1
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Nguyen HL, Hieu HK, Nguyen TQ, Nhung NTA, Li MS. Neuropilin-1 Protein May Serve as a Receptor for SARS-CoV-2 Infection: Evidence from Molecular Dynamics Simulations. J Phys Chem B 2024; 128:7141-7147. [PMID: 39010661 DOI: 10.1021/acs.jpcb.4c03119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The binding of the virus to host cells is the first step in viral infection. Human cell angiotensin converting enzyme 2 (ACE2) is the most popular receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), while other receptors have recently been observed in experiments. Neuropilin-1 protein (NRP1) is one of them, but the mechanism of its binding to the wild type (WT) and different variants of the virus remain unclear at the atomic level. In this work, all-atom umbrella sampling simulations were performed to clarify the binding mechanism of NRP1 to the spike protein fragments 679-685 of the WT, Delta, and Omicron BA.1 variants. We found that the Delta variant binds most strongly to NRP1, while the affinity for Omicron BA.1 slightly decreases for NRP1 compared to that of WT, and the van der Waals interaction plays a key role in stabilizing the studied complexes. The change in the protonation state of the His amino acid results in different binding free energies between variants. Consistent with the experiment, decreasing the pH was shown to increase the binding affinity of the virus to NRP1. Our results indicate that Delta and Omicron mutations not only affect fusogenicity but also affect NRP1 binding. In addition, we argue that viral evolution does not further improve NRP1 binding affinity which remains in the μM range but may increase immune evasion.
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Affiliation(s)
- Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, 03 Quang Trung, Hai Chau, Da Nang 550000, Viet Nam
| | - Ho Khac Hieu
- Faculty of Environmental and Natural Sciences, Duy Tan University, 03 Quang Trung, Hai Chau, Da Nang 550000, Viet Nam
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Hai Chau, Da Nang 550000, Viet Nam
| | - Thai Quoc Nguyen
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap 81000, Vietnam
| | - Nguyen Thi Ai Nhung
- Department of Chemistry, University of Sciences, Hue University, Hue 530000, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, Warsaw 02-668, Poland
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2
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Nagorska A, Tomás RMF, Tasnim A, Robb NC, Gibson MI. Cryopreserved Kidney Epithelial (Vero) Cell Monolayers for Rapid Viral Quantification, Enabled by a Combination of Macromolecular Cryoprotectants. Biomacromolecules 2024. [PMID: 39051654 DOI: 10.1021/acs.biomac.4c00760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Plaque assays quantify the amount of active, replicating virus to study and detect infectious diseases by application of samples to monolayers of cultured cells. Due to the time taken in thawing, propagating, plating, counting, and then conducting the assay, the process can take over a week to gather data. Here, we introduce assay-ready cryopreserved Vero monolayers in multiwell plates, which can be used directly from the freezer with no cell culture to accelerate the process of plaque determination. Standard dimethyl sulfoxide cryopreservation resulted in just 25% recovery, but addition of polyampholytes (macromolecular cryoprotectants) increased post-thaw recovery and viability in 12- and 24-well plate formats. Variability between individual wells was reduced by chemically induced ice nucleation to prevent supercooling. Cryopreserved cells were used to determine influenza viral plaques in just 24 h, matching results from nonfrozen controls. This innovation may accelerate viral detection and quantification and facilitate automation by eliminating extensive cell culturing.
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Affiliation(s)
- Agnieszka Nagorska
- CryoLogyx Ltd, Venture Centre, University of Warwick Science Park, Coventry CV4 7EZ, U.K
| | - Ruben M F Tomás
- CryoLogyx Ltd, Venture Centre, University of Warwick Science Park, Coventry CV4 7EZ, U.K
| | - Afifah Tasnim
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, U.K
| | - Nicole C Robb
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, U.K
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, U.K
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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3
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Hu Z, López-Muñoz AD, Kosik I, Li T, Callahan V, Brooks K, Yee DS, Holly J, Santos JJS, Castro Brant A, Johnson RF, Takeda K, Zheng ZM, Brenchley JM, Yewdell JW, Fox JM. Recombinant OC43 SARS-CoV-2 spike replacement virus: An improved BSL-2 proxy virus for SARS-CoV-2 neutralization assays. Proc Natl Acad Sci U S A 2024; 121:e2310421121. [PMID: 38976733 PMCID: PMC11260102 DOI: 10.1073/pnas.2310421121] [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: 06/20/2023] [Accepted: 05/24/2024] [Indexed: 07/10/2024] Open
Abstract
We generated a replication-competent OC43 human seasonal coronavirus (CoV) expressing the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike in place of the native spike (rOC43-CoV2 S). This virus is highly attenuated relative to OC43 and SARS-CoV-2 in cultured cells and animals and is classified as a biosafety level 2 (BSL-2) agent by the NIH biosafety committee. Neutralization of rOC43-CoV2 S and SARS-CoV-2 by S-specific monoclonal antibodies and human sera is highly correlated, unlike recombinant vesicular stomatitis virus-CoV2 S. Single-dose immunization with rOC43-CoV2 S generates high levels of neutralizing antibodies against SARS-CoV-2 and fully protects human ACE2 transgenic mice from SARS-CoV-2 lethal challenge, despite nondetectable replication in respiratory and nonrespiratory organs. rOC43-CoV2 S induces S-specific serum and airway mucosal immunoglobulin A and IgG responses in rhesus macaques. rOC43-CoV2 S has enormous value as a BSL-2 agent to measure S-specific antibodies in the context of a bona fide CoV and is a candidate live attenuated SARS-CoV-2 mucosal vaccine that preferentially replicates in the upper airway.
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Affiliation(s)
- Zhe Hu
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Alberto Domingo López-Muñoz
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Ivan Kosik
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Tiansheng Li
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Victoria Callahan
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Kelsie Brooks
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Debra S. Yee
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Jaroslav Holly
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Jefferson J. S. Santos
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Ayslan Castro Brant
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, National Cancer Institute, NIH, Frederick, MD21702
| | - Reed F. Johnson
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Kazuyo Takeda
- Microscopy and Imaging Core Facility, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, National Cancer Institute, NIH, Frederick, MD21702
| | - Jason M. Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Jonathan W. Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Julie M. Fox
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
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4
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Jeong GU, Hwang I, Lee W, Choi JH, Yoon GY, Kim HS, Yang JS, Kim KC, Lee JY, Kim SJ, Kwon YC, Kim KD. Generation of a lethal mouse model expressing human ACE2 and TMPRSS2 for SARS-CoV-2 infection and pathogenesis. Exp Mol Med 2024; 56:1221-1229. [PMID: 38816566 PMCID: PMC11148094 DOI: 10.1038/s12276-024-01197-z] [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: 08/27/2023] [Revised: 12/18/2023] [Accepted: 12/26/2023] [Indexed: 06/01/2024] Open
Abstract
Mouse models expressing human ACE2 for coronavirus disease 2019 have been frequently used to understand its pathogenesis and develop therapeutic strategies against SARS-CoV-2. Given that human TMPRSS2 supports viral entry, replication, and pathogenesis, we established a double-transgenic mouse model expressing both human ACE2 and TMPRSS2 for SARS-CoV-2 infection. Co-overexpression of both genes increased viral infectivity in vitro and in vivo. Double-transgenic mice showed significant body weight loss, clinical disease symptoms, acute lung injury, lung inflammation, and lethality in response to viral infection, indicating that they were highly susceptible to SARS-CoV-2. Pretreatment with the TMPRSS2 inhibitor, nafamostat, effectively reduced virus-induced weight loss, viral replication, and mortality in the double-transgenic mice. Moreover, the susceptibility and differential pathogenesis of SARS-CoV-2 variants were demonstrated in this animal model. Together, our results demonstrate that double-transgenic mice could provide a highly susceptible mouse model for viral infection to understand SARS-CoV-2 pathogenesis and evaluate antiviral therapeutics against coronavirus disease 2019.
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Affiliation(s)
- Gi Uk Jeong
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Insu Hwang
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
- Division of Vaccine Development Coordination, Center for Vaccine Research, National Institute of Infectious Diseases, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Wooseong Lee
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Ji Hyun Choi
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Gun Young Yoon
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Hae Soo Kim
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Jeong-Sun Yang
- Center for Emerging Virus Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Kyung-Chang Kim
- Center for Emerging Virus Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Joo-Yeon Lee
- Center for Emerging Virus Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Seong-Jun Kim
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Young-Chan Kwon
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea.
- Medical Chemistry and Pharmacology, University of Science and Technology (UST), Daejeon, Republic of Korea.
| | - Kyun-Do Kim
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea.
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5
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Tanneti NS, Patel AK, Tan LH, Marques AD, Perera RAPM, Sherrill-Mix S, Kelly BJ, Renner DM, Collman RG, Rodino K, Lee C, Bushman FD, Cohen NA, Weiss SR. Comparison of SARS-CoV-2 variants of concern in primary human nasal cultures demonstrates Delta as most cytopathic and Omicron as fastest replicating. mBio 2024; 15:e0312923. [PMID: 38477472 PMCID: PMC11005367 DOI: 10.1128/mbio.03129-23] [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: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
The SARS-CoV-2 pandemic was marked with emerging viral variants, some of which were designated as variants of concern (VOCs) due to selection and rapid circulation in the human population. Here, we elucidate functional features of each VOC linked to variations in replication rate. Patient-derived primary nasal cultures grown at air-liquid interface were used to model upper respiratory infection and compared to cell lines derived from human lung epithelia. All VOCs replicated to higher titers than the ancestral virus, suggesting a selection for replication efficiency. In primary nasal cultures, Omicron replicated to the highest titers at early time points, followed by Delta, paralleling comparative studies of population sampling. All SARS-CoV-2 viruses entered the cell primarily via a transmembrane serine protease 2 (TMPRSS2)-dependent pathway, and Omicron was more likely to use an endosomal route of entry. All VOCs activated and overcame dsRNA-induced cellular responses, including interferon (IFN) signaling, oligoadenylate ribonuclease L degradation, and protein kinase R activation. Among the VOCs, Omicron infection induced expression of the most IFN and IFN-stimulated genes. Infections in nasal cultures resulted in cellular damage, including a compromise of cell barrier integrity and loss of nasal cilia and ciliary beating function, especially during Delta infection. Overall, Omicron was optimized for replication in the upper respiratory tract and least favorable in the lower respiratory cell line, and Delta was the most cytopathic for both upper and lower respiratory cells. Our findings highlight the functional differences among VOCs at the cellular level and imply distinct mechanisms of pathogenesis in infected individuals. IMPORTANCE Comparative analysis of infections by SARS-CoV-2 ancestral virus and variants of concern, including Alpha, Beta, Delta, and Omicron, indicated that variants were selected for efficiency in replication. In infections of patient-derived primary nasal cultures grown at air-liquid interface to model upper respiratory infection, Omicron reached the highest titers at early time points, a finding that was confirmed by parallel population sampling studies. While all infections overcame dsRNA-mediated host responses, infections with Omicron induced the strongest interferon and interferon-stimulated gene response. In both primary nasal cultures and lower respiratory cell line, infections by Delta were most damaging to the cells as indicated by syncytia formation, loss of cell barrier integrity, and nasal ciliary function.
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Affiliation(s)
- Nikhila S. Tanneti
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Anant K. Patel
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Li Hui Tan
- Department of Otorhinolaryngology- Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrew D. Marques
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ranawaka A. P. M. Perera
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Brendan J. Kelly
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David M. Renner
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ronald G. Collman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kyle Rodino
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Carole Lee
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Noam A. Cohen
- Department of Otorhinolaryngology- Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Corporal Michael J. Crescenz VA Medical Center, Surgical Services, Philadelphia, Pennsylvania, USA
- Monell Chemical Senses Center, Philadelphia, Pennsylvania, USA
| | - Susan R. Weiss
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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6
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Hiono T, Sakaue H, Tomioka A, Kaji H, Sasaki M, Orba Y, Sawa H, Kuno A. Combinatorial Approach with Mass Spectrometry and Lectin Microarray Dissected Site-Specific Glycostem and Glycoleaf Features of the Virion-Derived Spike Protein of Ancestral and γ Variant SARS-CoV-2 Strains. J Proteome Res 2024; 23:1408-1419. [PMID: 38536229 DOI: 10.1021/acs.jproteome.3c00874] [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] [Indexed: 04/06/2024]
Abstract
The coronavirus disease (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has impacted public health globally. As the glycosylation of viral envelope glycoproteins is strongly associated with their immunogenicity, intensive studies have been conducted on the glycans of the glycoprotein of SARS-CoV-2, the spike (S) protein. Here, we conducted intensive glycoproteomic analyses of the SARS-CoV-2 S protein of ancestral and γ-variant strains using a combinatorial approach with two different technologies: mass spectrometry (MS) and lectin microarrays (LMA). Our unique MS1-based glycoproteomic technique, Glyco-RIDGE, in addition to MS2-based Byonic search, identified 1448 (ancestral strain) and 1785 (γ-variant strain) site-specific glycan compositions, respectively. Asparagine at amino acid position 20 (N20) is mainly glycosylated within two successive potential glycosylation sites, N17 and N20, of the γ-variant S protein; however, we found low-frequency glycosylation at N17. Our novel approaches, glycostem mapping and glycoleaf scoring, also illustrate the moderately branched/extended, highly fucosylated, and less sialylated natures of the glycoforms of S proteins. Subsequent LMA analysis emphasized the intensive end-capping of glycans by Lewis fucoses, which complemented the glycoproteomic features. These results illustrate the high-resolution glycoproteomic features of the SARS-CoV-2 S protein, contributing to vaccine design and understanding of viral protein synthesis.
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Affiliation(s)
- Takahiro Hiono
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
| | - Hiroaki Sakaue
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
| | - Azusa Tomioka
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
| | - Hiroyuki Kaji
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
| | - Michihito Sasaki
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
| | - Yasuko Orba
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
| | - Hirofumi Sawa
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
| | - Atsushi Kuno
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
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7
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Steiner S, Kratzel A, Barut GT, Lang RM, Aguiar Moreira E, Thomann L, Kelly JN, Thiel V. SARS-CoV-2 biology and host interactions. Nat Rev Microbiol 2024; 22:206-225. [PMID: 38225365 DOI: 10.1038/s41579-023-01003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 01/17/2024]
Abstract
The zoonotic emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing coronavirus disease 2019 (COVID-19) pandemic have profoundly affected our society. The rapid spread and continuous evolution of new SARS-CoV-2 variants continue to threaten global public health. Recent scientific advances have dissected many of the molecular and cellular mechanisms involved in coronavirus infections, and large-scale screens have uncovered novel host-cell factors that are vitally important for the virus life cycle. In this Review, we provide an updated summary of the SARS-CoV-2 life cycle, gene function and virus-host interactions, including recent landmark findings on general aspects of coronavirus biology and newly discovered host factors necessary for virus replication.
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Affiliation(s)
- Silvio Steiner
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - G Tuba Barut
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Reto M Lang
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Etori Aguiar Moreira
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lisa Thomann
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center, Jena, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
- European Virus Bioinformatics Center, Jena, Germany.
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8
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Tsumita T, Takeda R, Maishi N, Hida Y, Sasaki M, Orba Y, Sato A, Toba S, Ito W, Teshirogi T, Sakurai Y, Iba T, Naito H, Ando H, Watanabe H, Mizuno A, Nakanishi T, Matsuda A, Zixiao R, Lee J, Iimura T, Sawa H, Hida K. Viral uptake and pathophysiology of the lung endothelial cells in age-associated severe SARS-CoV-2 infection models. Aging Cell 2024; 23:e14050. [PMID: 38098255 PMCID: PMC10861199 DOI: 10.1111/acel.14050] [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: 07/11/2023] [Revised: 10/10/2023] [Accepted: 11/13/2023] [Indexed: 12/20/2023] Open
Abstract
Thrombosis is the major cause of death in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and the pathology of vascular endothelial cells (ECs) has received much attention. Although there is evidence of the infection of ECs in human autopsy tissues, their detailed pathophysiology remains unclear due to the lack of animal model to study it. We used a mouse-adapted SARS-CoV-2 virus strain in young and mid-aged mice. Only mid-aged mice developed fatal pneumonia with thrombosis. Pulmonary ECs were isolated from these infected mice and RNA-Seq was performed. The pulmonary EC transcriptome revealed that significantly higher levels of viral genes were detected in ECs from mid-aged mice with upregulation of viral response genes such as DDX58 and IRF7. In addition, the thrombogenesis-related genes encoding PLAT, PF4, F3 PAI-1, and P-selectin were upregulated. In addition, the inflammation-related molecules such as CXCL2 and CXCL10 were upregulated in the mid-aged ECs upon viral infection. Our mouse model demonstrated that SARS-CoV-2 virus entry into aged vascular ECs upregulated thrombogenesis and inflammation-related genes and led to fatal pneumonia with thrombosis. Current results of EC transcriptome showed that EC uptake virus and become thrombogenic by activating neutrophils and platelets in the aged mice, suggesting age-associated EC response as a novel finding in human severe COVID-19.
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Affiliation(s)
- Takuya Tsumita
- Department of Vascular Biology and Molecular Pathology, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Ryo Takeda
- Department of Vascular Biology and Molecular Pathology, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
- Department of Oral Diagnosis and Medicine, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Nako Maishi
- Department of Vascular Biology and Molecular Pathology, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Yasuhiro Hida
- Department of Advanced Robotic and Endoscopic SurgeryFujita Health UniversityToyoakeJapan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, International Institute for Zoonosis ControlHokkaido UniversitySapporoJapan
| | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis ControlHokkaido UniversitySapporoJapan
- International Collaboration Unit, International Institute for Zoonosis ControlHokkaido UniversitySapporoJapan
| | - Akihiko Sato
- Division of Molecular Pathobiology, International Institute for Zoonosis ControlHokkaido UniversitySapporoJapan
- Drug Discovery and Disease Research LaboratoryShionogi and Co., Ltd.OsakaJapan
| | - Shinsuke Toba
- Division of Molecular Pathobiology, International Institute for Zoonosis ControlHokkaido UniversitySapporoJapan
- Drug Discovery and Disease Research LaboratoryShionogi and Co., Ltd.OsakaJapan
| | - Wataru Ito
- Department of Vascular Biology and Molecular Pathology, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
- Department of Oral and Maxillofacial Surgery, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Takahito Teshirogi
- Department of Vascular Biology and Molecular Pathology, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
- Department of Dental Anesthesiology, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Yuya Sakurai
- Department of Vascular Biology and Molecular Pathology, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
- Department of Dental Anesthesiology, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Tomohiro Iba
- Department of Vascular Physiology, Graduate School of Medical SciencesKanazawa UniversityKanazawaJapan
- Department of Cellular and Molecular Function Analysis, Graduate School of Medical SciencesKanazawa UniversityKanazawaJapan
| | - Hisamichi Naito
- Department of Vascular Physiology, Graduate School of Medical SciencesKanazawa UniversityKanazawaJapan
| | - Hitoshi Ando
- Department of Cellular and Molecular Function Analysis, Graduate School of Medical SciencesKanazawa UniversityKanazawaJapan
| | - Haruhisa Watanabe
- Department of Pharmacology, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Amane Mizuno
- Department of Vascular Biology and Molecular Pathology, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Toshiki Nakanishi
- Department of Vascular Biology and Molecular Pathology, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Aya Matsuda
- Department of Vascular Biology and Molecular Pathology, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Ren Zixiao
- Department of Vascular Biology and Molecular Pathology, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
- Department of Oral and Maxillofacial Surgery, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Ji‐Won Lee
- Department of Pharmacology, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Tadahiro Iimura
- Department of Pharmacology, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, International Institute for Zoonosis ControlHokkaido UniversitySapporoJapan
- International Collaboration Unit, International Institute for Zoonosis ControlHokkaido UniversitySapporoJapan
- One Health Research CenterHokkaido UniversitySapporoJapan
- Institute for Vaccine Research and DevelopmentHokkaido UniversitySapporoJapan
| | - Kyoko Hida
- Department of Vascular Biology and Molecular Pathology, Faculty and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
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9
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Avila-Herrera A, Kimbrel JA, Manuel Martí J, Thissen J, Saada EA, Weisenberger T, Arrildt KT, Segelke BW, Allen JE, Zemla A, Borucki MK. Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies. PLoS One 2024; 19:e0289198. [PMID: 38271318 PMCID: PMC10810540 DOI: 10.1371/journal.pone.0289198] [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: 07/12/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Viral populations in natural infections can have a high degree of sequence diversity, which can directly impact immune escape. However, antibody potency is often tested in vitro with a relatively clonal viral populations, such as laboratory virus or pseudotyped virus stocks, which may not accurately represent the genetic diversity of circulating viral genotypes. This can affect the validity of viral phenotype assays, such as antibody neutralization assays. To address this issue, we tested whether recombinant virus carrying SARS-CoV-2 spike (VSV-SARS-CoV-2-S) stocks could be made more genetically diverse by passage, and if a stock passaged under selective pressure was more capable of escaping monoclonal antibody (mAb) neutralization than unpassaged stock or than viral stock passaged without selective pressures. We passaged VSV-SARS-CoV-2-S four times concurrently in three cell lines and then six times with or without polyclonal antiserum selection pressure. All three of the monoclonal antibodies tested neutralized the viral population present in the unpassaged stock. The viral inoculum derived from serial passage without antiserum selection pressure was neutralized by two of the three mAbs. However, the viral inoculum derived from serial passage under antiserum selection pressure escaped neutralization by all three mAbs. Deep sequencing revealed the rapid acquisition of multiple mutations associated with antibody escape in the VSV-SARS-CoV-2-S that had been passaged in the presence of antiserum, including key mutations present in currently circulating Omicron subvariants. These data indicate that viral stock that was generated under polyclonal antiserum selection pressure better reflects the natural environment of the circulating virus and may yield more biologically relevant outcomes in phenotypic assays. Thus, mAb assessment assays that utilize a more genetically diverse, biologically relevant, virus stock may yield data that are relevant for prediction of mAb efficacy and for enhancing biosurveillance.
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Affiliation(s)
- Aram Avila-Herrera
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - Jeffrey A. Kimbrel
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Jose Manuel Martí
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - James Thissen
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Edwin A. Saada
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Tracy Weisenberger
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Kathryn T. Arrildt
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Brent W. Segelke
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Jonathan E. Allen
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - Adam Zemla
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - Monica K. Borucki
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
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10
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Harari S, Miller D, Fleishon S, Burstein D, Stern A. Using big sequencing data to identify chronic SARS-Coronavirus-2 infections. Nat Commun 2024; 15:648. [PMID: 38245511 PMCID: PMC10799923 DOI: 10.1038/s41467-024-44803-4] [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: 09/04/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
The evolution of SARS-Coronavirus-2 (SARS-CoV-2) has been characterized by the periodic emergence of highly divergent variants. One leading hypothesis suggests these variants may have emerged during chronic infections of immunocompromised individuals, but limited data from these cases hinders comprehensive analyses. Here, we harnessed millions of SARS-CoV-2 genomes to identify potential chronic infections and used language models (LM) to infer chronic-associated mutations. First, we mined the SARS-CoV-2 phylogeny and identified chronic-like clades with identical metadata (location, age, and sex) spanning over 21 days, suggesting a prolonged infection. We inferred 271 chronic-like clades, which exhibited characteristics similar to confirmed chronic infections. Chronic-associated mutations were often high-fitness immune-evasive mutations located in the spike receptor-binding domain (RBD), yet a minority were unique to chronic infections and absent in global settings. The probability of observing high-fitness RBD mutations was 10-20 times higher in chronic infections than in global transmission chains. The majority of RBD mutations in BA.1/BA.2 chronic-like clades bore predictive value, i.e., went on to display global success. Finally, we used our LM to infer hundreds of additional chronic-like clades in the absence of metadata. Our approach allows mining extensive sequencing data and providing insights into future evolutionary patterns of SARS-CoV-2.
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Affiliation(s)
- Sheri Harari
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Danielle Miller
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Shay Fleishon
- Israeli Health Intelligence Agency, Public Health Division, Ministry of Health, Jerusalem, Israel
| | - David Burstein
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel.
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel.
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11
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Sasaki M, Sugi T, Iida S, Hirata Y, Kusakabe S, Konishi K, Itakura Y, Tabata K, Kishimoto M, Kobayashi H, Ariizumi T, Intaruck K, Nobori H, Toba S, Sato A, Matsuno K, Yamagishi J, Suzuki T, Hall WW, Orba Y, Sawa H. Combination therapy with oral antiviral and anti-inflammatory drugs improves the efficacy of delayed treatment in a COVID-19 hamster model. EBioMedicine 2024; 99:104950. [PMID: 38159532 PMCID: PMC10792455 DOI: 10.1016/j.ebiom.2023.104950] [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: 06/21/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Pulmonary infection with SARS-CoV-2 stimulates host immune responses and can also result in the progression of dysregulated and critical inflammation. Throughout the pandemic, the management and treatment of COVID-19 has been continuously updated with a range of antiviral drugs and immunomodulators. Monotherapy with oral antivirals has proven to be effective in the treatment of COVID-19. However, treatment should be initiated in the early stages of infection to ensure beneficial therapeutic outcomes, and there is still room for further consideration on therapeutic strategies using antivirals. METHODS We studied the therapeutic effects of monotherapy with the oral antiviral ensitrelvir or the anti-inflammatory corticosteroid methylprednisolone and combination therapy with ensitrelvir and methylprednisolone in a delayed dosing model of hamsters infected with SARS-CoV-2. FINDINGS Combination therapy with ensitrelvir and methylprednisolone improved respiratory conditions and reduced the development of pneumonia in hamsters even when the treatment was started after 2 days post-infection. The combination therapy led to a differential histological and transcriptomic pattern in comparison to either of the monotherapies, with reduced lung damage and down-regulation of expression of genes involved in the inflammatory response. Furthermore, we found that the combination treatment is effective in case of infection with either the highly pathogenic delta or circulating omicron variants. INTERPRETATION Our results demonstrate the advantage of combination therapy with antiviral and corticosteroid drugs in COVID-19 treatment from the perspective of lung pathology and host inflammatory responses. FUNDING Funding bodies are described in the Acknowledgments section.
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Affiliation(s)
- Michihito Sasaki
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan.
| | - Tatsuki Sugi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shun Iida
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuichiro Hirata
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shinji Kusakabe
- Division of Anti-Virus Drug Research, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Drug Discovery & Disease Research Laboratory, Shionogi & Co., Ltd., Osaka, Japan
| | - Kei Konishi
- Division of Anti-Virus Drug Research, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Drug Discovery & Disease Research Laboratory, Shionogi & Co., Ltd., Osaka, Japan
| | - Yukari Itakura
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Koshiro Tabata
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Mai Kishimoto
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hiroko Kobayashi
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Takuma Ariizumi
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kittiya Intaruck
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Haruaki Nobori
- Drug Discovery & Disease Research Laboratory, Shionogi & Co., Ltd., Osaka, Japan
| | - Shinsuke Toba
- Division of Anti-Virus Drug Research, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Drug Discovery & Disease Research Laboratory, Shionogi & Co., Ltd., Osaka, Japan
| | - Akihiko Sato
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan; Division of Anti-Virus Drug Research, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Drug Discovery & Disease Research Laboratory, Shionogi & Co., Ltd., Osaka, Japan
| | - Keita Matsuno
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Junya Yamagishi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - William W Hall
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; National Virus Reference Laboratory, School of Medicine, University College of Dublin, Ireland; Global Virus Network, Baltimore, Maryland, USA
| | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Division of Anti-Virus Drug Research, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Hirofumi Sawa
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Division of Anti-Virus Drug Research, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan; Global Virus Network, Baltimore, Maryland, USA
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12
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Tanneti NS, Patel AK, Tan LH, Marques AD, Perera RAPM, Sherrill-Mix S, Kelly BJ, Renner DM, Collman RG, Rodino K, Lee C, Bushman FD, Cohen NA, Weiss SR. Comparison of SARS-CoV-2 variants of concern in primary human nasal cultures demonstrates Delta as most cytopathic and Omicron as fastest replicating. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.553565. [PMID: 37662273 PMCID: PMC10473756 DOI: 10.1101/2023.08.24.553565] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The SARS-CoV-2 pandemic was marked with emerging viral variants, some of which were designated as variants of concern (VOCs) due to selection and rapid circulation in the human population. Here we elucidate functional features of each VOC linked to variations in replication rate. Patient-derived primary nasal cultures grown at air-liquid-interface (ALI) were used to model upper-respiratory infection and human lung epithelial cell lines used to model lower-respiratory infection. All VOCs replicated to higher titers than the ancestral virus, suggesting a selection for replication efficiency. In primary nasal cultures, Omicron replicated to the highest titers at early time points, followed by Delta, paralleling comparative studies of population sampling. All SARS-CoV-2 viruses entered the cell primarily via a transmembrane serine protease 2 (TMPRSS2)-dependent pathway, and Omicron was more likely to use an endosomal route of entry. All VOCs activated and overcame dsRNA-induced cellular responses including interferon (IFN) signaling, oligoadenylate ribonuclease L degradation and protein kinase R activation. Among the VOCs, Omicron infection induced expression of the most IFN and IFN stimulated genes. Infections in nasal cultures resulted in cellular damage, including a compromise of cell-barrier integrity and loss of nasal cilia and ciliary beating function, especially during Delta infection. Overall, Omicron was optimized for replication in the upper-respiratory system and least-favorable in the lower-respiratory cell line; and Delta was the most cytopathic for both upper and lower respiratory cells. Our findings highlight the functional differences among VOCs at the cellular level and imply distinct mechanisms of pathogenesis in infected individuals.
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Affiliation(s)
| | | | - Li Hui Tan
- Department of Otorhinolaryngology- Head and Neck Surgery
| | | | | | | | - Brendan J Kelly
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | | | - Ronald G Collman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Kyle Rodino
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | | | | | - Noam A Cohen
- Department of Otorhinolaryngology- Head and Neck Surgery
- Corporal Michael J. Crescenz VA Medical Center, Surgical Services, Philadelphia, USA
- Monell Chemical Senses Center, Philadelphia, USA
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13
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Abhinand CS, Prabhakaran AA, Krishnamurthy A, Raju R, Keshava Prasad TS, Nair AS, Rajasekharan KN, Oommen OV, Sudhakaran PR. SARS-CoV-2 variants infectivity prediction and therapeutic peptide design using computational approaches. J Biomol Struct Dyn 2023; 41:11166-11177. [PMID: 36572420 DOI: 10.1080/07391102.2022.2160819] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022]
Abstract
The outbreak of severe acute respiratory coronavirus 2 (SARS-CoV-2) has created a public health emergency globally. SARS-CoV-2 enters the human cell through the binding of the spike protein to human angiotensin converting enzyme 2 (ACE2) receptor. Significant changes have been reported in the mutational landscape of SARS-CoV-2 in the receptor binding domain (RBD) of S protein, subsequent to evolution of the pandemic. The present study examines the correlation between the binding affinity of mutated S-proteins and the rate of viral infectivity. For this, the binding affinity of SARS-CoV and variants of SARS-CoV-2 towards ACE2 was computationally determined. Subsequently, the RBD mutations were classified on the basis of the number of strains identified with respect to each mutation and the resulting variation in the binding affinity was computationally examined. The molecular docking studies indicated a significant correlation between the Z-Rank score of mutated S proteins and the rate of infectivity, suitable for predicting SARS-CoV-2 infectivity. Accordingly, a 30-mer peptide was designed and the inhibitory properties were computationally analyzed. Single amino acid-wise mutation was performed subsequently to identify the peptide with the highest binding affinity. Molecular dynamics and free energy calculations were then performed to examine the stability of the peptide-protein complexes. Additionally, selected peptides were synthesized and screened using a colorimetric assay. Together, this study developed a model to predict the rate of infectivity of SARS-CoV-2 variants and propose a potential peptide that can be used as an inhibitor for the viral entry to human.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chandran S Abhinand
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Athira A Prabhakaran
- Inter-University Centre for Genomics and Gene Technology, University of Kerala, Thiruvananthapuram, Kerala, India
| | | | - Rajesh Raju
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
- Center for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, India
| | | | - Achuthsankar S Nair
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
| | | | - Oommen V Oommen
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Perumana R Sudhakaran
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
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14
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de Vries M, Ciabattoni GO, Rodriguez-Rodriguez BA, Crosse KM, Papandrea D, Samanovic MI, Dimartino D, Marier C, Mulligan MJ, Heguy A, Desvignes L, Duerr R, Dittmann M. Generation of quality-controlled SARS-CoV-2 variant stocks. Nat Protoc 2023; 18:3821-3855. [PMID: 37833423 DOI: 10.1038/s41596-023-00897-6] [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: 01/17/2023] [Accepted: 07/28/2023] [Indexed: 10/15/2023]
Abstract
One of the main challenges in the fight against coronavirus disease 2019 (COVID-19) stems from the ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into multiple variants. To address this hurdle, research groups around the world have independently developed protocols to isolate these variants from clinical samples. These isolates are then used in translational and basic research-for example, in vaccine development, drug screening or characterizing SARS-CoV-2 biology and pathogenesis. However, over the course of the COVID-19 pandemic, we have learned that the introduction of artefacts during both in vitro isolation and subsequent propagation to virus stocks can lessen the validity and reproducibility of data. We propose a rigorous pipeline for the generation of high-quality SARS-CoV-2 variant clonal isolates that minimizes the acquisition of mutations and introduces stringent controls to detect them. Overall, the process includes eight stages: (i) cell maintenance, (ii) isolation of SARS-CoV-2 from clinical specimens, (iii) determination of infectious virus titers by plaque assay, (iv) clonal isolation by plaque purification, (v) whole-virus-genome deep-sequencing, (vi and vii) amplification of selected virus clones to master and working stocks and (viii) sucrose purification. This comprehensive protocol will enable researchers to generate reliable SARS-CoV-2 variant inoculates for in vitro and in vivo experimentation and will facilitate comparisons and collaborative work. Quality-controlled working stocks for most applications can be generated from acquired biorepository virus within 1 month. An additional 5-8 d are required when virus is isolated from clinical swab material, and another 6-7 d is needed for sucrose-purifying the stocks.
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Affiliation(s)
- Maren de Vries
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Grace O Ciabattoni
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Keaton M Crosse
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Dominick Papandrea
- High Containment Laboratories-Office of Science and Research, NYU Langone Health, New York, NY, USA
| | - Marie I Samanovic
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Dacia Dimartino
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY, USA
| | - Christian Marier
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY, USA
| | - Mark J Mulligan
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Adriana Heguy
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Ludovic Desvignes
- High Containment Laboratories-Office of Science and Research, NYU Langone Health, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Ralf Duerr
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Meike Dittmann
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA.
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15
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O’Reilly S, Kenny G, Alrawahneh T, Francois N, Gu L, Angeliadis M, de Masson d’Autume V, Garcia Leon A, Feeney ER, Yousif O, Cotter A, de Barra E, Horgan M, Mallon PWG, Gautier V. Development of a novel medium throughput flow-cytometry based micro-neutralisation test for SARS-CoV-2 with applications in clinical vaccine trials and antibody screening. PLoS One 2023; 18:e0294262. [PMID: 38033116 PMCID: PMC10688860 DOI: 10.1371/journal.pone.0294262] [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: 11/16/2022] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Quantifying neutralising capacity of circulating SARS-COV-2 antibodies is critical in evaluating protective humoral immune responses generated post-infection/post-vaccination. Here we describe a novel medium-throughput flow cytometry-based micro-neutralisation test to evaluate Neutralising Antibody (NAb) responses against live SARS-CoV-2 Wild Type and Variants of Concern (VOC) in convalescent/vaccinated populations. Flow Cytometry-Based Micro-Neutralisation Test (Micro-NT) was performed in 96-well plates using clinical isolates WT-B, WT-B.1.177.18 and/or VOCs Beta and Omicron. Plasma samples (All Ireland Infectious Diseases (AIID) Cohort) were serially diluted (8 points, half-log) from 1:20 and pre-incubated with SARS-CoV-2 (1h, 37°C). Virus-plasma mixture were added onto Vero E6 or Vero E6/TMPRSS2 cells for 18h. Percentage infected cells was analysed by automated flow cytometry following trypsinisation, fixation and SARS-CoV-2 Nucleoprotein intracellular staining. Half-maximal Neutralisation Titres (NT50) were determined using non-linear regression. Our assay was compared to Plaque Reduction Neutralisation Test (PRNT) and validated against the First WHO International Standard for anti-SARS-CoV-2 immunoglobulin. Both Micro-NT and PRNT achieved comparable NT50 values. Further validation showed adequate correlation with PRNT using a panel of secondary standards of clinical convalescent and vaccinated plasma samples. We found the assay to be reproducible through measuring both repeatability and intermediate precision. Screening 190 convalescent samples and 11 COVID-19 naive controls (AIID cohort) we demonstrated that Micro-NT has broad dynamic range differentiating NT50s <1/20 to >1/5000. We could also characterise immune-escape VOC Beta and Omicron BA.5, achieving fold-reductions in neutralising capacity similar to those published. Our flow cytometry-based Micro-NT is a robust and reliable assay to quantify NAb titres, and has been selected as an endpoint in clinical trials.
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Affiliation(s)
- Sophie O’Reilly
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Grace Kenny
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
- Department of Infectious Diseases, St Vincent’s University Hospital, Elm Park, Dublin, Ireland
| | - Tamara Alrawahneh
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Nathan Francois
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Lili Gu
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Matthew Angeliadis
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Valentin de Masson d’Autume
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Alejandro Garcia Leon
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Eoin R. Feeney
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
- Department of Infectious Diseases, St Vincent’s University Hospital, Elm Park, Dublin, Ireland
| | - Obada Yousif
- Endocrinology Department, Wexford General Hospital, Carricklawn, Wexford, Ireland
| | - Aoife Cotter
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
- Department of Infectious Diseases, Mater Misericordiae University Hospital, Eccles St, Dublin, Ireland
| | - Eoghan de Barra
- Department of Infectious Diseases, Beaumont Hospital, Beaumont, Dublin, Ireland
- Department of International Health and Tropical Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Mary Horgan
- Department of Infectious Diseases, Cork University Hospital, Wilton, Cork, Ireland
| | - Patrick W. G. Mallon
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
- Department of Infectious Diseases, St Vincent’s University Hospital, Elm Park, Dublin, Ireland
| | - Virginie Gautier
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Belfield, Dublin 4, Ireland
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16
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Kipfer ET, Hauser D, Lett MJ, Otte F, Urda L, Zhang Y, Lang CMR, Chami M, Mittelholzer C, Klimkait T. Rapid cloning-free mutagenesis of new SARS-CoV-2 variants using a novel reverse genetics platform. eLife 2023; 12:RP89035. [PMID: 37988285 PMCID: PMC10662946 DOI: 10.7554/elife.89035] [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] [Indexed: 11/23/2023] Open
Abstract
Reverse genetic systems enable the engineering of RNA virus genomes and are instrumental in studying RNA virus biology. With the recent outbreak of the coronavirus disease 2019 pandemic, already established methods were challenged by the large genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein we present an elaborated strategy for the rapid and straightforward rescue of recombinant plus-stranded RNA viruses with high sequence fidelity using the example of SARS-CoV-2. The strategy called CLEVER (CLoning-free and Exchangeable system for Virus Engineering and Rescue) is based on the intracellular recombination of transfected overlapping DNA fragments allowing the direct mutagenesis within the initial PCR-amplification step. Furthermore, by introducing a linker fragment - harboring all heterologous sequences - viral RNA can directly serve as a template for manipulating and rescuing recombinant mutant virus, without any cloning step. Overall, this strategy will facilitate recombinant SARS-CoV-2 rescue and accelerate its manipulation. Using our protocol, newly emerging variants can quickly be engineered to further elucidate their biology. To demonstrate its potential as a reverse genetics platform for plus-stranded RNA viruses, the protocol has been successfully applied for the cloning-free rescue of recombinant Chikungunya and Dengue virus.
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Affiliation(s)
- Enja Tatjana Kipfer
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - David Hauser
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Martin J Lett
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Fabian Otte
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Lorena Urda
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Yuepeng Zhang
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Christopher MR Lang
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Mohamed Chami
- BioEM Lab, Biozentrum, University of Basel, MattenstrasseBaselSwitzerland
| | | | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
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17
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Uemura K, Nobori H, Sato A, Toba S, Kusakabe S, Sasaki M, Tabata K, Matsuno K, Maeda N, Ito S, Tanaka M, Anraku Y, Kita S, Ishii M, Kanamitsu K, Orba Y, Matsuura Y, Hall WW, Sawa H, Kida H, Matsuda A, Maenaka K. 2-thiouridine is a broad-spectrum antiviral nucleoside analogue against positive-strand RNA viruses. Proc Natl Acad Sci U S A 2023; 120:e2304139120. [PMID: 37831739 PMCID: PMC10589713 DOI: 10.1073/pnas.2304139120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/23/2023] [Indexed: 10/15/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections are causing significant morbidity and mortality worldwide. Furthermore, over 1 million cases of newly emerging or re-emerging viral infections, specifically dengue virus (DENV), are known to occur annually. Because no virus-specific and fully effective treatments against these or many other viruses have been approved, there is an urgent need for novel, effective therapeutic agents. Here, we identified 2-thiouridine (s2U) as a broad-spectrum antiviral ribonucleoside analogue that exhibited antiviral activity against several positive-sense single-stranded RNA (ssRNA+) viruses, such as DENV, SARS-CoV-2, and its variants of concern, including the currently circulating Omicron subvariants. s2U inhibits RNA synthesis catalyzed by viral RNA-dependent RNA polymerase, thereby reducing viral RNA replication, which improved the survival rate of mice infected with DENV2 or SARS-CoV-2 in our animal models. Our findings demonstrate that s2U is a potential broad-spectrum antiviral agent not only against DENV and SARS-CoV-2 but other ssRNA+ viruses.
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Affiliation(s)
- Kentaro Uemura
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
- Drug Discovery and Disease Research Laboratory, Shionogi & Co. Ltd., Osaka561-0825, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- Laboratory of Virus Control, Center for Infectious Disease Education and Research, Osaka University, Osaka565-0871, Japan
| | - Haruaki Nobori
- Drug Discovery and Disease Research Laboratory, Shionogi & Co. Ltd., Osaka561-0825, Japan
| | - Akihiko Sato
- Drug Discovery and Disease Research Laboratory, Shionogi & Co. Ltd., Osaka561-0825, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo001-0021, Japan
| | - Shinsuke Toba
- Drug Discovery and Disease Research Laboratory, Shionogi & Co. Ltd., Osaka561-0825, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Shinji Kusakabe
- Drug Discovery and Disease Research Laboratory, Shionogi & Co. Ltd., Osaka561-0825, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Koshiro Tabata
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Keita Matsuno
- Unit of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- One Health Research Center, Hokkaido University, Sapporo001-0020, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Naoyoshi Maeda
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
| | - Shiori Ito
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
| | - Mayu Tanaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
| | - Yuki Anraku
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
| | - Shunsuke Kita
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
| | - Mayumi Ishii
- Lead Exploration Unit, Drug Discovery Initiative, The University of Tokyo, Tokyo113-0033, Japan
| | - Kayoko Kanamitsu
- Lead Exploration Unit, Drug Discovery Initiative, The University of Tokyo, Tokyo113-0033, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Yoshiharu Matsuura
- Laboratory of Virus Control, Center for Infectious Disease Education and Research, Osaka University, Osaka565-0871, Japan
| | - William W. Hall
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- National Virus Reference Laboratory, School of Medicine, University College of Dublin, DublinD04, Ireland
- Global Virus Network, Baltimore, MD21201
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo001-0021, Japan
- One Health Research Center, Hokkaido University, Sapporo001-0020, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- Global Virus Network, Baltimore, MD21201
| | - Hiroshi Kida
- Laboratory for Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Akira Matsuda
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo001-0021, Japan
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo060-0812, Japan
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18
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Kipfer E, Hauser D, Lett MJ, Otte F, Urda L, Zhang Y, Lang CMR, Chami M, Mittelholzer C, Klimkait T. Rapid cloning-free mutagenesis of new SARS-CoV-2 variants using a novel reverse genetics platform. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540343. [PMID: 37292682 PMCID: PMC10245781 DOI: 10.1101/2023.05.11.540343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Reverse genetic systems enable the engineering of RNA virus genomes and are instrumental in studying RNA virus biology. With the recent outbreak of the COVID-19 pandemic, already established methods were challenged by the large genome of SARS-CoV-2. Herein we present an elaborated strategy for the rapid and straightforward rescue of recombinant plus-stranded RNA viruses with high sequence fidelity, using the example of SARS-CoV-2. The strategy called CLEVER (CLoning-free and Exchangeable system for Virus Engineering and Rescue) is based on the intracellular recombination of transfected overlapping DNA fragments allowing the direct mutagenesis within the initial PCR-amplification step. Furthermore, by introducing a linker fragment - harboring all heterologous sequences - viral RNA can directly serve as a template for manipulating and rescuing recombinant mutant virus, without any cloning step. Overall, this strategy will facilitate recombinant SARS-CoV-2 rescue and accelerate its manipulation. Using our protocol, newly emerging variants can quickly be engineered to further elucidate their biology. To demonstrate its potential as a reverse genetics platform for plus-stranded RNA viruses, the protocol has been successfully applied for the cloning-free rescue of recombinant Chikungunya and Dengue virus.
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Affiliation(s)
- Enja Kipfer
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - David Hauser
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Martin J. Lett
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Fabian Otte
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Lorena Urda
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Yuepeng Zhang
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Christopher M. R. Lang
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Mohamed Chami
- BioEM Lab, Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Christian Mittelholzer
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
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19
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Khalafalla AI, Ishag HZA, Albalushi HIA, Al-Hammadi ZMAH, Al Yammahi SMS, Shah AAM, Al Muhairi SSM. Isolation and genetic characterization of MERS-CoV from dromedary camels in the United Arab Emirates. Front Vet Sci 2023; 10:1182165. [PMID: 37720473 PMCID: PMC10500840 DOI: 10.3389/fvets.2023.1182165] [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: 03/08/2023] [Accepted: 08/14/2023] [Indexed: 09/19/2023] Open
Abstract
Background The study of coronaviruses has grown significantly in recent years.Middle East respiratory syndrome coronavirus (MERS-CoV) replicates in various cell types, and quick development has been made of assays for its growth and quantification. However, only a few viral isolates are now available for investigation with full characterization. The current study aimed to isolate MERS-CoV from nasal swabs of dromedary camels and molecularly analyze the virus in order to detect strain-specific mutations and ascertain lineage classification. Methods We isolated the virus in Vero cells and adapted it for in vitro cultivation. The isolates were subjected to complete genome sequencing using next-generation sequencing followed by phylogenetic, mutation, and recombination analysis of the sequences. Results A total of five viral isolates were obtained in Vero cells and adapted to in vitro cultures. Phylogenetic analysis classified all the isolates within clade B3. Four isolates clustered close to the MERS-CoV isolate camel/KFU-HKU-I/2017 (GenBank ID: MN758606.1) with nucleotide identity 99.90-99.91%. The later isolate clustered close to the MERS-CoV isolate Al-Hasa-SA2407/2016 (GenBank ID: MN654975.1) with a sequence identity of 99.86%. Furthermore, the isolates contained several amino acids substitutions in ORF1a (32), ORF1ab (25), S (2), ORF3 (4), ORF4b (4), M (3), ORF8b (1), and the N protein (1). The analysis further identified a recombination event in one of the reported sequences (OQ423284/MERS-CoV/dromedary/UAE-Al Ain/13/2016). Conclusion Data presented in this study indicated the need for continuous identification and characterization of MERS-CoV to monitor virus circulation in the region, which is necessary to develop effective control measures. The mutations described in this investigation might not accurately represent the virus's natural evolution as artificial mutations may develop during cell culture passage. The isolated MERS-CoV strains would be helpful in new live attenuated vaccine development and efficacy studies.
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20
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Olarte-Castillo XA, Licitra BN, André NM, Sierra MA, Mason CE, Goodman LB, Whittaker GR. Intra-host variation in the spike S1/S2 region of a feline coronavirus type-1 in a cat with persistent infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551356. [PMID: 37577589 PMCID: PMC10418068 DOI: 10.1101/2023.07.31.551356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Feline coronavirus type 1 (FCoV-1) is widely known for causing feline infectious peritonitis (FIP), a systemic infection that is often fatal, with the virus known as the FIPV biotype. However, subclinical disease also occurs, in which cats may not show signs and intermittently shed the virus, including in feces, possibly for long periods of time. This virus is known as the FECV biotype. Progression of FECV to FIPV has been linked to several genomic changes, however a specific region of the viral spike protein at the interface of the spike S1 and S2 domains has been especially implicated. In this study, we followed a cat (#576) for six years from 2017, at which time FCoV-1 was detected in feces and conjunctival swabs, until 2022, when the animal was euthanized based on a diagnosis of alimentary small cell lymphoma. Over this time period, the cat was clinically diagnosed with inflammatory bowel disease and chronic rhinitis, and cardiac problems were also suspected. Using hybridization capture targeting the spike (S) gene of FCoV followed by next-generation sequencing, we screened 27 clinical samples. We detected FCoV-1 in 4 samples taken in 2017 (intestine and nasal tissue, feces, and conjunctiva), and 3 samples taken in 2022 (feces, and intestinal and heart tissue), but not in fecal samples taken in 2019 and 2020. Next, we focused on the S1/S2 region within S, which contains the furin cleavage site (FCS), a key regulator of viral transmission and pathogenesis. We show that the FCoV-1 variants obtained from feces in 2017 and 2022 were identical, while the ones from conjunctiva (2017), heart (2022), and intestine (2017 and 2022) were distinct. Sequence comparison of all the variants obtained showed that most of the non-synonymous changes in the S1/S2 region occur within the FCS. In the heart, we found two variants that differed by a single nucleotide, resulting in distinct FCS motifs that differ in one amino acid. It is predicted that one of these FCS motifs will down-regulate spike cleavability. The variant from the conjunctiva (2017) had a 6-nucleotide in-frame insertion that resulted in a longer and more exposed S1/S2 loop, which is predicted to be more accessible to the furin protease. Our studies indicate that FCoV-1 can independently persist in the gastrointestinal tract and heart of a cat over a long period of time without evidence of typical FIP signs, with intermittent viral shedding from the gastrointestinal and respiratory tracts.
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21
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Adler JM, Martin Vidal R, Voß A, Kunder S, Nascimento M, Abdelgawad A, Langner C, Vladimirova D, Osterrieder N, Gruber AD, Kunec D, Trimpert J. A non-transmissible live attenuated SARS-CoV-2 vaccine. Mol Ther 2023; 31:2391-2407. [PMID: 37263272 PMCID: PMC10214529 DOI: 10.1016/j.ymthe.2023.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 03/23/2023] [Accepted: 05/05/2023] [Indexed: 06/03/2023] Open
Abstract
Live attenuated vaccines (LAVs) administered via the mucosal route may offer better control of the COVID-19 pandemic than non-replicating vaccines injected intramuscularly. Conceptionally, LAVs have several advantages, including presentation of the entire antigenic repertoire of the virus, and the induction of strong mucosal immunity. Thus, immunity induced by LAV could offer superior protection against future surges of COVID-19 cases caused by emerging SARS-CoV-2 variants. However, LAVs carry the risk of unintentional transmission. To address this issue, we investigated whether transmission of a SARS-CoV-2 LAV candidate can be blocked by removing the furin cleavage site (FCS) from the spike protein. The level of protection and immunity induced by the attenuated virus with the intact FCS was virtually identical to the one induced by the attenuated virus lacking the FCS. Most importantly, removal of the FCS completely abolished horizontal transmission of vaccine virus between cohoused hamsters. Furthermore, the vaccine was safe in immunosuppressed animals and showed no tendency to recombine in vitro or in vivo with a SARS-CoV-2 field strain. These results indicate that removal of the FCS from SARS-CoV-2 LAV is a promising strategy to increase vaccine safety and prevent vaccine transmission without compromising vaccine efficacy.
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Affiliation(s)
- Julia M Adler
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | | | - Anne Voß
- Institut für Tierpathologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Sandra Kunder
- Institut für Tierpathologie, Freie Universität Berlin, 14163 Berlin, Germany
| | | | - Azza Abdelgawad
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Christine Langner
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Daria Vladimirova
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | | | - Achim D Gruber
- Institut für Tierpathologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Dusan Kunec
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany.
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22
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Spinello A, D'Anna L, Bignon E, Miclot T, Grandemange S, Terenzi A, Barone G, Barbault F, Monari A. Mechanism of the Covalent Inhibition of Human Transmembrane Protease Serine 2 as an Original Antiviral Strategy. J Phys Chem B 2023. [PMID: 37428676 DOI: 10.1021/acs.jpcb.3c02910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
The Transmembrane Protease Serine 2 (TMPRSS2) is a human enzyme which is involved in the maturation and post-translation of different proteins. In addition to being overexpressed in cancer cells, TMPRSS2 plays a further fundamental role in favoring viral infections by allowing the fusion of the virus envelope with the cellular membrane, notably in SARS-CoV-2. In this contribution, we resort to multiscale molecular modeling to unravel the structural and dynamical features of TMPRSS2 and its interaction with a model lipid bilayer. Furthermore, we shed light on the mechanism of action of a potential inhibitor (nafamostat), determining the free-energy profile associated with the inhibition reaction and showing the facile poisoning of the enzyme. Our study, while providing the first atomistically resolved mechanism of TMPRSS2 inhibition, is also fundamental in furnishing a solid framework for further rational design targeting transmembrane proteases in a host-directed antiviral strategy.
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Affiliation(s)
- Angelo Spinello
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo, 90126 Palermo, Italy
| | - Luisa D'Anna
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo, 90126 Palermo, Italy
| | - Emmanuelle Bignon
- Université de Lorraine and CNRS, UMR 7019 LPCT, F-54000 Nancy, France
| | - Tom Miclot
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo, 90126 Palermo, Italy
- Université de Lorraine and CNRS, UMR 7019 LPCT, F-54000 Nancy, France
| | | | - Alessio Terenzi
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo, 90126 Palermo, Italy
| | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo, 90126 Palermo, Italy
| | | | - Antonio Monari
- Université Paris Cité and CNRS, ITODYS, F-75006 Paris, France
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23
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von Delft A, Hall MD, Kwong AD, Purcell LA, Saikatendu KS, Schmitz U, Tallarico JA, Lee AA. Accelerating antiviral drug discovery: lessons from COVID-19. Nat Rev Drug Discov 2023; 22:585-603. [PMID: 37173515 PMCID: PMC10176316 DOI: 10.1038/s41573-023-00692-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2023] [Indexed: 05/15/2023]
Abstract
During the coronavirus disease 2019 (COVID-19) pandemic, a wave of rapid and collaborative drug discovery efforts took place in academia and industry, culminating in several therapeutics being discovered, approved and deployed in a 2-year time frame. This article summarizes the collective experience of several pharmaceutical companies and academic collaborations that were active in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antiviral discovery. We outline our opinions and experiences on key stages in the small-molecule drug discovery process: target selection, medicinal chemistry, antiviral assays, animal efficacy and attempts to pre-empt resistance. We propose strategies that could accelerate future efforts and argue that a key bottleneck is the lack of quality chemical probes around understudied viral targets, which would serve as a starting point for drug discovery. Considering the small size of the viral proteome, comprehensively building an arsenal of probes for proteins in viruses of pandemic concern is a worthwhile and tractable challenge for the community.
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Affiliation(s)
- Annette von Delft
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Oxford Biomedical Research Centre, National Institute for Health Research, University of Oxford, Oxford, UK.
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | | | | | | | | | | | - Alpha A Lee
- PostEra, Inc., Cambridge, MA, USA.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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24
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Chen C, Zhu R, Hodge EA, Díaz-Salinas MA, Nguyen A, Munro JB, Lee KK. hACE2-Induced Allosteric Activation in SARS-CoV versus SARS-CoV-2 Spike Assemblies Revealed by Structural Dynamics. ACS Infect Dis 2023; 9:1180-1189. [PMID: 37166130 PMCID: PMC10228703 DOI: 10.1021/acsinfecdis.3c00010] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Indexed: 05/12/2023]
Abstract
SARS-CoV and SARS-CoV-2 cell entry begins when spike glycoprotein (S) docks with the human ACE2 (hACE2) receptor. While the two coronaviruses share a common receptor and architecture of S, they exhibit differences in interactions with hACE2 as well as differences in proteolytic processing of S that trigger the fusion machine. Understanding how those differences impact S activation is key to understand its function and viral pathogenesis. Here, we investigate hACE2-induced activation in SARS-CoV and SARS-CoV-2 S using hydrogen/deuterium-exchange mass spectrometry (HDX-MS). HDX-MS revealed differences in dynamics in unbound S, including open/closed conformational switching and D614G-induced S stability. Upon hACE2 binding, notable differences in transduction of allosteric changes were observed extending from the receptor binding domain to regions proximal to proteolytic cleavage sites and the fusion peptide. Furthermore, we report that dimeric hACE2, the native oligomeric form of the receptor, does not lead to any more pronounced structural effect in S compared to saturated monomeric hACE2 binding. These experiments provide mechanistic insights into receptor-induced activation of Sarbecovirus spike proteins.
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Affiliation(s)
- Chengbo Chen
- Department
of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, USA
- Biological
Physics Structure and Design Program, University
of Washington, Seattle, Washington 98195, USA
| | - Richard Zhu
- Department
of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Edgar A. Hodge
- Department
of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Marco A. Díaz-Salinas
- Department
of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Adam Nguyen
- Biological
Physics Structure and Design Program, University
of Washington, Seattle, Washington 98195, USA
| | - James B. Munro
- Department
of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Kelly K. Lee
- Department
of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, USA
- Biological
Physics Structure and Design Program, University
of Washington, Seattle, Washington 98195, USA
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25
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Olivier T, Blomet J, Desmecht D. Central role of lung macrophages in SARS-CoV-2 physiopathology: a cross-model single-cell RNA-seq perspective. Front Immunol 2023; 14:1197588. [PMID: 37350967 PMCID: PMC10282834 DOI: 10.3389/fimmu.2023.1197588] [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: 03/31/2023] [Accepted: 05/19/2023] [Indexed: 06/24/2023] Open
Abstract
Cytokine storms are considered a driving factor in coronavirus disease 2019 (COVID-19) severity. However, the triggering and resolution of this cytokine production, as well as the link between this phenomenon and infected cells, are still poorly understood. In this study, a cross-species scRNA-seq analysis showed that cytokine-producing macrophages together with pneumocytes were found to be the main contributors of viral transcripts in both Syrian hamsters and African green monkeys. Whatever the cell type, viral read-bearing cells show an apoptotic phenotype. A comparison of SARS-CoV-2 entry receptor candidates showed that Fc receptors are better correlated with infected cells than ACE2, NRP1, or AXL. Although both species show similar interferon responses, differences in adaptive immunity were highlighted. Lastly, Fc receptor and cytokine upregulation in M1 macrophages was found to correlate with a comprehensive interferon response. Based on these results, we propose a model in which lung macrophages play a central role in COVID-19 severity through antibody-dependent enhancement.
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Affiliation(s)
- Thibaut Olivier
- GAS Department, Prevor Research Laboratories, Valmondois, France
- Department of Pathology, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liege, Liège, Belgium
| | - Joël Blomet
- GAS Department, Prevor Research Laboratories, Valmondois, France
| | - Daniel Desmecht
- Department of Pathology, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liege, Liège, Belgium
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26
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Abas AH, Tallei TE, Fatimawali F, Celik I, Alhumaydhi FA, Emran TB, Dhama K, Rabaan AA, Garout MA, Halwani MA, Al Mutair A, Alhumaid S, Harapan H. 4’-fluorouridine as a potential COVID-19 oral drug?: a review. F1000Res 2023; 11:410. [DOI: 10.12688/f1000research.109701.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
The available antiviral drugs against coronavirus disease 2019 (COVID-19) are limited. Oral drugs that can be prescribed to non-hospitalized patients are required. The 4′-fluoruridine, a nucleoside analog similar to remdesivir, is one of the promising candidates for COVID-19 oral therapy due to its ability to stall viral RdRp. Available data suggested that 4'-fluorouridine has antiviral activity against the respiratory syncytial virus, hepatitis C virus, lymphocytic choriomeningitis virus, and other RNA viruses, including SARS-CoV-2. In vivo study revealed that SARS-CoV-2 is highly susceptible to 4'-fluorouridine and was effective with a single daily dose versus molnupiravir administered twice daily. Although 4'-fluorouridine is considered as strong candidates, further studies are required to determine its efficacy in the patients and it’s genetic effects on humans. In this review, we the antiviral activity of 4′-fluorouridine is reviewed and compared it to other drugs currently in development. The current literature on 4′-fluorouridine's antiviral activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is compiled and discussed.
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27
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Kim SH, Kearns FL, Rosenfeld MA, Votapka L, Casalino L, Papanikolas M, Amaro RE, Freeman R. SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101346. [PMID: 37077408 PMCID: PMC10080732 DOI: 10.1016/j.xcrp.2023.101346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/07/2023] [Accepted: 03/07/2023] [Indexed: 05/03/2023]
Abstract
Viral variants of concern continue to arise for SARS-CoV-2, potentially impacting both methods for detection and mechanisms of action. Here, we investigate the effect of an evolving spike positive charge in SARS-CoV-2 variants and subsequent interactions with heparan sulfate and the angiotensin converting enzyme 2 (ACE2) in the glycocalyx. We show that the positively charged Omicron variant evolved enhanced binding rates to the negatively charged glycocalyx. Moreover, we discover that while the Omicron spike-ACE2 affinity is comparable to that of the Delta variant, the Omicron spike interactions with heparan sulfate are significantly enhanced, giving rise to a ternary complex of spike-heparan sulfate-ACE2 with a large proportion of double-bound and triple-bound ACE2. Our findings suggest that SARS-CoV-2 variants evolve to be more dependent on heparan sulfate in viral attachment and infection. This discovery enables us to engineer a second-generation lateral-flow test strip that harnesses both heparin and ACE2 to reliably detect all variants of concern, including Omicron.
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Affiliation(s)
- Sang Hoon Kim
- Department of Applied Physical Sciences, University of North Carolina - Chapel Hill, 1112 Murray Hall, CB#3050, Chapel Hill, NC 27599-2100, USA
| | - Fiona L Kearns
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Mia A Rosenfeld
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Lane Votapka
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Micah Papanikolas
- Department of Applied Physical Sciences, University of North Carolina - Chapel Hill, 1112 Murray Hall, CB#3050, Chapel Hill, NC 27599-2100, USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina - Chapel Hill, 1112 Murray Hall, CB#3050, Chapel Hill, NC 27599-2100, USA
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28
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Furusawa Y, Kiso M, Iida S, Uraki R, Hirata Y, Imai M, Suzuki T, Yamayoshi S, Kawaoka Y. In SARS-CoV-2 delta variants, Spike-P681R and D950N promote membrane fusion, Spike-P681R enhances spike cleavage, but neither substitution affects pathogenicity in hamsters. EBioMedicine 2023; 91:104561. [PMID: 37043872 PMCID: PMC10083686 DOI: 10.1016/j.ebiom.2023.104561] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/18/2023] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 delta (B.1.617.2 lineage) variant was first identified at the end of 2020 and possessed two unique amino acid substitutions in its spike protein: S-P681R, at the S1/S2 cleavage site, and S-D950N, in the HR1 of the S2 subunit. However, the roles of these substitutions in virus phenotypes have not been fully characterized. METHODS We used reverse genetics to generate Wuhan-D614G viruses with these substitutions and delta viruses lacking these substitutions and explored how these changes affected their viral characteristics in vitro and in vivo. FINDINGS S-P681R enhanced spike cleavage and membrane fusion, whereas S-D950N slightly promoted membrane fusion. Although S-681R reduced the virus replicative ability especially in VeroE6 cells, neither substitution affected virus replication in Calu-3 cells and hamsters. The pathogenicity of all recombinant viruses tested in hamsters was slightly but not significantly affected. INTERPRETATION Our observations suggest that the S-P681R and S-D950N substitutions alone do not increase virus pathogenicity, despite of their enhancement of spike cleavage or fusogenicity. FUNDING A full list of funding bodies that contributed to this study can be found under Acknowledgments.
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Affiliation(s)
- Yuri Furusawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan; The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Maki Kiso
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Shun Iida
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ryuta Uraki
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan; The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Yuichiro Hirata
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masaki Imai
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan; The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan; International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Seiya Yamayoshi
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan; The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan; International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
| | - Yoshihiro Kawaoka
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan; The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan; Pandemic Preparedness, Infection, and Advanced Research Center, The University of Tokyo, Tokyo, Japan; Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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29
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Alsmadi MM. The investigation of the complex population-drug-drug interaction between ritonavir-boosted lopinavir and chloroquine or ivermectin using physiologically-based pharmacokinetic modeling. Drug Metab Pers Ther 2023; 38:87-105. [PMID: 36205215 DOI: 10.1515/dmpt-2022-0130] [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: 04/29/2022] [Accepted: 08/19/2022] [Indexed: 11/07/2022]
Abstract
OBJECTIVES Therapy failure caused by complex population-drug-drug (PDDI) interactions including CYP3A4 can be predicted using mechanistic physiologically-based pharmacokinetic (PBPK) modeling. A synergy between ritonavir-boosted lopinavir (LPVr), ivermectin, and chloroquine was suggested to improve COVID-19 treatment. This work aimed to study the PDDI of the two CYP3A4 substrates (ivermectin and chloroquine) with LPVr in mild-to-moderate COVID-19 adults, geriatrics, and pregnancy populations. METHODS The PDDI of LPVr with ivermectin or chloroquine was investigated. Pearson's correlations between plasma, saliva, and lung interstitial fluid (ISF) levels were evaluated. Target site (lung epithelial lining fluid [ELF]) levels of ivermectin and chloroquine were estimated. RESULTS Upon LPVr coadministration, while the chloroquine plasma levels were reduced by 30, 40, and 20%, the ivermectin plasma levels were increased by a minimum of 425, 234, and 453% in adults, geriatrics, and pregnancy populations, respectively. The established correlation equations can be useful in therapeutic drug monitoring (TDM) and dosing regimen optimization. CONCLUSIONS Neither chloroquine nor ivermectin reached therapeutic ELF levels in the presence of LPVr despite reaching toxic ivermectin plasma levels. PBPK modeling, guided with TDM in saliva, can be advantageous to evaluate the probability of reaching therapeutic ELF levels in the presence of PDDI, especially in home-treated patients.
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Affiliation(s)
- Mo'tasem M Alsmadi
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
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30
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Schindewolf C, Lokugamage K, Vu MN, Johnson BA, Scharton D, Plante JA, Kalveram B, Crocquet-Valdes PA, Sotcheff S, Jaworski E, Alvarado RE, Debbink K, Daugherty MD, Weaver SC, Routh AL, Walker DH, Plante KS, Menachery VD. SARS-CoV-2 Uses Nonstructural Protein 16 To Evade Restriction by IFIT1 and IFIT3. J Virol 2023; 97:e0153222. [PMID: 36722972 PMCID: PMC9973020 DOI: 10.1128/jvi.01532-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/13/2023] [Indexed: 02/02/2023] Open
Abstract
Understanding the molecular basis of innate immune evasion by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important consideration for designing the next wave of therapeutics. Here, we investigate the role of the nonstructural protein 16 (NSP16) of SARS-CoV-2 in infection and pathogenesis. NSP16, a ribonucleoside 2'-O-methyltransferase (MTase), catalyzes the transfer of a methyl group to mRNA as part of the capping process. Based on observations with other CoVs, we hypothesized that NSP16 2'-O-MTase function protects SARS-CoV-2 from cap-sensing host restriction. Therefore, we engineered SARS-CoV-2 with a mutation that disrupts a conserved residue in the active site of NSP16. We subsequently show that this mutant is attenuated both in vitro and in vivo, using a hamster model of SARS-CoV-2 infection. Mechanistically, we confirm that the NSP16 mutant is more sensitive than wild-type SARS-CoV-2 to type I interferon (IFN-I) in vitro. Furthermore, silencing IFIT1 or IFIT3, IFN-stimulated genes that sense a lack of 2'-O-methylation, partially restores fitness to the NSP16 mutant. Finally, we demonstrate that sinefungin, an MTase inhibitor that binds the catalytic site of NSP16, sensitizes wild-type SARS-CoV-2 to IFN-I treatment and attenuates viral replication. Overall, our findings highlight the importance of SARS-CoV-2 NSP16 in evading host innate immunity and suggest a target for future antiviral therapies. IMPORTANCE Similar to other coronaviruses, disruption of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) NSP16 function attenuates viral replication in a type I interferon-dependent manner. In vivo, our results show reduced disease and viral replication at late times in the hamster lung, but an earlier titer deficit for the NSP16 mutant (dNSP16) in the upper airway. In addition, our results confirm a role for IFIT1 but also demonstrate the necessity of IFIT3 in mediating dNSP16 attenuation. Finally, we show that targeting NSP16 activity with a 2'-O-methyltransferase inhibitor in combination with type I interferon offers a novel avenue for antiviral development.
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Affiliation(s)
- Craig Schindewolf
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
| | - Kumari Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Michelle N. Vu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Bryan A. Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Dionna Scharton
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jessica A. Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, USA
| | - Birte Kalveram
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | | | - Stephanea Sotcheff
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Elizabeth Jaworski
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Rojelio E. Alvarado
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas, USA
| | - Kari Debbink
- Department of Microbiology and Immunology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Matthew D. Daugherty
- Department of Molecular Biology, University of California, San Diego, California, USA
| | - Scott C. Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, USA
| | - Andrew L. Routh
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - David H. Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Disease, University of Texas Medical Branch, Galveston, Texas, USA
| | - Kenneth S. Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, USA
| | - Vineet D. Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, USA
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31
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Toelzer C, Gupta K, Berger I, Schaffitzel C. Cryo-EM reveals binding of linoleic acid to SARS-CoV-2 spike glycoprotein, suggesting an antiviral treatment strategy. Acta Crystallogr D Struct Biol 2023; 79:111-121. [PMID: 36762857 PMCID: PMC9912919 DOI: 10.1107/s2059798323000049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/03/2023] [Indexed: 01/21/2023] Open
Abstract
The COVID-19 pandemic and concomitant lockdowns presented a global health challenge and triggered unprecedented research efforts to elucidate the molecular mechanisms and pathogenicity of SARS-CoV-2. The spike glycoprotein decorating the surface of SARS-CoV-2 virions is a prime target for vaccine development, antibody therapy and serology as it binds the host cell receptor and is central for viral cell entry. The electron cryo-microscopy structure of the spike protein revealed a hydrophobic pocket in the receptor-binding domain that is occupied by an essential fatty acid, linoleic acid (LA). The LA-bound spike protein adopts a non-infectious locked conformation which is more stable than the infectious form and shields important immunogenic epitopes. Here, the impact of LA binding on viral infectivity and replication, and the evolutionary conservation of the pocket in other highly pathogenic coronaviruses, including SARS-CoV-2 variants of concern (VOCs), are reviewed. The importance of LA metabolic products, the eicosanoids, in regulating the human immune response and inflammation is highlighted. Lipid and fatty-acid binding to a hydrophobic pocket in proteins on the virion surface appears to be a broader strategy employed by viruses, including picornaviruses and Zika virus. Ligand binding stabilizes their protein structure and assembly, and downregulates infectivity. In the case of rhinoviruses, this has been exploited to develop small-molecule antiviral drugs that bind to the hydrophobic pocket. The results suggest a COVID-19 antiviral treatment based on the LA-binding pocket.
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Affiliation(s)
- Christine Toelzer
- School of Biochemistry, University of Bristol, 1 Tankard’s Close, Bristol BS8 1TD, United Kingdom
- Bristol Synthetic Biology Centre: BrisSynBio, 24 Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| | - Kapil Gupta
- Imophoron Ltd, St Philips Central, Albert Road, Bristol BS2 0XJ, United Kingdom
| | - Imre Berger
- School of Biochemistry, University of Bristol, 1 Tankard’s Close, Bristol BS8 1TD, United Kingdom
- Bristol Synthetic Biology Centre: BrisSynBio, 24 Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Christiane Schaffitzel
- School of Biochemistry, University of Bristol, 1 Tankard’s Close, Bristol BS8 1TD, United Kingdom
- Bristol Synthetic Biology Centre: BrisSynBio, 24 Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
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32
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Atypical Mutational Spectrum of SARS-CoV-2 Replicating in the Presence of Ribavirin. Antimicrob Agents Chemother 2023; 67:e0131522. [PMID: 36602354 PMCID: PMC9872624 DOI: 10.1128/aac.01315-22] [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] [Indexed: 01/06/2023] Open
Abstract
We report that ribavirin exerts an inhibitory and mutagenic activity on SARS-CoV-2-infecting Vero cells, with a therapeutic index higher than 10. Deep sequencing analysis of the mutant spectrum of SARS-CoV-2 replicating in the absence or presence of ribavirin indicated an increase in the number of mutations, but not in deletions, and modification of diversity indices, expected from a mutagenic activity. Notably, the major mutation types enhanced by replication in the presence of ribavirin were A→G and U→C transitions, a pattern which is opposite to the dominance of G→A and C→U transitions previously described for most RNA viruses. Implications of the inhibitory activity of ribavirin, and the atypical mutational bias produced on SARS-CoV-2, for the search for synergistic anti-COVID-19 lethal mutagen combinations are discussed.
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33
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Sasaki M, Tabata K, Kishimoto M, Itakura Y, Kobayashi H, Ariizumi T, Uemura K, Toba S, Kusakabe S, Maruyama Y, Iida S, Nakajima N, Suzuki T, Yoshida S, Nobori H, Sanaki T, Kato T, Shishido T, Hall WW, Orba Y, Sato A, Sawa H. S-217622, a SARS-CoV-2 main protease inhibitor, decreases viral load and ameliorates COVID-19 severity in hamsters. Sci Transl Med 2023; 15:eabq4064. [PMID: 36327352 PMCID: PMC9765455 DOI: 10.1126/scitranslmed.abq4064] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In parallel with vaccination, oral antiviral agents are highly anticipated to act as countermeasures for the treatment of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Oral antiviral medication demands not only high antiviral activity but also target specificity, favorable oral bioavailability, and high metabolic stability. Although a large number of compounds have been identified as potential inhibitors of SARS-CoV-2 infection in vitro, few have proven to be effective in vivo. Here, we show that oral administration of S-217622 (ensitrelvir), an inhibitor of SARS-CoV-2 main protease (Mpro; also known as 3C-like protease), decreases viral load and ameliorates disease severity in SARS-CoV-2-infected hamsters. S-217622 inhibited viral proliferation at low nanomolar to submicromolar concentrations in cells. Oral administration of S-217622 demonstrated favorable pharmacokinetic properties and accelerated recovery from acute SARS-CoV-2 infection in hamster recipients. Moreover, S-217622 exerted antiviral activity against SARS-CoV-2 variants of concern, including the highly pathogenic Delta variant and the recently emerged Omicron BA.5 and BA.2.75 variants. Overall, our study provides evidence that S-217622, an antiviral agent that is under evaluation in a phase 3 clinical trial (clinical trial registration no. jRCT2031210350), has remarkable antiviral potency and efficacy against SARS-CoV-2 and is a prospective oral therapeutic option for COVID-19.
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Affiliation(s)
- Michihito Sasaki
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Corresponding author. (M.S.); (H.S.)
| | - Koshiro Tabata
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Mai Kishimoto
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Yukari Itakura
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Hiroko Kobayashi
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Takuma Ariizumi
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Kentaro Uemura
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan.,Laboratory of Biomolecular Science, Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, 060-0812, Japan
| | - Shinsuke Toba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Shinji Kusakabe
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Yuki Maruyama
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Shun Iida
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Noriko Nakajima
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | | | | | | | | | | | - William W. Hall
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan.,National Virus Reference Laboratory, School of Medicine, University College of Dublin, 4, Ireland.,Global Virus Network, Baltimore, MD, 21201, USA
| | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan
| | - Akihiko Sato
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan.,Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan.,Global Virus Network, Baltimore, MD, 21201, USA.,Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, 001-0021, Japan.,One Health Research Center, Hokkaido University, Sapporo, 001-0020, Japan.,Corresponding author. (M.S.); (H.S.)
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Heindl MR, Böttcher-Friebertshäuser E. The role of influenza-A virus and coronavirus viral glycoprotein cleavage in host adaptation. Curr Opin Virol 2023; 58:101303. [PMID: 36753938 PMCID: PMC9847222 DOI: 10.1016/j.coviro.2023.101303] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 01/19/2023]
Abstract
While receptor binding is well recognized as a factor in influenza-A virus (IAV) and coronavirus (CoV) host adaptation, the role of viral glycoprotein cleavage has not been studied in detail so far. Interestingly, recent studies suggest that host species may differ in their protease repertoire available for cleavage. Furthermore, it was shown for certain bat-derived CoVs that proteolytic activation provides a critical barrier to infect human cells. Understanding the role of glycoprotein cleavage in different species and how IAV and CoVs adapt to a new protease repertoire may allow evaluating the zoonotic potential and risk posed by these viruses. Here, we summarize the current knowledge on the emergence of a multibasic cleavage site (CS) in the glycoproteins of IAVs and CoVs in different host species. Additionally, we discuss the role of transmembrane serine protease 2 (TMPRSS2) in virus activation and entry and a role of neuropilin-1 in acquisition of a multibasic CS in different hosts.
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Hayashida K, Garcia A, Moonga LC, Sugi T, Takuya K, Kawase M, Kodama F, Nagasaka A, Ishiguro N, Takada A, Kajihara M, Nao N, Shingai M, Kida H, Suzuki Y, Hall WW, Sawa H, Yamagishi J. Field-deployable multiplex detection method of SARS-CoV-2 and influenza virus using loop-mediated isothermal amplification and DNA chromatography. PLoS One 2023; 18:e0285861. [PMID: 37192155 DOI: 10.1371/journal.pone.0285861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/03/2023] [Indexed: 05/18/2023] Open
Abstract
A novel multiplex loop-mediated isothermal amplification (LAMP) method combined with DNA chromatography was developed for the simultaneous detection of three important respiratory disease-causing viruses: severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A virus, and influenza B virus. Amplification was performed at a constant temperature, and a positive result was confirmed by a visible colored band. An in-house drying protocol with trehalose was used to prepare the dried format multiplex LAMP test. Using this dried multiplex LAMP test, the analytical sensitivity was determined to be 100 copies for each viral target and 100-1000 copies for the simultaneous detection of mixed targets. The multiplex LAMP system was validated using clinical COVID-19 specimens and compared with the real-time qRT-PCR method as a reference test. The determined sensitivity of the multiplex LAMP system for SARS-CoV-2 was 71% (95% CI: 0.62-0.79) for cycle threshold (Ct) ≤ 35 samples and 61% (95% CI: 0.53-0.69) for Ct ≤40 samples. The specificity was 99% (95%CI: 0.92-1.00) for Ct ≤35 samples and 100% (95%CI: 0.92-1.00) for the Ct ≤40 samples. The developed simple, rapid, low-cost, and laboratory-free multiplex LAMP system for the two major important respiratory viral diseases, COVID-19 and influenza, is a promising field-deployable diagnosis tool for the possible future 'twindemic, ' especially in resource-limited settings.
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Affiliation(s)
- Kyoko Hayashida
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Alejandro Garcia
- UCD Centre for Experimental Pathogen Host Research, University College Dublin, Belfield, Ireland
| | - Lavel Chinyama Moonga
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Tatsuki Sugi
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | | | | | | | | | - Nobuhisa Ishiguro
- Division of Infection Control, Hokkaido University Hospital, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Ayato Takada
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naganori Nao
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Masashi Shingai
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hiroshi Kida
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan
| | - William W Hall
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Ireland
- Global Virus Network, Baltimore, Maryland, United States of America
| | - Hirofumi Sawa
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan
- Global Virus Network, Baltimore, Maryland, United States of America
| | - Junya Yamagishi
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
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Production and characterization of lentivirus vector-based SARS-CoV-2 pseudoviruses with dual reporters: Evaluation of anti-SARS-CoV-2 viral effect of Korean Red Ginseng. J Ginseng Res 2023; 47:123-132. [PMID: 35855181 PMCID: PMC9283196 DOI: 10.1016/j.jgr.2022.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 01/09/2023] Open
Abstract
Background Pseudotyped virus systems that incorporate viral proteins have been widely employed for the rapid determination of the effectiveness and neutralizing activity of drug and vaccine candidates in biosafety level 2 facilities. We report an efficient method for producing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pseudovirus with dual luciferase and fluorescent protein reporters. Moreover, using the established method, we also aimed to investigate whether Korean Red Ginseng (KRG), a valuable Korean herbal medicine, can attenuate infectivity of the pseudotyped virus. Methods A pseudovirus of SARS-CoV-2 (SARS-2pv) was constructed and efficiently produced using lentivirus vector systems available in the public domain by the introduction of critical mutations in the cytoplasmic tail of the spike protein. KRG extract was dose-dependently treated to Calu-3 cells during SARS2-pv treatment to evaluate the protective activity against SARS-CoV-2. Results The use of Calu-3 cells or the expression of angiotensin-converting enzyme 2 (ACE2) in HEK293T cells enabled SARS-2pv infection of host cells. Coexpression of transmembrane protease serine subtype 2 (TMPRSS2), which is the activator of spike protein, with ACE2 dramatically elevated luciferase activity, confirming the importance of the TMPRSS2-mediated pathway during SARS-CoV-2 entry. Our pseudovirus assay also revealed that KRG elicited resistance to SARS-CoV-2 infection in lung cells, suggesting its beneficial health effect. Conclusion The method demonstrated the production of SARS-2pv for the analysis of vaccine or drug candidates. When KRG was assessed by the method, it protected host cells from coronavirus infection. Further studies will be followed for demonstrating this potential benefit.
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Chan K, Farias AG, Lee H, Guvenc F, Mero P, Brown KR, Ward H, Billmann M, Aulakh K, Astori A, Haider S, Marcon E, Braunschweig U, Pu S, Habsid A, Yan Tong AH, Christie-Holmes N, Budylowski P, Ghalami A, Mubareka S, Maguire F, Banerjee A, Mossman KL, Greenblatt J, Gray-Owen SD, Raught B, Blencowe BJ, Taipale M, Myers C, Moffat J. Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors. Heliyon 2023; 9:e12744. [PMID: 36597481 PMCID: PMC9800021 DOI: 10.1016/j.heliyon.2022.e12744] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
SARS-CoV-2 depends on host cell components for infection and replication. Identification of virus-host dependencies offers an effective way to elucidate mechanisms involved in viral infection and replication. If druggable, host factor dependencies may present an attractive strategy for anti-viral therapy. In this study, we performed genome wide CRISPR knockout screens in Vero E6 cells and four human cell lines including Calu-3, UM-UC-4, HEK-293 and HuH-7 to identify genetic regulators of SARS-CoV-2 infection. Our findings identified only ACE2, the cognate SARS-CoV-2 entry receptor, as a common host dependency factor across all cell lines, while other host genes identified were largely cell line specific, including known factors TMPRSS2 and CTSL. Several of the discovered host-dependency factors converged on pathways involved in cell signalling, immune-related pathways, and chromatin modification. Notably, the chromatin modifier gene KMT2C in Calu-3 cells had the strongest impact in preventing SARS-CoV-2 infection when perturbed.
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Affiliation(s)
- Katherine Chan
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1,Corresponding author
| | - Adrian Granda Farias
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1,Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Hunsang Lee
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Furkan Guvenc
- Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Patricia Mero
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Kevin R. Brown
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Henry Ward
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Kamaldeep Aulakh
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Audrey Astori
- Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Shahan Haider
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Edyta Marcon
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Ulrich Braunschweig
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Shuye Pu
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Andrea Habsid
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Amy Hin Yan Tong
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Natasha Christie-Holmes
- Combined Containment Level 3 Unit, Temerty Faculty of Medicine, University of Toronto Toronto, Ontario, Canada, M5S3E1
| | - Patrick Budylowski
- Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Ayoob Ghalami
- Office of Environmental Health & Safety, University of Toronto, Toronto, Ontario, Canada
| | - Samira Mubareka
- Sunnybrook Research Institute, Toronto, Ontario, Canada, M5S3E1,Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada
| | - Finlay Maguire
- Department of Community Health and Epidemiology, Faculty of Medicine Dalhousie University, Halifax, Nova Scotia, Canada,Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Karen L. Mossman
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jack Greenblatt
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1,Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Scott D. Gray-Owen
- Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Brian Raught
- Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Benjamin J. Blencowe
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1,Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Mikko Taipale
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1,Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Chad Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Jason Moffat
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1,Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8,Institute for Biomedical Engineering, Rosebrugh Building, 164 College Street, Room 407, University of Toronto, Toronto, Ontario, Canada, M5S3G9,Corresponding author. Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
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Guo C, Tsai SJ, Ai Y, Li M, Anaya E, Pekosz A, Cox A, Gould SJ. The D614G mutation redirects SARS-CoV-2 spike to lysosomes and suppresses deleterious traits of the furin cleavage site insertion mutation. SCIENCE ADVANCES 2022; 8:eade5085. [PMID: 36563151 PMCID: PMC9788772 DOI: 10.1126/sciadv.ade5085] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) egress occurs by lysosomal exocytosis. We show that the Spike D614G mutation enhances Spike trafficking to lysosomes, drives Spike-mediated reprogramming of lysosomes, and reduces cell surface Spike expression by ~3-fold. D614G is not a human-specific adaptation. Rather, it is an adaptation to the earlier furin cleavage site insertion (FCSI) mutation that occurred at the genesis of SARS-CoV-2. While advantageous to the virus, furin cleavage of spike has deleterious effects on spike structure and function, inhibiting its trafficking to lysosomes and impairing its infectivity by the transmembrane serine protease 2(TMPRSS2)-independent, endolysosomal pathway. D614G restores spike trafficking to lysosomes and enhances the earliest events in SARS-CoV-2 infectivity, while spike mutations that restore SARS-CoV-2's TMPRSS2-independent infectivity restore spike's trafficking to lysosomes. Together, these and other results show that D614G is an intragenic suppressor of deleterious traits linked to the FCSI and lend additional support to the endolysosomal model of SARS-CoV-2 egress and entry.
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Affiliation(s)
- Chenxu Guo
- Department of Biological Chemistry, Johns Hopkins University, School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Shang-Jui Tsai
- Department of Biological Chemistry, Johns Hopkins University, School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Yiwei Ai
- Department of Biological Chemistry, Johns Hopkins University, School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Maggie Li
- Department of Microbiology and Immunology, Johns Hopkins University, School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | - Eduardo Anaya
- Department of Microbiology and Immunology, Johns Hopkins University, School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | - Andrew Pekosz
- Department of Microbiology and Immunology, Johns Hopkins University, School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | - Andrea Cox
- Department of Medicine, Department of Microbiology and Immunology, Johns Hopkins University, School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Stephen J. Gould
- Department of Biological Chemistry, Johns Hopkins University, School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205, USA
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Sirijatuphat R, Leelarasamee A, Puangpet T, Thitithanyanont A. A Pilot Study of 0.4% Povidone-Iodine Nasal Spray to Eradicate SARS-CoV-2 in the Nasopharynx. Infect Drug Resist 2022; 15:7529-7536. [PMID: 36575672 PMCID: PMC9790155 DOI: 10.2147/idr.s391630] [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: 10/04/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Purpose This study aimed to evaluate the virucidal efficacy of 0.4% povidone-iodine (PVP-I) nasal spray against SARS-CoV-2 in the patients' nasopharynx at 3 minutes and 4 hours after PVP-I exposure. Patients and Methods The study was an open-label, before and after design, single-arm pilot study of adult patients with RT-PCR-confirmed COVID-19 within 24 hours. All patients received three puffs of 0.4% PVP-I nasal spray in each nostril. Nasopharyngeal (NP) swabs were collected before the PVP-I spray (baseline, left NP samples), and at 3 minutes (left and right NP samples) and 4 hours post-PVP-I spray (right NP samples). All swabs were coded to blind assessors and transported to diagnostic laboratory and tested by RT-PCR and cultured to measure the viable SARS-CoV-2 within 24 hours after collection. Results Fourteen patients were enrolled but viable SARS-CoV-2 was cultured from 12 patients (85.7%). The median viral titer at baseline was 3.5 log TCID50/mL (IQR 2.8-4.0 log TCID50/mL). At 3 minutes post-PVP-I spray via the left nostril, viral titers were reduced in 8 patients (66.7%). At 3 minutes post-PVP-I, the median viral titer was 3.4 log TCID50/mL (IQR 1.8-4.4 log TCID50/mL) (P=0.162). At 4 hours post-PVP-I spray via the right nostril, 6 of 11 patients (54.5%) had either the same or minimal change in viral titers. The median viral titer 3 minutes post-PVP-I spray was 2.7 log TCID50/mL (IQR 2.0-3.9 log TCID50/mL). Four hours post-PVP-I spray the median titer was 2.8 log TCID50/mL (IQR 2.2-3.9 log TCID50/mL) (P=0.704). No adverse effects of 0.4% PVP-I nasal spray were detected. Conclusion The 0.4% PVP-I nasal spray demonstrated minimal virucidal efficacy at 3 minutes post-exposure. At 4 hours post-exposure, the viral titer was considerably unchanged from baseline in 10 cases. The 0.4% PVP-I nasal spray showed poor virucidal activity and is unlikely to reduce transmission of SARS-CoV-2 in prophylaxis use.
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Affiliation(s)
- Rujipas Sirijatuphat
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Amorn Leelarasamee
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand,Faculty of Medicine, Siam University, Bangkok, Thailand,Correspondence: Amorn Leelarasamee, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Thanon Wang Lang, Siriraj, Bangkoknoi, Bangkok, 10700, Thailand, Tel/Fax +66 2 419 7783, Email
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McCann N, Castellino FJ. Cell Entry and Unusual Replication of SARS-CoV-2. Curr Drug Targets 2022; 23:1539-1554. [PMID: 36239725 DOI: 10.2174/1389450124666221014102927] [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: 06/17/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND SARS-CoV-2 is the causative virus for the CoVID-19 pandemic that has frequently mutated to continue to infect and resist available vaccines. Emerging new variants of the virus have complicated notions of immunity conferred by vaccines versus immunity that results from infection. While we continue to progress from epidemic to endemic as a result of this collective immunity, the pandemic remains a morbid and mortal problem. OBJECTIVE The SARS-CoV-2 virus has a very complex manner of replication. The spike protein, one of the four structural proteins of the encapsulated virus, is central to the ability of the virus to penetrate cells to replicate. The objective of this review is to summarize these complex features of viral replication. METHODS A review of the recent literature was performed on the biology of SARS-CoV-2 infection from published work from PubMed and works reported to preprint servers, e.g., bioRxiv and medRxiv. RESULTS AND CONCLUSION The complex molecular and cellular biology involved in SARS-CoV-2 replication and the origination of >30 proteins from a single open reading frame (ORF) have been summarized, as well as the structural biology of spike protein, a critical factor in the cellular entry of the virus, which is a necessary feature for it to replicate and cause disease.
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Affiliation(s)
- Nathan McCann
- Department of Chemistry and Biochemistry and W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46530, USA
| | - Francis J Castellino
- Department of Chemistry and Biochemistry and W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46530, USA
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41
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Li J, Xue Y, Wang X, Smith LS, He B, Liu S, Zhu H. Tissue- and cell-expression of druggable host proteins provide insights into repurposing drugs for COVID-19. Clin Transl Sci 2022; 15:2796-2811. [PMID: 36259251 PMCID: PMC9747131 DOI: 10.1111/cts.13400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 08/18/2022] [Accepted: 08/23/2022] [Indexed: 01/26/2023] Open
Abstract
Several human host proteins play important roles in the lifecycle of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Many drugs targeting these host proteins have been investigated as potential therapeutics for coronavirus disease 2019 (COVID-19). The tissue-specific expressions of selected host proteins were summarized using proteomics data retrieved from the Human Protein Atlas, ProteomicsDB, Human Proteome Map databases, and a clinical COVID-19 study. Protein expression features in different cell lines were summarized based on recent proteomics studies. The half-maximal effective concentration or half-maximal inhibitory concentration values were collected from in vitro studies. The pharmacokinetic data were mainly from studies in healthy subjects or non-COVID-19 patients. Considerable tissue-specific expression patterns were observed for several host proteins. ACE2 expression in the lungs was significantly lower than in many other tissues (e.g., the kidneys and intestines); TMPRSS2 expression in the lungs was significantly lower than in other tissues (e.g., the prostate and intestines). The expression levels of endocytosis-associated proteins CTSL, CLTC, NPC1, and PIKfyve in the lungs were comparable to or higher than most other tissues. TMPRSS2 expression was markedly different between cell lines, which could be associated with the cell-dependent antiviral activities of several drugs. Drug delivery receptor ICAM1 and CTSB were expressed at a higher level in the lungs than in other tissues. In conclusion, the cell- and tissue-specific proteomics data could help interpret the in vitro antiviral activities of host-directed drugs in various cells and aid the transition of the in vitro findings to clinical research to develop safe and effective therapeutics for COVID-19.
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Affiliation(s)
- Jiapeng Li
- Department of Clinical PharmacyUniversity of Michigan College of PharmacyAnn ArborMichiganUSA
| | - Yanling Xue
- Department of Clinical PharmacyUniversity of Michigan College of PharmacyAnn ArborMichiganUSA
| | - Xinwen Wang
- Department of Pharmaceutical SciencesNortheast Ohio Medical University College of PharmacyRootstownOhioUSA
| | - Logan S. Smith
- Department of Clinical PharmacyUniversity of Michigan College of PharmacyAnn ArborMichiganUSA
| | - Bing He
- Department of Computational Medicine and BioinformaticsUniversity of MichiganAnn ArborMichiganUSA
| | - Shuhan Liu
- Department of Clinical PharmacyUniversity of Michigan College of PharmacyAnn ArborMichiganUSA
| | - Hao‐Jie Zhu
- Department of Clinical PharmacyUniversity of Michigan College of PharmacyAnn ArborMichiganUSA
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Ruan D, Ye ZW, Yuan S, Li Z, Zhang W, Ong CP, Tang K, Ka Ki Tam TT, Guo J, Xuan Y, Huang Y, Zhang Q, Lee CL, Lu L, Chiu PCN, Yeung WSB, Liu F, Jin DY, Liu P. Human early syncytiotrophoblasts are highly susceptible to SARS-CoV-2 infection. Cell Rep Med 2022; 3:100849. [PMID: 36495872 PMCID: PMC9671691 DOI: 10.1016/j.xcrm.2022.100849] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 08/23/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
Direct in vivo investigation of human placenta trophoblast's susceptibility to SARS-CoV-2 is challenging. Here we report that human trophoblast stem cells (hTSCs) and their derivatives are susceptible to SARS-CoV-2 infection, which reveals heterogeneity in hTSC cultures. Early syncytiotrophoblasts (eSTBs) generated from hTSCs have enriched transcriptomic features of peri-implantation trophoblasts, express high levels of angiotensin-converting enzyme 2 (ACE2), and are productively infected by SARS-CoV-2 and its Delta and Omicron variants to produce virions. Antiviral drugs suppress SARS-CoV-2 replication in eSTBs and antagonize the virus-induced blockage of STB maturation. Although less susceptible to SARS-CoV-2 infection, trophoblast organoids originating from hTSCs show detectable viral replication reminiscent of the uncommon placental infection. These findings implicate possible risk of COVID-19 infection in peri-implantation embryos, which may go unnoticed. Stem cell-derived human trophoblasts such as eSTBs can potentially provide unlimited amounts of normal and genome-edited cells and facilitate coronavirus research and antiviral discovery.
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Affiliation(s)
- Degong Ruan
- Centre for Translational Stem Cell Biology, The University of Hong Kong, Hong Kong Special Administrative Region, China; Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Zi-Wei Ye
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Shuofeng Yuan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Zhuoxuan Li
- Stem Cell & Regenerative Medicine Consortium, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Weiyu Zhang
- Centre for Translational Stem Cell Biology, The University of Hong Kong, Hong Kong Special Administrative Region, China; Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Chon Phin Ong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kaiming Tang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Timothy Theodore Ka Ki Tam
- Stem Cell & Regenerative Medicine Consortium, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Jilong Guo
- Stem Cell & Regenerative Medicine Consortium, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yiyi Xuan
- Stem Cell & Regenerative Medicine Consortium, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yunying Huang
- Stem Cell & Regenerative Medicine Consortium, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Qingqing Zhang
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Cheuk-Lun Lee
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Liming Lu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Philip C N Chiu
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - William S B Yeung
- Centre for Translational Stem Cell Biology, The University of Hong Kong, Hong Kong Special Administrative Region, China; Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China; Department of Obstetrics and Gynaecology, School of Clinical Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Fang Liu
- Centre for Translational Stem Cell Biology, The University of Hong Kong, Hong Kong Special Administrative Region, China; Foshan Stomatology Hospital, School of Medicine, Foshan University, No. 5 Hebing Road, Foshan, Guangdong Province, China.
| | - Dong-Yan Jin
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.
| | - Pentao Liu
- Centre for Translational Stem Cell Biology, The University of Hong Kong, Hong Kong Special Administrative Region, China; Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China; Stem Cell & Regenerative Medicine Consortium, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.
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Pires De Souza GA, Le Bideau M, Boschi C, Wurtz N, Colson P, Aherfi S, Devaux C, La Scola B. Choosing a cellular model to study SARS-CoV-2. Front Cell Infect Microbiol 2022; 12:1003608. [PMID: 36339347 PMCID: PMC9634005 DOI: 10.3389/fcimb.2022.1003608] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/03/2022] [Indexed: 08/04/2023] Open
Abstract
As new pathogens emerge, new challenges must be faced. This is no different in infectious disease research, where identifying the best tools available in laboratories to conduct an investigation can, at least initially, be particularly complicated. However, in the context of an emerging virus, such as SARS-CoV-2, which was recently detected in China and has become a global threat to healthcare systems, developing models of infection and pathogenesis is urgently required. Cell-based approaches are crucial to understanding coronavirus infection biology, growth kinetics, and tropism. Usually, laboratory cell lines are the first line in experimental models to study viral pathogenicity and perform assays aimed at screening antiviral compounds which are efficient at blocking the replication of emerging viruses, saving time and resources, reducing the use of experimental animals. However, determining the ideal cell type can be challenging, especially when several researchers have to adapt their studies to specific requirements. This review strives to guide scientists who are venturing into studying SARS-CoV-2 and help them choose the right cellular models. It revisits basic concepts of virology and presents the currently available in vitro models, their advantages and disadvantages, and the known consequences of each choice.
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Affiliation(s)
- Gabriel Augusto Pires De Souza
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Marion Le Bideau
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Céline Boschi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Christian Devaux
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Department of Biological Sciences (INSB), Centre National de la Recherche Scientifique, Marseille, France
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
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44
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Hao Y, Wang Y, Wang M, Zhou L, Shi J, Cao J, Wang D. The origins of COVID-19 pandemic: A brief overview. Transbound Emerg Dis 2022; 69:3181-3197. [PMID: 36218169 PMCID: PMC9874793 DOI: 10.1111/tbed.14732] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 02/06/2023]
Abstract
The novel coronavirus disease (COVID-19) outbreak that emerged at the end of 2019 has now swept the world for more than 2 years, causing immeasurable damage to the lives and economies of the world. It has drawn so much attention to discovering how the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated and entered the human body. The current argument revolves around two contradictory theories: a scenario of laboratory spillover events and human contact with zoonotic diseases. Here, we reviewed the transmission, pathogenesis, possible hosts, as well as the genome and protein structure of SARS-CoV-2, which play key roles in the COVID-19 pandemic. We believe the coronavirus was originally transmitted to human by animals rather than by a laboratory leak. However, there still needs more investigations to determine the source of the pandemic. Understanding how COVID-19 emerged is vital to developing global strategies for mitigating future outbreaks.
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Affiliation(s)
- Ying‐Jian Hao
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Yu‐Lan Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Mei‐Yue Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Lan Zhou
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Jian‐Yun Shi
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Ji‐Min Cao
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - De‐Ping Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
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45
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Iwata-Yoshikawa N, Kakizaki M, Shiwa-Sudo N, Okura T, Tahara M, Fukushi S, Maeda K, Kawase M, Asanuma H, Tomita Y, Takayama I, Matsuyama S, Shirato K, Suzuki T, Nagata N, Takeda M. Essential role of TMPRSS2 in SARS-CoV-2 infection in murine airways. Nat Commun 2022; 13:6100. [PMID: 36243815 PMCID: PMC9568946 DOI: 10.1038/s41467-022-33911-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/07/2022] [Indexed: 12/24/2022] Open
Abstract
In cultured cells, SARS-CoV-2 infects cells via multiple pathways using different host proteases. Recent studies have shown that the furin and TMPRSS2 (furin/TMPRSS2)-dependent pathway plays a minor role in infection of the Omicron variant. Here, we confirm that Omicron uses the furin/TMPRSS2-dependent pathway inefficiently and enters cells mainly using the cathepsin-dependent endocytosis pathway in TMPRSS2-expressing VeroE6/TMPRSS2 and Calu-3 cells. This is the case despite efficient cleavage of the spike protein of Omicron. However, in the airways of TMPRSS2-knockout mice, Omicron infection is significantly reduced. We furthermore show that propagation of the mouse-adapted SARS-CoV-2 QHmusX strain and human clinical isolates of Beta and Gamma is reduced in TMPRSS2-knockout mice. Therefore, the Omicron variant isn't an exception in using TMPRSS2 in vivo, and analysis with TMPRSS2-knockout mice is important when evaluating SARS-CoV-2 variants. In conclusion, this study shows that TMPRSS2 is critically important for SARS-CoV-2 infection of murine airways, including the Omicron variant.
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Affiliation(s)
- Naoko Iwata-Yoshikawa
- grid.410795.e0000 0001 2220 1880Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masatoshi Kakizaki
- grid.410795.e0000 0001 2220 1880Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Nozomi Shiwa-Sudo
- grid.410795.e0000 0001 2220 1880Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takashi Okura
- grid.410795.e0000 0001 2220 1880Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Maino Tahara
- grid.410795.e0000 0001 2220 1880Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shuetsu Fukushi
- grid.410795.e0000 0001 2220 1880Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ken Maeda
- grid.410795.e0000 0001 2220 1880Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, Japan
| | - Miyuki Kawase
- grid.410795.e0000 0001 2220 1880Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideki Asanuma
- grid.410795.e0000 0001 2220 1880Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuriko Tomita
- grid.410795.e0000 0001 2220 1880Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ikuyo Takayama
- grid.410795.e0000 0001 2220 1880Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shutoku Matsuyama
- grid.410795.e0000 0001 2220 1880Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuya Shirato
- grid.410795.e0000 0001 2220 1880Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- grid.410795.e0000 0001 2220 1880Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Noriyo Nagata
- grid.410795.e0000 0001 2220 1880Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Takeda
- grid.410795.e0000 0001 2220 1880Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan ,grid.26999.3d0000 0001 2151 536XDepartment of Microbiology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
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46
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Hirose Y, Shindo N, Mori M, Onitsuka S, Isogai H, Hamada R, Hiramoto T, Ochi J, Takahashi D, Ueda T, Caaveiro JMM, Yoshida Y, Ohdo S, Matsunaga N, Toba S, Sasaki M, Orba Y, Sawa H, Sato A, Kawanishi E, Ojida A. Discovery of Chlorofluoroacetamide-Based Covalent Inhibitors for Severe Acute Respiratory Syndrome Coronavirus 2 3CL Protease. J Med Chem 2022; 65:13852-13865. [PMID: 36229406 DOI: 10.1021/acs.jmedchem.2c01081] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has necessitated the development of antiviral agents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 3C-like protease (3CLpro) is a promising target for COVID-19 treatment. Here, we report a new class of covalent inhibitors of 3CLpro that possess chlorofluoroacetamide (CFA) as a cysteine-reactive warhead. Based on an aza-peptide scaffold, we synthesized a series of CFA derivatives in enantiopure form and evaluated their biochemical efficiency. The data revealed that 8a (YH-6) with the R configuration at the CFA unit strongly blocks SARS-CoV-2 replication in infected cells, and its potency is comparable to that of nirmatrelvir. X-ray structural analysis showed that YH-6 formed a covalent bond with Cys145 at the catalytic center of 3CLpro. The strong antiviral activity and favorable pharmacokinetic properties of YH-6 suggest its potential as a lead compound for the treatment of COVID-19.
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Affiliation(s)
- Yuya Hirose
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka812-8582, Japan
| | - Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka812-8582, Japan
| | - Makiko Mori
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka812-8582, Japan
| | - Satsuki Onitsuka
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka812-8582, Japan
| | - Hikaru Isogai
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka812-8582, Japan
| | - Rui Hamada
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka812-8582, Japan
| | - Tadanari Hiramoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka812-8582, Japan
| | - Jinta Ochi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka812-8582, Japan
| | - Daisuke Takahashi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka812-8582, Japan
| | - Tadashi Ueda
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka812-8582, Japan
| | - Jose M M Caaveiro
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka812-8582, Japan
| | - Yuya Yoshida
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka812-8582, Japan
| | - Shigehiro Ohdo
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka812-8582, Japan
| | - Naoya Matsunaga
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka812-8582, Japan
| | - Shinsuke Toba
- International Institute for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo001-0020, Japan.,Drug Discovery and Disease Research Laboratory, Shionogi & Co. Ltd., 3-1-1 Futaba-cho, Toyonaka, Osaka561-0825, Japan
| | - Michihito Sasaki
- International Institute for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo001-0020, Japan
| | - Yasuko Orba
- International Institute for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo001-0020, Japan
| | - Hirofumi Sawa
- International Institute for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo001-0020, Japan.,One Health Research Center, Hokkaido University, North 18, West 9 Kita-ku, Sapporo060-0818, Japan.,Global Virus Network, 725 West Lombard St. Room S413, Baltimore, Maryland21201, United States
| | - Akihiko Sato
- International Institute for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo001-0020, Japan.,Drug Discovery and Disease Research Laboratory, Shionogi & Co. Ltd., 3-1-1 Futaba-cho, Toyonaka, Osaka561-0825, Japan
| | - Eiji Kawanishi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka812-8582, Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka812-8582, Japan
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Shimizu H, Kodama M, Matsumoto M, Orba Y, Sasaki M, Sato A, Sawa H, Nakayama KI. LIGHTHOUSE illuminates therapeutics for a variety of diseases including COVID-19. iScience 2022; 25:105314. [PMID: 36246574 PMCID: PMC9549714 DOI: 10.1016/j.isci.2022.105314] [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: 04/15/2022] [Revised: 08/08/2022] [Accepted: 10/05/2022] [Indexed: 11/26/2022] Open
Abstract
One of the bottlenecks in the application of basic research findings to patients is the enormous cost, time, and effort required for high-throughput screening of potential drugs for given therapeutic targets. Here we have developed LIGHTHOUSE, a graph-based deep learning approach for discovery of the hidden principles underlying the association of small-molecule compounds with target proteins. Without any 3D structural information for proteins or chemicals, LIGHTHOUSE estimates protein-compound scores that incorporate known evolutionary relations and available experimental data. It identified therapeutics for cancer, lifestyle related disease, and bacterial infection. Moreover, LIGHTHOUSE predicted ethoxzolamide as a therapeutic for coronavirus disease 2019 (COVID-19), and this agent was indeed effective against alpha, beta, gamma, and delta variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that are rampant worldwide. We envision that LIGHTHOUSE will help accelerate drug discovery and fill the gap between bench side and bedside. LIGHTHOUSE discovers therapeutics solely on the basis of the primary sequence The predictions of LIGHTHOUSE against multiple diseases were experimentally correct LIGHTHOUSE facilitates optimization of lead compounds as well
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Affiliation(s)
- Hideyuki Shimizu
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA,Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA 02115, USA,Department of AI Systems Medicine, M&D Data Science Center, Tokyo Medical and Dental University, Tokyo 113-8510, Japan,Corresponding author
| | - Manabu Kodama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Masaki Matsumoto
- Department of Omics and Systems Biology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 060-8638, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 060-8638, Japan
| | - Akihiko Sato
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 060-8638, Japan,Drug Discovery and Disease Research Laboratory, Shionogi & Co. Ltd., Osaka 561-0825, Japan
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 060-8638, Japan,International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo 060-8638, Japan,One Health Research Center, Hokkaido University, Sapporo 060-8638, Japan,Global Virus Network, Baltimore, MD 21201, USA,Hokkaido University, Institute for Vaccine Research and Development (HU-IVReD)
| | - Keiichi I. Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan,Corresponding author
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48
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Valleriani F, Jurisic L, Di Pancrazio C, Irelli R, Ciarrocchi E, Martino M, Cocco A, Di Felice E, Colaianni ML, Decaro N, Bonfini B, Lorusso A, Di Teodoro G. A Deletion Encompassing the Furin Cleavage Site in the Spike Encoding Gene Does Not Alter SARS-CoV-2 Replication in Lung Tissues of Mink and Neutralization by Convalescent Human Serum Samples. Pathogens 2022; 11:1152. [PMID: 36297209 PMCID: PMC9609486 DOI: 10.3390/pathogens11101152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/26/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023] Open
Abstract
SARS-CoV-2 has been shown to lose the furin polybasic cleavage site (FCS) following adaptation on cell culture. Deletion occurring in this region, which may include also the FCS flanking regions, seem not to affect virus replication in vitro; however, a chimeric SARS-CoV-2 virus without the sole FCS motif has been associated with lower virulence in mice and lower neutralization values. Moreover, SARS-CoV-2 virus lacking the FCS was shed to lower titers from experimentally infected ferrets and was not transmitted to cohoused sentinel animals, unlike wild-type virus. In this study, we investigated the replication kinetics and cellular tropism of a SARS-CoV-2 isolate carrying a 10-amino acid deletion in the spike protein spanning the FCS in lung ex vivo organ cultures of mink. Furthermore, we tested the neutralization capabilities of human convalescent SARS-CoV-2 positive serum samples against this virus. We showed that this deletion did not significantly hamper neither ex vivo replication nor neutralization activity by convalescent serum samples. This study highlights the importance of the preliminary phenotypic characterization of emerging viruses in ex vivo models and demonstrates that mink lung tissues are permissive to the replication of a mutant form of SARS-CoV-2 showing a deletion spanning the FCS. Notably, we also highlight the need for sequencing viral stocks before any infection study as large deletions may occur leading to the misinterpretation of results.
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Affiliation(s)
- Fabrizia Valleriani
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
| | - Lucija Jurisic
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
- Faculty of Veterinary Medicine, University of Teramo, 64100 Teramo, Italy
| | - Chiara Di Pancrazio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
| | - Roberta Irelli
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
| | - Eugenia Ciarrocchi
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
| | - Michele Martino
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
| | - Antonio Cocco
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
| | - Elisabetta Di Felice
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
| | | | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari, 70010 Bari, Italy
| | - Barbara Bonfini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
| | - Giovanni Di Teodoro
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
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49
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Asghar A, Imran HM, Bano N, Maalik S, Mushtaq S, Hussain A, Varjani S, Aleya L, Iqbal HMN, Bilal M. SARS-COV-2/COVID-19: scenario, epidemiology, adaptive mutations, and environmental factors. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:69117-69136. [PMID: 35947257 PMCID: PMC9363873 DOI: 10.1007/s11356-022-22333-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
The coronavirus pandemic of 2019 has already exerted an enormous impact. For over a year, the worldwide pandemic has ravaged the whole globe, with approximately 250 million verified human infection cases and a mortality rate surpassing 4 million. While the genetic makeup of the related pathogen (SARS-CoV-2) was identified, many unknown facets remain a mystery, comprising the virus's origin and evolutionary trend. There were many rumors that SARS-CoV-2 was human-borne and its evolution was predicted many years ago, but scientific investigation proved them wrong and concluded that bats might be the origin of SARS-CoV-2 and pangolins act as intermediary species to transmit the virus from bats to humans. Airborne droplets were found to be the leading cause of human-to-human transmission of this virus, but later studies showed that contaminated surfaces and other environmental factors are also involved in its transmission. The evolution of different SARS-CoV-2 variants worsens the condition and has become a challenge to overcome this pandemic. The emergence of COVID-19 is still a mystery, and scientists are unable to explain the exact origin of SARS-CoV-2. This review sheds light on the possible origin of SARS-CoV-2, its transmission, and the key factors that worsen the situation.
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Affiliation(s)
- Asma Asghar
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Hafiz Muhammad Imran
- Department of Biochemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Naheed Bano
- Department of Fisheries & Aquaculture, MNS-University of Agriculture, Multan, Pakistan
| | - Sadia Maalik
- Department of Zoology, Government College Women University, Sialkot, Pakistan
| | - Sajida Mushtaq
- Department of Zoology, Government College Women University, Sialkot, Pakistan
| | - Asim Hussain
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Sunita Varjani
- Gujarat Pollution Control Board, Gandhinagar, 382 010, Gujarat, India
| | - Lotfi Aleya
- Chrono-Environment Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, Besançon, France
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, 64849, Monterrey, Mexico
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China.
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Feng XL, Yu D, Zhang M, Li X, Zou QC, Ma W, Han JB, Xu L, Yang C, Qu W, Deng ZH, Long J, Long Y, Li M, Yao YG, Dong XQ, Zeng J, Li MH. Characteristics of replication and pathogenicity of SARS-CoV-2 Alpha and Delta isolates. Virol Sin 2022; 37:804-812. [PMID: 36167254 PMCID: PMC9507998 DOI: 10.1016/j.virs.2022.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/20/2022] [Indexed: 01/19/2023] Open
Abstract
The continuously arising of SARS-CoV-2 variants has been posting a great threat to public health safety globally, from B.1.17 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta) to B.1.1.529 (Omicron). The emerging or re-emerging of the SARS-CoV-2 variants of concern is calling for the constant monitoring of their epidemics, pathogenicity and immune escape. In this study, we aimed to characterize replication and pathogenicity of the Alpha and Delta variant strains isolated from patients infected in Laos. The amino acid mutations within the spike fragment of the isolates were determined via sequencing. The more efficient replication of the Alpha and Delta isolates was documented than the prototyped SARS-CoV-2 in Calu-3 and Caco-2 cells, while such features were not observed in Huh-7, Vero E6 and HPA-3 cells. We utilized both animal models of human ACE2 (hACE2) transgenic mice and hamsters to evaluate the pathogenesis of the isolates. The Alpha and Delta can replicate well in multiple organs and cause moderate to severe lung pathology in these animals. In conclusion, the spike protein of the isolated Alpha and Delta variant strains was characterized, and the replication and pathogenicity of the strains in the cells and animal models were also evaluated.
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Affiliation(s)
- Xiao-Li Feng
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Dandan Yu
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China,National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Mi Zhang
- Department of Infectious Diseases, Yunnan Provincial Infectious Diseases Hospital, Kunming, 650301, China
| | - Xiaohong Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Qing-Cui Zou
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Wentai Ma
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101, China,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian-Bao Han
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Ling Xu
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China,National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Cuixian Yang
- Department of Infectious Diseases, Yunnan Provincial Infectious Diseases Hospital, Kunming, 650301, China
| | - Wang Qu
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Zhong-Hua Deng
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Junyi Long
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Yanghaopeng Long
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Mingkun Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101, China,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yong-Gang Yao
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China,National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Xing-Qi Dong
- Department of Infectious Diseases, Yunnan Provincial Infectious Diseases Hospital, Kunming, 650301, China,Corresponding authors.
| | - Jianxiong Zeng
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China,National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China,Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China,Corresponding authors.
| | - Ming-Hua Li
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Corresponding authors.
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