1
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Carr CR, Crawford KHD, Murphy M, Galloway JG, Haddox HK, Matsen FA, Andersen KG, King NP, Bloom JD. Deep mutational scanning reveals functional constraints and antibody-escape potential of Lassa virus glycoprotein complex. Immunity 2024; 57:2061-2076.e11. [PMID: 39013466 PMCID: PMC11390330 DOI: 10.1016/j.immuni.2024.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/23/2024] [Accepted: 06/20/2024] [Indexed: 07/18/2024]
Abstract
Lassa virus is estimated to cause thousands of human deaths per year, primarily due to spillovers from its natural host, Mastomys rodents. Efforts to create vaccines and antibody therapeutics must account for the evolutionary variability of the Lassa virus's glycoprotein complex (GPC), which mediates viral entry into cells and is the target of neutralizing antibodies. To map the evolutionary space accessible to GPC, we used pseudovirus deep mutational scanning to measure how nearly all GPC amino-acid mutations affected cell entry and antibody neutralization. Our experiments defined functional constraints throughout GPC. We quantified how GPC mutations affected neutralization with a panel of monoclonal antibodies. All antibodies tested were escaped by mutations that existed among natural Lassa virus lineages. Overall, our work describes a biosafety-level-2 method to elucidate the mutational space accessible to GPC and shows how prospective characterization of antigenic variation could aid the design of therapeutics and vaccines.
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Affiliation(s)
- Caleb R Carr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Katharine H D Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Michael Murphy
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jared G Galloway
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Hugh K Haddox
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Frederick A Matsen
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Statistics, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA.
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2
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Tse AL, Acreman CM, Ricardo-Lax I, Berrigan J, Lasso G, Balogun T, Kearns FL, Casalino L, McClain GL, Chandran AM, Lemeunier C, Amaro RE, Rice CM, Jangra RK, McLellan JS, Chandran K, Miller EH. Distinct pathway for evolution of enhanced receptor binding and cell entry in SARS-like bat coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600393. [PMID: 38979151 PMCID: PMC11230278 DOI: 10.1101/2024.06.24.600393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Understanding the zoonotic risks posed by bat coronaviruses (CoVs) is critical for pandemic preparedness. Herein, we generated recombinant vesicular stomatitis viruses (rVSVs) bearing spikes from divergent bat CoVs to investigate their cell entry mechanisms. Unexpectedly, the successful recovery of rVSVs bearing the spike from SHC014, a SARS-like bat CoV, was associated with the acquisition of a novel substitution in the S2 fusion peptide-proximal region (FPPR). This substitution enhanced viral entry in both VSV and coronavirus contexts by increasing the availability of the spike receptor-binding domain to recognize its cellular receptor, ACE2. A second substitution in the spike N-terminal domain, uncovered through forward-genetic selection, interacted epistatically with the FPPR substitution to synergistically enhance spike:ACE2 interaction and viral entry. Our findings identify genetic pathways for adaptation by bat CoVs during spillover and host-to-host transmission, fitness trade-offs inherent to these pathways, and potential Achilles' heels that could be targeted with countermeasures.
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3
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Jacob-Dolan C, Lifton M, Powers OC, Miller J, Hachmann NP, Vu M, Surve N, Mazurek CR, Fisher JL, Rodrigues S, Patio RC, Anand T, Le Gars M, Sadoff J, Schmidt AG, Barouch DH. B cell somatic hypermutation following COVID-19 vaccination with Ad26.COV2.S. iScience 2024; 27:109716. [PMID: 38655202 PMCID: PMC11035370 DOI: 10.1016/j.isci.2024.109716] [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: 10/02/2023] [Revised: 02/02/2024] [Accepted: 04/07/2024] [Indexed: 04/26/2024] Open
Abstract
The viral vector-based COVID-19 vaccine Ad26.COV2.S has been recommended by the WHO since 2021 and has been administered to over 200 million people. Prior studies have shown that Ad26.COV2.S induces durable neutralizing antibodies (NAbs) that increase in coverage of variants over time, even in the absence of boosting or infection. Here, we studied humoral responses following Ad26.COV2.S vaccination in individuals enrolled in the initial Phase 1/2a trial of Ad26.COV2.S in 2020. Through 8 months post vaccination, serum NAb responses increased to variants, including B.1.351 (Beta) and B.1.617.2 (Delta), without additional boosting or infection. The level of somatic hypermutation, measured by nucleotide changes in the VDJ region of the heavy and light antibody chains, increased in Spike-specific B cells. Highly mutated mAbs from these sequences neutralized more SARS-CoV-2 variants than less mutated comparators. These findings suggest that the increase in NAb breadth over time following Ad26.COV2.S vaccination is mediated by affinity maturation.
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Affiliation(s)
- Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Department of Microbiology, Boston, MA, USA
- Harvard Medical School, Department of Immunology, Boston, MA, USA
| | - Michelle Lifton
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Olivia C. Powers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jessica Miller
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Nicole P. Hachmann
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Mya Vu
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
| | - Nehalee Surve
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Camille R. Mazurek
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jana L. Fisher
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Stefanie Rodrigues
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Robert C. Patio
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Trisha Anand
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Mathieu Le Gars
- Janssen Vaccines and Prevention B.V., Leiden, the Netherlands
| | - Jerald Sadoff
- Janssen Vaccines and Prevention B.V., Leiden, the Netherlands
| | - Aaron G. Schmidt
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Department of Microbiology, Boston, MA, USA
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Department of Immunology, Boston, MA, USA
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4
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Duan H, Zhang E, Ren G, Cheng Y, Yang B, Liu L, Jolicoeur N, Hu H, Xu Y, Liu B. Exploring immune evasion of SARS-CoV-2 variants using a pseudotyped system. Heliyon 2024; 10:e29939. [PMID: 38699727 PMCID: PMC11063423 DOI: 10.1016/j.heliyon.2024.e29939] [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: 03/05/2024] [Revised: 03/18/2024] [Accepted: 04/17/2024] [Indexed: 05/05/2024] Open
Abstract
In the United States, coronavirus disease 2019 (COVID-19) cases have consistently been linked to the prevailing variant XBB.1.5 of SARS-CoV-2 since late 2022. A system has been developed for producing and infecting cells with a pseudovirus (PsV) of SARS-CoV-2 to investigate the infection in a Biosafety Level 2 (BSL-2) laboratory. This system utilizes a lentiviral vector carrying ZsGreen1 and Firefly luciferase (Fluc) dual reporter genes, facilitating the analysis of experimental results. In addition, we have created a panel of PsV variants that depict both previous and presently circulating mutations found in circulating SARS-CoV-2 strains. A series of PsVs includes the prototype SARS-CoV-2, Delta B.1.617.2, BA.5, XBB.1, and XBB.1.5. To facilitate the study of infections caused by different variants of SARS-CoV-2 PsV, we have developed a HEK-293T cell line expressing mCherry and human angiotensin converting enzyme 2 (ACE2). To validate whether different SARS-CoV-2 PsV variants can be used for neutralization assays, we employed serum from rats immunized with the PF-D-Trimer protein vaccine to investigate its inhibitory effect on the infectivity of various SARS-CoV-2 PsV variants. According to our observations, the XBB variant, particularly XBB.1.5, exhibits stronger immune evasion capabilities than the prototype SARS-CoV-2, Delta B.1.617.2, and BA.5 PsV variants. Hence, utilizing the neutralization test, this study has the capability to forecast the effectiveness in preventing future SARS-CoV-2 variants infections.
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Affiliation(s)
- Haixiao Duan
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Ershuai Zhang
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Ge Ren
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Yining Cheng
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Binfeng Yang
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
| | - Lirong Liu
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
| | | | - Han Hu
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Yan Xu
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
| | - Binlei Liu
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
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5
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Dufloo J, Sanjuán R. Temperature impacts SARS-CoV-2 spike fusogenicity and evolution. mBio 2024; 15:e0336023. [PMID: 38411986 PMCID: PMC11005339 DOI: 10.1128/mbio.03360-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/29/2024] [Indexed: 02/28/2024] Open
Abstract
SARS-CoV-2 infects both the upper and lower respiratory tracts, which are characterized by different temperatures (33°C and 37°C, respectively). In addition, fever is a common COVID-19 symptom. SARS-CoV-2 has been shown to replicate more efficiently at low temperatures, but the effect of temperature on different viral proteins remains poorly understood. Here, we investigate how temperature affects the SARS-CoV-2 spike function and evolution. We first observed that increasing temperature from 33°C to 37°C or 39°C increased spike-mediated cell-cell fusion. We then experimentally evolved a recombinant vesicular stomatitis virus expressing the SARS-CoV-2 spike at these different temperatures. We found that spike-mediated cell-cell fusion was maintained during evolution at 39°C but was lost in a high proportion of viruses that evolved at 33°C or 37°C. Consistently, sequencing of the spikes evolved at 33°C or 37°C revealed the accumulation of mutations around the furin cleavage site, a region that determines cell-cell fusion, whereas this did not occur in spikes evolved at 39°C. Finally, using site-directed mutagenesis, we found that disruption of the furin cleavage site had a temperature-dependent effect on spike-induced cell-cell fusion and viral fitness. Our results suggest that variations in body temperature may affect the activity and diversification of the SARS-CoV-2 spike. IMPORTANCE When it infects humans, SARS-CoV-2 is exposed to different temperatures (e.g., replication site and fever). Temperature has been shown to strongly impact SARS-CoV-2 replication, but how it affects the activity and evolution of the spike protein remains poorly understood. Here, we first show that high temperatures increase the SARS-CoV-2 spike fusogenicity. Then, we demonstrate that the evolution of the spike activity and variants depends on temperature. Finally, we show that the functional effect of specific spike mutations is temperature-dependent. Overall, our results suggest that temperature may be a factor influencing the activity and adaptation of the SARS-CoV-2 spike in vivo, which will help understanding viral tropism, pathogenesis, and evolution.
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Affiliation(s)
- Jérémy Dufloo
- Institute for Integrative Systems Biology, Consejo Superior de Investigaciones Científicas-Universitat de València, Paterna, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology, Consejo Superior de Investigaciones Científicas-Universitat de València, Paterna, València, Spain
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6
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Greville G, Cremen S, O'Neill S, Azarian S, Brady G, McCormack W, Dyer AH, Bourke NM, Touzelet O, Courtney D, Power UF, Dowling P, Gallagher TK, Bamford CGG, Robinson MW. Type 1 interferon auto-antibodies are elevated in patients with decompensated liver cirrhosis. Clin Exp Immunol 2024; 215:177-189. [PMID: 37917972 PMCID: PMC10847822 DOI: 10.1093/cei/uxad119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 09/12/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023] Open
Abstract
Patients with decompensated liver cirrhosis, in particular those classified as Childs-Pugh class C, are at increased risk of severe coronavirus disease-2019 (COVID-19) upon infection with severe acute respiratory coronavirus 2 (SARS-CoV-2). The biological mechanisms underlying this are unknown. We aimed to examine the levels of serum intrinsic antiviral proteins as well as alterations in the innate antiviral immune response in patients with decompensated liver cirrhosis. Serum from 53 SARS-CoV-2 unexposed and unvaccinated individuals, with decompensated liver cirrhosis undergoing assessment for liver transplantation, were screened using SARS-CoV-2 pseudoparticle and SARS-CoV-2 virus assays. The ability of serum to inhibit interferon (IFN) signalling was assessed using a cell-based reporter assay. Severity of liver disease was assessed using two clinical scoring systems, the Child-Pugh class and the MELD-Na score. In the presence of serum from SARS-CoV-2 unexposed patients with decompensated liver cirrhosis there was no association between SARS-CoV-2 pseudoparticle infection or live SARS-CoV-2 virus infection and severity of liver disease. Type I IFNs are a key component of the innate antiviral response. Serum from patients with decompensated liver cirrhosis contained elevated levels of auto-antibodies capable of binding IFN-α2b compared to healthy controls. High MELD-Na scores were associated with the ability of these auto-antibodies to neutralize type I IFN signalling by IFN-α2b but not IFN-β1a. Our results demonstrate that neutralizing auto-antibodies targeting IFN-α2b are increased in patients with high MELD-Na scores. The presence of neutralizing type I IFN-specific auto-antibodies may increase the likelihood of viral infections, including severe COVID-19, in patients with decompensated liver cirrhosis.
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Affiliation(s)
- Gordon Greville
- Department of Biology, Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - Sinead Cremen
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Shauna O'Neill
- Department of Biology, Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - Sarah Azarian
- Department of Biology, Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - Gareth Brady
- Discipline of Clinical Medicine, School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - William McCormack
- Discipline of Clinical Medicine, School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Adam H Dyer
- Discipline of Medical Gerontology, School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Nollaig M Bourke
- Discipline of Medical Gerontology, School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Olivier Touzelet
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, Northern Ireland
| | - David Courtney
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, Northern Ireland
| | - Ultan F Power
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, Northern Ireland
| | - Paul Dowling
- Department of Biology, Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - Tom K Gallagher
- Department of Hepatopancreaticobiliary and Transplant Surgery, St. Vincent's University Hospital, Dublin, Ireland
| | - Connor G G Bamford
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, Northern Ireland
- School of Biological Sciences and Institute for Global Food Security (IGFS), Queen's University Belfast, Belfast, Northern Ireland
| | - Mark W Robinson
- Department of Biology, Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
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7
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Carr CR, Crawford KHD, Murphy M, Galloway JG, Haddox HK, Matsen FA, Andersen KG, King NP, Bloom JD. Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.579020. [PMID: 38370709 PMCID: PMC10871245 DOI: 10.1101/2024.02.05.579020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Lassa virus is estimated to cause thousands of human deaths per year, primarily due to spillovers from its natural host, Mastomys rodents. Efforts to create vaccines and antibody therapeutics must account for the evolutionary variability of Lassa virus's glycoprotein complex (GPC), which mediates viral entry into cells and is the target of neutralizing antibodies. To map the evolutionary space accessible to GPC, we use pseudovirus deep mutational scanning to measure how nearly all GPC amino-acid mutations affect cell entry and antibody neutralization. Our experiments define functional constraints throughout GPC. We quantify how GPC mutations affect neutralization by a panel of monoclonal antibodies and show that all antibodies are escaped by mutations that exist among natural Lassa virus lineages. Overall, our work describes a biosafety-level-2 method to elucidate the mutational space accessible to GPC and shows how prospective characterization of antigenic variation could aid design of therapeutics and vaccines.
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Affiliation(s)
- Caleb R. Carr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98109, USA
| | - Katharine H. D. Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98109, USA
| | - Michael Murphy
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jared G. Galloway
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Hugh K. Haddox
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Frederick A. Matsen
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Statistics, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
- Lead contact
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8
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Zhang DQ, Ma QH, Yang MC, Belyakova YY, Yang ZF, Radulov PS, Chen RH, Yang LJ, Wei JY, Peng YT, Zheng WY, Yaremenko IA, Terent'ev AO, Coghi P, Wong VKW. Peroxide derivatives as SARS-CoV-2 entry inhibitors. Virus Res 2024; 340:199295. [PMID: 38081457 PMCID: PMC10733699 DOI: 10.1016/j.virusres.2023.199295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 11/14/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 2019 (COVID-19) pandemic. Host cell invasion is mediated by the interaction of the viral spike protein (S) with human angiotensin-converting enzyme 2 (ACE2) through the receptor-binding domain (RBD). In this work, bio-layer interferometry (BLI) was used to screen a series of fifty-two peroxides, including aminoperoxides and bridged 1,2,4 - trioxolanes (ozonides), with the aim of identifying small molecules that interfere with the RBD-ACE2 interaction. We found that two compounds, compound 21 and 29, exhibit the activity to inhibit RBD-ACE2. They are further demonstrated to inhibit SARS-CoV-2 cell entry, as shown in pseudovirus assay and experiment with authentic SARS-CoV-2. A comprehensive in silico analysis was carried out to study the physicochemical and pharmacokinetic properties, revealing that both compounds have good physicochemical properties as well as good bioavailability. Our results highlight the potential of small molecules targeting RBD inhibitors as potential therapeutic drugs for COVID-19.
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Affiliation(s)
- Ding-Qi Zhang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Qin-Hai Ma
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Meng-Chu Yang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Yulia Yu Belyakova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Zi-Feng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Peter S Radulov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Rui-Hong Chen
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Li-Jun Yang
- Institute of Translational Medicine, Zhejiang Shuren University, Hangzhou, China
| | - Jing-Yuan Wei
- School of Pharmacy, Macau University of Science and Technology, Macau, China
| | - Yu-Tong Peng
- School of Pharmacy, Macau University of Science and Technology, Macau, China
| | - Wu-Yan Zheng
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Ivan A Yaremenko
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation; Faculty of Chemical and Pharmaceutical Technology and Biomedical Products, D .I . Mendeleev University of Chemical Technology of Russia, Moscow, Russian Federation
| | - Alexander O Terent'ev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.
| | - Paolo Coghi
- School of Pharmacy, Macau University of Science and Technology, Macau, China.
| | - Vincent Kam Wai Wong
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
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9
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McMahan K, Wegmann F, Aid M, Sciacca M, Liu J, Hachmann NP, Miller J, Jacob-Dolan C, Powers O, Hope D, Wu C, Pereira J, Murdza T, Mazurek CR, Hoyt A, Boon ACM, Davis-Gardner M, Suthar MS, Martinot AJ, Boursiquot M, Cook A, Pessaint L, Lewis MG, Andersen H, Tolboom J, Serroyen J, Solforosi L, Costes LMM, Zahn RC, Barouch DH. Mucosal boosting enhances vaccine protection against SARS-CoV-2 in macaques. Nature 2024; 626:385-391. [PMID: 38096903 PMCID: PMC10849944 DOI: 10.1038/s41586-023-06951-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 12/07/2023] [Indexed: 01/26/2024]
Abstract
A limitation of current SARS-CoV-2 vaccines is that they provide minimal protection against infection with current Omicron subvariants1,2, although they still provide protection against severe disease. Enhanced mucosal immunity may be required to block infection and onward transmission. Intranasal administration of current vaccines has proven inconsistent3-7, suggesting that alternative immunization strategies may be required. Here we show that intratracheal boosting with a bivalent Ad26-based SARS-CoV-2 vaccine results in substantial induction of mucosal humoral and cellular immunity and near-complete protection against SARS-CoV-2 BQ.1.1 challenge. A total of 40 previously immunized rhesus macaques were boosted with a bivalent Ad26 vaccine by the intramuscular, intranasal and intratracheal routes, or with a bivalent mRNA vaccine by the intranasal route. Ad26 boosting by the intratracheal route led to a substantial expansion of mucosal neutralizing antibodies, IgG and IgA binding antibodies, and CD8+ and CD4+ T cell responses, which exceeded those induced by Ad26 boosting by the intramuscular and intranasal routes. Intratracheal Ad26 boosting also led to robust upregulation of cytokine, natural killer, and T and B cell pathways in the lungs. After challenge with a high dose of SARS-CoV-2 BQ.1.1, intratracheal Ad26 boosting provided near-complete protection, whereas the other boosting strategies proved less effective. Protective efficacy correlated best with mucosal humoral and cellular immune responses. These data demonstrate that these immunization strategies induce robust mucosal immunity, suggesting the feasibility of developing vaccines that block respiratory viral infections.
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Affiliation(s)
- Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Frank Wegmann
- Janssen Vaccines and Prevention, Leiden, Netherlands
| | - Malika Aid
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Michaela Sciacca
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Nicole P Hachmann
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jessica Miller
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Olivia Powers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - David Hope
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Cindy Wu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Juliana Pereira
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Tetyana Murdza
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Camille R Mazurek
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Amelia Hoyt
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | | | | | - Amanda J Martinot
- Tufts University Cummings School of Veterinary Medicine, Grafton, MA, USA
| | | | | | | | | | | | | | - Jan Serroyen
- Janssen Vaccines and Prevention, Leiden, Netherlands
| | | | | | - Roland C Zahn
- Janssen Vaccines and Prevention, Leiden, Netherlands
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
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10
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Fan J, Li S, Zhang Y, Zheng J, Wang D, Liao Y, Cui Z, Zhao D, Barouch DH, Yu J. Early Emerging SARS-CoV-2 Spike Mutants Are Diversified in Virologic Properties but Elicit Compromised Antibody Responses. Viruses 2023; 15:2401. [PMID: 38140642 PMCID: PMC10747620 DOI: 10.3390/v15122401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Despite the effective antivirals and vaccines, COVID-19 remains a public health concern. The mutations that occurred during the early stage of the pandemic can be valuable in assessing the viral fitness and evolutionary trajectory. In this study, we analyzed a panel of 2969 spike sequences deposited in GISAID before April 2020 and characterized nine representative spike single-point mutants in detail. Compared with the WA01/2020, most (8 out of 9) mutants demonstrated an equivalent or diminished protein expression or processing, pseudovirus infectivity, and cell-cell fusion. Interestingly, most of the mutants in native form elicited minimum antibody responses in mice despite unaltered CD4+ and CD8+ T cell responses. The mutants remained sensitive to the antisera and the type I interferon. Taken together, these data suggest that the early emerging mutants are virologically divergent, and some of which showed transmission fitness. Our findings have important implications for the retrospective tracing of the early SARS-CoV-2 transmission and future pandemic preparedness.
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Affiliation(s)
- Junhao Fan
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510182, China;
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
| | - Shixiong Li
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yao Zhang
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jihao Zheng
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
| | - Dongfang Wang
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
| | - Yunxi Liao
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; (Y.L.); (D.Z.)
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Zhibo Cui
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Dongyu Zhao
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; (Y.L.); (D.Z.)
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jingyou Yu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510182, China;
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
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11
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Beitari S, Agbayani G, Hewitt M, Duque D, Bavananthasivam J, Sandhu JK, Akache B, Hadžisejdić I, Tran A. Effectiveness of VSV vectored SARS-CoV-2 spike when administered through intranasal, intramuscular or a combination of both. Sci Rep 2023; 13:21390. [PMID: 38049498 PMCID: PMC10695950 DOI: 10.1038/s41598-023-48397-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/26/2023] [Indexed: 12/06/2023] Open
Abstract
A critical feature of the VSV vector platform is the ability to pseudotype the virus with different glycoproteins from other viruses, thus altering cellular tropism of the recombinant virus. The route of administration is critical in triggering local and systemic immune response and protection. Most of the vaccine platforms used at the forefront are administered by intramuscular injection. However, it is not known at what level ACE2 is expressed on the surface of skeletal muscle cells, which will have a significant impact on the efficiency of a VSV-SARS-CoV-2 spike vaccine to mount a protective immune response when administered intramuscularly. In this study, we investigate the immunogenicity and efficacy of a prime-boost immunization regimen administered intranasally (IN), intramuscularly (IM), or combinations of the two. We determined that the prime-boost combinations of IM followed by IN immunization (IM + IN) or IN followed by IN immunization (IN + IN) exhibited strong spike-specific IgG, IgA and T cell response in vaccinated K18 knock-in mice. Hamsters vaccinated with two doses of VSV expressing SARS-CoV-2 spike, both delivered by IN or IM + IN, showed strong protection against SARS-CoV-2 variants of concern Alpha and Delta. This protection was also observed in aged hamsters. Our study underscores the highly crucial role immunization routes have with the VSV vector platform to elicit a strong and protective immune response.
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Affiliation(s)
- Saina Beitari
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Gerard Agbayani
- Immunomodulation, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Melissa Hewitt
- Preclinical Imaging, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Diana Duque
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Jegarubee Bavananthasivam
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Jagdeep K Sandhu
- Preclinical Imaging, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Bassel Akache
- Immunomodulation, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Ita Hadžisejdić
- Clinical Department of Pathology and Cytology Clinical Hospital Center Rijeka, University of Rijeka, Rijeka, Croatia
| | - Anh Tran
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada.
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12
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Cantoni D, Wilkie C, Bentley EM, Mayora-Neto M, Wright E, Scott S, Ray S, Castillo-Olivares J, Heeney JL, Mattiuzzo G, Temperton NJ. Correlation between pseudotyped virus and authentic virus neutralisation assays, a systematic review and meta-analysis of the literature. Front Immunol 2023; 14:1184362. [PMID: 37790941 PMCID: PMC10544934 DOI: 10.3389/fimmu.2023.1184362] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 08/28/2023] [Indexed: 10/05/2023] Open
Abstract
Background The virus neutralization assay is a principal method to assess the efficacy of antibodies in blocking viral entry. Due to biosafety handling requirements of viruses classified as hazard group 3 or 4, pseudotyped viruses can be used as a safer alternative. However, it is often queried how well the results derived from pseudotyped viruses correlate with authentic virus. This systematic review and meta-analysis was designed to comprehensively evaluate the correlation between the two assays. Methods Using PubMed and Google Scholar, reports that incorporated neutralisation assays with both pseudotyped virus, authentic virus, and the application of a mathematical formula to assess the relationship between the results, were selected for review. Our searches identified 67 reports, of which 22 underwent a three-level meta-analysis. Results The three-level meta-analysis revealed a high level of correlation between pseudotyped viruses and authentic viruses when used in an neutralisation assay. Reports that were not included in the meta-analysis also showed a high degree of correlation, with the exception of lentiviral-based pseudotyped Ebola viruses. Conclusion Pseudotyped viruses identified in this report can be used as a surrogate for authentic virus, though care must be taken in considering which pseudotype core to use when generating new uncharacterised pseudotyped viruses.
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Affiliation(s)
- Diego Cantoni
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Craig Wilkie
- School of Mathematics & Statistics, University of Glasgow, Glasgow, United Kingdom
| | - Emma M. Bentley
- Medicines and Healthcare Products Regulatory Agency, South Mimms, United Kingdom
| | - Martin Mayora-Neto
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Chatham, United Kingdom
| | - Edward Wright
- Viral Pseudotype Unit, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Simon Scott
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Chatham, United Kingdom
| | - Surajit Ray
- School of Mathematics & Statistics, University of Glasgow, Glasgow, United Kingdom
| | - Javier Castillo-Olivares
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge University, Cambridge, United Kingdom
| | - Jonathan Luke Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge University, Cambridge, United Kingdom
- DIOSynVax, University of Cambridge, Cambridge, United Kingdom
| | - Giada Mattiuzzo
- Medicines and Healthcare Products Regulatory Agency, South Mimms, United Kingdom
| | - Nigel James Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Chatham, United Kingdom
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13
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Luo H, Lv L, Yi J, Zhou Y, Liu C. Establishment of Replication Deficient Vesicular Stomatitis Virus for Studies of PEDV Spike-Mediated Cell Entry and Its Inhibition. Microorganisms 2023; 11:2075. [PMID: 37630636 PMCID: PMC10457912 DOI: 10.3390/microorganisms11082075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
The porcine epidemic diarrhea virus (PEDV) is a highly contagious and virulent enteric coronavirus that causes severe enteric disease in pigs worldwide. PEDV infection causes profound diarrhea, vomiting, and dehydration in pigs of all ages, resulting in high mortality rates, particularly among neonatal piglets. The spike glycoprotein (S) of PEDV plays a crucial role in binding to the host cell receptor and facilitating fusion between the viral and host membranes. Pseudotyped viral particles featuring the PEDV S protein are valuable tools for investigating virus entry, identifying neutralizing antibodies, and developing small molecules to impede virus replication. In this study, we used a codon-optimized PEDV S protein to generate recombinant pseudotyped vesicular stomatitis virus (VSV) particles (rVSV-ΔG-EGFP-S). The full-length S protein was efficiently incorporated into VSV particles. The S protein pseudotyped VSV exhibited infectivity towards permissive cell lines of PEDV. Moreover, we identified a new permissive cell line, JHH7, which showed robust support for PEDV replication. In contrast to the SARS-CoV-2 spike protein, the removal of amino acids from the cytoplasmic tail resulted in reduced efficiency of viral pseudotyping. Furthermore, we demonstrated that 25-hydroxycholesterol inhibited rVSV-ΔG-EGFP-S entry, while human APN facilitated rVSV-ΔG-EGFP-S entry through the use of ANPEP knockout Huh7 cells. Finally, by transducing swine intestinal organoids with the rVSV-ΔG-EGFP-S virus, we observed efficient infection of the swine intestinal organoids by the PEDV spike-pseudotyped VSV. Our work offers valuable tools for studying the cellular entry of PEDV and developing interventions to curb its transmission.
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Affiliation(s)
- Huaye Luo
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (H.L.); (L.L.); (J.Y.); (Y.Z.)
| | - Lilei Lv
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (H.L.); (L.L.); (J.Y.); (Y.Z.)
| | - Jingxuan Yi
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (H.L.); (L.L.); (J.Y.); (Y.Z.)
| | - Yanjun Zhou
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (H.L.); (L.L.); (J.Y.); (Y.Z.)
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Changlong Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (H.L.); (L.L.); (J.Y.); (Y.Z.)
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou 225009, China
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14
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Dong T, Wang M, Liu J, Ma P, Pang S, Liu W, Liu A. Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives. Chem Sci 2023; 14:6149-6206. [PMID: 37325147 PMCID: PMC10266450 DOI: 10.1039/d2sc06665c] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced severe public healthcare issues and weakened the global economy significantly. Although SARS-CoV-2 infection is not as fatal as the initial outbreak, many infected victims suffer from long COVID. Therefore, rapid and large-scale testing is critical in managing patients and alleviating its transmission. Herein, we review the recent advances in techniques to detect SARS-CoV-2. The sensing principles are detailed together with their application domains and analytical performances. In addition, the advantages and limits of each method are discussed and analyzed. Besides molecular diagnostics and antigen and antibody tests, we also review neutralizing antibodies and emerging SARS-CoV-2 variants. Further, the characteristics of the mutational locations in the different variants with epidemiological features are summarized. Finally, the challenges and possible strategies are prospected to develop new assays to meet different diagnostic needs. Thus, this comprehensive and systematic review of SARS-CoV-2 detection technologies may provide insightful guidance and direction for developing tools for the diagnosis and analysis of SARS-CoV-2 to support public healthcare and effective long-term pandemic management and control.
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Affiliation(s)
- Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
- School of Pharmacy, Medical College, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Junchong Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Pengxin Ma
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Wanjian Liu
- Qingdao Hightop Biotech Co., Ltd 369 Hedong Road, Hi-tech Industrial Development Zone Qingdao 266112 China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
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15
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Sengar A, Cervantes M, Bondalapati ST, Hess T, Kasson PM. Single-Virus Fusion Measurements Reveal Multiple Mechanistically Equivalent Pathways for SARS-CoV-2 Entry. J Virol 2023; 97:e0199222. [PMID: 37133381 PMCID: PMC10231210 DOI: 10.1128/jvi.01992-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/11/2023] [Indexed: 05/04/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds to cell surface receptors and is activated for membrane fusion and cell entry via proteolytic cleavage. Phenomenological data have shown that SARS-CoV-2 can be activated for entry at either the cell surface or in endosomes, but the relative roles in different cell types and mechanisms of entry have been debated. Here, we used single-virus fusion experiments and exogenously controlled proteases to probe activation directly. We found that plasma membrane and an appropriate protease are sufficient to support SARS-CoV-2 pseudovirus fusion. Furthermore, fusion kinetics of SARS-CoV-2 pseudoviruses are indistinguishable no matter which of a broad range of proteases is used to activate the virus. This suggests that the fusion mechanism is insensitive to protease identity or even whether activation occurs before or after receptor binding. These data support a model for opportunistic fusion by SARS-CoV-2 in which the subcellular location of entry likely depends on the differential activity of airway, cellsurface, and endosomal proteases, but all support infection. Inhibition of any single host protease may thus reduce infection in some cells but may be less clinically robust. IMPORTANCE SARS-CoV-2 can use multiple pathways to infect cells, as demonstrated recently when new viral variants switched dominant infection pathways. Here, we used single-virus fusion experiments together with biochemical reconstitution to show that these multiple pathways coexist simultaneously and specifically that the virus can be activated by different proteases in different cellular compartments with mechanistically identical effects. The consequences of this are that the virus is evolutionarily plastic and that therapies targeting viral entry should address multiple pathways at once to achieve optimal clinical effects.
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Affiliation(s)
- Anjali Sengar
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Marcos Cervantes
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Sai T. Bondalapati
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Tobin Hess
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Peter M. Kasson
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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16
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Yu J, Thomas PV, Sciacca M, Wu C, Liu J, He X, Miller J, Hachmann NP, Surve N, McMahan K, Jacob-Dolan C, Powers O, Hall K, Barrett J, Hope D, Mazurek CR, Murdza T, Chang WC, Golub E, Rees PA, Peterson CE, Hajduczki A, Chen WH, Martinez EJ, Hussin E, Lange C, Gong H, Matyas GR, Rao M, Suthar M, Boursiquot M, Cook A, Pessaint L, Lewis MG, Andersen H, Bolton DL, Michael NL, Joyce MG, Modjarrad K, Barouch DH. Ad26.COV2.S and SARS-CoV-2 spike protein ferritin nanoparticle vaccine protect against SARS-CoV-2 Omicron BA.5 challenge in macaques. Cell Rep Med 2023; 4:101018. [PMID: 37023746 PMCID: PMC10040355 DOI: 10.1016/j.xcrm.2023.101018] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 02/13/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines demonstrate reduced protection against acquisition of BA.5 subvariant but are still effective against severe disease. However, immune correlates of protection against BA.5 remain unknown. We report the immunogenicity and protective efficacy of vaccine regimens consisting of the vector-based Ad26.COV2.S vaccine and the adjuvanted spike ferritin nanoparticle (SpFN) vaccine against a high-dose, mismatched Omicron BA.5 challenge in macaques. The SpFNx3 and Ad26 + SpFNx2 regimens elicit higher antibody responses than Ad26x3, whereas the Ad26 + SpFNx2 and Ad26x3 regimens induce higher CD8 T cell responses than SpFNx3. The Ad26 + SpFNx2 regimen elicits the highest CD4 T cell responses. All three regimens suppress peak and day 4 viral loads in the respiratory tract, which correlate with both humoral and cellular immune responses. This study demonstrates that both homologous and heterologous regimens involving Ad26.COV2.S and SpFN vaccines provide robust protection against a mismatched BA.5 challenge in macaques.
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Affiliation(s)
- Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Paul V Thomas
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Michaela Sciacca
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Cindy Wu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Xuan He
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jessica Miller
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Nicole P Hachmann
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Nehalee Surve
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA; Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Olivia Powers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Kevin Hall
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Julia Barrett
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - David Hope
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Camille R Mazurek
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Tetyana Murdza
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - William C Chang
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA
| | - Emily Golub
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Phyllis A Rees
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Caroline E Peterson
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Agnes Hajduczki
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Wei-Hung Chen
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Elizabeth J Martinez
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Elizabeth Hussin
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Camille Lange
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Hua Gong
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Gary R Matyas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Mangala Rao
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | | | | | | | | | | | - Diane L Bolton
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Nelson L Michael
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
| | - M Gordon Joyce
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA.
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17
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Borghi M, Gallinaro A, Pirillo MF, Canitano A, Michelini Z, De Angelis ML, Cecchetti S, Tinari A, Falce C, Mariotti S, Capocefalo A, Chiantore MV, Iacobino A, Di Virgilio A, van Gils MJ, Sanders RW, Lo Presti A, Nisini R, Negri D, Cara A. Different configurations of SARS-CoV-2 spike protein delivered by integrase-defective lentiviral vectors induce persistent functional immune responses, characterized by distinct immunogenicity profiles. Front Immunol 2023; 14:1147953. [PMID: 37090707 PMCID: PMC10113491 DOI: 10.3389/fimmu.2023.1147953] [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: 01/19/2023] [Accepted: 03/13/2023] [Indexed: 04/08/2023] Open
Abstract
Several COVID-19 vaccine strategies utilizing new formulations for the induction of neutralizing antibodies (nAbs) and T cell immunity are still under evaluation in preclinical and clinical studies. Here we used Simian Immunodeficiency Virus (SIV)-based integrase defective lentiviral vector (IDLV) delivering different conformations of membrane-tethered Spike protein in the mouse immunogenicity model, with the aim of inducing persistent nAbs against multiple SARS-CoV-2 variants of concern (VoC). Spike modifications included prefusion-stabilizing double proline (2P) substitutions, mutations at the furin cleavage site (FCS), D614G mutation and truncation of the cytoplasmic tail (delta21) of ancestral and Beta (B.1.351) Spike, the latter mutation to markedly improve IDLV membrane-tethering. BALB/c mice were injected once with IDLV delivering the different forms of Spike or the recombinant trimeric Spike protein with 2P substitutions and FCS mutations in association with a squalene-based adjuvant. Anti-receptor binding domain (RBD) binding Abs, nAbs and T cell responses were detected up to six months from a single immunization with escalating doses of vaccines in all mice, but with different levels and kinetics. Results indicated that IDLV delivering the Spike protein with all the combined modifications, outperformed the other candidates in terms of T cell immunity and level of both binding Abs and nAbs soon after the single immunization and persistence over time, showing the best capacity to neutralize all formerly circulating VoC Alpha, Beta, Gamma and Delta. Although present, the lowest response was detected against Omicron variants (BA.1, BA.2 and BA.4/5), suggesting that the magnitude of immune evasion may be related to the higher genetic distance of Omicron as indicated by increased number of amino acid substitutions in Spike acquired during virus evolution.
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Affiliation(s)
- Martina Borghi
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | | | - Andrea Canitano
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Zuleika Michelini
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Laura De Angelis
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Serena Cecchetti
- Confocal Microscopy Unit, Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Antonella Tinari
- Center for Gender Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Chiara Falce
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Sabrina Mariotti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Antonio Capocefalo
- Department of Veterinary Public Health & Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | | | - Angelo Iacobino
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Antonio Di Virgilio
- Center for Animal Research and Welfare, Istituto Superiore di Sanità, Rome, Italy
| | - Marit J. van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Rogier W. Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | | | - Roberto Nisini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Donatella Negri
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
- *Correspondence: Donatella Negri, ; Andrea Cara,
| | - Andrea Cara
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
- *Correspondence: Donatella Negri, ; Andrea Cara,
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18
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Jacob-Dolan C, Yu J, McMahan K, Giffin V, Chandrashekar A, Martinot AJ, Anioke T, Powers OC, Hall K, Hope D, Miller J, Hachmann NP, Chung B, Gardner S, Sellers D, Barrett J, Lewis MG, Andersen H, Kleanthous H, Seo KW, Lee SJ, Park YW, Kim H, Barouch DH. Immunogenicity and protective efficacy of GBP510/AS03 vaccine against SARS-CoV-2 delta challenge in rhesus macaques. NPJ Vaccines 2023; 8:23. [PMID: 36823160 PMCID: PMC9947939 DOI: 10.1038/s41541-023-00622-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
Despite the availability of several effective SARS-CoV-2 vaccines, additional vaccines will be required for optimal global vaccination. In this study, we investigate the immunogenicity and protective efficacy of the GBP510 protein subunit vaccine adjuvanted with AS03, which has recently been authorized for marketing in South Korea under the trade name SKYCovioneTM. The antigen in GBP510/AS03 is a two-part recombinant nanoparticle, which displays 60 receptor binding domain (RBD) proteins of SARS-CoV-2 Spike on its surface. In this study we show that GBP510/AS03 induced robust immune responses in rhesus macaques and protected against a high-dose SARS-CoV-2 Delta challenge. We vaccinated macaques with two or three doses of GBP510/AS03 matched to the ancestral Wuhan strain of SARS-CoV-2 or with two doses of GBP510/AS03 matched to the ancestral strain and one dose matched to the Beta strain. Following the challenge with Delta, the vaccinated macaques rapidly controlled the virus in bronchoalveolar lavage and nasal swabs. Binding and neutralizing antibody responses prior to challenge correlated with protection against viral replication postchallenge. These data are consistent with data with this vaccine from the phase 3 clinical trial.
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Affiliation(s)
- Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Victoria Giffin
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Amanda J Martinot
- Tufts Cummings School of Veterinary Medicine, North Grafton, MA, 01536, USA
| | - Tochi Anioke
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Olivia C Powers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Kevin Hall
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - David Hope
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Jessica Miller
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Nichole P Hachmann
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Benjamin Chung
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Sarah Gardner
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Daniel Sellers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Julia Barrett
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | | | | | | | - Ki-Woen Seo
- Department of Research and Development, SK bioscience 310 Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Su Jeen Lee
- Department of Research and Development, SK bioscience 310 Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Yong Wook Park
- Department of Research and Development, SK bioscience 310 Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Hun Kim
- Department of Research and Development, SK bioscience 310 Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, 02115, USA.
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19
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Cytoplasmic Tail Truncation Stabilizes S1-S2 Association and Enhances S Protein Incorporation into SARS-CoV-2 Pseudovirions. J Virol 2023; 97:e0165022. [PMID: 36790205 PMCID: PMC10062125 DOI: 10.1128/jvi.01650-22] [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: 02/16/2023] Open
Abstract
Truncations of the cytoplasmic tail (CT) of entry proteins of enveloped viruses dramatically increase the infectivity of pseudoviruses (PVs) bearing these proteins. Several mechanisms have been proposed to explain this enhanced entry, including an increase in cell surface expression. However, alternative explanations have also been forwarded, and the underlying mechanisms for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) S protein remain undetermined. Here, we show that the partial or complete deletion of the CT (residues 19 to 35) does not modify SARS-CoV-2 S protein expression on the cell surface when the S2 subunit is measured, whereas it is significantly increased when the S1 subunit is measured. We also show that the higher level of S1 in these CT-truncated S proteins reflects the decreased dissociation of the S1 subunit from the S2 subunit. In addition, we demonstrate that CT truncation further promotes S protein incorporation into PV particles, as indicated by biochemical analyses and cryo-electron microscopy. Thus, our data show that two distinct mechanisms contribute to the markedly increased infectivity of PVs carrying CT-truncated SARS-CoV-2 S proteins and help clarify the interpretation of the results of studies employing such PVs. IMPORTANCE Various forms of PVs have been used as tools to evaluate vaccine efficacy and study virus entry steps. When PV infectivity is inherently low, such as that of SARS-CoV-2, a CT-truncated version of the viral entry glycoprotein is widely used to enhance PV infectivity, but the mechanism underlying this enhanced PV infectivity has been unclear. Here, our study identified two mechanisms by which the CT truncation of the SARS-CoV-2 S protein dramatically increases PV infectivity: a reduction of S1 shedding and an increase in S protein incorporation into PV particles. An understanding of these mechanisms can clarify the mechanistic bases for the differences observed among various assays employing such PVs.
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20
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Validation and Establishment of the SARS-CoV-2 Lentivirus Surrogate Neutralization Assay as a Prescreening Tool for the Plaque Reduction Neutralization Test. Microbiol Spectr 2023; 11:e0378922. [PMID: 36602312 PMCID: PMC9927366 DOI: 10.1128/spectrum.03789-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Neutralization assays are important for understanding and quantifying neutralizing antibody responses toward severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 lentivirus surrogate neutralization assay (SCLSNA) can be used in biosafety level 2 (BSL-2) laboratories and has been shown to be a reliable alternative approach to the plaque reduction neutralization test (PRNT). In this study, we optimized and validated the SCLSNA to assess its ability as a comparator and prescreening method to support the PRNT. Comparability between the PRNT and SCLSNA was determined through clinical sensitivity and specificity evaluations. Clinical sensitivity and specificity assays produced acceptable results, with 100% (95% confidence interval [CI], 94% to 100%) specificity and 100% (95% CI, 94% to 100%) sensitivity against ancestral Wuhan spike-pseudotyped lentivirus. The sensitivity and specificity against B.1.1.7 spike-pseudotyped lentivirus were 88.3% (95% CI, 77.8% to 94.2%) and 100% (95% CI, 94% to 100%), respectively. Assay precision measuring intra-assay variability produced acceptable results for high (50% PRNT [PRNT50], 1:≥640), mid (PRNT50, 1:160), and low (PRNT50, 1:40) antibody titer concentration ranges based on the PRNT50, with coefficients of variation (CVs) of 14.21%, 12.47%, and 13.28%, respectively. Intermediate precision indicated acceptable ranges for the high and mid concentrations, with CVs of 15.52% and 16.09%, respectively. However, the low concentration did not meet the acceptance criteria, with a CV of 26.42%. Acceptable ranges were found in the robustness evaluation for both intra-assay and interassay variability. In summary, the validation parameters tested met the acceptance criteria, making the SCLSNA method fit for its intended purpose, which can be used to support the PRNT. IMPORTANCE Neutralization studies play an important role in providing guidance and justification for vaccine administration and helping prevent the spread of diseases. The neutralization data generated in our laboratory have been included in the decision-making process of the National Advisory Committee on Immunization (NACI) in Canada. During the coronavirus 2019 (COVID-19) pandemic, the plaque reduction neutralization test (PRNT) has been the gold standard for determining neutralization of SARS-CoV-2. We validated a SARS-CoV-2 lentivirus surrogate neutralization assay (SCLSNA) as an alternative method to help support the PRNT. The advantages of using the SCLSNA is that it can process more samples, is less tedious to perform, and can be used in laboratories with a lower biosafety level. The use of the SCLSNA can further expand our capabilities to help fulfill the requirements for NACI and other important collaborations.
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21
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Hu L, Tang Y, Mei L, Liang M, Huang J, Wang X, Wu L, Jiang J, Li L, Long F, Xiao J, Tan L, Lu S, Peng T. A new intracellular targeting motif in the cytoplasmic tail of the spike protein may act as a target to inhibit SARS-CoV-2 assembly. Antiviral Res 2023; 209:105509. [PMID: 36572190 PMCID: PMC9788845 DOI: 10.1016/j.antiviral.2022.105509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022]
Abstract
Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a threat to global public health, underscoring the urgent need for the development of preventive and therapeutic measures. The spike (S) protein of SARS-CoV-2, which mediates receptor binding and subsequent membrane fusion to promote viral entry, is a major target for current drug development and vaccine design. The S protein comprises a large N-terminal extracellular domain, a transmembrane domain, and a short cytoplasmic tail (CT) at the C-terminus. CT truncation of the S protein has been previously reported to promote the infectivity of SARS-CoV and SARS-CoV-2 pseudoviruses. However, the underlying molecular mechanism has not been precisely elucidated. In addition, the CT of various viral membrane glycoproteins play an essential role in the assembly of virions, yet the role of the S protein CT in SARS-CoV-2 infection remains unclear. In this study, through constructing a series of mutations of the CT of the S protein and analyzing their impact on the packaging of the SARS-CoV-2 pseudovirus and live SARS-CoV-2 virus, we identified V1264L1265 as a new intracellular targeting motif in the CT of the S protein, that regulates the transport and subcellular localization of the spike protein through the interactions with cytoskeleton and vesicular transport-related proteins, ARPC3, SCAMP3, and TUBB8, thereby modulating SARS-CoV-2 pseudovirus and live SARS-CoV-2 virion assembly. Either disrupting the V1264L1265 motif or reducing the expression of ARPC3, SCAMP3, and TUBB8 significantly repressed the assembly of the live SARS-CoV-2 virion, raising the possibility that the V1264L1265 motif and the host responsive pathways involved could be new drug targets for the treatment of SARS-CoV-2 infection. Our results extend the understanding of the role played by the S protein CT in the assembly of pseudoviruses and live SARS-CoV-2 virions, which will facilitate the application of pseudoviruses to the study of SARS-CoV-2 and provide potential strategies for the treatment of SARS-CoV-2 infection.
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Affiliation(s)
- Longbo Hu
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China,Corresponding author
| | - Yongjie Tang
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Lingling Mei
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Mengdi Liang
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Jinxian Huang
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Xufei Wang
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Liping Wu
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Jiajing Jiang
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Leyi Li
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Fei Long
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Jing Xiao
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Long Tan
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Shaohua Lu
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Tao Peng
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China,Guangdong South China Vaccine, Guangzhou, China,Greater Bay Area Innovative Vaccine Technology Development Center, Guangzhou International Bio-island Laboratory, China,Corresponding author. State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
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22
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Wang Y, Zhou Z, Wu X, Li T, Wu J, Cai M, Nie J, Wang W, Cui Z. Pseudotyped Viruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1407:1-27. [PMID: 36920689 DOI: 10.1007/978-981-99-0113-5_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Pseudotyped viruses have been constructed for many viruses. They can mimic the authentic virus and have many advantages compared to authentic viruses. Thus, they have been widely used as a surrogate of authentic virus for viral function analysis, detection of neutralizing antibodies, screening viral entry inhibitors, and others. This chapter reviewed the progress in the field of pseudotyped viruses in general, including the definition and the advantages of pseudotyped viruses, their potential usage, different strategies or vectors used for the construction of pseudotyped viruses, and factors that affect the construction of pseudotyped viruses.
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Affiliation(s)
- Youchun Wang
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Kunming, China.
| | - Zehua Zhou
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China
| | - Xi Wu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China
| | - Tao Li
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China
| | - Jiajing Wu
- Beijing Yunling Biotechnology Co., Ltd., Beijing, China
| | - Meina Cai
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China
| | - Jianhui Nie
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China
| | - Wenbo Wang
- Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China
| | - Zhimin Cui
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China
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23
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Development of Fluorescence-Tagged SARS-CoV-2 Virus-like Particles by a Tri-Cistronic Vector Expression System for Investigating the Cellular Entry of SARS-CoV-2. Viruses 2022; 14:v14122825. [PMID: 36560829 PMCID: PMC9786960 DOI: 10.3390/v14122825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) has caused the pandemic that began late December 2019. The co-expression of SARS-CoV-2 structural proteins in cells could assemble into several types of virus-like particles (VLPs) without a viral RNA genome. VLPs containing S proteins with the structural and functional properties of authentic virions are safe materials to exploit for virus-cell entry and vaccine development. In this study, to generate SARS-CoV-2 VLPs (SCoV2-SEM VLPs) composed of three structural proteins including spike (S), envelop (E) protein and membrane (M) protein, a tri-cistronic vector expression system was established in a cell line co-expressing SARS-CoV-2 S, E and M proteins. The SCoV2-SEM VLPs were harvested from the cultured medium, and three structure proteins were confirmed by Western blot assay. A negative-stain TEM assay demonstrated the size of the SCoV2-SEM VLPs with a diameter of about 90 nm. To further characterize the infectious properties of SCoV2-SEM VLPs, the VLPs (atto647N-SCoV2-SEM VLPs) were fluorescence-labeled by conjugation with atto-647N and visualized under confocal microscopy at a single-particle resolution. The results of the infection assay revealed that atto647N-SCoV2-SEM VLPs attached to the surface of the HEK293T cells at the pre-binding phase in a ACE2-dependent manner. At the post-infection phase, atto647N-SCoV2-SEM VLPs either fused with the cellular membrane or internalized into the cytoplasm with mCherry-rab5-positive early endosomes. Moreover, fusion with the cellular membrane and the internalization with early endosomes could be inhibited by the treatment of camostat (a pharmacological inhibitor of TMPRSS2) and chlorpromazine (an endocytosis inhibitor), respectively. These results elucidated that SCoV2-SEM VLPs behave similarly to the authentic live SARS-CoV-2 virus, suggesting that the development of SCoV2-SEM VLPs provide a realistic and safe experimental model for studying the infectious mechanism of SARS-CoV-2.
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24
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Yu J, Thomas PV, McMahan K, Jacob-Dolan C, Liu J, He X, Hope D, Martinez EJ, Chen WH, Sciacca M, Hachmann NP, Lifton M, Miller J, Powers OC, Hall K, Wu C, Barrett J, Swafford I, Currier JR, King J, Corbitt C, Chang WC, Golub E, Rees PA, Peterson CE, Hajduczki A, Hussin E, Lange C, Gong H, Matyas GR, Rao M, Paquin-Proulx D, Gromowski GD, Lewis MG, Andersen H, Davis-Gardner M, Suthar MS, Michael NL, Bolton DL, Joyce MG, Modjarrad K, Barouch DH. Protection against SARS-CoV-2 Omicron BA.1 variant challenge in macaques by prime-boost vaccination with Ad26.COV2.S and SpFN. SCIENCE ADVANCES 2022; 8:eade4433. [PMID: 36417525 PMCID: PMC9683731 DOI: 10.1126/sciadv.ade4433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and waning immunity call for next-generation vaccine strategies. Here, we assessed the immunogenicity and protective efficacy of two SARS-CoV-2 vaccines targeting the WA1/2020 spike protein, Ad26.COV2.S (Ad26) and Spike ferritin Nanoparticle (SpFN), in nonhuman primates, delivered as either a homologous (SpFN/SpFN and Ad26/Ad26) or heterologous (Ad26/SpFN) prime-boost regimen. The Ad26/SpFN regimen elicited the highest CD4 T cell and memory B cell responses, the SpFN/SpFN regimen generated the highest binding and neutralizing antibody responses, and the Ad26/Ad26 regimen generated the most robust CD8 T cell responses. Despite these differences, protective efficacy against SARS-CoV-2 Omicron BA.1 challenge was similar for all three regimens. After challenge, all vaccinated monkeys showed significantly reduced peak and day 4 viral loads in both bronchoalveolar lavage and nasal swabs as compared with sham animals. The efficacy conferred by these three immunologically distinct vaccine regimens suggests that both humoral and cellular immunity contribute to protection against SARS-CoV-2 Omicron challenge.
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Affiliation(s)
- Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Paul V. Thomas
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02215, USA
- Harvard Medical School, Boston, MA 02215, USA
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Xuan He
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - David Hope
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Elizabeth J. Martinez
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Wei-Hung Chen
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Michaela Sciacca
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Nicole P. Hachmann
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Michelle Lifton
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Jessica Miller
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Olivia C. Powers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Kevin Hall
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Cindy Wu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Julia Barrett
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Isabella Swafford
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Jeffrey R. Currier
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Jocelyn King
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Courtney Corbitt
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - William C. Chang
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
| | - Emily Golub
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Phyllis A. Rees
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Caroline E. Peterson
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Agnes Hajduczki
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Elizabeth Hussin
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Camille Lange
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Hua Gong
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Gary R. Matyas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Mangala Rao
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Dominic Paquin-Proulx
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Gregory D. Gromowski
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | | | | | | | - Mehul S. Suthar
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Nelson L. Michael
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
| | - Diane L. Bolton
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - M. Gordon Joyce
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02215, USA
- Harvard Medical School, Boston, MA 02215, USA
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25
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Collier ARY, Miller J, Hachmann NP, McMahan K, Liu J, Apraku Bondzie E, Gallup L, Rowe M, Schonberg E, Thai S, Barrett J, Borducchi EN, Bouffard E, Jacob-Dolan C, Mazurek CR, Mutoni A, Powers O, Sciacca M, Surve N, VanWyk H, Wu C, Barouch DH. Immunogenicity of the BA.5 Bivalent mRNA Vaccine Boosters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.10.24.513619. [PMID: 36324798 PMCID: PMC9628195 DOI: 10.1101/2022.10.24.513619] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Waning immunity following mRNA vaccination and the emergence of SARS-CoV-2 variants has led to reduced mRNA vaccine efficacy against both symptomatic infection and severe disease. Bivalent mRNA boosters expressing the Omicron BA.5 and ancestral WA1/2020 Spike proteins have been developed and approved, because BA.5 is currently the dominant SARS-CoV-2 variant and substantially evades neutralizing antibodies (NAbs). Our data show that BA.5 NAb titers were comparable following monovalent and bivalent mRNA boosters.
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Affiliation(s)
| | | | | | | | - Jinyan Liu
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | - Lydia Gallup
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Marjorie Rowe
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | - Siline Thai
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Julia Barrett
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | | | | | | | - Audrey Mutoni
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Olivia Powers
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | - Nehalee Surve
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Haley VanWyk
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Cindy Wu
- Beth Israel Deaconess Medical Center, Boston, MA, USA
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26
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Ratnapriya S, Braun AR, Cervera H, Carlson D, Ding S, Paulson C, Mishra N, Sachs JN, Aldrich C, Finzi A, Herschhorn A. Broad Tricyclic Ring Inhibitors Block SARS-CoV-2 Spike Function Required for Viral Entry. ACS Infect Dis 2022; 8:2045-2058. [PMID: 36153947 PMCID: PMC9528568 DOI: 10.1021/acsinfecdis.1c00658] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Indexed: 01/29/2023]
Abstract
The entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into host cells requires binding of the viral spike glycoprotein to the angiotensin-converting enzyme 2 (ACE2) receptor, which triggers subsequent conformational changes to facilitate viral and cellular fusion at the plasma membrane or following endocytosis. Here, we experimentally identified selective and broad inhibitors of SARS-CoV-2 entry that share a tricyclic ring (or similar) structure. The inhibitory effect was restricted to early steps during infection and the entry inhibitors interacted with the receptor binding domain of the SARS-CoV-2 spike but did not significantly interfere with receptor (ACE2) binding. Instead, some of these compounds induced conformational changes or affected spike assembly and blocked SARS-CoV-2 spike cell-cell fusion activity. The broad inhibitors define a highly conserved binding pocket that is present on the spikes of SARS-CoV-1, SARS-CoV-2, and all circulating SARS-CoV-2 variants tested and block SARS-CoV spike activity required for mediating viral entry. These compounds provide new insights into the SARS-CoV-2 spike topography, as well as into critical steps on the entry pathway, and can serve as lead candidates for the development of broad-range entry inhibitors against SARS-CoVs.
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Affiliation(s)
- Sneha Ratnapriya
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Anthony R. Braun
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Héctor Cervera
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Danielle Carlson
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Carolyn Paulson
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Neeraj Mishra
- Department of Medicinal Chemistry, University of Minnesota, 8-101 WDH, 308 Harvard Street SE, Minneapolis, MN, 55455, United States; Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Jonathan N. Sachs
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Courtney Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 8-101 WDH, 308 Harvard Street SE, Minneapolis, MN, 55455, United States; Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Alon Herschhorn
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Microbiology, Immunology, and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, Minnesota 55455, USA
- The College of Veterinary Medicine Graduate Program, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA
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27
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Nkolola JP, Yu J, Wan H, Chang A, McMahan K, Anioke T, Jacob-Dolan C, Powers O, Ye T, Chandrashekar A, Sellers D, Barrett J, Loo YM, Esser MT, Carnahan RH, Crowe JE, Barouch DH. A bivalent SARS-CoV-2 monoclonal antibody combination does not affect the immunogenicity of a vector-based COVID-19 vaccine in macaques. Sci Transl Med 2022; 14:eabo6160. [PMID: 35857623 PMCID: PMC9348747 DOI: 10.1126/scitranslmed.abo6160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/21/2022] [Indexed: 11/06/2022]
Abstract
Human monoclonal antibodies (mAbs) that target the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) offer a promising approach for the prevention and treatment of coronavirus disease 2019 (COVID-19). Given suboptimal global vaccination rates, waning immunity in vaccinated individuals, and the emergence of SARS-CoV-2 variants of concern, the use of mAbs for COVID-19 prevention may increase and may need to be administered together with vaccines in certain settings. However, it is unknown whether administration of mAbs will affect the immunogenicity of SARS-CoV-2 vaccines. Using an adenovirus vector-based SARS-CoV-2 vaccine, we show that simultaneous administration of the vaccine with SARS-CoV-2 mAbs does not diminish vaccine-induced humoral or cellular immunity in cynomolgus macaques. These results suggest that SARS-CoV-2 mAbs and viral vector-based SARS-CoV-2 vaccines can be administered together without loss of potency of either product. Additional studies will be required to evaluate coadministration of mAbs with other vaccine platforms.
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Affiliation(s)
- Joseph P. Nkolola
- Center for Virology & Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Jingyou Yu
- Center for Virology & Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Huahua Wan
- Center for Virology & Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Aiquan Chang
- Center for Virology & Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Katherine McMahan
- Center for Virology & Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Tochi Anioke
- Center for Virology & Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Catherine Jacob-Dolan
- Center for Virology & Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Olivia Powers
- Center for Virology & Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Tianyi Ye
- Center for Virology & Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Abishek Chandrashekar
- Center for Virology & Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Daniel Sellers
- Center for Virology & Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Julia Barrett
- Center for Virology & Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Yueh-Ming Loo
- Microbial Sciences, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Mark T. Esser
- Microbial Sciences, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Robert H. Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Dan H. Barouch
- Center for Virology & Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
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28
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Ao Z, Ouyang MJ, Olukitibi TA, Warner B, Vendramelli R, Truong T, Meilleur C, Zhang M, Kung S, Fowke KR, Kobasa D, Yao X. A Recombinant VSV-Based Bivalent Vaccine Effectively Protects against Both SARS-CoV-2 and Influenza A Virus Infection. J Virol 2022; 96:e0133722. [PMID: 36069551 PMCID: PMC9517730 DOI: 10.1128/jvi.01337-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 12/03/2022] Open
Abstract
COVID-19 and influenza are both highly contagious respiratory diseases that have been serious threats to global public health. It is necessary to develop a bivalent vaccine to control these two infectious diseases simultaneously. In this study, we generated three attenuated replicating recombinant vesicular stomatitis virus (rVSV)-based vaccine candidates against both SARS-CoV-2 and influenza viruses. These rVSV-based vaccines coexpress SARS-CoV-2 Delta spike protein (SP) bearing the C-terminal 17 amino acid (aa) deletion (SPΔC) and I742A point mutation, or the SPΔC with a deletion of S2 domain, or the RBD domain, and a tandem repeat harboring four copies of the highly conserved influenza M2 ectodomain (M2e) that fused with the Ebola glycoprotein DC-targeting/activation domain. Animal immunization studies have shown that these rVSV bivalent vaccines induced efficient humoral and cellular immune responses against both SARS-CoV-2 SP and influenza M2 protein, including high levels of neutralizing antibodies against SARS-CoV-2 Delta and other variant SP-pseudovirus infections. Importantly, immunization of the rVSV bivalent vaccines effectively protected hamsters or mice against the challenges of SARS-CoV-2 Delta variant and lethal H1N1 and H3N2 influenza viruses and significantly reduced respiratory viral loads. Overall, this study provides convincing evidence for the high efficacy of this bivalent vaccine platform to be used and/or easily adapted to produce new vaccines against new or reemerging SARS-CoV-2 variants and influenza A virus infections. IMPORTANCE Given that both COVID-19 and influenza are preferably transmitted through respiratory droplets during the same seasons, it is highly advantageous to develop a bivalent vaccine that could simultaneously protect against both COVID-19 and influenza. In this study, we generated the attenuated replicating recombinant vesicular stomatitis virus (rVSV)-based vaccine candidates that target both spike protein of SARS-Cov-2 Delta variant and the conserved influenza M2 domain. Importantly, these vaccine candidates effectively protected hamsters or mice against the challenges of SARS-CoV-2 Delta variant and lethal H1N1 and H3N2 influenza viruses and significantly reduced respiratory viral loads.
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Affiliation(s)
- Zhujun Ao
- Laboratory of Molecular Human Retrovirology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Maggie J. Ouyang
- Laboratory of Molecular Human Retrovirology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Titus A. Olukitibi
- Laboratory of Molecular Human Retrovirology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Bryce Warner
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Robert Vendramelli
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Thang Truong
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Courtney Meilleur
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Manli Zhang
- Department of Immunology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sam Kung
- Department of Immunology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Keith R. Fowke
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Darwyn Kobasa
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Xiaojian Yao
- Laboratory of Molecular Human Retrovirology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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29
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Pastorio C, Zech F, Noettger S, Jung C, Jacob T, Sanderson T, Sparrer KMJ, Kirchhoff F. Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA.1 and BA.2. Cell Host Microbe 2022; 30:1255-1268.e5. [PMID: 35931073 PMCID: PMC9289044 DOI: 10.1016/j.chom.2022.07.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/29/2022] [Accepted: 07/12/2022] [Indexed: 12/02/2022]
Abstract
SARS-CoV-2 Omicron rapidly outcompeted other variants and currently dominates the COVID-19 pandemic. Its enhanced transmission and immune evasion are thought to be driven by numerous mutations in the Omicron Spike protein. Here, we systematically introduced BA.1 and/or BA.2 Omicron Spike mutations into the ancestral Spike protein and examined the impacts on Spike function, processing, and susceptibility to neutralization. Individual mutations of S371F/L, S375F, and T376A in the ACE2-receptor-binding domain as well as Q954H and N969K in the hinge region 1 impaired infectivity, while changes to G339D, D614G, N764K, and L981F moderately enhanced it. Most mutations in the N-terminal region and receptor-binding domain reduced the sensitivity of the Spike protein to neutralization by sera from individuals vaccinated with the BNT162b2 vaccine and by therapeutic antibodies. Our results represent a systematic functional analysis of Omicron Spike adaptations that have allowed this SARS-CoV-2 variant to dominate the current pandemic.
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Affiliation(s)
- Chiara Pastorio
- Institute of Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany
| | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany
| | - Sabrina Noettger
- Institute of Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany
| | - Christoph Jung
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany; Electrochemical Energy Storage, Helmholtz-Institute-Ulm (HIU), 89081 Ulm, Germany; Karlsruhe Institute of Technology (KIT), 76344 Karlsruhe, Germany
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany
| | | | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany.
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30
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Wu X, Liu J, Zhang H, Zhou H, Wang W, Ma Y, Shen S, Cai X, Huang A, Wang D. Immunomolecular assay based on selective virion capture by spike antibody and viral nucleic acid amplification for detecting intact SARS-CoV-2 particles. J Nanobiotechnology 2022; 20:399. [PMID: 36064407 PMCID: PMC9444083 DOI: 10.1186/s12951-022-01558-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/08/2022] [Indexed: 11/17/2022] Open
Abstract
Background Effective therapeutics and vaccines for coronavirus disease 2019 (COVID-19) are currently lacking because of the mutation and immune escape of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Based on the propagation characteristics of SARS-CoV-2, rapid and accurate detection of complete virions from clinical samples and the environment is critical for assessing infection risk and containing further COVID-19 outbreaks. However, currently applicable methods cannot achieve large-scale clinical application due to factors such as the high viral load, cumbersome virus isolation steps, demanding environmental conditions, and long experimental periods. In this study, we developed an immuno molecular detection method combining capture of the viral spike glycoprotein with monoclonal antibodies and nucleic acid amplification via quantitative reverse transcription PCR to rapidly and accurately detect complete virions. Results After constructing a novel pseudovirus, screening for specific antibodies, and optimizing the detection parameters, the assay achieved a limit of detection of 9 × 102 transduction units/mL of viral titer with high confidence (~ 95%) and excellent stability against human serum and common virus/pseudovirus. The coefficients of variation were 1.0 ~ 2.0% for intra-assay and inter-assay analyses, respectively. Compared with reverse transcription-PCR, the immunomolecular method more accurately quantified complete virions. SARS-CoV-2/pseudovirus was more stable on plastic and paper compared with aluminum and copper in the detection of SARS-CoV-2 pseudovirus under different conditions. Complete virions were detected up to 96 h after they were applied to these surfaces (except for copper), although the titer of the virions was greatly reduced. Conclusion Convenient, inexpensive, and accurate complete virus detection can be applied to many fields, including monitoring the infectivity of convalescent and post-discharge patients and assessing high-risk environments (isolation rooms, operating rooms, patient living environments, and cold chain logistics). This method can also be used to detect intact virions, including Hepatitis B and C viruses, human immunodeficiency virus, influenza, and the partial pulmonary virus, which may further improve the accuracy of diagnoses and facilitate individualized and precise treatments. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12951-022-01558-8.
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Affiliation(s)
- Xiaoli Wu
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Department of Infectious Diseases, Institute for Viral Hepatitis, Chongqing Medical University, Yuzhong, 400016, Chongqing, China.,College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, Yuzhong, China
| | - Junye Liu
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Department of Infectious Diseases, Institute for Viral Hepatitis, Chongqing Medical University, Yuzhong, 400016, Chongqing, China
| | - Hongpeng Zhang
- Department of Blood Transfusion, Women and Children's Hospital of Chongqing Medical University, Chongqing, 401147, China.,Department of Blood Transfusion, Chongqing Health Center for Women and Children, Chongqing, 401147, China
| | - Hua Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, Yuzhong, China
| | - Wen Wang
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Department of Infectious Diseases, Institute for Viral Hepatitis, Chongqing Medical University, Yuzhong, 400016, Chongqing, China
| | - Yuanyan Ma
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Department of Infectious Diseases, Institute for Viral Hepatitis, Chongqing Medical University, Yuzhong, 400016, Chongqing, China
| | - Shimei Shen
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Department of Infectious Diseases, Institute for Viral Hepatitis, Chongqing Medical University, Yuzhong, 400016, Chongqing, China
| | - Xuefei Cai
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Department of Infectious Diseases, Institute for Viral Hepatitis, Chongqing Medical University, Yuzhong, 400016, Chongqing, China
| | - Ailong Huang
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Department of Infectious Diseases, Institute for Viral Hepatitis, Chongqing Medical University, Yuzhong, 400016, Chongqing, China
| | - Deqiang Wang
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Department of Infectious Diseases, Institute for Viral Hepatitis, Chongqing Medical University, Yuzhong, 400016, Chongqing, China. .,College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, Yuzhong, China.
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31
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Liu J, Yu J, McMahan K, Jacob-Dolan C, He X, Giffin V, Wu C, Sciacca M, Powers O, Nampanya F, Miller J, Lifton M, Hope D, Hall K, Hachmann NP, Chung B, Anioke T, Li W, Muench J, Gamblin A, Boursiquot M, Cook A, Lewis MG, Andersen H, Barouch DH. CD8 T Cells Contribute to Vaccine Protection Against SARS-CoV-2 in Macaques. Sci Immunol 2022; 7:eabq7647. [PMID: 35943359 PMCID: PMC9407944 DOI: 10.1126/sciimmunol.abq7647] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Spike-specific neutralizing antibodies (NAbs) are generally considered key correlates of vaccine protection against SARS-CoV-2 infection. Recently, robust vaccine prevention of severe disease with SARS-CoV-2 variants that largely escape NAb responses has been reported, suggesting a role for other immune parameters for virologic control. However, direct data demonstrating a role of CD8+ T cells in vaccine protection has not yet been reported. In this study, we show that vaccine-elicited CD8+ T cells contribute substantially to virologic control following SARS-CoV-2 challenge in rhesus macaques. We vaccinated 30 macaques with a single immunization of the adenovirus vector-based vaccine Ad26.COV2.S or sham and then challenged them with 5x105 TCID50 SARS-CoV-2 B.1.617.2 (Delta) by the intranasal and intratracheal routes. All vaccinated animals were infected by this high-dose challenge but showed rapid virologic control in nasal swabs and bronchoalveolar lavage by day 4 following challenge. However, administration of an anti-CD8α or anti-CD8β depleting monoclonal antibody in vaccinated animals prior to SARS-CoV-2 challenge resulted in higher levels of peak and day 4 virus in both the upper and lower respiratory tracts. These data demonstrate that CD8+ T cells contribute substantially to vaccine protection against SARS-CoV-2 replication in macaques.
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Affiliation(s)
- Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Xuan He
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Victoria Giffin
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Cindy Wu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Michaela Sciacca
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Olivia Powers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Felix Nampanya
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Jessica Miller
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Michelle Lifton
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - David Hope
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Kevin Hall
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Nicole P Hachmann
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Benjamin Chung
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Tochi Anioke
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Wenjun Li
- University of Massachusetts, Lowell, MA 01854, USA
| | | | | | | | | | | | | | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
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32
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Nanishi E, McGrath ME, O'Meara TR, Barman S, Yu J, Wan H, Dillen CA, Menon M, Seo HS, Song K, Xu AZ, Sebastian L, Brook B, Bosco AN, Borriello F, Ernst RK, Barouch DH, Dhe-Paganon S, Levy O, Frieman MB, Dowling DJ. mRNA booster vaccination protects aged mice against the SARS-CoV-2 Omicron variant. Commun Biol 2022; 5:790. [PMID: 35933439 PMCID: PMC9357006 DOI: 10.1038/s42003-022-03765-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/25/2022] [Indexed: 01/04/2023] Open
Abstract
The SARS-CoV-2 Omicron variant evades vaccine-induced immunity. While a booster dose of ancestral mRNA vaccines effectively elicits neutralizing antibodies against variants, its efficacy against Omicron in older adults, who are at the greatest risk of severe disease, is not fully elucidated. Here, we evaluate multiple longitudinal immunization regimens of mRNA BNT162b2 to assess the effects of a booster dose provided >8 months after the primary immunization series across the murine lifespan, including in aged 21-month-old mice. Boosting dramatically enhances humoral and cell-mediated responses with evidence of Omicron cross-recognition. Furthermore, while younger mice are protected without a booster dose, boosting provides sterilizing immunity against Omicron-induced lung infection in aged 21-month-old mice. Correlational analyses reveal that neutralizing activity against Omicron is strongly associated with protection. Overall, our findings indicate age-dependent vaccine efficacy and demonstrate the potential benefit of mRNA booster immunization to protect vulnerable older populations against SARS-CoV-2 variants. A longitudinal study in mice reveals that a booster dose of mRNA vaccine BNT162b2 enhances humoral and cell-mediated responses and provides sterilizing immunity against Omicron-induced lung infection in aged animals.
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Affiliation(s)
- Etsuro Nanishi
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Marisa E McGrath
- Department of Microbiology and Immunology, The Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Timothy R O'Meara
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Soumik Barman
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Huahua Wan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Carly A Dillen
- Department of Microbiology and Immunology, The Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Manisha Menon
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Kijun Song
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andrew Z Xu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Luke Sebastian
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Byron Brook
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Anna-Nicole Bosco
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Francesco Borriello
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Division of Immunology, Boston Children's Hospital, Boston, MA, USA.,Generate Biomedicines, Cambridge, MA, USA
| | - Robert K Ernst
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ofer Levy
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Matthew B Frieman
- Department of Microbiology and Immunology, The Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - David J Dowling
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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33
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Tan CS, Collier ARY, Yu J, Liu J, Chandrashekar A, McMahan K, Jacob-Dolan C, He X, Roy V, Hauser BM, Munt JE, Mallory ML, Mattocks M, Powers JM, Meganck RM, Rowe M, Hemond R, Bondzie EA, Jaegle KH, Baric RS, Schmidt AG, Alter G, Le Gars M, Sadoff J, Barouch DH. Durability of Heterologous and Homologous COVID-19 Vaccine Boosts. JAMA Netw Open 2022; 5:e2226335. [PMID: 35947380 PMCID: PMC9366542 DOI: 10.1001/jamanetworkopen.2022.26335] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
IMPORTANCE Antibody responses elicited by current messenger RNA (mRNA) COVID-19 vaccines decline rapidly and require repeated boosting. OBJECTIVE To evaluate the immunogenicity and durability of heterologous and homologous prime-boost regimens involving the adenovirus vector vaccine Ad26.COV2.S and the mRNA vaccine BNT162b2. DESIGN, SETTING, AND PARTICIPANTS In this cohort study at a single clinical site in Boston, Massachusetts, 68 individuals who were vaccinated at least 6 months previously with 2 immunizations of BNT162b2 were boosted with either Ad26.COV2.S or BNT162b2. Enrollment of participants occurred from August 12, 2021, to October 25, 2021, and this study involved 4 months of follow-up. Data analysis was performed from November 2021 to February 2022. EXPOSURES Participants who were previously vaccinated with BNT162b2 received a boost with either Ad26.COV2.S or BNT162b2. MAIN OUTCOMES AND MEASURES Humoral immune responses were assessed by neutralizing, binding, and functional antibody responses for 16 weeks following the boost. CD8+ and CD4+ T-cell responses were evaluated by intracellular cytokine staining assays. RESULTS Among 68 participants who were originally vaccinated with BNT162b2 and boosted with Ad26.COV2.S (41 participants; median [range] age, 36 [23-84] years) or BNT162b2 (27 participants; median [range] age, 35 [23-76] years), 56 participants (82%) were female, 7 (10%) were Asian, 4 (6%) were Black, 4 (6%) were Hispanic or Latino, 3 (4%) were more than 1 race, and 53 (78%) were White. Both vaccines were found to be associated with increased humoral and cellular immune responses, including against SARS-CoV-2 variants of concern. BNT162b2 boosting was associated with a rapid increase of Omicron neutralizing antibodies that peaked at a median (IQR) titer of 1018 (699-1646) at week 2 and declined by 6.9-fold to a median (IQR) titer of 148 (95-266) by week 16. Ad26.COV2.S boosting was associated with increased Omicron neutralizing antibodies titers that peaked at a median (IQR) of 859 (467-1838) week 4 and declined by 2.1-fold to a median (IQR) of 403 (208-1130) by week 16. CONCLUSIONS AND RELEVANCE Heterologous Ad26.COV2.S boosting was associated with durable humoral and cellular immune responses in individuals who originally received the BNT162b2 vaccine. These data suggest potential benefits of heterologous prime-boost vaccine regimens for SARS-CoV-2.
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Affiliation(s)
- C. Sabrina Tan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Ai-ris Y. Collier
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Xuan He
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Vicky Roy
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge
| | - Blake M. Hauser
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge
| | | | | | | | | | | | - Marjorie Rowe
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Rachel Hemond
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Esther A. Bondzie
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Kate H. Jaegle
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | - Aaron G. Schmidt
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge
| | - Galit Alter
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge
| | | | - Jerald Sadoff
- Janssen Vaccines and Prevention, Leiden, Netherlands
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
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34
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Gebre MS, Rauch S, Roth N, Gergen J, Yu J, Liu X, Cole AC, Mueller SO, Petsch B, Barouch DH. mRNA vaccines induce rapid antibody responses in mice. NPJ Vaccines 2022; 7:88. [PMID: 35915094 PMCID: PMC9340693 DOI: 10.1038/s41541-022-00511-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/01/2022] [Indexed: 12/05/2022] Open
Abstract
mRNA vaccines can be developed and produced quickly, making them prime candidates for immediate outbreak responses. Furthermore, clinical trials have demonstrated rapid protection following mRNA vaccination. Thus, we sought to investigate how quickly mRNA vaccines elicit antibody responses compared to other vaccine modalities. We first compared the immune kinetics of mRNA and DNA vaccines expressing SARS-CoV-2 spike in mice. We observed rapid induction of antigen-specific binding and neutralizing antibodies by day 5 following mRNA (4 µg/mouse), but not DNA (50 µg/mouse), immunization. Comparing innate responses hours post immunization, the mRNA vaccine induced increased levels of IL-5, IL-6, and MCP-1 cytokines which maybe promoting humoral responses downstream. We then evaluated the immune kinetics of an HIV-1 mRNA vaccine in comparison to DNA, protein, and rhesus adenovirus 52 (RhAd52) vaccines of the same HIV-1 envelope antigen in mice. Again, induction of envelope-specific antibodies was observed by day 5 following mRNA vaccination, whereas antibodies were detected by day 7–14 following DNA, protein, and RhAd52 vaccination. Thus, eliciting rapid humoral immunity may be a unique and advantageous property of mRNA vaccines for controlling infectious disease outbreaks.
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Affiliation(s)
- Makda S Gebre
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | | | | | | | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Xiaowen Liu
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Andrew C Cole
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | | | | | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA. .,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
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35
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Yan LN, Zhao ZX, Wang ZD, Xiao X, Liu PP, Zhang WK, Gu XL, Li B, Yu LP, Yu XJ. Neutralizing antibodies and cellular immune response after two doses of inactivated SARS-CoV-2 vaccine in China. Expert Rev Vaccines 2022; 21:1465-1473. [PMID: 35861138 DOI: 10.1080/14760584.2022.2104714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND As of 2022, inactivated SARS-CoV-2 vaccines had been used in more than 91 countries. However, limited information was available on the immune responses of the inactivated SARS-CoV-2 vaccine in the real world. METHODS We used SARS-CoV-2 pseudovirus to determine neutralizing antibodies (NAbs) to wild type and several global variants and utilized enzyme-linked immunosorbent assay to investigate IFN-γ-secreting T-cell responses to SARS-CoV-2 among 240 vaccinees after two doses of inactivated vaccine in China. RESULTS A majority of vaccinees (>90%) have developed robust NAbs and T-cell responses to SARS-CoV-2 in the first two months after the second dose. After six months, only 37.0% and 44.0% of vaccinees had NAbs and T-cell immunity to SARS-CoV-2, respectively. Immune serum retained most of neutralizing potency against Alpha and Iota variants, but significantly lost neutralizing potency against Beta, Kappa, Delta, and Omicron variants. Only 40% vaccine-sera remained low-level neutralization activities to Omicron, with a 14.7-fold decrease compared to wild type. CONCLUSION The inactivated SARS-CoV-2 vaccine stimulated robust NAbs and T-cell immune responses in the first two months after the second dose but the immune effect drops rapidly, which highlights that a third or more dose boost shot may be required to boost immunity against SARS-CoV-2.
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Affiliation(s)
- Li-Na Yan
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, Hubei, P.R. China
| | - Zhong-Xin Zhao
- Department of Laboratory Medicine, Linyi People's Hospital, Linyi, Shandong, P.R. China
| | - Zhen-Dong Wang
- School of Public Health, Xi'an Medical University, Xi'an, Shanxi, P.R. China
| | - Xiao Xiao
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, Hubei, P.R. China
| | - Pan-Pan Liu
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, Hubei, P.R. China
| | - Wen-Kang Zhang
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, Hubei, P.R. China
| | - Xiao-Lan Gu
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, Hubei, P.R. China
| | - Bang Li
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, Hubei, P.R. China
| | - Li-Ping Yu
- School of Nursing, Wuhan University, Wuhan, Hubei, P.R. China
| | - Xue-Jie Yu
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, Hubei, P.R. China
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36
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Fujioka Y, Kashiwagi S, Yoshida A, Satoh AO, Fujioka M, Amano M, Yamauchi Y, Ohba Y. A method for the generation of pseudovirus particles bearing SARS coronavirus spike protein in high yields. Cell Struct Funct 2022; 47:43-53. [PMID: 35491102 PMCID: PMC10511058 DOI: 10.1247/csf.21047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 04/19/2022] [Indexed: 12/17/2023] Open
Abstract
The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has threatened human health and the global economy. Development of additional vaccines and therapeutics is urgently required, but such development with live virus must be conducted with biosafety level 3 confinement. Pseudotyped viruses have been widely adopted for studies of virus entry and pharmaceutical development to overcome this restriction. Here we describe a modified protocol to generate vesicular stomatitis virus (VSV) pseudotyped with SARS-CoV or SARS-CoV-2 spike protein in high yield. We found that a large proportion of pseudovirions produced with the conventional transient expression system lacked coronavirus spike protein at their surface as a result of inhibition of parental VSV infection by overexpression of this protein. Establishment of stable cell lines with an optimal expression level of coronavirus spike protein allowed the efficient production of progeny pseudoviruses decorated with spike protein. This improved VSV pseudovirus production method should facilitate studies of coronavirus entry and development of antiviral agents.Key words: severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, pseudovirus, vesicular stomatitis virus (VSV), spike protein.
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Affiliation(s)
- Yoichiro Fujioka
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, N12W6, Kita-ku, Sapporo 060-8612, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Sayaka Kashiwagi
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, N12W6, Kita-ku, Sapporo 060-8612, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Aiko Yoshida
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, N12W6, Kita-ku, Sapporo 060-8612, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Aya O. Satoh
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Mari Fujioka
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Maho Amano
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Yohei Yamauchi
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Yusuke Ohba
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, N12W6, Kita-ku, Sapporo 060-8612, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
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37
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Yarovaya OI, Shcherbakov DN, Borisevich SS, Sokolova AS, Gureev MA, Khamitov EM, Rudometova NB, Zybkina AV, Mordvinova ED, Zaykovskaya AV, Rogachev AD, Pyankov OV, Maksyutov RA, Salakhutdinov NF. Borneol Ester Derivatives as Entry Inhibitors of a Wide Spectrum of SARS-CoV-2 Viruses. Viruses 2022; 14:v14061295. [PMID: 35746766 PMCID: PMC9228966 DOI: 10.3390/v14061295] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 12/13/2022] Open
Abstract
In the present work we studied the antiviral activity of the home library of monoterpenoid derivatives using the pseudoviral systems of our development, which have glycoproteins of the SARS-CoV-2 virus strains Wuhan and Delta on their surface. We found that borneol derivatives with a tertiary nitrogen atom can exhibit activity at the early stages of viral replication. In order to search for potential binding sites of ligands with glycoprotein, we carried out additional biological tests to study the inhibition of the re-receptor-binding domain of protein S. For the compounds that showed activity on the pseudoviral system, a study using three strains of the infectious SARS-CoV-2 virus was carried out. As a result, two leader compounds were found that showed activity on the Wuhan, Delta, and Omicron strains. Based on the biological results, we searched for the potential binding site of the leader compounds using molecular dynamics and molecular docking methods. We suggested that the compounds can bind in conserved regions of the central helices and/or heptad repeats of glycoprotein S of SARS-CoV-2 viruses.
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Affiliation(s)
- Olga I. Yarovaya
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev ave., 9, 630090 Novosibirsk, Russia; (A.S.S.); (E.D.M.); (A.D.R.); (N.F.S.)
- Correspondence:
| | - Dmitriy N. Shcherbakov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.B.R.); (A.V.Z.); (A.V.Z.); (O.V.P.); (R.A.M.)
| | - Sophia S. Borisevich
- Laboratory of Chemical Physics Ufa Institute of Chemistry, Ufa Federal Research Center, RAS, Octyabrya pr., 71, 450054 Ufa, Russia; (S.S.B.); (E.M.K.)
| | - Anastasiya S. Sokolova
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev ave., 9, 630090 Novosibirsk, Russia; (A.S.S.); (E.D.M.); (A.D.R.); (N.F.S.)
| | - Maxim A. Gureev
- Research Center “Digital Biodesign and Personalized Healthcare”, I.M. Sechenov First Moscow State Medical University, Trubetskaya str., 8/2, 119991 Moscow, Russia;
- Department of Computational Biology, Sirius University of Science and Technology, Olympic Ave., 1, 354340 Sochi, Russia
| | - Edward M. Khamitov
- Laboratory of Chemical Physics Ufa Institute of Chemistry, Ufa Federal Research Center, RAS, Octyabrya pr., 71, 450054 Ufa, Russia; (S.S.B.); (E.M.K.)
| | - Nadezda B. Rudometova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.B.R.); (A.V.Z.); (A.V.Z.); (O.V.P.); (R.A.M.)
| | - Anastasiya V. Zybkina
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.B.R.); (A.V.Z.); (A.V.Z.); (O.V.P.); (R.A.M.)
| | - Ekaterina D. Mordvinova
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev ave., 9, 630090 Novosibirsk, Russia; (A.S.S.); (E.D.M.); (A.D.R.); (N.F.S.)
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.B.R.); (A.V.Z.); (A.V.Z.); (O.V.P.); (R.A.M.)
| | - Anna V. Zaykovskaya
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.B.R.); (A.V.Z.); (A.V.Z.); (O.V.P.); (R.A.M.)
| | - Artem D. Rogachev
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev ave., 9, 630090 Novosibirsk, Russia; (A.S.S.); (E.D.M.); (A.D.R.); (N.F.S.)
| | - Oleg V. Pyankov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.B.R.); (A.V.Z.); (A.V.Z.); (O.V.P.); (R.A.M.)
| | - Rinat A. Maksyutov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.B.R.); (A.V.Z.); (A.V.Z.); (O.V.P.); (R.A.M.)
| | - Nariman F. Salakhutdinov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev ave., 9, 630090 Novosibirsk, Russia; (A.S.S.); (E.D.M.); (A.D.R.); (N.F.S.)
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Torres JL, Ozorowski G, Andreano E, Liu H, Copps J, Piccini G, Donnici L, Conti M, Planchais C, Planas D, Manganaro N, Pantano E, Paciello I, Pileri P, Bruel T, Montomoli E, Mouquet H, Schwartz O, Sala C, De Francesco R, Wilson IA, Rappuoli R, Ward AB. Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody. Proc Natl Acad Sci U S A 2022; 119:e2120976119. [PMID: 35549549 PMCID: PMC9171815 DOI: 10.1073/pnas.2120976119] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/04/2022] [Indexed: 11/18/2022] Open
Abstract
As the coronavirus disease 2019 (COVID-19) pandemic continues, there is a strong need for highly potent monoclonal antibodies (mAbs) that are resistant against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VoCs). Here, we evaluate the potency of the previously described mAb J08 against these variants using cell-based assays and delve into the molecular details of the binding interaction using cryoelectron microscopy (cryo-EM) and X-ray crystallography. We show that mAb J08 has low nanomolar affinity against most VoCs and binds high on the receptor binding domain (RBD) ridge, away from many VoC mutations. These findings further validate the phase II/III human clinical trial underway using mAb J08 as a monoclonal therapy.
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Affiliation(s)
- Jonathan L. Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Emanuele Andreano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, 53100 Siena, Italy
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | | | - Lorena Donnici
- Istituto Nazionale Genetica Molecolare INGM “Romeo ed Enrica Invernizzi”, 20122 Milan, Italy
| | - Matteo Conti
- Istituto Nazionale Genetica Molecolare INGM “Romeo ed Enrica Invernizzi”, 20122 Milan, Italy
| | - Cyril Planchais
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, INSERM U1222, 75015 Paris, France
| | - Delphine Planas
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, 75015 Paris, France
- Vaccine Research Institute, 94000 Creteil, France
| | - Noemi Manganaro
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, 53100 Siena, Italy
| | - Elisa Pantano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, 53100 Siena, Italy
| | - Ida Paciello
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, 53100 Siena, Italy
| | - Piero Pileri
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, 53100 Siena, Italy
| | - Timothée Bruel
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, 75015 Paris, France
- Vaccine Research Institute, 94000 Creteil, France
| | - Emanuele Montomoli
- VisMederi S.r.l, 53100 Siena, Italy
- VisMederi Research S.r.l., 53100 Siena, Italy
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy
| | - Hugo Mouquet
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, INSERM U1222, 75015 Paris, France
| | - Olivier Schwartz
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, 75015 Paris, France
- Vaccine Research Institute, 94000 Creteil, France
| | - Claudia Sala
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, 53100 Siena, Italy
| | - Raffaele De Francesco
- Istituto Nazionale Genetica Molecolare INGM “Romeo ed Enrica Invernizzi”, 20122 Milan, Italy
- Department of Pharmacological and Biomolecular Sciences DiSFeB, University of Milan, 20122 Milan, Italy
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Rino Rappuoli
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, 53100 Siena, Italy
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
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39
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Chandrashekar A, Yu J, McMahan K, Jacob-Dolan C, Liu J, He X, Hope D, Anioke T, Barrett J, Chung B, Hachmann NP, Lifton M, Miller J, Powers O, Sciacca M, Sellers D, Siamatu M, Surve N, VanWyk H, Wan H, Wu C, Pessaint L, Valentin D, Van Ry A, Muench J, Boursiquot M, Cook A, Velasco J, Teow E, Boon ACM, Suthar MS, Jain N, Martinot AJ, Lewis MG, Andersen H, Barouch DH. Vaccine protection against the SARS-CoV-2 Omicron variant in macaques. Cell 2022; 185:1549-1555.e11. [PMID: 35427477 PMCID: PMC8926910 DOI: 10.1016/j.cell.2022.03.024] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/28/2022] [Accepted: 03/14/2022] [Indexed: 12/12/2022]
Abstract
The rapid spread of the SARS-CoV-2 Omicron (B.1.1.529) variant, including in highly vaccinated populations, has raised important questions about the efficacy of current vaccines. In this study, we show that the mRNA-based BNT162b2 vaccine and the adenovirus-vector-based Ad26.COV2.S vaccine provide robust protection against high-dose challenge with the SARS-CoV-2 Omicron variant in cynomolgus macaques. We vaccinated 30 macaques with homologous and heterologous prime-boost regimens with BNT162b2 and Ad26.COV2.S. Following Omicron challenge, vaccinated macaques demonstrated rapid control of virus in bronchoalveolar lavage, and most vaccinated animals also controlled virus in nasal swabs. However, 4 vaccinated animals that had moderate Omicron-neutralizing antibody titers and undetectable Omicron CD8+ T cell responses failed to control virus in the upper respiratory tract. Moreover, virologic control correlated with both antibody and T cell responses. These data suggest that both humoral and cellular immune responses contribute to vaccine protection against a highly mutated SARS-CoV-2 variant.
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Affiliation(s)
- Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Xuan He
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - David Hope
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Tochi Anioke
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Julia Barrett
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Benjamin Chung
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Nicole P Hachmann
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Michelle Lifton
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Jessica Miller
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Olivia Powers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Michaela Sciacca
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Daniel Sellers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Mazuba Siamatu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Nehalee Surve
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Haley VanWyk
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Huahua Wan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Cindy Wu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | | | | | | | | | | | | | | | | | | | | | - Neharika Jain
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - Amanda J Martinot
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | | | | | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
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40
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Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic demonstrates the threat posed by novel coronaviruses to human health. Coronaviruses share a highly conserved cell entry mechanism mediated by the spike protein, the sole product of the S gene. The structural dynamics by which the spike protein orchestrates infection illuminate how antibodies neutralize virions and how S mutations contribute to viral fitness. Here, we review the process by which spike engages its proteinaceous receptor, angiotensin converting enzyme 2 (ACE2), and how host proteases prime and subsequently enable efficient membrane fusion between virions and target cells. We highlight mutations common among severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern and discuss implications for cell entry. Ultimately, we provide a model by which sarbecoviruses are activated for fusion competency and offer a framework for understanding the interplay between humoral immunity and the molecular evolution of the SARS-CoV-2 Spike. In particular, we emphasize the relevance of the Canyon Hypothesis (M. G. Rossmann, J Biol Chem 264:14587-14590, 1989) for understanding evolutionary trajectories of viral entry proteins during sustained intraspecies transmission of a novel viral pathogen.
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Affiliation(s)
- Kyle A. Wolf
- Department of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Interdiscipinary Ph.D. Program in Structural and Computational Biology and Quantitative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason C. Kwan
- Department of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jeremy P. Kamil
- Department of Microbiology and Immunology, Louisiana State University Health Shreveport, Shreveport, Louisiana, USA
- Center for Excellence in Emerging Viral Threats, Louisiana State University Health Shreveport, Shreveport, Louisiana, USA
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41
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Collier ARY, Brown CM, McMahan KA, Yu J, Liu J, Jacob-Dolan C, Chandrashekar A, Tierney D, Ansel JL, Rowe M, Sellers D, Ahmad K, Aguayo R, Anioke T, Gardner S, Siamatu M, Bermudez Rivera L, Hacker MR, Madoff LC, Barouch DH. Characterization of immune responses in fully vaccinated individuals after breakthrough infection with the SARS-CoV-2 delta variant. Sci Transl Med 2022; 14:eabn6150. [PMID: 35258323 PMCID: PMC8995036 DOI: 10.1126/scitranslmed.abn6150] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/25/2022] [Indexed: 01/06/2023]
Abstract
Breakthrough infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have been reported frequently in vaccinated individuals with waning immunity. In particular, a cluster of over 1000 infections with the SARS-CoV-2 delta variant was identified in a predominantly fully vaccinated population in Provincetown, Massachusetts in July 2021. In this study, vaccinated individuals who tested positive for SARS-CoV-2 (n = 16) demonstrated substantially higher serum antibody responses than vaccinated individuals who tested negative for SARS-CoV-2 (n = 23), including 32-fold higher binding antibody titers and 31-fold higher neutralizing antibody titers against the SARS-CoV-2 delta variant. Vaccinated individuals who tested positive also showed higher mucosal antibody responses in nasal secretions and higher spike protein-specific CD8+ T cell responses in peripheral blood than did vaccinated individuals who tested negative. These data demonstrate that fully vaccinated individuals developed robust anamnestic antibody and T cell responses after infection with the SARS-CoV-2 delta variant. Moreover, these findings suggest that population immunity will likely increase over time by a combination of widespread vaccination and breakthrough infections.
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Affiliation(s)
- Ai-ris Y. Collier
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA 02115
- Harvard Medical School, Boston, MA, USA 02115
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, MA, USA 02215
| | | | - Katherine A. McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA 02115
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA 02115
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA 02115
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA 02115
- Harvard Medical School, Boston, MA, USA 02115
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA 02115
| | - Dylan Tierney
- Massachusetts Department of Public Health, Boston, MA, USA 02108
| | - Jessica L. Ansel
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA 02115
| | - Marjorie Rowe
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA 02115
| | - Daniel Sellers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA 02115
| | - Kunza Ahmad
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA 02115
| | - Ricardo Aguayo
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA 02115
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, MA, USA 02215
| | - Tochi Anioke
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA 02115
| | - Sarah Gardner
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA 02115
| | - Mazuba Siamatu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA 02115
| | - Lorraine Bermudez Rivera
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA 02115
| | - Michele R. Hacker
- Harvard Medical School, Boston, MA, USA 02115
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, MA, USA 02215
| | | | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA 02115
- Harvard Medical School, Boston, MA, USA 02115
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA 02139
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42
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Li S, Fan S, Li N, Shen Y, Xiang X, Chen W, Xia J, Han X, Cui M, Huang Y. The N1038S Substitution and 1153EQTRPKKSV 1162 Deletion of the S2 Subunit of QX-Type Avian Infectious Bronchitis Virus Can Synergistically Enhance Viral Proliferation. Front Microbiol 2022; 13:829218. [PMID: 35432239 PMCID: PMC9006875 DOI: 10.3389/fmicb.2022.829218] [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: 12/05/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
The S2 subunit of infectious bronchitis virus (IBV) plays a critical role in the process of IBV infection. A comparison between the S2 subunit sequence of chicken embryo kidney cell (CEK) adapted virulent QX-like IBV strain SczyC30 (hereafter referred to as zy30) and its CEK-attenuated strain, SczyC100, revealed an N1038S substitution in S2 subunit and a 1154EQTRPKKSV1162 residue deletion in the C-terminus of the S2 subunit. In order to explore whether these two mutations are related to changes in the biological characteristics of IBV, we firstly constructed an infectious clone of zy30 using a bacterial artificial chromosome (BAC), which combines the transcription of infectious IBV genomic RNA in non-susceptible BHK-21 cells with the amplification of rescued virus rzy30 in CEK cells. Then, three recombinant viruses, including an rzy30S2-N1038S strain that contained the N1038S substitution, an rzy30S2-CT9△ strain that contained the 1154EQTRPKKSV1162 deletion, and an rzy30S2-N1038S-CT9△ strain that contained both mutations, were constructed using rescued virus rzy30 as the backbone. The results showed that each mutation did not significantly affect the replication titer in CEK cells but reduced pathogenicity in chickens, while in combination, the N1038S substitution and 1154EQTRPKKSV1162 deletion improved the proliferation efficiency in CEK cells and reduced pathogenicity, compared to rzy30 strain. The contribution made by the 1154EQTRPKKSV1162 deletion in reducing pathogenicity was higher than that of N1038S substitution. Our results revealed that the N1038S substitution and 1154EQTRPKKSV1162 deletion in S2 subunit were deeply involved in the replication efficiency of IBV and contributed to reduction of viral pathogenicity.
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Affiliation(s)
- Shuyun Li
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shunyi Fan
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Nianning Li
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yuxi Shen
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xuelian Xiang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Wen Chen
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jing Xia
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinfeng Han
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Min Cui
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yong Huang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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43
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Thakur N, Gallo G, Newman J, Peacock TP, Biasetti L, Hall CN, Wright E, Barclay W, Bailey D. SARS-CoV-2 variants of concern alpha, beta, gamma and delta have extended ACE2 receptor host ranges. J Gen Virol 2022; 103. [PMID: 35377298 DOI: 10.1099/jgv.0.001735] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Following the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in PR China in late 2019 a number of variants have emerged, with two of these - alpha and delta - subsequently growing to global prevalence. One characteristic of these variants are changes within the spike protein, in particular the receptor-binding domain (RBD). From a public health perspective, these changes have important implications for increased transmissibility and immune escape; however, their presence could also modify the intrinsic host range of the virus. Using viral pseudotyping, we examined whether the variants of concern (VOCs) alpha, beta, gamma and delta have differing host angiotensin-converting enzyme 2 (ACE2) receptor usage patterns, focusing on a range of relevant mammalian ACE2 proteins. All four VOCs were able to overcome a previous restriction for mouse ACE2, with demonstrable differences also seen for individual VOCs with rat, ferret or civet ACE2 receptors, changes that we subsequently attributed to N501Y and E484K substitutions within the spike RBD.
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Affiliation(s)
- Nazia Thakur
- The Pirbright Institute, Guildford, Surrey, GU24 0NF, UK.,Nuffield Department of Medicine, The Jenner Institute, Oxford, OX3 7DQ, UK
| | - Giulia Gallo
- The Pirbright Institute, Guildford, Surrey, GU24 0NF, UK
| | - Joseph Newman
- The Pirbright Institute, Guildford, Surrey, GU24 0NF, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College - London, W2 1PG, UK
| | - Luca Biasetti
- School of Psychology and Neuroscience, University of Sussex, Falmer, BN1 9QH, UK
| | - Catherine N Hall
- School of Psychology and Neuroscience, University of Sussex, Falmer, BN1 9QH, UK
| | - Edward Wright
- Viral Pseudotype Unit, School of Life Sciences, University of Sussex, Falmer, BN1 9QG, UK
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College - London, W2 1PG, UK
| | - Dalan Bailey
- The Pirbright Institute, Guildford, Surrey, GU24 0NF, UK
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Yan LN, Liu PP, Li XG, Zhou SJ, Li H, Wang ZY, Shen F, Lu BC, Long Y, Xiao X, Wang ZD, Li D, Han HJ, Yu H, Zhou SH, Lv WL, Yu XJ. Neutralizing Antibodies and Cellular Immune Responses Against SARS-CoV-2 Sustained One and a Half Years After Natural Infection. Front Microbiol 2022; 12:803031. [PMID: 35310397 PMCID: PMC8928406 DOI: 10.3389/fmicb.2021.803031] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/20/2021] [Indexed: 12/23/2022] Open
Abstract
Background COVID-19 has caused more than 2.6 billion infections and several million deaths since its outbreak 2 years ago. We know very little about the long-term cellular immune responses and the kinetics of neutralizing antibodies (NAbs) to SARS-CoV-2 because it has emerged only recently in the human population. Methods We collected blood samples from individuals who were from the first wave of the COVID-19 epidemic in Wuhan between December 30, 2019, and February 24, 2020. We analyzed NAbs to SARS-CoV-2 using pseudoviruses and IgG antibodies to SARS-CoV-2 spike (S) and nucleocapsid (N) protein using enzyme-linked immunosorbent assay in patients’ sera and determined SARS-CoV-2-specific T-cell responses of patients with ELISpot assays. Results We found that 91.9% (57/62) and 88.9% (40/45) of COVID-19 patients had NAbs against SARS-CoV-2 in a year (10–11 months) and one and a half years (17–18 months), respectively, after the onset of illness, indicating that NAbs against SARS-CoV-2 waned slowly and possibly persisted over a long period time. Over 80% of patients had IgG antibodies to SARS-CoV-2 S and N protein one and a half years after illness onset. Most patients also had robust memory T-cell responses against SARS-CoV-2 one and a half years after the illness. Among the patients, 95.6% (43/45) had an IFN-γ-secreting T-cell response and 93.8% (15/16) had an IL-2-secreting T-cell response. The T-cell responses to SARS-CoV-2 were positively correlated with antibodies (including neutralizing antibodies and IgG antibodies to S and N protein) in COVID-19 patients. Eighty percent (4/5) of neutralizing antibody-negative patients also had SARS-CoV-2-specific T-cell response. After long-term infection, protective immunity was independent of disease severity, sex, and age. Conclusions We concluded that SARS-CoV-2 infection elicited a robust and persistent neutralizing antibody and memory T-cell response in COVID-19 patients, indicating that these sustained immune responses, among most SARS-CoV-2-infected people, may play a crucial role in protection against reinfection.
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Affiliation(s)
- Li-Na Yan
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, China
| | - Pan-Pan Liu
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, China
| | - Xu-Gui Li
- The Department of Clinical Laboratory Medicine, Hubei 672 Orthopaedics Hospital, Wuhan, China
| | - Shi-Jing Zhou
- The Department of Clinical Laboratory Medicine, Hubei 672 Orthopaedics Hospital, Wuhan, China
| | - Hao Li
- The First School of Clinical Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Zhi-Yin Wang
- Department of Clinical Laboratory Medicine, Hubei University of Chinese Medicine Huangjiahu Hospital, Wuhan, China
| | - Feng Shen
- College of Acupuncture and Orthopedics, Hubei University of Chinese Medicine, Wuhan, China
| | - Bi-Chao Lu
- Clinical College, Hubei University of Chinese Medicine, Wuhan, China
| | - Yu Long
- Clinical College, Hubei University of Chinese Medicine, Wuhan, China
| | - Xiao Xiao
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, China
| | - Zhen-Dong Wang
- School of Public Health, Xi'an Medical University, Xi'an, China
| | - Dan Li
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, China
| | - Hui-Ju Han
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, China
| | - Hao Yu
- Department of Neuroscience, Cell Biology, and Anatomy, University of Texas Medical Branch, Galveston, TX, United States
| | - Shu-Han Zhou
- Clinical College, Hubei University of Chinese Medicine, Wuhan, China
| | - Wen-Liang Lv
- Clinical College, Hubei University of Chinese Medicine, Wuhan, China
| | - Xue-Jie Yu
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, China
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Dalvie NC, Tostanoski LH, Rodriguez-Aponte SA, Kaur K, Bajoria S, Kumru OS, Martinot AJ, Chandrashekar A, McMahan K, Mercado NB, Yu J, Chang A, Giffin VM, Nampanya F, Patel S, Bowman L, Naranjo CA, Yun D, Flinchbaugh Z, Pessaint L, Brown R, Velasco J, Teow E, Cook A, Andersen H, Lewis MG, Camp DL, Silverman JM, Nagar GS, Rao HD, Lothe RR, Chandrasekharan R, Rajurkar MP, Shaligram US, Kleanthous H, Joshi SB, Volkin DB, Biswas S, Love JC, Barouch DH. SARS-CoV-2 receptor binding domain displayed on HBsAg virus-like particles elicits protective immunity in macaques. SCIENCE ADVANCES 2022; 8:eabl6015. [PMID: 35294244 PMCID: PMC8926328 DOI: 10.1126/sciadv.abl6015] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/25/2022] [Indexed: 05/16/2023]
Abstract
Authorized vaccines against SARS-CoV-2 remain less available in low- and middle-income countries due to insufficient supply, high costs, and storage requirements. Global immunity could still benefit from new vaccines using widely available, safe adjuvants, such as alum and protein subunits, suited to low-cost production in existing manufacturing facilities. Here, a clinical-stage vaccine candidate comprising a SARS-CoV-2 receptor binding domain-hepatitis B surface antigen virus-like particle elicited protective immunity in cynomolgus macaques. Titers of neutralizing antibodies (>104) induced by this candidate were above the range of protection for other licensed vaccines in nonhuman primates. Including CpG 1018 did not significantly improve the immunological responses. Vaccinated animals challenged with SARS-CoV-2 showed reduced median viral loads in bronchoalveolar lavage (~3.4 log10) and nasal mucosa (~2.9 log10) versus sham controls. These data support the potential benefit of this design for a low-cost modular vaccine platform for SARS-CoV-2 and other variants of concern or betacoronaviruses.
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Affiliation(s)
- Neil C. Dalvie
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lisa H. Tostanoski
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Sergio A. Rodriguez-Aponte
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kawaljit Kaur
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Sakshi Bajoria
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Ozan S. Kumru
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Amanda J. Martinot
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Departments of Infectious Diseases and Global Health and Comparative Pathobiology, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Noe B. Mercado
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Aiquan Chang
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Victoria M. Giffin
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Felix Nampanya
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Shivani Patel
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lesley Bowman
- SpyBiotech Limited, Oxford Business Park North, Oxford OX4 2JZ, UK
| | - Christopher A. Naranjo
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dongsoo Yun
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | | | | | | | | | | | | | - Danielle L. Camp
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | | | | | | | | | | | | | - Sangeeta B. Joshi
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - David B. Volkin
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Sumi Biswas
- SpyBiotech Limited, Oxford Business Park North, Oxford OX4 2JZ, UK
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - J. Christopher Love
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
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Mahrokhian SH, Tostanoski LH, Jacob-Dolan C, Zahn RC, Wegmann F, McMahan K, Yu J, Gebre MS, Bondzie EA, Wan H, Powers O, Ye T, Barrett J, Schuitemaker H, Barouch DH. Durability and expansion of neutralizing antibody breadth following Ad26.COV2.S vaccination of mice. NPJ Vaccines 2022; 7:23. [PMID: 35197477 PMCID: PMC8866515 DOI: 10.1038/s41541-022-00454-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/31/2022] [Indexed: 11/30/2022] Open
Abstract
Emerging SARS-CoV-2 variants with the potential to escape binding and neutralizing antibody responses pose a threat to vaccine efficacy. We recently reported expansion of broadly neutralizing activity of vaccine-elicited antibodies in humans 8 months following a single immunization with Ad26.COV2.S. Here, we assessed the 15-month durability of antibody responses and their neutralizing capacity to B.1.617.2 (delta) and B.1.351 (beta) variants following a single immunization of Ad26.COV2.S in mice. We report the persistence of binding and neutralizing antibody titers following immunization with a concomitant increase in neutralizing antibody breadth to delta and beta variants over time. Evaluation of bone marrow and spleen at 15 months postimmunization revealed that Ad26.COV2.S-immunized mice tissues contained spike-specific antibody-secreting cells. We conclude that immunization with Ad26.COV2.S elicits a robust immune response against SARS-CoV-2 spike, which expands over time to neutralize delta and beta variants more robustly, and seeds bone marrow and spleen with long-lived spike-specific antibody-secreting cells. These data extend previous findings in humans and support the use of a mouse model as a potential tool to further explore the dynamics of the humoral immune response following vaccination with Ad26.COV2.S.
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Affiliation(s)
- Shant H Mahrokhian
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
- Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Lisa H Tostanoski
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Roland C Zahn
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
| | - Frank Wegmann
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Makda S Gebre
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Esther A Bondzie
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Huahua Wan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Olivia Powers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Tianyi Ye
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Julia Barrett
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | | | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
- Harvard Medical School, Boston, MA, 02115, USA.
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA.
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115, USA.
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Chandrashekar A, Yu J, McMahan K, Jacob-Dolan C, Liu J, He X, Hope D, Anioke T, Barrett J, Chung B, Hachmann NP, Lifton M, Miller J, Powers O, Sciacca M, Sellers D, Siamatu M, Surve N, VanWyk H, Wan H, Wu C, Pessaint L, Valentin D, Van Ry A, Muench J, Boursiquot M, Cook A, Velasco J, Teow E, Boon AC, Suthar MS, Jain N, Martinot AJ, Lewis MG, Andersen H, Barouch DH. Vaccine Protection Against the SARS-CoV-2 Omicron Variant in Macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.02.06.479285. [PMID: 35169798 PMCID: PMC8845420 DOI: 10.1101/2022.02.06.479285] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND The rapid spread of the SARS-CoV-2 Omicron (B.1.1.529) variant, including in highly vaccinated populations, has raised important questions about the efficacy of current vaccines. Immune correlates of vaccine protection against Omicron are not known. METHODS 30 cynomolgus macaques were immunized with homologous and heterologous prime-boost regimens with the mRNA-based BNT162b2 vaccine and the adenovirus vector-based Ad26.COV2.S vaccine. Following vaccination, animals were challenged with the SARS-CoV-2 Omicron variant by the intranasal and intratracheal routes. RESULTS Omicron neutralizing antibodies were observed following the boost immunization and were higher in animals that received BNT162b2, whereas Omicron CD8+ T cell responses were higher in animals that received Ad26.COV2.S. Following Omicron challenge, sham controls showed more prolonged virus in nasal swabs than in bronchoalveolar lavage. Vaccinated macaques demonstrated rapid control of virus in bronchoalveolar lavage, and most vaccinated animals also controlled virus in nasal swabs, showing that current vaccines provide substantial protection against Omicron in this model. However, vaccinated animals that had moderate levels of Omicron neutralizing antibodies but negligible Omicron CD8+ T cell responses failed to control virus in the upper respiratory tract. Virologic control correlated with both antibody and T cell responses. CONCLUSIONS BNT162b2 and Ad26.COV2.S provided robust protection against high-dose challenge with the SARS-CoV-2 Omicron variant in macaques. Protection against this highly mutated SARS-CoV-2 variant correlated with both humoral and cellular immune responses.
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Affiliation(s)
- Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Xuan He
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - David Hope
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Tochi Anioke
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Julia Barrett
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Benjamin Chung
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Nicole P. Hachmann
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Michelle Lifton
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jessica Miller
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Olivia Powers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Michaela Sciacca
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Daniel Sellers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Mazuba Siamatu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Nehalee Surve
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Haley VanWyk
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Huahua Wan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Cindy Wu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | | | | | | | | | | | | | | | | | | | - Neharika Jain
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - Amanda J. Martinot
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | | | | | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
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48
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Xiang Q, Li L, Wu J, Tian M, Fu Y. Application of pseudovirus system in the development of vaccine, antiviral-drugs, and neutralizing antibodies. Microbiol Res 2022; 258:126993. [PMID: 35240544 PMCID: PMC8848573 DOI: 10.1016/j.micres.2022.126993] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/12/2022] [Accepted: 02/13/2022] [Indexed: 12/16/2022]
Abstract
Pseudoviruses are viral particles coated with a heterologous envelope protein, which mediates the entry of pseudoviruses as efficiently as that of the live viruses possessing high pathogenicity and infectivity. Due to the deletion of the envelope protein gene and the absence of pathogenic genes, pseudoviruses have no autonomous replication ability and can infect host cells for only a single cycle. In addition, pseudoviruses have the desired characteristics of high safety, strong operability, and can be easily used to perform rapid throughput detection. Therefore, pseudoviruses are widely employed in the mechanistic investigation of viral infection, the screening and evaluation of monoclonal antibodies and antiviral drugs, and the detection of neutralizing antibody titers in serum after vaccination. In this review, we will discuss the construction of pseudoviruses based on different packaging systems, their current applications especially in the research of SARS-CoV-2, limitations, and further directions.
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Affiliation(s)
- Qi Xiang
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Linhao Li
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jie Wu
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Miao Tian
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yang Fu
- School of Medicine, Southern University of Science and Technology, Shenzhen, China.
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49
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Yu J, Collins ND, Mercado NB, McMahan K, Chandrashekar A, Liu J, Anioke T, Chang A, Giffin VM, Hope DL, Sellers D, Nampanya F, Gardner S, Barrett J, Wan H, Velasco J, Teow E, Cook A, Van Ry A, Pessaint L, Andersen H, Lewis MG, Hofer C, Burke DS, Barkei EK, King HAD, Subra C, Bolton D, Modjarrad K, Michael NL, Barouch DH. Protective Efficacy of Gastrointestinal SARS-CoV-2 Delivery against Intranasal and Intratracheal SARS-CoV-2 Challenge in Rhesus Macaques. J Virol 2022; 96:e0159921. [PMID: 34705557 PMCID: PMC8791250 DOI: 10.1128/jvi.01599-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 10/26/2021] [Indexed: 12/21/2022] Open
Abstract
Live oral vaccines have been explored for their protective efficacy against respiratory viruses, particularly for adenovirus serotypes 4 and 7. The potential of a live oral vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), however, remains unclear. In this study, we assessed the immunogenicity of live SARS-CoV-2 delivered to the gastrointestinal tract in rhesus macaques and its protective efficacy against intranasal and intratracheal SARS-CoV-2 challenge. Postpyloric administration of SARS-CoV-2 by esophagogastroduodenoscopy resulted in limited virus replication in the gastrointestinal tract and minimal to no induction of mucosal antibody titers in rectal swabs, nasal swabs, and bronchoalveolar lavage fluid. Low levels of serum neutralizing antibodies were induced and correlated with modestly diminished viral loads in nasal swabs and bronchoalveolar lavage fluid following intranasal and intratracheal SARS-CoV-2 challenge. Overall, our data show that postpyloric inoculation of live SARS-CoV-2 is weakly immunogenic and confers partial protection against respiratory SARS-CoV-2 challenge in rhesus macaques. IMPORTANCE SARS-CoV-2 remains a global threat, despite the rapid deployment but limited coverage of multiple vaccines. Alternative vaccine strategies that have favorable manufacturing timelines, greater ease of distribution, and improved coverage may offer significant public health benefits, especially in resource-limited settings. Live oral vaccines have the potential to address some of these limitations; however, no studies have yet been conducted to assess the immunogenicity and protective efficacy of a live oral vaccine against SARS-CoV-2. Here, we report that oral administration of live SARS-CoV-2 in nonhuman primates may offer prophylactic benefits, but the formulation and route of administration will require further optimization.
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Affiliation(s)
- Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Noe B. Mercado
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Tochi Anioke
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Aiquan Chang
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Victoria M. Giffin
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - David L. Hope
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel Sellers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Felix Nampanya
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Sarah Gardner
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Julia Barrett
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Huahua Wan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | | | | | | | | | - Christian Hofer
- Veterinary Services Program, Center for Enabling Capabilities, Walter Reed Army Institute for Research, Silver Spring, Maryland, USA
| | - Donald S. Burke
- Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Erica K. Barkei
- Veterinary Services Program, Center for Enabling Capabilities, Walter Reed Army Institute for Research, Silver Spring, Maryland, USA
| | - Hannah A. D. King
- Henry Jackson Foundation, Bethesda, Maryland, USA
- Military HIV Research Program, Center for Infectious Disease Research, Walter Reed Army Institute for Research, Silver Spring, Maryland, USA
| | - Caroline Subra
- Henry Jackson Foundation, Bethesda, Maryland, USA
- Military HIV Research Program, Center for Infectious Disease Research, Walter Reed Army Institute for Research, Silver Spring, Maryland, USA
| | - Diane Bolton
- Henry Jackson Foundation, Bethesda, Maryland, USA
- Military HIV Research Program, Center for Infectious Disease Research, Walter Reed Army Institute for Research, Silver Spring, Maryland, USA
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Center for Infectious Disease Research, Walter Reed Army Institute for Research, Silver Spring, Maryland, USA
| | - Nelson L. Michael
- Center for Infectious Disease Research, Walter Reed Army Institute for Research, Silver Spring, Maryland, USA
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
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50
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) glycoprotein mediates viral entry and membrane fusion. Its cleavage at S1/S2 and S2′ sites during the biosynthesis in virus producer cells and viral entry are critical for viral infection and transmission. In contrast, the biological significance of the junction region between both cleavage sites for S protein synthesis and function is less understood. By analyzing the conservation and structure of S protein, we found that intrachain contacts formed by the conserved tyrosine (Y) residue 756 (Y756) with three α-helices contribute to the spike’s conformational stability. When Y756 is mutated to an amino acid residue that can provide hydrogen bonds, S protein could be expressed as a cleaved form, but not vice versa. Also, the L753 mutation linked to the Y756 hydrogen bond prevents the S protein from being cleaved. Y756 and L753 mutations alter S protein subcellular localization. Importantly, Y756 and L753 mutations are demonstrated to reduce the infectivity of the SARS-CoV-2 pseudoviruses by interfering with the incorporation of S protein into pseudovirus particles and causing the pseudoviruses to lose their sensitivity to neutralizing antibodies. Furthermore, both mutations affect the assembly and production of SARS-CoV-2 virus-like particles in cell culture. Together, our findings reveal for the first time a critical role for the conserved L753-LQ-Y756 motif between S1/S2 and S2′ cleavage sites in S protein synthesis and processing as well as virus assembly and infection. IMPORTANCE The continuous emergence of SARS-CoV-2 variants such as the delta or lambda lineage caused the continuation of the COVID-19 epidemic and challenged the effectiveness of the existing vaccines. Logically, the spike (S) protein mutation has attracted much concern. However, the key amino acids in S protein for its structure and function are still not very clear. In this study, we discovered for the first time that the conserved residues Y756 and L753 at the junction between the S1/S2 and S2′ sites are very important, like the S2′ cleavage site R815, for the synthesis and processing of S protein such as protease cleavage, and that the mutations severely interfered with the incorporation of S protein into pseudotyped virus particles and SARS-CoV-2 virus-like particles. Consequently, we delineate the novel potential target for the design of broad-spectrum antiviral drugs in the future, especially in the emergence of SARS-CoV-2 variants.
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