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Bhattacharya M, Chatterjee S, Lee SS, Dhama K, Chakraborty C. Antibody evasion associated with the RBD significant mutations in several emerging SARS-CoV-2 variants and its subvariants. Drug Resist Updat 2023; 71:101008. [PMID: 37757651 DOI: 10.1016/j.drup.2023.101008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]
Abstract
Since the origin of the wild strain of SARS-CoV-2, several variants have emerged, which were designated as VOC, VOI, and VUM from time to time. The Omicron variant is noted as the recent VOC. After the origin of the Omicron variant on November 2021, several subvariants of Omicron have originated subsequently, like BA.1/2, BA.2.75/2.75.2, BA.4/5, BF.7, BQ.1/1.1, XBB.1/1.5, etc. which are circulated throughout the globe. Scientists reported that antibody escape is a common phenomenon observed in all the previous VOCs, VOIs, including Omicron and its subvariants. The mutations in the NTD (N-terminal domain) and RBD (Receptor-binding domain) of the spike of these variants and subvariants are responsible for antibody escape. At the same time, it has been noted that spike RBD mutations have been increasing in the last few months. This review illustrates significant RBD mutations namely R346T, K417N/T, L452R, N460K E484A/K/Q, and N501Y found in the previous emerging SARS-CoV-2 variants, including Omicron and its subvariants in high frequency and their role in antibody evasion and immune evasion. The review also describes the different classes of nAb responsible for antibody escape in SARS-CoV-2 variants and the molecular perspective of the mutation in nAb escape. It will help the future researchers to develop efficient vaccines which can finally prevent the pandemic.
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Affiliation(s)
- Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Srijan Chatterjee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata 700126, West Bengal, India.
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2
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Heijnen L, Elsinga G, de Graaf M, Molenkamp R, Koopmans MPG, Medema G. Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Sci Total Environ 2021; 799:149456. [PMID: 34371414 PMCID: PMC8332926 DOI: 10.1016/j.scitotenv.2021.149456] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/15/2021] [Accepted: 07/31/2021] [Indexed: 04/15/2023]
Abstract
Wastewater surveillance has shown to be a valuable and efficient tool to obtain information about the trends of COVID-19 in the community. Since the recent emergence of new variants, associated with increased transmissibility and/or antibody escape (variants of concern), there is an urgent need for methods that enable specific and timely detection and quantification of the occurrence of these variants in the community. In this study, we demonstrate the use of RT-ddPCR on wastewater samples for specific detection of mutation N501Y. This assay enabled simultaneous enumeration of lineage B.1.351 (containing the 501Y mutation) and Wild Type (WT, containing 501N) SARS-CoV-2 RNA. Detection of N501Y was possible in samples with mixtures of WT with low proportions of B.1.351 (0.5%) and could accurately determine the proportion of N501Y and WT in mixtures of SARS-CoV-2 RNA. The application to raw sewage samples from the cities of Amsterdam and Utrecht demonstrated that this method can be applied to wastewater samples. The emergence of N501Y in Amsterdam and Utrecht wastewater aligned with the emergence of B.1.1.7 as causative agent of COVID-19 in the Netherlands, indicating that RT-ddPCR of wastewater samples can be used to monitor the emergence of the N501Y mutation in the community. It also indicates that RT-ddPCR could be used for sensitive and accurate monitoring of current (like K417N, K417T, E484K, L452R) or future mutations present in SARS-CoV-2 variants of concern. Monitoring these mutations can be used to obtain insight in the introduction and spread of VOC and support public health decision-making regarding measures to limit viral spread or allocation of testing or vaccination.
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Affiliation(s)
- Leo Heijnen
- KWR Water Research Institute, Nieuwegein, the Netherlands.
| | - Goffe Elsinga
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Gertjan Medema
- KWR Water Research Institute, Nieuwegein, the Netherlands
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3
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Heijnen L, Elsinga G, de Graaf M, Molenkamp R, Koopmans MPG, Medema G. Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Sci Total Environ 2021; 799:149456. [PMID: 34371414 DOI: 10.1101/2021.03.25.21254324] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/15/2021] [Accepted: 07/31/2021] [Indexed: 05/20/2023]
Abstract
Wastewater surveillance has shown to be a valuable and efficient tool to obtain information about the trends of COVID-19 in the community. Since the recent emergence of new variants, associated with increased transmissibility and/or antibody escape (variants of concern), there is an urgent need for methods that enable specific and timely detection and quantification of the occurrence of these variants in the community. In this study, we demonstrate the use of RT-ddPCR on wastewater samples for specific detection of mutation N501Y. This assay enabled simultaneous enumeration of lineage B.1.351 (containing the 501Y mutation) and Wild Type (WT, containing 501N) SARS-CoV-2 RNA. Detection of N501Y was possible in samples with mixtures of WT with low proportions of B.1.351 (0.5%) and could accurately determine the proportion of N501Y and WT in mixtures of SARS-CoV-2 RNA. The application to raw sewage samples from the cities of Amsterdam and Utrecht demonstrated that this method can be applied to wastewater samples. The emergence of N501Y in Amsterdam and Utrecht wastewater aligned with the emergence of B.1.1.7 as causative agent of COVID-19 in the Netherlands, indicating that RT-ddPCR of wastewater samples can be used to monitor the emergence of the N501Y mutation in the community. It also indicates that RT-ddPCR could be used for sensitive and accurate monitoring of current (like K417N, K417T, E484K, L452R) or future mutations present in SARS-CoV-2 variants of concern. Monitoring these mutations can be used to obtain insight in the introduction and spread of VOC and support public health decision-making regarding measures to limit viral spread or allocation of testing or vaccination.
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Affiliation(s)
- Leo Heijnen
- KWR Water Research Institute, Nieuwegein, the Netherlands.
| | - Goffe Elsinga
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Gertjan Medema
- KWR Water Research Institute, Nieuwegein, the Netherlands
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4
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Alabbas AB, Alamri MA. Analyzing the Effect of Mutations in SARS-CoV2 Papain-Like Protease from Saudi Isolates on Protein Structure and Drug-Protein Binding: Molecular Modelling and Dynamics Studies. Saudi J Biol Sci 2021; 29:526-533. [PMID: 34548835 PMCID: PMC8447498 DOI: 10.1016/j.sjbs.2021.09.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 08/31/2021] [Accepted: 09/09/2021] [Indexed: 02/09/2023] Open
Abstract
The continuous and rapid development of the severe acute
respiratory syndrome coronavirus-2 (SARS-CoV-2) virus remains a health concern
especially with the emergence of numerous variants and mutations worldwide. As
with other RNA viruses, SARS-CoV-2 has a genetically high mutation rate. These
mutations have an impact on the virus characteristics, including
transmissibility, antigenicity and development of drug and vaccine resistance.
This work was pursued to identify the differences that exist in the papain-like
protease (PLPro) from 58 Saudi isolates in comparison to the
first reported sequence from Wuhan, China and determine their implications on
protein structure and the inhibitor binding. PLpro is a key
protease enzyme for the host cells invasion and viral proteolytic cleavage,
hence, it emerges as a valuable antiviral therapeutic target. Two mutations were
identified including D108G and A249V and shown to increase the molecular
flexibility of PLPro protein and alter the protein stability,
particularly with D108G mutation. The effect of these mutations on the stability
and dynamic behavior of PLPro structures as well as their
effect on the binding of a known inhibitor; GRL0617 were further investigated by
molecular docking and dynamic simulation.
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Affiliation(s)
- Alhumaidi B Alabbas
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
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5
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Voss C, Esmail S, Liu X, Knauer MJ, Ackloo S, Kaneko T, Lowes L, Stogios P, Seitova A, Hutchinson A, Yusifov F, Skarina T, Evdokimova E, Loppnau P, Ghiabi P, Haijan T, Zhong S, Abdoh H, Hedley BD, Bhayana V, Martin CM, Slessarev M, Chin-Yee B, Fraser DD, Chin-Yee I, Li SS. Epitope-specific antibody responses differentiate COVID-19 outcomes and variants of concern. JCI Insight 2021; 6:148855. [PMID: 34081630 PMCID: PMC8410046 DOI: 10.1172/jci.insight.148855] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/02/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUNDThe role of humoral immunity in COVID-19 is not fully understood, owing, in large part, to the complexity of antibodies produced in response to the SARS-CoV-2 infection. There is a pressing need for serology tests to assess patient-specific antibody response and predict clinical outcome.METHODSUsing SARS-CoV-2 proteome and peptide microarrays, we screened 146 COVID-19 patients' plasma samples to identify antigens and epitopes. This enabled us to develop a master epitope array and an epitope-specific agglutination assay to gauge antibody responses systematically and with high resolution.RESULTSWe identified linear epitopes from the spike (S) and nucleocapsid (N) proteins and showed that the epitopes enabled higher resolution antibody profiling than the S or N protein antigen. Specifically, we found that antibody responses to the S-811-825, S-881-895, and N-156-170 epitopes negatively or positively correlated with clinical severity or patient survival. Moreover, we found that the P681H and S235F mutations associated with the coronavirus variant of concern B.1.1.7 altered the specificity of the corresponding epitopes.CONCLUSIONEpitope-resolved antibody testing not only affords a high-resolution alternative to conventional immunoassays to delineate the complex humoral immunity to SARS-CoV-2 and differentiate between neutralizing and non-neutralizing antibodies, but it also may potentially be used to predict clinical outcome. The epitope peptides can be readily modified to detect antibodies against variants of concern in both the peptide array and latex agglutination formats.FUNDINGOntario Research Fund (ORF) COVID-19 Rapid Research Fund, Toronto COVID-19 Action Fund, Western University, Lawson Health Research Institute, London Health Sciences Foundation, and Academic Medical Organization of Southwestern Ontario (AMOSO) Innovation Fund.
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MESH Headings
- Agglutination Tests/methods
- Amino Acid Sequence
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Antibody Formation/immunology
- Antibody Specificity/immunology
- COVID-19/blood
- COVID-19/immunology
- COVID-19/mortality
- COVID-19 Serological Testing/methods
- Epitopes/immunology
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/immunology
- Humans
- Immunity, Humoral
- Microarray Analysis/methods
- Nucleocapsid/chemistry
- Nucleocapsid/genetics
- Nucleocapsid/immunology
- Peptides/immunology
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Severity of Illness Index
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
| | | | | | - Michael J. Knauer
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | | | | | - Lori Lowes
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Peter Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Peter Loppnau
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Pegah Ghiabi
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Taraneh Haijan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Husam Abdoh
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Benjamin D. Hedley
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Vipin Bhayana
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Claudio M. Martin
- Department of Medicine, Western University, London, Ontario, Canada
- London Health Sciences Centre, London, Ontario, Canada
| | - Marat Slessarev
- Department of Medicine, Western University, London, Ontario, Canada
- London Health Sciences Centre, London, Ontario, Canada
| | | | - Douglas D. Fraser
- Department of Medicine, Western University, London, Ontario, Canada
- London Health Sciences Centre, London, Ontario, Canada
- Department of Paediatrics, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Ian Chin-Yee
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
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6
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Vidal SJ, Collier ARY, Yu J, McMahan K, Tostanoski LH, Ventura JD, Aid M, Peter L, Jacob-Dolan C, Anioke T, Chang A, Wan H, Aguayo R, Ngo D, Gerszten RE, Seaman MS, Barouch DH. Correlates of Neutralization against SARS-CoV-2 Variants of Concern by Early Pandemic Sera. J Virol 2021; 95:e0040421. [PMID: 33893169 PMCID: PMC8223959 DOI: 10.1128/jvi.00404-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 04/20/2021] [Indexed: 12/23/2022] Open
Abstract
Emerging SARS-CoV-2 variants of concern that overcome natural and vaccine-induced immunity threaten to exacerbate the COVID-19 pandemic. Increasing evidence suggests that neutralizing antibody (NAb) responses are a primary mechanism of protection against infection. However, little is known about the extent and mechanisms by which natural immunity acquired during the early COVID-19 pandemic confers cross-neutralization of emerging variants. In this study, we investigated cross-neutralization of the B.1.1.7 and B.1.351 SARS-CoV-2 variants in a well-characterized cohort of early pandemic convalescent subjects. We observed modestly decreased cross-neutralization of B.1.1.7 but a substantial 4.8-fold reduction in cross-neutralization of B.1.351. Correlates of cross-neutralization included receptor binding domain (RBD) and N-terminal domain (NTD) binding antibodies, homologous NAb titers, and membrane-directed T cell responses. These data shed light on the cross-neutralization of emerging variants by early pandemic convalescent immune responses. IMPORTANCE Widespread immunity to SARS-CoV-2 will be necessary to end the COVID-19 pandemic. NAb responses are a critical component of immunity that can be stimulated by natural infection as well as vaccines. However, SARS-CoV-2 variants are emerging that contain mutations in the spike gene that promote evasion from NAb responses. These variants may therefore delay control of the COVID-19 pandemic. We studied whether NAb responses from early COVID-19 convalescent patients are effective against the two SARS-CoV-2 variants, B.1.1.7 and B.1.351. We observed that the B.1.351 variant demonstrates significantly reduced susceptibility to early pandemic NAb responses. We additionally characterized virological, immunological, and clinical features that correlate with cross-neutralization. These studies increase our understanding of emerging SARS-CoV-2 variants.
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Affiliation(s)
- Samuel J. Vidal
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital and Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ai-ris Y. Collier
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Lisa H. Tostanoski
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - John D. Ventura
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Malika Aid
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Lauren Peter
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Tochi Anioke
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Aiquan Chang
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
- Program in Immunology, Harvard Medical School, Boston, Massachusetts, USA
| | - Huahua Wan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Ricardo Aguayo
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Debby Ngo
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Robert E. Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, Massachusetts, USA
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7
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Zhao LP, Lybrand TP, Gilbert PB, Hawn TR, Schiffer JT, Stamatatos L, Payne TH, Carpp LN, Geraghty DE, Jerome KR. Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy. bioRxiv 2021:2021.06.15.448495. [PMID: 34159336 PMCID: PMC8219100 DOI: 10.1101/2021.06.15.448495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The emergence and establishment of SARS-CoV-2 variants of interest (VOI) and variants of concern (VOC) highlight the importance of genomic surveillance. We propose a statistical learning strategy (SLS) for identifying and spatiotemporally tracking potentially relevant Spike protein mutations. We analyzed 167,893 Spike protein sequences from US COVID-19 cases (excluding 21,391 sequences from VOI/VOC strains) deposited at GISAID from January 19, 2020 to March 15, 2021. Alignment against the reference Spike protein sequence led to the identification of viral residue variants (VRVs), i.e., residues harboring a substitution compared to the reference strain. Next, generalized additive models were applied to model VRV temporal dynamics, to identify VRVs with significant and substantial dynamics (false discovery rate q-value <0.01; maximum VRV proportion > 10% on at least one day). Unsupervised learning was then applied to hierarchically organize VRVs by spatiotemporal patterns and identify VRV-haplotypes. Finally, homology modelling was performed to gain insight into potential impact of VRVs on Spike protein structure. We identified 90 VRVs, 71 of which have not previously been observed in a VOI/VOC, and 35 of which have emerged recently and are durably present. Our analysis identifies 17 VRVs ∼91 days earlier than their first corresponding VOI/VOC publication. Unsupervised learning revealed eight VRV-haplotypes of 4 VRVs or more, suggesting two emerging strains (B1.1.222 and B.1.234). Structural modeling supported potential functional impact of the D1118H and L452R mutations. The SLS approach equally monitors all Spike residues over time, independently of existing phylogenic classifications, and is complementary to existing genomic surveillance methods.
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Affiliation(s)
- Lue Ping Zhao
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
| | - Terry P. Lybrand
- Quintepa Computing LLC; Nashville, TN, USA
- Department of Chemistry; Department of Pharmacology, Vanderbilt University; Nashville, TN, USA
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
| | - Thomas R. Hawn
- Department of Medicine, University of Washington School of Medicine; Seattle, WA, USA
- Department of Global Health, University of Washington; Seattle, WA, USA
| | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
- Department of Medicine, University of Washington School of Medicine; Seattle, WA, USA
| | - Leonidas Stamatatos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
- Department of Global Health, University of Washington; Seattle, WA, USA
| | - Thomas H. Payne
- Department of Medicine, University of Washington School of Medicine; Seattle, WA, USA
| | - Lindsay N. Carpp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
| | - Daniel E. Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle; WA, USA
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
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8
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Abstract
Several neutralizing monoclonal antibodies (mAbs) to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed and are now under evaluation in clinical trials. With the US Food and Drug Administration recently granting emergency use authorizations for neutralizing mAbs in non-hospitalized patients with mild-to-moderate COVID-19, there is an urgent need to discuss the broader potential of these novel therapies and to develop strategies to deploy them effectively in clinical practice, given limited initial availability. Here, we review the precedent for passive immunization and lessons learned from using antibody therapies for viral infections such as respiratory syncytial virus, Ebola virus and SARS-CoV infections. We then focus on the deployment of convalescent plasma and neutralizing mAbs for treatment of SARS-CoV-2. We review specific clinical questions, including the rationale for stratification of patients, potential biomarkers, known risk factors and temporal considerations for optimal clinical use. To answer these questions, there is a need to understand factors such as the kinetics of viral load and its correlation with clinical outcomes, endogenous antibody responses, pharmacokinetic properties of neutralizing mAbs and the potential benefit of combining antibodies to defend against emerging viral variants.
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MESH Headings
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Viral/therapeutic use
- Antibody-Dependent Enhancement
- COVID-19/immunology
- COVID-19/therapy
- COVID-19/virology
- Drug Development
- Drug Resistance, Viral/genetics
- Drug Resistance, Viral/immunology
- Humans
- Immunization, Passive/adverse effects
- Immunization, Passive/methods
- Models, Immunological
- Pandemics
- SARS-CoV-2/drug effects
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- COVID-19 Serotherapy
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Affiliation(s)
- Peter C Taylor
- Botnar Research Centre, University of Oxford, Oxford, UK.
| | | | | | | | | | - Robert L Gottlieb
- Baylor University Medical Center, Dallas, TX, USA
- Baylor Scott & White Research Institute, Dallas, TX, USA
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9
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Ahmad M, Beg BM, Majeed A, Areej S, Riffat S, Rasheed MA, Mahmood S, Mushtaq RMZ, Hafeez MA. Epidemiological and Clinical Characteristics of COVID-19: A Retrospective Multi-Center Study in Pakistan. Front Public Health 2021; 9:644199. [PMID: 33937174 PMCID: PMC8079641 DOI: 10.3389/fpubh.2021.644199] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 03/15/2021] [Indexed: 01/08/2023] Open
Abstract
The emergence of a pathogen responsible for a mysterious respiratory disease was identified in China and later called a novel coronavirus. This disease was named COVID-19. The present study seeks to determine the epidemiological and clinical characteristics of COVID-19 in Pakistan. This report will exhibit a linkage between epidemiology and clinical aspects which in turn can be helpful to prevent the transmission of the virus in Pakistan. A retrospective, multiple center study was performed by collecting the data from patients' with their demographics, epidemiological status, history of co-morbid conditions, and clinical manifestations of the disease. The data was collected from 31 public-sector and 2 private hospitals across Pakistan by on-field healthcare workers. A Chi-square test was applied to assess the relationship between categorical data entries. A total of 194 medical records were examined. The median age of these patients was found to be 34 years. A total of 53.6% active cases were present including 41.2% males and 12.4% females till the end of the study. Adults accounted for most of the cases (94.3%) of COVID-19. Fever (86.60%), cough (85.05%), fatigue (36.60%), dyspnea (24.74%), and gastrointestinal discomfort (10.31%) were among the most frequently reported signs and symptoms by the patients. However, 4.12% of the total patient population remained asymptomatic. The median duration of hospital stay was found to be 14 (0-19) days. The earliest source of the spread of the virus may be linked to the foreigners traveling to Pakistan. Spread among men was more as compared to women. A few cases were found to be positive, due to the direct contact with pets or livestock. Hypertension (7.73%), diabetes (4.64%), cardiovascular conditions (2.58%) were the most common co-morbidities. The percentage mortality was 2.50% with the highest mortality among elders.
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Affiliation(s)
- Mehmood Ahmad
- Department of Pharmacology, Riphah International University, Lahore, Pakistan
| | - Bilal Mahmood Beg
- Department of Pharmacology and Toxicology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Arfa Majeed
- Department of Pharmacology and Toxicology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Sadaf Areej
- Department of Pharmacology and Toxicology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Sualeha Riffat
- Department of Pharmacology, Riphah International University, Lahore, Pakistan
| | - Muhammad Adil Rasheed
- Department of Pharmacology and Toxicology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Sammina Mahmood
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
| | | | - Mian Abdul Hafeez
- Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan
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Pavelić K, Kraljević Pavelić S, Brix B, Goswami N. A Perspective on COVID-19 Management. J Clin Med 2021; 10:1586. [PMID: 33918624 PMCID: PMC8070140 DOI: 10.3390/jcm10081586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 12/15/2022] Open
Abstract
A novel coronavirus-Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2)-outbreak correlated with the global coronavirus disease 2019 (COVID-19) pandemic was declared by the WHO in March 2020, resulting in numerous counted cases attributed to SARS-CoV-2 worldwide. Herein, we discuss current knowledge on the available therapy options for patients diagnosed with COVID-19. Based on available scientific data, we present an overview of solutions in COVID-19 management by use of drugs, vaccines and antibodies. Many questions with non-conclusive answers on the measures for the management of the COVID-19 pandemic and its impact on health still exist-i.e., the actual infection percentage of the population, updated precise mortality data, variability in response to infection by the population, the nature of immunity and its duration, vaccine development issues, a fear that science might end up with excessive promises in response to COVID-19-and were raised among scientists. Indeed, science may or may not deliver results in real time. In the presented paper we discuss some consequences of disease, its detection and serological tests, some solutions to disease prevention and management, pitfalls and obstacles, including vaccination. The presented ideas and data herein are meant to contribute to the ongoing debate on COVID-19 without pre-selection of available information.
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Affiliation(s)
- Krešimir Pavelić
- Faculty of Medicine, Juraj Dobrila University of Pula, Zagrebačka 30, 52100 Pula, Croatia;
| | | | - Bianca Brix
- Physiology Division, Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, Neue Stiftingtalstraße 6/D.05, 8010 Graz, Austria;
| | - Nandu Goswami
- Physiology Division, Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, Neue Stiftingtalstraße 6/D.05, 8010 Graz, Austria;
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Garcia-Beltran WF, Lam EC, St. Denis K, Nitido AD, Garcia ZH, Hauser BM, Feldman J, Pavlovic MN, Gregory DJ, Poznansky MC, Sigal A, Schmidt AG, Iafrate AJ, Naranbhai V, Balazs AB. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. medRxiv 2021:2021.02.14.21251704. [PMID: 33619506 PMCID: PMC7899476 DOI: 10.1101/2021.02.14.21251704] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Vaccination elicits immune responses capable of potently neutralizing SARS-CoV-2. However, ongoing surveillance has revealed the emergence of variants harboring mutations in spike, the main target of neutralizing antibodies. To understand the impact of these variants, we evaluated the neutralization potency of 99 individuals that received one or two doses of either BNT162b2 or mRNA-1273 vaccines against pseudoviruses representing 10 globally circulating strains of SARS-CoV-2. Five of the 10 pseudoviruses, harboring receptor-binding domain mutations, including K417N/T, E484K, and N501Y, were highly resistant to neutralization. Crossneutralization of B.1.351 variants was comparable to SARS-CoV and bat-derived WIV1-CoV, suggesting that a relatively small number of mutations can mediate potent escape from vaccine responses. While the clinical impact of neutralization resistance remains uncertain, these results highlight the potential for variants to escape from neutralizing humoral immunity and emphasize the need to develop broadly protective interventions against the evolving pandemic.
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Affiliation(s)
- Wilfredo F. Garcia-Beltran
- These authors contributed equally
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, 02115, USA
| | - Evan C. Lam
- These authors contributed equally
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Kerri St. Denis
- These authors contributed equally
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Adam D. Nitido
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Zeidy H. Garcia
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Blake M. Hauser
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Maia N. Pavlovic
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, 02129, USA
| | - David J. Gregory
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, 02129, USA
- Pedriatric Infectious Disease, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | - Mark C. Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, 02129, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Alex Sigal
- Africa Health Research Institute, Durban, 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4041 South Africa
- Max Planck Institute for Infection Biology, Berlin, 10117, Germany
| | - Aaron G. Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - A. John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Vivek Naranbhai
- Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for the AIDS Programme of Research in South Africa, Durban, 4001, South Africa
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