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Costacurta F, Dodaro A, Bante D, Schöppe H, Peng JY, Sprenger B, He X, Moghadasi SA, Egger LM, Fleischmann J, Pavan M, Bassani D, Menin S, Rauch S, Krismer L, Sauerwein A, Heberle A, Rabensteiner T, Ho J, Harris RS, Stefan E, Schneider R, Dunzendorfer-Matt T, Naschberger A, Wang D, Kaserer T, Moro S, von Laer D, Heilmann E. A comprehensive study of SARS-CoV-2 main protease (Mpro) inhibitor-resistant mutants selected in a VSV-based system. PLoS Pathog 2024; 20:e1012522. [PMID: 39259728 PMCID: PMC11407635 DOI: 10.1371/journal.ppat.1012522] [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: 10/06/2023] [Revised: 09/17/2024] [Accepted: 08/19/2024] [Indexed: 09/13/2024] Open
Abstract
Nirmatrelvir was the first protease inhibitor specifically developed against the SARS-CoV-2 main protease (3CLpro/Mpro) and licensed for clinical use. As SARS-CoV-2 continues to spread, variants resistant to nirmatrelvir and other currently available treatments are likely to arise. This study aimed to identify and characterize mutations that confer resistance to nirmatrelvir. To safely generate Mpro resistance mutations, we passaged a previously developed, chimeric vesicular stomatitis virus (VSV-Mpro) with increasing, yet suboptimal concentrations of nirmatrelvir. Using Wuhan-1 and Omicron Mpro variants, we selected a large set of mutants. Some mutations are frequently present in GISAID, suggesting their relevance in SARS-CoV-2. The resistance phenotype of a subset of mutations was characterized against clinically available protease inhibitors (nirmatrelvir and ensitrelvir) with cell-based, biochemical and SARS-CoV-2 replicon assays. Moreover, we showed the putative molecular mechanism of resistance based on in silico molecular modelling. These findings have implications on the development of future generation Mpro inhibitors, will help to understand SARS-CoV-2 protease inhibitor resistance mechanisms and show the relevance of specific mutations, thereby informing treatment decisions.
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Affiliation(s)
- Francesco Costacurta
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Andrea Dodaro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padova, Italy
| | - David Bante
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Helge Schöppe
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Ju-Yi Peng
- Department of Infectious Diseases and Vaccines Research, MRL, Merck & Co., Inc., Rahway, New Jersey, United States of America
| | - Bernhard Sprenger
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Xi He
- Department of Infectious Diseases and Vaccines Research, MRL, Merck & Co., Inc., Rahway, New Jersey, United States of America
| | - Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Lisa Maria Egger
- Institute of Molecular Biochemistry, Biocentre, Medical University of Innsbruck, Innsbruck, Austria
| | - Jakob Fleischmann
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, Tyrol, Austria
- Tyrolean Cancer Research Institute (TKFI), Innsbruck, Tyrol, Austria
| | - Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padova, Italy
| | - Davide Bassani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padova, Italy
| | - Silvia Menin
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padova, Italy
| | - Stefanie Rauch
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Laura Krismer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Anna Sauerwein
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Anne Heberle
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Toni Rabensteiner
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Joses Ho
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore, Singapore
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, United States of America
| | - Eduard Stefan
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, Tyrol, Austria
- Tyrolean Cancer Research Institute (TKFI), Innsbruck, Tyrol, Austria
| | - Rainer Schneider
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | | | - Andreas Naschberger
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Dai Wang
- Department of Infectious Diseases and Vaccines Research, MRL, Merck & Co., Inc., Rahway, New Jersey, United States of America
| | - Teresa Kaserer
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padova, Italy
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Emmanuel Heilmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Tyrol, Austria
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Yahalom-Ronen Y, Melamed S, Politi B, Erez N, Tamir H, Bar-On L, Ryvkin J, Leshkowitz D, Israeli O, Weiss S, Ben-Shmuel A, Barlev-Gross M, Cherry Mimran L, Achdout H, Paran N, Israely T. Induction of Superior Systemic and Mucosal Protective Immunity to SARS-CoV-2 by Nasal Administration of a VSV-ΔG-Spike Vaccine. Vaccines (Basel) 2024; 12:491. [PMID: 38793742 PMCID: PMC11125831 DOI: 10.3390/vaccines12050491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/21/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
The emergence of rapidly spreading variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) poses a major challenge to vaccines' protective efficacy. Intramuscular (IM) vaccine administration induces short-lived immunity but does not prevent infection and transmission. New vaccination strategies are needed to extend the longevity of vaccine protection, induce mucosal and systemic immunity and prevent viral transmission. The intranasal (IN) administration of the VSV-ΔG-spike vaccine candidate directly to mucosal surfaces yielded superior mucosal and systemic immunity at lower vaccine doses. Compared to IM vaccination in the K18-hACE2 model, IN vaccination preferentially induced mucosal IgA and T-cells, reduced the viral load at the site of infection, and ameliorated disease-associated brain gene expression. IN vaccination was protective even one year after administration. As most of the world population has been vaccinated by IM injection, we demonstrate the potential of a heterologous IM + IN vaccination regimen to induce mucosal immunity while maintaining systemic immunity. Furthermore, the IM + IN regimen prevented virus transmission in a golden Syrian hamster co-caging model. Taken together, we show that IN vaccination with VSV-ΔG-spike, either as a homologous IN + IN regimen or as a boost following IM vaccination, has a favorable potential over IM vaccination in inducing efficient mucosal immunity, long-term protection and preventing virus transmission.
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Affiliation(s)
- Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Sharon Melamed
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Boaz Politi
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Noam Erez
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Hadas Tamir
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Liat Bar-On
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (L.B.-O.); (O.I.)
| | - Julia Ryvkin
- Bioinformatics Unit, Life Science Core Facilities, Weizmann Institute of Science, Rehovot 52621, Israel; (J.R.); (D.L.)
| | - Dena Leshkowitz
- Bioinformatics Unit, Life Science Core Facilities, Weizmann Institute of Science, Rehovot 52621, Israel; (J.R.); (D.L.)
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (L.B.-O.); (O.I.)
| | - Shay Weiss
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Amir Ben-Shmuel
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Moria Barlev-Gross
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Lilach Cherry Mimran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Hagit Achdout
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
| | - Tomer Israely
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel; (Y.Y.-R.); (S.M.); (B.P.); (N.E.); (H.T.); (S.W.); (A.B.-S.); (M.B.-G.); (L.C.M.); (H.A.)
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3
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Toister E, Cherry L, Lupu E, Monash A, Dor E, Levin L, Girshengorn M, Natan N, Chapman S, Shmaya S, Epstein E, Adar Y, Zichel R, Ophir Y, Diamant E. Development and Validation of a Plaque Assay to Determine the Titer of a Recombinant Live-Attenuated Viral Vaccine for SARS-CoV-2. Vaccines (Basel) 2024; 12:374. [PMID: 38675756 PMCID: PMC11054748 DOI: 10.3390/vaccines12040374] [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: 02/27/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in more than seven million deaths worldwide. To reduce viral spread, the Israel Institute for Biological Research (IIBR) developed and produced a new rVSV-SARS-CoV-2-S vaccine candidate (BriLife®) based on a platform of a genetically engineered vesicular stomatitis virus (VSV) vector that expresses the spike protein of SARS-CoV-2 instead of the VSV-G protein on the virus surface. Quantifying the virus titer to evaluate vaccine potency requires a reliable validated assay that meets all the stringent pharmacopeial requirements of a bioanalytical method. Here, for the first time, we present the development and extensive validation of a quantitative plaque assay using Vero E6 cells for the determination of the concentration of the rVSV-SARS-CoV-2-S viral vector. Three different vaccine preparations with varying titers (DP_low, DP_high, and QC sample) were tested according to a strict validation protocol. The newly developed plaque assay was found to be highly specific, accurate, precise, and robust. The mean deviations from the predetermined titers for the DP_low, DP_high, and QC preparations were 0.01, 0.02, and 0.09 log10, respectively. Moreover, the mean %CV values for intra-assay precision were 18.7%, 12.0%, and 6.0%, respectively. The virus titers did not deviate from the established values between cell passages 5 and 19, and no correlation was found between titer and passage. The validation results presented herein indicate that the newly developed plaque assay can be used to determine the concentration of the BriLife® vaccine, suggesting that the current protocol is a reliable methodology for validating plaque assays for other viral vaccines.
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Affiliation(s)
- Einat Toister
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (E.T.); (L.C.); (E.L.); (A.M.); (E.D.); (M.G.); (N.N.); (E.E.); (Y.A.); (R.Z.)
| | - Lilach Cherry
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (E.T.); (L.C.); (E.L.); (A.M.); (E.D.); (M.G.); (N.N.); (E.E.); (Y.A.); (R.Z.)
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 7410001, Israel;
| | - Edith Lupu
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (E.T.); (L.C.); (E.L.); (A.M.); (E.D.); (M.G.); (N.N.); (E.E.); (Y.A.); (R.Z.)
| | - Arik Monash
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (E.T.); (L.C.); (E.L.); (A.M.); (E.D.); (M.G.); (N.N.); (E.E.); (Y.A.); (R.Z.)
| | - Eyal Dor
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (E.T.); (L.C.); (E.L.); (A.M.); (E.D.); (M.G.); (N.N.); (E.E.); (Y.A.); (R.Z.)
| | - Lilach Levin
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (E.T.); (L.C.); (E.L.); (A.M.); (E.D.); (M.G.); (N.N.); (E.E.); (Y.A.); (R.Z.)
| | - Meni Girshengorn
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (E.T.); (L.C.); (E.L.); (A.M.); (E.D.); (M.G.); (N.N.); (E.E.); (Y.A.); (R.Z.)
| | - Niva Natan
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (E.T.); (L.C.); (E.L.); (A.M.); (E.D.); (M.G.); (N.N.); (E.E.); (Y.A.); (R.Z.)
| | - Shira Chapman
- Department of Pharmacology, Israel Institute for Biological Research, Ness Ziona 7410001, Israel;
| | - Shlomo Shmaya
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 7410001, Israel;
| | - Eyal Epstein
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (E.T.); (L.C.); (E.L.); (A.M.); (E.D.); (M.G.); (N.N.); (E.E.); (Y.A.); (R.Z.)
| | - Yaakov Adar
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (E.T.); (L.C.); (E.L.); (A.M.); (E.D.); (M.G.); (N.N.); (E.E.); (Y.A.); (R.Z.)
| | - Ran Zichel
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (E.T.); (L.C.); (E.L.); (A.M.); (E.D.); (M.G.); (N.N.); (E.E.); (Y.A.); (R.Z.)
| | - Yakir Ophir
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (E.T.); (L.C.); (E.L.); (A.M.); (E.D.); (M.G.); (N.N.); (E.E.); (Y.A.); (R.Z.)
- Department of Microbiology, Cornell University, Ithaca, NY 14850, USA
| | - Eran Diamant
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (E.T.); (L.C.); (E.L.); (A.M.); (E.D.); (M.G.); (N.N.); (E.E.); (Y.A.); (R.Z.)
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Todesco HM, Gafuik C, John CM, Roberts EL, Borys BS, Pawluk A, Kallos MS, Potts KG, Mahoney DJ. High-titer manufacturing of SARS-CoV-2 Spike-pseudotyped VSV in stirred-tank bioreactors. Mol Ther Methods Clin Dev 2024; 32:101189. [PMID: 38327804 PMCID: PMC10847022 DOI: 10.1016/j.omtm.2024.101189] [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: 04/26/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
Abstract
The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) pandemic highlighted the importance of vaccine innovation in public health. Hundreds of vaccines built on numerous technology platforms have been rapidly developed against SARS-CoV-2 since 2020. Like all vaccine platforms, an important bottleneck to viral-vectored vaccine development is manufacturing. Here, we describe a scalable manufacturing protocol for replication-competent SARS-CoV-2 Spike-pseudotyped vesicular stomatitis virus (S-VSV)-vectored vaccines using Vero cells grown on microcarriers in a stirred-tank bioreactor. Using Cytodex 1 microcarriers over 6 days of fed-batch culture, Vero cells grew to a density of 3.95 ± 0.42 ×106 cells/mL in 1-L stirred-tank bioreactors. Ancestral strain S-VSV reached a peak titer of 2.05 ± 0.58 ×108 plaque-forming units (PFUs)/mL at 3 days postinfection. When compared to growth in plate-based cultures, this was a 29-fold increase in virus production, meaning a 1-L bioreactor produces the same amount of virus as 1,284 plates of 15 cm. In addition, the omicron BA.1 S-VSV reached a peak titer of 5.58 ± 0.35 × 106 PFU/mL. Quality control testing showed plate- and bioreactor-produced S-VSV had similar particle-to-PFU ratios and elicited comparable levels of neutralizing antibodies in immunized hamsters. This method should enhance preclinical and clinical development of pseudotyped VSV-vectored vaccines in future pandemics.
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Affiliation(s)
- Hayley M. Todesco
- Arnie Charbonneau Cancer Institute, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Disease, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
| | - Chris Gafuik
- Arnie Charbonneau Cancer Institute, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Disease, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
| | - Cini M. John
- Arnie Charbonneau Cancer Institute, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Disease, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
| | - Erin L. Roberts
- Department of Biomedical Engineering, Schulich School of Engineering, University of Calgary, Calgary, AB, Canada
| | - Breanna S. Borys
- Pharmaceutical Production Research Facility, Schulich School of Engineering, University of Calgary, Calgary, AB, Canada
| | - Alexis Pawluk
- Pharmaceutical Production Research Facility, Schulich School of Engineering, University of Calgary, Calgary, AB, Canada
| | - Michael S. Kallos
- Department of Biomedical Engineering, Schulich School of Engineering, University of Calgary, Calgary, AB, Canada
- Pharmaceutical Production Research Facility, Schulich School of Engineering, University of Calgary, Calgary, AB, Canada
| | - Kyle G. Potts
- Arnie Charbonneau Cancer Institute, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Disease, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
| | - Douglas J. Mahoney
- Arnie Charbonneau Cancer Institute, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Disease, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Microbiology, Immunology and Infectious Disease, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
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5
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Lundstrom K. COVID-19 Vaccines: Where Did We Stand at the End of 2023? Viruses 2024; 16:203. [PMID: 38399979 PMCID: PMC10893040 DOI: 10.3390/v16020203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Vaccine development against SARS-CoV-2 has been highly successful in slowing down the COVID-19 pandemic. A wide spectrum of approaches including vaccines based on whole viruses, protein subunits and peptides, viral vectors, and nucleic acids has been developed in parallel. For all types of COVID-19 vaccines, good safety and efficacy have been obtained in both preclinical animal studies and in clinical trials in humans. Moreover, emergency use authorization has been granted for the major types of COVID-19 vaccines. Although high safety has been demonstrated, rare cases of severe adverse events have been detected after global mass vaccinations. Emerging SARS-CoV-2 variants possessing enhanced infectivity have affected vaccine protection efficacy requiring re-design and re-engineering of novel COVID-19 vaccine candidates. Furthermore, insight is given into preparedness against emerging SARS-CoV-2 variants.
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Costacurta F, Dodaro A, Bante D, Schöppe H, Sprenger B, Moghadasi SA, Fleischmann J, Pavan M, Bassani D, Menin S, Rauch S, Krismer L, Sauerwein A, Heberle A, Rabensteiner T, Ho J, Harris RS, Stefan E, Schneider R, Kaserer T, Moro S, von Laer D, Heilmann E. A comprehensive study of SARS-CoV-2 main protease (M pro) inhibitor-resistant mutants selected in a VSV-based system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.558628. [PMID: 37808638 PMCID: PMC10557589 DOI: 10.1101/2023.09.22.558628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Nirmatrelvir was the first protease inhibitor (PI) specifically developed against the SARS-CoV-2 main protease (3CLpro/Mpro) and licensed for clinical use. As SARS-CoV-2 continues to spread, variants resistant to nirmatrelvir and other currently available treatments are likely to arise. This study aimed to identify and characterize mutations that confer resistance to nirmatrelvir. To safely generate Mpro resistance mutations, we passaged a previously developed, chimeric vesicular stomatitis virus (VSV-Mpro) with increasing, yet suboptimal concentrations of nirmatrelvir. Using Wuhan-1 and Omicron Mpro variants, we selected a large set of mutants. Some mutations are frequently present in GISAID, suggesting their relevance in SARS-CoV-2. The resistance phenotype of a subset of mutations was characterized against clinically available PIs (nirmatrelvir and ensitrelvir) with cell-based and biochemical assays. Moreover, we showed the putative molecular mechanism of resistance based on in silico molecular modelling. These findings have implications on the development of future generation Mpro inhibitors, will help to understand SARS-CoV-2 protease-inhibitor-resistance mechanisms and show the relevance of specific mutations in the clinic, thereby informing treatment decisions.
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Affiliation(s)
- Francesco Costacurta
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Andrea Dodaro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - David Bante
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Helge Schöppe
- Institute of Pharmacy/Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Bernhard Sprenger
- Department of Biochemistry, University of Innsbruck, Innsbruck, 6020, Austria
| | - Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, United States
| | - Jakob Fleischmann
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, Innsbruck, 6020, Tyrol, Austria
| | - Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Davide Bassani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Silvia Menin
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Stefanie Rauch
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Laura Krismer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Anna Sauerwein
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Anne Heberle
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Toni Rabensteiner
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Joses Ho
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, United States
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, United States
| | - Eduard Stefan
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, Innsbruck, 6020, Tyrol, Austria
| | - Rainer Schneider
- Department of Biochemistry, University of Innsbruck, Innsbruck, 6020, Austria
| | - Teresa Kaserer
- Institute of Pharmacy/Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Emmanuel Heilmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
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7
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Erez N, Achdout H, Yahalom-Ronen Y, Adutler-Lieber S, Bar-On L, Bar-Haim E, Politi B, Vitner EB, Tamir H, Melamed S, Paran N, Israely T. Identification of T-Cell Epitopes Using a Combined In-Silico and Experimental Approach in a Mouse Model for SARS-CoV-2. Curr Issues Mol Biol 2023; 45:7944-7955. [PMID: 37886945 PMCID: PMC10605721 DOI: 10.3390/cimb45100502] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Following viral infection, T-cells are crucial for an effective immune response to intracellular pathogens, including respiratory viruses. During the COVID-19 pandemic, diverse assays were required in pre-clinical trials to evaluate the immune response following vaccination against SARS-CoV-2 and assess the response following exposure to the virus. To assess the nature and potency of the cellular response to infection or vaccination, a reliable and specific activity assay was needed. A cellular activity assay based on the presentation of short peptides (epitopes) allows the identification of T cell epitopes displayed on different alleles of the MHC, shedding light on the strength of the immune response towards antigens and aiding in antigen design for vaccination. In this report, we describe two approaches for scanning T cell epitopes on the surface glycoprotein of the SARS-CoV-2 (spike), which is utilized for attachment and entry and serves as an antigen in many vaccine candidates. We demonstrate that epitope scanning is feasible using peptide libraries or computational scanning combined with a cellular activity assay. Our scans identified four CD8 T cell epitopes, including one novel undescribed epitope. These epitopes enabled us to establish a reliable T-cell response assay, which was examined and used in various experimental mouse models for SARS-CoV-2 infection and vaccination. These approaches could potentially aid in future antigen design for vaccination and establish cellular activity assays against uncharacterized antigens of emerging pathogens.
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Affiliation(s)
- Noam Erez
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
| | - Hagit Achdout
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
| | - Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
| | - Shimrit Adutler-Lieber
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
| | - Liat Bar-On
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (L.B.-O.); (E.B.-H.)
| | - Erez Bar-Haim
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (L.B.-O.); (E.B.-H.)
| | - Boaz Politi
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
| | - Einat B. Vitner
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
| | - Hadas Tamir
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
| | - Sharon Melamed
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
| | - Tomer Israely
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (H.A.); (Y.Y.-R.); (S.A.-L.); (B.P.); (E.B.V.); (H.T.); (S.M.); (N.P.)
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8
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Ko HJ, Kim YJ. Antigen Delivery Systems: Past, Present, and Future. Biomol Ther (Seoul) 2023; 31:370-387. [PMID: 37072288 PMCID: PMC10315343 DOI: 10.4062/biomolther.2023.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/07/2023] [Accepted: 03/22/2023] [Indexed: 04/20/2023] Open
Abstract
The COVID-19 pandemic has increased demand for safe and effective vaccines. Research to develop vaccines against diseases including Middle East respiratory syndrome, Ebolavirus, human immunodeficiency virus, and various cancers would also contribute to global well-being. For successful vaccine development, the advancement of technologies such as antigen (Ag) screening, Ag delivery systems and adjuvants, and manufacturing processes is essential. Ag delivery systems are required not only to deliver a sufficient amount of Ag for vaccination, but also to enhance immune response. In addition, Ag types and their delivery systems determine the manufacturing processes of the vaccine product. Here, we analyze the characteristics of various Ag delivery systems: plasmids, viral vectors, bacterial vectors, nanoparticles, self-assembled particles, natural and artificial cells, and extracellular vesicles. This review provides insight into the current vaccine landscape and highlights promising avenues of research for the development and improvement of Ag delivery systems.
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Affiliation(s)
- Hyun-Jeong Ko
- Laboratory of Microbiology and Immunology, Department of Pharmacy, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Yeon-Jeong Kim
- Laboratory of Microbiology and Immunology, College of Pharmacy, Inje University, Gimhae 50834, Republic of Korea
- Inje Institute of Pharmaceutical Science and Research, Inje University, Gimhae 50834, Republic of Korea
- Smart Marine Therapeutic Center, Inje University, Gimhae 50834, Republic of Korea
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9
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Yahalom-Ronen Y, Tamir H, Melamed S, Politi B, Achdout H, Erez N, Israeli O, Cohen-Gihon I, Chery Mimran L, Barlev-Gross M, Mandelboim M, Orr I, Feldmesser E, Weiss S, Beth-Din A, Paran N, Israely T. VSV-ΔG-Spike Candidate Vaccine Induces Protective Immunity and Protects K18-hACE2 Mice against SARS-CoV-2 Variants. Viruses 2023; 15:1364. [PMID: 37376662 DOI: 10.3390/v15061364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Since the emergence of the original SARS-CoV-2, several variants were described, raising questions as to the ability of recently developed vaccine platforms to induce immunity and provide protection against these variants. Here, we utilized the K18-hACE2 mouse model to show that VSV-ΔG-spike vaccination provides protection against several SARS-CoV-2 variants: alpha, beta, gamma, and delta. We show an overall robust immune response, regardless of variant identity, leading to reduction in viral load in target organs, prevention of morbidity and mortality, as well as prevention of severe brain immune response, which follows infection with various variants. Additionally, we provide a comprehensive comparison of the brain transcriptomic profile in response to infection with different variants of SARS-CoV-2 and show how vaccination prevents these disease manifestations. Taken together, these results highlight the robust VSV-ΔG-spike protective response against diverse SARS-CoV-2 variants, as well as its promising potential against newly arising variants.
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Affiliation(s)
- Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Hadas Tamir
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Sharon Melamed
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Boaz Politi
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Hagit Achdout
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Noam Erez
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Inbar Cohen-Gihon
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Lilach Chery Mimran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Moria Barlev-Gross
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Tel Hashomer, Ramat Gan 76100, Israel
| | - Irit Orr
- Bioinformatics Unit, Life Science Core Facilities, Weizmann Institute of Science, Rehovot 52621, Israel
| | - Ester Feldmesser
- Bioinformatics Unit, Life Science Core Facilities, Weizmann Institute of Science, Rehovot 52621, Israel
| | - Shay Weiss
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Adi Beth-Din
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Tomer Israely
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
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10
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Parham KA, Kim GN, Richer CG, Ninkov M, Wu K, Saeedian N, Li Y, Rashu R, Barr SD, Arts EJ, Haeryfar SMM, Kang CY, Troyer RM. Monovalent and trivalent VSV-based COVID-19 vaccines elicit neutralizing antibodies and CD8 + T cells against SARS-CoV-2 variants. iScience 2023; 26:106292. [PMID: 36915805 PMCID: PMC9970654 DOI: 10.1016/j.isci.2023.106292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 12/21/2022] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Recombinant vesicular stomatitis virus (rVSV) vaccines expressing spike proteins of Wuhan, Beta, and/or Delta variants of SARS-CoV-2 were generated and tested for induction of antibody and T cell immune responses following intramuscular delivery to mice. rVSV-Wuhan and rVSV-Delta vaccines and an rVSV-Trivalent (mixed rVSV-Wuhan, -Beta, -Delta) vaccine elicited potent neutralizing antibodies (nAbs) against live SARS-CoV-2 Wuhan (USAWA1), Beta (B.1.351), Delta (B.1.617.2), and Omicron (B.1.1.529) viruses. Prime-boost vaccination with rVSV-Beta was less effective in this capacity. Heterologous boosting of rVSV-Wuhan with rVSV-Delta induced strong nAb responses against Delta and Omicron viruses, with the rVSV-Trivalent vaccine consistently effective in inducing nAbs against all the SARS-CoV-2 variants tested. All vaccines, including rVSV-Beta, elicited a spike-specific immunodominant CD8+ T cell response. Collectively, rVSV vaccines targeting SARS-CoV-2 variants of concern may be considered in the global fight against COVID-19.
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Affiliation(s)
- Kate A Parham
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 3K7, Canada
| | - Gyoung Nyoun Kim
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 3K7, Canada
| | - Connor G Richer
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 3K7, Canada
| | - Marina Ninkov
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 3K7, Canada
| | - Kunyu Wu
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 3K7, Canada
| | - Nasrin Saeedian
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 3K7, Canada
| | - Yue Li
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 3K7, Canada
| | - Rasheduzzaman Rashu
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 3K7, Canada
| | - Stephen D Barr
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 3K7, Canada
| | - Eric J Arts
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 3K7, Canada
| | - S M Mansour Haeryfar
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 3K7, Canada
| | - C Yong Kang
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 3K7, Canada
| | - Ryan M Troyer
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 3K7, Canada
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11
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Naor M, Pinto GD, Davidov P, Abdrbo L. Rapidly Establishing an Ultra-Cold Supply Chain of Vaccines in Israel: Evidence for the Efficacy of Inoculation to Mitigate the COVID-19 Pandemic. Vaccines (Basel) 2023; 11:vaccines11020349. [PMID: 36851228 PMCID: PMC9959231 DOI: 10.3390/vaccines11020349] [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: 01/01/2023] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The agenda of this research was to investigate how to mitigate the spread of coronaviruses by rapidly establishing an ultra-cold supply chain of vaccines. Data analysis was conducted by linear regression utilizing a dataset publicly available from the Israel Ministry of Health regarding the daily rates of people vaccinated, tested, hospitalized, etc., since the start of the pandemic. The data provide statistical evidence for the efficacy of the Pfizer vaccines in diminishing a wide variety of disease factors, such as the number of patients who were lightly, moderately, or severely sick, and daily deaths, as well as the rate of spread (R-ratio) and number/percentage of people infected. Insightfully, the data corroborate how the first and second doses of the vaccines were able to decrease the wave of COVID-19, which hit Israel in January 2021, while the booster third dose was able to diminish a subsequent COVID-19 wave occurring in Israel in July 2021.
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Affiliation(s)
- Michael Naor
- School of Business Administration, Hebrew University, Jerusalem 9190501, Israel
- Correspondence:
| | - Gavriel David Pinto
- Industrial Engineering and Management, Azrieli College of Engineering, Jerusalem 9103501, Israel
| | - Pini Davidov
- Industrial Engineering and Management, Azrieli College of Engineering, Jerusalem 9103501, Israel
- UNEC Cognitive Economics Center, Azerbaijan State University of Economics, Baku AZ1001, Azerbaijan
| | - Lina Abdrbo
- Industrial Engineering and Management, Azrieli College of Engineering, Jerusalem 9103501, Israel
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12
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Heilmann E, Costacurta F, Moghadasi SA, Ye C, Pavan M, Bassani D, Volland A, Ascher C, Weiss AKH, Bante D, Harris RS, Moro S, Rupp B, Martinez-Sobrido L, von Laer D. SARS-CoV-2 3CL pro mutations selected in a VSV-based system confer resistance to nirmatrelvir, ensitrelvir, and GC376. Sci Transl Med 2023; 15:eabq7360. [PMID: 36194133 PMCID: PMC9765458 DOI: 10.1126/scitranslmed.abq7360] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/18/2022] [Accepted: 09/21/2022] [Indexed: 01/14/2023]
Abstract
Protease inhibitors are among the most powerful antiviral drugs. Nirmatrelvir is the first protease inhibitor specifically developed against the SARS-CoV-2 protease 3CLpro that has been licensed for clinical use. To identify mutations that confer resistance to this protease inhibitor, we engineered a chimeric vesicular stomatitis virus (VSV) that expressed a polyprotein composed of the VSV glycoprotein (G), the SARS-CoV-2 3CLpro, and the VSV polymerase (L). Viral replication was thus dependent on the autocatalytic processing of this precursor protein by 3CLpro and release of the functional viral proteins G and L, and replication of this chimeric VSV was effectively inhibited by nirmatrelvir. Using this system, we applied nirmatrelvir to select for resistance mutations. Resistance was confirmed by retesting nirmatrelvir against the selected mutations in additional VSV-based systems, in an independently developed cellular system, in a biochemical assay, and in a recombinant SARS-CoV-2 system. We demonstrate that some mutants are cross-resistant to ensitrelvir and GC376, whereas others are less resistant to these compounds. Furthermore, we found that most of these resistance mutations already existed in SARS-CoV-2 sequences that have been deposited in the NCBI and GISAID databases, indicating that these mutations were present in circulating SARS-CoV-2 strains.
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Affiliation(s)
- Emmanuel Heilmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Austria
| | - Francesco Costacurta
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Austria
| | - Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, United States
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX 78229, USA
| | - Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Davide Bassani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Andre Volland
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Austria
| | - Claudia Ascher
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, 6020, Austria
| | | | - David Bante
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Austria
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, United States
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, United States
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, United States
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Bernhard Rupp
- Division of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, 6020, Austria
- k.-k. Hofkristallamt, San Diego, CA 92084, United States
| | | | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Austria
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13
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Yuan F, Zheng A. Replicating-Competent VSV-Vectored Pseudotyped Viruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1407:329-348. [PMID: 36920706 DOI: 10.1007/978-981-99-0113-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Vesicular stomatitis virus (VSV) is prototype virus in the family of Rhabdoviridae. Reverse genetic platform has enabled the genetic manipulation of VSV as a powerful live viral vector. Replicating-competent VSV is constructed by replacing the original VSV glycoprotein gene with heterologous envelope genes. The resulting recombinant viruses are able to replicate in permissive cells and incorporate the foreign envelope proteins on the surface of the viral particle without changing the bullet-shape morphology. Correspondingly, the cell tropism of replicating-competent VSV is determined by the foreign envelope proteins. Replicating-competent VSVs have been successfully used for selecting critical viral receptors or host factors, screening mutants that escape therapeutic antibodies, and developing VSV-based live viral vaccines.
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Affiliation(s)
- Fei Yuan
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Aihua Zheng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
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14
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Du Y, Chen L, Shi Y. Booster COVID-19 vaccination against the SARS-CoV-2 Omicron variant: A systematic review. Hum Vaccin Immunother 2022; 18:2062983. [PMID: 35499517 PMCID: PMC9897643 DOI: 10.1080/21645515.2022.2062983] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/10/2022] [Accepted: 04/01/2022] [Indexed: 02/06/2023] Open
Abstract
There is a wealth of data suggesting that the effectiveness of existing vaccines against the Omicron variant, the most mutated SARS-CoV-2 variant to date, has been substantially reduced if only primary vaccination is administered. Therefore, the effectiveness of booster vaccination against the Omicron variant has become a topic of current interest. We conducted a comprehensive search in PubMed, Embase, and the Cochrane Library to collect various pseudovirus neutralization tests or live virus neutralization tests for the Omicron variant, with serum specimens from booster vaccinees. We extracted neutralization titers for the Omicron variant, the original strain, and the other variants before and after booster vaccination, and then manually calculated the fold increase or decrease in neutralization titers for the Omicron variant relative to the other variants, and the fold increase in neutralization titers for the Omicron variant after booster vaccination compared with that before booster vaccination. In the two-dose vaccination regimen, the neutralization titers against the Omicron variant decreased substantially compared to the original strain and other variants. However, after booster vaccination, both homologous and heterologous booster vaccination, the neutralization of serum antibodies against the Omicron variant was significantly improved, although still lower than that of the original strain and other variants. The booster vaccination program based on existing vaccines can produce broad but incomplete immunity against the Omicron variant.
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Affiliation(s)
- Yuxuan Du
- Department of Neonatology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Long Chen
- Department of Neonatology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Yuan Shi
- Department of Neonatology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
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15
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Espeseth AS, Yuan M, Citron M, Reiserova L, Morrow G, Wilson A, Horton M, Rukhman M, Kinek K, Hou F, Li SL, Li F, Choi Y, Heidecker G, Luo B, Wu G, Zhang L, Strable E, DeStefano J, Secore S, Mukhopadhyay TK, Richardson DD, Sayeed E, Welch LS, Bett AJ, Feinberg MB, Gupta SB, Cooper CL, Parks CL. Preclinical immunogenicity and efficacy of a candidate COVID-19 vaccine based on a vesicular stomatitis virus-SARS-CoV-2 chimera. EBioMedicine 2022; 82:104203. [PMID: 35915046 PMCID: PMC9338221 DOI: 10.1016/j.ebiom.2022.104203] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 12/17/2022] Open
Abstract
Background To investigate a vaccine technology with potential to protect against coronavirus disease 2019 (COVID-19) and reduce transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with a single vaccine dose, we developed a SARS-CoV-2 candidate vaccine using the live vesicular stomatitis virus (VSV) chimeric virus approach previously used to develop a licensed Ebola virus vaccine. Methods We generated a replication-competent chimeric VSV-SARS-CoV-2 vaccine candidate by replacing the VSV glycoprotein (G) gene with coding sequence for the SARS-CoV-2 Spike glycoprotein (S). Immunogenicity of the lead vaccine candidate (VSV∆G-SARS-CoV-2) was evaluated in cotton rats and golden Syrian hamsters, and protection from SARS-CoV-2 infection also was assessed in hamsters. Findings VSV∆G-SARS-CoV-2 delivered with a single intramuscular (IM) injection was immunogenic in cotton rats and hamsters and protected hamsters from weight loss following SARS-CoV-2 challenge. When mucosal vaccination was evaluated, cotton rats did not respond to the vaccine, whereas mucosal administration of VSV∆G-SARS-CoV-2 was found to be more immunogenic than IM injection in hamsters and induced immunity that significantly reduced SARS-CoV-2 challenge virus loads in both lung and nasal tissues. Interpretation VSV∆G-SARS-CoV-2 delivered by IM injection or mucosal administration was immunogenic in golden Syrian hamsters, and both vaccination methods effectively protected the lung from SARS-CoV-2 infection. Hamsters vaccinated by mucosal application of VSV∆G-SARS-CoV-2 also developed immunity that controlled SARS-CoV-2 replication in nasal tissue. Funding The study was funded by Merck Sharp & Dohme, Corp., a subsidiary of Merck & Co., Inc., Rahway, NJ, USA, and The International AIDS Vaccine Initiative, Inc. (IAVI), New York, USA. Parts of this research was supported by the Biomedical Advanced Research and Development Authority (BARDA) and the Defense Threat Reduction Agency (DTRA) of the US Department of Defense.
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Affiliation(s)
| | - Maoli Yuan
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | | | - Lucia Reiserova
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | - Gavin Morrow
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | - Aaron Wilson
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | | | - Mark Rukhman
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | | | - Fuxiang Hou
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | - Shui L Li
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | | | - Yesle Choi
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | | | - Bin Luo
- Merck & Co., Inc., Rahway, New Jersey, USA
| | - Guoxin Wu
- Merck & Co., Inc., Rahway, New Jersey, USA
| | - Lan Zhang
- Merck & Co., Inc., Rahway, New Jersey, USA
| | | | - Joanne DeStefano
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | | | | | | | - Eddy Sayeed
- The International AIDS Vaccine Initiative, Inc. (IAVI), New York, USA
| | - Lisa S Welch
- The International AIDS Vaccine Initiative, Inc. (IAVI), New York, USA; Currently at Clover Biopharmaceuticals, Boston, Massachusetts, USA
| | | | - Mark B Feinberg
- The International AIDS Vaccine Initiative, Inc. (IAVI), New York, USA
| | - Swati B Gupta
- The International AIDS Vaccine Initiative, Inc. (IAVI), New York, USA
| | - Christopher L Cooper
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | - Christopher L Parks
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA.
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rVSV-ΔG-SARS-CoV-2-S vaccine: repeated intramuscular (IM) toxicity, local tolerance, immunogenicity and biodistribution study in NZW rabbits. Arch Toxicol 2022; 96:2329-2339. [PMID: 35577986 PMCID: PMC9110212 DOI: 10.1007/s00204-022-03302-5] [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: 03/16/2022] [Accepted: 04/07/2022] [Indexed: 11/06/2022]
Abstract
BriLife®, a vector-based vaccine that utilizes the recombinant vesicular stomatitis virus (VSV) platform to express and present the spike antigen of SARS-CoV-2, is undergoing testing in a phase 2 clinical trial in Israel. A nonclinical repeated-dose (GLP) toxicity study in New Zealand white rabbits was performed to evaluate the potential toxicity, local tolerance, immunogenicity and biodistribution of the vaccine. rVSV-ΔG-SARS-CoV-2-S (or vehicle) was administered intramuscularly to two groups of animals (106, 107 PFU/animal, n = 10/sex/group) on three occasions, at 2-week intervals, followed by a 3-week recovery period. Systemic clinical signs, local reactions, body weight, body temperature, food consumption, ophthalmology, urinalysis, clinical pathology, C-reactive protein, viremia and antibody levels were monitored. Gross pathology was performed, followed by organs/tissues collection for biodistribution and histopathological evaluation. Treatment-related changes were restricted to multifocal minimal myofiber necrosis at the injection sites, and increased lymphocytic cellularity in the iliac and mesenteric lymph nodes and in the spleen. These changes were considered related to the inflammatory reaction elicited, and correlated with a trend for recovery. Detection of rVSV-ΔG-SARS-CoV-2-S vaccine RNA was noted in the regional iliac lymph node in animals assigned to the high-dose group, at both termination time points. A significant increase in binding and neutralizing antibody titers was observed following vaccination at both vaccine doses. In view of the findings, it was concluded that the rVSV-ΔG-SARS-CoV-2-S vaccine is safe. These results supported the initiation of clinical trials.
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17
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Fisher M, Manor A, Abramovitch H, Fatelevich E, Afrimov Y, Bilinsky G, Lupu E, Ben-Shmuel A, Glinert I, Madar-Balakirski N, Marcus H, Mechaly A. A Novel Quantitative Multi-Component Serological Assay for SARS-CoV-2 Vaccine Evaluation. Anal Chem 2022; 94:4380-4389. [PMID: 35230823 PMCID: PMC8903214 DOI: 10.1021/acs.analchem.1c05264] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/18/2022] [Indexed: 12/23/2022]
Abstract
A multi-component microarray, applying a novel analysis algorithm, was developed for quantitative evaluation of the SARS-CoV-2 vaccines' immunogenicity. The array enables simultaneous quantitation of IgG, IgM, and IgA, specific to the SARS-CoV-2 spike, receptor binding domain, and nucleocapsid proteins. The developed methodology is based on calculating an apparent immunoglobulin signal from the linear range of the fluorescent read-outs generated by scanning the microarray slides at different exposure times. A dedicated algorithm, employing a rigorous set of embedded conditions, then generates a normalized signal for each of the unique assays. Qualification of the multi-component array performance (evaluating linearity, extended dynamic-range, specificity, precision, and accuracy) was carried out with an in-house COVID-19, qRT-PCR positive serum, as well as pre-pandemic commercial negative sera. Results were compared to the WHO international standard for anti-SARS-CoV-2 immunoglobulins. Specific IgG, IgM, and IgA signals obtained by this array enabled successful discrimination between SARS-CoV-2 q-RT-PCR positive (seroconverted SARS-CoV-2 patients) and negative (naïve) samples. This array is currently used for evaluation of the humoral response to BriLife, the VSV-based Israeli vaccine during phase I/II clinical trials.
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Affiliation(s)
- Morly Fisher
- Department
of Infectious Diseases, Israel Institute
for Biological Research, 7410001 Ness-Ziona, Israel
| | - Alon Manor
- Department
of Environmental Physics, Israel Institute
for Biological Research, 7410001 Ness Ziona, Israel
| | - Hagar Abramovitch
- Department
of Quality Assurance, Israel Institute for
Biological Research, 7410001 Ness Ziona, Israel
| | - Ella Fatelevich
- Department
of Infectious Diseases, Israel Institute
for Biological Research, 7410001 Ness-Ziona, Israel
| | - Yafa Afrimov
- Department
of Infectious Diseases, Israel Institute
for Biological Research, 7410001 Ness-Ziona, Israel
| | - Gal Bilinsky
- Department
of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, 7410001 Ness Ziona, Israel
| | - Edith Lupu
- Department
of Biotechnology, Israel Institute for Biological
Research, 7410001 Ness Ziona, Israel
| | - Amir Ben-Shmuel
- Department
of Infectious Diseases, Israel Institute
for Biological Research, 7410001 Ness-Ziona, Israel
| | - Itai Glinert
- Department
of Infectious Diseases, Israel Institute
for Biological Research, 7410001 Ness-Ziona, Israel
| | - Noa Madar-Balakirski
- Department
of Pharmacology, Israel Institute for Biological
Research, 7410001 Ness Ziona, Israel
| | - Hadar Marcus
- Department
of Biotechnology, Israel Institute for Biological
Research, 7410001 Ness Ziona, Israel
| | - Adva Mechaly
- Department
of Infectious Diseases, Israel Institute
for Biological Research, 7410001 Ness-Ziona, Israel
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