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Witte L, Baharani VA, Schmidt F, Wang Z, Cho A, Raspe R, Guzman-Cardozo C, Muecksch F, Canis M, Park DJ, Gaebler C, Caskey M, Nussenzweig MC, Hatziioannou T, Bieniasz PD. Epistasis lowers the genetic barrier to SARS-CoV-2 neutralizing antibody escape. Nat Commun 2023; 14:302. [PMID: 36653360 PMCID: PMC9849103 DOI: 10.1038/s41467-023-35927-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023] Open
Abstract
Waves of SARS-CoV-2 infection have resulted from the emergence of viral variants with neutralizing antibody resistance mutations. Simultaneously, repeated antigen exposure has generated affinity matured B cells, producing broadly neutralizing receptor binding domain (RBD)-specific antibodies with activity against emergent variants. To determine how SARS-CoV-2 might escape these antibodies, we subjected chimeric viruses encoding spike proteins from ancestral, BA.1 or BA.2 variants to selection by 40 broadly neutralizing antibodies. We identify numerous examples of epistasis, whereby in vitro selected and naturally occurring substitutions in RBD epitopes that do not confer antibody resistance in the Wuhan-Hu-1 spike, do so in BA.1 or BA.2 spikes. As few as 2 or 3 of these substitutions in the BA.5 spike, confer resistance to nearly all of the 40 broadly neutralizing antibodies, and substantial resistance to plasma from most individuals. Thus, epistasis facilitates the acquisition of resistance to antibodies that remained effective against early omicron variants.
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Affiliation(s)
- Leander Witte
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, 10065, USA
| | - Viren A Baharani
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, 10065, USA
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, 10065, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - Raphael Raspe
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | | | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, 10065, USA
| | - Marie Canis
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, 10065, USA
| | - Debby J Park
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, 10065, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, 10065, USA.
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, 10065, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, 10065, USA.
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152
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Karges J, Giardini MA, Blacque O, Woodworth B, Siqueira-Neto JL, Cohen SM. Enantioselective inhibition of the SARS-CoV-2 main protease with rhenium(i) picolinic acid complexes. Chem Sci 2023; 14:711-720. [PMID: 36741526 PMCID: PMC9848156 DOI: 10.1039/d2sc05473f] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 12/12/2022] [Indexed: 12/14/2022] Open
Abstract
Infections of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have triggered a global pandemic with millions of deaths worldwide. Herein, the synthesis of functionalized Re(i) tricarbonyl complexes as inhibitors of the SARS-CoV-2 main protease, also referred to as the 3-chymotrypsin-like protease (3CLpro), is presented. The metal complexes were found to inhibit the activity of the enzyme with IC50 values in the low micromolar range. Mass spectrometry revealed that the metal complexes formed a coordinate covalent bond with the enzyme. Chiral separation of the enantiomers of the lead compound showed that one enantiomer was significantly more active than the other, consistent with specific binding and much like that observed for conventional organic small molecule inhibitors and druglike compounds. Evaluation of the lead compound against SARS-CoV-2 in a cell-based infection assay confirmed enantiospecific inhibition against the virus. This study represents a significant advancement in the use of metal complexes as coordinate covalent inhibitors of enzymes, as well as a novel starting point for the development of novel SARS-CoV-2 inhibitors.
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Affiliation(s)
- Johannes Karges
- Department of Chemistry and Biochemistry, University of CaliforniaLa JollaSan DiegoCalifornia 92093USA
| | - Miriam A. Giardini
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of CaliforniaLa JollaSan DiegoCalifornia 92093USA
| | - Olivier Blacque
- Department of Chemistry, University of ZurichWinterthurerstrasse 190CH-8057ZurichSwitzerland
| | - Brendon Woodworth
- Department of Medicine, Division of Infectious Diseases, University of California San DiegoLa JollaCalifornia 92093USA
| | - Jair L. Siqueira-Neto
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of CaliforniaLa JollaSan DiegoCalifornia 92093USA
| | - Seth M. Cohen
- Department of Chemistry and Biochemistry, University of CaliforniaLa JollaSan DiegoCalifornia 92093USA
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153
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Kumar N, Kaushik R, Zhang KYJ, Uversky VN, Sahu U, Sood R, Bhatia S. A novel consensus-based computational pipeline for screening of antibody therapeutics for efficacy against SARS-CoV-2 variants of concern including Omicron variant. Proteins 2023; 91:798-806. [PMID: 36629264 DOI: 10.1002/prot.26467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 11/11/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
Multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to evolve carrying flexible amino acid substitutions in the spike protein's receptor binding domain (RBD). These substitutions modify the binding of the SARS-CoV-2 to human angiotensin-converting enzyme 2 (hACE2) receptor and have been implicated in altered host fitness, transmissibility, and efficacy against antibody therapeutics and vaccines. Reliably predicting the binding strength of SARS-CoV-2 variants RBD to hACE2 receptor and neutralizing antibodies (NAbs) can help assessing their fitness, and rapid deployment of effective antibody therapeutics, respectively. Here, we introduced a two-step computational framework with 3-fold validation that first identified dissociation constant as a reliable predictor of binding affinity in hetero- dimeric and trimeric protein complexes. The second step implements dissociation constant as descriptor of the binding strengths of SARS-CoV-2 variants RBD to hACE2 and NAbs. Then, we examined several variants of concerns (VOCs) such as Alpha, Beta, Gamma, Delta, and Omicron and demonstrated that these VOCs RBD bind to the hACE2 with enhanced affinity. Furthermore, the binding affinity of Omicron variant's RBD was reduced with majority of the RBD-directed NAbs, which is highly consistent with the experimental neutralization data. By studying the atomic contacts between RBD and NAbs, we revealed the molecular footprints of four NAbs (GH-12, P2B-1A1, Asarnow_3D11, and C118)-that may likely neutralize the recently emerged Omicron variant-facilitating enhanced binding affinity. Finally, our findings suggest a computational pathway that could aid researchers identify a range of current NAbs that may be effective against emerging SARS-CoV-2 variants.
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Affiliation(s)
- Naveen Kumar
- Zoonotic Diseases Group, ICAR-National Institute of High Security Animal Diseases, Bhopal, India
| | - Rahul Kaushik
- Biotechnology Research Center, Technology Innovation Institute, Abu Dhabi, UAE.,Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center 'Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences', Pushchino, Russia
| | - Upasana Sahu
- Zoonotic Diseases Group, ICAR-National Institute of High Security Animal Diseases, Bhopal, India
| | - Richa Sood
- Zoonotic Diseases Group, ICAR-National Institute of High Security Animal Diseases, Bhopal, India
| | - Sandeep Bhatia
- Zoonotic Diseases Group, ICAR-National Institute of High Security Animal Diseases, Bhopal, India
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154
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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 BIOINFORMATICS AND BIOTECHNOLOGY 2023; 4:e42700. [PMID: 36688013 PMCID: PMC9843602 DOI: 10.2196/42700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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155
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Zhao Y, Ni W, Liang S, Dong L, Xiang M, Cai Z, Niu D, Zhang Q, Wang D, Zheng Y, Zhang Z, Zhou D, Guo W, Pan Y, Wu X, Yang Y, Jing Z, Jiang Y, Chen Y, Yan H, Zhou Y, Xu K, Lan K. Vaccination with S pan, an antigen guided by SARS-CoV-2 S protein evolution, protects against challenge with viral variants in mice. Sci Transl Med 2023; 15:eabo3332. [PMID: 36599007 DOI: 10.1126/scitranslmed.abo3332] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
SARS-CoV-2 continues to accumulate mutations to evade immunity, leading to breakthrough infections after vaccination. How researchers can anticipate the evolutionary trajectory of the virus in advance in the design of next-generation vaccines requires investigation. Here, we performed a comprehensive study of 11,650,487 SARS-CoV-2 sequences, which revealed that the SARS-CoV-2 spike (S) protein evolved not randomly but into directional paths of either high infectivity plus low immune resistance or low infectivity plus high immune resistance. The viral infectivity and immune resistance of variants are generally incompatible, except for limited variants such as Beta and Kappa. The Omicron variant has the highest immune resistance but showed high infectivity in only one of the tested cell lines. To provide cross-clade immunity against variants that undergo diverse evolutionary pathways, we designed a new pan-vaccine antigen (Span). Span was designed by analyzing the homology of 2675 SARS-CoV-2 S protein sequences from the NCBI database before the Delta variant emerged. The refined Span protein harbors high-frequency residues at given positions that reflect cross-clade generality in sequence evolution. Compared with a prototype wild-type (Swt) vaccine, which, when administered to mice, induced serum with decreased neutralization activity against emerging variants, Span vaccination of mice elicited broad immunity to a wide range of variants, including those that emerged after our design. Moreover, vaccinating mice with a heterologous Span booster conferred complete protection against lethal infection with the Omicron variant. Our results highlight the importance and feasibility of a universal vaccine to fight against SARS-CoV-2 antigenic drift.
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Affiliation(s)
- Yongliang Zhao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China
| | - Wenjia Ni
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China
| | - Simeng Liang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China
| | - Lianghui Dong
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China
| | - Min Xiang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China
| | - Zeng Cai
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China.,Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University, Wuhan 430072, Hubei, P.R. China
| | - Danping Niu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China
| | - Qiuhan Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China
| | - Dehe Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China
| | - Yucheng Zheng
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China
| | - Zhen Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China
| | - Dan Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China
| | - Wenhua Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China
| | - Yongbing Pan
- Wuhan Institute of Biological Products Co. Ltd., Wuhan 430207, Hubei, P.R. China
| | - Xiaoli Wu
- Wuhan Institute of Biological Products Co. Ltd., Wuhan 430207, Hubei, P.R. China
| | - Yimin Yang
- Wuhan Institute of Biological Products Co. Ltd., Wuhan 430207, Hubei, P.R. China
| | - Zhaofei Jing
- Wuhan Institute of Biological Products Co. Ltd., Wuhan 430207, Hubei, P.R. China
| | - Yongzhong Jiang
- Hubei Provincial Center for Diseases Control and Prevention, Wuhan 430079, Hubei, P.R. China
| | - Yu Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China.,Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University, Wuhan 430072, Hubei, P.R. China
| | - Huan Yan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China.,Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University, Wuhan 430072, Hubei, P.R. China
| | - Yu Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China.,Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China.,Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430072, Hubei, P.R. China
| | - Ke Xu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China.,Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University, Wuhan 430072, Hubei, P.R. China.,Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China.,Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University, Wuhan 430072, Hubei, P.R. China.,Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, Hubei, P.R. China.,Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430072, Hubei, P.R. China
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156
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Lan S, Neilsen G, Slack RL, Cantara WA, Castaner AE, Lorson ZC, Lulkin N, Zhang H, Lee J, Cilento ME, Tedbury PR, Sarafianos SG. Nirmatrelvir Resistance in SARS-CoV-2 Omicron_BA.1 and WA1 Replicons and Escape Strategies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2022.12.31.522389. [PMID: 36656782 PMCID: PMC9844013 DOI: 10.1101/2022.12.31.522389] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The antiviral component of Paxlovid, nirmatrelvir (NIR), forms a covalent bond with Cys145 of SARS-CoV-2 nsp5. To explore NIR resistance we designed mutations to impair binding of NIR over substrate. Using 12 Omicron (BA.1) and WA.1 SARS-CoV-2 replicons, cell-based complementation and enzymatic assays, we showed that in both strains, E166V imparted high NIR resistance (∼55-fold), with major decrease in WA1 replicon fitness (∼20-fold), but not BA.1 (∼2-fold). WA1 replicon fitness was restored by L50F. These differences may contribute to a potentially lower barrier to resistance in Omicron than WA1. E166V is rare in untreated patients, albeit more prevalent in paxlovid-treated EPIC-HR clinical trial patients. Importantly, NIR-resistant replicons with E166V or E166V/L50F remained susceptible to a) the flexible GC376, and b) PF-00835231, which forms additional interactions. Molecular dynamics simulations show steric clashes between the rigid and bulky NIR t-butyl and β-branched V166 distancing the NIR warhead from its Cys145 target. In contrast, GC376, through "wiggling and jiggling" accommodates V166 and still covalently binds Cys145. PF-00835231 uses its strategically positioned methoxy-indole to form a β-sheet and overcome E166V. Drug design based on strategic flexibility and main chain-targeting may help develop second-generation nsp5-targeting antivirals efficient against NIR-resistant viruses.
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157
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Verstraete MM, Heinkel F, Li J, Cao S, Tran A, Halverson EC, Gene R, Stangle E, Silva-Moreno B, Arrafi S, Bavananthasivam J, Fung M, Eji-Lasisi M, Masterman S, Xanthoudakis S, Dixit S, Babcook J, Clavette B, Fogg M, Escobar-Cabrera E. Multivalent IgM scaffold enhances the therapeutic potential of variant-agnostic ACE2 decoys against SARS-CoV-2. MAbs 2023; 15:2212415. [PMID: 37229608 DOI: 10.1080/19420862.2023.2212415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023] Open
Abstract
As immunological selection for escape mutants continues to give rise to future SARS-CoV-2 variants, novel universal therapeutic strategies against ACE2-dependent viruses are needed. Here we present an IgM-based decavalent ACE2 decoy that has variant-agnostic efficacy. In immuno-, pseudovirus, and live virus assays, IgM ACE2 decoy had potency comparable or superior to leading SARS-CoV-2 IgG-based mAb therapeutics evaluated in the clinic, which were variant-sensitive in their potency. We found that increased ACE2 valency translated into increased apparent affinity for spike protein and superior potency in biological assays when decavalent IgM ACE2 was compared to tetravalent, bivalent, and monovalent ACE2 decoys. Furthermore, a single intranasal dose of IgM ACE2 decoy at 1 mg/kg conferred therapeutic benefit against SARS-CoV-2 Delta variant infection in a hamster model. Taken together, this engineered IgM ACE2 decoy represents a SARS-CoV-2 variant-agnostic therapeutic that leverages avidity to drive enhanced target binding, viral neutralization, and in vivo respiratory protection against SARS-CoV-2.
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Affiliation(s)
| | | | | | | | - Anh Tran
- Department of Human Health Therapeutics, National Research Council Canada, Ottawa, Canada
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158
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Hussen BM, Sabir DK, Karim Y, Karim KK, Hidayat HJ. RETRACTED ARTICLE: Genome sequence analysis of SARS-COV-2 isolated from a COVID-19 patient in Erbil, Iraq. APPLIED NANOSCIENCE 2023; 13:3147. [PMID: 35155057 PMCID: PMC8818371 DOI: 10.1007/s13204-021-02300-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/27/2021] [Indexed: 01/07/2023]
Affiliation(s)
- Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Iraq
| | - Dana Khdr Sabir
- Department of Medical Laboratory Sciences, University Charmo, Kurdistan Region, Iraq
| | - Yasin Karim
- Medical Research Center, Hawler Medical University, Kurdistan Region, Iraq
| | | | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University, Kurdistan Region, Iraq
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159
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Shimada N, Shinoda M, Takei H, Yoshida Y, Nishimura M, Kousaka M, Morikawa M, Sato T, Matsuse H, Shinkai M. A case of reinfection with a different variant of SARS-CoV-2: case report. THE EGYPTIAN JOURNAL OF INTERNAL MEDICINE 2023; 35:13. [PMID: 36785595 PMCID: PMC9907179 DOI: 10.1186/s43162-023-00194-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/24/2023] [Indexed: 02/11/2023] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) was previously thought to have a low reinfection rate, but there are concerns that the reinfection rate will increase with the emergence and spread of mutant variants. This report describes the case of a 36-year-old, non-immunosuppressed man who was infected twice by two different variants of COVID-19 within a relatively short period. Case presentation A 36-year-old Japanese man with no comorbidities was infected with the E484K variant (R.1 lineage) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Symptoms were mild and improved with symptomatic treatment alone. About four months later he presented to another outpatient department with high fever and headache. We diagnosed him as infected with the Alpha variant (B.1.1.7) of SARS-CoV-2 based on SARS-CoV-2 real-time reverse transcription polymerase chain reaction testing (RT-PCR). The patient was hospitalized with high fever. The patient received treatment in the form of anti-inflammatory therapy with corticosteroid and antibacterial chemotherapy. The patient improved without developing severe disease. Conclusion Concerns have been raised that the reinfection rate of COVID-19 will increase with the emergence of mutant variants. Particularly in mild cases, adequate amounts of neutralizing antibodies may not be produced, and reinfection may thus occur. Continued attention to sufficient infection control is thus essential.
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Affiliation(s)
- Nagashige Shimada
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan ,grid.470115.6Division of Respiratory Medicine, Department of Internal Medicine, Toho University Ohashi Medical Center, Tokyo, Japan
| | - Masahiro Shinoda
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan
| | - Hiroaki Takei
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan ,grid.470115.6Division of Respiratory Medicine, Department of Internal Medicine, Toho University Ohashi Medical Center, Tokyo, Japan
| | - Yuto Yoshida
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan ,grid.470115.6Division of Respiratory Medicine, Department of Internal Medicine, Toho University Ohashi Medical Center, Tokyo, Japan
| | - Masashi Nishimura
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan
| | - Mio Kousaka
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan
| | - Miwa Morikawa
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan
| | - Takashi Sato
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan
| | - Hiroto Matsuse
- grid.470115.6Division of Respiratory Medicine, Department of Internal Medicine, Toho University Ohashi Medical Center, Tokyo, Japan
| | - Masaharu Shinkai
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan
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160
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Wang X, Hu M, Liu B, Xu H, Jin Y, Wang B, Zhao Y, Wu J, Yue J, Ren H. Evaluating the effect of SARS-CoV-2 spike mutations with a linear doubly robust learner. Front Cell Infect Microbiol 2023; 13:1161445. [PMID: 37153142 PMCID: PMC10154619 DOI: 10.3389/fcimb.2023.1161445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Abstract
Driven by various mutations on the viral Spike protein, diverse variants of SARS-CoV-2 have emerged and prevailed repeatedly, significantly prolonging the pandemic. This phenomenon necessitates the identification of key Spike mutations for fitness enhancement. To address the need, this manuscript formulates a well-defined framework of causal inference methods for evaluating and identifying key Spike mutations to the viral fitness of SARS-CoV-2. In the context of large-scale genomes of SARS-CoV-2, it estimates the statistical contribution of mutations to viral fitness across lineages and therefore identifies important mutations. Further, identified key mutations are validated by computational methods to possess functional effects, including Spike stability, receptor-binding affinity, and potential for immune escape. Based on the effect score of each mutation, individual key fitness-enhancing mutations such as D614G and T478K are identified and studied. From individual mutations to protein domains, this paper recognizes key protein regions on the Spike protein, including the receptor-binding domain and the N-terminal domain. This research even makes further efforts to investigate viral fitness via mutational effect scores, allowing us to compute the fitness score of different SARS-CoV-2 strains and predict their transmission capacity based solely on their viral sequence. This prediction of viral fitness has been validated using BA.2.12.1, which is not used for regression training but well fits the prediction. To the best of our knowledge, this is the first research to apply causal inference models to mutational analysis on large-scale genomes of SARS-CoV-2. Our findings produce innovative and systematic insights into SARS-CoV-2 and promotes functional studies of its key mutations, serving as reliable guidance about mutations of interest.
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Affiliation(s)
| | | | | | | | | | | | | | - Jun Wu
- *Correspondence: Hongguang Ren, ; Junjie Yue, ; Jun Wu,
| | - Junjie Yue
- *Correspondence: Hongguang Ren, ; Junjie Yue, ; Jun Wu,
| | - Hongguang Ren
- *Correspondence: Hongguang Ren, ; Junjie Yue, ; Jun Wu,
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161
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Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution. Nature 2023; 614:521-529. [PMID: 36535326 PMCID: PMC9931576 DOI: 10.1038/s41586-022-05644-7] [Citation(s) in RCA: 147] [Impact Index Per Article: 147.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Continuous evolution of Omicron has led to a rapid and simultaneous emergence of numerous variants that display growth advantages over BA.5 (ref. 1). Despite their divergent evolutionary courses, mutations on their receptor-binding domain (RBD) converge on several hotspots. The driving force and destination of such sudden convergent evolution and its effect on humoral immunity remain unclear. Here we demonstrate that these convergent mutations can cause evasion of neutralizing antibody drugs and convalescent plasma, including those from BA.5 breakthrough infection, while maintaining sufficient ACE2-binding capability. BQ.1.1.10 (BQ.1.1 + Y144del), BA.4.6.3, XBB and CH.1.1 are the most antibody-evasive strains tested. To delineate the origin of the convergent evolution, we determined the escape mutation profiles and neutralization activity of monoclonal antibodies isolated from individuals who had BA.2 and BA.5 breakthrough infections2,3. Owing to humoral immune imprinting, BA.2 and especially BA.5 breakthrough infection reduced the diversity of the neutralizing antibody binding sites and increased proportions of non-neutralizing antibody clones, which, in turn, focused humoral immune pressure and promoted convergent evolution in the RBD. Moreover, we show that the convergent RBD mutations could be accurately inferred by deep mutational scanning profiles4,5, and the evolution trends of BA.2.75 and BA.5 subvariants could be well foreseen through constructed convergent pseudovirus mutants. These results suggest that current herd immunity and BA.5 vaccine boosters may not efficiently prevent the infection of Omicron convergent variants.
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162
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Boytz R, Słabicki M, Ramaswamy S, Patten J, Zou C, Meng C, Hurst BL, Wang J, Nowak RP, Yang PL, Sattler M, Stone RM, Griffin JD, Gray NS, Gummuluru S, Davey RA, Weisberg E. Anti-SARS-CoV-2 activity of targeted kinase inhibitors: Repurposing clinically available drugs for COVID-19 therapy. J Med Virol 2023; 95:e28157. [PMID: 36117402 PMCID: PMC9538324 DOI: 10.1002/jmv.28157] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 01/17/2023]
Abstract
Coronavirus disease 2019 (COVID-19) remains a major public health concern, and vaccine unavailability, hesitancy, or failure underscore the need for discovery of efficacious antiviral drug therapies. Numerous approved drugs target protein kinases associated with viral life cycle and symptoms of infection. Repurposing of kinase inhibitors is appealing as they have been vetted for safety and are more accessible for COVID-19 treatment. However, an understanding of drug mechanism is needed to improve our understanding of the factors involved in pathogenesis. We tested the in vitro activity of three kinase inhibitors against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), including inhibitors of AXL kinase, a host cell factor that contributes to successful SARS-CoV-2 infection. Using multiple cell-based assays and approaches, gilteritinib, nintedanib, and imatinib were thoroughly evaluated for activity against SARS-CoV-2 variants. Each drug exhibited antiviral activity, but with stark differences in potency, suggesting differences in host dependency for kinase targets. Importantly, for gilteritinib, the amount of compound needed to achieve 90% infection inhibition, at least in part involving blockade of spike protein-mediated viral entry and at concentrations not inducing phospholipidosis (PLD), approached a clinically achievable concentration. Knockout of AXL, a target of gilteritinib and nintedanib, impaired SARS-CoV-2 variant infectivity, supporting a role for AXL in SARS-CoV-2 infection and supporting further investigation of drug-mediated AXL inhibition as a COVID-19 treatment. This study supports further evaluation of AXL-targeting kinase inhibitors as potential antiviral agents and treatments for COVID-19. Additional mechanistic studies are needed to determine underlying differences in virus response.
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Affiliation(s)
- RuthMabel Boytz
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA
| | - Mikołaj Słabicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sita Ramaswamy
- Department of Microbiology, Boston University, Boston, MA
| | - J.J. Patten
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA
| | - Charles Zou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Chengcheng Meng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brett L. Hurst
- Institute for Antiviral Research, Utah State University, Logan, UT
| | - Jinhua Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Radosław P. Nowak
- Department of Medicine, Harvard Medical School, Boston, MA, USA,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Priscilla L. Yang
- Cancer Biology, Dana-Farber Cancer Institute, MA, USA,Department of Microbiology, Harvard Medical School, Boston, MA, USA; current address Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Martin Sattler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Richard M. Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - James D. Griffin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nathanael S. Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | - Robert A. Davey
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA
| | - Ellen Weisberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Department of Medicine, Harvard Medical School, Boston, MA, USA
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163
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Titers of antibodies against ancestral SARS-CoV-2 correlate with levels of neutralizing antibodies to multiple variants. NPJ Vaccines 2022; 7:174. [PMID: 36585405 PMCID: PMC9801350 DOI: 10.1038/s41541-022-00586-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/24/2022] [Indexed: 12/31/2022] Open
Abstract
Diagnostic assays currently used to monitor the efficacy of COVID-19 vaccines measure levels of antibodies to the receptor-binding domain of ancestral SARS-CoV-2 (RBDwt). However, the predictive value for protection against new variants of concern (VOCs) has not been firmly established. Here, we used bead-based arrays and flow cytometry to measure binding of antibodies to spike proteins and receptor-binding domains (RBDs) from VOCs in 12,000 serum samples. Effects of sera on RBD-ACE2 interactions were measured as a proxy for neutralizing antibodies. The samples were obtained from healthy individuals or patients on immunosuppressive therapy who had received two to four doses of COVID-19 vaccines and from COVID-19 convalescents. The results show that anti-RBDwt titers correlate with the levels of binding- and neutralizing antibodies against the Alpha, Beta, Gamma, Delta, Epsilon and Omicron variants. The benefit of multiplexed analysis lies in the ability to measure a wide range of anti-RBD titers using a single dilution of serum for each assay. The reactivity patterns also yield an internal reference for neutralizing activity and binding antibody units per milliliter (BAU/ml). Results obtained with sera from vaccinated healthy individuals and patients confirmed and extended results from previous studies on time-dependent waning of antibody levels and effects of immunosuppressive agents. We conclude that anti-RBDwt titers correlate with levels of neutralizing antibodies against VOCs and propose that our method may be implemented to enhance the precision and throughput of immunomonitoring.
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164
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Warger J, Gaudieri S. On the Evolutionary Trajectory of SARS-CoV-2: Host Immunity as a Driver of Adaptation in RNA Viruses. Viruses 2022; 15:70. [PMID: 36680110 PMCID: PMC9866609 DOI: 10.3390/v15010070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022] Open
Abstract
Host immunity can exert a complex array of selective pressures on a pathogen, which can drive highly mutable RNA viruses towards viral escape. The plasticity of a virus depends on its rate of mutation, as well as the balance of fitness cost and benefit of mutations, including viral adaptations to the host's immune response. Since its emergence, SARS-CoV-2 has diversified into genetically distinct variants, which are characterised often by clusters of mutations that bolster its capacity to escape human innate and adaptive immunity. Such viral escape is well documented in the context of other pandemic RNA viruses such as the human immunodeficiency virus (HIV) and influenza virus. This review describes the selection pressures the host's antiviral immunity exerts on SARS-CoV-2 and other RNA viruses, resulting in divergence of viral strains into more adapted forms. As RNA viruses obscure themselves from host immunity, they uncover weak points in their own armoury that can inform more comprehensive, long-lasting, and potentially cross-protective vaccine coverage.
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Affiliation(s)
- Jacob Warger
- School of Medicine and Pharmacology, University of Western Australia, Crawley, WA 6009, Australia
| | - Silvana Gaudieri
- School of Human Sciences, University of Western Australia, Crawley, WA 6009, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Mandurah, WA 6150, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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165
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Kwon HJ, Kosikova M, Tang W, Ortega-Rodriguez U, Radvak P, Xiang R, Mercer KE, Muskhelishvili L, Davis K, Ward JM, Kosik I, Holly J, Kang I, Yewdell JW, Plant EP, Chen WH, Shriver MC, Barnes RS, Pasetti MF, Zhou B, Wentworth DE, Xie H. Enhanced virulence and waning vaccine-elicited antibodies account for breakthrough infections caused by SARS-CoV-2 delta and beyond. iScience 2022; 25:105507. [PMID: 36373096 PMCID: PMC9635945 DOI: 10.1016/j.isci.2022.105507] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/05/2022] [Accepted: 11/01/2022] [Indexed: 11/08/2022] Open
Abstract
Here we interrogate the factors responsible for SARS-CoV-2 breakthrough infections in a K18-hACE2 transgenic mouse model. We show that Delta and the closely related Kappa variant cause viral pneumonia and severe lung lesions in K18-hACE2 mice. Human COVID-19 mRNA post-vaccination sera after the 2nd dose are significantly less efficient in neutralizing Delta/Kappa than early 614G virus in vitro and in vivo. By 5 months post-vaccination, ≥50% of donors lack detectable neutralizing antibodies against Delta and Kappa and all mice receiving 5-month post-vaccination sera die after the lethal challenges. Although a 3rd vaccine dose can boost antibody neutralization against Delta in vitro and in vivo, the mean log neutralization titers against the latest Omicron subvariants are 1/3-1/2 of those against the original 614D virus. Our results suggest that enhanced virulence, greater immune evasion, and waning of vaccine-elicited protection account for SARS-CoV-2 variants caused breakthrough infections.
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Affiliation(s)
- Hyung-Joon Kwon
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Martina Kosikova
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Weichun Tang
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Uriel Ortega-Rodriguez
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Peter Radvak
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Ruoxuan Xiang
- Division of Biostatistics, Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Kelly E. Mercer
- Biomarkers and Alternative Models Branch, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, AR, USA
| | | | - Kelly Davis
- Toxicologic Pathology Associates, Jefferson, AR, USA
| | | | - Ivan Kosik
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jaroslav Holly
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Insung Kang
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Jonathan W. Yewdell
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ewan P. Plant
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Wilbur H. Chen
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mallory C. Shriver
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Robin S. Barnes
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Marcela F. Pasetti
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Bin Zhou
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - David E. Wentworth
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Hang Xie
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
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166
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Potent SARS-CoV-2 neutralizing antibodies with therapeutic effects in two animal models. iScience 2022; 25:105596. [PMID: 36406861 PMCID: PMC9664764 DOI: 10.1016/j.isci.2022.105596] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/07/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022] Open
Abstract
The use of therapeutic neutralizing antibodies against SARS-CoV-2 infection has been highly effective. However, there remain few practical antibodies against viruses that are acquiring mutations. In this study, we created 494 monoclonal antibodies from patients with COVID-19-convalescent, and identified antibodies that exhibited the comparable neutralizing ability to clinically used antibodies in the neutralization assay using pseudovirus and authentic virus including variants of concerns. These antibodies have different profiles against various mutations, which were confirmed by cell-based assay and cryo-electron microscopy. To prevent antibody-dependent enhancement, N297A modification was introduced. Our antibodies showed a reduction of lung viral RNAs by therapeutic administration in a hamster model. In addition, an antibody cocktail consisting of three antibodies was also administered therapeutically to a macaque model, which resulted in reduced viral titers of swabs and lungs and reduced lung tissue damage scores. These results showed that our antibodies have sufficient antiviral activity as therapeutic candidates.
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167
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Sertraline Is an Effective SARS-CoV-2 Entry Inhibitor Targeting the Spike Protein. J Virol 2022; 96:e0124522. [PMID: 36468859 PMCID: PMC9769394 DOI: 10.1128/jvi.01245-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The global spread of the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the continuously emerging new variants underscore an urgent need for effective therapeutics for the treatment of coronavirus disease 2019 (COVID-19). Here, we screened several FDA-approved amphiphilic drugs and determined that sertraline (SRT) exhibits potent antiviral activity against infection of SARS-CoV-2 pseudovirus (PsV) and authentic virus in vitro. It effectively inhibits SARS-CoV-2 spike (S)-mediated cell-cell fusion. SRT targets the early stage of viral entry. It can bind to the S1 subunit of the S protein, especially the receptor binding domain (RBD), thus blocking S-hACE2 interaction and interfering with the proteolysis process of S protein. SRT is also effective against infection with SARS-CoV-2 PsV variants, including the newly emerging Omicron. The combination of SRT and other antivirals exhibits a strong synergistic effect against infection of SARS-CoV-2 PsV. The antiviral activity of SRT is independent of serotonin transporter expression. Moreover, SRT effectively inhibits infection of SARS-CoV-2 PsV and alleviates the inflammation process and lung pathological alterations in transduced mice in vivo. Therefore, SRT shows promise as a treatment option for COVID-19. IMPORTANCE The study shows SRT is an effective entry inhibitor against infection of SARS-CoV-2, which is currently prevalent globally. SRT targets the S protein of SARS-CoV-2 and is effective against a panel of SARS-CoV-2 variants. It also could be used in combination to prevent SARS-CoV-2 infection. More importantly, with long history of clinical use and proven safety, SRT might be particularly suitable to treat infection of SARS-CoV-2 in the central nervous system and optimized for treatment in older people, pregnant women, and COVID-19 patients with heart complications, which are associated with severity and mortality of COVID-19.
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168
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Oo KZ, Htun ZW, Aung NM, Win KK, Linn KZ, Htoo SP, Aung PK, Oo TW, Zaw MT, Ko LY, Tun KM, Myint K, Lwin KK. Genomic Tracking of SARS-CoV-2 Variants in Myanmar. Vaccines (Basel) 2022; 11:6. [PMID: 36679850 PMCID: PMC9862072 DOI: 10.3390/vaccines11010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
In December 2019, the COVID-19 disease started in Wuhan, China. The WHO declared a pandemic on 12 March 2020, and the disease started in Myanmar on 23 March 2020. In December 2020, different variants were brought worldwide, threatening global health. To counter those threats, Myanmar started the COVID-19 variant surveillance program in late 2020. Whole genome sequencing was done six times between January 2021 and March 2022. Among them, 83 samples with a PCR threshold cycle of less than 25 were chosen. Then, we used MiSeq FGx for sequencing and Illumina DRAGEN COVIDSeq pipeline, command line interface, GISAID, and MEGA version 7 for data analysis. In January 2021, no variant was detected. The second run, during the rise of cases in June 2021, showed Alpha, Delta, and Kappa variants. The third and the fourth runs in August and December showed only a Delta variant. Omicron and Delta variants were detected during the fifth run in January 2022. The sixth run in March 2022 showed only Omicron BA.2. Amino acid mutation at the receptor binding domain of Spike glycoprotein started since the second run coupling with high transmission, recurrence, and vaccine escape. We also found the mutation at the primer targets used in current RT-PCR platforms, but there was no mutation at the existing antiviral drug targets. The occurrence of multiple variants and mutations claimed vigilance at ports of entry and preparedness for effective control measures. Genomic surveillance with the observation of evolutionary data is required to predict imminent threats of the current disease and diagnose emerging infectious diseases.
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Affiliation(s)
- Khine Zaw Oo
- Defence Services Medical Research Centre, Biological Toxin Research Department, Nay Pyi Taw 15021, Myanmar
| | - Zaw Win Htun
- Defence Services Medical Research Centre, Biological Toxin Research Department, Nay Pyi Taw 15021, Myanmar
| | - Nay Myo Aung
- Defence Services Medical Research Centre, Biological Toxin Research Department, Nay Pyi Taw 15021, Myanmar
| | - Ko Ko Win
- Defence Services Medical Research Centre, Biological Toxin Research Department, Nay Pyi Taw 15021, Myanmar
| | - Kyaw Zawl Linn
- Defence Services Medical Research Centre, Biological Toxin Research Department, Nay Pyi Taw 15021, Myanmar
| | - Sett Paing Htoo
- Defence Services Medical Research Centre, Biological Toxin Research Department, Nay Pyi Taw 15021, Myanmar
| | - Phyo Kyaw Aung
- Defence Services Medical Research Centre, Biological Toxin Research Department, Nay Pyi Taw 15021, Myanmar
| | - Thet Wai Oo
- Defence Services Medical Research Centre, Biological Toxin Research Department, Nay Pyi Taw 15021, Myanmar
| | - Myo Thiha Zaw
- Defence Services Medical Research Centre, Biological Toxin Research Department, Nay Pyi Taw 15021, Myanmar
| | - Linn Yuzana Ko
- Defence Services Medical Research Centre, Biological Toxin Research Department, Nay Pyi Taw 15021, Myanmar
| | - Kyaw Myo Tun
- Defence Services Medical Research Centre, Biological Toxin Research Department, Nay Pyi Taw 15021, Myanmar
| | - Kyee Myint
- Defence Services Medical Research Centre, Biological Toxin Research Department, Nay Pyi Taw 15021, Myanmar
| | - Ko Ko Lwin
- Directorate of Medical Services, Nay Pyi Taw 15013, Myanmar
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169
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Guenthoer J, Lilly M, Starr TN, Dadonaite B, Lovendahl KN, Croft JT, Stoddard CI, Chohan V, Ding S, Ruiz F, Kopp MS, Finzi A, Bloom JD, Chu HY, Lee KK, Overbaugh J. Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.15.520606. [PMID: 36561191 PMCID: PMC9774213 DOI: 10.1101/2022.12.15.520606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The antiviral benefit of antibodies can be compromised by viral escape especially for rapidly evolving viruses. Therefore, durable, effective antibodies must be both broad and potent to counter newly emerging, diverse strains. Discovery of such antibodies is critically important for SARS-CoV-2 as the global emergence of new variants of concern (VOC) has compromised the efficacy of therapeutic antibodies and vaccines. We describe a collection of broad and potent neutralizing monoclonal antibodies (mAbs) isolated from an individual who experienced a breakthrough infection with the Delta VOC. Four mAbs potently neutralize the Wuhan-Hu-1 vaccine strain, the Delta VOC, and also retain potency against the Omicron VOCs, including recently circulating BA.4/BA.5, in both pseudovirus-based and live virus assays, and one also potently neutralizes SARS-CoV-1. The potency of these mAbs was greater against Omicron VOCs than all but one of the mAbs that had been approved for therapeutic applications. The mAbs target distinct epitopes on the spike glycoprotein, three in the receptor binding domain (RBD) and one in an invariant region downstream of the RBD in subdomain 1 (SD1). The escape pathways we defined at single amino acid resolution with deep mutational scanning show they target conserved, functionally constrained regions of the glycoprotein, suggesting escape could incur a fitness cost. Overall, these mAbs are novel in their breadth across VOCs, their epitope specificity, and include a highly potent mAb targeting a rare epitope outside of the RBD in SD1.
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170
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Parigger L, Krassnigg A, Schopper T, Singh A, Tappler K, Köchl K, Hetmann M, Gruber K, Steinkellner G, Gruber CC. Recent changes in the mutational dynamics of the SARS-CoV-2 main protease substantiate the danger of emerging resistance to antiviral drugs. Front Med (Lausanne) 2022; 9:1061142. [PMID: 36590977 PMCID: PMC9794616 DOI: 10.3389/fmed.2022.1061142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Introduction The current coronavirus pandemic is being combated worldwide by nontherapeutic measures and massive vaccination programs. Nevertheless, therapeutic options such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main-protease (Mpro) inhibitors are essential due to the ongoing evolution toward escape from natural or induced immunity. While antiviral strategies are vulnerable to the effects of viral mutation, the relatively conserved Mpro makes an attractive drug target: Nirmatrelvir, an antiviral targeting its active site, has been authorized for conditional or emergency use in several countries since December 2021, and a number of other inhibitors are under clinical evaluation. We analyzed recent SARS-CoV-2 genomic data, since early detection of potential resistances supports a timely counteraction in drug development and deployment, and discovered accelerated mutational dynamics of Mpro since early December 2021. Methods We performed a comparative analysis of 10.5 million SARS-CoV-2 genome sequences available by June 2022 at GISAID to the NCBI reference genome sequence NC_045512.2. Amino-acid exchanges within high-quality regions in 69,878 unique Mpro sequences were identified and time- and in-depth sequence analyses including a structural representation of mutational dynamics were performed using in-house software. Results The analysis showed a significant recent event of mutational dynamics in Mpro. We report a remarkable increase in mutational variability in an eight-residue long consecutive region (R188-G195) near the active site since December 2021. Discussion The increased mutational variability in close proximity to an antiviral-drug binding site as described herein may suggest the onset of the development of antiviral resistance. This emerging diversity urgently needs to be further monitored and considered in ongoing drug development and lead optimization.
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Affiliation(s)
- Lena Parigger
- Innophore GmbH, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | | | - Amit Singh
- Innophore GmbH, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Katharina Tappler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Michael Hetmann
- Innophore GmbH, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Karl Gruber
- Innophore GmbH, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Georg Steinkellner
- Innophore GmbH, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Christian C. Gruber
- Innophore GmbH, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
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171
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Fan C, Cohen AA, Park M, Hung AFH, Keeffe JR, Gnanapragasam PNP, Lee YE, Gao H, Kakutani LM, Wu Z, Kleanthous H, Malecek KE, Williams JC, Bjorkman PJ. Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes. Immunity 2022; 55:2419-2435.e10. [PMID: 36370711 PMCID: PMC9606073 DOI: 10.1016/j.immuni.2022.10.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/07/2022] [Accepted: 10/24/2022] [Indexed: 01/21/2023]
Abstract
Increased immune evasion by SARS-CoV-2 variants of concern highlights the need for new therapeutic neutralizing antibodies. Immunization with nanoparticles co-displaying spike receptor-binding domains (RBDs) from eight sarbecoviruses (mosaic-8 RBD-nanoparticles) efficiently elicits cross-reactive polyclonal antibodies against conserved sarbecovirus RBD epitopes. Here, we identified monoclonal antibodies (mAbs) capable of cross-reactive binding and neutralization of animal sarbecoviruses and SARS-CoV-2 variants by screening single mouse B cells secreting IgGs that bind two or more sarbecovirus RBDs. Single-particle cryo-EM structures of antibody-spike complexes, including a Fab-Omicron complex, mapped neutralizing mAbs to conserved class 1/4 RBD epitopes. Structural analyses revealed neutralization mechanisms, potentials for intra-spike trimer cross-linking by IgGs, and induced changes in trimer upon Fab binding. In addition, we identified a mAb-resembling Bebtelovimab, an EUA-approved human class 3 anti-RBD mAb. These results support using mosaic RBD-nanoparticle vaccination to generate and identify therapeutic pan-sarbecovirus and pan-variant mAbs.
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Affiliation(s)
- Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Miso Park
- Department of Molecular Medicine, City of Hope, Duarte, CA 91010, USA
| | | | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Yu E Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leesa M Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ziyan Wu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Kathryn E Malecek
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - John C Williams
- Department of Molecular Medicine, City of Hope, Duarte, CA 91010, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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172
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Yu TC, Thornton ZT, Hannon WW, DeWitt WS, Radford CE, Matsen FA, Bloom JD. A biophysical model of viral escape from polyclonal antibodies. Virus Evol 2022; 8:veac110. [PMID: 36582502 PMCID: PMC9793855 DOI: 10.1093/ve/veac110] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/12/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
A challenge in studying viral immune escape is determining how mutations combine to escape polyclonal antibodies, which can potentially target multiple distinct viral epitopes. Here we introduce a biophysical model of this process that partitions the total polyclonal antibody activity by epitope and then quantifies how each viral mutation affects the antibody activity against each epitope. We develop software that can use deep mutational scanning data to infer these properties for polyclonal antibody mixtures. We validate this software using a computationally simulated deep mutational scanning experiment and demonstrate that it enables the prediction of escape by arbitrary combinations of mutations. The software described in this paper is available at https://jbloomlab.github.io/polyclonal.
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Affiliation(s)
- Timothy C Yu
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacifc Street, Seattle, WA 98195, USA
| | - Zorian T Thornton
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
| | - William W Hannon
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacifc Street, Seattle, WA 98195, USA
| | - William S DeWitt
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
| | - Caelan E Radford
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacifc Street, Seattle, WA 98195, USA
| | - Frederick A Matsen
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, 1100 Fairview Ave N, Seattle, WA 98109, USA
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173
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Liu Y, Arase H. Neutralizing and enhancing antibodies against SARS-CoV-2. Inflamm Regen 2022; 42:58. [PMID: 36471381 PMCID: PMC9720987 DOI: 10.1186/s41232-022-00233-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/30/2022] [Indexed: 12/12/2022] Open
Abstract
The high transmissibility and rapid global spread of SARS-CoV-2 since 2019 has led to a huge burden on healthcare worldwide. Anti-SARS-CoV-2 neutralizing antibodies play an important role in not only protecting against infection but also in clearing the virus and are essential to providing long-term immunity. On the other hand, antibodies against the virus are not always protective. With the emergence of SARS-CoV-2 immune escape variants, vaccine design strategies as well as antibody-mediated therapeutic approaches have become more important. We review some of the findings on SARS-CoV-2 antibodies, focusing on both basic research and clinical applications.
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Affiliation(s)
- Yafei Liu
- grid.136593.b0000 0004 0373 3971Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Osaka, 565-0871 Japan
| | - Hisashi Arase
- grid.136593.b0000 0004 0373 3971Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Osaka, 565-0871 Japan
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174
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Forte E, Des Soye BJ, Melani RD, Hollas MAR, Kafader JO, Sha BE, Schneider JR, Kelleher NL. Divergent Antibody Repertoires Found for Omicron versus Wuhan SARS-CoV-2 Strains Using Ig-MS. J Proteome Res 2022; 21:2987-2997. [PMID: 36343328 PMCID: PMC9668041 DOI: 10.1021/acs.jproteome.2c00514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Indexed: 11/09/2022]
Abstract
SARS-CoV-2 Omicron (B.1.1.529) and its subvariants are currently the most common variants of concern worldwide, featuring numerous mutations in the spike protein and elsewhere that collectively make Omicron variants more transmissible and more resistant to antibody-mediated neutralization provided by vaccination, previous infections, and monoclonal antibody therapies than their predecessors. We recently reported the creation and characterization of Ig-MS, a new mass spectrometry-based serology platform that can define the repertoire of antibodies against an antigen of interest at single proteoform resolution. Here, we applied Ig-MS to investigate the evolution of plasma antibody repertoires against the receptor-binding domain (RBD) of SARS-CoV-2 in response to the booster shot and natural viral infection. We also assessed the capacity for antibody repertoires generated in response to vaccination and/or infection with the Omicron variant to bind to both Wuhan- and Omicron-RBDs. Our results show that (1) the booster increases antibody titers against both Wuhan- and Omicron- RBDs and elicits an Omicron-specific response and (2) vaccination and infection act synergistically in generating anti-RBD antibody repertoires able to bind both Wuhan- and Omicron-RBDs with variant-specific antibodies.
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Affiliation(s)
- Eleonora Forte
- Proteomics Center of Excellence, Evanston, IL, 60208, USA
- Department of Surgery, Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | | | - Rafael D. Melani
- Proteomics Center of Excellence, Evanston, IL, 60208, USA
- Department of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | | | | | - Beverly E. Sha
- Division of Infectious Diseases, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Jeffrey R. Schneider
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Neil L. Kelleher
- Proteomics Center of Excellence, Evanston, IL, 60208, USA
- Department of Surgery, Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
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175
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Mise-Omata S, Ikeda M, Takeshita M, Uwamino Y, Wakui M, Arai T, Yoshifuji A, Murano K, Siomi H, Nakagawara K, Ohyagi M, Ando M, Hasegawa N, Saya H, Murata M, Fukunaga K, Namkoong H, Lu X, Yamasaki S, Yoshimura A. Memory B Cells and Memory T Cells Induced by SARS-CoV-2 Booster Vaccination or Infection Show Different Dynamics and Responsiveness to the Omicron Variant. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:2104-2113. [PMID: 36426984 DOI: 10.4049/jimmunol.2200525] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/21/2022] [Indexed: 01/04/2023]
Abstract
Although the immunological memory produced by BNT162b2 vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been well studied and established, further information using different racial cohorts is necessary to understand the overall immunological response to vaccination. We evaluated memory B and T cell responses to the severe acute respiratory syndrome coronavirus 2 spike protein before and after the third booster using a Japanese cohort. Although the Ab titer against the spike receptor-binding domain (RBD) decreased significantly 8 mo after the second vaccination, the number of memory B cells continued to increase, whereas the number of memory T cells decreased slowly. Memory B and T cells from unvaccinated infected patients showed similar kinetics. After the third vaccination, the Ab titer increased to the level of the second vaccination, and memory B cells increased at significantly higher levels before the booster, whereas memory T cells recovered close to the second vaccination levels. In memory T cells, the frequency of CXCR5+CXCR3+CCR6- circulating follicular Th1 was positively correlated with RBD-specific Ab-secreting B cells. For the response to variant RBDs, although 60-80% of memory B cells could bind to the omicron RBD, their avidity was low, whereas memory T cells show an equal response to the omicron spike. Thus, the persistent presence of memory B and T cells will quickly upregulate Ab production and T cell responses after omicron strain infection, which prevents severe illness and death due to coronavirus disease 2019.
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Affiliation(s)
- Setsuko Mise-Omata
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Mari Ikeda
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Masaru Takeshita
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yoshifumi Uwamino
- Department of Laboratory Medicine, Keio University School of Medicine, Tokyo, Japan.,Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Masatoshi Wakui
- Department of Laboratory Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Tomoko Arai
- Clinical Laboratory, Keio University Hospital, Tokyo, Japan
| | - Ayumi Yoshifuji
- Division of Nephrology, Department of Internal Medicine, Tokyo Saiseikai Central Hospital, Tokyo, Japan
| | - Kensaku Murano
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Kensuke Nakagawara
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan.,Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Masaki Ohyagi
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Makoto Ando
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Naoki Hasegawa
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Hideyuki Saya
- Division of Gene Regulation, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
| | - Mitsuru Murata
- Department of Laboratory Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Ho Namkoong
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Xiuyuan Lu
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan; and
| | - Sho Yamasaki
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan; and.,Department of Molecular Immunology, Research Institute Microbial Disease, Osaka University, Osaka, Japan
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
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176
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Chi H, Wang L, Liu C, Cheng X, Zheng H, Lv L, Tan Y, Zhang N, Zhao S, Wu M, Luo D, Qiu H, Feng R, Fu W, Zhang J, Xiong X, Zhang Y, Zu S, Chen Q, Ye Q, Yan X, Hu Y, Zhang Z, Yan R, Yin J, Lei P, Wang W, Lang G, Shao J, Deng Y, Wang X, Qin C. An Engineered IgG-VHH Bispecific Antibody against SARS-CoV-2 and Its Variants. SMALL METHODS 2022; 6:e2200932. [PMID: 36300882 PMCID: PMC9874498 DOI: 10.1002/smtd.202200932] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/30/2022] [Indexed: 06/16/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) neutralizing antibodies are shown to be effective therapeutics for providing coronavirus disease 2019 (COVID-19) protection. However, recurrent variants arise and facilitate significant escape from current antibody therapeutics. Bispecific antibodies (bsAbs) represent a unique platform to increase antibody breadth and to reduce neutralization escape. Herein, a novel immunoglobulin G-variable domains of heavy-chain-only antibody (IgG-VHH) format bsAb derived from a potent human antibody R15-F7 and a humanized nanobody P14-F8-35 are rationally engineered. The resulting bsAb SYZJ001 efficiently neutralizes wild-type SARS-CoV-2 as well as the alpha, beta, gamma, and delta variants, with superior efficacy to its parental antibodies. Cryo-electron microscopy structural analysis reveals that R15-F7 and P14-F8-35 bind to nonoverlapping epitopes within the RBD and sterically hindered ACE2 receptor binding. Most importantly, SYZJ001 shows potent prophylactic and therapeutic efficacy against SARS-CoV-2 in three established mouse models. Collectively, the current results demonstrate that the novel bsAb format is feasible and effective, suggesting great potential as an inspiring antiviral strategy.
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Affiliation(s)
- Hang Chi
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071China
| | - Lei Wang
- CAS Key Laboratory of Infection and ImmunityNational Laboratory of MacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Chanjuan Liu
- Department of Innovation Research and DevelopmentSanyou Biopharmaceuticals (Shanghai) Co., LtdShanghai201114China
| | - Xiaohe Cheng
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071China
| | - Hailiang Zheng
- Department of Innovation Research and DevelopmentSanyou Biopharmaceuticals (Shanghai) Co., LtdShanghai201114China
| | - Lilang Lv
- ZJ Bio‐Tech InstituteShanghai ZJ Bio‐Tech Co., Ltd.Shanghai201114China
| | - Yongcong Tan
- Department of Innovation Research and DevelopmentSanyou Biopharmaceuticals (Shanghai) Co., LtdShanghai201114China
| | - Nana Zhang
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071China
| | - Suoqun Zhao
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071China
| | - Mei Wu
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071China
| | - Dan Luo
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071China
| | - Hongying Qiu
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071China
| | - Rui Feng
- CAS Key Laboratory of Infection and ImmunityNational Laboratory of MacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
| | - Wangjun Fu
- CAS Key Laboratory of Infection and ImmunityNational Laboratory of MacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Jie Zhang
- ZJ Bio‐Tech InstituteShanghai ZJ Bio‐Tech Co., Ltd.Shanghai201114China
| | - Xiaochuan Xiong
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071China
| | - Yifei Zhang
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071China
| | - Shulong Zu
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071China
| | - Qi Chen
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071China
| | - Qing Ye
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071China
| | - Xintian Yan
- Department of Innovation Research and DevelopmentSanyou Biopharmaceuticals (Shanghai) Co., LtdShanghai201114China
| | - Yuhao Hu
- Department of Innovation Research and DevelopmentSanyou Biopharmaceuticals (Shanghai) Co., LtdShanghai201114China
| | - Zhen Zhang
- Department of Innovation Research and DevelopmentSanyou Biopharmaceuticals (Shanghai) Co., LtdShanghai201114China
| | - Run Yan
- Department of Innovation Research and DevelopmentSanyou Biopharmaceuticals (Shanghai) Co., LtdShanghai201114China
| | - Jiangfeng Yin
- Department of Innovation Research and DevelopmentSanyou Biopharmaceuticals (Shanghai) Co., LtdShanghai201114China
| | - Pan Lei
- Department of Innovation Research and DevelopmentSanyou Biopharmaceuticals (Shanghai) Co., LtdShanghai201114China
| | - Wanjing Wang
- Department of Innovation Research and DevelopmentSanyou Biopharmaceuticals (Shanghai) Co., LtdShanghai201114China
| | - Guojun Lang
- Department of Innovation Research and DevelopmentSanyou Biopharmaceuticals (Shanghai) Co., LtdShanghai201114China
| | - Junbin Shao
- ZJ Bio‐Tech InstituteShanghai ZJ Bio‐Tech Co., Ltd.Shanghai201114China
| | - Yongqiang Deng
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071China
| | - Xiangxi Wang
- CAS Key Laboratory of Infection and ImmunityNational Laboratory of MacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Chengfeng Qin
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071China
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177
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Lustig G, Ganga Y, Rodel H, Tegally H, Jackson L, Cele S, Khan K, Jule Z, Reedoy K, Karim F, Bernstein M, Moosa MYS, Archary D, de Oliveira T, Lessells R, Abdool Karim SS, Sigal A. SARS-CoV-2 evolves increased infection elicited cell death and fusion in an immunosuppressed individual. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.11.23.22282673. [PMID: 36451879 PMCID: PMC9709797 DOI: 10.1101/2022.11.23.22282673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The milder clinical manifestations of Omicron infection relative to pre-Omicron SARS CoV-2 raises the possibility that extensive evolution results in reduced pathogenicity. To test this hypothesis, we quantified induction of cell fusion and cell death in SARS CoV-2 evolved from ancestral virus during long-term infection. Both cell fusion and death were reduced in Omicron BA.1 infection relative to ancestral virus. Evolved virus was isolated at different times during a 6-month infection in an immunosuppressed individual with advanced HIV disease. The virus isolated 16 days post-reported symptom onset induced fusogenicity and cell death at levels similar to BA.1. However, fusogenicity was increased in virus isolated at 6 months post-symptoms to levels intermediate between BA.1 and ancestral SARS-CoV-2. Similarly, infected cell death showed a graded increase from earlier to later isolates. These results may indicate that, at least by the cellular measures used here, evolution in long-term infection does not necessarily attenuate the virus.
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Affiliation(s)
- Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Yashica Ganga
- Africa Health Research Institute, Durban, South Africa
| | - Hylton Rodel
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | | | - Sandile Cele
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Zesuliwe Jule
- Africa Health Research Institute, Durban, South Africa
| | - Kajal Reedoy
- Africa Health Research Institute, Durban, South Africa
| | - Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Derseree Archary
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Global Health, University of Washington, Seattle, USA
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Alex Sigal
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
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178
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Bian L, Liu J, Gao F, Gao Q, He Q, Mao Q, Wu X, Xu M, Liang Z. Research progress on vaccine efficacy against SARS-CoV-2 variants of concern. Hum Vaccin Immunother 2022; 18:2057161. [PMID: 35438600 PMCID: PMC9115786 DOI: 10.1080/21645515.2022.2057161] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 03/08/2022] [Accepted: 03/21/2022] [Indexed: 01/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate worldwide and a variety of variants have emerged. Variants of concern (VOC) designated by the World Health Organization (WHO) have triggered epidemic waves due to their strong infectivity or pathogenicity and potential immune escape, among other reasons. Although large-scale vaccination campaigns undertaken globally have contributed to the improved control of SARS-CoV-2, the efficacies of current vaccines against VOCs have declined to various degrees. In particular, the highly infectious Delta and Omicron variants have caused recent epidemics and prompted concerns about control measures. This review summarizes current VOCs, the protective efficacy of vaccines against VOCs, and the shortcomings in methods for evaluating vaccine efficacy. In addition, strategies for responding to variants are proposed for future epidemic prevention and control as well as for vaccine research and development.
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Affiliation(s)
- Lianlian Bian
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Jianyang Liu
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Fan Gao
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Qiushuang Gao
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Qian He
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Qunying Mao
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Xing Wu
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Miao Xu
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Zhenglun Liang
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
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179
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Ouyang WO, Tan TJ, Lei R, Song G, Kieffer C, Andrabi R, Matreyek KA, Wu NC. Probing the biophysical constraints of SARS-CoV-2 spike N-terminal domain using deep mutational scanning. SCIENCE ADVANCES 2022; 8:eadd7221. [PMID: 36417523 PMCID: PMC9683733 DOI: 10.1126/sciadv.add7221] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Increasing the expression level of the SARS-CoV-2 spike (S) protein has been critical for COVID-19 vaccine development. While previous efforts largely focused on engineering the receptor-binding domain (RBD) and the S2 subunit, the amino-terminal domain (NTD) has been long overlooked because of the limited understanding of its biophysical constraints. In this study, the effects of thousands of NTD single mutations on S protein expression were quantified by deep mutational scanning. Our results revealed that in terms of S protein expression, the mutational tolerability of NTD residues was inversely correlated with their proximity to the RBD and S2. We also identified NTD mutations at the interdomain interface that increased S protein expression without altering its antigenicity. Overall, this study not only advances the understanding of the biophysical constraints of the NTD but also provides invaluable insights into S-based immunogen design.
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Affiliation(s)
- Wenhao O. Ouyang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Timothy J.C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruipeng Lei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Collin Kieffer
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kenneth A. Matreyek
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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180
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Ling Z, Yi C, Sun X, Yang Z, Sun B. Broad strategies for neutralizing SARS-CoV-2 and other human coronaviruses with monoclonal antibodies. SCIENCE CHINA. LIFE SCIENCES 2022; 66:658-678. [PMID: 36443513 PMCID: PMC9707277 DOI: 10.1007/s11427-022-2215-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/04/2022] [Indexed: 11/30/2022]
Abstract
Antibody therapeutics and vaccines for coronavirus disease 2019 (COVID-19) have been approved in many countries, with most being developed based on the original strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 has an exceptional ability to mutate under the pressure of host immunity, especially the immune-dominant spike protein of the virus, which is the target of both antibody drugs and vaccines. Given the continuous evolution of the virus and the identification of critical mutation sites, the World Health Organization (WHO) has named 5 variants of concern (VOCs): 4 are previously circulating VOCs, and 1 is currently circulating (Omicron). Due to multiple mutations in the spike protein, the recently emerged Omicron and descendent lineages have been shown to have the strongest ability to evade the neutralizing antibody (NAb) effects of current antibody drugs and vaccines. The development and characterization of broadly neutralizing antibodies (bNAbs) will provide broad strategies for the control of the sophisticated virus SARS-CoV-2. In this review, we describe how the virus evolves to escape NAbs and the potential neutralization mechanisms that associated with bNAbs. We also summarize progress in the development of bNAbs against SARS-CoV-2, human coronaviruses (CoVs) and other emerging pathogens and highlight their scientific and clinical significance.
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Affiliation(s)
- Zhiyang Ling
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunyan Yi
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyu Sun
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhuo Yang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing Sun
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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181
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Egia-Mendikute L, Bosch A, Prieto-Fernández E, Vila-Vecilla L, Zanetti SR, Lee SY, Jiménez-Lasheras B, García del Río A, Antoñana-Vildosola A, de Blas A, Velasco-Beltrán P, Serrano-Maciá M, Iruzubieta P, Mehrpouyan M, Goldberg EM, Bornheimer SJ, Embade N, Martínez-Chantar ML, López-Hoyos M, Mato JM, Millet Ó, Palazón A. A flow cytometry-based neutralization assay for simultaneous evaluation of blocking antibodies against SARS-CoV-2 variants. Front Immunol 2022; 13:1014309. [PMID: 36505411 PMCID: PMC9730237 DOI: 10.3389/fimmu.2022.1014309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/09/2022] [Indexed: 11/25/2022] Open
Abstract
Vaccines against SARS-CoV-2 have alleviated infection rates, hospitalization and deaths associated with COVID-19. In order to monitor humoral immunity, several serology tests have been developed, but the recent emergence of variants of concern has revealed the need for assays that predict the neutralizing capacity of antibodies in a fast and adaptable manner. Sensitive and fast neutralization assays would allow a timely evaluation of immunity against emerging variants and support drug and vaccine discovery efforts. Here we describe a simple, fast, and cell-free multiplexed flow cytometry assay to interrogate the ability of antibodies to prevent the interaction of Angiotensin-converting enzyme 2 (ACE2) and the receptor binding domain (RBD) of the original Wuhan-1 SARS-CoV-2 strain and emerging variants simultaneously, as a surrogate neutralization assay. Using this method, we demonstrate that serum antibodies collected from representative individuals at different time-points during the pandemic present variable neutralizing activity against emerging variants, such as Omicron BA.1 and South African B.1.351. Importantly, antibodies present in samples collected during 2021, before the third dose of the vaccine was administered, do not confer complete neutralization against Omicron BA.1, as opposed to samples collected in 2022 which show significant neutralizing activity. The proposed approach has a comparable performance to other established surrogate methods such as cell-based assays using pseudotyped lentiviral particles expressing the spike of SARS-CoV-2, as demonstrated by the assessment of the blocking activity of therapeutic antibodies (i.e. Imdevimab) and serum samples. This method offers a scalable, cost effective and adaptable platform for the dynamic evaluation of antibody protection in affected populations against variants of SARS-CoV-2.
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Affiliation(s)
- Leire Egia-Mendikute
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Alexandre Bosch
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Endika Prieto-Fernández
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Laura Vila-Vecilla
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Samanta Romina Zanetti
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - So Young Lee
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Borja Jiménez-Lasheras
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Ana García del Río
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Asier Antoñana-Vildosola
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Ander de Blas
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Paloma Velasco-Beltrán
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Marina Serrano-Maciá
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Paula Iruzubieta
- Servicio Inmunología, Hospital Universitario Marqués de Valdecilla-IDIVAL, Cantabria, Spain
| | | | | | | | - Nieves Embade
- Precision Medicine and Metabolism Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - María L. Martínez-Chantar
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Marcos López-Hoyos
- Servicio Inmunología, Hospital Universitario Marqués de Valdecilla-IDIVAL, Cantabria, Spain
| | - José M. Mato
- Precision Medicine and Metabolism Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Óscar Millet
- Precision Medicine and Metabolism Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Asís Palazón
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain,Ikerbasque, Basque Foundation for Science, Bizkaia, Spain,*Correspondence: Asís Palazón,
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182
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Xie L, Li J, Ai Y, He H, Chen X, Yin M, Li W, Huang W, Luo MY, He J. Current strategies for SARS-CoV-2 molecular detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:4625-4642. [PMID: 36349688 DOI: 10.1039/d2ay01313d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The molecular detection of SARS-CoV-2 is extremely important for the discovery and prevention of pandemic dissemination. Because SARS-CoV-2 is not always present in the samples that can be collected, the sample chosen for testing has inevitably become the key to the SARS-CoV-2 positive cases screening. The nucleotide amplification strategy mainly includes Q-PCR assays and isothermal amplification assays. The Q-PCR assay is the most used SARS-CoV-2 detection assay. Due to heavy expenditures and other drawbacks, isothermal amplification cannot replace the dominant position of the Q-PCR assay. The antibody-based detection combined with Q-PCR can help to find more positive cases than only using nucleotide amplification-based assays. Pooled testing based on Q-PCR significantly increases efficiency and reduces the cost of massive-scale screening. The endless stream of variants emerging across the world poses a great challenge to SARS-CoV-2 molecular detection. The multi-target assays and several other strategies have proved to be efficient in the detection of mutated SARS-CoV-2 variants. Further research work should concentrate on: (1) identifying more ideal sample plucking strategies, (2) ameliorating the Q-PCR primer and probes targeted toward mutated SARS-CoV-2 variants, (3) exploring more economical and precise isothermal amplification assays, and (4) developing more advanced strategies for antibody/antigen or engineered antibodies to ameliorate the antibody/antigen-based strategy.
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Affiliation(s)
- Lei Xie
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Junlin Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Ying Ai
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510080, China
| | - Haolan He
- Guangzhou Eighth People's Hospital, Guangzhou 510080, China
| | - Xiuyun Chen
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Mingyu Yin
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Wanxi Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Wenguan Huang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Min-Yi Luo
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Jinyang He
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
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183
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Acosta‐Gutiérrez S, Buckley J, Battaglia G. The Role of Host Cell Glycans on Virus Infectivity: The SARS-CoV-2 Case. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 10:e2201853. [PMID: 36417571 PMCID: PMC9811451 DOI: 10.1002/advs.202201853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Glycans are ubiquitously expressed sugars, coating the cell and protein surfaces. They are found on many proteins as either short and branched chains or long chains sticking out from special membrane proteins, known as proteoglycans. This sugar cushion, the glycocalyx, modulates specific interactions and protects the cell. Here it is shown that both the expression of proteoglycans and the glycans expressed on the surface of both the host and virus proteins have a critical role in modulating viral attachment to the cell. A mathematical model using SARS-Cov-2 as an archetypical virus to study the glycan role during infection is proposed. It is shown that this occurs via a tug-of-war of forces. On one side, the multivalent molecular recognition that viral proteins have toward specific host glycans and receptors. On the other side, the glycan steric repulsion that a virus must overcome to approach such specific receptors. By balancing both interactions, viral tropism can be predicted. In other words, the authors can map out the cells susceptible to virus infection in terms of receptors and proteoglycans compositions.
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Affiliation(s)
- Silvia Acosta‐Gutiérrez
- Institute for the Physics of Living SystemsUniversity College LondonLondonCentral LondonUK
- Institute of Structural and Molecular BiologyUniversity College LondonLondonCentral LondonUK
- Department of ChemistryUniversity College London20 Gordon StLondonCentral LondonWC1H 0AJUK
| | - Joseph Buckley
- Institute for the Physics of Living SystemsUniversity College LondonLondonCentral LondonUK
- Institute of Structural and Molecular BiologyUniversity College LondonLondonCentral LondonUK
- Department of ChemistryUniversity College London20 Gordon StLondonCentral LondonWC1H 0AJUK
| | - Giuseppe Battaglia
- Institute for the Physics of Living SystemsUniversity College LondonLondonCentral LondonUK
- Institute of Structural and Molecular BiologyUniversity College LondonLondonCentral LondonUK
- Department of ChemistryUniversity College London20 Gordon StLondonCentral LondonWC1H 0AJUK
- Institute for Bioengineering of Catalunya (IBEC)The Barcelona Institute of Science and TechnologyBarcelonaBarcelona08028Spain
- Catalan Institution for Research and Advances Studies (ICREA)BarcelonaSpain
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184
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Chan KC, Song Y, Xu Z, Shang C, Zhou R. SARS-CoV-2 Delta Variant: Interplay between Individual Mutations and Their Allosteric Synergy. Biomolecules 2022; 12:biom12121742. [PMID: 36551170 PMCID: PMC9775976 DOI: 10.3390/biom12121742] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/17/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022] Open
Abstract
Since its first appearance in April 2021, B.1.617.2, also termed variant Delta, catalyzed one major worldwide wave dominating the second year of coronavirus disease 2019 (COVID-19) pandemic. Despite its quick disappearance worldwide, the strong virulence caused by a few point mutations remains an unsolved problem largely. Along with the other two sublineages, the Delta variant harbors an accumulation of Spike protein mutations, including the previously identified L452R, E484Q, and the newly emerged T478K on its receptor binding domain (RBD). We used molecular dynamics (MD) simulations, in combination with free energy perturbation (FEP) calculations, to examine the effects of two combinative mutation sets, L452R + E484Q and L452R + T478K. Our dynamic trajectories reveal an enhancement in binding affinity between mutated RBD and the common receptor protein angiotensin converting enzyme 2 (ACE2) through a net increase in the buried molecular surface area of the binary complex. This enhanced binding, mediated through Gln493, sets the same stage for all three sublineages due to the presence of L452R mutation. The other mutation component, E484Q or T478K, was found to impact the RBD-ACE2 binding and help the variant to evade several monoclonal antibodies (mAbs) in a distinct manner. Especially for L452R + T478K, synergies between mutations are mediated through a complex residual and water interaction network and further enhance its binding to ACE2. Taking together, this study demonstrates that new variants of SARS-CoV-2 accomplish both "attack" (infection) and "defense" (antibody neutralization escape) with the same "polished sword" (mutated Spike RBD).
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Affiliation(s)
- Kevin C. Chan
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Shanghai Institute for Advanced Study, Zhejiang University, 799 Dangui Road, Shanghai 201203, China
| | - Yi Song
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zheng Xu
- BirenTech Research, Shanghai 201112, China
| | - Chun Shang
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Shanghai Institute for Advanced Study, Zhejiang University, 799 Dangui Road, Shanghai 201203, China
- Department of Chemistry, Columbia University, New York, NY 10027, USA
- The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Correspondence:
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185
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Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1. Nat Commun 2022; 13:7011. [PMID: 36384919 PMCID: PMC9668218 DOI: 10.1038/s41467-022-34506-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/26/2022] [Indexed: 11/17/2022] Open
Abstract
The Omicron BA.1 variant emerged in late 2021 and quickly spread across the world. Compared to the earlier SARS-CoV-2 variants, BA.1 has many mutations, some of which are known to enable antibody escape. Many of these antibody-escape mutations individually decrease the spike receptor-binding domain (RBD) affinity for ACE2, but BA.1 still binds ACE2 with high affinity. The fitness and evolution of the BA.1 lineage is therefore driven by the combined effects of numerous mutations. Here, we systematically map the epistatic interactions between the 15 mutations in the RBD of BA.1 relative to the Wuhan Hu-1 strain. Specifically, we measure the ACE2 affinity of all possible combinations of these 15 mutations (215 = 32,768 genotypes), spanning all possible evolutionary intermediates from the ancestral Wuhan Hu-1 strain to BA.1. We find that immune escape mutations in BA.1 individually reduce ACE2 affinity but are compensated by epistatic interactions with other affinity-enhancing mutations, including Q498R and N501Y. Thus, the ability of BA.1 to evade immunity while maintaining ACE2 affinity is contingent on acquiring multiple interacting mutations. Our results implicate compensatory epistasis as a key factor driving substantial evolutionary change for SARS-CoV-2 and are consistent with Omicron BA.1 arising from a chronic infection.
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186
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Updated vaccine protects against SARS-CoV-2 variants including Omicron (B.1.1.529) and prevents transmission in hamsters. Nat Commun 2022; 13:6644. [PMID: 36333374 PMCID: PMC9636174 DOI: 10.1038/s41467-022-34439-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
Current COVID-19 vaccines are based on prototypic spike sequences from ancestral 2019 SARS-CoV-2 strains. However, the ongoing pandemic is fueled by variants of concern (VOC) escaping vaccine-mediated protection. Here we demonstrate how immunization in hamsters using prototypic spike expressed from yellow fever 17D (YF17D) as vector blocks ancestral virus (B lineage) and VOC Alpha (B.1.1.7) yet fails to fully protect from Beta (B.1.351). However, the same YF17D vectored vaccine candidate with an evolved antigen induced considerably improved neutralizing antibody responses against VOCs Beta, Gamma (P.1) and the recently predominant Omicron (B.1.1.529), while maintaining immunogenicity against ancestral virus and VOC Delta (B.1.617.2). Thus vaccinated animals resisted challenge by all VOCs, including vigorous high titre exposure to the most difficult to cover Beta, Delta and Omicron variants, eliminating detectable virus and markedly improving lung pathology. Finally, vaccinated hamsters did not transmit Delta variant to non-vaccinated cage mates. Overall, our data illustrate how current first-generation COVID-19 vaccines may need to be updated to maintain efficacy against emerging VOCs and their spread at community level.
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187
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Miliu A, Lavergne A, Succo T, Laizé C, Andrieu A, Enfissi A, Enouf V, Van der Werf S, Blanchet D, Demar M, Carod JF, Carage T, Flamand C, Tirera S, Simon-Lorière E, Rousseau C, Rousset D. Dynamics of SARS-CoV-2 lineages in French Guiana in 2020-2021: 4 epidemic waves with cross-influences from Europe and South America. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 105:105370. [PMID: 36184049 PMCID: PMC9529336 DOI: 10.1016/j.meegid.2022.105370] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 11/30/2022]
Abstract
Since the first cases of SARS-CoV-2 infection in Wuhan in December 2019, this RNA virus gave rise to different viral lineages with different virological, epidemiological and immunological properties. Here we describe the dynamics of circulation of SARS-CoV-2 lineages in an Amazonian South American French overseas territory, French Guiana (FG). The data analyzed are based on the general epidemic course, and genomic surveillance data come from whole genome sequencing (WGS) as well as typing PCRs. From March 2020 to October 2021, four COVID-19 epidemic waves were observed in FG with an evolution of viral lineages influenced by virus introductions from continental France and above all by land-based introductions from neighbouring countries. The third epidemic wave from March to June 2021 was driven by a predominant Gamma introduced from Brazil and a less frequent Alpha introduced from France. This coexistence was completely substituted by Delta that initiated the fourth epidemic wave.
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Affiliation(s)
- Alexandra Miliu
- Santé publique France, Regional unit French Guiana, Cayenne, French Guiana.
| | - Anne Lavergne
- National Reference Center for Respiratory Viruses, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Tiphanie Succo
- Santé publique France, Regional unit French Guiana, Cayenne, French Guiana
| | - Claire Laizé
- Agence régionale de santé (ARS) Guyane, Cayenne, French Guiana
| | - Audrey Andrieu
- Santé publique France, Regional unit French Guiana, Cayenne, French Guiana
| | - Antoine Enfissi
- National Reference Center for Respiratory Viruses, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Vincent Enouf
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Sylvie Van der Werf
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France.
| | - Denis Blanchet
- Clinical Laboratory, Centre Hospitalier de Cayenne (CHC), Cayenne, French Guiana
| | - Magalie Demar
- Clinical Laboratory, Centre Hospitalier de Cayenne (CHC), Cayenne, French Guiana.
| | - Jean-François Carod
- Clinical laboratory of Centre Hospitalier de l'Ouest Guyanais (CHOG), Saint Laurent du Maroni, French Guiana.
| | - Thierry Carage
- Carage laboratory associated to Kourou hospital center (CHK), Kourou, French Guiana
| | - Claude Flamand
- National Reference Center for Respiratory Viruses, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Sourakhata Tirera
- National Reference Center for Respiratory Viruses, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Etienne Simon-Lorière
- Institut Pasteur, Université de Paris, G5 Evolutionary Genomics of RNA viruses, 75015 Paris, France.
| | - Cyril Rousseau
- Santé publique France, Regional unit French Guiana, Cayenne, French Guiana
| | - Dominique Rousset
- National Reference Center for Respiratory Viruses, Institut Pasteur de la Guyane, Cayenne, French Guiana.
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188
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In silico analysis of SARS-CoV-2 spike protein N501Y and N501T mutation effects on human ACE2 binding. J Mol Graph Model 2022; 116:108260. [PMID: 35809511 PMCID: PMC9247859 DOI: 10.1016/j.jmgm.2022.108260] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 05/05/2022] [Accepted: 06/21/2022] [Indexed: 12/14/2022]
Abstract
The SARS-CoV-2 is an RNA-based virus and the most vital step of its survival is the attachment to hACE2 through its spike protein. Although SARS-CoV-2 has the ability to maintain high accurate replication and it can be accepted as a low mutation risked virus, it already showed more than nine thousand mutations in spike protein, of which 44 mutations are located within a 3.2 Å interacting distance from the hACE2 receptor. Mutations on spike protein, N501Y and N501T raised serious concerns for higher transmissibility and resistance towards current vaccines. In the current study, the mutational outcomes of N501Y and N501T on the hACE2-SARS CoV-2 spike protein complexation were analyzed by employing all-atom classic molecular dynamics (MD) simulations. These simulations revealed that both N501Y and N501T mutations increased the binding strength of spike protein to the host hACE2, predicted by binding free energy analysis via MM/GBSA rescoring scheme. This study highlights the importance of energy-based analysis for identifying mutational outcomes and will shed light on handling long-term and effective treatment strategies including repurposing anti-viral drugs, anti-SARS-CoV-2 antibodies, vaccines, and antisense based-therapies.
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189
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Bhadane R, Salo-Ahen OMH. High-Throughput Molecular Dynamics-Based Alchemical Free Energy Calculations for Predicting the Binding Free Energy Change Associated with the Selected Omicron Mutations in the Spike Receptor-Binding Domain of SARS-CoV-2. Biomedicines 2022; 10:2779. [PMID: 36359299 PMCID: PMC9687918 DOI: 10.3390/biomedicines10112779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/17/2022] [Accepted: 10/25/2022] [Indexed: 11/10/2023] Open
Abstract
The ongoing pandemic caused by SARS-CoV-2 has gone through various phases. Since the initial outbreak, the virus has mutated several times, with some lineages showing even stronger infectivity and faster spread than the original virus. Among all the variants, omicron is currently classified as a variant of concern (VOC) by the World Health Organization, as the previously circulating variants have been replaced by it. In this work, we have focused on the mutations observed in omicron sub lineages BA.1, BA.2, BA.4 and BA.5, particularly at the receptor-binding domain (RBD) of the spike protein that is responsible for the interactions with the host ACE2 receptor and binding of antibodies. Studying such mutations is particularly important for understanding the viral infectivity, spread of the disease and for tracking the escape routes of this virus from antibodies. Molecular dynamics (MD) based alchemical free energy calculations have been shown to be very accurate in predicting the free energy change, due to a mutation that could have a deleterious or a stabilizing effect on either the protein itself or its binding affinity to another protein. Here, we investigated the significance of five spike RBD mutations on the stability of the spike protein binding to ACE2 by free energy calculations using high throughput MD simulations. For comparison, we also used conventional MD simulations combined with a Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) based approach, and compared our results with the available experimental data. Overall, the alchemical free energy calculations performed far better than the MM-GBSA approach in predicting the individual impact of the mutations. When considering the experimental variation, the alchemical free energy method was able to produce a relatively accurate prediction for N501Y, the mutant that has previously been reported to increase the binding affinity to hACE2. On the other hand, the other individual mutations seem not to have a significant effect on the spike RBD binding affinity towards hACE2.
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Affiliation(s)
- Rajendra Bhadane
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland
| | - Outi M. H. Salo-Ahen
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland
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190
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Lam JH, Shivhare D, Chia TW, Chew SL, Sinsinbar G, Aw TY, Wong S, Venkataraman S, Lim FWI, Vandepapeliere P, Nallani M. Artificial Cell Membrane Polymersome-Based Intranasal Beta Spike Formulation as a Second Generation Covid-19 Vaccine. ACS NANO 2022; 16:16757-16775. [PMID: 36223228 PMCID: PMC9578649 DOI: 10.1021/acsnano.2c06350] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/06/2022] [Indexed: 05/25/2023]
Abstract
Current parenteral coronavirus disease 2019 (Covid-19) vaccines inadequately protect against infection of the upper respiratory tract. Additionally, antibodies generated by wild type (WT) spike-based vaccines poorly neutralize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. To address the need for a second-generation vaccine, we have initiated a preclinical program to produce and evaluate a potential candidate. Our vaccine consists of recombinant Beta spike protein coadministered with synthetic CpG adjuvant. Both components are encapsulated within artificial cell membrane (ACM) polymersomes, synthetic nanovesicles efficiently internalized by antigen presenting cells, including dendritic cells, enabling targeted delivery of cargo for enhanced immune responses. ACM vaccine is immunogenic in C57BL/6 mice and Golden Syrian hamsters, evoking high serum IgG and neutralizing responses. Compared to an ACM-WT spike vaccine that generates predominantly WT-neutralizing antibodies, the ACM-Beta spike vaccine induces antibodies that neutralize WT and Beta viruses equally. Intramuscular (IM)-immunized hamsters are strongly protected from weight loss and other clinical symptoms after the Beta challenge but show delayed viral clearance in the upper airway. With intranasal (IN) immunization, however, neutralizing antibodies are generated in the upper airway concomitant with rapid and potent reduction of viral load. Moreover, antibodies are cross-neutralizing and show good activity against Omicron. Safety is evaluated in New Zealand white rabbits in a repeated dose toxicological study under Good Laboratory Practice (GLP) conditions. Three doses, IM or IN, at two-week intervals do not induce an adverse effect or systemic toxicity. Cumulatively, these results support the application for a Phase 1 clinical trial of ACM-polymersome-based Covid-19 vaccine (ClinicalTrials.gov identifier: NCT05385991).
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Affiliation(s)
- Jian Hang Lam
- ACM Biolabs Pte Ltd., 71
Nanyang Drive, #02M-02, NTU Innovation Center, 638075, Singapore
| | - Devendra Shivhare
- ACM Biolabs Pte Ltd., 71
Nanyang Drive, #02M-02, NTU Innovation Center, 638075, Singapore
| | - Teck Wan Chia
- ACM Biolabs Pte Ltd., 71
Nanyang Drive, #02M-02, NTU Innovation Center, 638075, Singapore
| | - Suet Li Chew
- ACM Biolabs Pte Ltd., 71
Nanyang Drive, #02M-02, NTU Innovation Center, 638075, Singapore
| | - Gaurav Sinsinbar
- ACM Biolabs Pte Ltd., 71
Nanyang Drive, #02M-02, NTU Innovation Center, 638075, Singapore
| | - Ting Yan Aw
- ACM Biolabs Pte Ltd., 71
Nanyang Drive, #02M-02, NTU Innovation Center, 638075, Singapore
| | - Siamy Wong
- ACM Biolabs Pte Ltd., 71
Nanyang Drive, #02M-02, NTU Innovation Center, 638075, Singapore
| | - Shrinivas Venkataraman
- ACM Biolabs Pte Ltd., 71
Nanyang Drive, #02M-02, NTU Innovation Center, 638075, Singapore
| | - Francesca Wei Inng Lim
- Department of Hematology, Singapore General
Hospital, Outram Road, Block 7, Level 2, 169608,
Singapore
| | | | - Madhavan Nallani
- ACM Biolabs Pte Ltd., 71
Nanyang Drive, #02M-02, NTU Innovation Center, 638075, Singapore
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191
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Cuypers L, Dellicour S, Hong SL, Potter BI, Verhasselt B, Vereecke N, Lambrechts L, Durkin K, Bours V, Klamer S, Bayon-Vicente G, Vael C, Ariën KK, De Mendonca R, Soetens O, Michel C, Bearzatto B, Naesens R, Gras J, Vankeerberghen A, Matheeussen V, Martens G, Obbels D, Lemmens A, Van den Poel B, Van Even E, De Rauw K, Waumans L, Reynders M, Degosserie J, Maes P, André E, Baele G. Two Years of Genomic Surveillance in Belgium during the SARS-CoV-2 Pandemic to Attain Country-Wide Coverage and Monitor the Introduction and Spread of Emerging Variants. Viruses 2022; 14:2301. [PMID: 36298856 PMCID: PMC9612291 DOI: 10.3390/v14102301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/21/2022] Open
Abstract
An adequate SARS-CoV-2 genomic surveillance strategy has proven to be essential for countries to obtain a thorough understanding of the variants and lineages being imported and successfully established within their borders. During 2020, genomic surveillance in Belgium was not structurally implemented but performed by individual research laboratories that had to acquire the necessary funds themselves to perform this important task. At the start of 2021, a nationwide genomic surveillance consortium was established in Belgium to markedly increase the country's genomic sequencing efforts (both in terms of intensity and representativeness), to perform quality control among participating laboratories, and to enable coordination and collaboration of research projects and publications. We here discuss the genomic surveillance efforts in Belgium before and after the establishment of its genomic sequencing consortium, provide an overview of the specifics of the consortium, and explore more details regarding the scientific studies that have been published as a result of the increased number of Belgian SARS-CoV-2 genomes that have become available.
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Affiliation(s)
- Lize Cuypers
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1000 Brussels, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Samuel L. Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Barney I. Potter
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Bruno Verhasselt
- Department of Diagnostic Sciences, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
| | - Nick Vereecke
- PathoSense BV, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Laurens Lambrechts
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Keith Durkin
- Laboratory of Human Genetics, GIGA Research Institute, 4000 Liège, Belgium
| | - Vincent Bours
- Laboratory of Human Genetics, GIGA Research Institute, 4000 Liège, Belgium
- Department of Human Genetics, University Hospital of Liège, 4000 Liège, Belgium
| | - Sofieke Klamer
- Scientific Directorate of Epidemiology and Public Health, Sciensano, 1050 Brussels, Belgium
| | - Guillaume Bayon-Vicente
- Department of Proteomic and Microbiology, Research Institute for Biosciences, University of Mons, 7000 Mons, Belgium
| | - Carl Vael
- Clinical Laboratory, AZ Klina, 2930 Brasschaat, Belgium
| | - Kevin K. Ariën
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium
- Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Department of Biomedical Sciences, University of Antwerp, 2000 Antwerp, Belgium
| | - Ricardo De Mendonca
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, 1000 Brussels, Belgium
| | - Oriane Soetens
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Charlotte Michel
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), 1000 Brussels, Belgium
| | - Bertrand Bearzatto
- Center for Applied Molecular Technologies (CTMA), Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain (UCLouvain), 1000 Brussels, Belgium
| | - Reinout Naesens
- Department of Medical Microbiology, Ziekenhuis Netwerk Antwerpen, 2020 Antwerp, Belgium
| | - Jeremie Gras
- Institute of Pathology and Genetics (IPG), 6041 Gosselies, Belgium
| | - Anne Vankeerberghen
- Laboratory of Molecular Biology, Campus Aalst-Asse-Ninove, Onze-Lieve-Vrouwziekenhuis, 9300 Aalst, Belgium
| | - Veerle Matheeussen
- Laboratory of Medical Microbiology, Department of Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610 Wilrijk, Belgium
| | - Geert Martens
- Department of Laboratory Medicine, AZ Delta General Hospital, 8800 Roeselare, Belgium
| | - Dagmar Obbels
- Clinical Laboratory, Imelda Hospital, 2820 Bonheiden, Belgium
| | - Ann Lemmens
- Laboratory of Clinical Biology, AZ Sint-Maarten Hospital, 2800 Mechelen, Belgium
| | - Bea Van den Poel
- Clinical Laboratory, General Hospital Jan Portaels, 1800 Vilvoorde, Belgium
| | - Ellen Van Even
- Clinical Laboratory of Microbiology, HH Hospital Lier, 2500 Lier, Belgium
| | - Klara De Rauw
- Laboratory of Clinical Biology, AZ Sint Lucas Hospital, 9000 Ghent, Belgium
| | - Luc Waumans
- Clinical Laboratory, Jessa Hospital, 3500 Hasselt, Belgium
| | - Marijke Reynders
- Department of Laboratory Medicine, Medical Microbiology, AZ Sint-Jan Bruges-Ostend AV, 8000 Bruges, Belgium
| | - Jonathan Degosserie
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, CHU UCL Namur, 5530 Yvoir, Belgium
- Next Generation Sequencing Platform, Molecular Diagnostic Center, CHU UCL Namur, 5530 Yvoir, Belgium
| | - Piet Maes
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Emmanuel André
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
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192
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Iša P, Taboada B, García-López R, Boukadida C, Ramírez-González JE, Vázquez-Pérez JA, Hernández-Terán A, Romero-Espinoza JÁ, Muñoz-Medina JE, Grajales-Muñiz C, Rincón-Rubio A, Matías-Florentino M, Sanchez-Flores A, Mendieta-Condado E, Barrera-Badillo G, López S, Hernández-Rivas L, López-Martínez I, Ávila-Ríos S, Arias CF. Metagenomic analysis reveals differences in the co-occurrence and abundance of viral species in SARS-CoV-2 patients with different severity of disease. BMC Infect Dis 2022; 22:792. [PMID: 36261802 PMCID: PMC9580447 DOI: 10.1186/s12879-022-07783-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/06/2022] [Indexed: 11/22/2022] Open
Abstract
Background SARS-CoV-2 infections have a wide spectrum of clinical manifestations whose causes are not completely understood. Some human conditions predispose to severe outcome, like old age or the presence of comorbidities, but many other facets, including coinfections with other viruses, remain poorly characterized.
Methods In this study, the eukaryotic fraction of the respiratory virome of 120 COVID-19 patients was characterized through whole metagenomic sequencing. Results Genetic material from respiratory viruses was detected in 25% of all samples, whereas human viruses other than SARS-CoV-2 were found in 80% of them. Samples from hospitalized and deceased patients presented a higher prevalence of different viruses when compared to ambulatory individuals. Small circular DNA viruses from the Anneloviridae (Torque teno midi virus 8, TTV-like mini virus 19 and 26) and Cycloviridae families (Human associated cyclovirus 10), Human betaherpesvirus 6, were found to be significantly more abundant in samples from deceased and hospitalized patients compared to samples from ambulatory individuals. Similarly, Rotavirus A, Measles morbillivirus and Alphapapilomavirus 10 were significantly more prevalent in deceased patients compared to hospitalized and ambulatory individuals. Conclusions Results show the suitability of using metagenomics to characterize a broader peripheric virological landscape of the eukaryotic virome in SARS-CoV-2 infected patients with distinct disease outcomes. Identified prevalent viruses in hospitalized and deceased patients may prove important for the targeted exploration of coinfections that may impact prognosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07783-8.
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Affiliation(s)
- Pavel Iša
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | | | | | | | | | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Concepción Grajales-Muñiz
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Alma Rincón-Rubio
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Margarita Matías-Florentino
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Edgar Mendieta-Condado
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Ciudad de Mexico, Mexico
| | - Gisela Barrera-Badillo
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Ciudad de Mexico, Mexico
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Lucía Hernández-Rivas
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Ciudad de Mexico, Mexico
| | - Irma López-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Ciudad de Mexico, Mexico
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Carlos F Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Mannsverk S, Bergholm J, Palanisamy N, Ellström P, Kaden R, Lindh J, Lennerstrand J. SARS-CoV-2 variants of concern and spike protein mutational dynamics in a Swedish cohort during 2021, studied by Nanopore sequencing. Virol J 2022; 19:164. [PMID: 36258215 DOI: 10.1186/s12985-022-01896-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/08/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Since the beginning of the COVID-19 pandemic, new variants of significance to public health have emerged. Consequently, early detection of new mutations and variants through whole-genome sequencing remains crucial to assist health officials in employing appropriate public health measures. METHODS We utilized the ARTIC Network SARS-CoV-2 tiled amplicon approach and Nanopore sequencing to sequence 4,674 COVID-19 positive patient samples from Uppsala County, Sweden, between week 15 and 52 in 2021. Using this data, we mapped the circulating variants of concern (VOC) in the county over time and analysed the Spike (S) protein mutational dynamics in the Delta variant throughout 2021. RESULTS The distribution of the SARS-CoV-2 VOC matched the national VOC distribution in Sweden, in 2021. In the S protein of the Delta variant, we detected mutations attributable to variants under monitoring and variants of interest (e.g., E484Q, Q613H, Q677H, A222V and Y145H) and future VOC (e.g., T95I and Y144 deletion, which are signature mutations in the Omicron variant). We also frequently detected some less well-described S protein mutations in our Delta sequences, that might play a role in shaping future emerging variants. These include A262S, Q675K, I850L, Q1201H, V1228L and M1237I. Lastly, we observed that some of the Delta variant's signature mutations were underrepresented in our study due to artifacts of the used bioinformatics tools, approach and sequencing method. We therefore discuss some pitfalls and considerations when sequencing SARS-CoV-2 genomes. CONCLUSION Our results suggest that genomic surveillance in a small, representative cohort can be used to make predictions about the circulating variants nationally. Moreover, we show that detection of transient mutations in currently circulating variants can give valuable clues to signature mutations of future VOC. Here we suggest six such mutations, that we detected frequently in the Delta variant during 2021. Lastly, we report multiple systematic errors that occurred when following the ARTIC Network SARS-CoV-2 tiled amplicon approach using the V3 primers and Nanopore sequencing, which led to the masking of some of the important signature mutations in the Delta sequences.
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Affiliation(s)
- Steinar Mannsverk
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden.,Department of Cell and Molecular Biology, Uppsala University, 752 37, Uppsala, Sweden
| | - Julia Bergholm
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden
| | | | - Patrik Ellström
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden
| | - René Kaden
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden
| | - Johan Lindh
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden
| | - Johan Lennerstrand
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden.
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194
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Susceptibility to SARS-CoV-2 Omicron following ChAdOx1 nCoV-19 and BNT162b2 versus CoronaVac vaccination. iScience 2022; 25:105379. [PMID: 36277260 PMCID: PMC9575314 DOI: 10.1016/j.isci.2022.105379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 09/29/2022] [Accepted: 10/13/2022] [Indexed: 11/24/2022] Open
Abstract
The emergence of SARS-CoV-2 variants raises concerns of reduced COVID-19 vaccine efficacy. We investigated the humoral immunity in uninfected and previously infected ChAdOx1 nCoV-19, BNT162b2 and CoronaVac vaccinees, who have received complete regimes of vaccines by means of a SARS-CoV-2 surrogate virus blocking test. The ChAdOx1 nCoV-19 (p = 0.0013) and BNT162b2 (p = 0.0005) vaccines induced significant higher blocking activity with longer durability against the Spike (S) protein receptor binding domain (RBD) of wild type SARS-CoV-2 than the CoronaVac vaccine in uninfected vaccinees. Prior infection improved protection in the CoronaVac vaccinees. Subsequent investigation on the breadth of SARS-CoV-2 vaccine-induced antibody blocking responses, revealed that all vaccine platforms cross-protected uninfected vaccinees against all variant of concerns, except Omicron. Prior infection protected the ChAdOx1 nCoV-19 and BNT162b2 vaccinees against Omicron but not CoronaVac vaccinees. Our study suggests that vaccines that induce broader sterilizing immunity are essential to fight against fast-emerging variants. ChAdOx1 nCoV-19, BNT162b2, and CoronaVac did not protect against Omicron variant Combination of prior infection and ChAdOx1 nCoV-19 or BNT162b2 cross-protected against Omicron variant The CoronaVac vaccine had no protective effect against Omicron regardless of infection status Prolonged target antigen exposure and target diversification are key for next SARS-CoV-2 vaccines
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195
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SARS-CoV-2 Variant-Specific Infectivity and Immune Profiles Are Detectable in a Humanized Lung Mouse Model. Viruses 2022; 14:v14102272. [PMID: 36298826 PMCID: PMC9612296 DOI: 10.3390/v14102272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/09/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
Small animal models that accurately model pathogenesis of SARS-CoV-2 variants are required for ongoing research efforts. We modified our human immune system mouse model to support replication of SARS-CoV-2 by implantation of human lung tissue into the mice to create TKO-BLT-Lung (L) mice and compared infection with two different variants in a humanized lung model. Infection of TKO-BLT-L mice with SARS-CoV-2 recapitulated the higher infectivity of the B.1.1.7 variant with more animals becoming infected and higher sustained viral loads compared to mice challenged with an early B lineage (614D) virus. Viral lesions were observed in lung organoids but no differences were detected between the viral variants as expected. Partially overlapping but distinct immune profiles were also observed between the variants with a greater Th1 profile in VIDO-01 and greater Th2 profile in B.1.1.7 infection. Overall, the TKO-BLT-L mouse supported SARS-CoV-2 infection, recapitulated key known similarities and differences in infectivity and pathogenesis as well as revealing previously unreported differences in immune responses between the two viral variants. Thus, the TKO-BLT-L model may serve as a useful animal model to study the immunopathobiology of newly emerging variants in the context of genuine human lung tissue and immune cells.
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196
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Taft JM, Weber CR, Gao B, Ehling RA, Han J, Frei L, Metcalfe SW, Overath MD, Yermanos A, Kelton W, Reddy ST. Deep mutational learning predicts ACE2 binding and antibody escape to combinatorial mutations in the SARS-CoV-2 receptor-binding domain. Cell 2022; 185:4008-4022.e14. [PMID: 36150393 PMCID: PMC9428596 DOI: 10.1016/j.cell.2022.08.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 06/22/2022] [Accepted: 08/25/2022] [Indexed: 01/26/2023]
Abstract
The continual evolution of SARS-CoV-2 and the emergence of variants that show resistance to vaccines and neutralizing antibodies threaten to prolong the COVID-19 pandemic. Selection and emergence of SARS-CoV-2 variants are driven in part by mutations within the viral spike protein and in particular the ACE2 receptor-binding domain (RBD), a primary target site for neutralizing antibodies. Here, we develop deep mutational learning (DML), a machine-learning-guided protein engineering technology, which is used to investigate a massive sequence space of combinatorial mutations, representing billions of RBD variants, by accurately predicting their impact on ACE2 binding and antibody escape. A highly diverse landscape of possible SARS-CoV-2 variants is identified that could emerge from a multitude of evolutionary trajectories. DML may be used for predictive profiling on current and prospective variants, including highly mutated variants such as Omicron, thus guiding the development of therapeutic antibody treatments and vaccines for COVID-19.
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Affiliation(s)
- Joseph M. Taft
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland,Botnar Research Centre for Child Health, Basel 4058, Switzerland
| | - Cédric R. Weber
- Alloy Therapeutics (Switzerland) AG, Basel 4058, Switzerland
| | - Beichen Gao
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland,Botnar Research Centre for Child Health, Basel 4058, Switzerland
| | - Roy A. Ehling
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Jiami Han
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland,Botnar Research Centre for Child Health, Basel 4058, Switzerland
| | - Lester Frei
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland,Botnar Research Centre for Child Health, Basel 4058, Switzerland
| | - Sean W. Metcalfe
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Max D. Overath
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland,Botnar Research Centre for Child Health, Basel 4058, Switzerland,Department of Biology, Institute of Microbiology and Immunology, ETH Zurich, Zurich 8093, Switzerland,Department of Pathology and Immunology, University of Geneva, Geneva 1211, Switzerland
| | - William Kelton
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand
| | - Sai T. Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland,Botnar Research Centre for Child Health, Basel 4058, Switzerland,Corresponding author
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197
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Özbay Kurt FG, Lepper A, Gerhards C, Roemer M, Lasser S, Arkhypov I, Bitsch R, Bugert P, Altevogt P, Gouttefangeas C, Neumaier M, Utikal J, Umansky V. Booster dose of mRNA vaccine augments waning T cell and antibody responses against SARS-CoV-2. Front Immunol 2022; 13:1012526. [PMID: 36311732 PMCID: PMC9597683 DOI: 10.3389/fimmu.2022.1012526] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/26/2022] [Indexed: 12/03/2022] Open
Abstract
A gradual decay in humoral and cellular immune responses over time upon SAR1S-CoV-2 vaccination may cause a lack of protective immunity. We conducted a longitudinal analysis of antibodies, T cells, and monocytes in 25 participants vaccinated with mRNA or ChAdOx1-S up to 12 weeks after the 3rd (booster) dose with mRNA vaccine. We observed a substantial increase in antibodies and CD8 T cells specific for the spike protein of SARS-CoV-2 after vaccination. Moreover, vaccination induced activated T cells expressing CD69, CD137 and producing IFN-γ and TNF-α. Virus-specific CD8 T cells showed predominantly memory phenotype. Although the level of antibodies and frequency of virus-specific T cells reduced 4-6 months after the 2nd dose, they were augmented after the 3rd dose followed by a decrease later. Importantly, T cells generated after the 3rd vaccination were also reactive against Omicron variant, indicated by a similar level of IFN-γ production after stimulation with Omicron peptides. Breakthrough infection in participants vaccinated with two doses induced more SARS-CoV-2-specific T cells than the booster vaccination. We found an upregulation of PD-L1 expression on monocytes but no accumulation of myeloid cells with MDSC-like immunosuppressive phenotype after the vaccination. Our results indicate that the 3rd vaccination fosters antibody and T cell immune response independently from vaccine type used for the first two injections. However, such immune response is attenuated over time, suggesting thereby the need for further vaccinations.
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Affiliation(s)
- Feyza Gül Özbay Kurt
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany
- DKFZ-Hector Cancer Institute, University Medical Center Mannheim, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Alisa Lepper
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany
- DKFZ-Hector Cancer Institute, University Medical Center Mannheim, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Catharina Gerhards
- Institute for Clinical Chemistry, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Mathis Roemer
- Institute for Clinical Chemistry, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Samantha Lasser
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany
- DKFZ-Hector Cancer Institute, University Medical Center Mannheim, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Ihor Arkhypov
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany
- DKFZ-Hector Cancer Institute, University Medical Center Mannheim, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Rebekka Bitsch
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany
- DKFZ-Hector Cancer Institute, University Medical Center Mannheim, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Peter Bugert
- German Red Cross Blood Service Baden-Württemberg – Hessen, Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Peter Altevogt
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany
- DKFZ-Hector Cancer Institute, University Medical Center Mannheim, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Cécile Gouttefangeas
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Michael Neumaier
- Institute for Clinical Chemistry, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Jochen Utikal
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany
- DKFZ-Hector Cancer Institute, University Medical Center Mannheim, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Viktor Umansky
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany
- DKFZ-Hector Cancer Institute, University Medical Center Mannheim, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
- *Correspondence: Viktor Umansky,
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Jaago M, Rähni A, Pupina N, Pihlak A, Sadam H, Tuvikene J, Avarlaid A, Planken A, Planken M, Haring L, Vasar E, Baćević M, Lambert F, Kalso E, Pussinen P, Tienari PJ, Vaheri A, Lindholm D, Timmusk T, Ghaemmaghami AM, Palm K. Differential patterns of cross-reactive antibody response against SARS-CoV-2 spike protein detected for chronically ill and healthy COVID-19 naïve individuals. Sci Rep 2022; 12:16817. [PMID: 36207326 PMCID: PMC9540097 DOI: 10.1038/s41598-022-20849-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
Immunity to previously encountered viruses can alter response to unrelated pathogens. We reasoned that similar mechanism may also involve SARS-CoV-2 and thereby affect the specificity and the quality of the immune response against the virus. Here, we employed high-throughput next generation phage display method to explore the link between antibody immune response to previously encountered antigens and spike (S) glycoprotein. By profiling the antibody response in COVID-19 naïve individuals with a diverse clinical history (including cardiovascular, neurological, or oncological diseases), we identified 15 highly antigenic epitopes on spike protein that showed cross-reactivity with antigens of seasonal, persistent, latent or chronic infections from common human viruses. We observed varying degrees of cross-reactivity of different viral antigens with S in an epitope-specific manner. The data show that pre-existing SARS-CoV-2 S1 and S2 cross-reactive serum antibody is readily detectable in pre-pandemic cohort. In the severe COVID-19 cases, we found differential antibody response to the 15 defined antigenic and cross-reactive epitopes on spike. We also noted that despite the high mutation rates of Omicron (B.1.1.529) variants of SARS-CoV-2, some of the epitopes overlapped with the described mutations. Finally, we propose that the resolved epitopes on spike if targeted by re-called antibody response from SARS-CoV-2 infections or vaccinations can function in chronically ill COVID-19 naïve/unvaccinated individuals as immunogenic targets to boost antibodies augmenting the chronic conditions. Understanding the relationships between prior antigen exposure at the antibody epitope level and the immune response to subsequent infections with viruses from a different strain is paramount to guiding strategies to exit the COVID-19 pandemic.
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Affiliation(s)
- Mariliis Jaago
- Protobios LLC, Tallinn, Estonia.,Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Annika Rähni
- Protobios LLC, Tallinn, Estonia.,Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | | | | | - Helle Sadam
- Protobios LLC, Tallinn, Estonia.,Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Jürgen Tuvikene
- Protobios LLC, Tallinn, Estonia.,Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.,DXLabs LLC, Tallinn, Estonia
| | - Annela Avarlaid
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Anu Planken
- North Estonia Medical Centre Foundation, Tallinn, Estonia
| | - Margus Planken
- North Estonia Medical Centre Foundation, Tallinn, Estonia
| | - Liina Haring
- Institute of Clinical Medicine, Psychiatry Clinic of Tartu University Hospital, University of Tartu, Tartu, Estonia
| | - Eero Vasar
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.,Center of Excellence for Genomics and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Miljana Baćević
- Dental Biomaterial Research Unit (d-BRU), Faculty of Medicine, University of Liege, Liege, Belgium
| | - France Lambert
- Department of Periodontology and Oral Surgery, Faculty of Medicine, University of Liege, Liege, Belgium
| | - Eija Kalso
- Department of Anaesthesiology, Intensive Care and Pain Medicine, Helsinki University Hospital, Helsinki, Finland.,SleepWell Research Programme, Department of Pharmacology, University of Helsinki, Helsinki, Finland
| | - Pirkko Pussinen
- Oral and Maxillofacial Diseases, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Pentti J Tienari
- Translational Immunology Research Program, Department of Neurology, Neurocenter, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Antti Vaheri
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Dan Lindholm
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Tõnis Timmusk
- Protobios LLC, Tallinn, Estonia.,Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Amir M Ghaemmaghami
- Immunology and Immuno-Bioengineering Group, School of Life Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, United Kingdom
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199
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Fluorescent nanodiamond-based spin-enhanced lateral flow immunoassay for detection of SARS-CoV-2 nucleocapsid protein and spike protein from different variants. Anal Chim Acta 2022; 1230:340389. [PMID: 36192062 PMCID: PMC9472599 DOI: 10.1016/j.aca.2022.340389] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/30/2022] [Accepted: 09/09/2022] [Indexed: 11/24/2022]
Abstract
SARS-CoV-2 viruses, responsible for the COVID-19 pandemic, continues to evolve into new mutations, which poses a significant threat to public health. Current testing methods have some limitations, such as long turnaround times, high costs, and professional laboratory requirements. In this report, the novel Spin-Enhanced Lateral Flow Immunoassay (SELFIA) platform and fluorescent nanodiamond (FND) reporter were utilized for the rapid detection of SARS-CoV-2 nucleocapsid and spike antigens from different variants, including wild-type (Wuhan-1), Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529). The SARS-CoV-2 antibodies were conjugated with FND via nonspecific binding, enabling the detection of SARS-CoV-2 antigens via both direct and competitive SELFIA format. Direct SELFIA was performed by directly adding the SARS-CoV-2 antibodies-conjugated FND on the antigens-immobilized nitrocellulose (NC) membrane. Conversely, the SARS-CoV-2 antigen-containing sample was first incubated with the antibodies-conjugated FND, and then dropped on the antigen-immobilized NC membrane to carry out the competitive SELFIA. The results suggested that S44F anti-S IgG antibody can be efficiently used for the detection of wild-type, Alpha, Delta, and Omicron variants spike antigens. Findings were comparable in direct SELFIA, competitive SELFIA, and ELISA. A detection limit of 1.94, 0.77, 1.14, 1.91, and 1.68 ng/mL can be achieved for SARS-CoV-2 N protein, wild-type, Alpha, Delta, and Omicron S proteins, respectively, via competitive SELFIA assay. These results suggest that a direct SELFIA assay can be used for antibody/antigen pair screening in diagnosis development, while the competitive SELFIA assay can serve as an accurate quantitative diagnostic tool. The simplicity and rapidity of the SELFIA platform were demonstrated, which can be leveraged in the detection of other infectious diseases in the near future.
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200
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Takke A, Zarekar M, Muthuraman V, Ashar A, Patil K, Badhavkar A, Trivedi J, Khargekar N, Madkaikar M, Banerjee A. Comparative study of clinical features and vaccination status in Omicron and non-Omicron infected patients during the third wave in Mumbai, India. J Family Med Prim Care 2022; 11:6135-6142. [PMID: 36618147 PMCID: PMC9810849 DOI: 10.4103/jfmpc.jfmpc_430_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 11/11/2022] Open
Abstract
Objectives The Omicron variant-mediated COVID-19 wave is responsible for a global tsunami of cases. There is scarce data about the clinical and epidemiological characteristic analyses of the third wave. We present the data of COVID-19 patients from Mumbai region during the early third wave by taking S-gene target failure (SGTF) as a proxy for probable Omicron cases. Methods We collected retrospective data of RT-PCR-confirmed (COVID-19) patients, and measured the proportion of possible Omicron cases by SGTF. We segregated and analyzed the clinical and lab data of patients with outcomes such as differing symptoms, vaccination coverage, previous infection, and travel history. We also performed a trend analysis of Mumbai's COVID-19 data before and during the third wave. Results All patients had mild clinical symptoms while few were asymptomatic. Myalgia was more significantly present in SGTF/Omicron cases compared to non-SGTF/Delta patients. Out of the total 101 COVID-positive individuals, 94 individuals (93%) had taken two doses of COVID vaccine. Among these 94 individuals, 9 (8.9%) had been previously infected with COVID 19 in the first or second waves. 77.7% of the previously infected were now infected with Omicron variant and only 22.3% by a non-Omicron variant. Conclusion Rapid rise and fall during the third wave in Mumbai was due to Omicron cases gradually replacing Delta. The overall milder clinical spectrum in both Omicron and Delta cases imply that vaccines might not be effective against re-infection but can attenuate disease severity and mortality, as evident by high coverage of vaccination in the country.
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Affiliation(s)
- Apurva Takke
- ICMR- National Institute of Immunohaematology (NIIH), KEM Hospital Campus, Mumbai, Maharashtra, India
| | - Mohini Zarekar
- ICMR- National Institute of Immunohaematology (NIIH), KEM Hospital Campus, Mumbai, Maharashtra, India
| | - Vigneshwaran Muthuraman
- ICMR- National Institute of Immunohaematology (NIIH), KEM Hospital Campus, Mumbai, Maharashtra, India
| | - Aditee Ashar
- ICMR- National Institute of Immunohaematology (NIIH), KEM Hospital Campus, Mumbai, Maharashtra, India
| | - Kranti Patil
- ICMR- National Institute of Immunohaematology (NIIH), KEM Hospital Campus, Mumbai, Maharashtra, India
| | - Anagha Badhavkar
- ICMR- National Institute of Immunohaematology (NIIH), KEM Hospital Campus, Mumbai, Maharashtra, India
| | - Jayshil Trivedi
- ICMR- National Institute of Immunohaematology (NIIH), KEM Hospital Campus, Mumbai, Maharashtra, India
| | - Naveen Khargekar
- ICMR- National Institute of Immunohaematology (NIIH), KEM Hospital Campus, Mumbai, Maharashtra, India
| | - Manisha Madkaikar
- ICMR- National Institute of Immunohaematology (NIIH), KEM Hospital Campus, Mumbai, Maharashtra, India
| | - Anindita Banerjee
- ICMR- National Institute of Immunohaematology (NIIH), KEM Hospital Campus, Mumbai, Maharashtra, India,Address for correspondence: Dr. Anindita Banerjee, Scientist E (Medical), Head, Department of Transfusion Transmitted Diseases, ICMR- National Institute of Immunohaematology, 13th Floor, New Multistoreyed Building, KEM Hospital Campus, Parel, Mumbai - 400 012, Maharashtra, India. E-mail:
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