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Al-Hatamleh MA, Abusalah MA, Hatmal MM, Alshaer W, Ahmad S, Mohd-Zahid MH, Rahman ENSE, Yean CY, Alias IZ, Uskoković V, Mohamud R. Understanding the challenges to COVID-19 vaccines and treatment options, herd immunity and probability of reinfection. J Taibah Univ Med Sci 2023; 18:600-638. [PMID: 36570799 PMCID: PMC9758618 DOI: 10.1016/j.jtumed.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/29/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Unlike pandemics in the past, the outbreak of coronavirus disease 2019 (COVID-19), which rapidly spread worldwide, was met with a different approach to control and measures implemented across affected countries. The lack of understanding of the fundamental nature of the outbreak continues to make COVID-19 challenging to manage for both healthcare practitioners and the scientific community. Challenges to vaccine development and evaluation, current therapeutic options, convalescent plasma therapy, herd immunity, and the emergence of reinfection and new variants remain the major obstacles to combating COVID-19. This review discusses these challenges in the management of COVID-19 at length and highlights the mechanisms needed to provide better understanding of this pandemic.
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Affiliation(s)
- Mohammad A.I. Al-Hatamleh
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Mai A. Abusalah
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Zarqa University, Zarqa, Jordan
| | - Ma'mon M. Hatmal
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, Zarqa, Jordan
| | - Walhan Alshaer
- Cell Therapy Center (CTC), The University of Jordan, Amman, Jordan
| | - Suhana Ahmad
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Manali H. Mohd-Zahid
- Department of Chemical Pathology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Engku Nur Syafirah E.A. Rahman
- Department of Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Chan Y. Yean
- Department of Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Iskandar Z. Alias
- Department of Chemical Pathology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | | | - Rohimah Mohamud
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
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2
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Lung fibrosis: Post-COVID-19 complications and evidences. Int Immunopharmacol 2023; 116:109418. [PMID: 36736220 PMCID: PMC9633631 DOI: 10.1016/j.intimp.2022.109418] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/13/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND COVID 19, a lethal viral outbreak that devastated lives and the economy across the globe witnessed non-compensable respiratory illnesses in patients. As been evaluated in reports, patients receiving long-term treatment are more prone to acquire Pulmonary Fibrosis (PF). Repetitive damage and repair of alveolar tissues increase oxidative stress, inflammation and elevated production of fibrotic proteins ultimately disrupting normal lung physiology skewing the balance towards the fibrotic milieu. AIM In the present work, we have discussed several important pathways which are involved in post-COVID PF. Further, we have also highlighted the rationale for the use of antifibrotic agents for post-COVID PF to decrease the burden and improve pulmonary functions in COVID-19 patients. CONCLUSION Based on the available literature and recent incidences, it is crucial to monitor COVID-19 patients over a period of time to rule out the possibility of residual effects. There is a need for concrete evidence to deeply understand the mechanisms responsible for PF in COVID-19 patients.
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Abavisani M, Rahimian K, Mahdavi B, Tokhanbigli S, Mollapour Siasakht M, Farhadi A, Kodori M, Mahmanzar M, Meshkat Z. Mutations in SARS-CoV-2 structural proteins: a global analysis. Virol J 2022; 19:220. [PMID: 36528612 PMCID: PMC9759450 DOI: 10.1186/s12985-022-01951-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Emergence of new variants mainly variants of concerns (VOC) is caused by mutations in main structural proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therefore, we aimed to investigate the mutations among structural proteins of SARS-CoV-2 globally. METHODS We analyzed samples of amino-acid sequences (AASs) for envelope (E), membrane (M), nucleocapsid (N), and spike (S) proteins from the declaration of the coronavirus 2019 (COVID-19) as pandemic to January 2022. The presence and location of mutations were then investigated by aligning the sequences to the reference sequence and categorizing them based on frequency and continent. Finally, the related human genes with the viral structural genes were discovered, and their interactions were reported. RESULTS The results indicated that the most relative mutations among the E, M, N, and S AASs occurred in the regions of 7 to 14, 66 to 88, 164 to 205, and 508 to 635 AAs, respectively. The most frequent mutations in E, M, N, and S proteins were T9I, I82T, R203M/R203K, and D614G. D614G was the most frequent mutation in all six geographical areas. Following D614G, L18F, A222V, E484K, and N501Y, respectively, were ranked as the most frequent mutations in S protein globally. Besides, A-kinase Anchoring Protein 8 Like (AKAP8L) was shown as the linkage unit between M, E, and E cluster genes. CONCLUSION Screening the structural protein mutations can help scientists introduce better drug and vaccine development strategies.
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Affiliation(s)
- Mohammad Abavisani
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, School of Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Karim Rahimian
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Bahar Mahdavi
- Department of Molecular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Samaneh Tokhanbigli
- Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, Pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Mahsa Mollapour Siasakht
- Department of Biochemistry, Erasmus University Medical Center, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Amin Farhadi
- Department of Biology, Payame Noor University, Tehran, Iran
| | - Mansoor Kodori
- Non Communicable Diseases Research Center, Bam University of Medical Sciences, Bam, Iran
| | - Mohammadamin Mahmanzar
- Department of Bioinformatics, Kish International Campus University of Tehran, Kish, Iran.
| | - Zahra Meshkat
- Department of Microbiology and Virology, School of Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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4
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Wurtzer S, Levert M, Dhenain E, Accrombessi H, Manco S, Fagour N, Goulet M, Boudaud N, Gaillard L, Bertrand I, Challant J, Masnada S, Azimi S, Gillon-Ritz M, Robin A, Mouchel JM, Sig O, Moulin L. From Alpha to Omicron BA.2: New digital RT-PCR approach and challenges for SARS-CoV-2 VOC monitoring and normalization of variant dynamics in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157740. [PMID: 35917966 PMCID: PMC9338838 DOI: 10.1016/j.scitotenv.2022.157740] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 05/17/2023]
Abstract
Throughout the COVID-19 pandemic, new variants have continuously emerged and spread in populations. Among these, variants of concern (VOC) have been the main culprits of successive epidemic waves, due to their transmissibility, pathogenicity or ability to escape the immune response. Quantification of the SARS-CoV-2 genomes in raw wastewater is a reliable approach well-described and widely deployed worldwide to monitor the spread of SARS-CoV-2 in human populations connected to sewage systems. Discrimination of VOCs in wastewater is also a major issue and can be achieved by genome sequencing or by detection of specific mutations suggesting the presence of VOCs. This study aimed to date the emergence of these VOCs (from Alpha to Omicron BA.2) by monitoring wastewater from the greater Paris area, France, but also to model the propagation dynamics of these VOCs and to characterize the replacement kinetics of the prevalent populations. These dynamics were compared to various individual-centered public health data, such as regional incidence and the proportions of VOCs identified by sequencing of strains isolated from patient. The viral dynamics in wastewater highlighted the impact of the vaccination strategy on the viral circulation within human populations but also suggested its potential effect on the selection of variants most likely to be propagated in immunized populations. Normalization of concentrations to capture population movements appeared statistically more reliable using variations in local drinking water consumption rather than using PMMoV concentrations because PMMoV fecal shedding was subject to variability and was not sufficiently relevant in this study. The dynamics of viral spread was observed earlier (about 13 days on the wave related to Omicron VOC) in raw wastewater than the regional incidence alerting to a possible risk of decorrelation between incidence and actual virus circulation probably resulting from a lower severity of infection in vaccinated populations.
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Affiliation(s)
- Sebastien Wurtzer
- Eau de Paris, Research & Development, 33 avenue Jean Jaures, FR-94200 Ivry sur Seine, France.
| | - Morgane Levert
- Sorbonne Universite, CNRS, EPHE, UMR 7619 Metis, e-LTER Zone Atelier Seine, F-75005 Paris, France
| | - Eloïse Dhenain
- Sorbonne Universite, CNRS, EPHE, UMR 7619 Metis, e-LTER Zone Atelier Seine, F-75005 Paris, France
| | - Heberte Accrombessi
- Eau de Paris, Research & Development, 33 avenue Jean Jaures, FR-94200 Ivry sur Seine, France
| | - Sandra Manco
- Eau de Paris, Research & Development, 33 avenue Jean Jaures, FR-94200 Ivry sur Seine, France
| | - Nathalie Fagour
- Eau de Paris, Research & Development, 33 avenue Jean Jaures, FR-94200 Ivry sur Seine, France
| | - Marion Goulet
- Eau de Paris, Research & Development, 33 avenue Jean Jaures, FR-94200 Ivry sur Seine, France
| | | | - Lucie Gaillard
- ACTALIA, Food Safety Department, F-50000 Saint-Lô, France
| | | | - Julie Challant
- University of Lorraine, CNRS, LCPME, F-54000 Nancy, France
| | - Sophie Masnada
- SIAM - STV, Avenue de la courtiere, FR-77400 Saint Thibault des vignes, France
| | - Sam Azimi
- SIAAP, Innovation Department, 82 Avenue Kléber, FR-92700 Colombes, France
| | - Miguel Gillon-Ritz
- Direction de la Proprete et de l'Eau - Service Technique de l'Eau et de l'Assainissement, Rue du Commandeur, FR-75014 Paris, France
| | - Alban Robin
- Eau de Paris, Research & Development, 33 avenue Jean Jaures, FR-94200 Ivry sur Seine, France
| | - Jean-Marie Mouchel
- Sorbonne Universite, CNRS, EPHE, UMR 7619 Metis, e-LTER Zone Atelier Seine, F-75005 Paris, France
| | - Obepine Sig
- Sorbonne Universite, CNRS, EPHE, UMR 7619 Metis, e-LTER Zone Atelier Seine, F-75005 Paris, France
| | - Laurent Moulin
- Eau de Paris, Research & Development, 33 avenue Jean Jaures, FR-94200 Ivry sur Seine, France
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Kumar A, Ladha A, Choudhury A, Ikbal AMA, Bhattacharjee B, Das T, Gupta G, Sharma C, Sarbajna A, Mandal SC, Choudhury MD, Ali N, Slama P, Rezaei N, Palit P, Tiwari ON. The chimera of S1 and N proteins of SARS-CoV-2: can it be a potential vaccine candidate for COVID-19? Expert Rev Vaccines 2022; 21:1071-1086. [PMID: 35604776 DOI: 10.1080/14760584.2022.2081156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has emerged as one of the biggest global health issues. Spike protein (S) and nucleoprotein (N), the major immunogenic components of SARS-CoV-2, have been shown to be involved in the attachment and replication of the virus inside the host cell. AREAS COVERED Several investigations have shown that the SARS-CoV-2 nucleoprotein can elicit a cell-mediated immune response capable of regulating viral replication and lowering viral burden. However, the development of an effective vaccine that can stop the transmission of SARS-CoV-2 remains a matter of concern. Literature was retrieved using the keywords COVID-19 vaccine, role of nucleoprotein as vaccine candidate, spike protein, nucleoprotein immune responses against SARS-CoV-2, and chimera vaccine in PubMed, Google Scholar, and Google. EXPERT OPINION We have focussed on the use of chimera protein, consisting of N and S-1 protein components of SARS-CoV-2, as a potential vaccine candidate. This may act as a polyvalent mixed recombinant protein vaccine to elicit a strong T and B cell immune response, which will be capable of neutralizing the wild and mutated variants of SARS-CoV-2, and also restricting its attachment, replication, and budding in the host cell.
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Affiliation(s)
- Amresh Kumar
- Department of Life Sciences and Bioinformatics, Assam University, Silchar, India
| | - Amit Ladha
- Area of Biotechnology and Bioinformatics, NIIT University, Neemrana, India
| | - Ankita Choudhury
- Department of Pharmaceutical Sciences, Allama TR College of Pharmacy, Hospital Rd, Srigouri, India
| | - Abu Md Ashif Ikbal
- Department of Pharmacy, Tripura University (A Central University), Suryamaninagar, Tripura (W), India
| | - Bedanta Bhattacharjee
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, India
| | - Tanmay Das
- Department of Business Administration, Assam University Silchar, India
| | - Gaurav Gupta
- Area of Biotechnology and Bioinformatics, NIIT University, Neemrana, India.,Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Chhavi Sharma
- Area of Biotechnology and Bioinformatics, NIIT University, Neemrana, India
| | - Adity Sarbajna
- Department of Zoology, Surendranath College, Kolkata, India
| | - Subhash C Mandal
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | | | - Nahid Ali
- Division of Immunology, Department of Infectious Diseases, INDIAN INSTITUTE OF CHEMICAL BIOLOGY, Kolkata, India
| | - Petr Slama
- Laboratory of Animal Immunology and Biotechnology, Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, Brno, Czech Republic
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden
| | - Partha Palit
- Department of Pharmaceutical Sciences Drug Discovery research Laboratory, Assam University, Silchar, India
| | - Onkar Nath Tiwari
- Centre for Conservation and Utilisation of Blue Green Algae (CCUBGA), Division of Microbiology, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
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Strohl WR, Ku Z, An Z, Carroll SF, Keyt BA, Strohl LM. Passive Immunotherapy Against SARS-CoV-2: From Plasma-Based Therapy to Single Potent Antibodies in the Race to Stay Ahead of the Variants. BioDrugs 2022; 36:231-323. [PMID: 35476216 PMCID: PMC9043892 DOI: 10.1007/s40259-022-00529-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 12/15/2022]
Abstract
The COVID-19 pandemic is now approaching 2 years old, with more than 440 million people infected and nearly six million dead worldwide, making it the most significant pandemic since the 1918 influenza pandemic. The severity and significance of SARS-CoV-2 was recognized immediately upon discovery, leading to innumerable companies and institutes designing and generating vaccines and therapeutic antibodies literally as soon as recombinant SARS-CoV-2 spike protein sequence was available. Within months of the pandemic start, several antibodies had been generated, tested, and moved into clinical trials, including Eli Lilly's bamlanivimab and etesevimab, Regeneron's mixture of imdevimab and casirivimab, Vir's sotrovimab, Celltrion's regdanvimab, and Lilly's bebtelovimab. These antibodies all have now received at least Emergency Use Authorizations (EUAs) and some have received full approval in select countries. To date, more than three dozen antibodies or antibody combinations have been forwarded into clinical trials. These antibodies to SARS-CoV-2 all target the receptor-binding domain (RBD), with some blocking the ability of the RBD to bind human ACE2, while others bind core regions of the RBD to modulate spike stability or ability to fuse to host cell membranes. While these antibodies were being discovered and developed, new variants of SARS-CoV-2 have cropped up in real time, altering the antibody landscape on a moving basis. Over the past year, the search has widened to find antibodies capable of neutralizing the wide array of variants that have arisen, including Alpha, Beta, Gamma, Delta, and Omicron. The recent rise and dominance of the Omicron family of variants, including the rather disparate BA.1 and BA.2 variants, demonstrate the need to continue to find new approaches to neutralize the rapidly evolving SARS-CoV-2 virus. This review highlights both convalescent plasma- and polyclonal antibody-based approaches as well as the top approximately 50 antibodies to SARS-CoV-2, their epitopes, their ability to bind to SARS-CoV-2 variants, and how they are delivered. New approaches to antibody constructs, including single domain antibodies, bispecific antibodies, IgA- and IgM-based antibodies, and modified ACE2-Fc fusion proteins, are also described. Finally, antibodies being developed for palliative care of COVID-19 disease, including the ramifications of cytokine release syndrome (CRS) and acute respiratory distress syndrome (ARDS), are described.
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Affiliation(s)
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Sciences Center, Houston, TX USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Sciences Center, Houston, TX USA
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7
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Liu Z, Wu H, Egland KA, Gilliland TC, Dunn MD, Luke TC, Sullivan EJ, Klimstra WB, Bausch CL, Whelan SPJ. Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. Hum Vaccin Immunother 2022; 18:1940652. [PMID: 34228597 PMCID: PMC8290372 DOI: 10.1080/21645515.2021.1940652] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/16/2021] [Accepted: 06/02/2021] [Indexed: 12/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with amino-acid substitutions and deletions in spike protein (S) can reduce the effectiveness of monoclonal antibodies (mAbs) and may compromise immunity induced by vaccines. We report a polyclonal, fully human, anti-SARS-CoV-2 immunoglobulin produced in transchromosomic bovines (Tc-hIgG-SARS-CoV-2) hyperimmunized with two doses of plasmid DNA encoding the SARS-CoV-2 Wuhan strain S gene, followed by repeated immunization with S protein purified from insect cells. The resulting Tc-hIgG-SARS-CoV-2, termed SAB-185, efficiently neutralizes SARS-CoV-2, and vesicular stomatitis virus (VSV) SARS-CoV-2 chimeras in vitro. Neutralization potency was retained for S variants including S477N, E484K, and N501Y, substitutions present in recent variants of concern. In contrast to the ease of selection of escape variants with mAbs and convalescent human plasma, we were unable to isolate VSV-SARS-CoV-2 mutants resistant to Tc-hIgG-SARS-CoV-2 neutralization. This fully human immunoglobulin that potently inhibits SARS-CoV-2 infection may provide an effective therapeutic to combat COVID-19.
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Affiliation(s)
- Zhuoming Liu
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Hua Wu
- , SAB Biotherapeutics Inc, Sioux Fall, SD, USA
| | | | | | - Matthew D. Dunn
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | | | | | - Sean P. J. Whelan
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
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8
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Dol J, Boulos L, Somerville M, Saxinger L, Doroshenko A, Hastings S, Reynolds B, Gallant A, Shin HD, Wong H, Crowther D, Macdonald M, Martin-Misener R, McCulloch H, Tricco AC, Curran JA. Health system impacts of SARS-CoV - 2 variants of concern: a rapid review. BMC Health Serv Res 2022; 22:544. [PMID: 35461246 PMCID: PMC9034743 DOI: 10.1186/s12913-022-07847-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 03/21/2022] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND As of November 25th 2021, four SARS-CoV - 2 variants of concern (VOC: Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2)) have been detected. Variable degrees of increased transmissibility of the VOC have been documented, with potential implications for hospital and health system capacity and control measures. This rapid review aimed to provide a synthesis of evidence related to health system responses to the emergence of VOC worldwide. METHODS Seven databases were searched up to September 27, 2021, for terms related to VOC. Titles, abstracts, and full-text documents were screened independently by two reviewers. Data were extracted independently by two reviewers using a standardized form. Studies were included if they reported on at least one of the VOC and health system outcomes. RESULTS Of the 4877 articles retrieved, 59 studies were included, which used a wide range of designs and methods. Most of the studies reported on Alpha, and all except two reported on impacts for capacity planning related to hospitalization, intensive care admissions, and mortality. Most studies (73.4%) observed an increase in hospitalization, but findings on increased admission to intensive care units were mixed (50%). Most studies (63.4%) that reported mortality data found an increased risk of death due to VOC, although health system capacity may influence this. No studies reported on screening staff and visitors or cohorting patients based on VOC. CONCLUSION While the findings should be interpreted with caution as most of the sources identified were preprints, evidence is trending towards an increased risk of hospitalization and, potentially, mortality due to VOC compared to wild-type SARS-CoV - 2. There is little evidence on the need for, and the effect of, changes to health system arrangements in response to VOC transmission.
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Affiliation(s)
- Justine Dol
- Faculty of Health, Dalhousie University, Halifax, NS, Canada
| | - Leah Boulos
- Maritime SPOR SUPPORT Unit, Halifax, NS, Canada
| | - Mari Somerville
- School of Nursing, Dalhousie University, Halifax, NS, Canada
| | - Lynora Saxinger
- Division of Infectious Diseases, Departments of Medicine and Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Alexander Doroshenko
- Division of Preventive Medicine, Faculty of Medicine and Dentistry, University of Alberta, Calgary, AB, Canada
| | | | | | - Allyson Gallant
- Faculty of Health, Dalhousie University, Halifax, NS, Canada
| | | | - Helen Wong
- Faculty of Health, Dalhousie University, Halifax, NS, Canada
| | - Daniel Crowther
- School of Nursing, Dalhousie University, Halifax, NS, Canada
| | | | | | | | - Andrea C Tricco
- Knowledge Translation Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health, Toronto, ON, Canada
- Epidemiology Division and Institute for Health Policy, Management, and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Queen's Collaboration for Health Care Quality Joanna Briggs Institute Centre of Excellence, School of Nursing, Queen's University, Toronto, ON, Canada
| | - Janet A Curran
- School of Nursing, Dalhousie University, Halifax, NS, Canada.
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9
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Wang J, Yang Y, Liang T, Yang N, Li T, Zheng C, Ning N, Luo D, Yang X, He Z, Yang G, Li B, Gao J, Yu W, Gong S, Huang Y, Li J, Wang H, Zhang H, Zhang T, Li P, Li Y, Dai J, Zhang X, Li B, Yu X, Wang H. Longitudinal and proteome-wide analyses of antibodies in COVID-19 patients reveal features of the humoral immune response to SARS-CoV-2. J Adv Res 2022; 37:209-219. [PMID: 35475278 PMCID: PMC8313818 DOI: 10.1016/j.jare.2021.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/12/2021] [Accepted: 07/23/2021] [Indexed: 12/11/2022] Open
Abstract
Introduction The SARS-CoV-2 pandemic has endangered global health, the world economy, and societal values. Despite intensive measures taken around the world, morbidity and mortality remain high as many countries face new waves of infection and the spread of new variants. Worryingly, more and more variants are now being identified, such as 501Y.V1 (B.1.1.7) in the UK, 501Y.V2 (B.1.351) in South Africa, 501Y.V3 in Manaus, Brazil, and B.1.617/B.1.618 in India, which could lead to a severe epidemic rebound. Moreover, some variants have a stronger immune escape ability. To control the new SARS-CoV-2 variant, we may need to develop and redesign new vaccines repeatedly. So it is important to investigate how our immune system combats and responds to SARS-CoV-2 infection to develop safe and effective medical interventions. Objectives In this study, we performed a longitudinal and proteome-wide analysis of antibodies in the COVID-19 patients to revealed some immune processes of COVID-19 patients against SARS-CoV-2 and found some dominant epitopes of a potential vaccine. Methods Microarray assay, Antibody depletion assays, Neutralization assay. Results We profiled a B-cell linear epitope landscape of SARS-CoV-2 and identified the epitopes specifically recognized by either IgM, IgG, or IgA. We found that epitopes more frequently recognized by IgM are enriched in non-structural proteins. We further identified epitopes with different immune responses in severe and mild patients. Moreover, we identified 12 dominant epitopes eliciting antibodies in most COVID-19 patients and identified five key amino acids of epitopes. Furthermore, we found epitope S-82 and S-15 are perfect immunogenic peptides and should be considered in vaccine design. Conclusion This data provide useful information and rich resources for improving our understanding of viral infection and developing a novel vaccine/neutralizing antibodies for the treatment of SARS-CoV-2.
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Affiliation(s)
- Jianxin Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yongfei Yang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Te Liang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Ning Yang
- Department of Clinical Laboratory, The Fifth Medical Center of PLA General Hospital, No.100 West Fourth Ring Road, Beijing 100039, China
| | - Tao Li
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Chang Zheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Nianzhi Ning
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Deyan Luo
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Xiaolan Yang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Zhili He
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Guang Yang
- Department of Clinical Laboratory, The Fifth Medical Center of PLA General Hospital, No.100 West Fourth Ring Road, Beijing 100039, China
| | - Bo Li
- Department of Clinical Laboratory, The Fifth Medical Center of PLA General Hospital, No.100 West Fourth Ring Road, Beijing 100039, China
| | - Jie Gao
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Wenjing Yu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Saisai Gong
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yanyu Huang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Jiajia Li
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Hongye Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Hao Zhang
- Department of Clinical Laboratory, The Fifth Medical Center of PLA General Hospital, No.100 West Fourth Ring Road, Beijing 100039, China
| | - Tian Zhang
- Department of Clinical Laboratory, The Fifth Medical Center of PLA General Hospital, No.100 West Fourth Ring Road, Beijing 100039, China
| | - Peiran Li
- Department of Clinical Laboratory, The Fifth Medical Center of PLA General Hospital, No.100 West Fourth Ring Road, Beijing 100039, China
| | - Yongli Li
- Department of Clinical Laboratory, The Fifth Medical Center of PLA General Hospital, No.100 West Fourth Ring Road, Beijing 100039, China
| | - Jiayu Dai
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xiaomei Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Boan Li
- Department of Clinical Laboratory, The Fifth Medical Center of PLA General Hospital, No.100 West Fourth Ring Road, Beijing 100039, China
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Hui Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
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10
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Wolf JM, Kipper D, Borges GR, Streck AF, Lunge VR. Temporal spread and evolution of SARS-CoV-2 in the second pandemic wave in Brazil. J Med Virol 2022; 94:926-936. [PMID: 34596904 PMCID: PMC8661965 DOI: 10.1002/jmv.27371] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/11/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic spread rapidly and this scenario is concerning in South America, mainly in Brazil that presented more than 21 million coronavirus disease 2019 cases and 590 000 deaths. The recent emergence of novel lineages carrying several mutations in the spike protein has raised additional public health concerns worldwide. The present study describes the temporal spreading and evolution of SARS-CoV2 in the beginning of the second pandemic wave in Brazil, highlighting the fast dissemination of the two major concerning variants (P.1 and P.2). A total of 2507 SARS-CoV-2 whole-genome sequences (WGSs) with available information from the country (Brazil) and sampling date (July 2020-February 2021), were obtained and the frequencies of the lineages were evaluated in the period of the growing second pandemic wave. The results demonstrated the increasing prevalence of P.1 and P.2 lineages in the period evaluated. P.2 lineage was first detected in the middle of 2020, but a high increase occurred only in the last trimester of this same year and the spreading to all Brazilian regions. P.1 lineage emerged even later, first in the North region in December 2020 and really fast dissemination to all other Brazilian regions in January and February 2021. All SARS-CoV-2 WGSs of P.1 and P.2 were further separately evaluated with a Bayesian approach. The rates of nucleotide and amino acid substitutions were statistically higher in P.1 than P.2 (p < 0.01). The phylodynamic analysis demonstrated that P.2 gradually spread in all the country from September 2020 to January 2021, while P.1 disseminated even faster from December 2020 to February 2021. Skyline plots of both lineages demonstrated a slight rise in the spreading for P.2 and exponential growth for P.1. In conclusion, these data demonstrated that the P.1 (recently renamed as Gamma) and P.2 lineages have predominated in the second pandemic wave due to the very high spreading across all geographic regions in Brazil at the end of 2020 and beginning of 2021.
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Affiliation(s)
- Jonas M. Wolf
- Laboratório de Diagnóstico Molecular, Programa de Pós‐Graduação em Biologia Celular e Molecular Aplicada à SaúdeUniversidade Luterana do Brasil, ULBRACanoasRio Grande do SulBrazil
- Laboratório de Diagnóstico MolecularUniversidade Luterana do BrasilCanoasRio Grande do SulBrazil
| | - Diéssy Kipper
- Laboratório de Diagnóstico em Medicina VeterináriaUniversidade de Caxias do Sul, UCSCaxias do SulRio Grande do SulBrazil
| | - Gabriela R. Borges
- Laboratório de Diagnóstico MolecularUniversidade Luterana do BrasilCanoasRio Grande do SulBrazil
| | - André F. Streck
- Laboratório de Diagnóstico em Medicina VeterináriaUniversidade de Caxias do Sul, UCSCaxias do SulRio Grande do SulBrazil
| | - Vagner R. Lunge
- Laboratório de Diagnóstico Molecular, Programa de Pós‐Graduação em Biologia Celular e Molecular Aplicada à SaúdeUniversidade Luterana do Brasil, ULBRACanoasRio Grande do SulBrazil
- Laboratório de Diagnóstico MolecularUniversidade Luterana do BrasilCanoasRio Grande do SulBrazil
- Simbios BiotecnologiaCachoeirinhaRio Grande do SulBrazil
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11
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He WT, Musharrafieh R, Song G, Dueker K, Tse LV, Martinez DR, Schäfer A, Callaghan S, Yong P, Beutler N, Torres JL, Volk RM, Zhou P, Yuan M, Liu H, Anzanello F, Capozzola T, Parren M, Garcia E, Rawlings SA, Smith DM, Wilson IA, Safonova Y, Ward AB, Rogers TF, Baric RS, Gralinski LE, Burton DR, Andrabi R. Targeted isolation of panels of diverse human protective broadly neutralizing antibodies against SARS-like viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.09.08.459480. [PMID: 35169804 PMCID: PMC8845431 DOI: 10.1101/2021.09.08.459480] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The emergence of current SARS-CoV-2 variants of concern (VOCs) and potential future spillovers of SARS-like coronaviruses into humans pose a major threat to human health and the global economy 1-7 . Development of broadly effective coronavirus vaccines that can mitigate these threats is needed 8, 9 . Notably, several recent studies have revealed that vaccination of recovered COVID-19 donors results in enhanced nAb responses compared to SARS-CoV-2 infection or vaccination alone 10-13 . Here, we utilized a targeted donor selection strategy to isolate a large panel of broadly neutralizing antibodies (bnAbs) to sarbecoviruses from two such donors. Many of the bnAbs are remarkably effective in neutralization against sarbecoviruses that use ACE2 for viral entry and a substantial fraction also show notable binding to non-ACE2-using sarbecoviruses. The bnAbs are equally effective against most SARS-CoV-2 VOCs and many neutralize the Omicron variant. Neutralization breadth is achieved by bnAb binding to epitopes on a relatively conserved face of the receptor binding domain (RBD) as opposed to strain-specific nAbs to the receptor binding site that are commonly elicited in SARS-CoV-2 infection and vaccination 14-18 . Consistent with targeting of conserved sites, select RBD bnAbs exhibited in vivo protective efficacy against diverse SARS-like coronaviruses in a prophylaxis challenge model. The generation of a large panel of potent bnAbs provides new opportunities and choices for next-generation antibody prophylactic and therapeutic applications and, importantly, provides a molecular basis for effective design of pan-sarbecovirus vaccines.
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Affiliation(s)
- Wan-ting He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rami Musharrafieh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Katharina Dueker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Longping V. Tse
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David R. Martinez
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexandra Schäfer
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sean Callaghan
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter Yong
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan L. Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Reid M. Volk
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Panpan Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fabio Anzanello
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tazio Capozzola
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mara Parren
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Elijah Garcia
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Stephen A. Rawlings
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Davey M. Smith
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 9203
| | - Yana Safonova
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew B. Ward
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Thomas F. Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Ralph S. Baric
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Departments of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lisa E. Gralinski
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
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12
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Pattabiraman C, Prasad P, George AK, Sreenivas D, Rasheed R, Reddy NVK, Desai A, Vasanthapuram R. Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. Wellcome Open Res 2022; 6:110. [PMID: 35243004 PMCID: PMC8857524 DOI: 10.12688/wellcomeopenres.16768.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2022] [Indexed: 12/18/2022] Open
Abstract
Background: As the coronavirus disease 2019 (COVID-19) pandemic continues, the selection of genomic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) associated with higher transmission, more severe disease, re-infection, and immune escape are a cause for concern. Such variants have been reported from the UK (B.1.1.7), South Africa (B.1.351) and, Brazil (P.1/B.1.1.28). We performed this study to track the importation, spread, and emergence of variants locally. Methods: We sequenced whole genomes of SARS-CoV-2 from international travellers (n=75) entering Karnataka, South India, between Dec 22, 2020 and Jan 31, 2021, and from positive cases in the city of Bengaluru (n=108), between Nov 22, 2020- Jan 22, 2021, as well as a local outbreak. We present the lineage distribution and analysis of these sequences. Results: Genomes from the study group into 34 lineages. Variant B.1.1.7 was introduced by international travel (24/73, 32.9%). Lineage B.1.36 and B.1 formed a major fraction of both imported (B.1.36: 20/73, 27.4%; B.1: 14/73, 19.2%), and circulating viruses (B.1.36: 45/103; 43.7%,. B.1: 26/103; 25.2%). The lineage B.1.36 was also associated with a local outbreak. We detected nine amino acid changes, previously associated with immune escape, spread across multiple lineages. The N440K change was detected in 45/162 (27.7%) of the sequences, 37 of these were in the B.1.36 lineage (37/65, 56.92%) Conclusions: Our data support the idea that variants of concern spread by travel. Viruses with amino acid replacements associated with immune escape are already circulating. It is critical to check transmission and monitor changes in SARS-CoV-2 locally.
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Affiliation(s)
- Chitra Pattabiraman
- Neurovirology, National Institute of Mental Health and Neurosciences, India, Bangalore, Karnataka, 560029, India
| | - Pramada Prasad
- Neurovirology, National Institute of Mental Health and Neurosciences, India, Bangalore, Karnataka, 560029, India
| | - Anson K. George
- Neurovirology, National Institute of Mental Health and Neurosciences, India, Bangalore, Karnataka, 560029, India
| | - Darshan Sreenivas
- Neurovirology, National Institute of Mental Health and Neurosciences, India, Bangalore, Karnataka, 560029, India
| | - Risha Rasheed
- Neurovirology, National Institute of Mental Health and Neurosciences, India, Bangalore, Karnataka, 560029, India
| | - Nakka Vijay Kiran Reddy
- Neurovirology, National Institute of Mental Health and Neurosciences, India, Bangalore, Karnataka, 560029, India
| | - Anita Desai
- Neurovirology, National Institute of Mental Health and Neurosciences, India, Bangalore, Karnataka, 560029, India
| | - Ravi Vasanthapuram
- Nodal Officer Genetic Confirmation of SARS-CoV-2, Government of Karnataka, Bengaluru, India
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13
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Ozer EA, Simons LM, Adewumi OM, Fowotade AA, Omoruyi EC, Adeniji JA, Olayinka OA, Dean TJ, Zayas J, Bhimalli PP, Ash MK, Maiga AI, Somboro AM, Maiga M, Godzik A, Schneider JR, Mamede JI, Taiwo BO, Hultquist JF, Lorenzo-Redondo R. Multiple expansions of globally uncommon SARS-CoV-2 lineages in Nigeria. Nat Commun 2022; 13:688. [PMID: 35115515 PMCID: PMC8813984 DOI: 10.1038/s41467-022-28317-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/18/2022] [Indexed: 12/28/2022] Open
Abstract
Disparities in SARS-CoV-2 genomic surveillance have limited our understanding of the viral population dynamics and may delay identification of globally important variants. Despite being the most populated country in Africa, Nigeria has remained critically under sampled. Here, we report sequences from 378 SARS-CoV-2 isolates collected in Oyo State, Nigeria between July 2020 and August 2021. In early 2021, most isolates belonged to the Alpha "variant of concern" (VOC) or the Eta lineage. Eta outcompeted Alpha in Nigeria and across West Africa, persisting in the region even after expansion of an otherwise rare Delta sub-lineage. Spike protein from the Eta variant conferred increased infectivity and decreased neutralization by convalescent sera in vitro. Phylodynamic reconstructions suggest that Eta originated in West Africa before spreading globally and represented a VOC in early 2021. These results demonstrate a distinct distribution of SARS-CoV-2 lineages in Nigeria, and emphasize the need for improved genomic surveillance worldwide.
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Affiliation(s)
- Egon A Ozer
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
| | - Lacy M Simons
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
| | - Olubusuyi M Adewumi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeola A Fowotade
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Biorepository and Clinical Virology Laboratory, College of Medicine, University College Hospital, University of Ibadan, Ibadan, Nigeria
| | - Ewean C Omoruyi
- Biorepository and Clinical Virology Laboratory, College of Medicine, University College Hospital, University of Ibadan, Ibadan, Nigeria
| | - Johnson A Adeniji
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oluseyi A Olayinka
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Taylor J Dean
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
| | - Janet Zayas
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Pavan P Bhimalli
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Michelle K Ash
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Almoustapha I Maiga
- University Clinical Research Center (UCRC), University of Sciences, Techniques et Technologies of Bamako (USTTB), Bamako, Mali
| | - Anou M Somboro
- University Clinical Research Center (UCRC), University of Sciences, Techniques et Technologies of Bamako (USTTB), Bamako, Mali
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mamoudou Maiga
- University Clinical Research Center (UCRC), University of Sciences, Techniques et Technologies of Bamako (USTTB), Bamako, Mali
- Biomedical Engineering and Preventive Medicine Department, Northwestern University, Evanston, IL, USA
| | - Adam Godzik
- Biosciences Division, University of California Riverside School of Medicine, Riverside, CA, USA
| | - Jeffrey R Schneider
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - João I Mamede
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Babafemi O Taiwo
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Judd F Hultquist
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA.
| | - Ramon Lorenzo-Redondo
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA.
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14
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Hassan S, West KA, Conry‐Cantilena K, De Giorgi V. Regulatory challenges of convalescent plasma collection during the evolving stages of COVID-19 pandemic in the United States. Transfusion 2022; 62:483-492. [PMID: 34778974 PMCID: PMC8661755 DOI: 10.1111/trf.16751] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 12/25/2022]
Affiliation(s)
- Sajjad Hassan
- Department of Transfusion MedicineNIH Clinical Center, National Institutes of HealthBethesdaMarylandUSA
| | - Kamille A. West
- Department of Transfusion MedicineNIH Clinical Center, National Institutes of HealthBethesdaMarylandUSA
| | - Kathleen Conry‐Cantilena
- Department of Transfusion MedicineNIH Clinical Center, National Institutes of HealthBethesdaMarylandUSA
| | - Valeria De Giorgi
- Department of Transfusion MedicineNIH Clinical Center, National Institutes of HealthBethesdaMarylandUSA
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15
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Zhou P, Yuan M, Song G, Beutler N, Shaabani N, Huang D, He WT, Zhu X, Callaghan S, Yong P, Anzanello F, Peng L, Ricketts J, Parren M, Garcia E, Rawlings SA, Smith DM, Nemazee D, Teijaro JR, Rogers TF, Wilson IA, Burton DR, Andrabi R. A human antibody reveals a conserved site on beta-coronavirus spike proteins and confers protection against SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.03.30.437769. [PMID: 33821273 PMCID: PMC8020973 DOI: 10.1101/2021.03.30.437769] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Broadly neutralizing antibodies (bnAbs) to coronaviruses (CoVs) are valuable in their own right as prophylactic and therapeutic reagents to treat diverse CoVs and, importantly, as templates for rational pan-CoV vaccine design. We recently described a bnAb, CC40.8, from a coronavirus disease 2019 (COVID-19)-convalescent donor that exhibits broad reactivity with human beta-coronaviruses (β-CoVs). Here, we showed that CC40.8 targets the conserved S2 stem-helix region of the coronavirus spike fusion machinery. We determined a crystal structure of CC40.8 Fab with a SARS-CoV-2 S2 stem-peptide at 1.6 Å resolution and found that the peptide adopted a mainly helical structure. Conserved residues in β-CoVs interacted with CC40.8 antibody, thereby providing a molecular basis for its broad reactivity. CC40.8 exhibited in vivo protective efficacy against SARS-CoV-2 challenge in two animal models. In both models, CC40.8-treated animals exhibited less weight loss and reduced lung viral titers compared to controls. Furthermore, we noted CC40.8-like bnAbs are relatively rare in human COVID-19 infection and therefore their elicitation may require rational structure-based vaccine design strategies. Overall, our study describes a target on β-CoV spike proteins for protective antibodies that may facilitate the development of pan-β-CoV vaccines. SUMMARY A human mAb isolated from a COVID-19 donor defines a protective cross-neutralizing epitope for pan-β-CoV vaccine design strategies.
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Affiliation(s)
- Panpan Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Namir Shaabani
- Department of Immunology and Microbiology, 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
| | - Wan-ting He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sean Callaghan
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter Yong
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fabio Anzanello
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James Ricketts
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mara Parren
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Elijah Garcia
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Stephen A. Rawlings
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Davey M. Smith
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R. Teijaro
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Thomas F. Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, 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
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
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16
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Oluwagbemi OO, Oladipo EK, Dairo EO, Ayeni AE, Irewolede BA, Jimah EM, Oyewole MP, Olawale BM, Adegoke HM, Ogunleye AJ. Computational construction of a glycoprotein multi-epitope subunit vaccine candidate for old and new South-African SARS-CoV-2 virus strains. INFORMATICS IN MEDICINE UNLOCKED 2022; 28:100845. [PMID: 35071728 PMCID: PMC8760845 DOI: 10.1016/j.imu.2022.100845] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/28/2021] [Accepted: 01/01/2022] [Indexed: 12/19/2022] Open
Abstract
The discovery of a new SARS-CoV-2 virus strain in South Africa presents a major public health threat, therefore contributing to increased infections and transmission rates during the second wave of the global pandemic. This study lays the groundwork for the development of a novel subunit vaccine candidate from the circulating strains of South African SARS-CoV-2 and provides an understanding of the molecular epidemiological trend of the circulating strains. A total of 475 whole-genome nucleotide sequences from South Africa submitted between December 1, 2020 and February 15, 2021 available at the GISAID database were retrieved based on its size, coverage level and hosts. To obtain the distribution of the clades and lineages of South African SARS-CoV-2 circulating strains, the metadata of the sequence retrieved were subjected to an epidemiological analysis. There was a prediction of the cytotoxic T lymphocytes (CTL), Helper T cells (HTL) and B-cell epitopes. Furthermore, there was allergenicity, antigenicity and toxicity predictions on the epitopes. The analysis of the physicochemical properties of the vaccine construct was performed; the secondary structure, tertiary structure and B-cell 3D conformational structure of the vaccine construct were predicted. Also, molecular binding simulations and dynamics simulations were adopted in the prediction of the vaccine construct's stability and binding affinity with TLRs. Result obtained from the metadata analysis indicated lineage B.1.351 to be in higher circulation among various circulating strains of SARS-CoV-2 in South Africa and GH has the highest number of circulating clades. The construct of the novel vaccine was antigenic, non-allergenic and non-toxic. The Instability index (II) score and aliphatic index were estimated as 41.74 and 78.72 respectively. The computed half-life in mammalian reticulocytes was 4.4 h in vitro, for yeast and in E. coli was >20 h and >10 h in vivo respectively. The grand average of hydropathicity (GRAVY) score is estimated to be -0.129, signifying the hydrophilic nature of the protein. The molecular docking indicates that the vaccine construct has a high binding affinity towards the TLRs with TLR 3 having the highest binding energy (-1203.2 kcal/mol) and TLR 9 with the lowest (-1559.5 kcal/mol). These results show that the vaccine construct is promising and should be evaluated using animal model.
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Affiliation(s)
- Olugbenga Oluseun Oluwagbemi
- Department of Computer Science and Information Technology, Sol Plaatje University, 8301, Kimberley, South Africa
- Department of Mathematical Sciences, Stellenbosch University, 7602, Matieland, South Africa
- National Institute of Theoretical and Computational Sciences (NiTheCS), South Africa
| | - Elijah Kolawole Oladipo
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Emmanuel Oluwatobi Dairo
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Ayodele Eugene Ayeni
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Medical Microbiology and Parasitology, Faculty of Basic Medical Sciences, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | - Esther Moradeyo Jimah
- Department of Medical Microbiology and Parasitology, University of Ilorin, Kwara State, Nigeria
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Moyosoluwa Precious Oyewole
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Boluwatife Mary Olawale
- Reproduction and Bioinformatics Unit, Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | | | - Adewale Joseph Ogunleye
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Moscow Oblast, Russian Federation
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17
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Tan S, Banwell MG, Ye WC, Lan P, White LV. The Inhibition of RNA Viruses by Amaryllidaceae Alkaloids: Opportunities for the Development of Broad-Spectrum Anti-Coronavirus Drugs. Chem Asian J 2022; 17:e202101215. [PMID: 35032358 DOI: 10.1002/asia.202101215] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/06/2021] [Indexed: 12/16/2022]
Abstract
The global COVID-19 pandemic has claimed the lives of millions and disrupted nearly every aspect of human society. Currently, vaccines remain the only widely available medical means to address the cause of the pandemic, the SARS-CoV-2 virus. Unfortunately, current scientific consensus deems the emergence of vaccine-resistant SARS-CoV-2 variants highly likely. In this context, the design and development of broad-spectrum, small-molecule based antiviral drugs has been described as a potentially effective, alternative medical strategy to address circulating and re-emerging CoVs. Small molecules are well-suited to target the least-rapidly evolving structures within CoVs such as highly conserved RNA replication enzymes, and this renders them less vulnerable to evolved drug resistance. Examination of the vast literature describing the inhibition of RNA viruses by Amaryllidaceae alkaloids suggests that future, broad-spectrum anti-CoV drugs may be derived from this family of natural products.
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Affiliation(s)
- Shen Tan
- The Institute for Advanced and Applied Chemical Synthesis, Jinan University, Guangzhou, 510632, P. R. China
| | - Martin G Banwell
- The Institute for Advanced and Applied Chemical Synthesis, Jinan University, Guangzhou, 510632, P. R. China
| | - Wen-Cai Ye
- College of Pharmacy, Jinan University, Guangzhou, 510632, P. R. China
| | - Ping Lan
- The Institute for Advanced and Applied Chemical Synthesis, Jinan University, Guangzhou, 510632, P. R. China
| | - Lorenzo V White
- The Institute for Advanced and Applied Chemical Synthesis, Jinan University, Guangzhou, 510632, P. R. China
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18
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Negi N, Maurya SP, Singh R, Das BK. An update on host immunity correlates and prospects of re-infection in COVID-19. Int Rev Immunol 2021; 41:367-392. [PMID: 34961403 PMCID: PMC8787841 DOI: 10.1080/08830185.2021.2019727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/18/2021] [Accepted: 12/08/2021] [Indexed: 01/08/2023]
Abstract
Reinfection with SARS-CoV-2 is not frequent yet the incidence rate of it is increasing globally owing to the slow emergence of drift variants that pose a perpetual threat to vaccination strategies and have a greater propensity for disease reoccurrence. Long-term protection against SARS-CoV-2 reinfection relies on the induction of the innate as well as the adaptive immune response endowed with immune memory. However, a multitude of factors including the selection pressure, the waning immunity against SARS-CoV-2 over the first year after infection possibly favors evolution of more infectious immune escape variants, amplifying the risk of reinfection. Additionally, the correlates of immune protection, the novel SARS-CoV-2 variants of concern (VOC), the durability of the adaptive and mucosal immunity remain major challenges for the development of therapeutic and prophylactic interventions. Interestingly, a recent body of evidence indicated that the gastrointestinal (GI) tract is another important target organ for SARS-CoV-2 besides the respiratory system, potentially increasing the likelihood of reinfection by impacting the microbiome and the immune response via the gut-lung axis. In this review, we summarized the latest development in SARS-CoV-2 reinfection, and explored the untapped potential of trained immunity. We also highlighted the immune memory kinetics of the humoral and cell-mediated immune response, genetic drift of the emerging viral variants, and discussed the current challenges in vaccine development. Understanding the dynamics and the quality of immune response by unlocking the power of the innate, humoral and cell-mediated immunity during SARS-CoV-2 reinfection would open newer avenues for drug discovery and vaccine designs.
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Affiliation(s)
- Neema Negi
- Department of Chemical Sciences, University of Limerick, Limerick, Ireland
- Bernal Institute, University of Limerick,Limerick, Ireland
| | - Shesh Prakash Maurya
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Ravinder Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Bimal Kumar Das
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
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19
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McIntosh JA, Benkovics T, Silverman SM, Huffman MA, Kong J, Maligres PE, Itoh T, Yang H, Verma D, Pan W, Ho HI, Vroom J, Knight AM, Hurtak JA, Klapars A, Fryszkowska A, Morris WJ, Strotman NA, Murphy GS, Maloney KM, Fier PS. Engineered Ribosyl-1-Kinase Enables Concise Synthesis of Molnupiravir, an Antiviral for COVID-19. ACS CENTRAL SCIENCE 2021; 7:1980-1985. [PMID: 34963891 PMCID: PMC8704035 DOI: 10.1021/acscentsci.1c00608] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Indexed: 05/04/2023]
Abstract
Molnupiravir (MK-4482) is an investigational antiviral agent that is under development for the treatment of COVID-19. Given the potential high demand and urgency for this compound, it was critical to develop a short and sustainable synthesis from simple raw materials that would minimize the time needed to manufacture and supply molnupiravir. The route reported here is enabled through the invention of a novel biocatalytic cascade featuring an engineered ribosyl-1-kinase and uridine phosphorylase. These engineered enzymes were deployed with a pyruvate-oxidase-enabled phosphate recycling strategy. Compared to the initial route, this synthesis of molnupiravir is 70% shorter and approximately 7-fold higher yielding. Looking forward, the biocatalytic approach to molnupiravir outlined here is anticipated to have broad applications for streamlining the synthesis of nucleosides in general.
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Affiliation(s)
- John A. McIntosh
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Tamas Benkovics
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Steven M. Silverman
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Mark A. Huffman
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Jongrock Kong
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Peter E. Maligres
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Tetsuji Itoh
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Hao Yang
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Deeptak Verma
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Weilan Pan
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Hsing-I Ho
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Jonathan Vroom
- Codexis,
Inc., 200 Penobscot Drive, Redwood City, California 94063, United States
| | - Anders M. Knight
- Codexis,
Inc., 200 Penobscot Drive, Redwood City, California 94063, United States
| | - Jessica A. Hurtak
- Codexis,
Inc., 200 Penobscot Drive, Redwood City, California 94063, United States
| | - Artis Klapars
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Anna Fryszkowska
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - William J. Morris
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Neil A. Strotman
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Grant S. Murphy
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Kevin M. Maloney
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Patrick S. Fier
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
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20
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Chen RE, Gorman MJ, Zhu DY, Carreño JM, Yuan D, VanBlargan LA, Burdess S, Lauffenburger DA, Kim W, Turner JS, Droit L, Handley SA, Chahin S, Deepak P, O'Halloran JA, Paley MA, Presti RM, Wu GF, Krammer F, Alter G, Ellebedy AH, Kim AHJ, Diamond MS. Reduced antibody activity against SARS-CoV-2 B.1.617.2 delta virus in serum of mRNA-vaccinated individuals receiving tumor necrosis factor-α inhibitors. MED 2021; 2:1327-1341.e4. [PMID: 34812429 PMCID: PMC8599018 DOI: 10.1016/j.medj.2021.11.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/27/2021] [Accepted: 11/11/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Although vaccines effectively prevent coronavirus disease 2019 (COVID-19) in healthy individuals, they appear to be less immunogenic in individuals with chronic inflammatory disease (CID) or receiving chronic immunosuppression therapy. METHODS Here we assessed a cohort of 77 individuals with CID treated as monotherapy with chronic immunosuppressive drugs for antibody responses in serum against historical and variant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viruses after immunization with the BNT162b2 mRNA vaccine. FINDINGS Longitudinal analysis showed the greatest reductions in neutralizing antibodies and Fc effector function capacity in individuals treated with tumor necrosis factor alpha (TNF-α) inhibitors (TNFi), and this pattern appeared to be worse against the B.1.617.2 delta virus. Within 5 months of vaccination, serum neutralizing titers of all TNFi-treated individuals tested fell below the presumed threshold correlate for antibody-mediated protection. However, TNFi-treated individuals receiving a third mRNA vaccine dose boosted their serum neutralizing antibody titers by more than 16-fold. CONCLUSIONS Vaccine boosting or administration of long-acting prophylaxis (e.g., monoclonal antibodies) will likely be required to prevent SARS-CoV-2 infection in this susceptible population. FUNDING This study was supported by grants and contracts from the NIH (R01 AI157155, R01AI151178, and HHSN75N93019C00074; NIAID Centers of Excellence for Influenza Research and Response (CEIRR) contracts HHSN272201400008C and 75N93021C00014; and Collaborative Influenza Vaccine Innovation Centers [CIVIC] contract 75N93019C00051).
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Affiliation(s)
- Rita E Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Daniel Y Zhu
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dansu Yuan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Samantha Burdess
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Wooseob Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jackson S Turner
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lindsay Droit
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Salim Chahin
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Parakkal Deepak
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jane A O'Halloran
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael A Paley
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel M Presti
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, Saint Louis, MO, USA
| | - Gregory F Wu
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, Saint Louis, MO, USA
| | - Alfred H J Kim
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
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21
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Guo K, Barrett BS, Mickens KL, Vladar EK, Morrison JH, Hasenkrug KJ, Poeschla EM, Santiago ML. Interferon Resistance of Emerging SARS-CoV-2 Variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.20.436257. [PMID: 33758840 PMCID: PMC7986999 DOI: 10.1101/2021.03.20.436257] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The emergence of SARS-CoV-2 variants with enhanced transmissibility, pathogenesis and resistance to vaccines presents urgent challenges for curbing the COVID-19 pandemic. While Spike mutations that enhance virus infectivity or neutralizing antibody evasion may drive the emergence of these novel variants, studies documenting a critical role for interferon responses in the early control of SARS-CoV-2 infection, combined with the presence of viral genes that limit these responses, suggest that interferons may also influence SARS-CoV-2 evolution. Here, we compared the potency of 17 different human interferons against multiple viral lineages sampled during the course of the global outbreak, including ancestral and four major variants of concern. Our data reveal increased interferon resistance in emerging SARS-CoV-2 variants, suggesting that evasion of innate immunity may be a significant, ongoing driving force for SARS-CoV-2 evolution. These findings have implications for the increased lethality of emerging variants and highlight the interferon subtypes that may be most successful in the treatment of early infections.
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Affiliation(s)
- Kejun Guo
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Bradley S. Barrett
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Kaylee L. Mickens
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Ezster K. Vladar
- Division of Pulmonary Sciences and Critical Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - James H. Morrison
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Kim J. Hasenkrug
- Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Eric M. Poeschla
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Mario L. Santiago
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
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22
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Somerville M, Curran JA, Dol J, Boulos L, Saxinger L, Doroshenko A, Hastings S, Reynolds B, Gallant AJ, Shin HD, Wong H, Crowther D, Macdonald M, Martin-Misener R, Comeau J, McCulloch H, Tricco AC. Public health implications of SARS-CoV-2 variants of concern: a rapid scoping review. BMJ Open 2021; 11:e055781. [PMID: 34857582 PMCID: PMC8640198 DOI: 10.1136/bmjopen-2021-055781] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/22/2021] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES The four SARS-CoV-2 variants of concern (VOC; Alpha, Beta, Gamma and Delta) identified by May 2021 are highly transmissible, yet little is known about their impact on public health measures. We aimed to synthesise evidence related to public health measures and VOC. DESIGN A rapid scoping review. DATA SOURCES On 11 May 2021, seven databases (MEDLINE, Embase, the Cochrane Database of Systematic Reviews, Central Register of Controlled Trials, Epistemonikos' L-OVE on COVID-19, medRxiv, bioRxiv) were searched for terms related to VOC, public health measures, transmission and health systems. No limit was placed on date of publication. ELIGIBILITY CRITERIA Studies were included if they reported on any of the four VOCs and public health measures, and were available in English. Only studies reporting on data collected after October 2020, when the first VOC was reported, were included. DATA EXTRACTION AND SYNTHESIS Titles, abstracts and full-text articles were screened by two independent reviewers. Data extraction was completed by two independent reviewers using a standardised form. Data synthesis and reporting followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews guidelines. RESULTS Of the 37 included studies, the majority assessed the impact of Alpha (n=32) and were conducted in Europe (n=12) or the UK (n=9). Most were modelling studies (n=28) and preprints (n=28). The majority of studies reported on infection control measures (n=17), followed by modifying approaches to vaccines (n=13), physical distancing (n=6) and either mask wearing, testing or hand washing (n=2). Findings suggest an accelerated vaccine rollout is needed to mitigate the spread of VOC. CONCLUSIONS The increased severity of VOC requires proactive public health measures to control their spread. Further research is needed to strengthen the evidence for continued implementation of public health measures in conjunction with vaccine rollout. With no studies reporting on Delta, there is a need for further research on this and other emerging VOC on public health measures.
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Affiliation(s)
- Mari Somerville
- Faculty of Health, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Pediatrics, IWK Health, Halifax, Nova Scotia, Canada
| | - Janet A Curran
- Faculty of Health, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Pediatrics, IWK Health, Halifax, Nova Scotia, Canada
| | - Justine Dol
- Faculty of Health, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Leah Boulos
- Maritime SPOR SUPPORT Unit, Nova Scotia Health, Halifax, Nova Scotia, Canada
| | - Lynora Saxinger
- Division of Infectious Diseases, Department of Medicine, University of Alberta Faculty of Medicine and Dentistry, Edmonton, Alberta, Canada
| | - Alexander Doroshenko
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Stephanie Hastings
- Health Systems Evaluation and Evidence, Alberta Health Services, Calgary, Alberta, Canada
| | - Bearach Reynolds
- Department of Infectious Diseases, St Vincents Hospital, Dublin, Leinster, UK
- Evidence Synthesis Ireland, National University of Ireland, Galway, UK
| | - Allyson J Gallant
- Faculty of Health, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Helen Wong
- Faculty of Health, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Daniel Crowther
- Faculty of Health, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Marilyn Macdonald
- Faculty of Health, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Jeannette Comeau
- Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
- Division of Infectious Diseases, IWK Health, Halifax, Nova Scotia, Canada
| | - Holly McCulloch
- Department of Pediatrics, IWK Health, Halifax, Nova Scotia, Canada
| | - Andrea C Tricco
- Knowledge Translation Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Epidemiology Division and Institute for Health Policy, Management, and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Queen's Collaboration for Health Care Quality Joanna Briggs Institute Centre of Excellence, School of Nursing, Queen's University, Kingston, Ontario, Canada
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23
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Novazzi F, Genoni A, Spezia PG, Focosi D, Zago C, Colombo A, Cassani G, Pasciuta R, Tamborini A, Rossi A, Prestia M, Capuano R, Gasperina DD, Dentali F, Severgnini P, Ageno W, Gambarini C, Stefanelli P, Baj A, Maggi F. Introduction of SARS-CoV-2 variant of concern 20h/501Y.V2 (B.1.351) from Malawi to Italy. Emerg Microbes Infect 2021; 10:710-712. [PMID: 33739917 PMCID: PMC8043531 DOI: 10.1080/22221751.2021.1906757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 11/06/2022]
Abstract
We report here an imported case of SARS-CoV-2 variant of concern B.1.1.351 (also known as 20H/501Y.V2 or "South African variant" or VOC 202012/02) in a 66-years old symptomatic male who returned from Malawi to Italy.
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Affiliation(s)
| | - Angelo Genoni
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | | | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Cristian Zago
- Laboratory of Microbiology, ASST Sette Laghi, Varese, Italy
| | | | | | - Renee Pasciuta
- Laboratory of Microbiology, ASST Sette Laghi, Varese, Italy
| | | | - Agostino Rossi
- Laboratory of Microbiology, ASST Sette Laghi, Varese, Italy
| | | | | | - Daniela Dalla Gasperina
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
- Internal Medicine Unit, ASST Dei Sette Laghi, Varese, Italy
| | - Francesco Dentali
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
- Internal Medicine Unit, ASST Dei Sette Laghi, Varese, Italy
| | - Paolo Severgnini
- Anesthesia and Intensive Care, ASST Sette Laghi, Varese, Italy
- Biotechnology and Life Sciences Department, Varese, Italy
| | - Walter Ageno
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | | | | | - Andreina Baj
- Laboratory of Microbiology, ASST Sette Laghi, Varese, Italy
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Fabrizio Maggi
- Laboratory of Microbiology, ASST Sette Laghi, Varese, Italy
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
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24
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Salimi-Jeda A, Abbassi S, Mousavizadeh A, Esghaie M, Bokharaei-Salim F, Jeddi F, Shafaati M, Abdoli A. SARS-CoV-2: Current trends in emerging variants, pathogenesis, immune responses, potential therapeutic, and vaccine development strategies. Int Immunopharmacol 2021; 101:108232. [PMID: 34673335 PMCID: PMC8519814 DOI: 10.1016/j.intimp.2021.108232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/18/2021] [Accepted: 10/04/2021] [Indexed: 02/06/2023]
Abstract
More than a year after the SARS-CoV-2 pandemic, the Coronavirus disease 19 (COVID-19) is still a major global challenge for scientists to understand the different dimensions of infection and find ways to prevent, treat, and develop a vaccine. On January 30, 2020, the world health organization (WHO) officially announced this new virus as an international health emergency. While many biological and mechanisms of pathogenicity of this virus are still unclear, it seems that cytokine storm resulting from an immune response against the virus is considered the main culprit of the severity of the disease. Despite many global efforts to control the SARS-CoV-2, several problems and challenges have been posed in controlling the COVID-19 infection. These problems include the various mutations, the emergence of variants with high transmissibility, the short period of immunity against the virus, the possibility of reinfection in people improved, lack of specific drugs, and problems in the development of highly sensitive and specific vaccines. In this review, we summarized the results of the current trend and the latest research studies on the characteristics of the structure and genome of the SARS-CoV- 2, new mutations and variants of SARS-CoV-2, pathogenicity, immune response, virus diagnostic tests, potential treatment, and vaccine candidate.
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Affiliation(s)
- Ali Salimi-Jeda
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Sina Abbassi
- Department of Anesthesiology, Faculty of Medical Science, Tehran University of Medical Science, Tehran, Iran
| | - Atieh Mousavizadeh
- Department of Virology, Faculty of Medical Science, Tarbiat Modares University, Tehran, Iran
| | - Maryam Esghaie
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farah Bokharaei-Salim
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farhad Jeddi
- Department of Medical Genetics and Pathology, Faculty of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Maryam Shafaati
- Department of Microbiology, Jahrom Branch, Islamic Azad University, Fars, Iran
| | - Asghar Abdoli
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran.
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25
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Orf GS, Forberg K, Meyer TV, Mowerman I, Mohaimani A, Faron ML, Jennings C, Landay AL, Goldstein DY, Fox AS, Berg MG, Cloherty GA. SNP and Phylogenetic Characterization of Low Viral Load SARS-CoV-2 Specimens by Target Enrichment. FRONTIERS IN VIROLOGY 2021. [DOI: 10.3389/fviro.2021.765974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Background: Surveillance of SARS-CoV-2 across the globe has enabled detection of new variants and informed the public health response. With highly sensitive methods like qPCR widely adopted for diagnosis, the ability to sequence and characterize specimens with low titers needs to keep pace.Methods: Nucleic acids extracted from nasopharyngeal swabs collected from four sites in the United States in early 2020 were converted to NGS libraries to sequence SARS-CoV-2 genomes using metagenomic and xGen target enrichment approaches. Single nucleotide polymorphism (SNP) analysis and phylogeny were used to determine clade assignments and geographic origins of strains.Results: SARS-CoV-2-specific xGen enrichment enabled full genome coverage for 87 specimens with Ct values <29, corresponding to viral loads of >10,000 cp/ml. For samples with viral loads between 103 and 106 cp/ml, the median genome coverage for xGen was 99.1%, sequence depth was 605X, and the “on-target” rate was 57 ± 21%, compared to 13%, 2X and 0.001 ± 0.016%, respectively, for metagenomic sequencing alone. Phylogenetic analysis revealed the presence of most clades that existed at the time of the study, though clade GH dominated in the Midwest.Conclusions: Even as vaccines are being widely distributed, a high case load of SARS-CoV-2 infection persists around the world. Viral genetic surveillance has succeeded in warning the public of new variants in circulation and ensured that diagnostic tools remain resilient to a steadily increasing number of mutations. Target capture offers a means of characterizing low viral load samples which would normally pose a challenge for metagenomic sequencing.
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26
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Abstract
Since the start of the pandemic, SARS-CoV-2 has infected almost 200 million human hosts and is set to encounter and gain entry in many more in the coming months. As the coronavirus flourish, the evolutionary pressure selects those variants that can complete the infection cycle faster and reproduce in large numbers compared to others. This increase in infectivity and transmissibility coupled with the immune response from high viral load may cause moderate to severe disease. Whether this leads to enhanced virulence in the prevalent Alpha and Delta variants is still not clear. This review describes the different types of SARS-CoV-2 variants that are now prevalent, their emergence, the mutations responsible for their growth advantages, and how they affect vaccine efficacy and increase chances of reinfection. Finally, we have also summarized the efforts made to recognize and predict the mutations, which can cause immune escape and track their emergence through impactful genomic surveillance.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/immunology
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Binding Sites
- COVID-19/epidemiology
- COVID-19/pathology
- COVID-19/transmission
- COVID-19/virology
- COVID-19 Vaccines
- Genome, Viral
- Humans
- Immune Evasion/genetics
- Models, Molecular
- Mutation
- Phylogeny
- Protein Binding
- Protein Interaction Domains and Motifs
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/immunology
- SARS-CoV-2/classification
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Serine Endopeptidases/chemistry
- Serine Endopeptidases/genetics
- Serine Endopeptidases/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Virulence
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Affiliation(s)
- Raju Mukherjee
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
| | - Rohit Satardekar
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
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27
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van Dorp CH, Goldberg EE, Hengartner N, Ke R, Romero-Severson EO. Estimating the strength of selection for new SARS-CoV-2 variants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.29.21254233. [PMID: 33821289 PMCID: PMC8020992 DOI: 10.1101/2021.03.29.21254233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Controlling the SARS-CoV-2 pandemic becomes increasingly challenging as the virus adapts to human hosts through the continual emergence of more transmissible variants. Simply observing that a variant is increasing in frequency is relatively straightforward, but more sophisticated methodology is needed to determine whether a new variant is a global threat and the magnitude of its selective advantage. We present three methods for quantifying the strength of selection for new and emerging variants of SARS-CoV-2 relative to the background of contemporaneous variants. These methods range from a detailed model of dynamics within one country to a broad analysis across all countries, and they include alternative explanations such as migration and drift. We find evidence for strong selection favoring the D614G spike mutation and B.1.1.7 (Alpha), weaker selection favoring B.1.351 (Beta), and no advantage of R.1 after it spreads beyond Japan. Cutting back data to earlier time horizons reveals large uncertainty very soon after emergence, but that estimates of selection stabilize after several weeks. Our results also show substantial heterogeneity among countries, demonstrating the need for a truly global perspective on the molecular epidemiology of SARS-CoV-2.
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Affiliation(s)
- Christiaan H. van Dorp
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos NM, USA
| | - Emma E. Goldberg
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos NM, USA
- New Mexico Consortium, Los Alamos NM, USA
| | - Nick Hengartner
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos NM, USA
- New Mexico Consortium, Los Alamos NM, USA
| | - Ruian Ke
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos NM, USA
- New Mexico Consortium, Los Alamos NM, USA
| | - Ethan O. Romero-Severson
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos NM, USA
- New Mexico Consortium, Los Alamos NM, USA
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28
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A Potential Role of the CD47/SIRPalpha Axis in COVID-19 Pathogenesis. Curr Issues Mol Biol 2021; 43:1212-1225. [PMID: 34698067 PMCID: PMC8929144 DOI: 10.3390/cimb43030086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/15/2022] Open
Abstract
The coronavirus SARS-CoV-2 is the cause of the ongoing COVID-19 pandemic. Most SARS-CoV-2 infections are mild or even asymptomatic. However, a small fraction of infected individuals develops severe, life-threatening disease, which is caused by an uncontrolled immune response resulting in hyperinflammation. However, the factors predisposing individuals to severe disease remain poorly understood. Here, we show that levels of CD47, which is known to mediate immune escape in cancer and virus-infected cells, are elevated in SARS-CoV-2-infected Caco-2 cells, Calu-3 cells, and air-liquid interface cultures of primary human bronchial epithelial cells. Moreover, SARS-CoV-2 infection increases SIRPalpha levels, the binding partner of CD47, on primary human monocytes. Systematic literature searches further indicated that known risk factors such as older age and diabetes are associated with increased CD47 levels. High CD47 levels contribute to vascular disease, vasoconstriction, and hypertension, conditions that may predispose SARS-CoV-2-infected individuals to COVID-19-related complications such as pulmonary hypertension, lung fibrosis, myocardial injury, stroke, and acute kidney injury. Hence, age-related and virus-induced CD47 expression is a candidate mechanism potentially contributing to severe COVID-19, as well as a therapeutic target, which may be addressed by antibodies and small molecules. Further research will be needed to investigate the potential involvement of CD47 and SIRPalpha in COVID-19 pathology. Our data should encourage other research groups to consider the potential relevance of the CD47/ SIRPalpha axis in their COVID-19 research.
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29
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A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. Sci Rep 2021; 11:18428. [PMID: 34531417 PMCID: PMC8445915 DOI: 10.1038/s41598-021-97330-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/24/2021] [Indexed: 01/07/2023] Open
Abstract
Here we describe a homogeneous bioluminescent immunoassay based on the interaction between Fc-tagged SARS-CoV-2 Spike RBD and human ACE2, and its detection by secondary antibodies labeled with NanoLuc luciferase fragments LgBit and SmBit. The assay utility for the discovery of novel inhibitors was demonstrated with a panel of anti-RBD antibodies, ACE2-derived miniproteins and soluble ACE2. Studying the effect of RBD mutations on ACE2 binding showed that the N501Y mutation increased RBD apparent affinity toward ACE2 tenfold that resulted in escaping inhibition by some anti-RBD antibodies. In contrast, while E484K mutation did not highly change the binding affinity, it still escaped antibody inhibition likely due to changes in the epitope recognized by the antibody. Also, neutralizing antibodies (NAbs) from COVID-19 positive samples from two distinct regions (USA and Brazil) were successfully detected and the results further suggest the persistence of NAbs for at least 6 months post symptom onset. Finally, sera from vaccinated individuals were tested for NAbs and showed varying neutralizing activity after first and second doses, suggesting the assay can be used to assess immunity of vaccinated populations. Our results demonstrate the broad utility and ease of use of this methodology both for drug discovery and clinical research applications.
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30
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Zhang YN, Paynter J, Sou C, Fourfouris T, Wang Y, Abraham C, Ngo T, Zhang Y, He L, Zhu J. Mechanism of a COVID-19 nanoparticle vaccine candidate that elicits a broadly neutralizing antibody response to SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.26.437274. [PMID: 33791704 PMCID: PMC8010731 DOI: 10.1101/2021.03.26.437274] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Vaccines that induce potent neutralizing antibody (NAb) responses against emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are essential for combating the coronavirus disease 2019 (COVID-19) pandemic. We demonstrated that mouse plasma induced by self-assembling protein nanoparticles (SApNPs) that present 20 rationally designed S2GΔHR2 spikes of the ancestral Wuhan-Hu-1 strain can neutralize the B.1.1.7, B.1.351, P.1, and B.1.617 variants with the same potency. The adjuvant effect on vaccine-induced immunity was investigated by testing 16 formulations for the multilayered I3-01v9 SApNP. Using single-cell sorting, monoclonal antibodies (mAbs) with diverse neutralization breadth and potency were isolated from mice immunized with the receptor binding domain (RBD), S2GΔHR2 spike, and SApNP vaccines. The mechanism of vaccine-induced immunity was examined in mice. Compared with the soluble spike, the I3-01v9 SApNP showed 6-fold longer retention, 4-fold greater presentation on follicular dendritic cell dendrites, and 5-fold stronger germinal center reactions in lymph node follicles.
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Affiliation(s)
- Yi-Nan Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Jennifer Paynter
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Cindy Sou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Tatiana Fourfouris
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Ying Wang
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania 19140, USA
- Department of Microbiology and Immunology, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Ciril Abraham
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Timothy Ngo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Yi Zhang
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania 19140, USA
- Department of Microbiology and Immunology, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California 92037, USA
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31
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Zhou H, Dcosta BM, Samanovic MI, Mulligan MJ, Landau NR, Tada T. B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. mBio 2021; 12:e0138621. [PMID: 34311587 PMCID: PMC8406170 DOI: 10.1128/mbio.01386-21] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/21/2021] [Indexed: 11/20/2022] Open
Abstract
DNA sequence analysis recently identified the novel SARS-CoV-2 variant B.1.526 that is spreading at an alarming rate in the New York City area. Two versions of the variant were identified, both with the prevalent D614G mutation in the spike protein, together with four novel point mutations and with an E484K or S477N mutation in the receptor-binding domain, raising concerns of possible resistance to vaccine-elicited and therapeutic antibodies. We report that convalescent-phase sera and vaccine-elicited antibodies retain full neutralizing titer against the S477N B.1.526 variant and neutralize the E484K version with a modest 3.5-fold decrease in titer compared to D614G. The E484K version was neutralized with a 12-fold decrease in titer by the REGN10933 monoclonal antibody, but the combination cocktail with REGN10987 was fully active. The findings suggest that current vaccines and Regeneron therapeutic monoclonal antibodies will remain protective against the B.1.526 variants. The findings further support the value of widespread vaccination. IMPORTANCE A novel SARS-CoV-2 variant termed B.1.526 was recently identified in New York City and has been found to be spreading at an alarming rate. The variant has mutations in its spike protein that might allow it to escape neutralization by vaccine-elicited antibodies and might cause monoclonal antibody therapy for COVID-19 to be less successful. We report here that these fears are not substantiated; convalescent-phase sera and vaccine-elicited antibodies neutralized the B.1.526 variant. One of the Regeneron therapeutic monoclonal antibodies was less effective against the B.1.526 (E484K) variant but the two-antibody combination cocktail was fully active. The findings should assuage concerns that current vaccines will be ineffective against the B.1.526 (E484K) variant and suggest the importance of continued widespread vaccination.
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Affiliation(s)
- Hao Zhou
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Belinda M. Dcosta
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Marie I. Samanovic
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Mark J. Mulligan
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Nathaniel R. Landau
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
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32
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Rehn A, Braun P, Knüpfer M, Wölfel R, Antwerpen MH, Walter MC. Catching SARS-CoV-2 by Sequence Hybridization: a Comparative Analysis. mSystems 2021; 6:e0039221. [PMID: 34342536 PMCID: PMC8407296 DOI: 10.1128/msystems.00392-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/12/2021] [Indexed: 11/20/2022] Open
Abstract
Controlling and monitoring the still ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic regarding geographical distribution, evolution, and emergence of new mutations of the SARS-CoV-2 virus is only possible due to continuous next-generation sequencing (NGS) and sharing sequence data worldwide. Efficient sequencing strategies enable the retrieval of increasing numbers of high-quality, full-length genomes and are, hence, indispensable. Two opposed enrichment methods, tiling multiplex PCR and sequence hybridization by bait capture, have been established for SARS-CoV-2 sequencing and are both frequently used, depending on the quality of the patient sample and the question at hand. Here, we focused on the evaluation of the sequence hybridization method by studying five commercially available sequence capture bait panels with regard to sensitivity and capture efficiency. We discovered the SARS-CoV-2-specific panel of Twist Bioscience to be the most efficient panel, followed by two respiratory panels from Twist Bioscience and Illumina, respectively. Our results provide on the one hand a decision basis for the sequencing community including a computation for using the full capacity of the flow cell and on the other hand potential improvements for the manufacturers. IMPORTANCE Sequencing the genomes of the circulating SARS-CoV-2 strains is the only way to monitor the viral spread and evolution of the virus. Two different approaches, namely, tiling multiplex PCR and sequence hybridization by bait capture, are commonly used to fulfill this task. This study describes for the first time a combined approach of droplet digital PCR (ddPCR) and NGS to evaluate five commercially available sequence capture panels targeting SARS-CoV-2. In doing so, we were able to determine the most sensitive and efficient capture panel, distinguish the mode of action of the various bait panels, and compute the number of read pairs needed to recover a high-quality full-length genome. By calculating the minimum number of read pairs needed, we are providing optimized flow cell loading conditions for all sequencing laboratories worldwide that are striving for maximizing sequencing output and simultaneously minimizing time, costs, and sequencing resources.
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Affiliation(s)
| | - Peter Braun
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Mandy Knüpfer
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Roman Wölfel
- Bundeswehr Institute of Microbiology, Munich, Germany
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33
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Ying B, Whitener B, VanBlargan LA, Hassan AO, Shrihari S, Liang CY, Karl CE, Mackin S, Chen RE, Kafai NM, Wilks SH, Smith DJ, Carreño JM, Singh G, Krammer F, Carfi A, Elbashir S, Edwards DK, Thackray LB, Diamond MS. Protective activity of mRNA vaccines against ancestral and variant SARS-CoV-2 strains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.08.25.457693. [PMID: 34462745 PMCID: PMC8404887 DOI: 10.1101/2021.08.25.457693] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Although mRNA vaccines prevent COVID-19, variants jeopardize their efficacy as immunity wanes. Here, we assessed the immunogenicity and protective activity of historical (mRNA-1273, designed for Wuhan-1 spike) or modified (mRNA-1273.351, designed for B.1.351 spike) preclinical Moderna mRNA vaccines in 129S2 and K18-hACE2 mice. Immunization with high or low dose formulations of mRNA vaccines induced neutralizing antibodies in serum against ancestral SARS-CoV-2 and several variants, although levels were lower particularly against the B.1.617.2 (Delta) virus. Protection against weight loss and lung pathology was observed with all high-dose vaccines against all viruses. Nonetheless, low-dose formulations of the vaccines, which produced lower magnitude antibody and T cell responses, and serve as a possible model for waning immunity, showed breakthrough lung infection and pneumonia with B.1.617.2. Thus, as levels of immunity induced by mRNA vaccines decline, breakthrough infection and disease likely will occur with some SARS-CoV-2 variants, suggesting a need for additional booster regimens.
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Affiliation(s)
- Baoling Ying
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bradley Whitener
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura A. VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ahmed O. Hassan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Swathi Shrihari
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chieh-Yu Liang
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Courtney E. Karl
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine. St. Louis, MO, USA
| | - Samantha Mackin
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rita E. Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Natasha M. Kafai
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Samuel H. Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge UK
| | - Derek J. Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge UK
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | | - Larissa B. Thackray
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael S. Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine. St. Louis, MO, USA
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Ding C, He J, Zhang X, Jiang C, Sun Y, Zhang Y, Chen Q, He H, Li W, Xie J, Liu Z, Gao Y. Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. Front Immunol 2021; 12:693775. [PMID: 34484190 PMCID: PMC8416052 DOI: 10.3389/fimmu.2021.693775] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/27/2021] [Indexed: 11/16/2022] Open
Abstract
Small number of SARS-CoV-2 epidemic lineages did not efficiently exhibit a neutralization profile, while single amino acid mutation in the spike protein has not been confirmed in altering viral antigenicity resulting in immune escape. To identify crucial mutations in spike protein that escape humoral immune response, we evaluated the cross-neutralization of convalescent plasmas and RBD-specific monoclonal antibodies (mAbs) against various spike protein-based pseudoviruses. Three of 24 SARS-CoV-2 pseudoviruses containing different mutations in spike protein, including D614G, A475V, and E484Q, consistently showed an altered sensitivity to neutralization by convalescent plasmas. A475V and E484Q mutants are highly resistant to neutralization by mAb B38 and 2-4, suggesting that some crucial mutations in spike protein might evolve SARS-CoV-2 variants capable of escaping humoral immune response.
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Affiliation(s)
- Chengchao Ding
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China
| | - Jun He
- Department of Microbiology, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Xiangyu Zhang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China
| | - Chengcheng Jiang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China
| | - Yong Sun
- Department of Microbiology, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Yuqing Zhang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China
| | - Qingqing Chen
- Department of Microbiology, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Hongliang He
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China
| | - Wenting Li
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China
| | - Jiajia Xie
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China
| | - Zhirong Liu
- Department of Microbiology, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Yong Gao
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China
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35
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Malladi S, Patel UR, Rajmani RS, Singh R, Pandey S, Kumar S, Khaleeq S, van Vuren PJ, Riddell S, Goldie S, Gayathri S, Chakraborty D, Kalita P, Pramanick I, Agarwal N, Reddy P, Girish N, Upadhyaya A, Khan MS, Kanjo K, Bhat M, Mani S, Bhattacharyya S, Siddiqui S, Tyagi A, Jha S, Pandey R, Tripathi S, Dutta S, McAuley AJ, Singanallur N, Vasan SS, Ringe RP, Varadarajan R. Immunogenicity and Protective Efficacy of a Highly Thermotolerant, Trimeric SARS-CoV-2 Receptor Binding Domain Derivative. ACS Infect Dis 2021; 7:2546-2564. [PMID: 34260218 PMCID: PMC8996237 DOI: 10.1021/acsinfecdis.1c00276] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Indexed: 02/07/2023]
Abstract
The receptor binding domain (RBD) of SARS-CoV-2 is the primary target of neutralizing antibodies. We designed a trimeric, highly thermotolerant glycan engineered RBD by fusion to a heterologous, poorly immunogenic disulfide linked trimerization domain derived from cartilage matrix protein. The protein expressed at a yield of ∼80-100 mg/L in transiently transfected Expi293 cells, as well as CHO and HEK293 stable cell lines and formed homogeneous disulfide-linked trimers. When lyophilized, these possessed remarkable functional stability to transient thermal stress of up to 100 °C and were stable to long-term storage of over 4 weeks at 37 °C unlike an alternative RBD-trimer with a different trimerization domain. Two intramuscular immunizations with a human-compatible SWE adjuvanted formulation elicited antibodies with pseudoviral neutralizing titers in guinea pigs and mice that were 25-250 fold higher than corresponding values in human convalescent sera. Against the beta (B.1.351) variant of concern (VOC), pseudoviral neutralization titers for RBD trimer were ∼3-fold lower than against wildtype B.1 virus. RBD was also displayed on a designed ferritin-like Msdps2 nanoparticle. This showed decreased yield and immunogenicity relative to trimeric RBD. Replicative virus neutralization assays using mouse sera demonstrated that antibodies induced by the trimers neutralized all four VOC to date, namely B.1.1.7, B.1.351, P.1, and B.1.617.2 without significant differences. Trimeric RBD immunized hamsters were protected from viral challenge. The excellent immunogenicity, thermotolerance, and high yield of these immunogens suggest that they are a promising modality to combat COVID-19, including all SARS-CoV-2 VOC to date.
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Affiliation(s)
- Sameer
Kumar Malladi
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Unnatiben Rajeshbhai Patel
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Raju S. Rajmani
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Randhir Singh
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Suman Pandey
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Sahil Kumar
- Virology
Unit, Institute of Microbial Technology,
Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh 160036, India
| | - Sara Khaleeq
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Petrus Jansen van Vuren
- Australian
Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, Geelong 3220, Victoria, Australia
| | - Shane Riddell
- Australian
Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, Geelong 3220, Victoria, Australia
| | - Sarah Goldie
- Australian
Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, Geelong 3220, Victoria, Australia
| | - Savitha Gayathri
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Debajyoti Chakraborty
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Parismita Kalita
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Ishika Pramanick
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Nupur Agarwal
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Poorvi Reddy
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Nidhi Girish
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Aditya Upadhyaya
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Mohammad Suhail Khan
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Kawkab Kanjo
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Madhuraj Bhat
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Shailendra Mani
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster, Third Milestone, Gurugram-Faridabad
Expressway, Faridabad 121001, India
| | - Sankar Bhattacharyya
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster, Third Milestone, Gurugram-Faridabad
Expressway, Faridabad 121001, India
| | - Samreen Siddiqui
- Max Super
Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi 1100017, India
| | - Akansha Tyagi
- Max Super
Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi 1100017, India
| | - Sujeet Jha
- Max Super
Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi 1100017, India
| | - Rajesh Pandey
- Integrative
Genomics of Host-Pathogen (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Shashank Tripathi
- Department
of Microbiology & Cell Biology, Indian
Institute of Science, Bengaluru 560012, India
- Centre
for Infectious Disease Research, Indian
Institute of Science, Bengaluru 560012, India
| | - Somnath Dutta
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Alexander J. McAuley
- Australian
Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, Geelong 3220, Victoria, Australia
| | - Nagendrakumar
Balasubramanian Singanallur
- Australian
Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, Geelong 3220, Victoria, Australia
| | - Seshadri S. Vasan
- Australian
Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, Geelong 3220, Victoria, Australia
- Department
of Health Sciences, University of York, York YO10 5DD, United Kingdom
| | - Rajesh P. Ringe
- Virology
Unit, Institute of Microbial Technology,
Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh 160036, India
| | - Raghavan Varadarajan
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
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36
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Corbett KS, Gagne M, Wagner DA, Connell SO, Narpala SR, Flebbe DR, Andrew SF, Davis RL, Flynn B, Johnston TS, Stringham C, Lai L, Valentin D, Van Ry A, Flinchbaugh Z, Werner AP, Moliva JI, Sriparna M, O'Dell S, Schmidt SD, Tucker C, Choi A, Koch M, Bock KW, Minai M, Nagata BM, Alvarado GS, Henry AR, Laboune F, Schramm CA, Zhang Y, Wang L, Choe M, Boyoglu-Barnum S, Shi W, Lamb E, Nurmukhambetova ST, Provost SJ, Donaldson MM, Marquez J, Todd JPM, Cook A, Dodson A, Pekosz A, Boritz E, Ploquin A, Doria-Rose N, Pessaint L, Andersen H, Foulds KE, Misasi J, Wu K, Carfi A, Nason MC, Mascola J, Moore IN, Edwards DK, Lewis MG, Suthar MS, Roederer M, McDermott A, Douek DC, Sullivan NJ, Graham BS, Seder RA. Protection against SARS-CoV-2 Beta Variant in mRNA-1273 Boosted Nonhuman Primates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.08.11.456015. [PMID: 34426813 PMCID: PMC8382125 DOI: 10.1101/2021.08.11.456015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
UNLABELLED Neutralizing antibody responses gradually wane after vaccination with mRNA-1273 against several variants of concern (VOC), and additional boost vaccinations may be required to sustain immunity and protection. Here, we evaluated the immune responses in nonhuman primates that received 100 µg of mRNA-1273 vaccine at 0 and 4 weeks and were boosted at week 29 with mRNA-1273 (homologous) or mRNA-1273.β (heterologous), which encompasses the spike sequence of the B.1.351 (beta or β) variant. Reciprocal ID 50 pseudovirus neutralizing antibody geometric mean titers (GMT) against live SARS-CoV-2 D614G and the β variant, were 4700 and 765, respectively, at week 6, the peak of primary response, and 644 and 553, respectively, at a 5-month post-vaccination memory time point. Two weeks following homologous or heterologous boost β-specific reciprocal ID 50 GMT were 5000 and 3000, respectively. At week 38, animals were challenged in the upper and lower airway with the β variant. Two days post-challenge, viral replication was low to undetectable in both BAL and nasal swabs in most of the boosted animals. These data show that boosting with the homologous mRNA-1273 vaccine six months after primary immunization provides up to a 20-fold increase in neutralizing antibody responses across all VOC, which may be required to sustain high-level protection against severe disease, especially for at-risk populations. ONE-SENTENCE SUMMARY mRNA-1273 boosted nonhuman primates have increased immune responses and are protected against SARS-CoV-2 beta infection.
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37
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Gooch KE, Smith TRF, Salguero FJ, Fotheringham SA, Watson RJ, Dennis MJ, Handley A, Humphries HE, Longet S, Tipton T, Sarfas C, Sibley L, Slack GS, Rayner E, Ryan KA, Schultheis K, Ramos SJ, White A, Charlton S, Sharpe SA, Gleeson F, Humeau LM, Hall Y, Broderick KE, Carroll MW. One or two dose regimen of the SARS-CoV-2 synthetic DNA vaccine INO-4800 protects against respiratory tract disease burden in nonhuman primate challenge model. Vaccine 2021; 39:4885-4894. [PMID: 34253420 PMCID: PMC8220992 DOI: 10.1016/j.vaccine.2021.06.057] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/17/2021] [Accepted: 06/20/2021] [Indexed: 01/31/2023]
Abstract
Safe and effective vaccines will provide essential medical countermeasures to tackle the COVID-19 pandemic. Here, we assessed the safety, immunogenicity and efficacy of the intradermal delivery of INO-4800, a synthetic DNA vaccine candidate encoding the SARS-CoV-2 spike protein in the rhesus macaque model. Single and 2 dose vaccination regimens were evaluated. Vaccination induced both binding and neutralizing antibodies, along with IFN-γ-producing T cells against SARS-CoV-2. Upon administration of a high viral dose (5 × 106 pfu) via the intranasal and intratracheal routes we observed significantly reduced virus load in the lung and throat, in the vaccinated animals compared to controls. 2 doses of INO-4800 was associated with more robust vaccine-induced immune responses and improved viral protection. Importantly, histopathological examination of lung tissue provided no indication of vaccine-enhanced disease following SARS-CoV-2 challenge in INO-4800 immunized animals. This vaccine candidate is currently under clinical evaluation as a 2 dose regimen.
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Affiliation(s)
- Karen E Gooch
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | | | - Francisco J Salguero
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | - Susan A Fotheringham
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | - Robert J Watson
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | - Mike J Dennis
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | - Alastair Handley
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | - Holly E Humphries
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | - Stephanie Longet
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | - Tom Tipton
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | - Charlotte Sarfas
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | - Laura Sibley
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | - Gillian S Slack
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | - Emma Rayner
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | - Kathryn A Ryan
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | | | | | - Andrew White
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | - Sue Charlton
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | - Sally A Sharpe
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | | | | | - Yper Hall
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | | | - Miles W Carroll
- Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom; Wellcome Centre for Human Genetics, Nuffield Dept of Medicine, Oxford University, OX3 7BN, UK
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38
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Yi H, Wang J, Wang J, Lu Y, Zhang Y, Peng R, Lu J, Chen Z. The Emergence and Spread of Novel SARS-CoV-2 Variants. Front Public Health 2021; 9:696664. [PMID: 34409009 PMCID: PMC8364952 DOI: 10.3389/fpubh.2021.696664] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022] Open
Abstract
Since severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) began to spread in late 2019, laboratories around the world have widely used whole genome sequencing (WGS) to continuously monitor the changes in the viral genes and discovered multiple subtypes or branches evolved from SARS-CoV-2. Recently, several novel SARS-CoV-2 variants have been found to be more transmissible. They may affect the immune response caused by vaccines and natural infections and reduce the sensitivity to neutralizing antibodies. We analyze the distribution characteristics of prevalent SARS-CoV-2 variants and the frequency of mutant sites based on the data available from GISAID and PANGO by R 4.0.2 and ArcGIS 10.2. Our analysis suggests that B.1.1.7, B.1.351, and P.1 are more easily spreading than other variants, and the key mutations of S protein, including N501Y, E484K, and K417N/T, have high mutant frequencies, which may have become the main genotypes for the spread of SARS-CoV-2.
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Affiliation(s)
- Huaimin Yi
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jin Wang
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jiong Wang
- School of Public Health, Southern Medical University, Guangzhou, China
| | - Yuying Lu
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yali Zhang
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Ruihao Peng
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jiahai Lu
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Zeliang Chen
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shenyang, China
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39
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Faulkner N, Ng KW, Wu MY, Harvey R, Margaritis M, Paraskevopoulou S, Houlihan C, Hussain S, Greco M, Bolland W, Warchal S, Heaney J, Rickman H, Spyer M, Frampton D, Byott M, de Oliveira T, Sigal A, Kjaer S, Swanton C, Gandhi S, Beale R, Gamblin SJ, McCauley JW, Daniels RS, Howell M, Bauer D, Nastouli E, Kassiotis G. Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains. eLife 2021; 10:e69317. [PMID: 34323691 PMCID: PMC8352583 DOI: 10.7554/elife.69317] [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: 04/11/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022] Open
Abstract
Background The degree of heterotypic immunity induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains is a major determinant of the spread of emerging variants and the success of vaccination campaigns, but remains incompletely understood. Methods We examined the immunogenicity of SARS-CoV-2 variant B.1.1.7 (Alpha) that arose in the United Kingdom and spread globally. We determined titres of spike glycoprotein-binding antibodies and authentic virus neutralising antibodies induced by B.1.1.7 infection to infer homotypic and heterotypic immunity. Results Antibodies elicited by B.1.1.7 infection exhibited significantly reduced recognition and neutralisation of parental strains or of the South Africa variant B.1.351 (Beta) than of the infecting variant. The drop in cross-reactivity was significantly more pronounced following B.1.1.7 than parental strain infection. Conclusions The results indicate that heterotypic immunity induced by SARS-CoV-2 variants is asymmetric. Funding This work was supported by the Francis Crick Institute and the Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg.
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Affiliation(s)
- Nikhil Faulkner
- Retroviral ImmunologyLondonUnited Kingdom
- National Heart and Lung Institute, Imperial College LondonLondonUnited Kingdom
| | - Kevin W Ng
- Retroviral ImmunologyLondonUnited Kingdom
| | - Mary Y Wu
- High Throughput Screening STPLondonUnited Kingdom
| | - Ruth Harvey
- Worldwide Influenza CentreLondonUnited Kingdom
| | - Marios Margaritis
- Advanced Pathogen Diagnostics Unit UCLH NHS TrustLondonUnited Kingdom
| | | | - Catherine Houlihan
- Advanced Pathogen Diagnostics Unit UCLH NHS TrustLondonUnited Kingdom
- Division of Infection and ImmunityLondonUnited Kingdom
| | - Saira Hussain
- Worldwide Influenza CentreLondonUnited Kingdom
- RNA Virus Replication LaboratoryLondonUnited Kingdom
| | - Maria Greco
- RNA Virus Replication LaboratoryLondonUnited Kingdom
| | | | | | - Judith Heaney
- Advanced Pathogen Diagnostics Unit UCLH NHS TrustLondonUnited Kingdom
| | - Hannah Rickman
- Advanced Pathogen Diagnostics Unit UCLH NHS TrustLondonUnited Kingdom
| | - Moria Spyer
- Advanced Pathogen Diagnostics Unit UCLH NHS TrustLondonUnited Kingdom
- Department of Population, Policy and PracticeLondonUnited Kingdom
| | | | - Matthew Byott
- Advanced Pathogen Diagnostics Unit UCLH NHS TrustLondonUnited Kingdom
| | - Tulio de Oliveira
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
- KwaZulu-Natal Research Innovation and Sequencing PlatformDurbanSouth Africa
- Centre for the AIDS Programme of Research in South AfricaDurbanSouth Africa
- Department of Global Health, University of WashingtonSeattleUnited States
| | - Alex Sigal
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
- Africa Health Research InstituteDurbanSouth Africa
- Max Planck Institute for Infection BiologyBerlinGermany
| | | | - Charles Swanton
- Cancer Evolution and Genome Instability LaboratoryLondonUnited Kingdom
| | - Sonia Gandhi
- Neurodegradation Biology LaboratoryLondonUnited Kingdom
| | - Rupert Beale
- Cell Biology of Infection LaboratoryLondonUnited Kingdom
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | | | | | | | - David Bauer
- RNA Virus Replication LaboratoryLondonUnited Kingdom
| | - Eleni Nastouli
- Retroviral ImmunologyLondonUnited Kingdom
- Advanced Pathogen Diagnostics Unit UCLH NHS TrustLondonUnited Kingdom
- Department of Population, Policy and PracticeLondonUnited Kingdom
| | - George Kassiotis
- Retroviral ImmunologyLondonUnited Kingdom
- Department of Infectious Disease, St Mary's Hospital, Imperial College LondonLondonUnited Kingdom
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40
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da Silva KN, Gobatto ALN, Costa-Ferro ZSM, Cavalcante BRR, Caria ACI, de Aragão França LS, Nonaka CKV, de Macêdo Lima F, Lopes-Pacheco M, Rocco PRM, de Freitas Souza BS. Is there a place for mesenchymal stromal cell-based therapies in the therapeutic armamentarium against COVID-19? Stem Cell Res Ther 2021; 12:425. [PMID: 34315546 PMCID: PMC8314259 DOI: 10.1186/s13287-021-02502-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 07/04/2021] [Indexed: 02/07/2023] Open
Abstract
The COVID-19 pandemic, caused by the rapid global spread of the novel coronavirus (SARS-CoV-2), has caused healthcare systems to collapse and led to hundreds of thousands of deaths. The clinical spectrum of COVID-19 is not only limited to local pneumonia but also represents multiple organ involvement, with potential for systemic complications. One year after the pandemic, pathophysiological knowledge has evolved, and many therapeutic advances have occurred, but mortality rates are still elevated in severe/critical COVID-19 cases. Mesenchymal stromal cells (MSCs) can exert immunomodulatory, antiviral, and pro-regenerative paracrine/endocrine actions and are therefore promising candidates for MSC-based therapies. In this review, we discuss the rationale for MSC-based therapies based on currently available preclinical and clinical evidence of safety, potential efficacy, and mechanisms of action. Finally, we present a critical analysis of the risks, limitations, challenges, and opportunities that place MSC-based products as a therapeutic strategy that may complement the current arsenal against COVID-19 and reduce the pandemic's unmet medical needs.
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Affiliation(s)
- Kátia Nunes da Silva
- Goncalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rua Waldemar Falcão, 121, Candeal, Salvador, Bahia, 40296-710, Brazil
- D'Or Institute for Research and Education (IDOR), Salvador, Brazil
- Center for Biotechnology and Cell Therapy, São Rafael Hospital, Salvador, Brazil
| | | | - Zaquer Suzana Munhoz Costa-Ferro
- D'Or Institute for Research and Education (IDOR), Salvador, Brazil
- Center for Biotechnology and Cell Therapy, São Rafael Hospital, Salvador, Brazil
| | - Bruno Raphael Ribeiro Cavalcante
- Goncalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rua Waldemar Falcão, 121, Candeal, Salvador, Bahia, 40296-710, Brazil
| | - Alex Cleber Improta Caria
- Graduate Program in Medicine and Health, Faculty of Medicine, Federal University of Bahia, Salvador, Brazil
| | - Luciana Souza de Aragão França
- D'Or Institute for Research and Education (IDOR), Salvador, Brazil
- Center for Biotechnology and Cell Therapy, São Rafael Hospital, Salvador, Brazil
| | - Carolina Kymie Vasques Nonaka
- D'Or Institute for Research and Education (IDOR), Salvador, Brazil
- Center for Biotechnology and Cell Therapy, São Rafael Hospital, Salvador, Brazil
| | | | - Miquéias Lopes-Pacheco
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Patricia Rieken Macêdo Rocco
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- National Institute of Science and Technology for Regenerative Medicine, Rio de Janeiro, Rio de Janeiro, Brazil
- COVID-19 Virus Network, Ministry of Science and Technology, and Innovation, Rio de Janeiro, Brazil
| | - Bruno Solano de Freitas Souza
- Goncalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rua Waldemar Falcão, 121, Candeal, Salvador, Bahia, 40296-710, Brazil.
- D'Or Institute for Research and Education (IDOR), Salvador, Brazil.
- Center for Biotechnology and Cell Therapy, São Rafael Hospital, Salvador, Brazil.
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Rochman ND, Wolf YI, Faure G, Mutz P, Zhang F, Koonin EV. Ongoing global and regional adaptive evolution of SARS-CoV-2. Proc Natl Acad Sci U S A 2021; 118:e2104241118. [PMID: 34292871 PMCID: PMC8307621 DOI: 10.1073/pnas.2104241118] [Citation(s) in RCA: 152] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Understanding the trends in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution is paramount to control the COVID-19 pandemic. We analyzed more than 300,000 high-quality genome sequences of SARS-CoV-2 variants available as of January 2021. The results show that the ongoing evolution of SARS-CoV-2 during the pandemic is characterized primarily by purifying selection, but a small set of sites appear to evolve under positive selection. The receptor-binding domain of the spike protein and the region of the nucleocapsid protein associated with nuclear localization signals (NLS) are enriched with positively selected amino acid replacements. These replacements form a strongly connected network of apparent epistatic interactions and are signatures of major partitions in the SARS-CoV-2 phylogeny. Virus diversity within each geographic region has been steadily growing for the entirety of the pandemic, but analysis of the phylogenetic distances between pairs of regions reveals four distinct periods based on global partitioning of the tree and the emergence of key mutations. The initial period of rapid diversification into region-specific phylogenies that ended in February 2020 was followed by a major extinction event and global homogenization concomitant with the spread of D614G in the spike protein, ending in March 2020. The NLS-associated variants across multiple partitions rose to global prominence in March to July, during a period of stasis in terms of interregional diversity. Finally, beginning in July 2020, multiple mutations, some of which have since been demonstrated to enable antibody evasion, began to emerge associated with ongoing regional diversification, which might be indicative of speciation.
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Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894;
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Pascal Mutz
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142;
- HHMI, Massachusetts Institute of Technology, Cambridge, MA 02139
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894;
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42
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Hafezi B, Chan L, Knapp JP, Karimi N, Alizadeh K, Mehrani Y, Bridle BW, Karimi K. Cytokine Storm Syndrome in SARS-CoV-2 Infections: A Functional Role of Mast Cells. Cells 2021; 10:1761. [PMID: 34359931 PMCID: PMC8308097 DOI: 10.3390/cells10071761] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/27/2021] [Accepted: 07/09/2021] [Indexed: 02/06/2023] Open
Abstract
Cytokine storm syndrome is a cascade of escalated immune responses disposing the immune system to exhaustion, which might ultimately result in organ failure and fatal respiratory distress. Infection with severe acute respiratory syndrome-coronavirus-2 can result in uncontrolled production of cytokines and eventually the development of cytokine storm syndrome. Mast cells may react to viruses in collaboration with other cells and lung autopsy findings from patients that died from the coronavirus disease that emerged in 2019 (COVID-19) showed accumulation of mast cells in the lungs that was thought to be the cause of pulmonary edema, inflammation, and thrombosis. In this review, we present evidence that a cytokine response by mast cells may initiate inappropriate antiviral immune responses and cause the development of cytokine storm syndrome. We also explore the potential of mast cell activators as adjuvants for COVID-19 vaccines and discuss the medications that target the functions of mast cells and could be of value in the treatment of COVID-19. Recognition of the cytokine storm is crucial for proper treatment of patients and preventing the release of mast cell mediators, as impeding the impacts imposed by these mediators could reduce the severity of COVID-19.
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Affiliation(s)
- Bahareh Hafezi
- Department of Clinical Science, School of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad 9177948974, Iran; (B.H.); (N.K.)
| | - Lily Chan
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada; (L.C.); (J.P.K.); (Y.M.)
| | - Jason P. Knapp
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada; (L.C.); (J.P.K.); (Y.M.)
| | - Negar Karimi
- Department of Clinical Science, School of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad 9177948974, Iran; (B.H.); (N.K.)
| | - Kimia Alizadeh
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA;
| | - Yeganeh Mehrani
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada; (L.C.); (J.P.K.); (Y.M.)
| | - Byram W. Bridle
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada; (L.C.); (J.P.K.); (Y.M.)
| | - Khalil Karimi
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada; (L.C.); (J.P.K.); (Y.M.)
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Hauser BM, Sangesland M, Denis KJS, Windsor IW, Feldman J, Lam EC, Kannegieter T, Balazs AB, Lingwood D, Schmidt AG. Rationally designed immunogens enable immune focusing to the SARS-CoV-2 receptor binding motif. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.15.435440. [PMID: 33758851 PMCID: PMC7987010 DOI: 10.1101/2021.03.15.435440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Eliciting antibodies to surface-exposed viral glycoproteins can lead to protective responses that ultimately control and prevent future infections. Targeting functionally conserved epitopes may help reduce the likelihood of viral escape and aid in preventing the spread of related viruses with pandemic potential. One such functionally conserved viral epitope is the site to which a receptor must bind to facilitate viral entry. Here, we leveraged rational immunogen design strategies to focus humoral responses to the receptor binding motif (RBM) on the SARS-CoV-2 spike. Using glycan engineering and epitope scaffolding, we find an improved targeting of the serum response to the RBM in context of SARS-CoV-2 spike imprinting. Furthermore, we observed a robust SARS-CoV-2-neutralizing serum response with increased potency against related sarbecoviruses, SARS-CoV, WIV1-CoV, RaTG13-CoV, and SHC014-CoV. Thus, RBM focusing is a promising strategy to elicit breadth across emerging sarbecoviruses and represents an adaptable design approach for targeting conserved epitopes on other viral glycoproteins. ONE SENTENCE SUMMARY SARS-CoV-2 immune focusing with engineered immunogens.
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Muecksch F, Wise H, Templeton K, Batchelor B, Squires M, McCance K, Jarvis L, Malloy K, Furrie E, Richardson C, MacGuire J, Godber I, Burns A, Mavin S, Zhang F, Schmidt F, Bieniasz P, Jenks S, Hatziioannou T. Longitudinal variation in SARS-CoV-2 antibody levels and emergence of viral variants: implications for the ability of serological assays to predict immunity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.07.02.21259939. [PMID: 34268524 PMCID: PMC8282113 DOI: 10.1101/2021.07.02.21259939] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Serological assays are being deployed to monitor antibody responses in SARS-CoV-2 convalescents and vaccine recipients. There is a need to determine whether such assays can predict immunity, as antibody levels wane and viral variants emerge. METHODS We measured antibodies in a cohort of SARS-CoV-2 infected patients using several high-throughput serological tests and functional neutralization assays. The effects of time and spike protein sequence variation on the performance and predictive value of the various assays was assessed. FINDINGS Neutralizing antibody titers decreased over the first few months post-infection but stabilized thereafter, at about 30% of the level observed shortly after infection. Serological assays commonly used to measure antibodies against SARS-CoV-2 displayed a range of sensitivities that declined to varying extents over time. Quantitative measurements generated by serological assays based on the spike protein were better at predicting neutralizing antibody titers than assays based on nucleocapsid, but performance was variable and manufacturer positivity thresholds were not able to predict the presence or absence of detectable neutralizing activity. Even though there was some deterioration in correlation between serological measurements and functional neutralization activity, some assays maintained an ability to predict neutralizing titers, even against variants of concern. INTERPRETATION The ability of high throughput serological assays to predict neutralizing antibody titers is likely crucial for evaluation of immunity at the population scale. These data will facilitate the selection of the most suitable assays as surrogates of functional neutralizing activity and suggest that such measurements may have utility in clinical practice.
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Affiliation(s)
- Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10065
| | - Helen Wise
- Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA
| | - Kate Templeton
- Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA
| | - Becky Batchelor
- Western General Hospital, Crewe Road South, Edinburgh, EH4 2XU
| | - Maria Squires
- Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA
| | - Kirsty McCance
- Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA
| | - Lisa Jarvis
- SNBTS Microbiology Reference Laboratory, The Jack Copland Centre, 52 Research Avenue North, Heriot Watt Research Park, Edinburgh, EH14 4AP
| | - Kristen Malloy
- SNBTS Microbiology Reference Laboratory, The Jack Copland Centre, 52 Research Avenue North, Heriot Watt Research Park, Edinburgh, EH14 4AP
| | - Elizabeth Furrie
- Ninewells Hospital and Medical School, NHS Tayside, Dundee, DD1 9SY
| | | | | | - Ian Godber
- Queen Elizabeth University Hospital, Govan Road, Glasgow, G51 4TF
| | - Alana Burns
- Queen Elizabeth University Hospital, Govan Road, Glasgow, G51 4TF
| | - Sally Mavin
- Scottish Microbiology Reference Laboratory, NHS Highland, Inverness, IV2 3UJ
| | - Fengwen Zhang
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10065
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10065
| | - Paul Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10065
- Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York NY 10065
| | - Sara Jenks
- Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA
| | - Theodora Hatziioannou
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10065
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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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46
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Ozer EA, Simons LM, Adewumi OM, Fowotade AA, Omoruyi EC, Adeniji JA, Dean TJ, Zayas J, Bhimalli PP, Ash MK, Godzik A, Schneider JR, Mamede JI, Taiwo BO, Hultquist JF, Lorenzo-Redondo R. Coincident rapid expansion of two SARS-CoV-2 lineages with enhanced infectivity in Nigeria. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.04.09.21255206. [PMID: 33880483 PMCID: PMC8057251 DOI: 10.1101/2021.04.09.21255206] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The emergence of new SARS-CoV-2 variants with enhanced transmissibility or decreased susceptibility to immune responses is a major threat to global efforts to end the coronavirus disease 2019 (COVID-19) pandemic. Disparities in viral genomic surveillance capabilities and efforts have resulted in gaps in our understanding of the viral population dynamics across the globe. Nigeria, despite having the largest population of any nation in Africa, has had relatively little SARS-CoV-2 sequence data made publicly available. Here we report the whole-genome sequences of 74 SARS-CoV-2 isolates collected from individuals in Oyo State, Nigeria in January 2021. Most isolates belonged to either the B.1.1.7 Alpha "variant of concern" or the B.1.525 Eta lineage, which is currently considered a "variant of interest" containing multiple spike protein mutations previously associated with enhanced transmissibility and possible immune escape. Nigeria has the highest reported frequency of the B.1.525 lineage globally with phylogenetic characteristics consistent with a recent monophyletic origin and rapid expansion. Spike protein from the B.1.525 lineage displayed both increased infectivity and decreased neutralization by convalescent sera compared to Spike proteins from other clades. These results, along with indications that the virus is outpacing the B.1.1.7 lineage in Nigeria, suggest that the B.1.525 lineage represents another "variant of concern" and further underline the importance of genomic surveillance in undersampled regions across the globe.
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Affiliation(s)
- Egon A. Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Institute for Global Health, Chicago, IL, USA
| | - Lacy M. Simons
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Institute for Global Health, Chicago, IL, USA
| | - Olubusuyi M. Adewumi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeola A. Fowotade
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Biorepository and Clinical Virology Laboratory, College of Medicine, University College Hospital, University of Ibadan, Ibadan, Nigeria
| | - Ewean C. Omoruyi
- Biorepository and Clinical Virology Laboratory, College of Medicine, University College Hospital, University of Ibadan, Ibadan, Nigeria
| | - Johnson A. Adeniji
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Taylor J. Dean
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Institute for Global Health, Chicago, IL, USA
| | - Janet Zayas
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Pavan P. Bhimalli
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Michelle K. Ash
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Adam Godzik
- University of California Riverside School of Medicine, Biosciences Division, Riverside, CA, USA
| | - Jeffrey R. Schneider
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - João I. Mamede
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Babafemi O. Taiwo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Judd F. Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Institute for Global Health, Chicago, IL, USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Institute for Global Health, Chicago, IL, USA
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47
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Garritsen A, Scholzen A, van den Nieuwenhof DWA, Smits APF, Datema ES, van Galen LS, Kouwijzer MLCE. Two-tiered SARS-CoV-2 seroconversion screening in the Netherlands and stability of nucleocapsid, spike protein domain 1 and neutralizing antibodies. Infect Dis (Lond) 2021; 53:498-512. [PMID: 33684020 PMCID: PMC7967720 DOI: 10.1080/23744235.2021.1893378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/28/2021] [Accepted: 02/17/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Serological testing in the COVID-19 pandemic is mainly implemented to gain sero-epidemiological data, but can also retrospectively inform about suspected SARS-CoV-2 infection. METHOD We verified and applied a two-tiered testing strategy combining a SARS-CoV-2 receptor-binding domain (RBD)-specific lateral flow assay (LFA) with a nucleocapsid protein (NCP) IgG ELISA to assess seroconversion in n = 7241 individuals. The majority had experienced symptoms consistent with COVID-19, but had no access to RT-PCR testing. Longitudinal follow-up in n = 97 LFA + individuals was performed up to 20 weeks after initial infection using NCP and spike protein S1 domain (S1) IgG ELISAs and a surrogate virus neutralization test (sVNT). RESULTS Individuals reporting symptoms from January 2020 onwards showed seroconversion, as did a considerable proportion of asymptomatic individuals. Seroconversion for symptomatic and asymptomatic individuals was higher in an area with a known infection cluster compared to a low incidence area. Overall, 94% of individuals with a positive IgG result by LFA were confirmed by NCP ELISA. The proportion of ELISA-confirmed LFA results declined over time, in line with contracting NCP IgG titres during longitudinal follow-up. Neutralizing antibody activity was considerably more stable than S1 and NCP IgG titres, and both reach a plateau after approximately 100 d. The sVNT proved to be not only highly specific, but also more sensitive than the specificity-focussed two-tiered serology approach. CONCLUSIONS Our results demonstrate the high specificity of two-tiered serology testing and highlight the sVNT used as a valuable tool to support modelling of SARS-CoV-2 transmission dynamics, complement molecular testing and provide relevant information to individuals.
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48
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Giron CC, Laaksonen A, Barroso da Silva FL. Up State of the SARS-COV-2 Spike Homotrimer Favors an Increased Virulence for New Variants. FRONTIERS IN MEDICAL TECHNOLOGY 2021; 3:694347. [PMID: 35047936 PMCID: PMC8757851 DOI: 10.3389/fmedt.2021.694347] [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: 04/13/2021] [Accepted: 05/31/2021] [Indexed: 12/23/2022] Open
Abstract
The COVID-19 pandemic has spread worldwide. However, as soon as the first vaccines-the only scientifically verified and efficient therapeutic option thus far-were released, mutations combined into variants of SARS-CoV-2 that are more transmissible and virulent emerged, raising doubts about their efficiency. This study aims to explain possible molecular mechanisms responsible for the increased transmissibility and the increased rate of hospitalizations related to the new variants. A combination of theoretical methods was employed. Constant-pH Monte Carlo simulations were carried out to quantify the stability of several spike trimeric structures at different conformational states and the free energy of interactions between the receptor-binding domain (RBD) and angiotensin-converting enzyme II (ACE2) for the most worrying variants. Electrostatic epitopes were mapped using the PROCEEDpKa method. These analyses showed that the increased virulence is more likely to be due to the improved stability to the S trimer in the opened state, in which the virus can interact with the cellular receptor, ACE2, rather than due to alterations in the complexation RBD-ACE2, since the difference observed in the free energy values was small (although more attractive in general). Conversely, the South African/Beta variant (B.1.351), compared with the SARS-CoV-2 wild type (wt), is much more stable in the opened state with one or two RBDs in the up position than in the closed state with three RBDs in the down position favoring the infection. Such results contribute to understanding the natural history of disease and indicate possible strategies for developing new therapeutic molecules and adjusting the vaccine doses for higher B-cell antibody production.
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Affiliation(s)
- Carolina Corrêa Giron
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Hospital de Clínicas, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Aatto Laaksonen
- Arrhenius Laboratory, Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, China
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Iasi, Romania
- Division of Energy Science, Department of Engineering Sciences and Mathematics, Luleå University of Technology, Luleå, Sweden
| | - Fernando Luís Barroso da Silva
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States
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49
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Tada T, Dcosta BM, Samanovic MI, Herati RS, Cornelius A, Zhou H, Vaill A, Kazmierski W, Mulligan MJ, Landau NR. Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. mBio 2021; 12:e0069621. [PMID: 34060334 PMCID: PMC8262901 DOI: 10.1128/mbio.00696-21] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/28/2021] [Indexed: 12/21/2022] Open
Abstract
The increasing prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with spike protein mutations raises concerns that antibodies elicited by natural infection or vaccination and therapeutic monoclonal antibodies will become less effective. We show that convalescent-phase sera neutralize pseudotyped viruses with the B.1.1.7, B.1.351, B.1.1.248, COH.20G/677H, 20A.EU2, and mink cluster 5 spike proteins with only a minor loss in titer. Similarly, antibodies elicited by Pfizer BNT162b2 vaccination neutralized B.1.351 and B.1.1.248 with only a 3-fold decrease in titer, an effect attributable to E484K. Analysis of the Regeneron monoclonal antibodies REGN10933 and REGN10987 showed that REGN10933 has lost neutralizing activity against the B.1.351 and B.1.1.248 pseudotyped viruses, and the cocktail is 9- to 15-fold decreased in titer. These findings suggest that antibodies elicited by natural infection and by the Pfizer vaccine will maintain protection against the B.1.1.7, B.1.351, and B.1.1.248 variants but that monoclonal antibody therapy may be less effective for patients infected with B.1.351 or B.1.1.248 SARS-CoV-2. IMPORTANCE The rapid evolution of SARS-CoV-2 variants has raised concerns with regard to their potential to escape from vaccine-elicited antibodies and anti-spike protein monoclonal antibodies. We report here on an analysis of sera from recovered patients and vaccinated individuals and on neutralization by Regeneron therapeutic monoclonal antibodies. Overall, the variants were neutralized nearly as well as the wild-type pseudotyped virus. The B.1.351 variant was somewhat resistant to vaccine-elicited antibodies but was still readily neutralized. One of the two Regeneron therapeutic monoclonal antibodies seems to have lost most of its activity against the B.1.351 variant, raising concerns that the combination therapy might be less effective for some patients. The findings should alleviate concerns that vaccines will become ineffective but suggest the importance of continued surveillance for potential new variants.
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Affiliation(s)
- Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Belinda M. Dcosta
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Marie I. Samanovic
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Ramin S. Herati
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Amber Cornelius
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Hao Zhou
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Ada Vaill
- Biohaven Pharmaceuticals, Inc., New Haven, Connecticut, USA
| | - Wes Kazmierski
- Biohaven Pharmaceuticals, Inc., New Haven, Connecticut, USA
| | - Mark J. Mulligan
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Nathaniel R. Landau
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
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50
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Laiton-Donato K, Usme-Ciro JA, Franco-Muñoz C, Álvarez-Díaz DA, Ruiz-Moreno HA, Reales-González J, Prada DA, Corchuelo S, Herrera-Sepúlveda MT, Naizaque J, Santamaría G, Wiesner M, Walteros DM, Ospina Martínez ML, Mercado-Reyes M. Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. Front Med (Lausanne) 2021; 8:697605. [PMID: 34262921 PMCID: PMC8273171 DOI: 10.3389/fmed.2021.697605] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/31/2021] [Indexed: 12/02/2022] Open
Abstract
COVID-19 pandemics has led to genetic diversification of SARS-CoV-2 and the appearance of variants with potential impact in transmissibility and viral escape from acquired immunity. We report a new and highly divergent lineage containing 21 distinctive mutations (10 non-synonymous, eight synonymous, and three substitutions in non-coding regions). The amino acid changes L249S and E484K located at the CTD and RBD of the Spike protein could be of special interest due to their potential biological role in the virus-host relationship. Further studies are required for monitoring the epidemiologic impact of this new lineage.
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Affiliation(s)
| | - Jose A. Usme-Ciro
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
- Centro de Investigación en Salud para el Trópico - CIST, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta, Colombia
| | - Carlos Franco-Muñoz
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Diego A. Álvarez-Díaz
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | | | | | - Diego Andrés Prada
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Sheryll Corchuelo
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | | | - Julian Naizaque
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Gerardo Santamaría
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Magdalena Wiesner
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Diana Marcela Walteros
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | | | - Marcela Mercado-Reyes
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
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