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Singh J, Pandit P, McArthur AG, Banerjee A, Mossman K. Evolutionary trajectory of SARS-CoV-2 and emerging variants. Virol J 2021; 18:166. [PMID: 34389034 PMCID: PMC8361246 DOI: 10.1186/s12985-021-01633-w] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022] Open
Abstract
The emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and more recently, the independent evolution of multiple SARS-CoV-2 variants has generated renewed interest in virus evolution and cross-species transmission. While all known human coronaviruses (HCoVs) are speculated to have originated in animals, very little is known about their evolutionary history and factors that enable some CoVs to co-exist with humans as low pathogenic and endemic infections (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1), while others, such as SARS-CoV, MERS-CoV and SARS-CoV-2 have evolved to cause severe disease. In this review, we highlight the origins of all known HCoVs and map positively selected for mutations within HCoV proteins to discuss the evolutionary trajectory of SARS-CoV-2. Furthermore, we discuss emerging mutations within SARS-CoV-2 and variants of concern (VOC), along with highlighting the demonstrated or speculated impact of these mutations on virus transmission, pathogenicity, and neutralization by natural or vaccine-mediated immunity.
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Affiliation(s)
- Jalen Singh
- School of Interdisciplinary Science, McMaster University, Hamilton, ON, Canada
| | - Pranav Pandit
- EpiCenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
| | - Karen Mossman
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
- Department of Medicine, McMaster University, Hamilton, ON, Canada.
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada.
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302
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McCallum M, Walls AC, Sprouse KR, Bowen JE, Rosen L, Dang HV, deMarco A, Franko N, Tilles SW, Logue J, Miranda MC, Ahlrichs M, Carter L, Snell G, Pizzuto MS, Chu HY, Van Voorhis WC, Corti D, Veesler D. Molecular basis of immune evasion by the delta and kappa SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34401880 DOI: 10.1101/2021.08.11.455956] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Worldwide SARS-CoV-2 transmission leads to the recurrent emergence of variants, such as the recently described B.1.617.1 (kappa), B.1.617.2 (delta) and B.1.617.2+ (delta+). The B.1.617.2 (delta) variant of concern is causing a new wave of infections in many countries, mostly affecting unvaccinated individuals, and has become globally dominant. We show that these variants dampen the in vitro potency of vaccine-elicited serum neutralizing antibodies and provide a structural framework for describing the impact of individual mutations on immune evasion. Mutations in the B.1.617.1 (kappa) and B.1.617.2 (delta) spike glycoproteins abrogate recognition by several monoclonal antibodies via alteration of key antigenic sites, including an unexpected remodeling of the B.1.617.2 (delta) N-terminal domain. The binding affinity of the B.1.617.1 (kappa) and B.1.617.2 (delta) receptor-binding domain for ACE2 is comparable to the ancestral virus whereas B.1.617.2+ (delta+) exhibits markedly reduced affinity. We describe a previously uncharacterized class of N-terminal domain-directed human neutralizing monoclonal antibodies cross-reacting with several variants of concern, revealing a possible target for vaccine development.
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303
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Duerr R, Dimartino D, Marier C, Zappile P, Wang G, Lighter J, Elbel B, Troxel AB, Heguy A. Dominance of alpha and Iota variants in SARS-CoV-2 vaccine breakthrough infections in New York City. J Clin Invest 2021; 131:e152702. [PMID: 34375308 DOI: 10.1172/jci152702] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/05/2021] [Indexed: 11/17/2022] Open
Abstract
The efficacy of COVID-19 mRNA vaccines is high, but breakthrough infections still occur. We compared the SARS-CoV-2 genomes of 76 breakthrough cases after full vaccination with BNT162b2 (Pfizer/BioNTech), mRNA-1273 (Moderna), or JNJ-78436735 (Janssen) to unvaccinated controls (February-April 2021) in metropolitan New York, including their phylogenetic relationship, distribution of variants, and full spike mutation profiles. Their median age was 48 years; seven required hospitalization and one died. Most breakthrough infections (57/76) occurred with B.1.1.7 (Alpha) or B.1.526 (Iota). Among the 7 hospitalized cases, 4 were infected with B.1.1.7, including 1 death. Both unmatched and matched statistical analyses considering age, sex, vaccine type, and study month as covariates supported the null hypothesis of equal variant distributions between vaccinated and unvaccinated in chi-squared and McNemar tests (p>0.1) highlighting a high vaccine efficacy against B.1.1.7 and B.1.526. There was no clear association among breakthroughs between type of vaccine received and variant. In the vaccinated group, spike mutations in the N-terminal domain and receptor-binding domain that have been associated with immune evasion were overrepresented. The evolving dynamic of SARS-CoV-2 variants requires broad genomic analyses of breakthrough infections to provide real-life information on immune escape mediated by circulating variants and their spike mutations.
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Affiliation(s)
- Ralf Duerr
- Department of Microbiology, NYU Langone Health, New York, United States of America
| | - Dacia Dimartino
- Office for Science and Research, NYU Langone Health, New York, United States of America
| | - Christian Marier
- Office for Science and Research, NYU Langone Health, New York, United States of America
| | - Paul Zappile
- Office for Science and Research, NYU Langone Health, New York, United States of America
| | - Guiqing Wang
- Department of Pathology, NYU Langone Health, New York, United States of America
| | - Jennifer Lighter
- Department of Pediatric Infectious Diseases, NYU Langone Health, New York, United States of America
| | - Brian Elbel
- Department of Population Health, NYU Langone Health, New York, United States of America
| | - Andrea B Troxel
- Department of Population Health, NYU Langone Health, New York, United States of America
| | - Adriana Heguy
- NYU Langone Health, New York, United States of America
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304
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Leach A, Ilca FT, Akbar Z, Ferrari M, Bentley EM, Mattiuzzo G, Onuoha S, Miller A, Ali H, Rabbitts TH. A tetrameric ACE2 protein broadly neutralizes SARS-CoV-2 spike variants of concern with elevated potency. Antiviral Res 2021; 194:105147. [PMID: 34375715 PMCID: PMC8349458 DOI: 10.1016/j.antiviral.2021.105147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 01/06/2023]
Abstract
The SARS-CoV-2 receptor angiotensin converting enzyme 2 (ACE2) was previously engineered into a high affinity tetravalent format (ACE2-Fc-TD) that is a potential decoy protein in SARS-CoV-2 infection.We report that this protein shows greatly enhanced binding to SARS-CoV-2 spike proteins of the SARS-CoV-2 variants of concern B.1.1.7 (alpha variant, originally isolated in the United Kingdom) and B.1.351 (beta variant, originally isolated in South Africa) with picomolar compared with nanomolar Kd values. In addition, ACE2-Fc-TD displays greater neutralization of SARS-CoV-2 pseudotype viruses compared to a dimeric ACE2-Fc, with enhanced activity on variant B.1.351. This tetrameric decoy protein would be a valuable addition to SARS-CoV-2 therapeutic approaches, especially where vaccination cannot be used but also should there be any future coronavirus pandemics.
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Affiliation(s)
- Adam Leach
- Institute of Cancer Research, Centre for Cancer Drug Discovery, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - F Tudor Ilca
- Autolus Therapeutics Plc, 58 Wood Lane, London, W12 7RZ, UK
| | - Zulaikha Akbar
- Autolus Therapeutics Plc, 58 Wood Lane, London, W12 7RZ, UK
| | | | - Emma M Bentley
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Hertfordshire, EN6 3QG, UK
| | - Giada Mattiuzzo
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Hertfordshire, EN6 3QG, UK
| | - Shimobi Onuoha
- Autolus Therapeutics Plc, 58 Wood Lane, London, W12 7RZ, UK
| | - Ami Miller
- Institute of Cancer Research, Centre for Cancer Drug Discovery, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Hanif Ali
- Quadrucept Limited, 1010 Cambourne Road, Cambridge, CB23 6DW, UK
| | - Terence H Rabbitts
- Institute of Cancer Research, Centre for Cancer Drug Discovery, 15 Cotswold Road, Sutton, London, SM2 5NG, UK.
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305
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McCallum M, Bassi J, De Marco A, Chen A, Walls AC, Di Iulio J, Tortorici MA, Navarro MJ, Silacci-Fregni C, Saliba C, Sprouse KR, Agostini M, Pinto D, Culap K, Bianchi S, Jaconi S, Cameroni E, Bowen JE, Tilles SW, Pizzuto MS, Guastalla SB, Bona G, Pellanda AF, Garzoni C, Van Voorhis WC, Rosen LE, Snell G, Telenti A, Virgin HW, Piccoli L, Corti D, Veesler D. SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern. Science 2021; 373:648-654. [PMID: 34210893 PMCID: PMC9835956 DOI: 10.1126/science.abi7994] [Citation(s) in RCA: 296] [Impact Index Per Article: 98.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/25/2021] [Indexed: 01/16/2023]
Abstract
A novel variant of concern (VOC) named CAL.20C (B.1.427/B.1.429), which was originally detected in California, carries spike glycoprotein mutations S13I in the signal peptide, W152C in the N-terminal domain (NTD), and L452R in the receptor-binding domain (RBD). Plasma from individuals vaccinated with a Wuhan-1 isolate-based messenger RNA vaccine or from convalescent individuals exhibited neutralizing titers that were reduced 2- to 3.5-fold against the B.1.427/B.1.429 variant relative to wild-type pseudoviruses. The L452R mutation reduced neutralizing activity in 14 of 34 RBD-specific monoclonal antibodies (mAbs). The S13I and W152C mutations resulted in total loss of neutralization for 10 of 10 NTD-specific mAbs because the NTD antigenic supersite was remodeled by a shift of the signal peptide cleavage site and the formation of a new disulfide bond, as revealed by mass spectrometry and structural studies.
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MESH Headings
- 2019-nCoV Vaccine mRNA-1273
- Amino Acid Substitution
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Antigens, Viral/immunology
- BNT162 Vaccine
- COVID-19/immunology
- COVID-19/virology
- COVID-19 Vaccines/immunology
- Cryoelectron Microscopy
- Humans
- Immune Evasion
- Models, Molecular
- Mutation
- Neutralization Tests
- Protein Conformation
- Protein Domains
- Protein Interaction Domains and Motifs
- Protein Subunits/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alex Chen
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | | | - Mary-Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Siro Bianchi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sasha W Tilles
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | | | - Giovanni Bona
- Clinical Research Unit, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | | | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Wesley C Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | | | | | | | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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306
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Abstract
Selective pressures drive adaptive changes in the coronavirus spike proteins directing virus-cell entry. These changes are concentrated in the amino-terminal domains (NTDs) and the receptor-binding domains (RBDs) of complex modular spike protein trimers. The impact of this hypervariability on virus entry is often unclear, particularly with respect to sarbecovirus NTD variations. Therefore, we constructed indels and substitutions within hypervariable NTD regions and used severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus-like particles and quantitative virus-cell entry assays to elucidate spike structures controlling this initial infection stage. We identified NTD variations that increased SARS-CoV-2 spike protein-mediated membrane fusion and cell entry. Increased cell entry correlated with greater presentation of RBDs to ACE2 receptors. This revealed a significant allosteric effect, in that changes within the NTDs can orient RBDs for effective virus-cell binding. Yet, those NTD changes elevating receptor binding and membrane fusion also reduced interdomain associations, leaving spikes on virus-like particles susceptible to irreversible inactivation. These findings parallel those obtained decades ago, in which comparisons of murine coronavirus spike protein variants established inverse relationships between membrane fusion potential and virus stability. Considerable hypervariability in the SARS-CoV-2 spike protein NTDs also appear to be driven by counterbalancing pressures for effective virus-cell entry and durable extracellular virus infectivity. These forces may selectively amplify SARS-CoV-2 variants of concern.
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307
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Bourassa L, Perchetti GA, Phung Q, Lin MJ, Mills MG, Roychoudhury P, Harmon KG, Reed JC, Greninger AL. A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. J Clin Virol 2021; 141:104900. [PMID: 34171548 DOI: 10.1101/2021.05.05.21256527] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/09/2021] [Indexed: 05/27/2023]
Abstract
More than one year into a global pandemic, SARS-CoV-2 is now defined by a variety of rapidly evolving variant lineages. Several FDA authorized molecular diagnostic tests have been impacted by viral variation, while no reports of viral variation affecting antigen test performance have occurred to date. While determining the analytical sensitivity of the Quidel Sofia SARS Antigen FIA test (Sofia 2), we uncovered a high viral load specimen that repeatedly tested negative by this antigen test. Whole genome sequencing of the specimen uncovered two mutations, T205I and D399N, present in the nucleocapsid protein of the isolate. All six SARS-CoV-2 positive clinical specimens available in our laboratory with a D399N nucleocapsid mutation and CT < 31 were not detected by the Sofia 2 but detected by the Abbott BinaxNOW COVID-19 Ag Card, while clinical specimens with the T205I mutation were detected by both assays. Testing of recombinant SARS-CoV-2 nucleocapsid with these variants demonstrated an approximate 1000-fold loss in sensitivity for the Quidel Sofia SARS Antigen FIA test associated with the D399N mutation, while the BinaxNOW and Quidel Quickvue SARS Antigen tests were unaffected by the mutation. The D399N nucleocapsid mutation has been relatively uncommon to date, appearing in only 0.02% of genomes worldwide at time of writing. Our results demonstrate how routine pathogen genomics can be integrated into the clinical microbiology laboratory to investigate diagnostic edge cases, as well as the importance of profiling antigenic diversity outside of the spike protein for SARS-CoV-2 diagnostics.
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Affiliation(s)
- Lori Bourassa
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Garrett A Perchetti
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Quynh Phung
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Michelle J Lin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Margaret G Mills
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Viral and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kimberly G Harmon
- Department of Family Medicine, for Stanley Herring Department of Physical Medicine and Rehabilitation, University of Washington, Seattle, Washington, USA
| | - Jonathan C Reed
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Viral and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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308
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Galili U. COVID-19 variants as moving targets and how to stop them by glycoengineered whole-virus vaccines. Virulence 2021; 12:1717-1720. [PMID: 34304693 PMCID: PMC8346202 DOI: 10.1080/21505594.2021.1939924] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Uri Galili
- Department of Medicine, Rush Medical College, Chicago, IL, USA
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309
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Abstract
Recent studies have shown that persistent SARS-CoV-2 infections in immunocompromised patients can trigger the accumulation of an unusual high number of mutations with potential relevance at both biological and epidemiological levels. Here, we report a case of an immunocompromised patient (non-Hodgkin lymphoma patient under immunosuppressive therapy) with a persistent SARS-CoV-2 infection (marked by intermittent positivity) over at least 6 months. Viral genome sequencing was performed at days 1, 164, and 171 to evaluate SARS-CoV-2 evolution. Among the 15 single-nucleotide polymorphisms (SNPs) (11 leading to amino acid alterations) and 3 deletions accumulated during this long-term infection, four amino acid changes (V3G, S50L, N87S, and A222V) and two deletions (18-30del and 141-144del) occurred in the virus Spike protein. Although no convalescent plasma therapy was administered, some of the detected mutations have been independently reported in other chronically infected individuals, which supports a scenario of convergent adaptive evolution. This study shows that it is of the utmost relevance to monitor the SARS-CoV-2 evolution in immunocompromised individuals, not only to identify novel potentially adaptive mutations, but also to mitigate the risk of introducing “hyper-evolved” variants in the community. IMPORTANCE Tracking the within-patient evolution of SARS-CoV-2 is key to understanding how this pandemic virus shapes its genome toward immune evasion and survival. In the present study, by monitoring a long-term COVID-19 immunocompromised patient, we observed the concurrent emergence of mutations potentially associated with immune evasion and/or enhanced transmission, mostly targeting the SARS-CoV-2 key host-interacting protein and antigen. These findings show that the frequent oscillation in the immune status in immunocompromised individuals can trigger an accelerated virus evolution, thus consolidating this study model as an accelerated pathway to better understand SARS-CoV-2 adaptive traits and anticipate the emergence of variants of concern.
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310
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Pacl HT, Tipper JL, Sevalkar RR, Crouse A, Crowder C, Ahmad S, Ahmad A, Holder GD, Kuhlman CJ, Chinta KC, Nadeem S, Green TJ, Petit CM, Steyn AJC, Might M, Harrod KS. Water-soluble tocopherol derivatives inhibit SARS-CoV-2 RNA-dependent RNA polymerase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34282419 DOI: 10.1101/2021.07.13.449251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The recent emergence of a novel coronavirus, SARS-CoV-2, has led to the global pandemic of the severe disease COVID-19 in humans. While efforts to quickly identify effective antiviral therapies have focused largely on repurposing existing drugs 1-4 , the current standard of care, remdesivir, remains the only authorized antiviral intervention of COVID-19 and provides only modest clinical benefits 5 . Here we show that water-soluble derivatives of α-tocopherol have potent antiviral activity and synergize with remdesivir as inhibitors of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). Through an artificial-intelligence-driven in silico screen and in vitro viral inhibition assay, we identified D-α-tocopherol polyethylene glycol succinate (TPGS) as an effective antiviral against SARS-CoV-2 and β-coronaviruses more broadly that also displays strong synergy with remdesivir. We subsequently determined that TPGS and other water-soluble derivatives of α-tocopherol inhibit the transcriptional activity of purified SARS-CoV-2 RdRp and identified affinity binding sites for these compounds within a conserved, hydrophobic interface between SARS-CoV-2 nonstructural protein 7 and nonstructural protein 8 that is functionally implicated in the assembly of the SARS-CoV-2 RdRp 6 . In summary, we conclude that solubilizing modifications to α-tocopherol allow it to interact with the SARS-CoV-2 RdRp, making it an effective antiviral molecule alone and even more so in combination with remdesivir. These findings are significant given that many tocopherol derivatives, including TPGS, are considered safe for humans, orally bioavailable, and dramatically enhance the activity of the only approved antiviral for SARS-CoV-2 infection 7-9 .
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311
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Otto SP, Day T, Arino J, Colijn C, Dushoff J, Li M, Mechai S, Van Domselaar G, Wu J, Earn DJD, Ogden NH. The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic. Curr Biol 2021; 31:R918-R929. [PMID: 34314723 PMCID: PMC8220957 DOI: 10.1016/j.cub.2021.06.049] [Citation(s) in RCA: 190] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
One year into the global COVID-19 pandemic, the focus of attention has shifted to the emergence and spread of SARS-CoV-2 variants of concern (VOCs). After nearly a year of the pandemic with little evolutionary change affecting human health, several variants have now been shown to have substantial detrimental effects on transmission and severity of the virus. Public health officials, medical practitioners, scientists, and the broader community have since been scrambling to understand what these variants mean for diagnosis, treatment, and the control of the pandemic through nonpharmaceutical interventions and vaccines. Here we explore the evolutionary processes that are involved in the emergence of new variants, what we can expect in terms of the future emergence of VOCs, and what we can do to minimise their impact.
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Affiliation(s)
- Sarah P Otto
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Troy Day
- Department of Mathematics and Statistics, Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Julien Arino
- Department of Mathematics and Data Science Nexus, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Jonathan Dushoff
- Department of Biology and M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Michael Li
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON N1G 3W4, Canada
| | - Samir Mechai
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, St. Hyacinthe, QC J2S 2M2, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory - Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Jianhong Wu
- Laboratory for Industrial and Applied Mathematics, York University, Toronto, ON M3J 1P3, Canada
| | - David J D Earn
- Department of Mathematics and Statistics and M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Nicholas H Ogden
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, St. Hyacinthe, QC J2S 2M2, Canada
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312
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Gilliland T, Liu Y, Li R, Dunn M, Cottle E, Terada Y, Ryckman Z, Alcorn M, Vasilatos S, Lundy J, Larson D, Wu H, Luke T, Bausch C, Egland K, Sullivan E, Wang Z, Klimstra WB. Protection of human ACE2 transgenic Syrian hamsters from SARS CoV-2 variants by human polyclonal IgG from hyper-immunized transchromosomic bovines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34341790 DOI: 10.1101/2021.07.26.453840] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pandemic SARS CoV-2 has been undergoing rapid evolution during spread throughout the world resulting in the emergence of many Spike protein variants, some of which appear to either evade antibody neutralization, transmit more efficiently, or potentially exhibit increased virulence. This raises significant concerns regarding the long-term efficacy of protection elicited after primary infection and/or from vaccines derived from single virus Spike (S) genotypes, as well as the efficacy of anti-S monoclonal antibody based therapeutics. Here, we used fully human polyclonal human IgG (SAB-185), derived from hyperimmunization of transchromosomic bovines with DNA plasmids encoding the SARS-CoV-2 Wa-1 strain S protein or purified ectodomain of S protein, to examine the neutralizing capacity of SAB-185 in vitro and the protective efficacy of passive SAB-185 antibody (Ab) transfer in vivo . The Ab preparation was tested for neutralization against five variant SARS-CoV-2 strains: Munich (Spike D614G), UK (B.1.1.7), Brazil (P.1) and SA (B.1.3.5) variants, and a variant isolated from a chronically infected immunocompromised patient (Spike Δ144-146). For the in vivo studies, we used a new human ACE2 (hACE2) transgenic Syrian hamster model that exhibits lethality after SARS-Cov-2 challenge and the Munich, UK, SA and Δ144-146 variants. SAB-185 neutralized each of the SARS-CoV-2 strains equivalently on Vero E6 cells, however, a control convalescent human serum sample was less effective at neutralizing the SA variant. In the hamster model, prophylactic SAB-185 treatment protected the hamsters from fatal disease and minimized clinical signs of infection. These results suggest that SAB-185 may be an effective treatment for patients infected with SARS CoV-2 variants.
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313
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Fischer W, Giorgi EE, Chakraborty S, Nguyen K, Bhattacharya T, Theiler J, Goloboff PA, Yoon H, Abfalterer W, Foley BT, Tegally H, San JE, de Oliveira T, Gnanakaran S, Korber B. HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens. Cell Host Microbe 2021; 29:1093-1110. [PMID: 34242582 PMCID: PMC8173590 DOI: 10.1016/j.chom.2021.05.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Humanity is currently facing the challenge of two devastating pandemics caused by two very different RNA viruses: HIV-1, which has been with us for decades, and SARS-CoV-2, which has swept the world in the course of a single year. The same evolutionary strategies that drive HIV-1 evolution are at play in SARS-CoV-2. Single nucleotide mutations, multi-base insertions and deletions, recombination, and variation in surface glycans all generate the variability that, guided by natural selection, enables both HIV-1's extraordinary diversity and SARS-CoV-2's slower pace of mutation accumulation. Even though SARS-CoV-2 diversity is more limited, recently emergent SARS-CoV-2 variants carry Spike mutations that have important phenotypic consequences in terms of both antibody resistance and enhanced infectivity. We review and compare how these mutational patterns manifest in these two distinct viruses to provide the variability that fuels their evolution by natural selection.
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Affiliation(s)
- Will Fischer
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA; New Mexico Consortium, Los Alamos, New Mexico, 87545, USA
| | - Elena E Giorgi
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA; New Mexico Consortium, Los Alamos, New Mexico, 87545, USA
| | - Srirupa Chakraborty
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA; Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Kien Nguyen
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Tanmoy Bhattacharya
- T-2: Nuclear and Particle Physics, Astrophysics and Cosmology, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545 USA
| | - James Theiler
- ISR-3: Space Data Science and Systems, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Pablo A Goloboff
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas - Fundación Miguel Lillo, S. M. de Tucumán, Miguel Lillo 251 4000, Argentina; Research Associate, American Museum of Natural History, New York 10024, USA
| | - Hyejin Yoon
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Werner Abfalterer
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Brian T Foley
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sandrasegaram Gnanakaran
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Bette Korber
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA; New Mexico Consortium, Los Alamos, New Mexico, 87545, USA.
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314
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Abstract
The Severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 originated in bats and adapted to infect humans. Several SARS-CoV-2 strains have been identified. Genetic variation is fundamental to virus evolution and, in response to selection pressure, is manifested as the emergence of new strains and species adapted to different hosts or with novel pathogenicity. The combination of variation and selection forms a genetic footprint on the genome, consisting of the preferential accumulation of mutations in particular areas. Properties of betacoronaviruses contributing to variation and the emergence of new strains and species are beginning to be elucidated. To better understand their variation, we profiled the accumulation of mutations in all species in the genus Betacoronavirus, including SARS-CoV-2 and two other species that infect humans: SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Variation profiles identified both genetically stable and variable areas at homologous locations across species within the genus Betacoronavirus. The S glycoprotein is the most variable part of the genome and is structurally disordered. Other variable parts include proteins 3 and 7 and ORF8, which participate in replication and suppression of antiviral defense. In contrast, replication proteins in ORF1b are the least variable. Collectively, our results show that variation and structural disorder in the S glycoprotein is a general feature of all members of the genus Betacoronavirus, including SARS-CoV-2. These findings highlight the potential for the continual emergence of new species and strains with novel biological properties and indicate that the S glycoprotein has a critical role in host adaptation. IMPORTANCE Natural infection with SARS-CoV-2 and vaccines triggers the formation of antibodies against the S glycoprotein, which are detected by antibody-based diagnostic tests. Our analysis showed that variation in the S glycoprotein is a general feature of all species in the genus Betacoronavirus, including three species that infect humans: SARS-CoV, SARS-CoV-2, and MERS-CoV. The variable nature of the S glycoprotein provides an explanation for the emergence of SARS-CoV-2, the differentiation of SARS-CoV-2 into strains, and the probability of SARS-CoV-2 repeated infections in people. Variation of the S glycoprotein also has important implications for the reliability of SARS-CoV-2 antibody-based diagnostic tests and the design and deployment of vaccines and antiviral drugs. These findings indicate that adjustments to vaccine design and deployment and to antibody-based diagnostic tests are necessary to account for S glycoprotein variation.
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315
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Khateeb J, Li Y, Zhang H. Emerging SARS-CoV-2 variants of concern and potential intervention approaches. Crit Care 2021; 25:244. [PMID: 34253247 PMCID: PMC8274962 DOI: 10.1186/s13054-021-03662-x] [Citation(s) in RCA: 147] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 06/29/2021] [Indexed: 12/18/2022] Open
Abstract
The major variant of concerns (VOCs) have shared mutations in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike proteins, mostly on the S1 unit and resulted in higher transmissibility rate and affect viral virulence and clinical outcome. The spike protein mutations and other non-structural protein mutations in the VOCs may lead to escape approved vaccinations in certain extend. We will discuss these VOC mutations and discuss the need for combination therapeutic strategies targeting viral cycle and immune host responses.
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Affiliation(s)
- Jasmin Khateeb
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Unity Health Toronto, Room 619, LKSKI, 30 Bond Street, Toronto, ON, M5B1W8, Canada
- Department of Internal Medicine D, Rambam Health Care Campus, Haifa, Israel
| | - Yuchong Li
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Unity Health Toronto, Room 619, LKSKI, 30 Bond Street, Toronto, ON, M5B1W8, Canada
- The State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Haibo Zhang
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Unity Health Toronto, Room 619, LKSKI, 30 Bond Street, Toronto, ON, M5B1W8, Canada.
- The State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
- Departments of Anaesthesia and Physiology, Interdepartmental Division of Critical Care Medicine, University of Toronto, Toronto, ON, Canada.
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316
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Adam KM. Immunoinformatics approach for multi-epitope vaccine design against structural proteins and ORF1a polyprotein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Trop Dis Travel Med Vaccines 2021; 7:22. [PMID: 34238372 PMCID: PMC8266167 DOI: 10.1186/s40794-021-00147-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 06/25/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The lack of effective treatment against the highly infectious SARS-CoV-2 has aggravated the already catastrophic global health issue. Here, in an attempt to design an efficient vaccine, a thorough immunoinformatics approach was followed to predict the most suitable viral proteins epitopes for building that vaccine. METHODS The amino acid sequences of four structural proteins (S, M, N, E) along with one potentially antigenic accessory protein (ORF1a) of SARS-CoV-2 were inspected for the most appropriate epitopes to be used for building the vaccine construct. Several immunoinformatics tools were used to assess the antigenicity (VaxiJen server), immunogenicity (IEDB immunogenicity tool), allergenicity (AlgPred), toxigenicity (ToxinPred server), interferon-gamma inducing capacity (IFNepitope server), and the physicochemical properties of the construct (ProtParam tool). RESULTS The final candidate vaccine construct consisted of 468 amino acids, encompassing 29 epitopes. The CTL epitopes that passed the antigenicity, allergenicity, toxigenicity and immunogenicity assessment were four epitopes from S protein, one from M protein, two from N protein, 12 from the ORF1a polyprotein and none from E protein. While the HTL epitopes that passed the antigenicity, allergenicity, toxigenicity and INF-[Formula: see text] were one from S protein, three from M protein, six from the ORF1a polyprotein and none from N and E proteins. All the vaccine properties and its ability to trigger the humoral and cell-mediated immune response were validated computationally. Molecular modeling, docking to TLR3, simulation, and molecular dynamics were also carried out. Finally, a molecular clone using pET28::mAID expression plasmid vector was prepared. CONCLUSION The overall results of the study suggest that the final multi-epitope chimeric construct is a potential candidate for an efficient protective vaccine against SARS-CoV-2.
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Affiliation(s)
- Khalid Mohamed Adam
- College of Applied Medical Sciences, Medical and Engineering Complex, University of Bisha, Bisha, 61922, Kingdom of Saudi Arabia.
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317
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Barth RF, Buja LM, Barth AL, Carpenter DE, Parwani AV. A Comparison of the Clinical, Viral, Pathologic, and Immunologic Features of Severe Acute Respiratory Syndrome (SARS), Middle East Respiratory Syndrome (MERS), and Coronavirus 2019 (COVID-19) Diseases. Arch Pathol Lab Med 2021; 145:1194-1211. [PMID: 34232978 DOI: 10.5858/arpa.2020-0820-sa] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT -The purpose of this review is to compare three coronavirus diseases: severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and coronavirus disease 2019 (COVID-19) caused by SARS-CoV, MERS-CoV, and SARS-CoV-2 viruses, respectively. OBJECTIVE -To cover the following topics: clinical considerations, viral characteristics, pathology, immune response, pathogenesis, and the prognosis associated with each coronavirus human disease in humans. DATA SOURCES -Clinically, flu-like symptoms are usual at the time of presentation for all 3 diseases, but these vary from asymptomatic to severe multi-system involvement. The pathology associated with symptomatic SARS and COVID-19 has been well described, the most prominent of which is diffuse alveolar damage (DAD). The immune response to each of these viruses is highly complex and includes both humoral and cellular components that can have a significant impact on prognosis. In severe cases of COVID-19, a dysregulated innate host immune system can initiate a hyperinflammatory syndrome dominated by endothelial dysfunction that can lead to a hypercoagulable state with microthrombi, resulting in a systemic micro- and macro-vascular disease. CONCLUSIONS -The SARS and MERS epidemics have been limited, involving 7,500 and 2,500 individuals, respectively. In contrast, COVID-19 has resulted in a worldwide pandemic with over 177 million cases and 3.9 million deaths as of June 15, 2021, and fatality rates ranging from <0.1% to ~10% depending upon the country. Ending on a positive note, the development of a number of vaccines, at least six of which now are in clinical use, should mitigate and eventually control the devastating COVID-19 pandemic.
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Affiliation(s)
- Rolf F Barth
- Department of Pathology (RF Barth, Parwani), S.P. Technical Editor (Retired) Departments of Neurosurgery and Radiation Oncology (Carpenter), The Ohio State University Columbus, Ohio
| | - L Maximillian Buja
- Department of Pathology and Laboratory Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas (Buja)
| | - Alison L Barth
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA (AL Barth)
| | - David E Carpenter
- Department of Pathology (RF Barth, Parwani), S.P. Technical Editor (Retired) Departments of Neurosurgery and Radiation Oncology (Carpenter), The Ohio State University Columbus, Ohio
| | - Anil V Parwani
- Department of Pathology (RF Barth, Parwani), S.P. Technical Editor (Retired) Departments of Neurosurgery and Radiation Oncology (Carpenter), The Ohio State University Columbus, Ohio
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318
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Greaney AJ, Starr TN, Barnes CO, Weisblum Y, Schmidt F, Caskey M, Gaebler C, Cho A, Agudelo M, Finkin S, Wang Z, Poston D, Muecksch F, Hatziioannou T, Bieniasz PD, Robbiani DF, Nussenzweig MC, Bjorkman PJ, Bloom JD. Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies. Nat Commun 2021; 12:4196. [PMID: 34234131 PMCID: PMC8263750 DOI: 10.1038/s41467-021-24435-8] [Citation(s) in RCA: 251] [Impact Index Per Article: 83.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/11/2021] [Indexed: 11/28/2022] Open
Abstract
Monoclonal antibodies targeting a variety of epitopes have been isolated from individuals previously infected with SARS-CoV-2, but the relative contributions of these different antibody classes to the polyclonal response remains unclear. Here we use a yeast-display system to map all mutations to the viral spike receptor-binding domain (RBD) that escape binding by representatives of three potently neutralizing classes of anti-RBD antibodies with high-resolution structures. We compare the antibody-escape maps to similar maps for convalescent polyclonal plasmas, including plasmas from individuals from whom some of the antibodies were isolated. While the binding of polyclonal plasma antibodies are affected by mutations across multiple RBD epitopes, the plasma-escape maps most resemble those of a single class of antibodies that target an epitope on the RBD that includes site E484. Therefore, although the human immune system can produce antibodies that target diverse RBD epitopes, in practice the polyclonal response to infection is skewed towards a single class of antibodies targeting an epitope that is already undergoing rapid evolution.
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Affiliation(s)
- Allison J Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Tyler N Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Marianna Agudelo
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Shlomo Finkin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Daniel Poston
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | | | - Paul D Bieniasz
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Institute for Research in Biomedicine, Universita della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Michel C Nussenzweig
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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319
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Raman R, Patel KJ, Ranjan K. COVID-19: Unmasking Emerging SARS-CoV-2 Variants, Vaccines and Therapeutic Strategies. Biomolecules 2021; 11:993. [PMID: 34356617 PMCID: PMC8301790 DOI: 10.3390/biom11070993] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/26/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of the coronavirus disease 2019 (COVID-19) pandemic, which has been a topic of major concern for global human health. The challenge to restrain the COVID-19 pandemic is further compounded by the emergence of several SARS-CoV-2 variants viz. B.1.1.7 (Alpha), B.1.351 (Beta), P1 (Gamma) and B.1.617.2 (Delta), which show increased transmissibility and resistance towards vaccines and therapies. Importantly, there is convincing evidence of increased susceptibility to SARS-CoV-2 infection among individuals with dysregulated immune response and comorbidities. Herein, we provide a comprehensive perspective regarding vulnerability of SARS-CoV-2 infection in patients with underlying medical comorbidities. We discuss ongoing vaccine (mRNA, protein-based, viral vector-based, etc.) and therapeutic (monoclonal antibodies, small molecules, plasma therapy, etc.) modalities designed to curb the COVID-19 pandemic. We also discuss in detail, the challenges posed by different SARS-CoV-2 variants of concern (VOC) identified across the globe and their effects on therapeutic and prophylactic interventions.
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Affiliation(s)
- Renuka Raman
- Department of Surgery, Weill Cornell Medical College, New York, NY 10065, USA;
| | - Krishna J. Patel
- Mount Sinai Innovation Partners, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Kishu Ranjan
- School of Medicine, Yale University, New Haven, CT 06519, USA
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320
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Rezaei S, Sefidbakht Y, Uskoković V. Tracking the pipeline: immunoinformatics and the COVID-19 vaccine design. Brief Bioinform 2021; 22:6313266. [PMID: 34219142 DOI: 10.1093/bib/bbab241] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/23/2021] [Accepted: 06/04/2021] [Indexed: 12/23/2022] Open
Abstract
With the onset of the COVID-19 pandemic, the amount of data on genomic and proteomic sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) stored in various databases has exponentially grown. A large volume of these data has led to the production of equally immense sets of immunological data, which require rigorous computational approaches to sort through and make sense of. Immunoinformatics has emerged in the recent decades as a field capable of offering this approach by bridging experimental and theoretical immunology with state-of-the-art computational tools. Here, we discuss how immunoinformatics can assist in the development of high-performance vaccines and drug discovery needed to curb the spread of SARS-CoV-2. Immunoinformatics can provide a set of computational tools to extract meaningful connections from the large sets of COVID-19 patient data, which can be implemented in the design of effective vaccines. With this in mind, we represent a pipeline to identify the role of immunoinformatics in COVID-19 treatment and vaccine development. In this process, a number of free databases of protein sequences, structures and mutations are introduced, along with docking web servers for assessing the interaction between antibodies and the SARS-CoV-2 spike protein segments as most commonly considered antigens in vaccine design.
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Affiliation(s)
- Shokouh Rezaei
- Protein Research Center at Shahid Beheshti University, Tehran, Iran
| | - Yahya Sefidbakht
- Protein Research Center at Shahid Beheshti University, Tehran, Iran
| | - Vuk Uskoković
- Founder of the biotech startup, TardigradeNano, and formerly a Professor at University of Illinois in Chicago, Chapman University, and University of California in Irvine
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321
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Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, Ludden C, Reeve R, Rambaut A, Peacock SJ, Robertson DL. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol 2021; 19:409-424. [PMID: 34075212 PMCID: PMC8167834 DOI: 10.1038/s41579-021-00573-0] [Citation(s) in RCA: 2098] [Impact Index Per Article: 699.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 02/07/2023]
Abstract
Although most mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome are expected to be either deleterious and swiftly purged or relatively neutral, a small proportion will affect functional properties and may alter infectivity, disease severity or interactions with host immunity. The emergence of SARS-CoV-2 in late 2019 was followed by a period of relative evolutionary stasis lasting about 11 months. Since late 2020, however, SARS-CoV-2 evolution has been characterized by the emergence of sets of mutations, in the context of 'variants of concern', that impact virus characteristics, including transmissibility and antigenicity, probably in response to the changing immune profile of the human population. There is emerging evidence of reduced neutralization of some SARS-CoV-2 variants by postvaccination serum; however, a greater understanding of correlates of protection is required to evaluate how this may impact vaccine effectiveness. Nonetheless, manufacturers are preparing platforms for a possible update of vaccine sequences, and it is crucial that surveillance of genetic and antigenic changes in the global virus population is done alongside experiments to elucidate the phenotypic impacts of mutations. In this Review, we summarize the literature on mutations of the SARS-CoV-2 spike protein, the primary antigen, focusing on their impacts on antigenicity and contextualizing them in the protein structure, and discuss them in the context of observed mutation frequencies in global sequence datasets.
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Affiliation(s)
- William T Harvey
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Emma C Thomson
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | | | - Richard Reeve
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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322
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Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, Ludden C, Reeve R, Rambaut A, Peacock SJ, Robertson DL. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol 2021; 19:409-424. [PMID: 34075212 DOI: 10.1038/s41579-021-00573-02] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 05/26/2023]
Abstract
Although most mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome are expected to be either deleterious and swiftly purged or relatively neutral, a small proportion will affect functional properties and may alter infectivity, disease severity or interactions with host immunity. The emergence of SARS-CoV-2 in late 2019 was followed by a period of relative evolutionary stasis lasting about 11 months. Since late 2020, however, SARS-CoV-2 evolution has been characterized by the emergence of sets of mutations, in the context of 'variants of concern', that impact virus characteristics, including transmissibility and antigenicity, probably in response to the changing immune profile of the human population. There is emerging evidence of reduced neutralization of some SARS-CoV-2 variants by postvaccination serum; however, a greater understanding of correlates of protection is required to evaluate how this may impact vaccine effectiveness. Nonetheless, manufacturers are preparing platforms for a possible update of vaccine sequences, and it is crucial that surveillance of genetic and antigenic changes in the global virus population is done alongside experiments to elucidate the phenotypic impacts of mutations. In this Review, we summarize the literature on mutations of the SARS-CoV-2 spike protein, the primary antigen, focusing on their impacts on antigenicity and contextualizing them in the protein structure, and discuss them in the context of observed mutation frequencies in global sequence datasets.
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Affiliation(s)
- William T Harvey
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Emma C Thomson
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | | | - Richard Reeve
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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323
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Shen L, Bard JD, Triche TJ, Judkins AR, Biegel JA, Gai X. Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Emerg Microbes Infect 2021; 10:1293-1299. [PMID: 34125658 PMCID: PMC8238060 DOI: 10.1080/22221751.2021.1943540] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The SARS-CoV-2 B.1.1.7 lineage is highly infectious and as of April 2021 accounted for 92% of COVID-19 cases in Europe and 59% of COVID-19 cases in the U.S. It is defined by the N501Y mutation in the receptor-binding domain (RBD) of the Spike (S) protein, and a few other mutations. These include two mutations in the N terminal domain (NTD) of the S protein, HV69-70del and Y144del (also known as Y145del due to the presence of tyrosine at both positions). We recently identified several emerging SARS-CoV-2 variants of concerns, characterized by Membrane (M) protein mutations, including I82T and V70L. We now identify a sub-lineage of B.1.1.7 that emerged through sequential acquisitions of M:V70L in November 2020 followed by a novel S:D178H mutation first observed in early February 2021. The percentage of B.1.1.7 isolates in the US that belong to this sub-lineage increased from 0.15% in February 2021 to 1.8% in April 2021. To date, this sub-lineage appears to be U.S.-specific with reported cases in 31 states, including Hawaii. As of April 2021, it constituted 36.8% of all B.1.1.7 isolates in Washington. Phylogenetic analysis and transmission inference with Nextstrain suggest this sub-lineage likely originated in either California or Washington. Structural analysis revealed that the S:D178H mutation is in the NTD of the S protein and close to two other signature mutations of B.1.1.7, HV69-70del and Y144del. It is surface exposed and may alter NTD tertiary configuration or accessibility, and thus has the potential to affect neutralization by NTD directed antibodies.
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Affiliation(s)
- Lishuang Shen
- Children's Hospital Los Angles, Department of Pathology and Laboratory Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Jennifer Dien Bard
- Children's Hospital Los Angles, Department of Pathology and Laboratory Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Timothy J Triche
- Children's Hospital Los Angles, Department of Pathology and Laboratory Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Alexander R Judkins
- Children's Hospital Los Angles, Department of Pathology and Laboratory Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Jaclyn A Biegel
- Children's Hospital Los Angles, Department of Pathology and Laboratory Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Xiaowu Gai
- Children's Hospital Los Angles, Department of Pathology and Laboratory Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
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324
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Shah M, Woo HG. Molecular Perspectives of SARS-CoV-2: Pathology, Immune Evasion, and Therapeutic Interventions. Mol Cells 2021; 44:408-421. [PMID: 34059561 PMCID: PMC8245319 DOI: 10.14348/molcells.2021.0026] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) has not only affected human health but also diverted the focus of research and derailed the world economy over the past year. Recently, vaccination against COVID-19 has begun, but further studies on effective therapeutic agents are still needed. The severity of COVID-19 is attributable to several factors such as the dysfunctional host immune response manifested by uncontrolled viral replication, type I interferon suppression, and release of impaired cytokines by the infected resident and recruited cells. Due to the evolving pathophysiology and direct involvement of the host immune system in COVID-19, the use of immune-modulating drugs is still challenging. For the use of immune-modulating drugs in severe COVID-19, it is important to balance the fight between the aggravated immune system and suppression of immune defense against the virus that causes secondary infection. In addition, the interplaying events that occur during virus-host interactions, such as activation of the host immune system, immune evasion mechanism of the virus, and manifestation of different stages of COVID-19, are disjunctive and require thorough streamlining. This review provides an update on the immunotherapeutic interventions implemented to combat COVID-19 along with the understanding of molecular aspects of the immune evasion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which may provide opportunities to develop more effective and promising therapeutics.
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Affiliation(s)
- Masaud Shah
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Korea
| | - Hyun Goo Woo
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Korea
- Department of Biomedical Science, Graduate School of Ajou University, Suwon 16499, Korea
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325
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Meng B, Kemp SA, Papa G, Datir R, Ferreira IATM, Marelli S, Harvey WT, Lytras S, Mohamed A, Gallo G, Thakur N, Collier DA, Mlcochova P, Duncan LM, Carabelli AM, Kenyon JC, Lever AM, De Marco A, Saliba C, Culap K, Cameroni E, Matheson NJ, Piccoli L, Corti D, James LC, Robertson DL, Bailey D, Gupta RK. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Cell Rep 2021. [PMID: 34166617 DOI: 10.1101/2020.12.14.422555] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike ΔH69/V70 in multiple independent lineages, often occurring after acquisition of receptor binding motif replacements such as N439K and Y453F, known to increase binding affinity to the ACE2 receptor and confer antibody escape. In vitro, we show that, although ΔH69/V70 itself is not an antibody evasion mechanism, it increases infectivity associated with enhanced incorporation of cleaved spike into virions. ΔH69/V70 is able to partially rescue infectivity of spike proteins that have acquired N439K and Y453F escape mutations by increased spike incorporation. In addition, replacement of the H69 and V70 residues in the Alpha variant B.1.1.7 spike (where ΔH69/V70 occurs naturally) impairs spike incorporation and entry efficiency of the B.1.1.7 spike pseudotyped virus. Alpha variant B.1.1.7 spike mediates faster kinetics of cell-cell fusion than wild-type Wuhan-1 D614G, dependent on ΔH69/V70. Therefore, as ΔH69/V70 compensates for immune escape mutations that impair infectivity, continued surveillance for deletions with functional effects is warranted.
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Affiliation(s)
- Bo Meng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Steven A Kemp
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Division of Infection and Immunity, University College London, London, UK
| | - Guido Papa
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Rawlings Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Sara Marelli
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - William T Harvey
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK; MRC - University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Spyros Lytras
- MRC - University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | | | | | - Dami A Collier
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Division of Infection and Immunity, University College London, London, UK
| | - Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Lidia M Duncan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Julia C Kenyon
- Department of Medicine, University of Cambridge, Cambridge, UK; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Andrew M Lever
- Department of Medicine, University of Cambridge, Cambridge, UK; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK; NHS Blood and Transplant, Cambridge, UK
| | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Leo C James
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Africa Health Research Institute, Durban, South Africa.
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326
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Meng B, Kemp SA, Papa G, Datir R, Ferreira IATM, Marelli S, Harvey WT, Lytras S, Mohamed A, Gallo G, Thakur N, Collier DA, Mlcochova P, Duncan LM, Carabelli AM, Kenyon JC, Lever AM, De Marco A, Saliba C, Culap K, Cameroni E, Matheson NJ, Piccoli L, Corti D, James LC, Robertson DL, Bailey D, Gupta RK. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Cell Rep 2021; 35:109292. [PMID: 34166617 PMCID: PMC8185188 DOI: 10.1016/j.celrep.2021.109292] [Citation(s) in RCA: 284] [Impact Index Per Article: 94.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/29/2021] [Accepted: 06/02/2021] [Indexed: 12/23/2022] Open
Abstract
We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike ΔH69/V70 in multiple independent lineages, often occurring after acquisition of receptor binding motif replacements such as N439K and Y453F, known to increase binding affinity to the ACE2 receptor and confer antibody escape. In vitro, we show that, although ΔH69/V70 itself is not an antibody evasion mechanism, it increases infectivity associated with enhanced incorporation of cleaved spike into virions. ΔH69/V70 is able to partially rescue infectivity of spike proteins that have acquired N439K and Y453F escape mutations by increased spike incorporation. In addition, replacement of the H69 and V70 residues in the Alpha variant B.1.1.7 spike (where ΔH69/V70 occurs naturally) impairs spike incorporation and entry efficiency of the B.1.1.7 spike pseudotyped virus. Alpha variant B.1.1.7 spike mediates faster kinetics of cell-cell fusion than wild-type Wuhan-1 D614G, dependent on ΔH69/V70. Therefore, as ΔH69/V70 compensates for immune escape mutations that impair infectivity, continued surveillance for deletions with functional effects is warranted.
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Affiliation(s)
- Bo Meng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Steven A Kemp
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Division of Infection and Immunity, University College London, London, UK
| | - Guido Papa
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Rawlings Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Sara Marelli
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - William T Harvey
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK; MRC - University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Spyros Lytras
- MRC - University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | | | | | - Dami A Collier
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Division of Infection and Immunity, University College London, London, UK
| | - Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Lidia M Duncan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Julia C Kenyon
- Department of Medicine, University of Cambridge, Cambridge, UK; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Andrew M Lever
- Department of Medicine, University of Cambridge, Cambridge, UK; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK; NHS Blood and Transplant, Cambridge, UK
| | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Leo C James
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Africa Health Research Institute, Durban, South Africa.
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327
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de Vries RD, Rockx B, Haagmans BL, Herfst S, Koopmans MP, de Swart RL. Animal models of SARS-CoV-2 transmission. Curr Opin Virol 2021; 50:8-16. [PMID: 34256352 PMCID: PMC8238653 DOI: 10.1016/j.coviro.2021.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023]
Abstract
SARS-CoV-2 emerged in China as a zoonotic virus in December 2019. The virus proved to be human-to-human transmissible and its global spread resulted in the ongoing COVID-19 pandemic, associated with high morbidity and mortality. Vaccines were developed at an unprecedented speed and proved to be efficacious in preventing disease, but it remains to be determined if vaccines are able to interrupt transmission. Moreover, virus variants of concern continue to emerge that appear more transmissible and/or less sensitive to virus-specific immune responses. Here, we briefly review the role of animal models in assessing prophylactic and therapeutic options to interrupt SARS-CoV-2 transmission.
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Affiliation(s)
- Rory D de Vries
- Department Viroscience, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Barry Rockx
- Department Viroscience, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Bart L Haagmans
- Department Viroscience, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Sander Herfst
- Department Viroscience, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Marion Pg Koopmans
- Department Viroscience, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Rik L de Swart
- Department Viroscience, Erasmus MC, University Medical Center Rotterdam, The Netherlands.
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328
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Duerr R, Crosse KM, Valero-Jimenez AM, Dittmann M. SARS-CoV-2 Portrayed against HIV: Contrary Viral Strategies in Similar Disguise. Microorganisms 2021; 9:1389. [PMID: 34198973 PMCID: PMC8307803 DOI: 10.3390/microorganisms9071389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 and HIV are zoonotic viruses that rapidly reached pandemic scale, causing global losses and fear. The COVID-19 and AIDS pandemics ignited massive efforts worldwide to develop antiviral strategies and characterize viral architectures, biological and immunological properties, and clinical outcomes. Although both viruses have a comparable appearance as enveloped viruses with positive-stranded RNA and envelope spikes mediating cellular entry, the entry process, downstream biological and immunological pathways, clinical outcomes, and disease courses are strikingly different. This review provides a systemic comparison of both viruses' structural and functional characteristics, delineating their distinct strategies for efficient spread.
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Affiliation(s)
- Ralf Duerr
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA; (K.M.C.); (A.M.V.-J.); (M.D.)
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329
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Lodi L, Moriondo M, Pucci A, Pisano L, Ricci S, Indolfi G, Azzari C. Chronic asymptomatic SARS-CoV-2 infection in the immunocompromised patient: new challenges and urgent needs. Clin Infect Dis 2021; 74:553. [PMID: 34157075 DOI: 10.1093/cid/ciab538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Lorenzo Lodi
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy.,Immunology and Molecular Microbiology Unit, Meyer Children's University Hospital, Florence, Italy
| | - Maria Moriondo
- Immunology and Molecular Microbiology Unit, Meyer Children's University Hospital, Florence, Italy
| | - Alessandra Pucci
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy
| | - Laura Pisano
- Immunology and Molecular Microbiology Unit, Meyer Children's University Hospital, Florence, Italy
| | - Silvia Ricci
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy.,Immunology and Molecular Microbiology Unit, Meyer Children's University Hospital, Florence, Italy
| | - Giuseppe Indolfi
- Department of Pediatrics, Meyer Children's University Hospital, Florence, Italy.,NEUROFARBA Department, University of Florence, Florence, Italy
| | - Chiara Azzari
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy.,Immunology and Molecular Microbiology Unit, Meyer Children's University Hospital, Florence, Italy
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330
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COVID-19: Structural Considerations for Virus Pathogenesis, Therapeutic Strategies and Vaccine Design in the Novel SARS-CoV-2 Variants Era. Mol Biotechnol 2021; 63:885-897. [PMID: 34145550 PMCID: PMC8213040 DOI: 10.1007/s12033-021-00353-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/08/2021] [Indexed: 02/08/2023]
Abstract
COVID-19 pandemic caused by SARS-CoV-2 globally impacted the humanity causing tragic outcomes; costing millions of lives, destroying economies and demolishing public health infrastructures. The emergence of vaccines using various ingenious approaches in less than a year was deemed the light at the end of the tunnel. However, recent emergence of variants of SARS-CoV-2 in several parts of the world revealed that another hurdle is ahead in the fight against COVID-19. This review will highlight how SARS-CoV-2 mutations, creating different virus variants could potentially impact virus pathogenesis as well as different therapy approaches and vaccine design.
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331
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Bourassa L, Perchetti GA, Phung Q, Lin MJ, Mills MG, Roychoudhury P, Harmon KG, Reed JC, Greninger AL. A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. J Clin Virol 2021; 141:104900. [PMID: 34171548 PMCID: PMC8219478 DOI: 10.1016/j.jcv.2021.104900] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023]
Abstract
More than one year into a global pandemic, SARS-CoV-2 is now defined by a variety of rapidly evolving variant lineages. Several FDA authorized molecular diagnostic tests have been impacted by viral variation, while no reports of viral variation affecting antigen test performance have occurred to date. While determining the analytical sensitivity of the Quidel Sofia SARS Antigen FIA test (Sofia 2), we uncovered a high viral load specimen that repeatedly tested negative by this antigen test. Whole genome sequencing of the specimen uncovered two mutations, T205I and D399N, present in the nucleocapsid protein of the isolate. All six SARS-CoV-2 positive clinical specimens available in our laboratory with a D399N nucleocapsid mutation and CT < 31 were not detected by the Sofia 2 but detected by the Abbott BinaxNOW COVID-19 Ag Card, while clinical specimens with the T205I mutation were detected by both assays. Testing of recombinant SARS-CoV-2 nucleocapsid with these variants demonstrated an approximate 1000-fold loss in sensitivity for the Quidel Sofia SARS Antigen FIA test associated with the D399N mutation, while the BinaxNOW and Quidel Quickvue SARS Antigen tests were unaffected by the mutation. The D399N nucleocapsid mutation has been relatively uncommon to date, appearing in only 0.02% of genomes worldwide at time of writing. Our results demonstrate how routine pathogen genomics can be integrated into the clinical microbiology laboratory to investigate diagnostic edge cases, as well as the importance of profiling antigenic diversity outside of the spike protein for SARS-CoV-2 diagnostics.
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Affiliation(s)
- Lori Bourassa
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Garrett A Perchetti
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Quynh Phung
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Michelle J Lin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Margaret G Mills
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Viral and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kimberly G Harmon
- Department of Family Medicine, for Stanley Herring Department of Physical Medicine and Rehabilitation, University of Washington, Seattle, Washington, USA
| | - Jonathan C Reed
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Viral and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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332
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Motozono C, Toyoda M, Zahradnik J, Saito A, Nasser H, Tan TS, Ngare I, Kimura I, Uriu K, Kosugi Y, Yue Y, Shimizu R, Ito J, Torii S, Yonekawa A, Shimono N, Nagasaki Y, Minami R, Toya T, Sekiya N, Fukuhara T, Matsuura Y, Schreiber G, Ikeda T, Nakagawa S, Ueno T, Sato K. SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Cell Host Microbe 2021; 29:1124-1136.e11. [PMID: 34171266 PMCID: PMC8205251 DOI: 10.1016/j.chom.2021.06.006] [Citation(s) in RCA: 336] [Impact Index Per Article: 112.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/22/2021] [Accepted: 06/09/2021] [Indexed: 01/15/2023]
Abstract
Many SARS-CoV-2 variants with naturally acquired mutations have emerged. These mutations can affect viral properties such as infectivity and immune resistance. Although the sensitivity of naturally occurring SARS-CoV-2 variants to humoral immunity has been investigated, sensitivity to human leukocyte antigen (HLA)-restricted cellular immunity remains largely unexplored. Here, we demonstrate that two recently emerging mutations in the receptor-binding domain of the SARS-CoV-2 spike protein, L452R (in B.1.427/429 and B.1.617) and Y453F (in B.1.1.298), confer escape from HLA-A24-restricted cellular immunity. These mutations reinforce affinity toward the host entry receptor ACE2. Notably, the L452R mutation increases spike stability, viral infectivity, viral fusogenicity, and thereby promotes viral replication. These data suggest that HLA-restricted cellular immunity potentially affects the evolution of viral phenotypes and that a further threat of the SARS-CoV-2 pandemic is escape from cellular immunity.
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Affiliation(s)
- Chihiro Motozono
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Mako Toyoda
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Jiri Zahradnik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 8892192, Japan; Center for Animal Disease Control, University of Miyazaki, Miyazaki 8892192, Japan; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 8892192, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan; Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia 41511, Egypt
| | - Toong Seng Tan
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Isaac Ngare
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Izumi Kimura
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Yusuke Kosugi
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Yuan Yue
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Shiho Torii
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan; Division of Microbiology and Immunology, Center for Infectious Diseases Education and Research, Osaka University, Osaka 5650871, Japan; Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan
| | - Akiko Yonekawa
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 8128582, Japan
| | - Nobuyuki Shimono
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 8128582, Japan
| | - Yoji Nagasaki
- Division of Infectious Diseases, Clinical Research Institute, National Hospitalization Organization, Kyushu Medical Center, Fukuoka 8108563, Japan
| | - Rumi Minami
- Internal Medicine, Clinical Research Institute, National Hospital Organization, Kyushu Medical Center, Fukuoka 8108563, Japan
| | - Takashi Toya
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo 1138677, Japan
| | - Noritaka Sekiya
- Department of Infection Prevention and Control, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo 1138677, Japan; Department of Clinical Laboratory, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo 1138677, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Hokkaido 0608638, Japan
| | - Yoshiharu Matsuura
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan; Division of Microbiology and Immunology, Center for Infectious Diseases Education and Research, Osaka University, Osaka 5650871, Japan; Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan
| | - Gideon Schreiber
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan.
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan.
| | - Takamasa Ueno
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan.
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan.
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333
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Understanding individual SARS-CoV-2 proteins for targeted drug development against COVID-19. Mol Cell Biol 2021; 41:e0018521. [PMID: 34124934 PMCID: PMC8384068 DOI: 10.1128/mcb.00185-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the COVID-19 pandemic, responsible for millions of deaths globally. Even with effective vaccines, SARS-CoV-2 will likely maintain a hold in the human population through gaps in efficacy, percent vaccinated, and arising new strains. Therefore, understanding how SARS-CoV-2 causes widespread tissue damage and the development of targeted pharmacological treatments will be critical in fighting this virus and preparing for future outbreaks. Herein, we summarize the progress made thus far by using in vitro or in vivo models to investigate individual SARS-CoV-2 proteins and their pathogenic mechanisms. We have grouped the SARS-CoV-2 proteins into three categories: host entry, self-acting, and host interacting. This review focuses on the self-acting and host-interacting SARS-CoV-2 proteins and summarizes current knowledge on how these proteins promote virus replication and disrupt host systems, as well as drugs that target the virus and virus interacting host proteins. Encouragingly, many of these drugs are currently in clinical trials for the treatment of COVID-19. Future coronavirus outbreaks will most likely be caused by new virus strains that evade vaccine protection through mutations in entry proteins. Therefore, study of individual self-acting and host-interacting SARS-CoV-2 proteins for targeted therapeutic interventions is not only essential for fighting COVID-19 but also valuable against future coronavirus outbreaks.
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334
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Sherman EJ, Mirabelli C, Tang VT, Khan TG, Kennedy AA, Graham SE, Willer CJ, Tai AW, Sexton JZ, Wobus CE, Emmer BT. Identification of ACE2 modifiers by CRISPR screening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.06.10.447768. [PMID: 34127970 PMCID: PMC8202422 DOI: 10.1101/2021.06.10.447768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
SARS-CoV-2 infection is initiated by binding of the viral spike protein to its receptor, ACE2, on the surface of host cells. ACE2 expression is heterogeneous both in vivo and in immortalized cell lines, but the molecular pathways that govern ACE2 expression remain unclear. We now report high-throughput CRISPR screens for functional modifiers of ACE2 surface abundance. We identified 35 genes whose disruption was associated with a change in the surface abundance of ACE2 in HuH7 cells. Enriched among these ACE2 regulators were established transcription factors, epigenetic regulators, and functional networks. We further characterized individual cell lines with disruption of SMAD4, EP300, PIAS1 , or BAMBI and found these genes to regulate ACE2 at the mRNA level and to influence cellular susceptibility to SARS-CoV-2 infection. Collectively, our findings clarify the host factors involved in SARS-CoV-2 entry and suggest potential targets for therapeutic development.
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335
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Corti D, Purcell LA, Snell G, Veesler D. Tackling COVID-19 with neutralizing monoclonal antibodies. Cell 2021; 184:3086-3108. [PMID: 34087172 PMCID: PMC8152891 DOI: 10.1016/j.cell.2021.05.005] [Citation(s) in RCA: 235] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/25/2021] [Accepted: 05/04/2021] [Indexed: 12/12/2022]
Abstract
Monoclonal antibodies (mAbs) have revolutionized the treatment of several human diseases, including cancer and autoimmunity and inflammatory conditions, and represent a new frontier for the treatment of infectious diseases. In the last 20 years, innovative methods have allowed the rapid isolation of mAbs from convalescent subjects, humanized mice, or libraries assembled in vitro and have proven that mAbs can be effective countermeasures against emerging pathogens. During the past year, an unprecedentedly large number of mAbs have been developed to fight coronavirus disease 2019 (COVID-19). Lessons learned from this pandemic will pave the way for the development of more mAb-based therapeutics for other infectious diseases. Here, we provide an overview of SARS-CoV-2-neutralizing mAbs, including their origin, specificity, structure, antiviral and immunological mechanisms of action, and resistance to circulating variants, as well as a snapshot of the clinical trials of approved or late-stage mAb therapeutics.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/immunology
- Angiotensin-Converting Enzyme 2/metabolism
- Animals
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibodies, Viral/therapeutic use
- COVID-19/pathology
- COVID-19/virology
- Humans
- SARS-CoV-2/immunology
- SARS-CoV-2/isolation & purification
- SARS-CoV-2/metabolism
- Spike Glycoprotein, Coronavirus/immunology
- COVID-19 Drug Treatment
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Affiliation(s)
- Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.
| | | | | | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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336
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Dupont L, Snell LB, Graham C, Seow J, Merrick B, Lechmere T, Hallett SR, Charalampous T, Alcolea-Medina A, Huettner I, Maguire TJA, Acors S, Almeida N, Cox D, Dickenson RE, Galao RP, Jimenez-Guardeño JM, Kouphou N, Lista MJ, Pickering S, Ortega-Prieto AM, Wilson H, Winstone H, Fairhead C, Su J, Nebbia G, Batra R, Neil S, Shankar-Hari M, Edgeworth JD, Malim MH, Doores KJ. Antibody longevity and cross-neutralizing activity following SARS-CoV-2 wave 1 and B.1.1.7 infections. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.06.07.21258351. [PMID: 34127977 PMCID: PMC8202432 DOI: 10.1101/2021.06.07.21258351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
As SARS-CoV-2 variants continue to emerge globally, a major challenge for COVID-19 vaccination is the generation of a durable antibody response with cross-neutralizing activity against both current and newly emerging viral variants. Cross-neutralizing activity against major variants of concern (B.1.1.7, P.1 and B.1.351) has been observed following vaccination, albeit at a reduced potency, but whether vaccines based on the Spike glycoprotein of these viral variants will produce a superior cross-neutralizing antibody response has not been fully investigated. Here, we used sera from individuals infected in wave 1 in the UK to study the long-term cross-neutralization up to 10 months post onset of symptoms (POS), as well as sera from individuals infected with the B.1.1.7 variant to compare cross-neutralizing activity profiles. We show that neutralizing antibodies with cross-neutralizing activity can be detected from wave 1 up to 10 months POS. Although neutralization of B.1.1.7 and B.1.351 is lower, the difference in neutralization potency decreases at later timepoints suggesting continued antibody maturation and improved tolerance to Spike mutations. Interestingly, we found that B.1.1.7 infection also generates a cross-neutralizing antibody response, which, although still less potent against B.1.351, can neutralize parental wave 1 virus to a similar degree as B.1.1.7. These findings have implications for the optimization of vaccines that protect against newly emerging viral variants.
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Affiliation(s)
- Liane Dupont
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Luke B Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Blair Merrick
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Thomas Lechmere
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Sadie R Hallett
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Themoula Charalampous
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Adela Alcolea-Medina
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Thomas J A Maguire
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Sam Acors
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Nathalia Almeida
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Daniel Cox
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Ruth E Dickenson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Rui Pedro Galao
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jose M Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Neophytos Kouphou
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Marie Jose Lista
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Ana Maria Ortega-Prieto
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Harry Wilson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Helena Winstone
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Cassandra Fairhead
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Jia Su
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Stuart Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Manu Shankar-Hari
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jonathan D Edgeworth
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
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337
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Graham C, Seow J, Huettner I, Khan H, Kouphou N, Acors S, Winstone H, Pickering S, Galao RP, Dupont L, Lista MJ, Jimenez-Guardeño JM, Laing AG, Wu Y, Joseph M, Muir L, van Gils MJ, Ng WM, Duyvesteyn HME, Zhao Y, Bowden TA, Shankar-Hari M, Rosa A, Cherepanov P, McCoy LE, Hayday AC, Neil SJD, Malim MH, Doores KJ. Neutralization potency of monoclonal antibodies recognizing dominant and subdominant epitopes on SARS-CoV-2 Spike is impacted by the B.1.1.7 variant. Immunity 2021; 54:1276-1289.e6. [PMID: 33836142 PMCID: PMC8015430 DOI: 10.1016/j.immuni.2021.03.023] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/05/2021] [Accepted: 03/29/2021] [Indexed: 01/21/2023]
Abstract
Interaction of the SARS-CoV-2 Spike receptor binding domain (RBD) with the receptor ACE2 on host cells is essential for viral entry. RBD is the dominant target for neutralizing antibodies, and several neutralizing epitopes on RBD have been molecularly characterized. Analysis of circulating SARS-CoV-2 variants has revealed mutations arising in the RBD, N-terminal domain (NTD) and S2 subunits of Spike. To understand how these mutations affect Spike antigenicity, we isolated and characterized >100 monoclonal antibodies targeting epitopes on RBD, NTD, and S2 from SARS-CoV-2-infected individuals. Approximately 45% showed neutralizing activity, of which ∼20% were NTD specific. NTD-specific antibodies formed two distinct groups: the first was highly potent against infectious virus, whereas the second was less potent and displayed glycan-dependant neutralization activity. Mutations present in B.1.1.7 Spike frequently conferred neutralization resistance to NTD-specific antibodies. This work demonstrates that neutralizing antibodies targeting subdominant epitopes should be considered when investigating antigenic drift in emerging variants.
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Affiliation(s)
- Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Hataf Khan
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Neophytos Kouphou
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Sam Acors
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Helena Winstone
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Rui Pedro Galao
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Liane Dupont
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Maria Jose Lista
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jose M Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Adam G Laing
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Yin Wu
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK; The Francis Crick Institute, UK
| | - Magdalene Joseph
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK; The Francis Crick Institute, UK
| | - Luke Muir
- Division of Infection and Immunity, University College London, London, UK
| | - Marit J van Gils
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Netherlands
| | - Weng M Ng
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Manu Shankar-Hari
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | | | | | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - Adrian C Hayday
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK; The Francis Crick Institute, UK
| | - Stuart J D Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK; Genotype-to-Phenotype UK National Virology Consortium
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK; Genotype-to-Phenotype UK National Virology Consortium
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK; Genotype-to-Phenotype UK National Virology Consortium.
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338
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Monrad I, Sahlertz SR, Nielsen SSF, Pedersen LØ, Petersen MS, Kobel CM, Tarpgaard IH, Storgaard M, Mortensen KL, Schleimann MH, Tolstrup M, Vibholm LK. Persistent Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Immunocompromised Host Displaying Treatment Induced Viral Evolution. Open Forum Infect Dis 2021; 8:ofab295. [PMID: 34258320 PMCID: PMC8244814 DOI: 10.1093/ofid/ofab295] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
We report a coronavirus disease 2019 case with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) persisting beyond 333 days in an immunocompromised patient with chronic lymphocytic leukemia, asymptomatically carrying infectious SARS-CoV-2 at day 197 postdiagnosis. In addition, viral sequencing indicates major changes in the spike protein over time, temporally associated with convalescent plasma treatment.
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Affiliation(s)
- Ida Monrad
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | - Stine Sofie Frank Nielsen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | | | - Carl Mathias Kobel
- Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Merete Storgaard
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Martin Tolstrup
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Line K Vibholm
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
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339
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Voss WN, Hou YJ, Johnson NV, Delidakis G, Kim JE, Javanmardi K, Horton AP, Bartzoka F, Paresi CJ, Tanno Y, Chou CW, Abbasi SA, Pickens W, George K, Boutz DR, Towers DM, McDaniel JR, Billick D, Goike J, Rowe L, Batra D, Pohl J, Lee J, Gangappa S, Sambhara S, Gadush M, Wang N, Person MD, Iverson BL, Gollihar JD, Dye JM, Herbert AS, Finkelstein IJ, Baric RS, McLellan JS, Georgiou G, Lavinder JJ, Ippolito GC. Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes. Science 2021; 372:1108-1112. [PMID: 33947773 PMCID: PMC8224265 DOI: 10.1126/science.abg5268] [Citation(s) in RCA: 172] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022]
Abstract
The molecular composition and binding epitopes of the immunoglobulin G (IgG) antibodies that circulate in blood plasma after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are unknown. Proteomic deconvolution of the IgG repertoire to the spike glycoprotein in convalescent subjects revealed that the response is directed predominantly (>80%) against epitopes residing outside the receptor binding domain (RBD). In one subject, just four IgG lineages accounted for 93.5% of the response, including an amino (N)-terminal domain (NTD)-directed antibody that was protective against lethal viral challenge. Genetic, structural, and functional characterization of a multidonor class of "public" antibodies revealed an NTD epitope that is recurrently mutated among emerging SARS-CoV-2 variants of concern. These data show that "public" NTD-directed and other non-RBD plasma antibodies are prevalent and have implications for SARS-CoV-2 protection and antibody escape.
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MESH Headings
- Animals
- Antibodies, Monoclonal/blood
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibody Affinity
- COVID-19/immunology
- COVID-19/prevention & control
- Epitopes/immunology
- Humans
- Immune Evasion
- Immunoglobulin G/blood
- Immunoglobulin G/chemistry
- Immunoglobulin G/immunology
- Immunoglobulin Heavy Chains/immunology
- Immunoglobulin Variable Region/immunology
- Mice
- Mice, Inbred BALB C
- Mutation
- Protein Domains
- Proteomics
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- William N Voss
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - George Delidakis
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jin Eyun Kim
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew P Horton
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Foteini Bartzoka
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Chelsea J Paresi
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Yuri Tanno
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Shawn A Abbasi
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Whitney Pickens
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Katia George
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Daniel R Boutz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, The University of Texas at Austin, Austin, TX, USA
| | - Dalton M Towers
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | | | - Daniel Billick
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jule Goike
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Lori Rowe
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Tulane National Primate Research Center Department of Microbiology 18703 Three Rivers Road Covington, LA, USA
| | - Dhwani Batra
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jan Pohl
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Justin Lee
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shivaprakash Gangappa
- Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Suryaprakash Sambhara
- Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michelle Gadush
- Center for Biomedical Research Support, The University of Texas at Austin, Austin, TX, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Maria D Person
- Center for Biomedical Research Support, The University of Texas at Austin, Austin, TX, USA
| | - Brent L Iverson
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Jimmy D Gollihar
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, The University of Texas at Austin, Austin, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - John M Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Andrew S Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - George Georgiou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Jason J Lavinder
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
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340
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Mengist HM, Kombe Kombe AJ, Mekonnen D, Abebaw A, Getachew M, Jin T. Mutations of SARS-CoV-2 spike protein: Implications on immune evasion and vaccine-induced immunity. Semin Immunol 2021; 55:101533. [PMID: 34836774 PMCID: PMC8604694 DOI: 10.1016/j.smim.2021.101533] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/09/2021] [Accepted: 11/16/2021] [Indexed: 02/04/2023]
Abstract
Responsible for more than 4.9 million deaths so far, COVID-19, caused by SARS-CoV-2, is instigating devastating effects on the global health care system whose impacts could be longer for the years to come. Acquiring a comprehensive knowledge of host-virus interaction is critical for designing effective vaccines and/or drugs. Understanding the evolution of the virus and the impact of genetic variability on host immune evasion and vaccine efficacy is helpful to design novel strategies to minimize the effects of the emerging variants of concern (VOC). Most vaccines under development and/or in current use target the spike protein owning to its unique function of host receptor binding, relatively conserved nature, potent immunogenicity in inducing neutralizing antibodies, and being a good target of T cell responses. However, emerging SARS-CoV-2 strains are exhibiting variability on the spike protein which could affect the efficacy of vaccines and antibody-based therapies in addition to enhancing viral immune evasion mechanisms. Currently, the degree to which mutations on the spike protein affect immunity and vaccination, and the ability of the current vaccines to confer protection against the emerging variants attracts much attention. This review discusses the implications of SARS-CoV-2 spike protein mutations on immune evasion and vaccine-induced immunity and forward directions which could contribute to future studies focusing on designing effective vaccines and/or immunotherapies to consider viral evolution. Combining vaccines derived from different regions of the spike protein that boost both the humoral and cellular wings of adaptive immunity could be the best options to cope with the emerging VOC.
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Affiliation(s)
- Hylemariam Mihiretie Mengist
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Arnaud John Kombe Kombe
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, Anhui, 230027, China
| | - Daniel Mekonnen
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, Anhui, 230027, China
| | - Abtie Abebaw
- Department of Medical Laboratory Science, College of Health Science, Debre Markos University, Debre Markos, 269, Ethiopia
| | - Melese Getachew
- Department of Clinical Pharmacy, College of Health Science, Debre Markos University, Debre Markos, 269, Ethiopia
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China; Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, Anhui, 230027, China; CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Science, Shanghai, 200031, China.
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341
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Dopazo J, Maya-Miles D, García F, Lorusso N, Calleja MÁ, Pareja MJ, López-Miranda J, Rodríguez-Baño J, Padillo J, Túnez I, Romero-Gómez M. Implementing Personalized Medicine in COVID-19 in Andalusia: An Opportunity to Transform the Healthcare System. J Pers Med 2021; 11:475. [PMID: 34073493 PMCID: PMC8226500 DOI: 10.3390/jpm11060475] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
The COVID-19 pandemic represents an unprecedented opportunity to exploit the advantages of personalized medicine for the prevention, diagnosis, treatment, surveillance and management of a new challenge in public health. COVID-19 infection is highly variable, ranging from asymptomatic infections to severe, life-threatening manifestations. Personalized medicine can play a key role in elucidating individual susceptibility to the infection as well as inter-individual variability in clinical course, prognosis and response to treatment. Integrating personalized medicine into clinical practice can also transform health care by enabling the design of preventive and therapeutic strategies tailored to individual profiles, improving the detection of outbreaks or defining transmission patterns at an increasingly local level. SARS-CoV2 genome sequencing, together with the assessment of specific patient genetic variants, will support clinical decision-makers and ultimately better ways to fight this disease. Additionally, it would facilitate a better stratification and selection of patients for clinical trials, thus increasing the likelihood of obtaining positive results. Lastly, defining a national strategy to implement in clinical practice all available tools of personalized medicine in COVID-19 could be challenging but linked to a positive transformation of the health care system. In this review, we provide an update of the achievements, promises, and challenges of personalized medicine in the fight against COVID-19 from susceptibility to natural history and response to therapy, as well as from surveillance to control measures and vaccination. We also discuss strategies to facilitate the adoption of this new paradigm for medical and public health measures during and after the pandemic in health care systems.
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Affiliation(s)
- Joaquín Dopazo
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Área de Bioinformática, Fundación progreso y Salud, Junta de Andalucía, 41013 Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Douglas Maya-Miles
- Instituto de Biomedicina de Sevilla (HUVR/HUVM/CSIC/US), 41013 Sevilla, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28029 Madrid, Spain
| | - Federico García
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria IBS, 18012 Granada, Spain
| | - Nicola Lorusso
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Dirección General de Salud Pública, Consejería de Salud y Familias, Junta de Andalucía, Spain
| | - Miguel Ángel Calleja
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Servicio de Farmacia, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain
| | - María Jesús Pareja
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Hospital Universitario de Valme, 41014 Sevilla, Spain
| | - José López-Miranda
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Servicio de Medicina Interna, Hospital Universitario Reina Sofía, 14004 Córdoba, Spain
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), 14004 Córdoba, Spain
- Departamento de Ciencias Médicas y Quirúrgicas, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Jesús Rodríguez-Baño
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Instituto de Biomedicina de Sevilla (HUVR/HUVM/CSIC/US), 41013 Sevilla, Spain;
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain
- Departamento de Medicina, Universidad de Sevilla, 41009 Sevilla, Spain
| | - Javier Padillo
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Instituto de Biomedicina de Sevilla (HUVR/HUVM/CSIC/US), 41013 Sevilla, Spain;
- Departamento de Cirugía, Universidad de Sevilla, 41009 Sevilla, Spain
- Servicio de Cirugía General y Digestiva, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
| | - Isaac Túnez
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Servicio de Medicina Interna, Hospital Universitario Reina Sofía, 14004 Córdoba, Spain
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), 14004 Córdoba, Spain
- Departamento de Bioquímica, Universidad de Córdoba, 14071 Córdoba, Spain
- Secretaría General de Investigación, Desarrollo e Innovación en Salud, Consejería de Salud y Familias de la Junta de Andalucía, 41020 Sevilla, Spain
| | - Manuel Romero-Gómez
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Instituto de Biomedicina de Sevilla (HUVR/HUVM/CSIC/US), 41013 Sevilla, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28029 Madrid, Spain
- Departamento de Medicina, Universidad de Sevilla, 41009 Sevilla, Spain
- Servicio de Aparato Digestivo, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
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Pucci F, Rooman M. Prediction and Evolution of the Molecular Fitness of SARS-CoV-2 Variants: Introducing SpikePro. Viruses 2021; 13:935. [PMID: 34070055 PMCID: PMC8158131 DOI: 10.3390/v13050935] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 12/18/2022] Open
Abstract
The understanding of the molecular mechanisms driving the fitness of the SARS-CoV-2 virus and its mutational evolution is still a critical issue. We built a simplified computational model, called SpikePro, to predict the SARS-CoV-2 fitness from the amino acid sequence and structure of the spike protein. It contains three contributions: the inter-human transmissibility of the virus predicted from the stability of the spike protein, the infectivity computed in terms of the affinity of the spike protein for the ACE2 receptor, and the ability of the virus to escape from the human immune response based on the binding affinity of the spike protein for a set of neutralizing antibodies. Our model reproduces well the available experimental, epidemiological and clinical data on the impact of variants on the biophysical characteristics of the virus. For example, it is able to identify circulating viral strains that, by increasing their fitness, recently became dominant at the population level. SpikePro is a useful, freely available instrument which predicts rapidly and with good accuracy the dangerousness of new viral strains. It can be integrated and play a fundamental role in the genomic surveillance programs of the SARS-CoV-2 virus that, despite all the efforts, remain time-consuming and expensive.
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Affiliation(s)
- Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium;
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium;
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
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343
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Pucci F, Rooman M. Prediction and Evolution of the Molecular Fitness of SARS-CoV-2 Variants: Introducing SpikePro. Viruses 2021; 13:v13050935. [PMID: 34070055 DOI: 10.1101/2021.04.11.439322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 05/25/2023] Open
Abstract
The understanding of the molecular mechanisms driving the fitness of the SARS-CoV-2 virus and its mutational evolution is still a critical issue. We built a simplified computational model, called SpikePro, to predict the SARS-CoV-2 fitness from the amino acid sequence and structure of the spike protein. It contains three contributions: the inter-human transmissibility of the virus predicted from the stability of the spike protein, the infectivity computed in terms of the affinity of the spike protein for the ACE2 receptor, and the ability of the virus to escape from the human immune response based on the binding affinity of the spike protein for a set of neutralizing antibodies. Our model reproduces well the available experimental, epidemiological and clinical data on the impact of variants on the biophysical characteristics of the virus. For example, it is able to identify circulating viral strains that, by increasing their fitness, recently became dominant at the population level. SpikePro is a useful, freely available instrument which predicts rapidly and with good accuracy the dangerousness of new viral strains. It can be integrated and play a fundamental role in the genomic surveillance programs of the SARS-CoV-2 virus that, despite all the efforts, remain time-consuming and expensive.
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Affiliation(s)
- Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
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344
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Boehm E, Kronig I, Neher RA, Eckerle I, Vetter P, Kaiser L. Novel SARS-CoV-2 variants: the pandemics within the pandemic. Clin Microbiol Infect 2021; 27:1109-1117. [PMID: 34015535 PMCID: PMC8127517 DOI: 10.1016/j.cmi.2021.05.022] [Citation(s) in RCA: 232] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/05/2021] [Accepted: 05/09/2021] [Indexed: 11/29/2022]
Abstract
Background Many new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been termed variants of concern/interest (VOC/I) because of the greater risk they pose due to possible enhanced transmissibility and/or severity, immune escape, diagnostic and/or treatment failure, and reduced vaccine efficacy. Aims We sought to review the current knowledge of emerging SARS-CoV-2 variants, particularly those deemed VOC/Is: B.1.351, B.1.1.7, and P.1. Sources MEDLINE and BioRxiv databases, as well as the grey literature, were searched for reports of SARS-CoV-2 variants since November 2020. Relevant articles and their references were screened. Content Mutations on the spike protein in particular may affect both affinity for the SARS-CoV-2 cell receptor ACEII and antibody binding. These VOC/Is often share similar mutation sets. The N501Y mutation is shared by the three main VOCs: B.1.1.7, first identified in the United Kingdom, P.1, originating from Brazil, and B.1.351, first described in South Africa. This mutation likely increases transmissibility by increasing affinity for ACEII. The B.1.351 and P.1 variants also display the E484K mutation which decreases binding of neutralizing antibodies, leading to partial immune escape; this favours reinfections, and decreases the in vitro efficacy of some antibody therapies or vaccines. Those mutations may also have phenotypical repercussions of greater severity. Furthermore, the accumulation of mutations poses a diagnostic risk (lowered when using multiplex assays), as seen for some assays targeting the S gene. With ongoing surveillance, many new VOC/Is have been identified. The emergence of the E484K mutation independently in different parts of the globe may reflect the adaptation of SARS-CoV-2 to humans against a background of increasing immunity. Implications These VOC/Is are increasing in frequency globally and pose challenges to any herd immunity approach to managing the pandemic. While vaccination is ongoing, vaccine updates may be prudent. The virus continues to adapt to transmission in humans, and further divergence from the initial Wuhan sequences is expected.
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Affiliation(s)
- Erik Boehm
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland.
| | - Ilona Kronig
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Richard A Neher
- Biozentrum, University of Basel, Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Isabella Eckerle
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Pauline Vetter
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Laurent Kaiser
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
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345
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Liu H, Yuan M, Huang D, Bangaru S, Zhao F, Lee CCD, Peng L, Barman S, Zhu X, Nemazee D, Burton DR, van Gils MJ, Sanders RW, Kornau HC, Reincke SM, Prüss H, Kreye J, Wu NC, Ward AB, Wilson IA. A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection. Cell Host Microbe 2021; 29:806-818.e6. [PMID: 33894127 PMCID: PMC8049401 DOI: 10.1016/j.chom.2021.04.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/26/2021] [Accepted: 04/12/2021] [Indexed: 12/15/2022]
Abstract
Coronaviruses have caused several human epidemics and pandemics including the ongoing coronavirus disease 2019 (COVID-19). Prophylactic vaccines and therapeutic antibodies have already shown striking effectiveness against COVID-19. Nevertheless, concerns remain about antigenic drift in SARS-CoV-2 as well as threats from other sarbecoviruses. Cross-neutralizing antibodies to SARS-related viruses provide opportunities to address such concerns. Here, we report on crystal structures of a cross-neutralizing antibody, CV38-142, in complex with the receptor-binding domains from SARS-CoV-2 and SARS-CoV. Recognition of the N343 glycosylation site and water-mediated interactions facilitate cross-reactivity of CV38-142 to SARS-related viruses, allowing the antibody to accommodate antigenic variation in these viruses. CV38-142 synergizes with other cross-neutralizing antibodies, notably COVA1-16, to enhance neutralization of SARS-CoV and SARS-CoV-2, including circulating variants of concern B.1.1.7 and B.1.351. Overall, this study provides valuable information for vaccine and therapeutic design to address current and future antigenic drift in SARS-CoV-2 and to protect against zoonotic SARS-related coronaviruses.
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Affiliation(s)
- Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sandhya Bangaru
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fangzhu Zhao
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chang-Chun D Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shawn Barman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Marit J van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Hans-Christian Kornau
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany; Neuroscience Research Center (NWFZ), Cluster NeuroCure, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - S Momsen Reincke
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany; Helmholtz Innovation Lab BaoBab, Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Harald Prüss
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany; Helmholtz Innovation Lab BaoBab, Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jakob Kreye
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany; Helmholtz Innovation Lab BaoBab, Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany; Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Nicholas C Wu
- Department of Biochemistry, 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; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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346
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Filkins L, SoRelle JA, Schoggins J, Park JY. Laboratory Action Plan for Emerging SARS-CoV-2 Variants. Clin Chem 2021; 67:720-723. [PMID: 33515256 DOI: 10.1093/clinchem/hvab020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 01/19/2021] [Indexed: 12/19/2022]
Affiliation(s)
- Laura Filkins
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX.,Department of Pathology and Laboratory Medicine, Children's Health System of Texas, Dallas, TX
| | - Jeffrey A SoRelle
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX.,Department of Pathology and Laboratory Medicine, Children's Health System of Texas, Dallas, TX
| | - John Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jason Y Park
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX.,Department of Pathology and Laboratory Medicine, Children's Health System of Texas, Dallas, TX.,McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX
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Abstract
Roughly 1 year after the first case of COVID-19 was identified and less than 1 year after the sequencing of SARS-CoV-2, multiple SARS-CoV-2 vaccines with demonstrated safety and efficacy in phase III clinical trials are available. The most promising vaccines have targeted the surface glycoprotein (S-protein) of SARS-CoV-2 and achieved an approximate 85%-95% reduction in the risk of symptomatic COVID-19, while retaining excellent safety profiles and modest side effects in the phase III clinical trials. The mRNA, replication-incompetent viral vector, and protein subunit vaccine technologies have all been successfully employed. Some novel SARS-CoV-2 variants evade but do not appear to fully overcome the potent immunity induced by these vaccines. Emerging real-world effectiveness data add evidence for protection from severe COVID-19. This is an impressive first demonstration of the effectiveness of the mRNA vaccine and vector vaccine platforms. The success of SARS-CoV-2 vaccine development should be credited to open science, industry partnerships, harmonization of clinical trials, and the altruism of study participants. The manufacturing and distribution of the emergency use-authorized SARS-CoV-2 vaccines are ongoing challenges. What remains now is to ensure broad and equitable global vaccination against COVID-19.
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Affiliation(s)
| | - Njira Lugogo
- Division of Pulmonary and Critical Care Medicine, and
| | | | - Anna S. Lok
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
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348
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Abstract
COVID-19 is characterized by a wide range of clinical manifestations, from asymptomatic to extremely severe. At the onset of the pandemic, it became clear that old age and chronic illness were the major risk factors. However, they do not fully explain the variety of symptoms and complications of the SARS-COV-2 coronavirus infection. The research on genetic risk factors for COVID-19 is still at its early stages. A number of mutations and polymorphisms have been identified that affect the structure and stability of proteins factors of susceptibility to SARS-COV-2 infection, as well as a predisposition to the development of respiratory failure and the need for intensive care. Most of the identified genetic factors are related to the function of the immune system. On the other hand, the genetic polymorphism of the virus itself affects the COVID-19 spread and severity of its course . The genome of the virus accumulates mutations and evolves towards increasing contagiousness, replicative ability and evasion from the host's immune system. Genetic determinants of the COVID-19 infection are potential therapeutic targets. Studying them will provide information for the development of drugs and vaccines to combat the pandemic.
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349
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Truong TT, Ryutov A, Pandey U, Yee R, Goldberg L, Bhojwani D, Aguayo-Hiraldo P, Pinsky BA, Pekosz A, Shen L, Boyd SD, Wirz OF, Röltgen K, Bootwalla M, Maglinte DT, Ostrow D, Ruble D, Han JH, Biegel JA, Li M, Huang C, Sahoo MK, Pannaraj PS, O'Gorman M, Judkins AR, Gai X, Dien Bard J. Increased viral variants in children and young adults with impaired humoral immunity and persistent SARS-CoV-2 infection: A consecutive case series. EBioMedicine 2021; 67:103355. [PMID: 33915337 PMCID: PMC8072072 DOI: 10.1016/j.ebiom.2021.103355] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/22/2021] [Accepted: 04/08/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND There is increasing concern that persistent infection of SARS-CoV-2 within immunocompromised hosts could serve as a reservoir for mutation accumulation and subsequent emergence of novel strains with the potential to evade immune responses. METHODS We describe three patients with acute lymphoblastic leukemia who were persistently positive for SARS-CoV-2 by real-time polymerase chain reaction. Viral viability from longitudinally-collected specimens was assessed. Whole-genome sequencing and serological studies were performed to measure viral evolution and evidence of immune escape. FINDINGS We found compelling evidence of ongoing replication and infectivity for up to 162 days from initial positive by subgenomic RNA, single-stranded RNA, and viral culture analysis. Our results reveal a broad spectrum of infectivity, host immune responses, and accumulation of mutations, some with the potential for immune escape. INTERPRETATION Our results highlight the potential need to reassess infection control precautions in the management and care of immunocompromised patients. Routine surveillance of mutations and evaluation of their potential impact on viral transmission and immune escape should be considered.
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Affiliation(s)
- Thao T Truong
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Alex Ryutov
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Utsav Pandey
- Department of Pathology, Westchester Medical Center/New York Medical College, Valhalla, NY, United States
| | - Rebecca Yee
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Lior Goldberg
- Department of Pediatrics, Cancer and Blood Disease Institute, Division of Hematology-Oncology, Children's Hospital Los Angeles, Los Angeles, CA, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Deepa Bhojwani
- Department of Pediatrics, Cancer and Blood Disease Institute, Division of Hematology-Oncology, Children's Hospital Los Angeles, Los Angeles, CA, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Paibel Aguayo-Hiraldo
- Department of Pediatrics, Cancer and Blood Disease Institute, Division of Hematology-Oncology, Children's Hospital Los Angeles, Los Angeles, CA, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA, United States; Department of Pediatrics, Cancer and Blood Disorder Institute, Transplant and Cellular Therapy Section, Children's Hospital Los Angeles, CA, United States
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Lishuang Shen
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Scott D Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States; Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, United States
| | - Oliver F Wirz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Katharina Röltgen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Moiz Bootwalla
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Dennis T Maglinte
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Dejerianne Ostrow
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - David Ruble
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Jennifer H Han
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Jaclyn A Biegel
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Maggie Li
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Pia S Pannaraj
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States; Department of Pediatrics, Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Maurice O'Gorman
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Alexander R Judkins
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Xiaowu Gai
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.
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350
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Kennedy NA, Goodhand JR, Bewshea C, Nice R, Chee D, Lin S, Chanchlani N, Butterworth J, Cooney R, Croft NM, Hart AL, Irving PM, Kok KB, Lamb CA, Limdi JK, Macdonald J, McGovern DP, Mehta SJ, Murray CD, Patel KV, Pollok RC, Raine T, Russell RK, Selinger CP, Smith PJ, Bowden J, McDonald TJ, Lees CW, Sebastian S, Powell N, Ahmad T. Anti-SARS-CoV-2 antibody responses are attenuated in patients with IBD treated with infliximab. Gut 2021; 70:865-875. [PMID: 33753421 PMCID: PMC7992387 DOI: 10.1136/gutjnl-2021-324388] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Antitumour necrosis factor (anti-TNF) drugs impair protective immunity following pneumococcal, influenza and viral hepatitis vaccination and increase the risk of serious respiratory infections. We sought to determine whether infliximab-treated patients with IBD have attenuated serological responses to SARS-CoV-2 infections. DESIGN Antibody responses in participants treated with infliximab were compared with a reference cohort treated with vedolizumab, a gut-selective anti-integrin α4β7 monoclonal antibody that is not associated with impaired vaccine responses or increased susceptibility to systemic infections. 6935 patients were recruited from 92 UK hospitals between 22 September and 23 December 2020. RESULTS Rates of symptomatic and proven SARS-CoV-2 infection were similar between groups. Seroprevalence was lower in infliximab-treated than vedolizumab-treated patients (3.4% (161/4685) vs 6.0% (134/2250), p<0.0001). Multivariable logistic regression analyses confirmed that infliximab (vs vedolizumab; OR 0.66 (95% CI 0.51 to 0.87), p=0.0027) and immunomodulator use (OR 0.70 (95% CI 0.53 to 0.92), p=0.012) were independently associated with lower seropositivity. In patients with confirmed SARS-CoV-2 infection, seroconversion was observed in fewer infliximab-treated than vedolizumab-treated patients (48% (39/81) vs 83% (30/36), p=0.00044) and the magnitude of anti-SARS-CoV-2 reactivity was lower (median 0.8 cut-off index (0.2-5.6) vs 37.0 (15.2-76.1), p<0.0001). CONCLUSIONS Infliximab is associated with attenuated serological responses to SARS-CoV-2 that were further blunted by immunomodulators used as concomitant therapy. Impaired serological responses to SARS-CoV-2 infection might have important implications for global public health policy and individual anti-TNF-treated patients. Serological testing and virus surveillance should be considered to detect suboptimal vaccine responses, persistent infection and viral evolution to inform public health policy. TRIAL REGISTRATION NUMBER ISRCTN45176516.
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Affiliation(s)
- Nicholas A Kennedy
- Department of Gastroenterology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - James R Goodhand
- Department of Gastroenterology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Claire Bewshea
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Rachel Nice
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
- Department of Biochemistry, Exeter Clinical Laboratory International, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Desmond Chee
- Department of Gastroenterology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Simeng Lin
- Department of Gastroenterology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Neil Chanchlani
- Department of Gastroenterology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Jeffrey Butterworth
- Department of Gastroenterology, Shrewsbury and Telford Hospital NHS Trust, Shrewsbury, UK
| | - Rachel Cooney
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Nicholas M Croft
- Department of Paediatric Gastroenterology, Royal London Hospital, Barts Health NHS Trust, London, UK
- Centre for Immunobiology, Blizard Institute, Barts and the London School of Medicine, Queen Mary University of London, London, UK
| | - Ailsa L Hart
- Department of Gastroenterology, St Mark's Hospital and Academic Institute, Harrow, London, UK
| | - Peter M Irving
- Department of Gastroenterology, Guy's and St Thomas' NHS Foundation Trust, London, UK
- School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Klaartje B Kok
- Centre for Immunobiology, Blizard Institute, Barts and the London School of Medicine, Queen Mary University of London, London, UK
- Department of Gastroenterology, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Christopher A Lamb
- Department of Gastroenterology, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Jimmy K Limdi
- Department of Gastroenterology, Pennine Acute Hospitals NHS Trust, Manchester, UK
- Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - Jonathan Macdonald
- Department of Gastroenterology, Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Dermot Pb McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shameer J Mehta
- Department of Gastroenterology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Charles D Murray
- Department of Gastroenterology, Royal Free London NHS Foundation Trust, London, UK
| | - Kamal V Patel
- Department of Gastroenterology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Richard Cg Pollok
- Department of Gastroenterology, St George's University Hospitals NHS Foundation Trust, London, UK
- Institute for Infection and Immunity, University of London, London, UK
| | - Timothy Raine
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Richard K Russell
- Department of Paediatric Gastroenterology, Royal Hospital for Sick Children, NHS Lothian, Edinburgh, UK
| | | | - Philip J Smith
- Department of Gastroenterology, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Jack Bowden
- Medical School, University of Exeter, Exeter, UK
| | - Timothy J McDonald
- Department of Biochemistry, Exeter Clinical Laboratory International, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Charlie W Lees
- Department of Gastroenterology, Western General Hospital, NHS Lothian, Edinburgh, UK
- Institute of Genetic and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Shaji Sebastian
- Department of Gastroenterology, Hull University Teaching Hospitals NHS Trust, Hull, UK
| | - Nicholas Powell
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Tariq Ahmad
- Department of Gastroenterology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
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