Here, we investigated the binding strength of Omicron with ACE2 and monoclonal antibodies that are either approved by the FDA for COVID-19 therapy or undergoing phase III clinical trials. Computational mutagenesis and free energy perturbation could confirm that Omicron RBD binds ACE2 ~2.5 times stronger than prototype SARS-CoV-2. Notably, three substitutions, i.e., T478K, Q493K, and Q498R, significantly contribute to the binding energies and almost doubled the electrostatic potential (ELE) of the RBDOmic–ACE2 complex. Omicron also harbors E484A substitution instead of the E484K that helped neutralization escape of Beta, Gamma, and Mu variants. Together, T478K, Q493K, Q498R, and E484A substitutions contribute to a significant drop in the ELE between RBDOmic–mAbs, particularly in etesevimab, bamlanivimab, and CT-p59. AZD1061 showed a slight drop in ELE and sotrovimab that binds a conserved epitope on the RBD; therefore, it could be used as a cocktail therapy in Omicron-driven COVID-19. In conclusion, we suggest that the Spike mutations prudently devised by the virus facilitate the receptor binding, weakening the mAbs binding to escape the immune response.
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MESH Headings
- Amino Acid Substitution
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/immunology
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibodies, Viral/therapeutic use
- COVID-19/genetics
- COVID-19/immunology
- Humans
- Immune Evasion
- Molecular Dynamics Simulation
- Mutation, Missense
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- COVID-19 Drug Treatment
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Affiliation(s)
- Masaud Shah
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
| | - Hyun Goo Woo
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
- Department of Biomedical Science, Graduate School, Ajou University, Suwon, South Korea
- *Correspondence: Hyun Goo Woo,
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31
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Chen Z, Zhang P, Matsuoka Y, Tsybovsky Y, West K, Santos C, Boyd LF, Nguyen H, Pomerenke A, Stephens T, Olia AS, De Giorgi V, Holbrook MR, Gross R, Postnikova E, Garza NL, Johnson RF, Margulies DH, Kwong PD, Alter HJ, Buchholz UJ, Lusso P, Farci P. Extremely potent monoclonal antibodies neutralize Omicron and other SARS-CoV-2 variants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022. [PMID: 35043120 DOI: 10.1101/2022.01.12.22269023] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has triggered a devastating global health, social and economic crisis. The RNA nature and broad circulation of this virus facilitate the accumulation of mutations, leading to the continuous emergence of variants of concern with increased transmissibility or pathogenicity 1 . This poses a major challenge to the effectiveness of current vaccines and therapeutic antibodies 1, 2 . Thus, there is an urgent need for effective therapeutic and preventive measures with a broad spectrum of action, especially against variants with an unparalleled number of mutations such as the recently emerged Omicron variant, which is rapidly spreading across the globe 3 . Here, we used combinatorial antibody phage-display libraries from convalescent COVID-19 patients to generate monoclonal antibodies against the receptor-binding domain of the SARS-CoV-2 spike protein with ultrapotent neutralizing activity. One such antibody, NE12, neutralizes an early isolate, the WA-1 strain, as well as the Alpha and Delta variants with half-maximal inhibitory concentrations at picomolar level. A second antibody, NA8, has an unusual breadth of neutralization, with picomolar activity against both the Beta and Omicron variants. The prophylactic and therapeutic efficacy of NE12 and NA8 was confirmed in preclinical studies in the golden Syrian hamster model. Analysis by cryo-EM illustrated the structural basis for the neutralization properties of NE12 and NA8. Potent and broadly neutralizing antibodies against conserved regions of the SARS-CoV-2 spike protein may play a key role against future variants of concern that evade immune control.
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