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Brady DK, Gurijala AR, Huang L, Hussain AA, Lingan AL, Pembridge OG, Ratangee BA, Sealy TT, Vallone KT, Clements TP. A guide to COVID-19 antiviral therapeutics: a summary and perspective of the antiviral weapons against SARS-CoV-2 infection. FEBS J 2024; 291:1632-1662. [PMID: 36266238 PMCID: PMC9874604 DOI: 10.1111/febs.16662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/11/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
Antiviral therapies are integral in the fight against SARS-CoV-2 (i.e. severe acute respiratory syndrome coronavirus 2), the causative agent of COVID-19. Antiviral therapeutics can be divided into categories based on how they combat the virus, including viral entry into the host cell, viral replication, protein trafficking, post-translational processing, and immune response regulation. Drugs that target how the virus enters the cell include: Evusheld, REGEN-COV, bamlanivimab and etesevimab, bebtelovimab, sotrovimab, Arbidol, nitazoxanide, and chloroquine. Drugs that prevent the virus from replicating include: Paxlovid, remdesivir, molnupiravir, favipiravir, ribavirin, and Kaletra. Drugs that interfere with protein trafficking and post-translational processing include nitazoxanide and ivermectin. Lastly, drugs that target immune response regulation include interferons and the use of anti-inflammatory drugs such as dexamethasone. Antiviral therapies offer an alternative solution for those unable or unwilling to be vaccinated and are a vital weapon in the battle against the global pandemic. Learning more about these therapies helps raise awareness in the general population about the options available to them with respect to aiding in the reduction of the severity of COVID-19 infection. In this 'A Guide To' article, we provide an in-depth insight into the development of antiviral therapeutics against SARS-CoV-2 and their ability to help fight COVID-19.
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Affiliation(s)
- Drugan K. Brady
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | - Aashi R. Gurijala
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | - Liyu Huang
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | - Ali A. Hussain
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | - Audrey L. Lingan
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | | | - Brina A. Ratangee
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | - Tristan T. Sealy
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | - Kyle T. Vallone
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
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2
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Sharma D, Rawat P, Greiff V, Janakiraman V, Gromiha MM. Predicting the immune escape of SARS-CoV-2 neutralizing antibodies upon mutation. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166959. [PMID: 37967796 DOI: 10.1016/j.bbadis.2023.166959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/25/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023]
Abstract
COVID-19 has resulted in millions of deaths and severe impact on economies worldwide. Moreover, the emergence of SARS-CoV-2 variants presented significant challenges in controlling the pandemic, particularly their potential to avoid the immune system and evade vaccine immunity. This has led to a growing need for research to predict how mutations in SARS-CoV-2 reduces the ability of antibodies to neutralize the virus. In this study, we assembled a set of 1813 mutations from the interface of SARS-CoV-2 spike protein's receptor binding domain (RBD) and neutralizing antibody complexes and developed a machine learning model to classify high or low escape mutations using interaction energy, inter-residue contacts and predicted binding free energy change. Our approach achieved an Area under the Receiver Operating Characteristics (ROC) Curve (AUC) of 0.91 using the Random Forest classifier on the test dataset with 217 mutations. The model was further utilized to predict the escape mutations on a dataset of 29,165 mutations located at the interface of 83 RBD-neutralizing antibody complexes. A small subset of this dataset was also validated based on available experimental data. We found that top 10 % high escape mutations were dominated by charged to nonpolar mutations whereas low escape mutations were dominated by polar to nonpolar mutations. We believe that the present method will allow prioritization of high/low escape mutations in the context of neutralizing antibodies targeting SARS-CoV-2 RBD region and assist antibody design for current and emerging variants.
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Affiliation(s)
- Divya Sharma
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - Puneet Rawat
- University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Victor Greiff
- University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Vani Janakiraman
- Infection Biology Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - M Michael Gromiha
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India; International Research Frontiers Initiative, School of Computing, Tokyo Institute of Technology, Yokohama 226-8501, Japan; Department of Computer Science, National University of Singapore, Singapore.
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3
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Ou BS, Baillet J, Picece VCT, Gale EC, Powell AE, Saouaf OM, Yan J, Nejatfard A, Lopez Hernandez H, Appel EA. Nanoparticle-Conjugated Toll-Like Receptor 9 Agonists Improve the Potency, Durability, and Breadth of COVID-19 Vaccines. ACS Nano 2024; 18:3214-3233. [PMID: 38215338 PMCID: PMC10832347 DOI: 10.1021/acsnano.3c09700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/04/2024] [Accepted: 01/09/2024] [Indexed: 01/14/2024]
Abstract
Development of effective vaccines for infectious diseases has been one of the most successful global health interventions in history. Though, while ideal subunit vaccines strongly rely on antigen and adjuvant(s) selection, the mode and time scale of exposure to the immune system has often been overlooked. Unfortunately, poor control over the delivery of many adjuvants, which play a key role in enhancing the quality and potency of immune responses, can limit their efficacy and cause off-target toxicities. There is a critical need for improved adjuvant delivery technologies to enhance their efficacy and boost vaccine performance. Nanoparticles have been shown to be ideal carriers for improving antigen delivery due to their shape and size, which mimic viral structures but have been generally less explored for adjuvant delivery. Here, we describe the design of self-assembled poly(ethylene glycol)-b-poly(lactic acid) nanoparticles decorated with CpG, a potent TLR9 agonist, to increase adjuvanticity in COVID-19 vaccines. By controlling the surface density of CpG, we show that intermediate valency is a key factor for TLR9 activation of immune cells. When delivered with the SARS-CoV-2 spike protein, CpG nanoparticle (CpG-NP) adjuvant greatly improves the magnitude and duration of antibody responses when compared to soluble CpG, and results in overall greater breadth of immunity against variants of concern. Moreover, encapsulation of CpG-NP into injectable polymeric-nanoparticle (PNP) hydrogels enhances the spatiotemporal control over codelivery of CpG-NP adjuvant and spike protein antigen such that a single immunization of hydrogel-based vaccines generates humoral responses comparable to those of a typical prime-boost regimen of soluble vaccines. These delivery technologies can potentially reduce the costs and burden of clinical vaccination, both of which are key elements in fighting a pandemic.
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Affiliation(s)
- Ben S. Ou
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Julie Baillet
- Department
of Materials Science & Engineering, Stanford University, Stanford, California 94305, United States
| | - Vittoria C. T.
M. Picece
- Department
of Materials Science & Engineering, Stanford University, Stanford, California 94305, United States
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Zurich 8093, Switzerland
| | - Emily C. Gale
- Department
of Biochemistry, Stanford University School
of Medicine, Stanford, California 94305, United States
| | - Abigail E. Powell
- Department
of Biochemistry, Stanford University School
of Medicine, Stanford, California 94305, United States
- Stanford
ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Olivia M. Saouaf
- Department
of Materials Science & Engineering, Stanford University, Stanford, California 94305, United States
| | - Jerry Yan
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Anahita Nejatfard
- Department
of Biochemistry, Stanford University School
of Medicine, Stanford, California 94305, United States
| | - Hector Lopez Hernandez
- Department
of Materials Science & Engineering, Stanford University, Stanford, California 94305, United States
| | - Eric A. Appel
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- Department
of Materials Science & Engineering, Stanford University, Stanford, California 94305, United States
- Stanford
ChEM-H, Stanford University, Stanford, California 94305, United States
- Department
of Pediatrics - Endocrinology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Woods
Institute for the Environment, Stanford
University, Stanford, California 94305, United States
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4
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Sun Y, Li Q, Luo Y, Zhu H, Xu F, Lu H, Yao P, Wang Z, Zhao W, Zhou Z. Development of an RBD-Fc fusion vaccine for COVID-19. Vaccine X 2024; 16:100444. [PMID: 38327768 PMCID: PMC10847155 DOI: 10.1016/j.jvacx.2024.100444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/09/2024] Open
Abstract
Although the global pandemic of SARS-CoV-2 has passed, there are still regional outbreaks that continue to jeopardize human health. Hence, there is still a great deal of interest in developing an efficient vaccine that can quickly and effectively prevent reemerging outbreaks of SARS-CoV-2. Delta variant was once a dominant strain in the world in 2021, and we first constructed a recombinant RBDdelta-Fc fusion vaccine by coupling the RBD of Delta variant with the human Fc fragment. This Fc fusion strategy increases the immunogenicity of the recombinant RBD vaccine, with a long-lasting high level of IgG antibodies and neutralizing antibodies induced by RBDdelta-Fc vaccine. This RBDdelta-Fc vaccine, as well as the RBD-Fc vaccine prepared in our previously study, could trigger a durable immune effect by the heterologous boosting immunity, and the RBD-Fc induced a quicker humoral immune response than the homologous immunization with inactivated vaccines. In conclusion, the Fc fusion strategy has a significant role in enhancing the immunogenicity of recombinant protein vaccines, thus promising the development of a safe and efficient vaccine for the heterologous boosting against SARS-CoV-2.
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Affiliation(s)
- Yisheng Sun
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Key Lab of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310015, China
| | - Qiaomin Li
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuanyuan Luo
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hanping Zhu
- Key Lab of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310015, China
| | - Fang Xu
- Key Lab of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310015, China
| | - Hangjing Lu
- Key Lab of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310015, China
| | - Pingping Yao
- Key Lab of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310015, China
| | - Zhen Wang
- Key Lab of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310015, China
| | - Wenbin Zhao
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhan Zhou
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China
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Sheehan J, Ardizzone CM, Khanna M, Trauth AJ, Hagensee ME, Ramsay AJ. Dynamics of Serum-Neutralizing Antibody Responses in Vaccinees through Multiple Doses of the BNT162b2 Vaccine. Vaccines (Basel) 2023; 11:1720. [PMID: 38006052 PMCID: PMC10675463 DOI: 10.3390/vaccines11111720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/08/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
SARS-CoV-2 mRNA vaccines are administered as effective prophylactic measures for reducing virus transmission rates and disease severity. To enhance the durability of post-vaccination immunity and combat SARS-CoV-2 variants, boosters have been administered to two-dose vaccinees. However, long-term humoral responses following booster vaccination are not well characterized. A 16-member cohort of healthy SARS-CoV-2 naïve participants were enrolled in this study during a three-dose BNT162b2 vaccine series. Serum samples were collected from vaccinees over 420 days and screened for antigen (Ag)-specific antibody titers, IgG subclass distribution, and neutralizing antibody (nAb) responses. Vaccine boosting restored peak Ag-specific titers with sustained α-RBD IgG and IgA antibody responses when measured at six months post-boost. RBD- and spike-specific IgG4 antibody levels were markedly elevated in three-dose but not two-dose immune sera. Although strong neutralization responses were detected in two- and three-dose vaccine sera, these rapidly decayed to pre-immune levels by four and six months, respectively. While boosters enhanced serum IgG Ab reactivity and nAb responses against variant strains, all variants tested showed resistance to two- and three-dose immune sera. Our data reflect the poor durability of vaccine-induced nAb responses which are a strong predictor of protection from symptomatic SARS-CoV-2 infection. The induction of IgG4-switched humoral responses may permit extended viral persistence via the downregulation of Fc-mediated effector functions.
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Affiliation(s)
- Jared Sheehan
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Caleb M. Ardizzone
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Mayank Khanna
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Amber J. Trauth
- Department of Internal Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Michael E. Hagensee
- Department of Internal Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Alistair J. Ramsay
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
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6
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Focosi D, McConnell S, Sullivan DJ, Casadevall A. Analysis of SARS-CoV-2 mutations associated with resistance to therapeutic monoclonal antibodies that emerge after treatment. Drug Resist Updat 2023; 71:100991. [PMID: 37572569 DOI: 10.1016/j.drup.2023.100991] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/18/2023] [Accepted: 07/30/2023] [Indexed: 08/14/2023]
Abstract
The mutation rate of the Omicron sublineage has led to baseline resistance against all previously authorized anti-Spike monoclonal antibodies (mAbs). Nevertheless, in case more antiviral mAbs will be authorized in the future, it is relevant to understand how frequently treatment-emergent resistance has emerged so far, under different combinations and in different patient subgroups. We report the results of a systematic review of the medical literature for case reports and case series for treatment-emergent immune escape, which is defined as emergence of a resistance-driving mutation in at least 20% of sequences in a given host at a given timepoint. We identified 32 publications detailing 216 cases that included different variants of concern (VOC) and found that the incidence of treatment emergent-resistance ranged from 10% to 50%. Most of the treatment-emergent resistance events occurred in immunocompromised patients. Interestingly, resistance also emerged against cocktails of two mAbs, albeit at lower frequencies. The heterogenous therapeutic management of those cases doesn't allow inferences about the clinical outcome in patients with treatment-emergent resistance. Furthermore, we noted a temporal correlation between the introduction of mAb therapies and a subsequent increase in SARS-CoV-2 sequences across the globe carrying mutations conferring resistance to that mAb, raising concern as to whether these had originated in mAb-treated individuals. Our findings confirm that treatment-emergent immune escape to anti-Spike mAbs represents a frequent and concerning phenomenon and suggests that these are associated with mAb use in immunosuppressed hosts.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Italy.
| | - Scott McConnell
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - David J Sullivan
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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7
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Ou BS, Saouaf OM, Yan J, Bruun TUJ, Baillet J, Zhou X, King NP, Appel EA. Broad and Durable Humoral Responses Following Single Hydrogel Immunization of SARS-CoV-2 Subunit Vaccine. Adv Healthc Mater 2023; 12:e2301495. [PMID: 37278391 DOI: 10.1002/adhm.202301495] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Indexed: 06/07/2023]
Abstract
Most vaccines require several immunizations to induce robust immunity, and indeed, most SARS-CoV-2 vaccines require an initial two-shot regimen followed by several boosters to maintain efficacy. Such a complex series of immunizations unfortunately increases the cost and complexity of populations-scale vaccination and reduces overall compliance and vaccination rate. In a rapidly evolving pandemic affected by the spread of immune-escaping variants, there is an urgent need to develop vaccines capable of providing robust and durable immunity. In this work, a single immunization SARS-CoV-2 subunit vaccine is developed that can rapidly generate potent, broad, and durable humoral immunity. Injectable polymer-nanoparticle (PNP) hydrogels are leveraged as a depot technology for the sustained delivery of a nanoparticle antigen (RND-NP) displaying multiple copies of the SARS-CoV-2 receptor-binding domain (RBD) and potent adjuvants including CpG and 3M-052. Compared to a clinically relevant prime-boost regimen with soluble vaccines formulated with CpG/alum or 3M-052/alum adjuvants, PNP hydrogel vaccines more rapidly generated higher, broader, and more durable antibody responses. Additionally, these single-immunization hydrogel-based vaccines elicit potent and consistent neutralizing responses. Overall, it is shown that PNP hydrogels elicit improved anti-COVID immune responses with only a single administration, demonstrating their potential as critical technologies to enhance overall pandemic readiness.
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Affiliation(s)
- Ben S Ou
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Olivia M Saouaf
- Department of Materials Science & Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Jerry Yan
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Theodora U J Bruun
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Julie Baillet
- Department of Materials Science & Engineering, Stanford University, Stanford, CA, 94305, USA
- CNRS, Bordeaux INP, LCPO, University of Bordeaux, Pessac, 33600, France
| | - Xueting Zhou
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA, 98109, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Eric A Appel
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Materials Science & Engineering, Stanford University, Stanford, CA, 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics-Endocrinology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Woods Institute for the Environment, Stanford University, Stanford, CA, 94305, USA
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8
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Albright C, Van Egeren D, Thakur A, Chakravarty A, White LF, Stoddard M. Antibody escape, the risk of serotype formation, and rapid immune waning: Modeling the implications of SARS-CoV-2 immune evasion. PLoS One 2023; 18:e0292099. [PMID: 37851632 PMCID: PMC10584102 DOI: 10.1371/journal.pone.0292099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/12/2023] [Indexed: 10/20/2023] Open
Abstract
As the COVID-19 pandemic progresses, widespread community transmission of SARS-CoV-2 has ushered in a volatile era of viral immune evasion rather than the much-heralded stability of "endemicity" or "herd immunity." At this point, an array of viral strains has rendered essentially all monoclonal antibody therapeutics obsolete and strongly undermined the impact of vaccinal immunity on SARS-CoV-2 transmission. In this work, we demonstrate that antibody escape resulting in evasion of pre-existing immunity is highly evolutionarily favored and likely to cause waves of short-term transmission. In the long-term, invading strains that induce weak cross-immunity against pre-existing strains may co-circulate with those pre-existing strains. This would result in the formation of serotypes that increase disease burden, complicate SARS-CoV-2 control, and raise the potential for increases in viral virulence. Less durable immunity does not drive positive selection as a trait, but such strains may transmit at high levels if they establish. Overall, our results draw attention to the importance of inter-strain cross-immunity as a driver of transmission trends and the importance of early immune evasion data to predict the trajectory of the pandemic.
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Affiliation(s)
| | - Debra Van Egeren
- Stanford University School of Medicine, Stanford, CA, United States of America
| | - Aditya Thakur
- Boston University, Boston, MA, United States of America
| | | | - Laura F. White
- Boston University School of Public Health, Boston, MA, United States of America
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9
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Hussein HA, Kandeil A, Gomaa M, Hassan RYA. Double-antibody-based nano-biosensing system for the onsite monitoring of SARS-CoV-2 variants. Microsyst Nanoeng 2023; 9:105. [PMID: 37614970 PMCID: PMC10442362 DOI: 10.1038/s41378-023-00578-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 08/25/2023]
Abstract
The fast and reliable diagnosis of COVID-19 is the foremost priority for promoting public health interventions. Therefore, double-antibody-based immunobiosensor chips were designed, constructed, and exploited for clinical diagnosis. Gold nanoparticles/tungsten oxide/carbon nanotubes (AuNPs/WO3/CNTs) were used as the active working sensor surface to support the chemical immobilization of a mixture of SARS-CoV-2 antibodies (anti-RBD-S and anti-RBD-S-anti-Llama monoclonal antibodies). The morphology and chemical functionalization of the fabricated disposable immunochips was characterized using scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy, cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS). After full assay optimization, the immunobiosensor showed a high sensitivity to detect SARS-CoV-2-S protein with limits of detection and quantification of 1.8 and 5.6 pg/mL, respectively. On the other hand, for the SARS-CoV-2 whole virus particle analysis, the detection and quantification limits were determined to be 5.7 and 17 pg/mL, respectively. The biosensor showed a highly selective response toward SARS-CoV-2, even in the presence of influenza, nontargeting human coronaviruses, and Middle East respiratory syndrome coronavirus (MERS-CoV). The immunochips exhibited distinct responses toward the variants of concern: B.1>C.36.3>Omicron> Delta> Alpha coronavirus variants. For biosensor validation, twenty-nine clinical specimens were analyzed, and the impedimetric responses were positively detected for two Delta samples, eighteen Omicron samples, and six B.1-type samples in addition to three negative samples. Eventually, the immunobiosensor was fabricated in the form of ready-to-use chips capable of sensitive detection of virus variants, especially variants of concern (VOC) and interest, in a specimen within 15 min. The chips provided instantaneous detection with the direct application of clinical samples and are considered a point-of-care device that could be used in public places and hot spots.
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Affiliation(s)
- Heba A. Hussein
- Virology Department, Animal Health Research Institute (AHRI), Agricultural Research Center (ARC), Giza, 12619 Egypt
- Biosensors Research Laboratory, Zewail City of Science and Technology, 6th October City, Giza, 12578 Egypt
| | - Ahmed Kandeil
- Center of Scientific Excellence for Influenza Viruses, Environmental Research Division, National Research Centre, Giza, 12622 Egypt
| | - Mokhtar Gomaa
- Center of Scientific Excellence for Influenza Viruses, Environmental Research Division, National Research Centre, Giza, 12622 Egypt
| | - Rabeay Y. A. Hassan
- Biosensors Research Laboratory, Zewail City of Science and Technology, 6th October City, Giza, 12578 Egypt
- Nanoscience Program, University of Science and Technology (UST), Zewail City of Science and Technology, Giza, 12578 Egypt
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10
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Jiao Y, Xing Y, Sun Y. Impact of E484Q and L452R Mutations on Structure and Binding Behavior of SARS-CoV-2 B.1.617.1 Using Deep Learning AlphaFold2, Molecular Docking and Dynamics Simulation. Int J Mol Sci 2023; 24:11564. [PMID: 37511322 PMCID: PMC10380202 DOI: 10.3390/ijms241411564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/04/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
During the outbreak of COVID-19, many SARS-CoV-2 variants presented key amino acid mutations that influenced their binding abilities with angiotensin-converting enzyme 2 (hACE2) and neutralizing antibodies. For the B.1.617 lineage, there had been fears that two key mutations, i.e., L452R and E484Q, would have additive effects on the evasion of neutralizing antibodies. In this paper, we systematically investigated the impact of the L452R and E484Q mutations on the structure and binding behavior of B.1.617.1 using deep learning AlphaFold2, molecular docking and dynamics simulation. We firstly predicted and verified the structure of the S protein containing L452R and E484Q mutations via the AlphaFold2-calculated pLDDT value and compared it with the experimental structure. Next, a molecular simulation was performed to reveal the structural and interaction stabilities of the S protein of the double mutant variant with hACE2. We found that the double mutations, L452R and E484Q, could lead to a decrease in hydrogen bonds and higher interaction energy between the S protein and hACE2, demonstrating the lower structural stability and the worse binding affinity in the long dynamic evolutional process, even though the molecular docking showed the lower binding energy score of the S1 RBD of the double mutant variant with hACE2 than that of the wild type (WT) with hACE2. In addition, docking to three approved neutralizing monoclonal antibodies (mAbs) showed a reduced binding affinity of the double mutant variant, suggesting a lower neutralization ability of the mAbs against the double mutant variant. Our study helps lay the foundation for further SARS-CoV-2 studies and provides bioinformatics and computational insights into how the double mutations lead to immune evasion, which could offer guidance for subsequent biomedical studies.
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Affiliation(s)
- Yanqi Jiao
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Yichen Xing
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Yao Sun
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
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11
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Acuña-Castillo C, Barrera-Avalos C, Bachelet VC, Milla LA, Inostroza-Molina A, Vidal M, Luraschi R, Vallejos-Vidal E, Mella-Torres A, Valdés D, Reyes-López FE, Imarai M, Rojas P, Sandino AM. An ecological study on reinfection rates using a large dataset of RT-qPCR tests for SARS-CoV-2 in Santiago of Chile. Front Public Health 2023; 11:1191377. [PMID: 37492136 PMCID: PMC10364051 DOI: 10.3389/fpubh.2023.1191377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/05/2023] [Indexed: 07/27/2023] Open
Abstract
Introduction As the SARS-CoV-2 continues to evolve, new variants pose a significant threat by potentially overriding the immunity conferred by vaccination and natural infection. This scenario can lead to an upswing in reinfections, amplified baseline epidemic activity, and localized outbreaks. In various global regions, estimates of breakthrough cases associated with the currently circulating viral variants, such as Omicron, have been reported. Nonetheless, specific data on the reinfection rate in Chile still needs to be included. Methods Our study has focused on estimating COVID-19 reinfections per wave based on a sample of 578,670 RT-qPCR tests conducted at the University of Santiago of Chile (USACH) from April 2020 to July 2022, encompassing 345,997 individuals. Results The analysis reveals that the highest rate of reinfections transpired during the fourth and fifth COVID-19 waves, primarily driven by the Omicron variant. These findings hold despite 80% of the Chilean population receiving complete vaccination under the primary scheme and 60% receiving at least one booster dose. On average, the interval between initial infection and reinfection was found to be 372 days. Interestingly, reinfection incidence was higher in women aged between 30 and 55. Additionally, the viral load during the second infection episode was lower, likely attributed to Chile's high vaccination rate. Discussion This study demonstrates that the Omicron variant is behind Chile's highest number of reinfection cases, underscoring its potential for immune evasion. This vital epidemiological information contributes to developing and implementing effective public health policies.
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Affiliation(s)
- Claudio Acuña-Castillo
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Carlos Barrera-Avalos
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Vivienne C. Bachelet
- Escuela de Medicina, Facultad de Ciencias Médicas, Universidad de Santiago de Chile, Santiago, Chile
| | - Luis A. Milla
- Centro de Investigaciones Biomédicas y Aplicadas, Escuela de Medicina, Facultad de Ciencias Médicas, Universidad de Santiago de Chile, Santiago, Chile
| | - Ailén Inostroza-Molina
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Mabel Vidal
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Roberto Luraschi
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Eva Vallejos-Vidal
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Centro de Nanociencia y Nanotecnología CEDENNA, Universidad de Santiago de Chile, Santiago, Chile
| | - Andrea Mella-Torres
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Daniel Valdés
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Felipe E. Reyes-López
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Mónica Imarai
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Patricio Rojas
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Ana María Sandino
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
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12
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Wuo M, Dugan AE, Halim M, Hauser BM, Feldman J, Caradonna TM, Zhang S, Pepi LE, Atyeo C, Fischinger S, Alter G, Garcia-Beltran WF, Azadi P, Hung D, Schmidt AG, Kiessling LL. Lectin Fingerprinting Distinguishes Antibody Neutralization in SARS-CoV-2. ACS Cent Sci 2023; 9:947-956. [PMID: 37252360 PMCID: PMC10214521 DOI: 10.1021/acscentsci.2c01471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Indexed: 05/31/2023]
Abstract
Enveloped viruses co-opt host glycosylation pathways to decorate their surface proteins. As viruses evolve, emerging strains can modify their glycosylation patterns to influence host interactions and subvert immune recognition. Still, changes in viral glycosylation or their impact on antibody protection cannot be predicted from genomic sequences alone. Using the highly glycosylated SARS-CoV-2 Spike protein as a model system, we present a lectin fingerprinting method that rapidly reports on changes in variant glycosylation state, which are linked to antibody neutralization. In the presence of antibodies or convalescent and vaccinated patient sera, unique lectin fingerprints emerge that distinguish neutralizing versus non-neutralizing antibodies. This information could not be inferred from direct binding interactions between antibodies and the Spike receptor-binding domain (RBD) binding data alone. Comparative glycoproteomics of the Spike RBD of wild-type (Wuhan-Hu-1) and Delta (B.1.617.2) variants reveal O-glycosylation differences as a key determinant of immune recognition differences. These data underscore the interplay between viral glycosylation and immune recognition and reveal lectin fingerprinting to be a rapid, sensitive, and high-throughput assay to distinguish the neutralization potential of antibodies that target critical viral glycoproteins.
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Affiliation(s)
- Michael
G. Wuo
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Amanda E. Dugan
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Melanie Halim
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Blake M. Hauser
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Jared Feldman
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Timothy M. Caradonna
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Shuting Zhang
- The
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02139, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Lauren E. Pepi
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Caroline Atyeo
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Stephanie Fischinger
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Galit Alter
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | | | - Parastoo Azadi
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Deb Hung
- The
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02139, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Aaron G. Schmidt
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
- Department
of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Laura L. Kiessling
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
- The
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Koch
Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts 02139, United States
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13
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Chatterjee S, Chakraborty A, Banik J, Mahindru S, Sharma AK, Mukherjee M. SNAP@CQD as a promising therapeutic vehicle against HCoVs: an overview. Drug Discov Today 2023; 28:103601. [PMID: 37119964 PMCID: PMC10140467 DOI: 10.1016/j.drudis.2023.103601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/04/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
This report discusses potential therapies for treating human coronaviruses (HCoVs) and their economic impact. Specifically, we explore therapeutics that can support the body's immune response, including immunoglobulin (Ig)A, IgG and T-cell responses, to inhibit the viral replication cycle and improve respiratory function. We hypothesize that carbon quantum dots conjugated with S-nitroso-N-acetylpenicillamine (SNAP) could be a synergistic alternative cure for treating respiratory injuries caused by HCoV infections. To achieve this, we propose developing aerosol sprays containing SNAP moieties that release nitric oxide and are conjugated onto promising nanostructured materials. These sprays could combat HCoVs by inhibiting viral replication and improving respiratory function. Furthermore, they could potentially provide other benefits, such as providing novel possibilities for nasal vaccines in the future. Teaser: Synergistic effect of carbon quantum dots and S-nitroso-N-acetylpenicillamine (SNAP) could be suggested as an alternative treatment for the respiratory damage caused by HCoV infections that further open possibilities of developing novel nasal vaccines.
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Affiliation(s)
- Satyaki Chatterjee
- Amity Institute of Click Chemistry Research and Studies (AICCRS), Amity University, Noida, U.P. - 201301, India
| | - Arnab Chakraborty
- Amity Institute of Click Chemistry Research and Studies (AICCRS), Amity University, Noida, U.P. - 201301, India
| | - Jyotiparna Banik
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON M5S 3E5, Canada
| | - Sanya Mahindru
- Amity Institute of Biotechnology, Amity University, Noida - 201303, India
| | - Arun K Sharma
- Department of Pharmacology, Amity Institute of Pharmacy, Amity University, Gurugram, Haryana - 122413, India
| | - Monalisa Mukherjee
- Amity Institute of Click Chemistry Research and Studies (AICCRS), Amity University, Noida, U.P. - 201301, India; Amity Institute of Biotechnology, Amity University, Noida - 201303, India.
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14
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Zhang RY, Zhou SH, Feng RR, Wen Y, Ding D, Zhang ZM, Wei HW, Guo J. Adjuvant-Free COVID-19 Vaccine with Glycoprotein Antigen Oxidized by Periodate Rapidly Elicits Potent Immune Responses. ACS Chem Biol 2023; 18:915-923. [PMID: 37009726 PMCID: PMC10081833 DOI: 10.1021/acschembio.3c00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/23/2023] [Indexed: 04/04/2023]
Abstract
Modification of antigens to improve their immunogenicity represents a promising direction for the development of protein vaccine. Here, we designed facilely prepared adjuvant-free vaccines in which the N-glycan of SARS-CoV-2 receptor-binding domain (RBD) glycoprotein was oxidized by sodium periodate. This strategy only minimally modifies the glycans and does not interfere with the epitope peptides. The RBD glycoprotein oxidized by high concentrations of periodate (RBDHO) significantly enhanced antigen uptake mediated by scavenger receptors and promoted the activation of antigen-presenting cells. Without any external adjuvant, two doses of RBDHO elicited 324- and 27-fold increases in IgG antibody titers and neutralizing antibody titers, respectively, compared to the unmodified RBD antigen. Meanwhile, the RBDHO vaccine could cross-neutralize all of the SARS-CoV-2 variants of concern. In addition, RBDHO effectively enhanced cellular immune responses. This study provides a new insight for the development of adjuvant-free protein vaccines.
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Affiliation(s)
- Ru-Yan Zhang
- Key Laboratory of Pesticide & Chemical Biology of
Ministry of Education, International Joint Research Center for Intelligent Biosensing
Technology and Health, Hubei International Scientific and Technological Cooperation Base
of Pesticide and Green Synthesis, College of Chemistry, Central China Normal
University, Wuhan 430079, China
| | - Shi-Hao Zhou
- Key Laboratory of Pesticide & Chemical Biology of
Ministry of Education, International Joint Research Center for Intelligent Biosensing
Technology and Health, Hubei International Scientific and Technological Cooperation Base
of Pesticide and Green Synthesis, College of Chemistry, Central China Normal
University, Wuhan 430079, China
| | - Ran-Ran Feng
- Key Laboratory of Pesticide & Chemical Biology of
Ministry of Education, International Joint Research Center for Intelligent Biosensing
Technology and Health, Hubei International Scientific and Technological Cooperation Base
of Pesticide and Green Synthesis, College of Chemistry, Central China Normal
University, Wuhan 430079, China
| | - Yu Wen
- Key Laboratory of Pesticide & Chemical Biology of
Ministry of Education, International Joint Research Center for Intelligent Biosensing
Technology and Health, Hubei International Scientific and Technological Cooperation Base
of Pesticide and Green Synthesis, College of Chemistry, Central China Normal
University, Wuhan 430079, China
| | - Dong Ding
- Key Laboratory of Pesticide & Chemical Biology of
Ministry of Education, International Joint Research Center for Intelligent Biosensing
Technology and Health, Hubei International Scientific and Technological Cooperation Base
of Pesticide and Green Synthesis, College of Chemistry, Central China Normal
University, Wuhan 430079, China
| | - Zhi-Ming Zhang
- Key Laboratory of Pesticide & Chemical Biology of
Ministry of Education, International Joint Research Center for Intelligent Biosensing
Technology and Health, Hubei International Scientific and Technological Cooperation Base
of Pesticide and Green Synthesis, College of Chemistry, Central China Normal
University, Wuhan 430079, China
| | - Hua-Wei Wei
- Jiangsu East-Mab Biomedical Technology
Co. Ltd, Nantong 226499, China
| | - Jun Guo
- Key Laboratory of Pesticide & Chemical Biology of
Ministry of Education, International Joint Research Center for Intelligent Biosensing
Technology and Health, Hubei International Scientific and Technological Cooperation Base
of Pesticide and Green Synthesis, College of Chemistry, Central China Normal
University, Wuhan 430079, China
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15
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Muñoz-Basagoiti J, Monteiro FLL, Krumpe LRH, Armario-Najera V, Shenoy SR, Perez-Zsolt D, Westgarth HJ, Villorbina G, Bomfim LM, Raïch-Regué D, Nogueras L, Henrich CJ, Gallemí M, Moreira FRR, Torres P, Wilson J, D’arc M, Marfil S, Herlinger AL, Pradenas E, Higa LM, Portero-Otin M, Trinité B, Twyman RM, Capell T, Tanuri A, Blanco J, Izquierdo-Useros N, Rech EL, Christou P, O’Keefe BR. Cyanovirin-N binds to select SARS-CoV-2 spike oligosaccharides outside of the receptor binding domain and blocks infection by SARS-CoV-2. Proc Natl Acad Sci U S A 2023; 120:e2214561120. [PMID: 36853940 PMCID: PMC10013841 DOI: 10.1073/pnas.2214561120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/12/2023] [Indexed: 03/01/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped positive stranded RNA virus which has caused the recent deadly pandemic called COVID-19. The SARS-CoV-2 virion is coated with a heavily glycosylated Spike glycoprotein which is responsible for attachment and entry into target cells. One, as yet unexploited strategy for preventing SARS-CoV-2 infections, is the targeting of the glycans on Spike. Lectins are carbohydrate-binding proteins produced by plants, algae, and cyanobacteria. Some lectins can neutralize enveloped viruses displaying external glycoproteins, offering an alternative therapeutic approach for the prevention of infection with virulent β-coronaviruses, such as SARS-CoV-2. Here we show that the cyanobacterial lectin cyanovirin-N (CV-N) can selectively target SARS-CoV-2 Spike oligosaccharides and inhibit SARS-CoV-2 infection in vitro and in vivo. CV-N neutralizes Delta and Omicron variants in vitro better than earlier circulating viral variants. CV-N binds selectively to Spike with a Kd as low as 15 nM and a stoichiometry of 2 CV-N: 1 Spike but does not bind to the receptor binding domain (RBD). Further mapping of CV-N binding sites on Spike shows that select high-mannose oligosaccharides in the S1 domain of Spike are targeted by CV-N. CV-N also reduced viral loads in the nares and lungs in vivo to protect hamsters against a lethal viral challenge. In summary, we present an anti-coronavirus agent that works by an unexploited mechanism and prevents infection by a broad range of SARS-CoV-2 strains.
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Affiliation(s)
| | - Fábio Luís Lima Monteiro
- Laboratory of Molecular Virology, Institute of Biology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro21941-90, Brazil
| | - Lauren R. H. Krumpe
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute-Frederick, NIH, Frederick, MD21702
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD21702
| | - Victoria Armario-Najera
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio Center, Lleida25198, Spain
| | - Shilpa R. Shenoy
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute-Frederick, NIH, Frederick, MD21702
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD21702
| | - Daniel Perez-Zsolt
- IrsiCaixa Acquired Immune Deficiency Syndrome Research Institute, Badalona08916, Spain
| | - Harrison James Westgarth
- Laboratory of Molecular Virology, Institute of Biology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro21941-90, Brazil
| | - Gemma Villorbina
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio Center, Lleida25198, Spain
| | - Larissa Maciel Bomfim
- Laboratory of Molecular Virology, Institute of Biology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro21941-90, Brazil
| | - Dàlia Raïch-Regué
- IrsiCaixa Acquired Immune Deficiency Syndrome Research Institute, Badalona08916, Spain
| | - Lara Nogueras
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio Center, Lleida25198, Spain
| | - Curtis J. Henrich
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute-Frederick, NIH, Frederick, MD21702
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD21702
| | - Marçal Gallemí
- IrsiCaixa Acquired Immune Deficiency Syndrome Research Institute, Badalona08916, Spain
| | - Filipe Romero Rebello Moreira
- Laboratory of Molecular Virology, Institute of Biology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro21941-90, Brazil
| | - Pascual Torres
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio Center, Lleida25198, Spain
| | - Jennifer Wilson
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute-Frederick, NIH, Frederick, MD21702
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD21702
| | - Mirela D’arc
- Laboratory of Diversity and Viral Diseases, Institute of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro21941-90, Brazil
| | - Silvia Marfil
- IrsiCaixa Acquired Immune Deficiency Syndrome Research Institute, Badalona08916, Spain
| | - Alice Laschuk Herlinger
- Laboratory of Molecular Virology, Institute of Biology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro21941-90, Brazil
| | - Edwards Pradenas
- IrsiCaixa Acquired Immune Deficiency Syndrome Research Institute, Badalona08916, Spain
| | - Luiza Mendonça Higa
- Laboratory of Molecular Virology, Institute of Biology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro21941-90, Brazil
| | - Manuel Portero-Otin
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio Center, Lleida25198, Spain
| | - Benjamin Trinité
- IrsiCaixa Acquired Immune Deficiency Syndrome Research Institute, Badalona08916, Spain
| | | | - Teresa Capell
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio Center, Lleida25198, Spain
| | - Amilcar Tanuri
- Laboratory of Molecular Virology, Institute of Biology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro21941-90, Brazil
| | - Julià Blanco
- IrsiCaixa Acquired Immune Deficiency Syndrome Research Institute, Badalona08916, Spain
- Germans Trias i Pujol Research Institute, Badalona08916, Spain
- Centro de Investigación Biomédica en Red Enfermedades Infecciosas, Madrid28029, Spain
- Universitat de Vic - Universitat Central de Catalunya, Vic08500, Spain
| | - Nuria Izquierdo-Useros
- IrsiCaixa Acquired Immune Deficiency Syndrome Research Institute, Badalona08916, Spain
- Germans Trias i Pujol Research Institute, Badalona08916, Spain
- Centro de Investigación Biomédica en Red Enfermedades Infecciosas, Madrid28029, Spain
| | - Elibio L. Rech
- Embrapa Genetic Resources and Biotechnology National Institute of Science and Technology in Synthetic Biology, Brasília70770-917, Brazil
| | - Paul Christou
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio Center, Lleida25198, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, Barcelona08010, Spain
| | - Barry R. O’Keefe
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute-Frederick, NIH, Frederick, MD21702
- Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Frederick, MD21702
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16
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Tolan NV, DeSimone MS, Fernandes MD, Lewis JE, Simmons DP, Schur PH, Brigl M, Tanasijevic MJ, Desjardins M, Sherman AC, Baden LR, Snyder M, Melanson SE. Lessons learned: A look back at the performance of nine COVID-19 serologic assays and their proposed utility. Clin Biochem 2023; 117:60-68. [PMID: 36878344 PMCID: PMC9985916 DOI: 10.1016/j.clinbiochem.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/07/2023]
Abstract
BACKGROUND Serologic assays for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been proposed to assist with the acute diagnosis of infection, support epidemiological studies, identify convalescent plasma donors, and evaluate vaccine response. METHODS We report an evaluation of nine serologic assays: Abbott (AB) and Epitope (EP) IgG and IgM, EUROIMMUN (EU) IgG and IgA, Roche anti-N (RN TOT) and anti-S (RS TOT) total antibody, and DiaSorin (DS) IgG. We evaluated 291 negative controls (NEG CTRL), 91 PCR positive (PCR POS) patients (179 samples), 126 convalescent plasma donors (CPD), 27 healthy vaccinated donors (VD), and 20 allogeneic hematopoietic stem cell transplant (HSCT) recipients (45 samples). RESULTS We observed good agreement with the method performance claims for specificity (93-100%) in NEG CTRL but only 85% for EU IgA. The sensitivity claims in the first 2 weeks of symptom onset was lower (26-61%) than performance claims based on > 2 weeks since PCR positivity. We observed high sensitivities (94-100%) in CPD except for AB IgM (77%), EP IgM (0%). Significantly higher RS TOT was observed for Moderna vaccine recipients then Pfizer (p-values < 0.0001). A sustained RS TOT response was observed for the five months following vaccination. HSCT recipients demonstrated significantly lower RS TOT than healthy VD (p < 0.0001) at dose 2 and 4 weeks after. CONCLUSIONS Our data suggests against the use of anti-SARS-CoV-2 assays to aid in acute diagnosis. RN TOT and RS TOT can readily identify past-resolved infection and vaccine response in the absence of native infection. We provide an estimate of expected antibody response in healthy VD over the time course of vaccination for which to compare antibody responses in immunosuppressed patients.
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Affiliation(s)
- Nicole V Tolan
- Brigham and Women's Hospital, Department of Pathology, Boston, MA, United States; Harvard Medical School, Boston, MA, United States.
| | - Mia S DeSimone
- Brigham and Women's Hospital, Department of Pathology, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - Maria D Fernandes
- Brigham and Women's Hospital, Department of Pathology, Boston, MA, United States
| | - Joshua E Lewis
- Brigham and Women's Hospital, Department of Pathology, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - Daimon P Simmons
- Brigham and Women's Hospital, Department of Pathology, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - Peter H Schur
- Brigham and Women's Hospital, Department of Pathology, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - Manfred Brigl
- Brigham and Women's Hospital, Department of Pathology, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - Milenko J Tanasijevic
- Brigham and Women's Hospital, Department of Pathology, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - Michaël Desjardins
- Harvard Medical School, Boston, MA, United States; Brigham and Women's Hospital, Department of Medicine, Division of Infectious Diseases, Boston, MA, United States
| | - Amy C Sherman
- Harvard Medical School, Boston, MA, United States; Brigham and Women's Hospital, Department of Medicine, Division of Infectious Diseases, Boston, MA, United States
| | - Lindsey R Baden
- Harvard Medical School, Boston, MA, United States; Brigham and Women's Hospital, Department of Medicine, Division of Infectious Diseases, Boston, MA, United States
| | | | - Stacy Ef Melanson
- Brigham and Women's Hospital, Department of Pathology, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
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17
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Cox M, Peacock TP, Harvey WT, Hughes J, Wright DW, Willett BJ, Thomson E, Gupta RK, Peacock SJ, Robertson DL, Carabelli AM. SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies. Nat Rev Microbiol 2023; 21:112-124. [PMID: 36307535 PMCID: PMC9616429 DOI: 10.1038/s41579-022-00809-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2022] [Indexed: 01/20/2023]
Abstract
Monoclonal antibodies (mAbs) offer a treatment option for individuals with severe COVID-19 and are especially important in high-risk individuals where vaccination is not an option. Given the importance of understanding the evolution of resistance to mAbs by SARS-CoV-2, we reviewed the available in vitro neutralization data for mAbs against live variants and viral constructs containing spike mutations of interest. Unfortunately, evasion of mAb-induced protection is being reported with new SARS-CoV-2 variants. The magnitude of neutralization reduction varied greatly among mAb-variant pairs. For example, sotrovimab retained its neutralization capacity against Omicron BA.1 but showed reduced efficacy against BA.2, BA.4 and BA.5, and BA.2.12.1. At present, only bebtelovimab has been reported to retain its efficacy against all SARS-CoV-2 variants considered here. Resistance to mAb neutralization was dominated by the action of epitope single amino acid substitutions in the spike protein. Although not all observed epitope mutations result in increased mAb evasion, amino acid substitutions at non-epitope positions and combinations of mutations also contribute to evasion of neutralization. This Review highlights the implications for the rational design of viral genomic surveillance and factors to consider for the development of novel mAb therapies.
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Affiliation(s)
- MacGregor Cox
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Thomas P Peacock
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Derek W Wright
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Brian J Willett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Emma Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
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18
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Kumar A, Asghar A, Singh HN, Faiq MA, Kumar S, Narayan RK, Kumar G, Dwivedi P, Sahni C, Jha RK, Kulandhasamy M, Prasoon P, Sesham K, Kant K, Pandey SN. SARS-CoV-2 Omicron Variant Genomic Sequences and Their Epidemiological Correlates Regarding the End of the Pandemic: In Silico Analysis. JMIR Bioinform Biotech 2023; 4:e42700. [PMID: 36688013 PMCID: PMC9843602 DOI: 10.2196/42700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/29/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Emergence of the new SARS-CoV-2 variant B.1.1.529 worried health policy makers worldwide due to a large number of mutations in its genomic sequence, especially in the spike protein region. The World Health Organization (WHO) designated this variant as a global variant of concern (VOC), which was named "Omicron." Following Omicron's emergence, a surge of new COVID-19 cases was reported globally, primarily in South Africa. OBJECTIVE The aim of this study was to understand whether Omicron had an epidemiological advantage over existing variants. METHODS We performed an in silico analysis of the complete genomic sequences of Omicron available on the Global Initiative on Sharing Avian Influenza Data (GISAID) database to analyze the functional impact of the mutations present in this variant on virus-host interactions in terms of viral transmissibility, virulence/lethality, and immune escape. In addition, we performed a correlation analysis of the relative proportion of the genomic sequences of specific SARS-CoV-2 variants (in the period from October 1 to November 29, 2021) with matched epidemiological data (new COVID-19 cases and deaths) from South Africa. RESULTS Compared with the current list of global VOCs/variants of interest (VOIs), as per the WHO, Omicron bears more sequence variation, specifically in the spike protein and host receptor-binding motif (RBM). Omicron showed the closest nucleotide and protein sequence homology with the Alpha variant for the complete sequence and the RBM. The mutations were found to be primarily condensed in the spike region (n=28-48) of the virus. Further mutational analysis showed enrichment for the mutations decreasing binding affinity to angiotensin-converting enzyme 2 receptor and receptor-binding domain protein expression, and for increasing the propensity of immune escape. An inverse correlation of Omicron with the Delta variant was noted (r=-0.99, P<.001; 95% CI -0.99 to -0.97) in the sequences reported from South Africa postemergence of the new variant, subsequently showing a decrease. There was a steep rise in new COVID-19 cases in parallel with the increase in the proportion of Omicron isolates since the report of the first case (74%-100%). By contrast, the incidence of new deaths did not increase (r=-0.04, P>.05; 95% CI -0.52 to 0.58). CONCLUSIONS In silico analysis of viral genomic sequences suggests that the Omicron variant has more remarkable immune-escape ability than existing VOCs/VOIs, including Delta, but reduced virulence/lethality than other reported variants. The higher power for immune escape for Omicron was a likely reason for the resurgence in COVID-19 cases and its rapid rise as the globally dominant strain. Being more infectious but less lethal than the existing variants, Omicron could have plausibly led to widespread unnoticed new, repeated, and vaccine breakthrough infections, raising the population-level immunity barrier against the emergence of new lethal variants. The Omicron variant could have thus paved the way for the end of the pandemic.
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Affiliation(s)
- Ashutosh Kumar
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Adil Asghar
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Himanshu N Singh
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Systems Biology Columbia University Irving Medical Center New York, NY United States
| | - Muneeb A Faiq
- Etiologically Elusive Disorders Research Network New Delhi India
- New York University Langone Health Center Robert I Grossman School of Medicine New York University New York, NY United States
| | - Sujeet Kumar
- Etiologically Elusive Disorders Research Network New Delhi India
- Center for Proteomics and Drug Discovery Amity Institute of Biotechnology Amity University, Maharashtra Mumbai India
| | - Ravi K Narayan
- Etiologically Elusive Disorders Research Network New Delhi India
- Dr BC Roy Multi-speciality Medical Research Centre Indian Institute of Technology Kharagpur India
| | - Gopichand Kumar
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Prakhar Dwivedi
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Chetan Sahni
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Anatomy Institute of Medical Sciences Banaras Hindu University Varanasi India
| | - Rakesh K Jha
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Maheswari Kulandhasamy
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Biochemistry Maulana Azad Medical College New Delhi India
| | - Pranav Prasoon
- Etiologically Elusive Disorders Research Network New Delhi India
- School of Medicine University of Pittsburgh Pittsburgh, PA United States
| | - Kishore Sesham
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Anatomy All India Institute of Medical Sciences-Mangalagiri Mangalagiri India
| | - Kamla Kant
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Microbiology All India Institute of Medical Sciences-Bathinda Bathinda India
| | - Sada N Pandey
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Zoology Banaras Hindu University Varanasi India
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19
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Li M, Ren Y, Aw ZQ, Chen B, Yang Z, Lei Y, Cheng L, Liang Q, Hong J, Yang Y, Chen J, Wong YH, Wei J, Shan S, Zhang S, Ge J, Wang R, Dong JZ, Chen Y, Shi X, Zhang Q, Zhang Z, Chu JJH, Wang X, Zhang L. Broadly neutralizing and protective nanobodies against SARS-CoV-2 Omicron subvariants BA.1, BA.2, and BA.4/5 and diverse sarbecoviruses. Nat Commun 2022; 13:7957. [PMID: 36575191 DOI: 10.1038/s41467-022-35642-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022] Open
Abstract
As SARS-CoV-2 Omicron and other variants of concern (VOCs) continue spreading worldwide, development of antibodies and vaccines to confer broad and protective activity is a global priority. Here, we report on the identification of a special group of nanobodies from immunized alpaca with potency against diverse VOCs including Omicron subvariants BA.1, BA.2 and BA.4/5, SARS-CoV-1, and major sarbecoviruses. Crystal structure analysis of one representative nanobody, 3-2A2-4, discovers a highly conserved epitope located between the cryptic and the outer face of the receptor binding domain (RBD), distinctive from the receptor ACE2 binding site. Cryo-EM and biochemical evaluation reveal that 3-2A2-4 interferes structural alteration of RBD required for ACE2 binding. Passive delivery of 3-2A2-4 protects K18-hACE2 mice from infection of authentic SARS-CoV-2 Delta and Omicron. Identification of these unique nanobodies will inform the development of next generation antibody therapies and design of pan-sarbecovirus vaccines.
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20
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Hauser BM, Feldman J, Sangesland M, Ronsard L, St Denis KJ, Sheehan ML, Cao Y, Boucau J, Windsor IW, Cheng AH, Vu ML, Cardoso MR, Kannegieter T, Balazs AB, Lingwood D, Garcia-Beltran WF, Schmidt AG. Cross-reactive SARS-CoV-2 epitope targeted across donors informs immunogen design. Cell Rep Med 2022; 3:100834. [PMID: 36423634 PMCID: PMC9663748 DOI: 10.1016/j.xcrm.2022.100834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/07/2022] [Accepted: 11/08/2022] [Indexed: 11/17/2022]
Abstract
The emergence of the antigenically distinct and highly transmissible Omicron variant highlights the possibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune escape due to viral evolution. This continued evolution, along with the possible introduction of new sarbecoviruses from zoonotic reservoirs, may evade host immunity elicited by current SARS-CoV-2 vaccines. Identifying cross-reactive antibodies and defining their epitope(s) can provide templates for rational immunogen design strategies for next-generation vaccines. Here, we characterize the receptor-binding-domain-directed, cross-reactive humoral repertoire across 10 human vaccinated donors. We identify cross-reactive antibodies from diverse gene rearrangements targeting two conserved receptor-binding domain epitopes. An engineered immunogen enriches antibody responses to one of these conserved epitopes in mice with pre-existing SARS-CoV-2 immunity; elicited responses neutralize SARS-CoV-2, variants, and related sarbecoviruses. These data show how immune focusing to a conserved epitope targeted by human cross-reactive antibodies may guide pan-sarbecovirus vaccine development, providing a template for identifying such epitopes and translating to immunogen design.
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Affiliation(s)
- Blake M Hauser
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Maya Sangesland
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Larance Ronsard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Kerri J St Denis
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Maegan L Sheehan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Yi Cao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ian W Windsor
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Laboratory of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Agnes H Cheng
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Mya L Vu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Ty Kannegieter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Wilfredo F Garcia-Beltran
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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21
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Torchia JA, Tavares AH, Carstensen LS, Chen DY, Huang J, Xiao T, Mukherjee S, Reeves PM, Tu H, Sluder AE, Chen B, Kotton DN, Bowen RA, Saeed M, Poznansky MC, Freeman GJ. Optimized ACE2 decoys neutralize antibody-resistant SARS-CoV-2 variants through functional receptor mimicry and treat infection in vivo. Sci Adv 2022; 8:eabq6527. [PMID: 36475798 PMCID: PMC9728973 DOI: 10.1126/sciadv.abq6527] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/01/2022] [Indexed: 05/14/2023]
Abstract
As severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) evolves to escape natural antibodies, it also loses sensitivity to therapeutic antibody drugs. By contrast, evolution selects for binding to ACE2, the cell-surface receptor required for SARS-CoV-2 infection. Consistent with this, we find that an ACE2 decoy neutralizes antibody-resistant variants, including Omicron, with no loss in potency. To identify design features necessary for in vivo activity, we compare several enzymatically inactive, Fc effector-silenced ACE2-Fc decoys. Inclusion of the ACE2 collectrin-like domain not only improves affinity for the S protein but also unexpectedly extends serum half-life and is necessary to reduce disease severity and viral titer in Syrian hamsters. Fc effector function is not required. The activity of ACE2 decoy receptors is due, in part, to their ability to trigger an irreversible structural change in the viral S protein. Our studies provide a new understanding of how ACE2 decoys function and support their development as therapeutics to treat ACE2-dependent coronaviruses.
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Affiliation(s)
- James A. Torchia
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Alexander H. Tavares
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Laura S. Carstensen
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Da-Yuan Chen
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University, Boston Medical Center, and The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Tianshu Xiao
- Division of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Sonia Mukherjee
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Patrick M. Reeves
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Hua Tu
- LakePharma Inc., San Carlos, CA 94070, USA
| | - Ann E. Sluder
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Bing Chen
- Division of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University, Boston Medical Center, and The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Richard A. Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Mohsan Saeed
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Mark C. Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Gordon J. Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
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22
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Malisheni MM, Bates M, Rizvanov AA, MacAry PA. SARS-CoV-2 Antibody Effectiveness Is Influenced by Non-Epitope Mutation/Binding-Induced Denaturation of the Epitope 3D Architecture. Pathogens 2022; 11. [PMID: 36558771 DOI: 10.3390/pathogens11121437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/16/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022] Open
Abstract
The public health threat from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to intensify with emerging variants of concern (VOC) aiming to render COVID-19 vaccines/infection-induced antibodies redundant. The SARS-CoV-2 spike protein is responsible for receptor binding and infection of host cells making it a legitimate antibody target. Antibodies mostly target epitopes in the receptor binding domain (RBD). Mutations occurring within epitopes influence antibody specificity and function by altering their 3D architecture. However, the mechanisms by which non-epitope mutations in the RBD influence antibody specificity and function remain a mystery. We used Protein Data Bank (PDB) deposited 3D structures for the original, Beta, Delta, BA.1, and BA.2 RBD proteins in complex with either neutralizing antibodies or Angiotensin-Converting Enzyme 2 (ACE2) to elucidate the structural and mechanistic basis for neutralizing antibody evasion driven by non-epitope amino acid substitutions in the RBD. Since the mechanism behind the extensively reported functional discrepancies between the same antibody when used individually and when used in an antibody cocktail is lacking, we explored the structural basis for this inconsistency. Finally, since SARS-CoV-2 antibodies are viral mutagens, we deciphered determinants for antibody-pressured amino acid substitutions. On the one hand, we show that non-epitope mutations in the RBD domain of SARS-CoV-2 VOC influence the formation of hydrogen bonds in the paratope-epitope interface by repositioning RBD amino-acid sidechains (AASCs). This increases the distance between complementary donor/acceptor atoms on paratope and epitope AASCs leading to weaker or the complete prevention of the formation of hydrogen bonds in the paratope-epitope interface. On the other hand, we show that SARS-CoV-2 VOC employ the same strategy to simultaneously search for complementary donor/acceptor atoms on ACE2 AASCs to form new interactions, potentially favoring increased viral transmission. Additionally, we illustrate that converting the spike protein to an RBD, a deletion mutation, also repositions epitope AASCs and that AASC interactions in the paratope-epitope interface vary when an antibody is used individually versus when utilized as a cocktail with other antibodies. Finally, we show that the process of substituting immunogenic RBD amino acids begins with the repositioning of their AASCs induced by immune/antibody pressure. We show that donor/acceptor atoms from any amino acid can determine cross-reactivity instead, provided they possess and present spatially pairing donor/acceptor atoms. By studying structural alignments for PDB deposited antibody-RBD 3D structures and relating them to published binding and neutralization profiles of the same antibodies, we demonstrate that minor structural alterations such as epitope AASC repositioning have a major impact on antibody effectiveness and, hence, should receive adequate attention given that protein structure dictates protein function.
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23
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Shafqat A, Omer MH, Ahmad O, Niaz M, Abdulkader HS, Shafqat S, Mushtaq AH, Shaik A, Elshaer AN, Kashir J, Alkattan K, Yaqinuddin A. SARS-CoV-2 epitopes inform future vaccination strategies. Front Immunol 2022; 13:1041185. [PMID: 36505475 PMCID: PMC9732895 DOI: 10.3389/fimmu.2022.1041185] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022] Open
Abstract
All currently approved COVID-19 vaccines utilize the spike protein as their immunogen. SARS-CoV-2 variants of concern (VOCs) contain mutations in the spike protein, enabling them to escape infection- and vaccination-induced immune responses to cause reinfection. New vaccines are hence being researched intensively. Studying SARS-CoV-2 epitopes is essential for vaccine design, as identifying targets of broadly neutralizing antibody responses and immunodominant T-cell epitopes reveal candidates for inclusion in next-generation COVID-19 vaccines. We summarize the major studies which have reported on SARS-CoV-2 antibody and T-cell epitopes thus far. These results suggest that a future of pan-coronavirus vaccines, which not only protect against SARS-CoV-2 but numerous other coronaviruses, may be possible. The T-cell epitopes of SARS-CoV-2 have gotten less attention than neutralizing antibody epitopes but may provide new strategies to control SARS-CoV-2 infection. T-cells target many SARS-CoV-2 antigens other than spike, recognizing numerous epitopes within these antigens, thereby limiting the chance of immune escape by VOCs that mainly possess spike protein mutations. Therefore, augmenting vaccination-induced T-cell responses against SARS-CoV-2 may provide adequate protection despite broad antibody escape by VOCs.
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Affiliation(s)
- Areez Shafqat
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia,*Correspondence: Areez Shafqat,
| | - Mohamed H. Omer
- School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Omar Ahmad
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Mahnoor Niaz
- Medical College, Aga Khan University, Karachi, Pakistan
| | | | | | | | - Abdullah Shaik
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | | | - Junaid Kashir
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia,Department of Comparative Medicine, King Faisal Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Khaled Alkattan
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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24
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Abstract
As many parts of the world continue to fight the innumerable waves of COVID-19 infection, SARS-CoV-2 continues to sculpt its antigenic determinants to enhance its virulence and evolvability. Several vaccines were developed and used around the world, and oral antiviral medications are being developed against SARS-CoV-2. However, studies showed that the virus is mutating in line with the antibody's neutralization escape; thus, new therapeutic alternatives are solicited. We hereby review the key role that miRNAs can play as epigenetic mediators of the cross-talk between SARS-CoV-2 and the host cells. The limitations resulting from the "virus intelligence" to escape and antagonize the host miRNAs as well as the possible mechanisms that could be used in the viral evasion strategies are discussed. Lastly, we suggest new therapeutic approaches based on viral miRNAs.
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Affiliation(s)
- Leyla Tahrani Hardin
- Department of Biomedical Sciences at the Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, 94103 CA, USA
| | - Nan Xiao
- Department of Biomedical Sciences at the Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, 94103 CA, USA
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25
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Brady T, Zhang T, Tuffy KM, Haskins N, Du Q, Lin J, Kaplan G, Novick S, Roe TL, Ren K, Rosenthal K, McTamney PM, Abram ME, Streicher K, Kelly EJ. Qualification of a Biolayer Interferometry Assay to Support AZD7442 Resistance Monitoring. Microbiol Spectr 2022; 10:e0103422. [PMID: 35993765 DOI: 10.1128/spectrum.01034-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
AZD7442, a combination of two long-acting monoclonal antibodies (tixagevimab [AZD8895] and cilgavimab [AZD1061]), has been authorized for the prevention and treatment of coronavirus disease 2019 (COVID-19). The rapid emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants requires methods capable of quickly characterizing resistance to AZD7442. To support AZD7442 resistance monitoring, a biolayer interferometry (BLI) assay was developed to screen the binding of tixagevimab and cilgavimab to SARS-CoV-2 spike proteins to reduce the number of viral variants for neutralization susceptibility verification. Six spike variants were chosen to assess the assay's performance: four with decreased affinity for tixagevimab (F486S:D614G and F486W:D614G proteins) or cilgavimab (S494L:D614G and K444R:D614G proteins) and two reference proteins (wild-type HexaPro and D614G protein). Equilibrium dissociation constant (KD) values from each spike protein were used to determine shifts in binding affinity. The assay's precision, range, linearity, and limits of quantitation were established. Qualification acceptance criteria determined whether the assay was fit for purpose. By bypassing protein purification, the BLI assay provided increased screening throughput. Although limited correlation between pseudotype neutralization and BLI data (50% inhibitory concentration versus KD) was observed for full immunoglobulins (IgGs), the correlations for antibody fragments (Fabs) were stronger and reflected a better comparison of antibody binding kinetics with neutralization potency. Therefore, despite strong assay performance characteristics, the use of full IgGs limited the screening utility of the assay; however, the Fab approach warrants further exploration as a rapid, high-throughput variant-screening method for future resistance-monitoring programs. IMPORTANCE SARS-CoV-2 variants harbor multiple substitutions in their spike trimers, potentially leading to breakthrough infections and clinical resistance to immune therapies. For this reason, a BLI assay was developed and qualified to evaluate the reliability of screening SARS-CoV-2 spike trimer variants against anti-SARS-CoV-2 monoclonal antibodies (MAbs) tixagevimab and cilgavimab, the components of AZD7442, prior to in vitro pseudovirus neutralization susceptibility verification testing. The assay bypasses protein purification with rapid assessment of the binding affinity of each MAb for each recombinant protein, potentially providing an efficient preliminary selection step, thus allowing a reduced testing burden in the more technically complex viral neutralization assays. Despite precise and specific measures, an avidity effect associated with MAb binding to the trimer confounded correlation with neutralization potency, negating the assay's utility as a surrogate for neutralizing antibody potency. Improved correlation with Fabs suggests that assay optimization could overcome any avidity limitation, warranting further exploration to support future resistance-monitoring programs.
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26
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Huang Q, Han X, Yan J. Structure-based neutralizing mechanisms for SARS-CoV-2 antibodies. Emerg Microbes Infect 2022; 11:2412-2422. [PMID: 36106670 PMCID: PMC9553185 DOI: 10.1080/22221751.2022.2125348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Qingrui Huang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaonan Han
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jinghua Yan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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27
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Wang C, Li Y, Kaplonek P, Gentili M, Fischinger S, Bowman KA, Sade-Feldman M, Kays KR, Regan J, Flynn JP, Goldberg MB, Hacohen N, Filbin MR, Lauffenburger DA, Alter G, Li JZ. The Kinetics of SARS-CoV-2 Antibody Development Is Associated with Clearance of RNAemia. mBio 2022; 13:e0157722. [PMID: 35762593 PMCID: PMC9426503 DOI: 10.1128/mbio.01577-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 01/23/2023] Open
Abstract
Persistent SARS-CoV-2 replication and systemic dissemination are linked to increased COVID-19 disease severity and mortality. However, the precise immune profiles that track with enhanced viral clearance, particularly from systemic RNAemia, remain incompletely defined. To define whether antibody characteristics, specificities, or functions that emerge during natural infection are linked to accelerated containment of viral replication, we examined the relationship of SARS-CoV-2-specific humoral immune evolution in the setting of SARS-CoV-2 plasma RNAemia, which is tightly associated with disease severity and death. On presentation to the emergency department, S-specific IgG3, IgA1, and Fc-γ-receptor (Fcγ R) binding antibodies were all inversely associated with higher baseline plasma RNAemia. Importantly, the rapid development of spike (S) and its subunit (S1/S2/receptor binding domain)-specific IgG, especially FcγR binding activity, were associated with clearance of RNAemia. These results point to a potentially critical and direct role for SARS-CoV-2-specific humoral immune clearance on viral dissemination, persistence, and disease outcome, providing novel insights for the development of more effective therapeutics to resolve COVID-19. IMPORTANCE We showed that persistent SARS-CoV-2 RNAemia is an independent predictor of severe COVID-19. We observed that SARS-CoV-2-targeted antibody maturation, specifically Fc-effector functions rather than neutralization, was strongly linked with the ability to rapidly clear viremia. This highlights the critical role of key humoral features in preventing viral dissemination or accelerating viremia clearance and provides insights for the design of next-generation monoclonal therapeutics. The main key points will be that (i) persistent SARS-CoV-2 plasma RNAemia independently predicts severe COVID-19 and (ii) specific humoral immune functions play a critical role in halting viral dissemination and controlling COVID-19 disease progression.
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Affiliation(s)
- Chuangqi Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Yijia Li
- Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Paulina Kaplonek
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Matteo Gentili
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Kathryn A. Bowman
- Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Massachusetts General Hospital, Boston, Massachusetts, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Kyle R. Kays
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | - James Regan
- Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - James P. Flynn
- Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Marcia B. Goldberg
- Massachusetts General Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael R. Filbin
- Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Douglas A. Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Galit Alter
- Massachusetts General Hospital, Boston, Massachusetts, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jonathan Z. Li
- Brigham and Women’s Hospital, Boston, Massachusetts, USA
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28
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Durmaz V, Köchl K, Krassnigg A, Parigger L, Hetmann M, Singh A, Nutz D, Korsunsky A, Kahler U, König C, Chang L, Krebs M, Bassetto R, Pavkov-Keller T, Resch V, Gruber K, Steinkellner G, Gruber CC. Structural bioinformatics analysis of SARS-CoV-2 variants reveals higher hACE2 receptor binding affinity for Omicron B.1.1.529 spike RBD compared to wild type reference. Sci Rep 2022; 12:14534. [PMID: 36008461 PMCID: PMC9406262 DOI: 10.1038/s41598-022-18507-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 08/08/2022] [Indexed: 01/16/2023] Open
Abstract
To date, more than 263 million people have been infected with SARS-CoV-2 during the COVID-19 pandemic. In many countries, the global spread occurred in multiple pandemic waves characterized by the emergence of new SARS-CoV-2 variants. Here we report a sequence and structural-bioinformatics analysis to estimate the effects of amino acid substitutions on the affinity of the SARS-CoV-2 spike receptor binding domain (RBD) to the human receptor hACE2. This is done through qualitative electrostatics and hydrophobicity analysis as well as molecular dynamics simulations used to develop a high-precision empirical scoring function (ESF) closely related to the linear interaction energy method and calibrated on a large set of experimental binding energies. For the latest variant of concern (VOC), B.1.1.529 Omicron, our Halo difference point cloud studies reveal the largest impact on the RBD binding interface compared to all other VOC. Moreover, according to our ESF model, Omicron achieves a much higher ACE2 binding affinity than the wild type and, in particular, the highest among all VOCs except Alpha and thus requires special attention and monitoring.
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Affiliation(s)
| | | | | | | | - Michael Hetmann
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria.,Austrian Centre of Industrial Biotechnology, 8010, Graz, Austria
| | - Amit Singh
- Innophore GmbH, 8010, Graz, Austria.,Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria
| | | | | | | | | | - Lee Chang
- AWS Diagnostic Development Initiative-Global Social Impact, Seattle, WA, 98109, USA
| | - Marius Krebs
- Amazon Web Services EMEA SARL, 80807, Muenchen, Germany
| | | | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria
| | | | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria.,Field of Excellence BioHealth-University of Graz, 8010, Graz, Austria
| | - Georg Steinkellner
- Innophore GmbH, 8010, Graz, Austria. .,Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria.
| | - Christian C Gruber
- Innophore GmbH, 8010, Graz, Austria. .,Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria.
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29
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Chaqroun A, Hartard C, Josse T, Taverniers A, Jeulin H, Gantzer C, Murray JM, Bertrand I, Schvoerer E. SARS-CoV-2 Variability in Patients and Wastewaters—Potential Immuno-Modulation during the Shift from Delta to Omicron. Biomedicines 2022; 10:biomedicines10092080. [PMID: 36140181 PMCID: PMC9496010 DOI: 10.3390/biomedicines10092080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/16/2022] Open
Abstract
The continuous emergence of SARS-CoV-2 variants favors potential co-infections and/or viral mutation events, leading to possible new biological properties. The aim of this work was to characterize SARS-CoV-2 genetic variability during the Delta–Omicron shift in patients and in a neighboring wastewater treatment plant (WWTP) in the same urban area. The surveillance of SARS-CoV-2 was performed by routine screening of positive samples by single nucleotide polymorphism analysis within the S gene. Moreover, additionally to national systematic whole genome sequencing (WGS) once a week in SARS-CoV-2-positive patients, WGS was also applied when mutational profiles were difficult to interpret by routine screening. Thus, WGS was performed on 414 respiratory samples and on four wastewater samples, northeastern France. This allowed us to report (i) the temporally concordant Delta to Omicron viral shift in patients and wastewaters; (ii) the characterization of 21J (Delta) and 21K (Omicron)/BA.1-21L (Omicron)/BA.2-BA.4 mixtures from humans or environmental samples; (iii) the mapping of composite mutations and the predicted impact on immune properties in the viral Spike protein.
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Affiliation(s)
- Ahlam Chaqroun
- CNRS, LCPME, Université de Lorraine, F-54000 Nancy, France
- Laboratoire de Virologie-Microbiologie, Hôpital Universitaire de Nancy, Université de Lorraine, F-54000 Nancy, France
| | - Cédric Hartard
- CNRS, LCPME, Université de Lorraine, F-54000 Nancy, France
- Laboratoire de Virologie-Microbiologie, Hôpital Universitaire de Nancy, Université de Lorraine, F-54000 Nancy, France
| | - Thomas Josse
- Laboratoire de Virologie-Microbiologie, Hôpital Universitaire de Nancy, Université de Lorraine, F-54000 Nancy, France
| | - Audrey Taverniers
- Laboratoire de Virologie-Microbiologie, Hôpital Universitaire de Nancy, Université de Lorraine, F-54000 Nancy, France
| | - Hélène Jeulin
- CNRS, LCPME, Université de Lorraine, F-54000 Nancy, France
- Laboratoire de Virologie-Microbiologie, Hôpital Universitaire de Nancy, Université de Lorraine, F-54000 Nancy, France
| | | | - John M. Murray
- School of Mathematics and Statistics, UNSW Sydney, Sydney, NSW 2052, Australia
| | | | | | - Evelyne Schvoerer
- CNRS, LCPME, Université de Lorraine, F-54000 Nancy, France
- Laboratoire de Virologie-Microbiologie, Hôpital Universitaire de Nancy, Université de Lorraine, F-54000 Nancy, France
- Correspondence: or
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30
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Hale M, Netland J, Chen Y, Thouvenel CD, Smith KN, Rich LM, Vanderwall ER, Miranda MC, Eggenberger J, Hao L, Watson MJ, Mundorff CC, Rodda LB, King NP, Guttman M, Gale M, Abraham J, Debley JS, Pepper M, Rawlings DJ. IgM antibodies derived from memory B cells are potent cross-variant neutralizers of SARS-CoV-2. J Exp Med 2022; 219:213384. [PMID: 35938988 PMCID: PMC9365875 DOI: 10.1084/jem.20220849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/22/2022] [Accepted: 07/12/2022] [Indexed: 01/14/2023] Open
Abstract
Humoral immunity to SARS-CoV-2 can be supplemented with polyclonal sera from convalescent donors or an engineered monoclonal antibody (mAb) product. While pentameric IgM antibodies are responsible for much of convalescent sera's neutralizing capacity, all available mAbs are based on the monomeric IgG antibody subtype. We now show that IgM mAbs derived from immune memory B cell receptors are potent neutralizers of SARS-CoV-2. IgM mAbs outperformed clonally identical IgG antibodies across a range of affinities and SARS-CoV-2 receptor-binding domain epitopes. Strikingly, efficacy against SARS-CoV-2 viral variants was retained for IgM but not for clonally identical IgG. To investigate the biological role for IgM memory in SARS-CoV-2, we also generated IgM mAbs from antigen-experienced IgM+ memory B cells in convalescent donors, identifying a potent neutralizing antibody. Our results highlight the therapeutic potential of IgM mAbs and inform our understanding of the role for IgM memory against a rapidly mutating pathogen.
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Affiliation(s)
- Malika Hale
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | - Jason Netland
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Yu Chen
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | | | | | - Lucille M. Rich
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | | | - Marcos C. Miranda
- Institute for Protein Design, University of Washington, Seattle, WA,Department of Biochemistry, University of Washington School of Medicine, Seattle, WA
| | - Julie Eggenberger
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Linhui Hao
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Michael J. Watson
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
| | | | - Lauren B. Rodda
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Neil P. King
- Institute for Protein Design, University of Washington, Seattle, WA,Department of Biochemistry, University of Washington School of Medicine, Seattle, WA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
| | - Michael Gale
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Jonathan Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA
| | - Jason S. Debley
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | - Marion Pepper
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - David J. Rawlings
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA,Department of Immunology, University of Washington School of Medicine, Seattle, WA,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA,Correspondence to David J. Rawlings:
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31
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Kudriavtsev AV, Vakhrusheva AV, Novosеletsky VN, Bozdaganyan ME, Shaitan KV, Kirpichnikov MP, Sokolova OS. Immune Escape Associated with RBD Omicron Mutations and SARS-CoV-2 Evolution Dynamics. Viruses 2022; 14:1603. [PMID: 35893668 DOI: 10.3390/v14081603] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
The evolution and the emergence of new mutations of viruses affect their transmissibility and/or pathogenicity features, depending on different evolutionary scenarios of virus adaptation to the host. A typical trade-off scenario of SARS-CoV-2 evolution has been proposed, which leads to the appearance of an Omicron strain with lowered lethality, yet enhanced transmissibility. This direction of evolution might be partly explained by virus adaptation to therapeutic agents and enhanced escape from vaccine-induced and natural immunity formed by other SARS-CoV-2 strains. Omicron’s high mutation rate in the Spike protein, as well as its previously described high genome mutation rate (Kandeel et al., 2021), revealed a gap between it and other SARS-CoV-2 strains, indicating the absence of a transitional evolutionary form to the Omicron strain. Therefore, Omicron has emerged as a new serotype divergent from the evolutionary lineage of other SARS-CoV-2 strains. Omicron is a rapidly evolving variant of high concern, whose new subvariants continue to manifest. Its further understanding and the further monitoring of key mutations that provide virus immune escape and/or high affinity towards the receptor could be useful for vaccine and therapeutic development in order to control the evolutionary direction of the COVID-19 pandemic.
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32
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Almanza G, Clark AE, Kouznetsova V, Olmedillas E, Castro A, Tsigelny IF, Wu Y, Gao GF, Leibel SL, Bray W, Ollmann Saphire E, Carlin AF, Zanetti M. Structure-selected RBM immunogens prime polyclonal memory responses that neutralize SARS-CoV-2 variants of concern. PLoS Pathog 2022; 18:e1010686. [PMID: 35862442 PMCID: PMC9302722 DOI: 10.1371/journal.ppat.1010686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 06/17/2022] [Indexed: 11/19/2022] Open
Abstract
Successful control of the COVID-19 pandemic depends on vaccines that prevent transmission. The full-length Spike protein is highly immunogenic but the majority of antibodies do not target the virus: ACE2 interface. In an effort to affect the quality of the antibody response focusing it to the receptor-binding motif (RBM) we generated a series of conformationally-constrained immunogens by inserting solvent-exposed RBM amino acid residues into hypervariable loops of an immunoglobulin molecule. Priming C57BL/6 mice with plasmid (p)DNA encoding these constructs yielded a rapid memory response to booster immunization with recombinant Spike protein. Immune sera antibodies bound strongly to the purified receptor-binding domain (RBD) and Spike proteins. pDNA primed for a consistent response with antibodies efficient at neutralizing authentic WA1 virus and three variants of concern (VOC), B.1.351, B.1.617.2, and BA.1. We demonstrate that immunogens built on structure selection can be used to influence the quality of the antibody response by focusing it to a conserved site of vulnerability shared between wildtype virus and VOCs, resulting in neutralizing antibodies across variants.
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33
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Chen J, Xu W, Li L, Yi L, Jiang Y, Hao P, Xu Z, Zou W, Li P, Gao Z, Tian M, Jin N, Ren L, Li C. Immunogenicity and protective potential of chimeric virus-like particles containing SARS-CoV-2 spike and H5N1 matrix 1 proteins. Front Cell Infect Microbiol 2022; 12:967493. [PMID: 35923799 PMCID: PMC9339902 DOI: 10.3389/fcimb.2022.967493] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 06/28/2022] [Indexed: 12/17/2022] Open
Abstract
Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), has posed a constant threat to human beings and the world economy for more than two years. Vaccination is the first choice to control and prevent the pandemic. However, an effective SARS-CoV-2 vaccine against the virus infection is still needed. This study designed and prepared four kinds of virus-like particles (VLPs) using an insect expression system. Two constructs encoded wild-type SARS-CoV-2 spike (S) fused with or without H5N1 matrix 1 (M1) (S and SM). The other two constructs contained a codon-optimized spike gene and/or M1 gene (mS and mSM) based on protein expression, stability, and ADE avoidance. The results showed that the VLP-based vaccine could induce high SARS-CoV-2 specific antibodies in mice, including specific IgG, IgG1, and IgG2a. Moreover, the mSM group has the most robust ability to stimulate humoral immunity and cellular immunity than the other VLPs, suggesting the mSM is the best immunogen. Further studies showed that the mSM combined with Al/CpG adjuvant could stimulate animals to produce sustained high-level antibodies and establish an effective protective barrier to protect mice from challenges with mouse-adapted strain. The vaccine based on mSM and Al/CpG adjuvant is a promising candidate vaccine to prevent the COVID-19 pandemic.
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Affiliation(s)
- Jing Chen
- College of Veterinary medicine, Key Lab for Zoonoses Research, Ministry of Education, Jilin University, Changchun, China
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Wang Xu
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Letian Li
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Lichao Yi
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yuhang Jiang
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Pengfei Hao
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Zhiqiang Xu
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Wancheng Zou
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Peiheng Li
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Zihan Gao
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Mingyao Tian
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Ningyi Jin
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- *Correspondence: Chang Li, ; Linzhu Ren, ; Ningyi Jin,
| | - Linzhu Ren
- College of Animal Sciences, Key Lab for Zoonoses Research, Ministry of Education, Jilin University, Changchun, China
- *Correspondence: Chang Li, ; Linzhu Ren, ; Ningyi Jin,
| | - Chang Li
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- *Correspondence: Chang Li, ; Linzhu Ren, ; Ningyi Jin,
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34
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Xiang Y, Huang W, Liu H, Sang Z, Nambulli S, Tubiana J, Williams KL, Duprex WP, Schneidman-Duhovny D, Wilson IA, Taylor DJ, Shi Y. Superimmunity by pan-sarbecovirus nanobodies. Cell Rep 2022; 39:111004. [PMID: 35738279 PMCID: PMC9174178 DOI: 10.1016/j.celrep.2022.111004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/09/2022] [Accepted: 06/03/2022] [Indexed: 11/23/2022] Open
Abstract
Vaccine boosters and infection can facilitate the development of SARS-CoV-2 antibodies with improved potency and breadth. Here, we observe superimmunity in a camelid extensively immunized with the SARS-CoV-2 receptor-binding domain (RBD). We rapidly isolate a large repertoire of specific ultra-high-affinity nanobodies that bind strongly to all known sarbecovirus clades using integrative proteomics. These pan-sarbecovirus nanobodies (psNbs) are highly effective against SARS-CoV and SARS-CoV-2 variants, including Omicron, with the best median neutralization potency at single-digit nanograms per milliliter. A highly potent, inhalable, and bispecific psNb (PiN-31) is also developed. Structural determinations of 13 psNbs with the SARS-CoV-2 spike or RBD reveal five epitope classes, providing insights into the mechanisms and evolution of their broad activities. The highly evolved psNbs target small, flat, and flexible epitopes that contain over 75% of conserved RBD surface residues. Their potencies are strongly and negatively correlated with the distance of the epitopes from the receptor binding sites.
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Affiliation(s)
- Yufei Xiang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Zhe Sang
- The University of Pittsburgh and Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA 15213, USA
| | - Sham Nambulli
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jérôme Tubiana
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel; Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Kevin L Williams
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - W Paul Duprex
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA; Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA; The University of Pittsburgh and Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA 15213, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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35
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Troyano-Hernáez P, Reinosa R, Holguín Á. Evolution of SARS-CoV-2 in Spain during the First Two Years of the Pandemic: Circulating Variants, Amino Acid Conservation, and Genetic Variability in Structural, Non-Structural, and Accessory Proteins. Int J Mol Sci 2022; 23:ijms23126394. [PMID: 35742840 PMCID: PMC9223475 DOI: 10.3390/ijms23126394] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 02/04/2023] Open
Abstract
Monitoring SARS-CoV-2’s genetic diversity and emerging mutations in this ongoing pandemic is crucial to understanding its evolution and ensuring the performance of COVID-19 diagnostic tests, vaccines, and therapies. Spain has been one of the main epicenters of COVID-19, reaching the highest number of cases and deaths per 100,000 population in Europe at the beginning of the pandemic. This study aims to investigate the epidemiology of SARS-CoV-2 in Spain and its 18 Autonomous Communities across the six epidemic waves established from February 2020 to January 2022. We report on the circulating SARS-CoV-2 variants in each epidemic wave and Spanish region and analyze the mutation frequency, amino acid (aa) conservation, and most frequent aa changes across each structural/non-structural/accessory viral protein among the Spanish sequences deposited in the GISAID database during the study period. The overall SARS-CoV-2 mutation frequency was 1.24 × 10−5. The aa conservation was >99% in the three types of protein, being non-structural the most conserved. Accessory proteins had more variable positions, while structural proteins presented more aa changes per sequence. Six main lineages spread successfully in Spain from 2020 to 2022. The presented data provide an insight into the SARS-CoV-2 circulation and genetic variability in Spain during the first two years of the pandemic.
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36
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Ding S, Ullah I, Gong SY, Grover JR, Mohammadi M, Chen Y, Vézina D, Beaudoin-Bussières G, Verma VT, Goyette G, Gaudette F, Richard J, Yang D, Smith AB, Pazgier M, Côté M, Abrams C, Kumar P, Mothes W, Uchil PD, Finzi A, Baron C. VE607 stabilizes SARS-CoV-2 Spike in the "RBD-up" conformation and inhibits viral entry. iScience 2022; 25:104528. [PMID: 35677392 PMCID: PMC9164512 DOI: 10.1016/j.isci.2022.104528] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/11/2022] [Accepted: 05/30/2022] [Indexed: 10/26/2022] Open
Abstract
SARS-CoV-2 infection of host cells starts by binding the Spike glycoprotein (S) to the ACE2 receptor. The S-ACE2 interaction is a potential target for therapies against COVID-19 as demonstrated by the development of immunotherapies blocking this interaction. VE607 - a commercially available compound composed of three stereoisomers - was described as an inhibitor of SARS-CoV-1. Here, we show that VE607 broadly inhibits pseudoviral particles bearing the Spike from major VOCs (D614G, Alpha, Beta, Gamma, Delta, Omicron - BA.1, and BA.2) as well as authentic SARS-CoV-2 at low micromolar concentrations. In silico docking, mutational analysis, and smFRET revealed that VE607 binds to the receptor binding domain (RBD)-ACE2 interface and stabilizes RBD in its "up" conformation. Prophylactic treatment with VE607 did not prevent SARS-CoV-2-induced mortality in K18-hACE2 mice, but it did reduce viral replication in the lungs by 37-fold. Thus, VE607 is an interesting lead for drug development for the treatment of SARS-CoV-2 infection.
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Affiliation(s)
- Shilei Ding
- Centre de recherche du CHUM, Montréal, QC, Canada
| | - Irfan Ullah
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shang Yu Gong
- Centre de recherche du CHUM, Montréal, QC, Canada,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Jonathan R. Grover
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Mohammadjavad Mohammadi
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Yaozong Chen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Dani Vézina
- Centre de recherche du CHUM, Montréal, QC, Canada,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Guillaume Beaudoin-Bussières
- Centre de recherche du CHUM, Montréal, QC, Canada,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Vijay Tailor Verma
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, Canada
| | | | | | - Jonathan Richard
- Centre de recherche du CHUM, Montréal, QC, Canada,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Derek Yang
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Amos B. Smith
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Cameron Abrams
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Pradeep D. Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Andrés Finzi
- Centre de recherche du CHUM, Montréal, QC, Canada,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada,Corresponding author
| | - Christian Baron
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, Canada,Corresponding author
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37
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Li T, Zhou B, Li Y, Huang S, Luo Z, Zhou Y, Lai Y, Gautam A, Bourgeau S, Wang S, Bao J, Tan J, Lavillette D, Li D. Isolation, characterization, and structure-based engineering of a neutralizing nanobody against SARS-CoV-2. Int J Biol Macromol 2022; 209:1379-1388. [PMID: 35460753 PMCID: PMC9020654 DOI: 10.1016/j.ijbiomac.2022.04.096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 11/29/2022]
Abstract
SARS-CoV-2 engages with human cells through the binding of its Spike receptor-binding domain (S-RBD) to the receptor ACE2. Molecular blocking of this engagement represents a proven strategy to treat COVID-19. Here, we report a single-chain antibody (nanobody, DL4) isolated from immunized alpaca with picomolar affinity to RBD. DL4 neutralizes SARS-CoV-2 pseudoviruses with an IC50 of 0.101 μg mL-1 (6.2 nM). A crystal structure of the DL4-RBD complex at 1.75-Å resolution unveils the interaction detail and reveals a direct competition mechanism for DL4's ACE2-blocking and hence neutralizing activity. The structural information allows us to rationally design a mutant with higher potency. Our work adds diversity of neutralizing nanobodies against SARS-CoV-2 and should encourage protein engineering to improve antibody affinities in general.
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Affiliation(s)
- Tingting Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China
| | - Bingjie Zhou
- University of CAS, Beijing 101408, China,CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China
| | - Yaning Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China,University of CAS, Beijing 101408, China
| | - Suqiong Huang
- University of CAS, Beijing 101408, China,CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China,College of Pharmacy, Chongqing Medical University, China
| | - Zhipu Luo
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Yuanze Zhou
- Nanjing Crycision Biotech Co., Ltd., Nanjing, China
| | - Yanling Lai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China,University of CAS, Beijing 101408, China
| | - Anupriya Gautam
- University of CAS, Beijing 101408, China,CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China
| | - Salome Bourgeau
- University of CAS, Beijing 101408, China,CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China,Institut National de la Santé et de la Recherche Médicale, École des Hautes Etudes en Santé Publique, Institut de Recherche en Santé, Environnement et Travail, Université de Rennes, F-35000 Rennes, France
| | - Shurui Wang
- Nanjing Crycision Biotech Co., Ltd., Nanjing, China
| | - Juan Bao
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China
| | - Jingquan Tan
- Nanjing Crycision Biotech Co., Ltd., Nanjing, China
| | - Dimitri Lavillette
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China; Pasteurien College, Soochow University, Jiangsu, China.
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China.
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Chuang ST, Papp H, Kuczmog A, Eells R, Condor Capcha JM, Shehadeh LA, Jakab F, Buchwald P. Methylene Blue Is a Nonspecific Protein-Protein Interaction Inhibitor with Potential for Repurposing as an Antiviral for COVID-19. Pharmaceuticals (Basel) 2022; 15:621. [PMID: 35631447 PMCID: PMC9144480 DOI: 10.3390/ph15050621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 02/07/2023] Open
Abstract
We have previously identified methylene blue, a tricyclic phenothiazine dye approved for clinical use for the treatment of methemoglobinemia and for other medical applications as a small-molecule inhibitor of the protein-protein interaction (PPI) between the spike protein of the SARS-CoV-2 coronavirus and ACE2, the first critical step of the attachment and entry of this coronavirus responsible for the COVID-19 pandemic. Here, we show that methylene blue concentration dependently inhibits this PPI for the spike protein of the original strain as well as for those of variants of concern such as the D614G mutant and delta (B.1.617.2) with IC50 in the low micromolar range (1-5 μM). Methylene blue also showed promiscuous activity and inhibited several other PPIs of viral proteins (e.g., HCoV-NL63-ACE2, hepatitis C virus E-CD81) as well as others (e.g., IL-2-IL-2Rα) with similar potency. This nonspecificity notwithstanding, methylene blue inhibited the entry of pseudoviruses bearing the spike protein of SARS-CoV-2 in hACE2-expressing host cells, both for the original strain and the delta variant. It also blocked SARS-CoV-2 (B.1.5) virus replication in Vero E6 cells with an IC50 in the low micromolar range (1.7 μM) when assayed using quantitative PCR of the viral RNA. Thus, while it seems to be a promiscuous PPI inhibitor with low micromolar activity and has a relatively narrow therapeutic index, methylene blue inhibits entry and replication of SARS-CoV-2, including several of its mutant variants, and has potential as a possible inexpensive, broad-spectrum, orally bioactive small-molecule antiviral for the prevention and treatment of COVID-19.
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Affiliation(s)
- Sung-Ting Chuang
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA;
| | - Henrietta Papp
- National Laboratory of Virology, University of Pécs, 7622 Pécs, Hungary; (H.P.); (A.K.); (F.J.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7622 Pécs, Hungary
| | - Anett Kuczmog
- National Laboratory of Virology, University of Pécs, 7622 Pécs, Hungary; (H.P.); (A.K.); (F.J.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7622 Pécs, Hungary
| | | | - Jose M. Condor Capcha
- Division of Cardiology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (J.M.C.C.); (L.A.S.)
- Interdisciplinary Stem Cell Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Lina A. Shehadeh
- Division of Cardiology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (J.M.C.C.); (L.A.S.)
- Interdisciplinary Stem Cell Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ferenc Jakab
- National Laboratory of Virology, University of Pécs, 7622 Pécs, Hungary; (H.P.); (A.K.); (F.J.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7622 Pécs, Hungary
| | - Peter Buchwald
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA;
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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Ng TI, Correia I, Seagal J, Degoey DA, Schrimpf MR, Hardee DJ, Noey EL, Kati WM. Antiviral Drug Discovery for the Treatment of COVID-19 Infections. Viruses 2022; 14:961. [PMID: 35632703 PMCID: PMC9143071 DOI: 10.3390/v14050961] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 02/04/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a recently emerged human coronavirus. COVID-19 vaccines have proven to be successful in protecting the vaccinated from infection, reducing the severity of disease, and deterring the transmission of infection. However, COVID-19 vaccination faces many challenges, such as the decline in vaccine-induced immunity over time, and the decrease in potency against some SARS-CoV-2 variants including the recently emerged Omicron variant, resulting in breakthrough infections. The challenges that COVID-19 vaccination is facing highlight the importance of the discovery of antivirals to serve as another means to tackle the pandemic. To date, neutralizing antibodies that block viral entry by targeting the viral spike protein make up the largest class of antivirals that has received US FDA emergency use authorization (EUA) for COVID-19 treatment. In addition to the spike protein, other key targets for the discovery of direct-acting antivirals include viral enzymes that are essential for SARS-CoV-2 replication, such as RNA-dependent RNA polymerase and proteases, as judged by US FDA approval for remdesivir, and EUA for Paxlovid (nirmatrelvir + ritonavir) for treating COVID-19 infections. This review presents an overview of the current status and future direction of antiviral drug discovery for treating SARS-CoV-2 infections, covering important antiviral targets such as the viral spike protein, non-structural protein (nsp) 3 papain-like protease, nsp5 main protease, and the nsp12/nsp7/nsp8 RNA-dependent RNA polymerase complex.
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40
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Gruell H, Vanshylla K, Weber T, Barnes CO, Kreer C, Klein F. Antibody-Mediated Neutralization of SARS-CoV-2. Immunity 2022; 55:925-944. [PMID: 35623355 PMCID: PMC9118976 DOI: 10.1016/j.immuni.2022.05.005] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 11/28/2022]
Abstract
Neutralizing antibodies can block infection, clear pathogens, and are essential to provide long-term immunity. Since the onset of the pandemic, SARS-CoV-2 neutralizing antibodies have been comprehensively investigated and critical information on their development, function, and potential use to prevent and treat COVID-19 have been revealed. With the emergence of SARS-CoV-2 immune escape variants, humoral immunity is being challenged, and a detailed understanding of neutralizing antibodies is essential to guide vaccine design strategies as well as antibody-mediated therapies. In this review, we summarize some of the key findings on SARS-CoV-2 neutralizing antibodies, with a focus on their clinical application.
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Affiliation(s)
- Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Kanika Vanshylla
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Timm Weber
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Christopher O Barnes
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.
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41
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Tolan NV, Sherman AC, Zhou G, Nabel KG, Desjardins M, Melanson S, Kanjilal S, Moheed S, Kupelian J, Kaufman RM, Ryan ET, LaRocque RC, Branda JA, Dighe AS, Abraham J, Baden LR, Charles RC, Turbett SE. The Effect of Vaccine Type and SARS-CoV-2 Lineage on Commercial SARS-CoV-2 Serologic and Pseudotype Neutralization Assays in mRNA Vaccine Recipients. Microbiol Spectr 2022; 10:e0021122. [PMID: 35311584 PMCID: PMC9045317 DOI: 10.1128/spectrum.00211-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/20/2022] [Indexed: 12/24/2022] Open
Abstract
The use of anti-spike (S) serologic assays as surrogate measurements of SARS-CoV-2 vaccine induced immunity will be an important clinical and epidemiological tool. The characteristics of a commercially available anti-S antibody assay (Roche Elecsys anti-SARS-CoV-2 S) were evaluated in a cohort of vaccine recipients. Levels were correlated with pseudotype neutralizing antibodies (NAb) across SARS-CoV-2 variants. We recruited adults receiving a two-dose series of mRNA-1273 or BNT162b2 and collected serum at scheduled intervals up to 8 months post-first vaccination. Anti-S and NAb levels were measured, and correlation was evaluated by (i) vaccine type and (ii) SARS-CoV-2 variant (wild-type, Alpha, Beta, Gamma, and three constructs Day 146*, Day 152*, and RBM-2). Forty-six mRNA vaccine recipients were enrolled. mRNA-1273 vaccine recipients had higher peak anti-S and NAb levels compared with BNT162b2 (P < 0.001 for anti-S levels; P < 0.05 for NAb levels). When anti-S and NAb levels were compared, there was good correlation (all r values ≥ 0.85) in both BNT162b2 and mRNA-1273 vaccine recipients across all evaluated variants; however, these correlations were nonlinear in nature. Lower correlation was identified between anti-S and NAb for the Beta variant (r = 0.88) compared with the wild-type (WT) strain (r = 0.94). Finally, the degree of neutralizing activity at any given anti-S level was lower for each variant compared with that of the WT strain, (P < 0.001). Although the Roche anti-S assay correlates well with NAb levels, this association is affected by vaccine type and SARS-CoV-2 variant. These variables must be considered when interpreting anti-S levels. IMPORTANCE We evaluated anti-spike antibody concentrations in healthy mRNA vaccinated individuals and compared these concentrations to values obtained from pseudotype neutralization assays targeting SARS-CoV-2 variants of concern to determine how well anti-spike antibodies correlate with neutralizing titers, which have been used as a marker of immunity from COVID-19 infection. We found high peak anti-spike concentrations in these individuals, with significantly higher levels seen in mRNA-1273 vaccine recipients. When we compared anti-spike and pseudotype neuralization titers, we identified good correlation; however, this correlation was affected by both vaccine type and variant, illustrating the difficulty of applying a "one size fits all" approach to anti-spike result interpretation. Our results support CDC recommendations to discourage anti-spike antibody testing to assess for immunity after vaccination and cautions providers in their interpretations of these results as a surrogate of protection in COVID-vaccinated individuals.
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Affiliation(s)
- Nicole V. Tolan
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Amy C. Sherman
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Guohai Zhou
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | | | - Michaël Desjardins
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Stacy Melanson
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Sanjat Kanjilal
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Serina Moheed
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - John Kupelian
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Richard M. Kaufman
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Edward T. Ryan
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Regina C. LaRocque
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - John A. Branda
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Anand S. Dighe
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan Abraham
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Lindsey R. Baden
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Richelle C. Charles
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sarah E. Turbett
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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Zhou T, Wang L, Misasi J, Pegu A, Zhang Y, Harris DR, Olia AS, Talana CA, Yang ES, Chen M, Choe M, Shi W, Teng IT, Creanga A, Jenkins C, Leung K, Liu T, Stancofski ESD, Stephens T, Zhang B, Tsybovsky Y, Graham BS, Mascola JR, Sullivan NJ, Kwong PD. Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529. Science 2022; 376:eabn8897. [PMID: 35324257 PMCID: PMC9580340 DOI: 10.1126/science.abn8897] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/19/2022] [Indexed: 12/14/2022]
Abstract
The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (Omicron) variant and its resistance to neutralization by vaccinee and convalescent sera are driving a search for monoclonal antibodies with potent neutralization. To provide insight into effective neutralization, we determined cryo-electron microscopy structures and evaluated receptor binding domain (RBD) antibodies for their ability to bind and neutralize B.1.1.529. Mutations altered 16% of the B.1.1.529 RBD surface, clustered on an RBD ridge overlapping the angiotensin-converting enzyme 2 (ACE2)-binding surface and reduced binding of most antibodies. Substantial inhibitory activity was retained by select monoclonal antibodies-including A23-58.1, B1-182.1, COV2-2196, S2E12, A19-46.1, S309, and LY-CoV1404-that accommodated these changes and neutralized B.1.1.529. We identified combinations of antibodies with synergistic neutralization. The analysis revealed structural mechanisms for maintenance of potent neutralization against emerging variants.
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Affiliation(s)
- Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John Misasi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amarendra Pegu
- 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
| | - Darcy R. Harris
- 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
| | - Chloe Adrienna Talana
- 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
| | - Man Chen
- 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
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian Creanga
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Claudia Jenkins
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tracy Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erik-Stephane D. Stancofski
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Barney S. Graham
- 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
| | - Nancy J. Sullivan
- 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
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Ruocco V, Strasser R. Transient Expression of Glycosylated SARS-CoV-2 Antigens in Nicotiana benthamiana. Plants (Basel) 2022; 11:1093. [PMID: 35448821 PMCID: PMC9033091 DOI: 10.3390/plants11081093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 12/14/2022]
Abstract
The current COVID-19 pandemic very dramatically shows that the world lacks preparedness for novel viral diseases. In addition to newly emerging viruses, many known pathogenic viruses such as influenza are constantly evolving, leading to frequent outbreaks with severe diseases and deaths. Hence, infectious viruses are a recurrent burden to our daily life, and powerful strategies to stop the spread of human pathogens and disease progression are of utmost importance. Transient plant-based protein expression is a technology that allows fast and highly flexible manufacturing of recombinant viral proteins and, thus, can contribute to infectious disease detection and prevention. This review highlights recent progress in the transient production of viral glycoproteins in N. benthamiana with a focus on SARS-CoV-2-derived viral antigens.
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Affiliation(s)
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria;
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44
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Jen GHH, Yen AMF, Hsu CY, Chen SLS, Chen THH. A pre-symptomatic incubation model for precision strategies of screening, quarantine, and isolation based on imported COVID-19 cases in Taiwan. Sci Rep 2022; 12:6053. [PMID: 35411061 PMCID: PMC8998162 DOI: 10.1038/s41598-022-09863-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 03/21/2022] [Indexed: 12/31/2022] Open
Abstract
Facing the emerging COVID viral variants and the uneven distribution of vaccine worldwide, imported pre-symptomatic COVID-19 cases play a pivotal role in border control strategies. A stochastic disease process and computer simulation experiments with Bayesian underpinning was therefore developed to model pre-symptomatic disease progression during incubation period on which we were based to provide precision strategies for containing the resultant epidemic caused by imported COVID-19 cases. We then applied the proposed model to data on 1051 imported COVID-19 cases among inbound passengers to Taiwan between March 2020 and April 2021. The overall daily rate (per 100,000) of pre-symptomatic COVID-19 cases was estimated as 106 (95% credible interval (CrI): 95–117) in March–June 2020, fell to 37 (95% CrI: 28–47) in July–September 2020 (p < 0.0001), resurged to 141 (95% CrI: 118–164) in October–December 2020 (p < 0.0001), and declined to 90 (95% CrI: 73–108) in January–April 2021 (p = 0.0004). Given the median dwelling time, over 82% cases would progress from pre-symptomatic to symptomatic phase in 5-day quarantine. The time required for quarantine given two real-time polymerase chain reaction (RT-PCR) tests depends on the risk of departing countries, testing and quarantine strategies, and whether the passengers have vaccine jabs. Our proposed four-compartment stochastic process and computer simulation experiments design underpinning Bayesian MCMC algorithm facilitated the development of precision strategies for imported COVID-19 cases.
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Affiliation(s)
- Amanda E Dugan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amanda L Peiffer
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA. .,The Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,The Koch Integrative Cancer Research Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
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46
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Wang CY, Hwang KP, Kuo HK, Peng WJ, Shen YH, Kuo BS, Huang JH, Liu H, Ho YH, Lin F, Ding S, Liu Z, Wu HT, Huang CT, Lee YJ, Liu MC, Yang YC, Lu PL, Tsai HC, Lee CH, Shi ZY, Liu CE, Liao CH, Chang FY, Cheng HC, Wang FD, Hou KL, Cheng J, Wang MS, Yang YT, Chiu HC, Jiang MH, Shih HY, Shen HY, Chang PY, Lan YR, Chen CT, Lin YL, Liang JJ, Liao CC, Chou YC, Morris MK, Hanson CV, Guirakhoo F, Hellerstein M, Yu HJ, King CC, Kemp T, Heppner DG, Monath TP. A multitope SARS-COV-2 vaccine provides long-lasting B cell and T cell immunity against Delta and Omicron variants. J Clin Invest 2022; 132:157707. [PMID: 35316221 PMCID: PMC9106357 DOI: 10.1172/jci157707] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/16/2022] [Indexed: 11/19/2022] Open
Abstract
Background The Delta and Omicron variants of SARS-CoV-2 are currently responsible for breakthrough infections due to waning immunity. We report phase I/II trial results of UB-612, a multitope subunit vaccine containing S1-RBD-sFc protein and rationally designed promiscuous peptides representing sarbecovirus conserved helper T cell and cytotoxic T lymphocyte epitopes on the nucleocapsid (N), membrane (M), and spike (S2) proteins. Method We conducted a phase I primary 2-dose (28 days apart) trial of 10, 30, or 100 μg UB-612 in 60 healthy young adults 20 to 55 years old, and 50 of them were boosted with 100 μg of UB-612 approximately 7 to 9 months after the second dose. A separate placebo-controlled and randomized phase II study was conducted with 2 doses of 100 μg of UB-612 (n = 3,875, 18–85 years old). We evaluated interim safety and immunogenicity of phase I until 14 days after the third (booster) dose and of phase II until 28 days after the second dose. Results No vaccine-related serious adverse events were recorded. The most common solicited adverse events were injection site pain and fatigue, mostly mild and transient. In both trials, UB-612 elicited respective neutralizing antibody titers similar to a panel of human convalescent sera. The most striking findings were long-lasting virus-neutralizing antibodies and broad T cell immunity against SARS-CoV-2 variants of concern (VoCs), including Delta and Omicron, and a strong booster-recalled memory immunity with high cross-reactive neutralizing titers against the Delta and Omicron VoCs. Conclusion UB-612 has presented a favorable safety profile, potent booster effect against VoCs, and long-lasting B and broad T cell immunity that warrants further development for both primary immunization and heterologous boosting of other COVID-19 vaccines. Trial Registration ClinicalTrials.gov: NCT04545749, NCT04773067, and NCT04967742. Funding UBI Asia, Vaxxinity Inc., and Taiwan Centers for Disease Control, Ministry of Health and Welfare.
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Affiliation(s)
| | - Kao-Pin Hwang
- Division of Infectious Diseases, China Medical University Children's Hospital, Taichung City, Taiwan
| | - Hui-Kai Kuo
- Designed Vaccine Translation Medical Center, UBI Asia, Hsinchu, Taiwan
| | - Wen-Jiun Peng
- Administrative Management Center, UBI Asia, Hsinchu, Taiwan
| | - Yea-Huei Shen
- Medical and Clinical Operation, StatPlus, Taipei, Taiwan
| | - Be-Sheng Kuo
- Preclinical and ImmunoPharmacology Center, UBI Asia, Hsinchu, Taiwan
| | | | | | - Yu-Hsin Ho
- Regulatory Affairs, UBI Asia, Hsinchu, Taiwan
| | - Feng Lin
- R&D Center, United Bioimedical, Inc., Hauppauge, United States of America
| | - Shuang Ding
- R&D Center, United Biomedical, Inc., Hauppauge, United States of America
| | - Zhi Liu
- R&D Center, United Biomedical, Inc., Hauppauge, United States of America
| | | | - Ching-Tai Huang
- Department of Infectious Disease, Chang Gung University, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Yuarn-Jang Lee
- Division of Infectious Diseases, Taipei Medical University Hospital, Taipei, Taiwan
| | - Ming-Che Liu
- R&D, Taipei Medical University Hospital, Taipei, Taiwan
| | - Yi-Ching Yang
- Ministry of Health and Welfare, National Cheng Kung University and Hospital, Tainan, Taiwan
| | - Po-Liang Lu
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Hung-Chin Tsai
- School of Medicine, Kaohsiung Veterans General Hospital, Kaoshiung, Taiwan
| | - Chen-Hsiang Lee
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Zhi-Yuan Shi
- Department of Medical Affairs, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chun-Eng Liu
- Department of Medical Affairs, Changhua Christian Hospital, Changhua, Taiwan
| | - Chun-Hsing Liao
- Department of Medical Affairs, Far Eastern Memorial Hospital, New Taipei, Taiwan
| | - Feng-Yee Chang
- Department of Internal Medicine, Tri-Service General Hospital, Taipei, Taiwan
| | - Hsiang-Cheng Cheng
- Department of Medical Affairs, Tri-Service General Hospital, Taipei, Taiwan
| | - Fu-Der Wang
- Department of Internal Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Kuo-Liang Hou
- Department of Preclinical Research, UBI Asia, Hsinchu, Taiwan
| | - Jennifer Cheng
- Department of Preclinical Research, UBI Asia, Hsinchu, Taiwan
| | - Min-Sheng Wang
- Department of Clinical Research, UBI Asia, Hsinchu, Taiwan
| | - Ya-Ting Yang
- Department of Preclinical Research, UBI Asia, Hsinchu, Taiwan
| | - Han-Chen Chiu
- Department of Medical Affairs, UBI Asia, Hsinchu, Taiwan
| | - Ming-Han Jiang
- Department of Preclinical Research, UBI Asia, Hsinchu, Taiwan
| | - Hao-Yu Shih
- Department of Preclinical Research, UBI Asia, Hsinchu, Taiwan
| | - Hsuan-Yu Shen
- Department of Clinical Research, UBI Asia, Hsinchu, Taiwan
| | - Po-Yen Chang
- Department of Clinical Research, UBI Asia, Hsinchu, Taiwan
| | - Yu-Rou Lan
- Department of Preclinical Research, UBI Asia, Hsinchu, Taiwan
| | - Chi-Tian Chen
- Biostatistics and Data Management, StatPlus, Taipei, Taiwan
| | - Yi-Ling Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jian-Jong Liang
- Biomedical Translation Research Center (bioTReC) Academia Sinica, Taipei, Taiwan
| | - Chun-Che Liao
- Department of Medical Affairs, Biomedical Translation Research Center (bioTReC) Academia Sinica, Taipei, Taiwan
| | - Yu-Chi Chou
- Department of Statistics, Biomedical Translation Research Center (bioTReC) Academia Sinica, Taipei, Taiwan
| | - Mary Kate Morris
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, United States of America
| | - Carl V Hanson
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, United States of America
| | - Farshad Guirakhoo
- Department of Clinical Research, Vaxxinity Inc., Dallas, United States of America
| | - Michael Hellerstein
- Department of Preclinical Research, Vaxxinity Inc., Dallas, United States of America
| | - Hui Jing Yu
- Department of Clinical Research, Vaxxinity Inc., Dallas, United States of America
| | - Chwan-Chuen King
- Department of Medical, Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Tracy Kemp
- Department of Clinical Research, Vaxxinity, Inc., Dallas, United States of America
| | - D Gray Heppner
- Department of Clinical Research, Vaxxinity, Inc., Dallas, United States of America
| | - Thomas P Monath
- Department of Clinical Research, Vaxxinity, Inc., Dallas, United States of America
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Abstract
The vaccine and drug discovery responses to COVID-19 have worked far better than could have been imagined. Yet by the end of 2021, more than 5 million people had died, and the pandemic continues to evolve and rage globally. This Review will describe how each of the vaccines, antibody therapies, and antiviral drugs that have been approved to date were built on decades of investment in technology and basic science. We will caution that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has so far proven a straightforward test of our pandemic preparedness, and we will recommend steps we should undertake now to prepare for, to minimize the effects of, and ideally to prevent future pandemics. Other Reviews in this series describe the interactions of SARS-CoV-2 with the immune system and those therapies that target the host response to infection.
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Affiliation(s)
- Aled M Edwards
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Ralph S Baric
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.,Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jeffrey B Ulmer
- TechImmune, Newport Beach, CA 92660, USA.,Immorna Biotherapeutics, Durham, NC 27703, USA
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48
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Cui Z, Liu P, Wang N, Wang L, Fan K, Zhu Q, Wang K, Chen R, Feng R, Jia Z, Yang M, Xu G, Zhu B, Fu W, Chu T, Feng L, Wang Y, Pei X, Yang P, Xie XS, Cao L, Cao Y, Wang X. Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron. Cell 2022; 185:860-871.e13. [PMID: 35120603 DOI: 10.1016/j.cell.2022.01.019] [Citation(s) in RCA: 250] [Impact Index Per Article: 125.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/10/2022] [Accepted: 01/20/2022] [Indexed: 12/11/2022]
Abstract
The SARS-CoV-2 Omicron variant with increased fitness is spreading rapidly worldwide. Analysis of cryo-EM structures of the spike (S) from Omicron reveals amino acid substitutions forging interactions that stably maintain an active conformation for receptor recognition. The relatively more compact domain organization confers improved stability and enhances attachment but compromises the efficiency of the viral fusion step. Alterations in local conformation, charge, and hydrophobic microenvironments underpin the modulation of the epitopes such that they are not recognized by most NTD- and RBD-antibodies, facilitating viral immune escape. Structure of the Omicron S bound with human ACE2, together with the analysis of sequence conservation in ACE2 binding region of 25 sarbecovirus members, as well as heatmaps of the immunogenic sites and their corresponding mutational frequencies, sheds light on conserved and structurally restrained regions that can be used for the development of broad-spectrum vaccines and therapeutics.
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49
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Ding S, Gong SY, Grover J, Mohammadi M, Chen Y, Vézina D, Beaudoin-Bussières G, Verma VT, Goyette G, Richard J, Yang D, Smith AB, Pazgier M, Côté M, Abrams C, Mothes W, Finzi A, Baron C. VE607 Stabilizes SARS-CoV-2 Spike In the "RBD-up" Conformation and Inhibits Viral Entry. bioRxiv 2022:2022.02.03.479007. [PMID: 35233570 PMCID: PMC8887069 DOI: 10.1101/2022.02.03.479007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
SARS-CoV-2 infection of host cells starts by binding of the Spike glycoprotein (S) to the ACE2 receptor. The S-ACE2 interaction is a potential target for therapies against COVID-19 as demonstrated by the development of immunotherapies blocking this interaction. Here, we present the commercially available VE607, comprised of three stereoisomers, that was originally described as an inhibitor of SARS-CoV-1. We show that VE607 specifically inhibits infection of SARS-CoV-1 and SARS-CoV-2 S-expressing pseudoviral particles as well as authentic SARS-CoV-2. VE607 stabilizes the receptor binding domain (RBD) in its "up" conformation. In silico docking and mutational analysis map the VE607 binding site at the RBD-ACE2 interface. The IC 50 values are in the low micromolar range for pseudoparticles derived from SARS-CoV-2 Wuhan/D614G as well as from variants of concern (Alpha, Beta, Gamma, Delta and Omicron), suggesting that VE607 has potential for the development of drugs against SARS-CoV-2 infections.
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50
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Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus is continuously evolving, and this poses a major threat to antibody therapies and currently authorized Coronavirus Disease 2019 (COVID-19) vaccines. It is therefore of utmost importance to investigate and predict the putative mutations on the spike protein that confer immune evasion. Antibodies are key components of the human immune system’s response to SARS-CoV-2, and the spike protein is a prime target of neutralizing antibodies (nAbs) as it plays critical roles in host cell recognition, fusion, and virus entry. The potency of therapeutic antibodies and vaccines partly depends on how readily the virus can escape neutralization. Recent structural and functional studies have mapped the epitope landscape of nAbs on the spike protein, which illustrates the footprints of several nAbs and the site of escape mutations. In this review, we discuss (1) the emerging SARS-CoV-2 variants; (2) the structural basis for antibody-mediated neutralization of SARS-CoV-2 and nAb classification; and (3) identification of the RBD escape mutations for several antibodies that resist antibody binding and neutralization. These escape maps are a valuable tool to predict SARS-CoV-2 fitness, and in conjunction with the structures of the spike-nAb complex, they can be utilized to facilitate the rational design of escape-resistant antibody therapeutics and vaccines.
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