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Geanes ES, McLennan R, Pierce SH, Menden HL, Paul O, Sampath V, Bradley T. SARS-CoV-2 envelope protein regulates innate immune tolerance. iScience 2024; 27:109975. [PMID: 38827398 PMCID: PMC11140213 DOI: 10.1016/j.isci.2024.109975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/01/2024] [Accepted: 05/10/2024] [Indexed: 06/04/2024] Open
Abstract
Severe COVID-19 often leads to secondary infections and sepsis that contribute to long hospital stays and mortality. However, our understanding of the precise immune mechanisms driving severe complications after SARS-CoV-2 infection remains incompletely understood. Here, we provide evidence that the SARS-CoV-2 envelope (E) protein initiates innate immune inflammation, via toll-like receptor 2 signaling, and establishes a sustained state of innate immune tolerance following initial activation. Monocytes in this tolerant state exhibit reduced responsiveness to secondary stimuli, releasing lower levels of cytokines and chemokines. Mice exposed to E protein before secondary lipopolysaccharide challenge show diminished pro-inflammatory cytokine expression in the lung, indicating that E protein drives this tolerant state in vivo. These findings highlight the potential of the SARS-CoV-2 E protein to induce innate immune tolerance, contributing to long-term immune dysfunction that could lead to susceptibility to subsequent infections, and uncovers therapeutic targets aimed at restoring immune function following SARS-CoV-2 infection.
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Affiliation(s)
- Eric S. Geanes
- Genomic Medicine Center, Children’s Mercy Research Institute, Kansas City, MO, USA
| | - Rebecca McLennan
- Genomic Medicine Center, Children’s Mercy Research Institute, Kansas City, MO, USA
| | - Stephen H. Pierce
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Heather L. Menden
- Division of Neonatology, Children’s Mercy Research Institute, Kansas City, MO, USA
| | - Oishi Paul
- Genomic Medicine Center, Children’s Mercy Research Institute, Kansas City, MO, USA
| | - Venkatesh Sampath
- Division of Neonatology, Children’s Mercy Research Institute, Kansas City, MO, USA
- Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA
| | - Todd Bradley
- Genomic Medicine Center, Children’s Mercy Research Institute, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
- Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA
- Department of Pediatrics, University of Kansas Medical Center, Kansas City, MO, USA
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2
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Abdul-Kareem HH, Al-Maqtoofi MY, Burghal AA. Impact of COVID-19 vaccination on saliva immune barriers: IgA, lysozyme, and lactoferrin. Arch Virol 2023; 168:293. [PMID: 37973637 DOI: 10.1007/s00705-023-05914-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/28/2023] [Indexed: 11/19/2023]
Abstract
Understanding the role of salivary constituents, such as lactoferrin, lysozyme, and secretory immunoglobulin A (sIgA), in immune protection and defense mechanisms against microbial invasion and colonization of the airways is important in light of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. The salivary immune barrier in individuals affected by COVID-19 may contribute to disease prognosis. Thus, the aim of the present review is to evaluate the effect of COVID-19 vaccines on the immunological composition of saliva. IgA antibodies generated by vaccination can neutralize the virus at mucosal surfaces, whereas antimicrobial peptides, such as lysozyme and lactoferrin, have broad-spectrum antimicrobial activity. Collectively, these components contribute to the protective immune response of the oral cavity and may help minimize viral transmission as well as the severity of COVID-19. Measuring the levels of these components in the saliva of COVID-19-vaccinated individuals can help in evaluating the vaccine's ability to induce mucosal immunity, and it might also provide insights into whether saliva can be used in diagnostics or surveillance for monitoring immune responses following vaccination. This also has implications for viral transmission.
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Affiliation(s)
| | - Marwan Y Al-Maqtoofi
- Biology Department, College of Science University of Basrah, Basrah, 61001, Iraq.
| | - Ahmed A Burghal
- Biology Department, College of Science University of Basrah, Basrah, 61001, Iraq
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3
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López-Monteon A, Balderas-Caballero AE, Domínguez-Guillén JA, Romero-Ramírez H, Baltierra-Uribe SL, Ramos-Ligonio A. Pfizer-BioNTech vaccine induces the production of cross-reactive antibodies against Trypanosoma cruzi proteins: A preliminary study. Trop Med Int Health 2023; 28:384-390. [PMID: 36879355 DOI: 10.1111/tmi.13869] [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: 03/08/2023]
Abstract
OBJECTIVE To evaluate the presence of cross-reactivity by anti-severe acute respiratory syndrome coronavirus 2 antibodies induced by the Pfizer-BioNTech vaccine against Trypanosoma cruzi proteins in a screening test. METHODS Forty-three serum samples were obtained from personnel at the Hospital General Naval de Alta Especialidad in Mexico City who received one or two doses of the vaccine and were tested for T. cruzi infection using four tests: two 'in house' enzyme-linked immunosorbent assays (ELISAs), a commercial ELISA diagnostic kit and an immunoblot test. RESULTS IgG antibodies against the T. cruzi proteins were present in the serum of unvaccinated subjects and subjects who had received one or two doses of the vaccine. The positivity of the samples against T. cruzi was ruled out by means of a Western Blot assay, where all samples were negative for T. cruzi. CONCLUSION The data suggest that people convalescing from coronavirus disease 2019 and those who received the Pfizer-BioNTech vaccine exhibit cross-reactive antibodies against T. cruzi antigens in ELISA assays.
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Affiliation(s)
- Aracely López-Monteon
- LADISER Inmunología y Biología Molecular, Facultad de Ciencias Químicas, Universidad Veracruzana, Orizaba, Mexico.,Asociacion Chagas con Ciencia y Conocimiento A.C. Orizaba, Veracruz, Mexico
| | | | | | | | | | - Angel Ramos-Ligonio
- LADISER Inmunología y Biología Molecular, Facultad de Ciencias Químicas, Universidad Veracruzana, Orizaba, Mexico.,Asociacion Chagas con Ciencia y Conocimiento A.C. Orizaba, Veracruz, Mexico
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4
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Hauser BM, Feldman J, Sangesland M, Ronsard L, St Denis KJ, Sheehan ML, Cao Y, Boucau J, Windsor IW, Cheng AH, Vu ML, Cardoso MR, Kannegieter T, Balazs AB, Lingwood D, Garcia-Beltran WF, Schmidt AG. Cross-reactive SARS-CoV-2 epitope targeted across donors informs immunogen design. Cell Rep Med 2022; 3:100834. [PMID: 36423634 PMCID: PMC9663748 DOI: 10.1016/j.xcrm.2022.100834] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/07/2022] [Accepted: 11/08/2022] [Indexed: 11/17/2022]
Abstract
The emergence of the antigenically distinct and highly transmissible Omicron variant highlights the possibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune escape due to viral evolution. This continued evolution, along with the possible introduction of new sarbecoviruses from zoonotic reservoirs, may evade host immunity elicited by current SARS-CoV-2 vaccines. Identifying cross-reactive antibodies and defining their epitope(s) can provide templates for rational immunogen design strategies for next-generation vaccines. Here, we characterize the receptor-binding-domain-directed, cross-reactive humoral repertoire across 10 human vaccinated donors. We identify cross-reactive antibodies from diverse gene rearrangements targeting two conserved receptor-binding domain epitopes. An engineered immunogen enriches antibody responses to one of these conserved epitopes in mice with pre-existing SARS-CoV-2 immunity; elicited responses neutralize SARS-CoV-2, variants, and related sarbecoviruses. These data show how immune focusing to a conserved epitope targeted by human cross-reactive antibodies may guide pan-sarbecovirus vaccine development, providing a template for identifying such epitopes and translating to immunogen design.
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Affiliation(s)
- Blake M Hauser
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Maya Sangesland
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Larance Ronsard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Kerri J St Denis
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Maegan L Sheehan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Yi Cao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ian W Windsor
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Laboratory of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Agnes H Cheng
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Mya L Vu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Ty Kannegieter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Wilfredo F Garcia-Beltran
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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5
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Jutel M, Torres MJ, Palomares O, Akdis CA, Eiwegger T, Untersmayr E, Barber D, Zemelka-Wiacek M, Kosowska A, Palmer E, Vieths S, Mahler V, Canonica WG, Nadeau K, Shamji MH, Agache I. COVID-19 vaccination in patients receiving allergen immunotherapy (AIT) or biologicals-EAACI recommendations. Allergy 2022; 77:2313-2336. [PMID: 35147230 PMCID: PMC9111382 DOI: 10.1111/all.15252] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/05/2022] [Accepted: 01/12/2022] [Indexed: 12/16/2022]
Abstract
Immune modulation is a key therapeutic approach for allergic diseases, asthma and autoimmunity. It can be achieved in an antigen-specific manner via allergen immunotherapy (AIT) or in an endotype-driven approach using biologicals that target the major pathways of the type 2 (T2) immune response: immunoglobulin (Ig)E, interleukin (IL)-5 and IL-4/IL-13 or non-type 2 response: anti-cytokine antibodies and B-cell depletion via anti-CD20. Coronavirus disease 2019 (COVID-19) vaccination provides an excellent opportunity to tackle the global pandemics and is currently being applied in an accelerated rhythm worldwide. The vaccine exerts its effects through immune modulation, induces and amplifies the response against the severe acute respiratory syndrome coronavirus (SARS-CoV-2). Thus, as there may be a discernible interference between these treatment modalities, recommendations on how they should be applied in sequence are expected. The European Academy of Allergy and Clinical Immunology (EAACI) assembled an expert panel under its Research and Outreach Committee (ROC). This expert panel evaluated the evidence and have formulated recommendations on the administration of COVID-19 vaccine in patients with allergic diseases and asthma receiving AIT or biologicals. The panel also formulated recommendations for COVID-19 vaccine in association with biologicals targeting the type 1 or type 3 immune response. In formulating recommendations, the panel evaluated the mechanisms of COVID-19 infection, of COVID-19 vaccine, of AIT and of biologicals and considered the data published for other anti-infectious vaccines administered concurrently with AIT or biologicals.
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Affiliation(s)
- Marek Jutel
- Department of Clinical Immunology, Wroclaw Medical University, Wroclaw, Poland
- ALL-MED Medical Research Institute, Wroclaw, Poland
| | - Maria J Torres
- Allergy Unit, Regional University Hospital of Malaga, IBIMA-UMA-ARADyAL-BIONAND, Malaga, Spain
| | - Oscar Palomares
- Department of Biochemistry and Molecular Biology, School of Chemistry, Complutense University of Madrid, Madrid, Spain
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Zurich, Switzerland
- Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - Thomas Eiwegger
- Division of Immunology and Allergy, The Department of 13 Pediatrics, Food Allergy and Anaphylaxis Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Translational Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Eva Untersmayr
- Institute of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Domingo Barber
- Facultad de Medicina, Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA), Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | | | - Anna Kosowska
- Department of Clinical Immunology, Wroclaw Medical University, Wroclaw, Poland
- ALL-MED Medical Research Institute, Wroclaw, Poland
| | - Elizabeth Palmer
- Immunomodulation and Tolerance Group, Allergy and Clinical Immunology, Inflammation, Repair and Development, National Heart and Lung Institute, Imperial College London. MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK
| | - Stefan Vieths
- Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Langen, Germany
| | | | - Walter G Canonica
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- Personalized Medicine Asthma, & Allergy Center-IRCCS Humanitas Research Hospital, Milan, Italy
| | - Kari Nadeau
- Division of Pulmonary, Allergy and Critical Care Medicine, Dept of Medicine, Stanford, California, USA
| | - Mohamed H Shamji
- Immunomodulation and Tolerance Group, Allergy and Clinical Immunology, Inflammation, Repair and Development, National Heart and Lung Institute, Imperial College London. MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK
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Cojocaru C, Cojocaru E, Turcanu A, Zaharia D. Clinical challenges of SARS‑CoV‑2 variants (Review). Exp Ther Med 2022; 23:416. [PMID: 35601074 PMCID: PMC9117961 DOI: 10.3892/etm.2022.11343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/08/2022] [Indexed: 11/06/2022] Open
Abstract
Since the first cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, there have been challenges recognizing the clinical features of SARS-CoV-2 and identifying therapeutic options. This has been compounded by viral mutations that affect clinical response and primary epidemiological indicators. Multiple variants of SARS-CoV-2 have been identified and classified on the basis of nomenclature implemented by scientific organizations and the World Health Organisation (WHO). A total of five variants of concern (VOCs) have been identified to date. The present study aimed to analyse clinical and epidemiological features of each variant. Based on these characteristics, predictions were made about potential future evolution. Considering the time and location of SARS-CoV-2 VOC emergence, it was hypothesised that mutations were not due to pressure caused by the vaccines introduced in December 2020 but were dependent on natural characteristics of the virus. In the process of adapting to the human body, SARS-CoV-2 is expected to undergo evolution to become more contagious but less deadly. SARS-CoV-2 was hypothesized to continue spread through isolated epidemic outbreaks due to the unimmunized population, mostly unvaccinated children and adults, and for coronaviruses to continue to present a public health problem.
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Affiliation(s)
- Cristian Cojocaru
- Medical III Department, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Elena Cojocaru
- Morpho‑Functional Sciences II Department, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Adina Turcanu
- Medical III Department, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Dragos Zaharia
- Department 4 Cardio‑thoracic Pathology, Faculty of Medicine, University of Medicine and Pharmacy ‘Carol Davila’, 050471 Bucharest, Romania
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7
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Yogev O, Weissbrod O, Battistoni G, Bressan D, Naamti A, Falciatori I, Berkyurek AC, Rasnic R, Hosmillo M, Ilan S, Grossman I, McCormick L, Honeycutt CC, Johnston T, Gagne M, Douek DC, Goodfellow I, Hannon GJ, Erlich Y. Genome wide screen of RNAi molecules against SARS-CoV-2 creates a broadly potent prophylaxis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.04.12.488010. [PMID: 35441162 PMCID: PMC9016640 DOI: 10.1101/2022.04.12.488010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Expanding the arsenal of prophylactic approaches against SARS-CoV-2 is of utmost importance, specifically those strategies that are resistant to antigenic drift in Spike. Here, we conducted a screen with over 16,000 RNAi triggers against the SARS-CoV-2 genome using a massively parallel assay to identify hyper-potent siRNAs. We selected 10 candidates for in vitro validation and found five siRNAs that exhibited hyper-potent activity with IC50<20pM and strong neutralisation in live virus experiments. We further enhanced the activity by combinatorial pairing of the siRNA candidates to develop siRNA cocktails and found that these cocktails are active against multiple types of variants of concern (VOC). We examined over 2,000 possible mutations to the siRNA target sites using saturation mutagenesis and identified broad protection against future variants. Finally, we demonstrated that intranasal administration of the siRNA cocktail effectively attenuates clinical signs and viral measures of disease in the Syrian hamster model. Our results pave the way to development of an additional layer of antiviral prophylaxis that is orthogonal to vaccines and monoclonal antibodies.
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Affiliation(s)
- Ohad Yogev
- Eleven Therapeutics, Cambridge, United Kingdom
| | | | - Giorgia Battistoni
- Eleven Therapeutics, Cambridge, United Kingdom
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, United Kingdom
| | - Dario Bressan
- Eleven Therapeutics, Cambridge, United Kingdom
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, United Kingdom
| | - Adi Naamti
- Eleven Therapeutics, Cambridge, United Kingdom
| | | | | | | | - Myra Hosmillo
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
| | | | | | - Lauren McCormick
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christopher C. Honeycutt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Timothy Johnston
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ian Goodfellow
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
| | - Gregory J. Hannon
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, United Kingdom
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8
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Stefanizzi P, Larocca AMV, Martinelli A, Soldano S, Dell'Aera M, Migliore G, Germinario CA, Vimercati L, Tafuri S, Bianchi FP. Immune response to one dose of BNT162b2 mRNA Covid-19 vaccine followed by SARS-CoV-2 infection: An Italian prospective observational study. Vaccine 2022; 40:1805-1809. [PMID: 35190212 PMCID: PMC8847089 DOI: 10.1016/j.vaccine.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 12/23/2021] [Accepted: 02/01/2022] [Indexed: 11/22/2022]
Abstract
INTRODUCTION A mass vaccination campaign against SARS-CoV-2 was initiated in European countries on December 27, 2020. This study compared the antibody response in a sample of healthcare workers (HCWs) who, after the first dose of the BNT162b2 mRNA vaccine, were infected with SARS-CoV-2 (infection group) with the response in a control group of HCWs immunized with two doses (vaccine group). METHODS This two-arm observational cohort study was carried out using routine health surveillance data obtained from HCWs at Bari Policlinico General Hospital (Italy). The antibody response was determined infection group and vaccine group. RESULTS Among the 100 HCWs, 25 (25.0%) were in the infection group and 75 (75.0%) in the full-vaccine group. At the serological evaluation, all of the HCWs tested positive, with a geometric mean titer (GMT) of 7106.8 (95 %CI = 5628.5-8973.4) and a statistically significant difference (p < 0.0001) between the infection group (GMT = 2139.7; 95 %CI = 1310.4-3493.6) and the vaccine group (GMT = 10603.6; 95 %CI = 8698.0-12926.8). DISCUSSION Our results shed light on the vaccine response of individuals in different risk categories. It also emphasizes the need for the continued use by HCWs of PPE and good practices during the window between the first and second anti-SARS-CoV-2 vaccinations.
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Affiliation(s)
- Pasquale Stefanizzi
- Department of Biomedical Science and Human Oncology, Aldo Moro University of Bari, Bari, Italy
| | | | - Andrea Martinelli
- Department of Biomedical Science and Human Oncology, Aldo Moro University of Bari, Bari, Italy
| | - Savino Soldano
- Hospital Direction, Bari Policlinico General Hospital, Bari, Italy
| | - Maria Dell'Aera
- Pharmacy Department, Bari Policlinico General Hospital, Bari, Italy
| | | | | | - Luigi Vimercati
- Interdisciplinary Department of Medicine, Aldo Moro University of Bari, Bari, Italy
| | - Silvio Tafuri
- Department of Biomedical Science and Human Oncology, Aldo Moro University of Bari, Bari, Italy.
| | - Francesco Paolo Bianchi
- Department of Biomedical Science and Human Oncology, Aldo Moro University of Bari, Bari, Italy
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9
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Yu Y, Esposito D, Kang Z, Lu J, Remaley AT, De Giorgi V, Chen LN, West K, Cao L. mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. Sci Rep 2022; 12:2628. [PMID: 35173254 PMCID: PMC8850441 DOI: 10.1038/s41598-022-06629-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 01/17/2022] [Indexed: 02/07/2023] Open
Abstract
Several variants of SARS-CoV-2 have emerged. Those with mutations in the angiotensin-converting enzyme (ACE2) receptor binding domain (RBD) are associated with increased transmission and severity. In this study, we developed both antibody quantification and functional neutralization assays. Analyses of both COVID-19 convalescent and diagnostic cohorts strongly support the use of RBD antibody levels as an excellent surrogate to biochemical neutralization activities. Data further revealed that the samples from mRNA vaccinated individuals had a median of 17 times higher RBD antibody levels and a similar degree of increased neutralization activities against RBD-ACE2 binding than those from natural infections. Our data showed that N501Y RBD had fivefold higher ACE2 binding than the original variant. While some antisera from naturally infected subjects had substantially reduced neutralization ability against N501Y RBD, all blood samples from vaccinated individuals were highly effective in neutralizing it. Thus, our data indicates that mRNA vaccination may generate more neutralizing RBD antibodies than natural immunity. It further suggests a potential need to maintain high RBD antibody levels to control the more infectious SARS-CoV-2 variants.
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Affiliation(s)
- Yunkai Yu
- Genetics Branch, Center for Cancer Research, National Cancer Institute, 37 Convent Dr. MSC 4265, Bldg 37, Rm 6040, Bethesda, MD, 20892, USA
| | - Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Zhigang Kang
- Genetics Branch, Center for Cancer Research, National Cancer Institute, 37 Convent Dr. MSC 4265, Bldg 37, Rm 6040, Bethesda, MD, 20892, USA
| | - Jianming Lu
- Codex BioSolutions, Inc, Gaithersburg, MD, USA
| | - Alan T Remaley
- Lipoprotein Metabolism Section, National Heat, Lung, and Blood Institute, Bethesda, MD, USA
| | - Valeria De Giorgi
- Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Leonard N Chen
- Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Kamille West
- Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Liang Cao
- Genetics Branch, Center for Cancer Research, National Cancer Institute, 37 Convent Dr. MSC 4265, Bldg 37, Rm 6040, Bethesda, MD, 20892, USA.
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10
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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: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [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. SARS-CoV-2 genomic surveillance has been important for informing pandemic responses but many regions remain under-sampled, limiting knowledge of circulating strains. Here, the authors sequence 378 isolates from Nigeria and identify two strains that appear to be important locally though globally uncommon.
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11
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Rabiul Islam M, Nasreen W, Anjum R, Shahriar M, Roy A, Dhama K, Ahmed Bhuiyan M. Characteristics of the SARS-CoV-2 Omicron (B.1.1.529) Variant and Emerging Impact on Global Public Health. CLINICAL PATHOLOGY (THOUSAND OAKS, VENTURA COUNTY, CALIF.) 2022; 15:2632010X221124908. [PMID: 36147794 PMCID: PMC9490387 DOI: 10.1177/2632010x221124908] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/22/2022] [Indexed: 01/07/2023]
Abstract
The discovery of the SARS-CoV-2 Omicron (B.1.1.529) variant has sparked alarm globally because of its rapid rate of infection and trespassing acquired immunity due to vaccination or natural infection. This heavily mutated variant is rapidly spreading around the world. Infected individuals with the Omicron variant may suffer from flu-like symptoms, and infected with the Delta variant frequently report low oxygen levels, high pulse rates, and a loss of smell and taste. Also, the Omicron variant causes asymptomatic or mild disease so far, and not any severe illness as like Delta, and this new variant has a 15% to 80% reduced risk of hospitalization than the Delta variant. Scientists are worried about the possibility of escaping the immunity by the Omicron variants and subvariants among fully vaccinated and recovered COVID-19 patients. Two doses of available vaccines are found to be partially ineffective in protecting this new variant, therefore, the third dose as a booster is recommended to enhance antibody level. Moreover, some antiviral drugs significantly reduce hospitalization or death among mild to severe COVID-19 patients. All authorized antiviral drugs are effective against viral replication for most SARS-CoV-2 variants, and particularly some monoclonal antibodies may not now be effective in treating COVID-19 patients. There is an urgent need to update existing vaccines, develop more effective and newer vaccines as well as additional monoclonal antibodies to counter Omicron. Therefore, along with close monitoring of Omicron characteristics, the present study suggests that health safety guidelines, mass immunization, early diagnosis, and search for effective antiviral drugs should be the approaches to fight against newer SARS-CoV-2 variants.
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Affiliation(s)
- Md Rabiul Islam
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Waheeda Nasreen
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Ramisa Anjum
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Mohammad Shahriar
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Arpita Roy
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
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12
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Miller IF, Metcalf CJE. Assessing the risk of vaccine-driven virulence evolution in SARS-CoV-2. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211021. [PMID: 35070341 PMCID: PMC8728167 DOI: 10.1098/rsos.211021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
The evolution of SARS-CoV-2 virulence, or lethality, threatens to exacerbate the burden of COVID-19 on society. How might COVID-19 vaccines alter selection for increased SARS-CoV-2 virulence? Framing current evidence surrounding SARS-CoV-2 biology and COVID-19 vaccines in the context of evolutionary theory indicates that prospects for virulence evolution remain uncertain. However, differential effects of vaccinal immunity on transmission and disease severity between respiratory compartments could select for increased virulence. To bound expectations for this outcome, we analyse an evo-epidemiological model. Synthesizing model predictions with vaccine efficacy data, we conclude that while vaccine-driven virulence remains a theoretical possibility, the risk is low if vaccines provide sustained robust protection against infection. Furthermore, we found that any increases in transmission concomitant with increases in virulence would be unlikely to threaten prospects for herd immunity in a highly immunized population. Given that virulence evolution would nevertheless impact unvaccinated individuals and populations with low vaccination rates, it is important to achieve high vaccination rates worldwide and ensure that vaccinal immunity provides robust protection against both infection and disease, potentially through the use of booster doses.
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Affiliation(s)
- Ian F. Miller
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - C. Jessica E. Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA
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13
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Günl F, Mecate-Zambrano A, Rehländer S, Hinse S, Ludwig S, Brunotte L. Shooting at a Moving Target-Effectiveness and Emerging Challenges for SARS-CoV-2 Vaccine Development. Vaccines (Basel) 2021; 9:1052. [PMID: 34696160 PMCID: PMC8540924 DOI: 10.3390/vaccines9101052] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 02/06/2023] Open
Abstract
Since late 2019 the newly emerged pandemic SARS-CoV-2, the causative agent of COVID-19, has hit the world with recurring waves of infections necessitating the global implementation of non-pharmaceutical interventions, including strict social distancing rules, the wearing of masks and the isolation of infected individuals in order to restrict virus transmissions and prevent the breakdown of our healthcare systems. These measures are not only challenging on an economic level but also have a strong impact on social lifestyles. Using traditional and novel technologies, highly efficient vaccines against SARS-CoV-2 were developed and underwent rapid clinical evaluation and approval to accelerate the immunization of the world population, aiming to end the pandemic and return to normality. However, the emergence of virus variants with improved transmission, enhanced fitness and partial immune escape from the first generation of vaccines poses new challenges, which are currently being addressed by scientists and pharmaceutical companies all over the world. In this ongoing pandemic, the evaluation of SARS-CoV-2 vaccines underlies diverse unpredictable dynamics, posed by the first broad application of the mRNA vaccine technology and their compliance, the occurrence of unexpected side effects and the rapid emergence of variations in the viral antigen. However, despite these hurdles, we conclude that the available SARS-CoV-2 vaccines are very safe and efficiently protect from severe COVID-19 and are thereby the most powerful tools to prevent further harm to our healthcare systems, economics and individual lives. This review summarizes the unprecedented pathways of vaccine development and approval during the ongoing SARS-CoV-2 pandemic. We focus on the real-world effectiveness and unexpected positive and negative side effects of the available vaccines and summarize the timeline of the applied adaptations to the recommended vaccination strategies in the light of emerging virus variants. Finally, we highlight upcoming strategies to improve the next generations of SARS-CoV-2 vaccines.
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Affiliation(s)
- Franziska Günl
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
| | - Angeles Mecate-Zambrano
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
- Interdisciplinary Centre for Clinical Research (IZKF), Medical Faculty, University of Münster, 48149 Münster, Germany
| | - Selina Rehländer
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
| | - Saskia Hinse
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
| | - Stephan Ludwig
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
- Interdisciplinary Centre for Clinical Research (IZKF), Medical Faculty, University of Münster, 48149 Münster, Germany
| | - Linda Brunotte
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
- Interdisciplinary Centre for Clinical Research (IZKF), Medical Faculty, University of Münster, 48149 Münster, Germany
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14
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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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15
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Wheeler SE, Shurin GV, Yost M, Anderson A, Pinto L, Wells A, Shurin MR. Differential Antibody Response to mRNA COVID-19 Vaccines in Healthy Subjects. Microbiol Spectr 2021; 9:e0034121. [PMID: 34346750 PMCID: PMC8552678 DOI: 10.1128/spectrum.00341-21] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/13/2021] [Indexed: 12/20/2022] Open
Abstract
Knowledge about development and duration of virus-specific antibodies after COVID-19 vaccination is important for understanding how to limit the pandemic via vaccination in different populations and societies. However, the clinical utility of postvaccination testing of antibody response and selection of targeted SARS-CoV-2 antigen(s) has not been established. The results of such testing from clinical teams independent from vaccine manufacturers are also limited. Here, we report the initial results of an ongoing clinical study on evaluation of antibody response to four different SARS-CoV-2 antigens after first and second dose of Pfizer and Moderna mRNA vaccines and at later time points. We revealed a peak of antibody induction after the vaccine boosting dose with a gradual decline of antibody levels at later time. Anti-nucleocapsid antibody was not induced by spike protein-encoding vaccines and this may continue to serve as a marker of previous SARS-CoV-2 infection. No differences between the two vaccines in terms of antibody response were revealed. Age and gender dependencies were determined to be minimal within the healthy adult (but not aged) population. Our results suggest that postvaccination testing of antibody response is an important and feasible tool for following people after vaccination and selecting individuals who might require a third dose of vaccine at an earlier time point or persons who may not need a second dose due to previous SARS-CoV-2 infection. IMPORTANCE Now that authorized vaccines for COVID-19 have been widely used, it is important to understand how they induce antivirus antibodies, which antigens are targeted, how long antibodies circulate, and how personal health conditions and age may affect this humoral immunity. Here, we report induction and time course of multiple anti-SARS-CoV-2 antibody responses in healthy individuals immunized with Pfizer and Moderna mRNA vaccines. We also determined the age and gender dependence of the antibody response and compared antibody levels to responses seen in those who have recovered from COVID-19. Our results suggest the importance of screening for antibody response to multiple antigens after vaccination in order to reveal individuals who require early and late additional boosting and those who may not need second dose due to prior SARS-CoV-2 infection.
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Affiliation(s)
- Sarah E. Wheeler
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Galina V. Shurin
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Mary Yost
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Adam Anderson
- Bio-Rad Laboratories, Inc., Benicia, California, USA
| | - Lisa Pinto
- Bio-Rad Laboratories, Inc., Benicia, California, USA
| | - Alan Wells
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Michael R. Shurin
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
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16
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Hasenkrug KJ, Feldmann F, Myers L, Santiago ML, Guo K, Barrett BS, Mickens KL, Carmody A, Okumura A, Rao D, Collins MM, Messer RJ, Lovaglio J, Shaia C, Rosenke R, van Doremalen N, Clancy C, Saturday G, Hanley P, Smith BJ, Meade-White K, Shupert WL, Hawman DW, Feldmann H. Recovery from Acute SARS-CoV-2 Infection and Development of Anamnestic Immune Responses in T Cell-Depleted Rhesus Macaques. mBio 2021; 12:e0150321. [PMID: 34311582 PMCID: PMC8406331 DOI: 10.1128/mbio.01503-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/21/2021] [Indexed: 12/16/2022] Open
Abstract
Severe coronavirus disease 2019 (COVID-19) has been associated with T cell lymphopenia, but no causal effect of T cell deficiency on disease severity has been established. To investigate the specific role of T cells in recovery from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, we studied rhesus macaques that were depleted of either CD4+, CD8+, or both T cell subsets prior to infection. Peak virus loads were similar in all groups, but the resolution of virus in the T cell-depleted animals was slightly delayed compared to that in controls. The T cell-depleted groups developed virus-neutralizing antibody responses and class switched to IgG. When reinfected 6 weeks later, the T cell-depleted animals showed anamnestic immune responses characterized by rapid induction of high-titer virus-neutralizing antibodies, faster control of virus loads, and reduced clinical signs. These results indicate that while T cells play a role in the recovery of rhesus macaques from acute SARS-CoV-2 infections, their depletion does not induce severe disease, and T cells do not account for the natural resistance of rhesus macaques to severe COVID-19. Neither primed CD4+ nor CD8+ T cells appeared critical for immunoglobulin class switching, the development of immunological memory, or protection from a second infection. IMPORTANCE Patients with severe COVID-19 often have decreased numbers of T cells, a cell type important in fighting most viral infections. However, it is not known whether the loss of T cells contributes to severe COVID-19 or is a consequence of it. We studied rhesus macaques, which develop only mild COVID-19, similar to most humans. Experimental depletion of T cells slightly prolonged their clearance of virus, but there was no increase in disease severity. Furthermore, they were able to develop protection from a second infection and produced antibodies capable of neutralizing the virus. They also developed immunological memory, which allows a much stronger and more rapid response upon a second infection. These results suggest that T cells are not critical for recovery from acute SARS-CoV-2 infections in this model and point toward B cell responses and antibodies as the essential mediators of protection from re-exposure.
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Affiliation(s)
- Kim J. Hasenkrug
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Lara Myers
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Mario L. Santiago
- Departments of Medicine, Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kejun Guo
- Departments of Medicine, Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Bradley S. Barrett
- Departments of Medicine, Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kaylee L. Mickens
- Departments of Medicine, Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Aaron Carmody
- Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Atsushi Okumura
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Deepashri Rao
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Madison M. Collins
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Ronald J. Messer
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Jamie Lovaglio
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Carl Shaia
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Rebecca Rosenke
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Neeltje van Doremalen
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Chad Clancy
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Greg Saturday
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Patrick Hanley
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Brian J. Smith
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Kimberly Meade-White
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - W. Lesley Shupert
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - David W. Hawman
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Heinz Feldmann
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
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17
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Singh J, Pandit P, McArthur AG, Banerjee A, Mossman K. Evolutionary trajectory of SARS-CoV-2 and emerging variants. Virol J 2021; 18:166. [PMID: 34389034 PMCID: PMC8361246 DOI: 10.1186/s12985-021-01633-w] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022] Open
Abstract
The emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and more recently, the independent evolution of multiple SARS-CoV-2 variants has generated renewed interest in virus evolution and cross-species transmission. While all known human coronaviruses (HCoVs) are speculated to have originated in animals, very little is known about their evolutionary history and factors that enable some CoVs to co-exist with humans as low pathogenic and endemic infections (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1), while others, such as SARS-CoV, MERS-CoV and SARS-CoV-2 have evolved to cause severe disease. In this review, we highlight the origins of all known HCoVs and map positively selected for mutations within HCoV proteins to discuss the evolutionary trajectory of SARS-CoV-2. Furthermore, we discuss emerging mutations within SARS-CoV-2 and variants of concern (VOC), along with highlighting the demonstrated or speculated impact of these mutations on virus transmission, pathogenicity, and neutralization by natural or vaccine-mediated immunity.
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Affiliation(s)
- Jalen Singh
- School of Interdisciplinary Science, McMaster University, Hamilton, ON, Canada
| | - Pranav Pandit
- EpiCenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
| | - Karen Mossman
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
- Department of Medicine, McMaster University, Hamilton, ON, Canada.
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada.
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18
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Gittens CL. Remote HRI: a Methodology for Maintaining COVID-19 Physical Distancing and Human Interaction Requirements in HRI Studies. INFORMATION SYSTEMS FRONTIERS : A JOURNAL OF RESEARCH AND INNOVATION 2021; 26:1-16. [PMID: 34366703 PMCID: PMC8335710 DOI: 10.1007/s10796-021-10162-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/16/2021] [Indexed: 06/01/2023]
Abstract
Observing how humans and robots interact is an integral part of understanding how they can effectively coexist. This ability to undertake these observations was taken for granted before the COVID-19 pandemic restricted the possibilities of performing HRI study-based interactions. We explore the problem of how HRI research can occur in a setting where physical separation is the most reliable way of preventing disease transmission. We present the results of an exploratory experiment that suggests Remote-HRI (R-HRI) studies may be a viable alternative to traditional face-to-face HRI studies. An R-HRI study minimizes or eliminates in-person interaction between the experimenter and the participant and implements a new protocol for interacting with the robot to minimize physical contact. Our results showed that participants interacting with the robot remotely experienced a higher cognitive workload, which may be due to minor cultural and technical factors. Importantly, however, we also found that whether participants interacted with the robot in-person (but socially distanced) or remotely over a network, their experience, perception of, and attitude towards the robot were unaffected.
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Affiliation(s)
- Curtis L. Gittens
- The University of the West Indies Cave Hill Campus, P.O. Box 64, Bridgetown, Barbados
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19
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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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20
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Abstract
Since emerging into the human population in late 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has reached across the globe to infect >80 million people. The coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 can range in severity from mild and asymptomatic to severe and fatal. Identifying risk factors for adverse outcomes in COVID-19 is a major challenge. In the context of the existing HIV-1 pandemic, whether COVID-19 disproportionately burdens people living with HIV-1 infection (PLWH) is unclear. The following discussion highlights pressing questions and challenges in the HIV-1 and SARS-CoV-2 syndemic, including (i) age, sex, and race as drivers of COVID-19 severity; (ii) whether chronic inflammation common in PLWH influences immune response; (iii) whether disease severity and trajectory models for COVID-19 ought to be calibrated for PLWH; (iv) vaccine considerations, and finally, (v) long-term health outcomes in PLWH that are further burdened by coinfection with SARS-CoV-2.
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Affiliation(s)
- Monty Montano
- Boston Claude D. Pepper Older Americans Independence Center, Boston, Massachusetts, USA
- Harvard University Center for AIDS Research, Boston, Massachusetts, USA
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21
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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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22
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Bhattarai N, Baral P, Gerstman BS, Chapagain PP. Structural and Dynamical Differences in the Spike Protein RBD in the SARS-CoV-2 Variants B.1.1.7 and B.1.351. J Phys Chem B 2021; 125:7101-7107. [PMID: 34110159 PMCID: PMC8204914 DOI: 10.1021/acs.jpcb.1c01626] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/25/2021] [Indexed: 12/13/2022]
Abstract
The novel coronavirus (SARS-CoV-2) pandemic that started in late 2019 is responsible for hundreds of millions of cases worldwide and millions of fatalities. Though vaccines are available, the virus is mutating to form new strains among which are the variants B.1.1.7 and B.1.351 that demonstrate increased transmissivity and infectivity. In this study, we performed molecular dynamics simulations to explore the role of the mutations in the interaction of the virus spike protein receptor binding domain (RBD) with the host receptor ACE2. We find that the hydrogen bond networks are rearranged in the variants and also that new hydrogen bonds are established between the RBD and ACE2 as a result of mutations. We investigated three variants: the wild-type (WT), B.1.1.7, and B.1.351. We find that the B.1.351 variant (also known as 501Y.V2) shows larger flexibility in the RBD loop segment involving residue K484, yet the RBD-ACE2 complex shows higher stability. Mutations that allow a more flexible interface that can result in a more stable complex may be a factor contributing to the increased infectivity of the mutated variants.
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Affiliation(s)
- Nisha Bhattarai
- Department of Physics, Florida
International University, Miami, Florida 33199, United
States
| | - Prabin Baral
- Department of Physics, Florida
International University, Miami, Florida 33199, United
States
| | - Bernard S. Gerstman
- Department of Physics, Florida
International University, Miami, Florida 33199, United
States
- Biomolecular Sciences Institute, Florida
International University, Miami, Florida 33199, United
States
| | - Prem P. Chapagain
- Department of Physics, Florida
International University, Miami, Florida 33199, United
States
- Biomolecular Sciences Institute, Florida
International University, Miami, Florida 33199, United
States
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23
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Lee E, Oh JE. Humoral Immunity against SARS-CoV-2 and the Impact on COVID-19 Pathogenesis. Mol Cells 2021; 44:392-400. [PMID: 34059562 PMCID: PMC8245316 DOI: 10.14348/molcells.2021.0075] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 02/07/2023] Open
Abstract
It has been more than a year since severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) first emerged. Many studies have provided insights into the various aspects of the immune response in coronavirus disease 2019 (COVID-19). Especially for antibody treatment and vaccine development, humoral immunity to SARS-CoV-2 has been studied extensively, though there is still much that is unknown and controversial. Here, we introduce key discoveries on the humoral immune responses in COVID-19, including the immune dynamics of antibody responses and correlations with disease severity, neutralizing antibodies and their cross-reactivity, how long the antibody and memory B-cell responses last, aberrant autoreactive antibodies generated in COVID-19 patients, and the efficacy of currently available therapeutic antibodies and vaccines against circulating SARS-CoV-2 variants, and highlight gaps in the current knowledge.
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Affiliation(s)
- Eunjin Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Ji Eun Oh
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- BioMedical Research Center, KAIST, Daejeon 34141, Korea
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24
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Jung MK, Shin EC. Phenotypes and Functions of SARS-CoV-2-Reactive T Cells. Mol Cells 2021; 44:401-407. [PMID: 34120892 PMCID: PMC8245315 DOI: 10.14348/molcells.2021.0079] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/09/2021] [Accepted: 05/12/2021] [Indexed: 12/27/2022] Open
Abstract
Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), which is an ongoing pandemic disease. SARS-CoV-2-specific CD4+ and CD8+ T-cell responses have been detected and characterized not only in COVID-19 patients and convalescents, but also unexposed individuals. Here, we review the phenotypes and functions of SARS-CoV-2-specific T cells in COVID-19 patients and the relationships between SARS-CoV-2-specific T-cell responses and COVID-19 severity. In addition, we describe the phenotypes and functions of SARS-CoV-2-specific memory T cells after recovery from COVID-19 and discuss the presence of SARS-CoV-2-reactive T cells in unexposed individuals and SARS-CoV-2-specific T-cell responses elicited by COVID-19 vaccines. A better understanding of T-cell responses is important for effective control of the current COVID-19 pandemic.
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Affiliation(s)
- Min Kyung Jung
- Laboratory of Immunology and Infectious Diseases, Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Eui-Cheol Shin
- Laboratory of Immunology and Infectious Diseases, Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- The Center for Epidemic Preparedness, KAIST, Daejeon 34141, Korea
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25
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Pucci F, Rooman M. Prediction and Evolution of the Molecular Fitness of SARS-CoV-2 Variants: Introducing SpikePro. Viruses 2021; 13:v13050935. [PMID: 34070055 DOI: 10.1101/2021.04.11.439322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 05/25/2023] Open
Abstract
The understanding of the molecular mechanisms driving the fitness of the SARS-CoV-2 virus and its mutational evolution is still a critical issue. We built a simplified computational model, called SpikePro, to predict the SARS-CoV-2 fitness from the amino acid sequence and structure of the spike protein. It contains three contributions: the inter-human transmissibility of the virus predicted from the stability of the spike protein, the infectivity computed in terms of the affinity of the spike protein for the ACE2 receptor, and the ability of the virus to escape from the human immune response based on the binding affinity of the spike protein for a set of neutralizing antibodies. Our model reproduces well the available experimental, epidemiological and clinical data on the impact of variants on the biophysical characteristics of the virus. For example, it is able to identify circulating viral strains that, by increasing their fitness, recently became dominant at the population level. SpikePro is a useful, freely available instrument which predicts rapidly and with good accuracy the dangerousness of new viral strains. It can be integrated and play a fundamental role in the genomic surveillance programs of the SARS-CoV-2 virus that, despite all the efforts, remain time-consuming and expensive.
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Affiliation(s)
- Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
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26
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Shakhany MQ, Salimifard K. Predicting the dynamical behavior of COVID-19 epidemic and the effect of control strategies. CHAOS, SOLITONS, AND FRACTALS 2021; 146:110823. [PMID: 33727767 PMCID: PMC7951801 DOI: 10.1016/j.chaos.2021.110823] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 05/03/2023]
Abstract
This paper uses transformed subsystem of ordinary differential equation s e i r s model, with vital dynamics of birth and death rates, and temporary immunity (of infectious individuals or vaccinated susceptible) to evaluate the disease-free D F E X ¯ D F E , and endemic E E X ¯ E E equilibrium points, using the Jacobian matrix eigenvalues λ i of both disease-free equilibrium X ¯ D F E , and endemic equilibrium X ¯ E E for COVID-19 infectious disease to show S, E, I, and R ratios to the population in time-series. In order to obtain the disease-free equilibrium point, globally asymptotically stable ( R 0 ≤ 1 ), the effect of control strategies has been added to the model (in order to decrease transmission rate β , and reinforce susceptible to recovered flow), to determine how much they are effective, in a mass immunization program. The effect of transmission rates β (from S to E) and α (from R to S) varies, and when vaccination effect ρ , is added to the model, disease-free equilibrium X ¯ D F E is globally asymptotically stable, and the endemic equilibrium point X ¯ E E , is locally unstable. The initial conditions for the decrease in transmission rates of β and α , reached the corresponding disease-free equilibrium X ¯ D F E locally unstable, and globally asymptotically stable for endemic equilibrium X ¯ E E . The initial conditions for the decrease in transmission rate s β and α , and increase in ρ , reached the corresponding disease-free equilibrium X ¯ D F E globally asymptotically stable, and locally unstable in endemic equilibrium X ¯ E E .
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Affiliation(s)
- Mohammad Qaleh Shakhany
- Persian Gulf University, Computational Intelligence & Intelligent Research Group, Mahini Street, Bushehr 75169-13798
| | - Khodakaram Salimifard
- Persian Gulf University, Computational Intelligence & Intelligent Research Group, Mahini Street, Bushehr 75169-13798
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27
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Li J, Giabbanelli P. Returning to a Normal Life via COVID-19 Vaccines in the United States: A Large-scale Agent-Based Simulation Study. JMIR Med Inform 2021; 9:e27419. [PMID: 33872188 PMCID: PMC8086790 DOI: 10.2196/27419] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/21/2021] [Accepted: 04/14/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND In 2020, COVID-19 has claimed more than 300,000 deaths in the United States alone. Although nonpharmaceutical interventions were implemented by federal and state governments in the United States, these efforts have failed to contain the virus. Following the Food and Drug Administration's approval of two COVID-19 vaccines, however, the hope for the return to normalcy has been renewed. This hope rests on an unprecedented nationwide vaccine campaign, which faces many logistical challenges and is also contingent on several factors whose values are currently unknown. OBJECTIVE We study the effectiveness of a nationwide vaccine campaign in response to different vaccine efficacies, the willingness of the population to be vaccinated, and the daily vaccine capacity under two different federal plans. To characterize the possible outcomes most accurately, we also account for the interactions between nonpharmaceutical interventions and vaccines through 6 scenarios that capture a range of possible impacts from nonpharmaceutical interventions. METHODS We used large-scale, cloud-based, agent-based simulations by implementing the vaccination campaign using COVASIM, an open-source agent-based model for COVID-19 that has been used in several peer-reviewed studies and accounts for individual heterogeneity and a multiplicity of contact networks. Several modifications to the parameters and simulation logic were made to better align the model with current evidence. We chose 6 nonpharmaceutical intervention scenarios and applied the vaccination intervention following both the plan proposed by Operation Warp Speed (former Trump administration) and the plan of one million vaccines per day, proposed by the Biden administration. We accounted for unknowns in vaccine efficacies and levels of population compliance by varying both parameters. For each experiment, the cumulative infection growth was fitted to a logistic growth model, and the carrying capacities and the growth rates were recorded. RESULTS For both vaccination plans and all nonpharmaceutical intervention scenarios, the presence of the vaccine intervention considerably lowers the total number of infections when life returns to normal, even when the population compliance to vaccines is as low as 20%. We noted an unintended consequence; given the vaccine availability estimates under both federal plans and the focus on vaccinating individuals by age categories, a significant reduction in nonpharmaceutical interventions results in a counterintuitive situation in which higher vaccine compliance then leads to more total infections. CONCLUSIONS Although potent, vaccines alone cannot effectively end the pandemic given the current availability estimates and the adopted vaccination strategy. Nonpharmaceutical interventions need to continue and be enforced to ensure high compliance so that the rate of immunity established by vaccination outpaces that induced by infections.
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Affiliation(s)
- Junjiang Li
- Department of Computer Science & Software Engineering, Miami University, Oxford, OH, United States
| | - Philippe Giabbanelli
- Department of Computer Science & Software Engineering, Miami University, Oxford, OH, United States
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28
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Hasenkrug KJ, Feldmann F, Myers L, Santiago ML, Guo K, Barrett BS, Mickens KL, Carmody A, Okumura A, Rao D, Collins MM, Messer RJ, Lovaglio J, Shaia C, Rosenke R, van Doremalen N, Clancy C, Saturday G, Hanley P, Smith B, Meade-White K, Shupert WL, Hawman DW, Feldmann H. Recovery from acute SARS-CoV-2 infection and development of anamnestic immune responses in T cell-depleted rhesus macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.02.438262. [PMID: 33821272 PMCID: PMC8020972 DOI: 10.1101/2021.04.02.438262] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
Abstract
Severe COVID-19 has been associated with T cell lymphopenia 1,2, but no causal effect of T cell deficiency on disease severity has been established. To investigate the specific role of T cells in recovery from SARS-CoV-2 infections we studied rhesus macaques that were depleted of either CD4+, CD8+ or both T cell subsets prior to infection. Peak virus loads were similar in all groups, but the resolution of virus in the T cell-depleted animals was slightly delayed compared to controls. The T cell-depleted groups developed virus-neutralizing antibody responses and also class-switched to IgG. When re-infected six weeks later, the T cell-depleted animals showed anamnestic immune responses characterized by rapid induction of high-titer virus-neutralizing antibodies, faster control of virus loads and reduced clinical signs. These results indicate that while T cells play a role in the recovery of rhesus macaques from acute SARS-CoV-2 infections, their depletion does not induce severe disease, and T cells do not account for the natural resistance of rhesus macaques to severe COVID-19. Neither primed CD4+ or CD8+ T cells appeared critical for immunoglobulin class switching, the development of immunological memory or protection from a second infection.
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Affiliation(s)
- Kim J. Hasenkrug
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Lara Myers
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Mario L. Santiago
- Departments of Medicine, Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Kejun Guo
- Departments of Medicine, Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Bradley S. Barrett
- Departments of Medicine, Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Kaylee L. Mickens
- Departments of Medicine, Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Aaron Carmody
- Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Atsushi Okumura
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Deepashri Rao
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Madison M. Collins
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Ronald J. Messer
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jamie Lovaglio
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Carl Shaia
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Rebecca Rosenke
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Neeltje van Doremalen
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Chad Clancy
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Greg Saturday
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Patrick Hanley
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Brian Smith
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kimberly Meade-White
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - W. Lesley Shupert
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - David W. Hawman
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Heinz Feldmann
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
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29
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33791698 DOI: 10.1101/2021.03.24.436620] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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 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 as 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 therapeutic monoclonal antibodies will remain protective against the B.1.526 variants. The findings further support the value of wide-spread vaccination.
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30
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Walls AC, Miranda MC, Pham MN, Schäfer A, Greaney A, Arunachalam PS, Navarro MJ, Tortorici MA, Rogers K, O'Connor MA, Shireff L, Ferrell DE, Brunette N, Kepl E, Bowen J, Zepeda SK, Starr T, Hsieh CL, Fiala B, Wrenn S, Pettie D, Sydeman C, Johnson M, Blackstone A, Ravichandran R, Ogohara C, Carter L, Tilles SW, Rappuoli R, O'Hagan DT, Van Der Most R, Van Voorhis WC, McLellan JS, Kleanthous H, Sheahan TP, Fuller DH, Villinger F, Bloom J, Pulendran B, Baric R, King N, Veesler D. Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.15.435528. [PMID: 33758839 PMCID: PMC7986998 DOI: 10.1101/2021.03.15.435528] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Understanding the ability of SARS-CoV-2 vaccine-elicited antibodies to neutralize and protect against emerging variants of concern and other sarbecoviruses is key for guiding vaccine development decisions and public health policies. We show that a clinical stage multivalent SARS-CoV-2 receptor-binding domain nanoparticle vaccine (SARS-CoV-2 RBD-NP) protects mice from SARS-CoV-2-induced disease after a single shot, indicating that the vaccine could allow dose-sparing. SARS-CoV-2 RBD-NP elicits high antibody titers in two non-human primate (NHP) models against multiple distinct RBD antigenic sites known to be recognized by neutralizing antibodies. We benchmarked NHP serum neutralizing activity elicited by RBD-NP against a lead prefusion-stabilized SARS-CoV-2 spike immunogen using a panel of single-residue spike mutants detected in clinical isolates as well as the B.1.1.7 and B.1.351 variants of concern. Polyclonal antibodies elicited by both vaccines are resilient to most RBD mutations tested, but the E484K substitution has similar negative consequences for neutralization, and exhibit modest but comparable neutralization breadth against distantly related sarbecoviruses. We demonstrate that mosaic and cocktail sarbecovirus RBD-NPs elicit broad sarbecovirus neutralizing activity, including against the SARS-CoV-2 B.1.351 variant, and protect mice against severe SARS-CoV challenge even in the absence of the SARS-CoV RBD in the vaccine. This study provides proof of principle that sarbecovirus RBD-NPs induce heterotypic protection and enables advancement of broadly protective sarbecovirus vaccines to the clinic.
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Affiliation(s)
- Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Marcos C Miranda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Minh N Pham
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Allison Greaney
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Mary-Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Kenneth Rogers
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA, 70560 USA
| | - Megan A O'Connor
- Washington National Primate Research Center, Seattle, WA 98121, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Lisa Shireff
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA, 70560 USA
| | - Douglas E Ferrell
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA, 70560 USA
| | - Natalie Brunette
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth Kepl
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - John Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Tyler Starr
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Samuel Wrenn
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Deleah Pettie
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Claire Sydeman
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Max Johnson
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alyssa Blackstone
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Cassandra Ogohara
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Sasha W Tilles
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | | | | | - Wesley C Van Voorhis
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Deborah H Fuller
- Washington National Primate Research Center, Seattle, WA 98121, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Francois Villinger
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA, 70560 USA
| | - Jesse Bloom
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Neil King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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31
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Santiago L, Uranga-Murillo I, Arias M, González-Ramírez AM, Macías-León J, Moreo E, Redrado S, García-García A, Taleb V, Lira-Navarrete E, Hurtado-Guerrero R, Aguilo N, del Mar Encabo-Berzosa M, Hidalgo S, Galvez EM, Ramirez-Labrada A, de Miguel D, Benito R, Miranda P, Fernández A, Domingo JM, Serrano L, Yuste C, Villanueva-Saz S, Paño-Pardo JR, Pardo J. Determination of the Concentration of IgG against the Spike Receptor-Binding Domain That Predicts the Viral Neutralizing Activity of Convalescent Plasma and Serum against SARS-CoV-2. BIOLOGY 2021; 10:208. [PMID: 33801808 PMCID: PMC8001978 DOI: 10.3390/biology10030208] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/01/2021] [Accepted: 03/06/2021] [Indexed: 12/22/2022]
Abstract
Several hundred millions of people have been diagnosed of coronavirus disease 2019 (COVID-19), causing millions of deaths and a high socioeconomic burden. SARS-CoV-2, the causative agent of COVID-19, induces both specific T- and B-cell responses, being antibodies against the virus detected a few days after infection. Passive immunization with hyperimmune plasma from convalescent patients has been proposed as a potentially useful treatment for COVID-19. Using an in-house quantitative ELISA test, we found that plasma from 177 convalescent donors contained IgG antibodies specific to the spike receptor-binding domain (RBD) of SARS-CoV-2, although at very different concentrations which correlated with previous disease severity and gender. Anti-RBD IgG plasma concentrations significantly correlated with the plasma viral neutralizing activity (VN) against SARS-CoV-2 in vitro. Similar results were found using an independent cohort of serum from 168 convalescent health workers. These results validate an in-house RBD IgG ELISA test in a large cohort of COVID-19 convalescent patients and indicate that plasma from all convalescent donors does not contain a high enough amount of anti-SARS-CoV-2-RBD neutralizing IgG to prevent SARS-CoV-2 infection in vitro. The use of quantitative anti-RBD IgG detection systems might help to predict the efficacy of the passive immunization using plasma from patients recovered from SARS-CoV-2.
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Affiliation(s)
- Llipsy Santiago
- Biomedical Research Centre of Aragón (CIBA), Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; (L.S.); (I.U.-M.); (S.H.); (D.d.M.); (R.B.)
| | - Iratxe Uranga-Murillo
- Biomedical Research Centre of Aragón (CIBA), Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; (L.S.); (I.U.-M.); (S.H.); (D.d.M.); (R.B.)
| | - Maykel Arias
- Instituto de Carboquímica (ICB), Consejo Superior de Investigaciones Científicas (CSIC), 50018 Zaragoza, Spain; (M.A.); (S.R.); (E.M.G.)
| | - Andrés Manuel González-Ramírez
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain; (A.M.G.-R.); (J.M.-L.); (A.G.-G.); (V.T.); (E.L.-N.); (R.H.-G.)
| | - Javier Macías-León
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain; (A.M.G.-R.); (J.M.-L.); (A.G.-G.); (V.T.); (E.L.-N.); (R.H.-G.)
| | - Eduardo Moreo
- Department Microbiology, Preventive Medicine and Public Health, University of Zaragoza, 50009 Zaragoza, Spain; (E.M.); (N.A.)
| | - Sergio Redrado
- Instituto de Carboquímica (ICB), Consejo Superior de Investigaciones Científicas (CSIC), 50018 Zaragoza, Spain; (M.A.); (S.R.); (E.M.G.)
| | - Ana García-García
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain; (A.M.G.-R.); (J.M.-L.); (A.G.-G.); (V.T.); (E.L.-N.); (R.H.-G.)
| | - Víctor Taleb
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain; (A.M.G.-R.); (J.M.-L.); (A.G.-G.); (V.T.); (E.L.-N.); (R.H.-G.)
| | - Erandi Lira-Navarrete
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain; (A.M.G.-R.); (J.M.-L.); (A.G.-G.); (V.T.); (E.L.-N.); (R.H.-G.)
| | - Ramón Hurtado-Guerrero
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain; (A.M.G.-R.); (J.M.-L.); (A.G.-G.); (V.T.); (E.L.-N.); (R.H.-G.)
- Aragon I+D Foundation (ARAID), 50018 Zaragoza, Spain
- Laboratorio de Microscopías Avanzada (LMA), Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Nacho Aguilo
- Department Microbiology, Preventive Medicine and Public Health, University of Zaragoza, 50009 Zaragoza, Spain; (E.M.); (N.A.)
| | | | - Sandra Hidalgo
- Biomedical Research Centre of Aragón (CIBA), Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; (L.S.); (I.U.-M.); (S.H.); (D.d.M.); (R.B.)
| | - Eva M. Galvez
- Instituto de Carboquímica (ICB), Consejo Superior de Investigaciones Científicas (CSIC), 50018 Zaragoza, Spain; (M.A.); (S.R.); (E.M.G.)
| | - Ariel Ramirez-Labrada
- Unidad de Nanotoxicología e Inmunotoxicología (UNATI), Biomedical Research Centre of Aragón (CIBA), Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain;
| | - Diego de Miguel
- Biomedical Research Centre of Aragón (CIBA), Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; (L.S.); (I.U.-M.); (S.H.); (D.d.M.); (R.B.)
| | - Rafael Benito
- Biomedical Research Centre of Aragón (CIBA), Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; (L.S.); (I.U.-M.); (S.H.); (D.d.M.); (R.B.)
- Department Microbiology, Preventive Medicine and Public Health, University of Zaragoza, 50009 Zaragoza, Spain; (E.M.); (N.A.)
- Servicio de Microbiología, Hospital Clinico Universitario Lozano Blesa, 50009 Zaragoza, Spain
| | - Patricia Miranda
- Banco de Sangre y Tejidos de Aragón, 50009 Zaragoza, Spain; (P.M.); (J.M.D.)
| | - Antonio Fernández
- Department Animal Pathology, University of Zaragoza, 50013 Zaragoza, Spain;
| | - José María Domingo
- Banco de Sangre y Tejidos de Aragón, 50009 Zaragoza, Spain; (P.M.); (J.M.D.)
| | - Laura Serrano
- Servicio de Prevención de Riesgos Laborales, Hospital Clínico Universitario Lozano Blesa, 50009 Zaragoza, Spain; (L.S.); (C.Y.)
| | - Cristina Yuste
- Servicio de Prevención de Riesgos Laborales, Hospital Clínico Universitario Lozano Blesa, 50009 Zaragoza, Spain; (L.S.); (C.Y.)
| | - Sergio Villanueva-Saz
- Department Pharmacology and Physiology, University of Zaragoza, 50013 Zaragoza, Spain;
| | - José Ramón Paño-Pardo
- Biomedical Research Centre of Aragón (CIBA), Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; (L.S.); (I.U.-M.); (S.H.); (D.d.M.); (R.B.)
- Servicio de Enfermedades Infecciosas, Hospital Clinico Universitario Lozano Blesa, 50009 Zaragoza, Spain
| | - Julián Pardo
- Biomedical Research Centre of Aragón (CIBA), Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; (L.S.); (I.U.-M.); (S.H.); (D.d.M.); (R.B.)
- Department Microbiology, Preventive Medicine and Public Health, University of Zaragoza, 50009 Zaragoza, Spain; (E.M.); (N.A.)
- Aragon I+D Foundation (ARAID), 50018 Zaragoza, Spain
- Centro de Investigación Biomédicaen Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 50018 Madrid, Spain
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Bashor L, Gagne RB, Bosco-Lauth A, Bowen R, Stenglein M, VandeWoude S. SARS-CoV-2 evolution in animals suggests mechanisms for rapid variant selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.05.434135. [PMID: 33758844 PMCID: PMC7987003 DOI: 10.1101/2021.03.05.434135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
SARS-CoV-2 spillback from humans into domestic and wild animals has been well-documented. We compared variants of cell culture-expanded SARS-CoV-2 inoculum and virus recovered from four species following experimental exposure. Five nonsynonymous changes in nsp12, S, N and M genes were near fixation in the inoculum, but reverted to wild-type sequences in RNA recovered from dogs, cats and hamsters within 1-3 days post-exposure. Fourteen emergent variants were detected in viruses recovered from animals, including substitutions at spike positions H69, N501, and D614, which also vary in human lineages of concern. The rapidity of in vitro and in vivo SARS-CoV-2 selection reveals residues with functional significance during host-switching, illustrating the potential for spillback reservoir hosts to accelerate evolution, and demonstrating plasticity of viral adaptation in animal models. ONE-SENTENCE SUMMARY SARS-CoV-2 variants rapidly arise in non-human hosts, revealing viral evolution and potential risk for human reinfection.
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Affiliation(s)
- Laura Bashor
- Department of Microbiology, Immunology, and Pathology, Colorado State University; Fort Collins, CO, 80523, USA
| | - Roderick B. Gagne
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine; Kennett Square, PA, 19348, USA
| | - Angela Bosco-Lauth
- Department of Biomedical Sciences, Colorado State University; Fort Collins, CO, 80523, USA
| | - Richard Bowen
- Department of Biomedical Sciences, Colorado State University; Fort Collins, CO, 80523, USA
| | - Mark Stenglein
- Department of Microbiology, Immunology, and Pathology, Colorado State University; Fort Collins, CO, 80523, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University; Fort Collins, CO, 80523, USA
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33
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Human Vaccines & Immunotherapeutics: news. Hum Vaccin Immunother 2021; 17:618-619. [PMID: 33734943 DOI: 10.1080/21645515.2021.1894892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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34
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Xu J, Xu K, Jung S, Conte A, Lieberman J, Muecksch F, Cetrulo Lorenzi JC, Park S, Wang Z, Tessarollo L, Bylund T, Chuang GY, Olia AS, Stephens T, Teng IT, Tsybovsky Y, Zhou T, Hatziioannou T, Bieniasz PD, Nussenzweig MC, Kwong PD, Casellas R. Multimeric nanobodies from camelid engineered mice and llamas potently neutralize SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33688659 DOI: 10.1101/2021.03.04.433768] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Since the start of the coronavirus disease-2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused more than 2 million deaths worldwide. Multiple vaccines have been deployed to date, but the continual evolution of the viral receptor-binding domain (RBD) has recently challenged their efficacy. In particular, SARS-CoV-2 variants originating in the U.K. (B.1.1.7), South Africa (B.1.351) and New York (B.1.526) have reduced neutralization activity from convalescent sera and compromised the efficacy of antibody cocktails that received emergency use authorization. Whereas vaccines can be updated periodically to account for emerging variants, complementary strategies are urgently needed to avert viral escape. One potential alternative is the use of camelid VHHs (also known as nanobodies), which due to their small size can recognize protein crevices that are inaccessible to conventional antibodies. Here, we isolate anti-RBD nanobodies from llamas and "nanomice" we engineered to produce VHHs cloned from alpacas, dromedaries and camels. Through binding assays and cryo-electron microscopy, we identified two sets of highly neutralizing nanobodies. The first group expresses VHHs that circumvent RBD antigenic drift by recognizing a region outside the ACE2-binding site that is conserved in coronaviruses but is not typically targeted by monoclonal antibodies. The second group is almost exclusively focused to the RBD-ACE2 interface and fails to neutralize pseudoviruses carrying the E484K or N501Y substitutions. Notably however, they do neutralize the RBD variants when expressed as homotrimers, rivaling the most potent antibodies produced to date against SARS-CoV-2. These findings demonstrate that multivalent nanobodies overcome SARS-CoV-2 variant mutations through two separate mechanisms: enhanced avidity for the ACE2 binding domain, and recognition of conserved epitopes largely inaccessible to human antibodies. Therefore, while new SARS-CoV-2 mutants will continue to emerge, nanobodies represent promising tools to prevent COVID-19 mortality when vaccines are compromised.
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35
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Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DDS, Mishra S, Crispim MAE, Sales FC, Hawryluk I, McCrone JT, Hulswit RJG, Franco LAM, Ramundo MS, de Jesus JG, Andrade PS, Coletti TM, Ferreira GM, Silva CAM, Manuli ER, Pereira RHM, Peixoto PS, Kraemer MU, Gaburo N, Camilo CDC, Hoeltgebaum H, Souza WM, Rocha EC, de Souza LM, de Pinho MC, Araujo LJT, Malta FSV, de Lima AB, Silva JDP, Zauli DAG, de S. Ferreira AC, Schnekenberg RP, Laydon DJ, Walker PGT, Schlüter HM, dos Santos ALP, Vidal MS, Del Caro VS, Filho RMF, dos Santos HM, Aguiar RS, Modena JLP, Nelson B, Hay JA, Monod M, Miscouridou X, Coupland H, Sonabend R, Vollmer M, Gandy A, Suchard MA, Bowden TA, Pond SLK, Wu CH, Ratmann O, Ferguson NM, Dye C, Loman NJ, Lemey P, Rambaut A, Fraiji NA, Carvalho MDPSS, Pybus OG, Flaxman S, Bhatt S, Sabino EC. Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.02.26.21252554. [PMID: 33688664 PMCID: PMC7941639 DOI: 10.1101/2021.02.26.21252554] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite high levels of previous infection there. Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around early November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.4-2.2 times more transmissible and 25-61% more likely to evade protective immunity elicited by previous infection with non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.
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Affiliation(s)
- Nuno R. Faria
- Department of Infectious Disease Epidemiology, Imperial College London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Zoology, University of Oxford, UK
| | - Thomas A. Mellan
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Charles Whittaker
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Ingra M. Claro
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Darlan da S. Candido
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Zoology, University of Oxford, UK
| | - Swapnil Mishra
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Myuki A. E. Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
| | - Flavia C. Sales
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Iwona Hawryluk
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - John T. McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Ruben J. G. Hulswit
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Lucas A. M. Franco
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mariana S. Ramundo
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Jaqueline G. de Jesus
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Pamela S. Andrade
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Thais M. Coletti
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Giulia M. Ferreira
- Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Camila A. M. Silva
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Erika R. Manuli
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | - Pedro S. Peixoto
- Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | | | | | | | | | - William M. Souza
- Virology Research Centre, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Esmenia C. Rocha
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Leandro M. de Souza
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mariana C. de Pinho
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Leonardo J. T Araujo
- Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil
| | | | | | | | | | | | | | - Daniel J. Laydon
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | | | | | | | | | | | | | | | - Renato S. Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - José L. P. Modena
- Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
| | - Bruce Nelson
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - James A. Hay
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, USA
- Center for Communicable Disease Dynamics, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Melodie Monod
- Department of Mathematics, Imperial College London, UK
| | | | - Helen Coupland
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Raphael Sonabend
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Michaela Vollmer
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Axel Gandy
- Department of Mathematics, Imperial College London, UK
| | - Marc A. Suchard
- Department of Biomathematics, Department of Biostatistics and Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Sergei L. K. Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, USA
| | - Chieh-Hsi Wu
- Mathematical Sciences, University of Southampton, Southampton, UK
| | | | - Neil M. Ferguson
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | | | - Nick J. Loman
- Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Nelson A. Fraiji
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria Clínica, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Maria do P. S. S. Carvalho
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria da Presidência, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, UK
| | - Seth Flaxman
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Samir Bhatt
- Department of Infectious Disease Epidemiology, Imperial College London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Denmark
| | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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Affiliation(s)
- John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York
| | - Paul A Offit
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia
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Wang L, Zhou T, Zhang Y, Yang ES, Schramm CA, Shi W, Pegu A, Oloninyi OK, Ransier A, Darko S, Narpala SR, Hatcher C, Martinez DR, Tsybovsky Y, Phung E, Abiona OM, Cale EM, Chang LA, Corbett KS, DiPiazza AT, Gordon IJ, Leung K, Liu T, Mason RD, Nazzari A, Novik L, Olia AS, Doria-Rose NA, Stephens T, Stringham CD, Talana CA, Teng IT, Wagner D, Widge AT, Zhang B, Roederer M, Ledgerwood JE, Ruckwardt TJ, Gaudinski MR, Baric RS, Graham BS, McDermott AB, Douek DC, Kwong PD, Mascola JR, Sullivan NJ, Misasi J. Antibodies with potent and broad neutralizing activity against antigenically diverse and highly transmissible SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.25.432969. [PMID: 33655252 PMCID: PMC7924272 DOI: 10.1101/2021.02.25.432969] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The emergence of highly transmissible SARS-CoV-2 variants of concern (VOC) that are resistant to therapeutic antibodies highlights the need for continuing discovery of broadly reactive antibodies. We identify four receptor-binding domain targeting antibodies from three early-outbreak convalescent donors with potent neutralizing activity against 12 variants including the B.1.1.7 and B.1.351 VOCs. Two of them are ultrapotent, with sub-nanomolar neutralization titers (IC50 <0.0006 to 0.0102 μ g/mL; IC80 < 0.0006 to 0.0251 μ g/mL). We define the structural and functional determinants of binding for all four VOC-targeting antibodies, and show that combinations of two antibodies decrease the in vitro generation of escape mutants, suggesting potential means to mitigate resistance development. These results define the basis of therapeutic cocktails against VOCs and suggest that targeted boosting of existing immunity may increase vaccine breadth against VOCs.
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Affiliation(s)
- Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chaim A. Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Olamide K. Oloninyi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy Ransier
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samuel Darko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sandeep R. Narpala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christian Hatcher
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David R. Martinez
- Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Emily Phung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Olubukola M. Abiona
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evan M. Cale
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren A. Chang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kizzmekia S. Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anthony T. DiPiazza
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ingelise J. Gordon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tracy Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rosemarie D. Mason
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra Nazzari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura Novik
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam S. Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole A. Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Christopher D. Stringham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chloe Adrienna Talana
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Danielle Wagner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alicia T. Widge
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julie E. Ledgerwood
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tracy J. Ruckwardt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Martin R. Gaudinski
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ralph S. Baric
- Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Barney S. Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian B. McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nancy J. Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John Misasi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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38
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Hodcroft EB, Domman DB, Snyder DJ, Oguntuyo KY, Van Diest M, Densmore KH, Schwalm KC, Femling J, Carroll JL, Scott RS, Whyte MM, Edwards MW, Hull NC, Kevil CG, Vanchiere JA, Lee B, Dinwiddie DL, Cooper VS, Kamil JP. Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.02.12.21251658. [PMID: 33594385 PMCID: PMC7885944 DOI: 10.1101/2021.02.12.21251658] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S) plays critical roles in host cell entry. Non-synonymous substitutions affecting S are not uncommon and have become fixed in a number of SARS-CoV-2 lineages. A subset of such mutations enable escape from neutralizing antibodies or are thought to enhance transmission through mechanisms such as increased affinity for the cell entry receptor, angiotensin-converting enzyme 2 (ACE2). Independent genomic surveillance programs based in New Mexico and Louisiana contemporaneously detected the rapid rise of numerous clade 20G (lineage B.1.2) infections carrying a Q677P substitution in S. The variant was first detected in the US on October 23, yet between 01 Dec 2020 and 19 Jan 2021 it rose to represent 27.8% and 11.3% of all SARS-CoV-2 genomes sequenced from Louisiana and New Mexico, respectively. Q677P cases have been detected predominantly in the south central and southwest United States; as of 03 Feb 2021, GISAID data show 499 viral sequences of this variant from the USA. Phylogenetic analyses revealed the independent evolution and spread of at least six distinct Q677H sub-lineages, with first collection dates ranging from mid-August to late November 2020. Four 677H clades from clade 20G (B.1.2), 20A (B.1.234), and 20B (B.1.1.220, and B.1.1.222) each contain roughly 100 or fewer sequenced cases, while a distinct pair of clade 20G clusters are represented by 754 and 298 cases, respectively. Although sampling bias and founder effects may have contributed to the rise of S:677 polymorphic variants, the proximity of this position to the polybasic cleavage site at the S1/S2 boundary are consistent with its potential functional relevance during cell entry, suggesting parallel evolution of a trait that may confer an advantage in spread or transmission. Taken together, our findings demonstrate simultaneous convergent evolution, thus providing an impetus to further evaluate S:677 polymorphisms for effects on proteolytic processing, cell tropism, and transmissibility.
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Affiliation(s)
- Emma B Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
| | - Daryl B Domman
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Daniel J Snyder
- Microbial Genome Sequencing Center, LLC, Pittsburgh, PA, USA
| | | | - Maarten Van Diest
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
| | - Kenneth H Densmore
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
| | - Kurt C Schwalm
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Jon Femling
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Jennifer L Carroll
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
| | - Rona S Scott
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
| | | | | | - Noah C Hull
- Wyoming Public Health Laboratory, Cheyenne, WY, USA
| | - Christopher G Kevil
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
| | - John A Vanchiere
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
| | - Benhur Lee
- Microbial Genome Sequencing Center, LLC, Pittsburgh, PA, USA
| | | | - Vaughn S Cooper
- University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Jeremy P Kamil
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
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39
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Lundstrom K. Viral Vectors for COVID-19 Vaccine Development. Viruses 2021; 13:317. [PMID: 33669550 PMCID: PMC7922679 DOI: 10.3390/v13020317] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 12/14/2022] Open
Abstract
Vaccine development against SARS-CoV-2 has been fierce due to the devastating COVID-19 pandemic and has included all potential approaches for providing the global community with safe and efficient vaccine candidates in the shortest possible timeframe. Viral vectors have played a central role especially using adenovirus-based vectors. Additionally, other viral vectors based on vaccinia viruses, measles viruses, rhabdoviruses, influenza viruses and lentiviruses have been subjected to vaccine development. Self-amplifying RNA virus vectors have been utilized for lipid nanoparticle-based delivery of RNA as COVID-19 vaccines. Several adenovirus-based vaccine candidates have elicited strong immune responses in immunized animals and protection against challenges in mice and primates has been achieved. Moreover, adenovirus-based vaccine candidates have been subjected to phase I to III clinical trials. Recently, the simian adenovirus-based ChAdOx1 vector expressing the SARS-CoV-2 S spike protein was approved for use in humans in the UK.
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40
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Saunders KO, Lee E, Parks R, Martinez DR, Li D, Chen H, Edwards RJ, Gobeil S, Barr M, Mansouri K, Alam SM, Sutherland LL, Cai F, Sanzone AM, Berry M, Manne K, Kapingidza AB, Azoitei M, Tse LV, Scobey TD, Spreng RL, Rountree RW, DeMarco CT, Denny TN, Woods CW, Petzold EW, Oguin TH, Sempowski GD, Gagne M, Douek DC, Tomai MA, Fox CB, Seder R, Wiehe K, Weissman D, Pardi N, Acharya P, Andersen H, Lewis MG, Moore IN, Montefiori DC, Baric RS, Haynes BF. SARS-CoV-2 vaccination induces neutralizing antibodies against pandemic and pre-emergent SARS-related coronaviruses in monkeys. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.17.431492. [PMID: 33619494 PMCID: PMC7899458 DOI: 10.1101/2021.02.17.431492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Betacoronaviruses (betaCoVs) caused the severe acute respiratory syndrome (SARS) and Middle East Respiratory Syndrome (MERS) outbreaks, and now the SARS-CoV-2 pandemic. Vaccines that elicit protective immune responses against SARS-CoV-2 and betaCoVs circulating in animals have the potential to prevent future betaCoV pandemics. Here, we show that immunization of macaques with a multimeric SARS-CoV-2 receptor binding domain (RBD) nanoparticle adjuvanted with 3M-052-Alum elicited cross-neutralizing antibody responses against SARS-CoV-1, SARS-CoV-2, batCoVs and the UK B.1.1.7 SARS-CoV-2 mutant virus. Nanoparticle vaccination resulted in a SARS-CoV-2 reciprocal geometric mean neutralization titer of 47,216, and robust protection against SARS-CoV-2 in macaque upper and lower respiratory tracts. Importantly, nucleoside-modified mRNA encoding a stabilized transmembrane spike or monomeric RBD protein also induced SARS-CoV-1 and batCoV cross-neutralizing antibodies, albeit at lower titers. These results demonstrate current mRNA vaccines may provide some protection from future zoonotic betaCoV outbreaks, and provide a platform for further development of pan-betaCoV nanoparticle vaccines.
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41
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Collier DA, De Marco A, Ferreira IATM, Meng B, Datir R, Walls AC, Kemp S SA, Bassi J, Pinto D, Fregni CS, Bianchi S, Tortorici MA, Bowen J, Culap K, Jaconi S, Cameroni E, Snell G, Pizzuto MS, Pellanda AF, Garzoni C, Riva A, Elmer A, Kingston N, Graves B, McCoy LE, Smith KG, Bradley JR, Temperton N, Ceron-Gutierrez L L, Barcenas-Morales G, Harvey W, Virgin HW, Lanzavecchia A, Piccoli L, Doffinger R, Wills M, Veesler D, Corti D, Gupta RK. SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.01.19.21249840. [PMID: 33619509 PMCID: PMC7899479 DOI: 10.1101/2021.01.19.21249840] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) transmission is uncontrolled in many parts of the world, compounded in some areas by higher transmission potential of the B1.1.7 variant now seen in 50 countries. It is unclear whether responses to SARS-CoV-2 vaccines based on the prototypic strain will be impacted by mutations found in B.1.1.7. Here we assessed immune responses following vaccination with mRNA-based vaccine BNT162b2. We measured neutralising antibody responses following a single immunization using pseudoviruses expressing the wild-type Spike protein or the 8 amino acid mutations found in the B.1.1.7 spike protein. The vaccine sera exhibited a broad range of neutralising titres against the wild-type pseudoviruses that were modestly reduced against B.1.1.7 variant. This reduction was also evident in sera from some convalescent patients. Decreased B.1.1.7 neutralisation was also observed with monoclonal antibodies targeting the N-terminal domain (9 out of 10), the Receptor Binding Motif (RBM) (5 out of 31), but not in neutralising mAbs binding outside the RBM. Introduction of the E484K mutation in a B.1.1.7 background to reflect newly emerging viruses in the UK led to a more substantial loss of neutralising activity by vaccine-elicited antibodies and mAbs (19 out of 31) over that conferred by the B.1.1.7 mutations alone. E484K emergence on a B.1.1.7 background represents a threat to the vaccine BNT162b.
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Affiliation(s)
- Dami A Collier
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rawlings Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Steven A Kemp S
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Siro Bianchi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - John Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Matteo S Pizzuto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Agostino Riva
- Division of Infectious Diseases, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Anne Elmer
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | | | | | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - Kenneth Gc Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge, Cambridge, UK
- NIHR Bioresource, Cambridge, UK
| | | | | | - Gabriela Barcenas-Morales
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital, UK
- Laboratorio de Inmunologia, S-Cuautitlán, UNAM, Mexico
| | - William Harvey
- Institute of Biodiversity, University of Glasgow, Glasgow, UK
| | | | - Antonio Lanzavecchia
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital, UK
| | - Mark Wills
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- University of KwaZulu Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- Department of Infectious Diseases, Cambridge University Hospitals NHS Trust, Cambridge UK
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42
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Liu H, Yuan M, Huang D, Bangaru S, Lee CCD, Peng L, Zhu X, Nemazee D, van Gils MJ, Sanders RW, Kornau HC, Reincke SM, Prüss H, Kreye J, Wu NC, Ward AB, Wilson IA. A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.11.430866. [PMID: 33594361 PMCID: PMC7885913 DOI: 10.1101/2021.02.11.430866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Coronaviruses have caused several epidemics and pandemics including the ongoing coronavirus disease 2019 (COVID-19). Some prophylactic vaccines and therapeutic antibodies have already showed striking effectiveness against COVID-19. Nevertheless, concerns remain about antigenic drift in SARS-CoV-2 as well as threats from other sarbecoviruses. Cross-neutralizing antibodies to SARS-related viruses provide opportunities to address such concerns. Here, we report on crystal structures of a cross-neutralizing antibody CV38-142 in complex with the receptor binding domains from SARS-CoV-2 and SARS-CoV. Our structural findings provide mechanistic insights into how this antibody can accommodate antigenic variation in these viruses. CV38-142 synergizes with other cross-neutralizing antibodies, in particular COVA1-16, to enhance neutralization of SARS-CoV-2 and SARS-CoV. Overall, this study provides valuable information for vaccine and therapeutic design to address current and future antigenic drift in SARS-CoV-2 and to protect against zoonotic coronaviruses.
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Affiliation(s)
- Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deli Huang
- Department of Immunology and Microbiology and Infection Prevention, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sandhya Bangaru
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chang-Chun D. Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linghang Peng
- Department of Immunology and Microbiology and Infection Prevention, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology and Infection Prevention, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marit J. van Gils
- Department of Medical Microbiology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Rogier W. Sanders
- Department of Medical Microbiology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Hans-Christian Kornau
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Neuroscience Research Center (NWFZ), Cluster NeuroCure, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - S. Momsen Reincke
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Harald Prüss
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jakob Kreye
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
- Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
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43
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Flores-Alanis A, Cruz-Rangel A, Rodríguez-Gómez F, González J, Torres-Guerrero CA, Delgado G, Cravioto A, Morales-Espinosa R. Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. Pathogens 2021; 10:184. [PMID: 33572190 PMCID: PMC7915391 DOI: 10.3390/pathogens10020184] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/02/2021] [Accepted: 02/06/2021] [Indexed: 12/16/2022] Open
Abstract
In December 2019, the first cases of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified in the city of Wuhan, China. Since then, it has spread worldwide with new mutations being reported. The aim of the present study was to monitor the changes in genetic diversity and track non-synonymous substitutions (dN) that could be implicated in the fitness of SARS-CoV-2 and its spread in different regions between December 2019 and November 2020. We analyzed 2213 complete genomes from six geographical regions worldwide, which were downloaded from GenBank and GISAID databases. Although SARS-CoV-2 presented low genetic diversity, there has been an increase over time, with the presence of several hotspot mutations throughout its genome. We identified seven frequent mutations that resulted in dN substitutions. Two of them, C14408T>P323L and A23403G>D614G, located in the nsp12 and Spike protein, respectively, emerged early in the pandemic and showed a considerable increase in frequency over time. Two other mutations, A1163T>I120F in nsp2 and G22992A>S477N in the Spike protein, emerged recently and have spread in Oceania and Europe. There were associations of P323L, D614G, R203K and G204R substitutions with disease severity. Continuous molecular surveillance of SARS-CoV-2 will be necessary to detect and describe the transmission dynamics of new variants of the virus with clinical relevance. This information is important to improve programs to control the virus.
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Affiliation(s)
- Alejandro Flores-Alanis
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04360, Mexico; (A.F.-A.); (G.D.); (A.C.)
| | - Armando Cruz-Rangel
- Laboratorio de Bioquímica de Enfermedades Crónicas, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
| | - Flor Rodríguez-Gómez
- Departamento de Ciencias Computacionales, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Guadalajara 44430, Jalisco, Mexico;
| | - James González
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | | | - Gabriela Delgado
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04360, Mexico; (A.F.-A.); (G.D.); (A.C.)
| | - Alejandro Cravioto
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04360, Mexico; (A.F.-A.); (G.D.); (A.C.)
| | - Rosario Morales-Espinosa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04360, Mexico; (A.F.-A.); (G.D.); (A.C.)
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Jangra S, Ye C, Rathnasinghe R, Stadlbauer D, Krammer F, Simon V, Martinez-Sobrido L, García-Sastre A, Schotsaert M. The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.01.26.21250543. [PMID: 33532796 PMCID: PMC7852247 DOI: 10.1101/2021.01.26.21250543] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
One year in the coronavirus disease 2019 (COVID-19) pandemic, the first vaccines are being rolled out under emergency use authorizations. It is of great concern that newly emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can escape antibody-mediated protection induced by previous infection or vaccination through mutations in the spike protein. The glutamate (E) to Lysine (K) substitution at position 484 (E484K) in the receptor binding domain (RBD) of the spike protein is present in the rapidly spreading variants of concern belonging to the B.1.351 and P.1 lineages. We performed in vitro microneutralization assays with both the USA-WA1/2020 virus and a recombinant (r)SARS-CoV-2 virus that is identical to USA-WA1/2020 except for the E484K mutation introduced in the spike RBD. We selected 34 sera from study participants based on their SARS-CoV-2 spike ELISA antibody titer (negative [N=4] versus weak [N=8], moderate [N=11] or strong positive [N=11]). In addition, we included sera from five individuals who received two doses of the Pfizer SARS-CoV-2 vaccine BNT162b2. Serum neutralization efficiency was lower against the E484K rSARS-CoV-2 (vaccination samples: 3.4 fold; convalescent low IgG: 2.4 fold, moderate IgG: 4.2 fold and high IgG: 2.6 fold) compared to USA-WA1/2020. For some of the convalescent donor sera with low or moderate IgG against the SARS-CoV-2 spike, the drop in neutralization efficiency resulted in neutralization ID50 values similar to negative control samples, with low or even absence of neutralization of the E484K rSARS-CoV-2. However, human sera with high neutralization titers against the USA-WA1/2020 strain were still able to neutralize the E484K rSARS-CoV-2. Therefore, it is important to aim for the highest titers possible induced by vaccination to enhance protection against newly emerging SARS-CoV-2 variants. Two vaccine doses may be needed for induction of high antibody titers against SARS-CoV-2. Postponing the second vaccination is suggested by some public health authorities in order to provide more individuals with a primer vaccination. Our data suggests that this may leave vaccinees less protected against newly emerging variants.
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Affiliation(s)
- Sonia Jangra
- Department of Microbiology, Icahn School of Medicine at
Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn
School of Medicine at Mount Sinai New York, NY, USA
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX,
USA
| | - Raveen Rathnasinghe
- Department of Microbiology, Icahn School of Medicine at
Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn
School of Medicine at Mount Sinai New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Stadlbauer
- Department of Microbiology, Icahn School of Medicine at
Mount Sinai New York, NY, USA
| | - PVI study group
- Department of Microbiology, Icahn School of Medicine at
Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, 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
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at
Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn
School of Medicine at Mount Sinai New York, NY, USA
- Department of Medicine, Division of Infectious Diseases,
Icahn School of Medicine at Mount Sinai New York, NY, USA
| | | | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at
Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn
School of Medicine at Mount Sinai New York, NY, USA
- Department of Medicine, Division of Infectious Diseases,
Icahn School of Medicine at Mount Sinai New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at
Mount Sinai New York, NY, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at
Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn
School of Medicine at Mount Sinai New York, NY, USA
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Xie X, Liu Y, Liu J, Zhang X, Zou J, Fontes-Garfias CR, Xia H, Swanson KA, Cutler M, Cooper D, Menachery VD, Weaver S, Dormitzer PR, Shi PY. Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K, and N501Y variants by BNT162b2 vaccine-elicited sera. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.27.427998. [PMID: 33532771 PMCID: PMC7852264 DOI: 10.1101/2021.01.27.427998] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We engineered three SARS-CoV-2 viruses containing key spike mutations from the newly emerged United Kingdom (UK) and South African (SA) variants: N501Y from UK and SA; 69/70-deletion+N501Y+D614G from UK; and E484K+N501Y+D614G from SA. Neutralization geometric mean titers (GMTs) of twenty BTN162b2 vaccine-elicited human sera against the three mutant viruses were 0.81- to 1.46-fold of the GMTs against parental virus, indicating small effects of these mutations on neutralization by sera elicited by two BNT162b2 doses.
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Affiliation(s)
- Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, U.S.A
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, U.S.A
| | - Jianying Liu
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, U.S.A
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, U.S.A
| | - Xianwen Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, U.S.A
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, U.S.A
| | - Camila R. Fontes-Garfias
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, U.S.A
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, U.S.A
| | | | - Mark Cutler
- Pfizer, 401 N Middletown Rd., Pearl River, NY 10960, U.S.A
| | - David Cooper
- Pfizer, 401 N Middletown Rd., Pearl River, NY 10960, U.S.A
| | - Vineet D. Menachery
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, U.S.A
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, U.S.A
| | - Scott Weaver
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, U.S.A
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, U.S.A
| | | | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, U.S.A
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, U.S.A
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, U.S.A
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, U.S.A
- Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, U.S.A
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Tan TJ, Yuan M, Kuzelka K, Padron GC, Beal JR, Chen X, Wang Y, Rivera-Cardona J, Zhu X, Stadtmueller BM, Brooke CB, Wilson IA, Wu NC. Sequence signatures of two IGHV3-53/3-66 public clonotypes to SARS-CoV-2 receptor binding domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.26.428356. [PMID: 33532781 PMCID: PMC7852275 DOI: 10.1101/2021.01.26.428356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Since the COVID-19 pandemic onset, the antibody response to SARS-CoV-2 has been extensively characterized. Antibodies to the receptor binding domain (RBD) on the spike protein are frequently encoded by IGHV3-53/3-66 with a short CDR H3. Germline-encoded sequence motifs in CDRs H1 and H2 play a major role, but whether any common motifs are present in CDR H3, which is often critical for binding specificity, have not been elucidated. Here, we identify two public clonotypes of IGHV3-53/3-66 RBD antibodies with a 9-residue CDR H3 that pair with different light chains. Distinct sequence motifs on CDR H3 are present in the two public clonotypes that appear to be related to differential light chain pairing. Additionally, we show that Y58F is a common somatic hypermutation that results in increased binding affinity of IGHV3-53/3-66 RBD antibodies with a short CDR H3. Overall, our results advance fundamental understanding of the antibody response to SARS-CoV-2.
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Affiliation(s)
- Timothy J.C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kaylee Kuzelka
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Gilberto C. Padron
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jacob R. Beal
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Xin Chen
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Joel Rivera-Cardona
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Beth M. Stadtmueller
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Christopher B. Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- 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
| | - Nicholas C. Wu
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Anand SP, Prévost J, Nayrac M, Beaudoin-Bussières G, Benlarbi M, Gasser R, Brassard N, Laumaea A, Gong SY, Bourassa C, Brunet-Ratnasingham E, Medjahed H, Gendron-Lepage G, Goyette G, Gokool L, Morrisseau C, Bégin P, Martel-Laferrière V, Tremblay C, Richard J, Bazin R, Duerr R, Kaufmann DE, Finzi A. Longitudinal analysis of humoral immunity against SARS-CoV-2 Spike in convalescent individuals up to 8 months post-symptom onset. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33532774 DOI: 10.1101/2021.01.25.428097] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Functional and lasting immune responses to the novel coronavirus (SARS-CoV-2) are currently under intense investigation as antibody titers in plasma have been shown to decline during convalescence. Since the absence of antibodies does not equate to absence of immune memory, we sought to determine the presence of SARS-CoV-2-specific memory B cells in COVID-19 convalescent patients. In this study, we report on the evolution of the overall humoral immune responses on 101 blood samples obtained from 32 COVID-19 convalescent patients between 16 and 233 days post-symptom onset. Our observations indicate that anti-Spike and anti-RBD IgM in plasma decay rapidly, whereas the reduction of IgG is less prominent. Neutralizing activity in convalescent plasma declines rapidly compared to Fc-effector functions. Concomitantly, the frequencies of RBD-specific IgM+ B cells wane significantly when compared to RBD-specific IgG+ B cells, which increase over time, and the number of IgG+ memory B cells which remain stable thereafter for up to 8 months after symptoms onset. With the recent approval of highly effective vaccines for COVID-19, data on the persistence of immune responses are of central importance. Even though overall circulating SARS-CoV-2 Spike-specific antibodies contract over time during convalescence, we demonstrate that RBD-specific B cells increase and persist up to 8 months post symptom onset. We also observe modest increases in RBD-specific IgG+ memory B cells and importantly, detectable IgG and sustained Fc-effector activity in plasma over the 8-month period. Our results add to the current understanding of immune memory following SARS-CoV-2 infection, which is critical for the prevention of secondary infections, vaccine efficacy and herd immunity against COVID-19.
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