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Al-Jamal H, Idriss S, Roufayel R, Abi Khattar Z, Fajloun Z, Sabatier JM. Treating COVID-19 with Medicinal Plants: Is It Even Conceivable? A Comprehensive Review. Viruses 2024; 16:320. [PMID: 38543686 PMCID: PMC10974729 DOI: 10.3390/v16030320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/15/2024] [Accepted: 02/18/2024] [Indexed: 05/23/2024] Open
Abstract
In 2020, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) challenged the world with a global outbreak that led to millions of deaths worldwide. Coronavirus disease 2019 (COVID-19) is the symptomatic manifestation of this virus, which can range from flu-like symptoms to utter clinical complications and even death. Since there was no clear medicine that could tackle this infection or lower its complications with minimal adverse effects on the patients' health, the world health organization (WHO) developed awareness programs to lower the infection rate and limit the fast spread of this virus. Although vaccines have been developed as preventative tools, people still prefer going back to traditional herbal medicine, which provides remarkable health benefits that can either prevent the viral infection or limit the progression of severe symptoms through different mechanistic pathways with relatively insignificant side effects. This comprehensive review provides scientific evidence elucidating the effect of 10 different plants against SARS-CoV-2, paving the way for further studies to reconsider plant-based extracts, rich in bioactive compounds, into more advanced clinical assessments in order to identify their impact on patients suffering from COVID-19.
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Affiliation(s)
- Hadi Al-Jamal
- Faculty of Public Health 3, Lebanese University, Tripoli 1100, Lebanon;
| | - Sara Idriss
- Laboratory of Applied Biotechnology (LBA3B), Azm Center for Research in Biotechnology and Its Applications, EDST, Lebanese University, Tripoli 1300, Lebanon;
| | - Rabih Roufayel
- College of Engineering and Technology, American University of the Middle East, Egaila 54200, Kuwait;
| | - Ziad Abi Khattar
- Faculty of Medicine and Medical Sciences, University of Balamand, Kalhat, Tripoli P.O. Box 100, Lebanon;
| | - Ziad Fajloun
- Laboratory of Applied Biotechnology (LBA3B), Azm Center for Research in Biotechnology and Its Applications, EDST, Lebanese University, Tripoli 1300, Lebanon;
- Department of Biology, Faculty of Sciences 3, Campus Michel Slayman Ras Maska, Lebanese University, Tripoli 1352, Lebanon
| | - Jean-Marc Sabatier
- INP, Inst Neurophysiopathol, Aix-Marseille Université, CNRS, 13385 Marseille, France
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2
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Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait BT, Darst SA, Campbell EA. Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain. Mol Cell 2023; 83:3921-3930.e7. [PMID: 37890482 PMCID: PMC10843261 DOI: 10.1016/j.molcel.2023.10.001] [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: 06/07/2023] [Revised: 08/28/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023]
Abstract
The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5' cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here, we determine high-resolution cryoelectron microscopy (cryo-EM) structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development.
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Affiliation(s)
- Gabriel I Small
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Olga Fedorova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Joshua Chandanani
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Anoosha Banerjee
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Tri-Institutional Program in Chemical Biology, The Rockefeller University, New York, New York, USA
| | - Young Joo Choi
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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3
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Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait B, Darst SA, Campbell EA. Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN Domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.558837. [PMID: 37808858 PMCID: PMC10557602 DOI: 10.1101/2023.09.25.558837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N-terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5'-cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here we determine high-resolution cryo-electron microscopy structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development.
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Affiliation(s)
- Gabriel I Small
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Olga Fedorova
- Department of Chemistry and Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Joshua Chandanani
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Anoosha Banerjee
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Young Joo Choi
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
- Present address: University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Brian Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
- Lead contact:
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4
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Mihalič F, Benz C, Kassa E, Lindqvist R, Simonetti L, Inturi R, Aronsson H, Andersson E, Chi CN, Davey NE, Överby AK, Jemth P, Ivarsson Y. Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets. Nat Commun 2023; 14:5636. [PMID: 37704626 PMCID: PMC10499821 DOI: 10.1038/s41467-023-41312-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
The virus life cycle depends on host-virus protein-protein interactions, which often involve a disordered protein region binding to a folded protein domain. Here, we used proteomic peptide phage display (ProP-PD) to identify peptides from the intrinsically disordered regions of the human proteome that bind to folded protein domains encoded by the SARS-CoV-2 genome. Eleven folded domains of SARS-CoV-2 proteins were found to bind 281 peptides from human proteins, and affinities of 31 interactions involving eight SARS-CoV-2 protein domains were determined (KD ∼ 7-300 μM). Key specificity residues of the peptides were established for six of the interactions. Two of the peptides, binding Nsp9 and Nsp16, respectively, inhibited viral replication. Our findings demonstrate how high-throughput peptide binding screens simultaneously identify potential host-virus interactions and peptides with antiviral properties. Furthermore, the high number of low-affinity interactions suggest that overexpression of viral proteins during infection may perturb multiple cellular pathways.
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Affiliation(s)
- Filip Mihalič
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Caroline Benz
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eszter Kassa
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Richard Lindqvist
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187, Umeå, Sweden
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Raviteja Inturi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Hanna Aronsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Anna K Överby
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187, Umeå, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden.
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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Zhou P, Song G, Liu H, Yuan M, He WT, Beutler N, Zhu X, Tse LV, Martinez DR, Schäfer A, Anzanello F, Yong P, Peng L, Dueker K, Musharrafieh R, Callaghan S, Capozzola T, Limbo O, Parren M, Garcia E, Rawlings SA, Smith DM, Nemazee D, Jardine JG, Safonova Y, Briney B, Rogers TF, Wilson IA, Baric RS, Gralinski LE, Burton DR, Andrabi R. Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause deadly disease. Immunity 2023; 56:669-686.e7. [PMID: 36889306 PMCID: PMC9933850 DOI: 10.1016/j.immuni.2023.02.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/10/2022] [Accepted: 02/10/2023] [Indexed: 02/18/2023]
Abstract
Pan-betacoronavirus neutralizing antibodies may hold the key to developing broadly protective vaccines against novel pandemic coronaviruses and to more effectively respond to SARS-CoV-2 variants. The emergence of Omicron and subvariants of SARS-CoV-2 illustrates the limitations of solely targeting the receptor-binding domain (RBD) of the spike (S) protein. Here, we isolated a large panel of broadly neutralizing antibodies (bnAbs) from SARS-CoV-2 recovered-vaccinated donors, which targets a conserved S2 region in the betacoronavirus spike fusion machinery. Select bnAbs showed broad in vivo protection against all three deadly betacoronaviruses, SARS-CoV-1, SARS-CoV-2, and MERS-CoV, which have spilled over into humans in the past two decades. Structural studies of these bnAbs delineated the molecular basis for their broad reactivity and revealed common antibody features targetable by broad vaccination strategies. These bnAbs provide new insights and opportunities for antibody-based interventions and for developing pan-betacoronavirus vaccines.
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Affiliation(s)
- Panpan Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wan-Ting He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Longping V Tse
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David R Martinez
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexandra Schäfer
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Fabio Anzanello
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter Yong
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Katharina Dueker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rami Musharrafieh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sean Callaghan
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tazio Capozzola
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oliver Limbo
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mara Parren
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Elijah Garcia
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Stephen A Rawlings
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Davey M Smith
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joseph G Jardine
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yana Safonova
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Thomas F Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Ian A Wilson
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Ralph S Baric
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Departments of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Lisa E Gralinski
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA.
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.
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A SARS-CoV-2-Related Virus from Malayan Pangolin Causes Lung Infection without Severe Disease in Human ACE2-Transgenic Mice. J Virol 2023; 97:e0171922. [PMID: 36688655 PMCID: PMC9972989 DOI: 10.1128/jvi.01719-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), which is caused by the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the most severe emerging infectious disease in the current century. The discovery of SARS-CoV-2-related coronaviruses (SARSr-CoV-2) in bats and pangolins in South Asian countries indicates that SARS-CoV-2 likely originated from wildlife. To date, two SARSr-CoV-2 strains have been isolated from pangolins seized in Guangxi and Guangdong by the customs agency of China, respectively. However, it remains unclear whether these viruses cause disease in animal models and whether they pose a transmission risk to humans. In this study, we investigated the biological features of a SARSr-CoV-2 strain isolated from a smuggled Malayan pangolin (Manis javanica) captured by the Guangxi customs agency, termed MpCoV-GX, in terms of receptor usage, cell tropism, and pathogenicity in wild-type BALB/c mice, human angiotensin-converting enzyme 2 (ACE2)-transgenic mice, and human ACE2 knock-in mice. We found that MpCoV-GX can utilize ACE2 from humans, pangolins, civets, bats, pigs, and mice for cell entry and infect cell lines derived from humans, monkeys, bats, minks, and pigs. The virus could infect three mouse models but showed limited pathogenicity, with mild peribronchial and perivascular inflammatory cell infiltration observed in lungs. Our results suggest that this SARSr-CoV-2 virus from pangolins has the potential for interspecies infection, but its pathogenicity is mild in mice. Future surveillance among these wildlife hosts of SARSr-CoV-2 is needed to monitor variants that may have higher pathogenicity and higher spillover risk. IMPORTANCE SARS-CoV-2, which likely spilled over from wildlife, is the third highly pathogenic human coronavirus. Being highly transmissible, it is perpetuating a pandemic and continuously posing a severe threat to global public health. Several SARS-CoV-2-related coronaviruses (SARSr-CoV-2) in bats and pangolins have been identified since the SARS-CoV-2 outbreak. It is therefore important to assess their potential of crossing species barriers for better understanding of their risk of future emergence. In this work, we investigated the biological features and pathogenicity of a SARSr-CoV-2 strain isolated from a smuggled Malayan pangolin, named MpCoV-GX. We found that MpCoV-GX can utilize ACE2 from 7 species for cell entry and infect cell lines derived from a variety of mammalian species. MpCoV-GX can infect mice expressing human ACE2 without causing severe disease. These findings suggest the potential of cross-species transmission of MpCoV-GX, and highlight the need of further surveillance of SARSr-CoV-2 in pangolins and other potential animal hosts.
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Hirunpattarasilp C, James G, Kwanthongdee J, Freitas F, Huo J, Sethi H, Kittler JT, Owens RJ, McCoy LE, Attwell D. SARS-CoV-2 triggers pericyte-mediated cerebral capillary constriction. Brain 2023; 146:727-738. [PMID: 35867861 PMCID: PMC9384509 DOI: 10.1093/brain/awac272] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/04/2022] [Accepted: 07/11/2022] [Indexed: 11/21/2022] Open
Abstract
The SARS-CoV-2 receptor, ACE2, is found on pericytes, contractile cells enwrapping capillaries that regulate brain, heart and kidney blood flow. ACE2 converts vasoconstricting angiotensin II into vasodilating angiotensin-(1-7). In brain slices from hamster, which has an ACE2 sequence similar to human ACE2, angiotensin II evoked a small pericyte-mediated capillary constriction via AT1 receptors, but evoked a large constriction when the SARS-CoV-2 receptor binding domain (RBD, original Wuhan variant) was present. A mutated non-binding RBD did not potentiate constriction. A similar RBD-potentiated capillary constriction occurred in human cortical slices, and was evoked in hamster brain slices by pseudotyped virions expressing SARS-CoV-2 spike protein. This constriction reflects an RBD-induced decrease in the conversion of angiotensin II to angiotensin-(1-7) mediated by removal of ACE2 from the cell surface membrane and was mimicked by blocking ACE2. The clinically used drug losartan inhibited the RBD-potentiated constriction. Thus, AT1 receptor blockers could be protective in COVID-19 by preventing pericyte-mediated blood flow reductions in the brain, and perhaps the heart and kidney.
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Affiliation(s)
- Chanawee Hirunpattarasilp
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, UK
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Talat Bang Khen, Lak Si, Bangkok, 10210, Thailand
| | - Greg James
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, UK
- Department of Neurosurgery, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Jaturon Kwanthongdee
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, UK
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Talat Bang Khen, Lak Si, Bangkok, 10210, Thailand
| | - Felipe Freitas
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, UK
| | - Jiandong Huo
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Protein Production UK, The Research Complex at Harwell, and Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0GD, UK
| | - Huma Sethi
- Division of Neurosurgery, National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| | - Josef T Kittler
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, UK
| | - Raymond J Owens
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Protein Production UK, The Research Complex at Harwell, and Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0GD, UK
| | - Laura E McCoy
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - David Attwell
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, UK
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8
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A C57BL/6 Mouse Model of SARS-CoV-2 Infection Recapitulates Age- and Sex-Based Differences in Human COVID-19 Disease and Recovery. Vaccines (Basel) 2022; 11:vaccines11010047. [PMID: 36679892 PMCID: PMC9860616 DOI: 10.3390/vaccines11010047] [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: 12/01/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
We present a comprehensive analysis of SARS-CoV-2 infection and recovery using wild type C57BL/6 mice and a mouse-adapted virus, and we demonstrate that this is an ideal model of infection and recovery that phenocopies acute human disease arising from the ancestral SARS-CoV-2. Disease severity and infection kinetics are age- and sex-dependent, as has been reported for humans, with older mice and males in particular exhibiting decreased viral clearance and increased mortality. We identified key parallels with human pathology, including intense virus positivity in bronchial epithelial cells, wide-spread alveolar involvement, recruitment of immune cells to the infected lungs, and acute bronchial epithelial cell death. Moreover, older animals experienced increased virus persistence, delayed dispersal of immune cells into lung parenchyma, and morphologic evidence of tissue damage and inflammation. Parallel analysis of SCID mice revealed that the adaptive immune response was not required for recovery from COVID disease symptoms nor early phase clearance of virus but was required for efficient clearance of virus at later stages of infection. Finally, transcriptional analyses indicated that induction and duration of key innate immune gene programs may explain differences in age-dependent disease severity. Importantly, these data demonstrate that SARS-CoV-2-mediated disease in C57BL/6 mice phenocopies human disease across ages and establishes a platform for future therapeutic and genetic screens for not just SARS-CoV-2 but also novel coronaviruses that have yet to emerge.
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9
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Davis M, Voss K, Turnbull JB, Gustin AT, Knoll M, Muruato A, Hsiang TY, Dinnon KH, Leist SR, Nickel K, Baric RS, Ladiges W, Akilesh S, Smith KD, Gale M. A C57BL/6 Mouse model of SARS-CoV-2 infection recapitulates age- and sex-based differences in human COVID-19 disease and recovery. RESEARCH SQUARE 2022:rs.3.rs-2194450. [PMID: 36415465 PMCID: PMC9681052 DOI: 10.21203/rs.3.rs-2194450/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We present a comprehensive analysis of SARS-CoV-2 infection and recovery in wild type C57BL/6 mice, demonstrating that this is an ideal model of infection and recovery that accurately phenocopies acute human disease arising from the ancestral SARS-CoV-2. Disease severity and infection kinetics are age- and sex-dependent, as has been reported for humans, with older mice and males in particular exhibiting decreased viral clearance and increased mortality. We identified key parallels with human pathology, including intense virus positivity in bronchial epithelial cells, wide-spread alveolar involvement, recruitment of immune cells to the infected lungs, and acute bronchial epithelial cell death. Moreover, older animals experienced increased virus persistence, delayed dispersal of immune cells into lung parenchyma, and morphologic evidence of tissue damage and inflammation. Parallel analysis of SCID mice revealed that the adaptive immune response was not required for recovery from COVID disease symptoms nor early phase clearance of virus but was required for efficient clearance of virus at later stages of infection. Finally, transcriptional analyses indicated that induction and duration of key innate immune gene programs may explain differences in age-dependent disease severity. Importantly, these data demonstrate that SARS-CoV-2-mediated disease in C57BL/6 mice accurately phenocopies human disease across ages and establishes a platform for future therapeutic and genetic screens for not just SARS-CoV-2 but also novel coronaviruses that have yet to emerge.
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10
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Dey R, Samadder A, Nandi S. Exploring the Targets of Novel Corona Virus and Docking-based Screening of Potential Natural Inhibitors to Combat COVID-19. Curr Top Med Chem 2022; 22:2410-2434. [PMID: 36281864 DOI: 10.2174/1568026623666221020163831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 09/07/2022] [Accepted: 09/21/2022] [Indexed: 01/20/2023]
Abstract
There is a need to explore natural compounds against COVID-19 due to their multitargeted actions against various targets of nCoV. They act on multiple sites rather than single targets against several diseases. Thus, there is a possibility that natural resources can be repurposed to combat COVID-19. However, the biochemical mechanisms of these inhibitors were not known. To reveal the mode of anti-nCoV action, structure-based docking plays a major role. The present study is an attempt to explore various potential targets of SARS-CoV-2 and the structure-based screening of various potential natural inhibitors to combat the novel coronavirus.
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Affiliation(s)
- Rishita Dey
- Department of Zoology, Cytogenetics and Molecular Biology Lab., University of Kalyani, Kalyani, Nadia, 741235, India.,Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur, 244713, India
| | - Asmita Samadder
- Department of Zoology, Cytogenetics and Molecular Biology Lab., University of Kalyani, Kalyani, Nadia, 741235, India
| | - Sisir Nandi
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur, 244713, India
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11
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Zhang Y, Wang S, Xia H, Guo J, He K, Huang C, Luo R, Chen Y, Xu K, Gao H, Sheng J, Li L. Identification of Monocytes Associated with Severe COVID-19 in the PBMCs of Severely Infected Patients Through Single-Cell Transcriptome Sequencing. ENGINEERING (BEIJING, CHINA) 2022; 17:161-169. [PMID: 34150352 PMCID: PMC8196473 DOI: 10.1016/j.eng.2021.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/07/2021] [Accepted: 05/17/2021] [Indexed: 05/15/2023]
Abstract
Understanding the immunological characteristics of monocytes-including the characteristics associated with fibrosis-in severe coronavirus disease 2019 (COVID-19) is crucial for understanding the pathogenic mechanism of the disease and preventing disease severity. In this study, we performed single-cell transcriptomic sequencing of peripheral blood samples collected from six healthy controls and 14 COVID-19 samples including severe, moderate, and convalescent samples from three severely/critically ill and four moderately ill patients. We found that the monocytes were strongly remodeled in the severely/critically ill patients with COVID-19, with an increased proportion of monocytes and seriously reduced diversity. In addition, we discovered two novel severe-disease-specific monocyte subsets: Mono 0 and Mono 5. These subsets expressed amphiregulin (AREG), epiregulin (EREG), and cytokine interleukin-18 (IL-18) gene, exhibited an enriched erythroblastic leukemia viral oncogene homolog (ErbB) signaling pathway, and appeared to exhibit pro-fibrogenic and pro-inflammation characteristics. We also found metabolic changes in Mono 0 and Mono 5, including increased glycolysis/gluconeogenesis and an increased hypoxia inducible factor-1 (HIF-1) signaling pathway. Notably, one pre-severe sample displayed a monocyte atlas similar to that of the severe/critical samples. In conclusion, our study discovered two novel severe-disease-specific monocyte subsets as potential predictors and therapeutic targets for severe COVID-19. Overall, this study provides potential predictors for severe disease and therapeutic targets for COVID-19 and thus provides a resource for further studies on COVID-19.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Shuting Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - He Xia
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Jing Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Kangxin He
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Chenjie Huang
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Rui Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Yanfei Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Kaijin Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Hainv Gao
- Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou 310022, China
| | - Jifang Sheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
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12
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Manangeeswaran M, Ireland DDC, Thacker SG, Lee HN, Kelley-Baker L, Lewkowicz AP, Rothlauf PW, Cornejo Pontelli M, Bloyet LM, Eckhaus MA, Mendoza MI, Whelan S, Verthelyi D. BSL2-compliant lethal mouse model of SARS-CoV-2 and variants of concern to evaluate therapeutics targeting the Spike protein. Front Immunol 2022; 13:919815. [PMID: 35967447 PMCID: PMC9367692 DOI: 10.3389/fimmu.2022.919815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/04/2022] [Indexed: 12/02/2022] Open
Abstract
Since first reported in 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is rapidly acquiring mutations, particularly in the spike protein, that can modulate pathogenicity, transmission and antibody evasion leading to successive waves of COVID19 infections despite an unprecedented mass vaccination necessitating continuous adaptation of therapeutics. Small animal models can facilitate understanding host-pathogen interactions, target selection for therapeutic drugs, and vaccine development, but availability and cost of studies in BSL3 facilities hinder progress. To generate a BSL2-compatible in vivo system that specifically recapitulates spike protein mediated disease we used replication competent, GFP tagged, recombinant Vesicular Stomatitis Virus where the VSV glycoprotein was replaced by the SARS-CoV-2 spike protein (rVSV-SARS2-S). We show that infection requires hACE2 and challenge of neonatal but not adult, K18-hACE2 transgenic mice (hACE2tg) leads to productive infection of the lungs and brains. Although disease progression was faster in SARS-CoV-2 infected mice, infection with both viruses resulted in neuronal infection and encephalitis with increased expression of Interferon-stimulated Irf7, Bst2, Ifi294, as well as CxCL10, CCL5, CLC2, and LILRB4, and both models were uniformly lethal. Further, prophylactic treatment targeting the Spike protein (Receptor Binding Domain) with antibodies resulted in similar levels of protection from lethal infection against rVSV-SARS2-S and SARS-CoV-2 viruses. Strikingly, challenge of neonatal hACE2tg mice with SARS-CoV-2 Variants of Concern (SARS-CoV-2-α, -β, ϒ, or Δ) or the corresponding rVSV-SARS2-S viruses (rVSV-SARS2-Spike-α, rVSV-SARS2-Spike-β, rVSV-SARS2-Spike-ϒ or rVSV-SARS2-Spike-Δ) resulted in increased lethality, suggesting that the Spike protein plays a key role in determining the virulence of each variant. Thus, we propose that rVSV-SARS2-S virus can be used to understand the effect of changes to SARS-CoV-2 spike protein on infection and to evaluate existing or experimental therapeutics targeting spike protein of current or future VOC of SARS-CoV-2 under BSL-2 conditions.
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Affiliation(s)
- Mohanraj Manangeeswaran
- Laboratory of Immunology, Center of Excellence in Infectious Disease and Inflammation, Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
- *Correspondence: Daniela Verthelyi, ; Mohanraj Manangeeswaran,
| | - Derek D. C. Ireland
- Laboratory of Immunology, Center of Excellence in Infectious Disease and Inflammation, Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Seth G. Thacker
- Laboratory of Immunology, Center of Excellence in Infectious Disease and Inflammation, Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Ha-Na Lee
- Laboratory of Immunology, Center of Excellence in Infectious Disease and Inflammation, Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Logan Kelley-Baker
- Laboratory of Immunology, Center of Excellence in Infectious Disease and Inflammation, Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Aaron P. Lewkowicz
- Laboratory of Immunology, Center of Excellence in Infectious Disease and Inflammation, Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Paul W. Rothlauf
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States
- Program in Virology, Harvard Medical School, Boston, MA, United States
| | - Marjorie Cornejo Pontelli
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Louis-Marie Bloyet
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Michael A. Eckhaus
- Division of Veterinary Resources, Office of Research Services, National Institutes of Health, Bethesda, MD, United States
| | - Mirian I. Mendoza
- Laboratory of Immunology, Center of Excellence in Infectious Disease and Inflammation, Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Sean Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Daniela Verthelyi
- Laboratory of Immunology, Center of Excellence in Infectious Disease and Inflammation, Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
- *Correspondence: Daniela Verthelyi, ; Mohanraj Manangeeswaran,
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13
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Bestion E, Halfon P, Mezouar S, Mège JL. Cell and Animal Models for SARS-CoV-2 Research. Viruses 2022; 14:1507. [PMID: 35891487 PMCID: PMC9319816 DOI: 10.3390/v14071507] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/29/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
During the last two years following the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, development of potent antiviral drugs and vaccines has been a global health priority. In this context, the understanding of virus pathophysiology, the identification of associated therapeutic targets, and the screening of potential effective compounds have been indispensable advancements. It was therefore of primary importance to develop experimental models that recapitulate the aspects of the human disease in the best way possible. This article reviews the information concerning available SARS-CoV-2 preclinical models during that time, including cell-based approaches and animal models. We discuss their evolution, their advantages, and drawbacks, as well as their relevance to drug effectiveness evaluation.
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Affiliation(s)
- Eloïne Bestion
- Microbe Evolution Phylogeny Infection, Institut pour la Recherche et le Developpement, Assistance Publique Hopitaux de Marseille, Aix-Marseille University, 13005 Marseille, France; (E.B.); (P.H.)
- Institue Hospitalo, Universitaire Mediterranée Infection, 13005 Marseille, France
- Genoscience Pharma, 13005 Marseille, France
| | - Philippe Halfon
- Microbe Evolution Phylogeny Infection, Institut pour la Recherche et le Developpement, Assistance Publique Hopitaux de Marseille, Aix-Marseille University, 13005 Marseille, France; (E.B.); (P.H.)
- Institue Hospitalo, Universitaire Mediterranée Infection, 13005 Marseille, France
- Genoscience Pharma, 13005 Marseille, France
| | - Soraya Mezouar
- Microbe Evolution Phylogeny Infection, Institut pour la Recherche et le Developpement, Assistance Publique Hopitaux de Marseille, Aix-Marseille University, 13005 Marseille, France; (E.B.); (P.H.)
- Institue Hospitalo, Universitaire Mediterranée Infection, 13005 Marseille, France
- Genoscience Pharma, 13005 Marseille, France
| | - Jean-Louis Mège
- Microbe Evolution Phylogeny Infection, Institut pour la Recherche et le Developpement, Assistance Publique Hopitaux de Marseille, Aix-Marseille University, 13005 Marseille, France; (E.B.); (P.H.)
- Institue Hospitalo, Universitaire Mediterranée Infection, 13005 Marseille, France
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14
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Lou Z, Rao Z. The Life of SARS-CoV-2 Inside Cells: Replication-Transcription Complex Assembly and Function. Annu Rev Biochem 2022; 91:381-401. [PMID: 35729072 DOI: 10.1146/annurev-biochem-052521-115653] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The persistence of the coronavirus disease 2019 (COVID-19) pandemic has resulted in increasingly disruptive impacts, and it has become the most devastating challenge to global health in a century. The rapid emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants challenges the currently available therapeutics for clinical application. Nonstructural proteins (also known as replicase proteins) with versatile biological functions play central roles in viral replication and transcription inside the host cells, and they are the most conserved target proteins among the SARS-CoV-2 variants. Specifically, they constitute the replication-transcription complexes (RTCs) dominating the synthesis of viral RNA. Knowledge of themolecular mechanisms of nonstructural proteins and their assembly into RTCs will benefit the development of antivirals targeting them against existing or potentially emerging variants. In this review, we summarize current knowledge of the structures and functions of coronavirus nonstructural proteins as well as the assembly and functions of RTCs in the life cycle of the virus.
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Affiliation(s)
- Zhiyong Lou
- Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; ,
| | - Zihe Rao
- Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; , .,Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,School of Life Sciences, Tsinghua University, Beijing, China.,State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Guangzhou Laboratory, Guangzhou, China
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15
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Wu L, Wu H, Ou T, Huang H, Duan L, Li W, Jiang W. Mapping theme trends and recognizing hot spots in viral pneumonia: a bibliometric analysis of global research. Am J Transl Res 2022; 14:2972-2987. [PMID: 35702075 PMCID: PMC9185022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/30/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The challenges that viral pneumonia poses to the global public health system remain daunting. In this study, an analysis of publications on viral pneumonia over the past two decades was conducted. Through this work, we hope to provide inspiration for future research on viral pneumonia. METHODS We extracted all of the English publications relevant to viral pneumonia published during 1999-2019 from Web of Science. GraphPad Prism, CiteSpace, and VOSviewer were used to collect and analyze the publication trends in related fields. RESULTS We identified 2,006 publications with 62,155 citations as of February 16, 2021. The United States accounted for the largest number of publications (34.2%), with the highest number of citations (27,616) and the highest h-index (78). China ranked second in the number of publications. Ctr Dis Control & Prevent proved to be the center of research cooperation. Clinical Infectious Diseases included the most papers published relating to the topic of viral pneumonia. Chan KH published the most papers in this field (25), while an article from Fouchier RAM presented the highest citation frequency (1,275). CONCLUSIONS According to the bibliometric analysis database and related software results, the United States dominates the field of viral pneumonia research. The key term extracted by VOSviewer has shifted to "Diagnosis and management", indicating a new trend for viral pneumonia research.
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Affiliation(s)
- Lixue Wu
- Department of Emergency and Critical Care Medicine, Changzheng Hospital, Naval Medical UniversityShanghai, 200003, China
| | - Hao Wu
- Department of Emergency and Critical Care Medicine, Changzheng Hospital, Naval Medical UniversityShanghai, 200003, China
| | - Tianle Ou
- College of Basic Medicine, Naval Medical UniversityShanghai, 200433, China
| | - Hao Huang
- Department of Emergency and Critical Care Medicine, Changzheng Hospital, Naval Medical UniversityShanghai, 200003, China
| | - Liwei Duan
- Department of Emergency and Critical Care Medicine, Changzheng Hospital, Naval Medical UniversityShanghai, 200003, China
| | - Wenfang Li
- Department of Emergency and Critical Care Medicine, Changzheng Hospital, Naval Medical UniversityShanghai, 200003, China
| | - Weiwei Jiang
- Department of Emergency and Critical Care Medicine, Changzheng Hospital, Naval Medical UniversityShanghai, 200003, China
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16
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Fu YS, Ho WY, Kang N, Tsai MJ, Wu J, Huang L, Weng CF. Pharmaceutical Prospects of Curcuminoids for the Remedy of COVID-19: Truth or Myth. Front Pharmacol 2022; 13:863082. [PMID: 35496320 PMCID: PMC9047796 DOI: 10.3389/fphar.2022.863082] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/01/2022] [Indexed: 01/09/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is a positive-strand RNA virus, and has rapidly spread worldwide as a pandemic. The vaccines, repurposed drugs, and specific treatments have led to a surge of novel therapies and guidelines nowadays; however, the epidemic of COVID-19 is not yet fully combated and is still in a vital crisis. In repositioning drugs, natural products are gaining attention because of the large therapeutic window and potent antiviral, immunomodulatory, anti-inflammatory, and antioxidant properties. Of note, the predominant curcumoid extracted from turmeric (Curcuma longa L.) including phenolic curcumin influences multiple signaling pathways and has demonstrated to possess anti-inflammatory, antioxidant, antimicrobial, hypoglycemic, wound healing, chemopreventive, chemosensitizing, and radiosensitizing spectrums. In this review, all pieces of current information related to curcumin-used for the treatment and prevention of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection through in vitro, in vivo, and in silico studies, clinical trials, and new formulation designs are retrieved to re-evaluate the applications based on the pharmaceutical efficacy of clinical therapy and to provide deep insights into knowledge and strategy about the curcumin's role as an immune booster, inflammatory modulator, and therapeutic agent against COVID-19. Moreover, this study will also afford a favorable application or approach with evidence based on the drug discovery and development, pharmacology, functional foods, and nutraceuticals for effectively fighting the COVID-19 pandemic.
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Affiliation(s)
- Yaw-Syan Fu
- Department of Basic Medical Science, Anatomy and Functional Physiology Section, Xiamen Medical College, Xiamen, China,Department of Basic Medical Science, Institute of Respiratory Disease, Xiamen Medical College, Xiamen, China
| | - Wan-Yi Ho
- Department of Anatomy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ning Kang
- Department of Otorhinolaryngology, the Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - May-Jywan Tsai
- Department of Neurosurgery, Neurological Institute, Neurological Institute, Taipei, Taiwan
| | - Jingyi Wu
- Department of Basic Medical Science, Anatomy and Functional Physiology Section, Xiamen Medical College, Xiamen, China
| | - Liyue Huang
- Department of Basic Medical Science, Anatomy and Functional Physiology Section, Xiamen Medical College, Xiamen, China
| | - Ching-Feng Weng
- Department of Basic Medical Science, Anatomy and Functional Physiology Section, Xiamen Medical College, Xiamen, China,Department of Basic Medical Science, Institute of Respiratory Disease, Xiamen Medical College, Xiamen, China,*Correspondence: Ching-Feng Weng, ,
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17
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Zhou P, Song G, He WT, Beutler N, Tse LV, Martinez DR, Schäfer A, Anzanello F, Yong P, Peng L, Dueker K, Musharrafieh R, Callaghan S, Capozzola T, Yuan M, Liu H, Limbo O, Parren M, Garcia E, Rawlings SA, Smith DM, Nemazee D, Jardine JG, Wilson IA, Safonova Y, Rogers TF, Baric RS, Gralinski LE, Burton DR, Andrabi R. Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause severe disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.03.04.479488. [PMID: 35291291 PMCID: PMC8923106 DOI: 10.1101/2022.03.04.479488] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Pan-betacoronavirus neutralizing antibodies may hold the key to developing broadly protective vaccines against coronaviruses that cause severe disease, for anticipating novel pandemic-causing viruses, and to respond more effectively to SARS-CoV-2 variants. The emergence of the Omicron variant of SARS-CoV-2 has illustrated the limitations of solely targeting the receptor binding domain (RBD) of the envelope Spike (S)-protein. Here, we isolated a large panel of broadly neutralizing antibodies (bnAbs) from SARS-CoV-2 recovered-vaccinated donors that target a conserved S2 region in the fusion machinery on betacoronavirus spikes. Select bnAbs show broad in vivo protection against all three pathogenic betacoronaviruses, SARS-CoV-1, SARS-CoV-2 and MERS-CoV, that have spilled over into humans in the past 20 years to cause severe disease. The bnAbs provide new opportunities for antibody-based interventions and key insights for developing pan-betacoronavirus vaccines.
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Affiliation(s)
- Panpan Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wan-ting He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Longping V. Tse
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David R. Martinez
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexandra Schäfer
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Fabio Anzanello
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter Yong
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Katharina Dueker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rami Musharrafieh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sean Callaghan
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tazio Capozzola
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oliver Limbo
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mara Parren
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Elijah Garcia
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Stephen A. Rawlings
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Davey M. Smith
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joseph G. Jardine
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yana Safonova
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Thomas F. Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Ralph S. Baric
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Departments of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Corresponding author. (R.S.B.); (L.E.G.); (D.R.B.); (R.A.)
| | - Lisa E. Gralinski
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Corresponding author. (R.S.B.); (L.E.G.); (D.R.B.); (R.A.)
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
- Corresponding author. (R.S.B.); (L.E.G.); (D.R.B.); (R.A.)
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Corresponding author. (R.S.B.); (L.E.G.); (D.R.B.); (R.A.)
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18
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Starr TN, Zepeda SK, Walls AC, Greaney AJ, Alkhovsky S, Veesler D, Bloom JD. ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. Nature 2022; 603:913-918. [PMID: 35114688 PMCID: PMC8967715 DOI: 10.1038/s41586-022-04464-z] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 01/25/2022] [Indexed: 11/08/2022]
Abstract
Two different sarbecoviruses have caused major human outbreaks in the past two decades1,2. Both of these sarbecoviruses, SARS-CoV-1 and SARS-CoV-2, engage ACE2 through the spike receptor-binding domain2-6. However, binding to ACE2 orthologues of humans, bats and other species has been observed only sporadically among the broader diversity of bat sarbecoviruses7-11. Here we use high-throughput assays12 to trace the evolutionary history of ACE2 binding across a diverse range of sarbecoviruses and ACE2 orthologues. We find that ACE2 binding is an ancestral trait of sarbecovirus receptor-binding domains that has subsequently been lost in some clades. Furthermore, we reveal that bat sarbecoviruses from outside Asia can bind to ACE2. Moreover, ACE2 binding is highly evolvable-for many sarbecovirus receptor-binding domains, there are single amino-acid mutations that enable binding to new ACE2 orthologues. However, the effects of individual mutations can differ considerably between viruses, as shown by the N501Y mutation, which enhances the human ACE2-binding affinity of several SARS-CoV-2 variants of concern12 but substantially decreases it for SARS-CoV-1. Our results point to the deep ancestral origin and evolutionary plasticity of ACE2 binding, broadening the range of sarbecoviruses that should be considered to have spillover potential.
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Affiliation(s)
- Tyler N Starr
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Allison J Greaney
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sergey Alkhovsky
- N.F. Gamleya National Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - David Veesler
- Howard Hughes Medical Institute, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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19
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Yan F, Li E, Wang T, Li Y, Liu J, Wang W, Qin T, Su R, Pei H, Wang S, Feng N, Zhao Y, Yang S, Xia X, Gao Y. Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. Front Immunol 2022; 13:821664. [PMID: 35197985 PMCID: PMC8858946 DOI: 10.3389/fimmu.2022.821664] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/13/2022] [Indexed: 12/15/2022] Open
Abstract
New emerging severe acute respiratory syndrome 2 (SARS-CoV-2) has caused a worldwide pandemic. Several animal models of coronavirus disease 2019 (COVID-19) have been developed and applied to antiviral research. In this study, two lethal mouse-adapted SARS-CoV-2 variants (BMA8 and C57MA14) with different virulence were generated from different hosts, which are characterized by high viral replication titers in the upper and lower respiratory tract, pulmonary pathology, cytokine storm, cellular tropism, lymphopenia, and neutrophilia. Two variants exhibit host genetics-related and age-dependent morbidity and mortality in mice, exquisitely reflecting the clinical manifestation of asymptomatic, moderate, and severe COVID-19 patients. Notably, both variants equally weaken the neutralization capacity of the serum derived from COVID-19 convalescent, but the C57MA14 variant showed a much higher virulence than the BMA8 variant in vitro. Q489H substitution in the receptor-binding domain (RBD) of BMA8 and C57MA14 variants results in the receptors of SARS-CoV-2 switching from human angiotensin-converting enzyme 2 (hACE2) to murine angiotensin-converting enzyme 2 (mACE2). Additionally, A22D and A36V mutation in E protein were first reported in our study, which potentially contributed to the virulence difference between the two variants. Of note, the protective efficacy of the novel bacterium-like particle (BLP) vaccine candidate was validated using the BMA8- or C57MA14-infected aged mouse model. The BMA8 variant- and C57MA14 variant-infected models provide a relatively inexpensive and accessible evaluation platform for assessing the efficacy of vaccines and novel therapeutic approaches. This will promote further research in the transmissibility and pathogenicity mechanisms of SARS-CoV-2.
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Affiliation(s)
- Feihu Yan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Entao Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Tiecheng Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yuanguo Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jun Liu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Weiqi Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Tian Qin
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- School of Life Sciences, Northeast Normal University, Changchun, China
| | - Rina Su
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
| | - Hongyan Pei
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
| | - Shen Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Na Feng
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yongkun Zhao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Songtao Yang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xianzhu Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yuwei Gao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- *Correspondence: Yuwei Gao,
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20
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Abstract
The recently encountered severe acute respiratory syndrome coronavirus 2 creates huge predicaments among various countries. Lack of specific treatment of COVID-19 disease demands urgency in drug design against SARS-CoV-2 targets. Nigella sativa the miraculous herb native to South and Southwest Asia and belonging to the family Ranunculaceae, due to its beneficial bioactive properties, was used by us for performing in silico study to analyze the potential of its compounds so that they can target and inhibit SARS-COV-2 proteins including its main protease, the papain-like protease, its helicase, and also the RNA-dependent RNApolymerase, RNA-binding protein, Endoribonuclease, receptor-binding domain, and the RNA-binding domain of nucleocapsid phosphoprotein. The procedure of molecular docking was done with the help of AutoDock–Vina 1.1.2. and along with it the ADMET properties of the best suited ligands were found and Lipinski screening was performed. Among 58 ligands screened, various compounds showed binding energy less than the standard drug chloroquine. Three compounds alpha-hederin, rutin, and nigellamine A2 had the least binding energy with the specific SARS-Cov-2 proteins suggesting their best potential as SARS-CoV-2 inhibitor. Hence, in the future, studies including the in vitro and also the in vivo studies can be carried out for analyzing their true potential and encourage use of nutraceuticals like Nigella sativa to inhibit this virus.
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21
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Yan W, Zheng Y, Zeng X, He B, Cheng W. Structural biology of SARS-CoV-2: open the door for novel therapies. Signal Transduct Target Ther 2022; 7:26. [PMID: 35087058 PMCID: PMC8793099 DOI: 10.1038/s41392-022-00884-5] [Citation(s) in RCA: 122] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 02/08/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the causative agent of the pandemic disease COVID-19, which is so far without efficacious treatment. The discovery of therapy reagents for treating COVID-19 are urgently needed, and the structures of the potential drug-target proteins in the viral life cycle are particularly important. SARS-CoV-2, a member of the Orthocoronavirinae subfamily containing the largest RNA genome, encodes 29 proteins including nonstructural, structural and accessory proteins which are involved in viral adsorption, entry and uncoating, nucleic acid replication and transcription, assembly and release, etc. These proteins individually act as a partner of the replication machinery or involved in forming the complexes with host cellular factors to participate in the essential physiological activities. This review summarizes the representative structures and typically potential therapy agents that target SARS-CoV-2 or some critical proteins for viral pathogenesis, providing insights into the mechanisms underlying viral infection, prevention of infection, and treatment. Indeed, these studies open the door for COVID therapies, leading to ways to prevent and treat COVID-19, especially, treatment of the disease caused by the viral variants are imperative.
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Affiliation(s)
- Weizhu Yan
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Yanhui Zheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Xiaotao Zeng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Bin He
- Department of Emergency Medicine, West China Hospital of Sichuan University, 610041, Chengdu, China.
- The First People's Hospital of Longquanyi District Chengdu, 610100, Chengdu, China.
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China.
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22
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Kalamvoki M, Norris V. A Defective Viral Particle Approach to COVID-19. Cells 2022; 11:302. [PMID: 35053418 PMCID: PMC8774189 DOI: 10.3390/cells11020302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/03/2021] [Accepted: 01/13/2022] [Indexed: 12/10/2022] Open
Abstract
The novel coronavirus SARS-CoV-2 has caused a pandemic resulting in millions of deaths worldwide. While multiple vaccines have been developed, insufficient vaccination combined with adaptive mutations create uncertainty for the future. Here, we discuss novel strategies to control COVID-19 relying on Defective Interfering Particles (DIPs) and related particles that arise naturally during an infection. Our intention is to encourage and to provide the basis for the implementation of such strategies by multi-disciplinary teams. We therefore provide an overview of SARS-CoV-2 for a multi-disciplinary readership that is specifically tailored to these strategies, we identify potential targets based on the current knowledge of the properties and functions of coronaviruses, and we propose specific strategies to engineer DIPs and other interfering or therapeutic nanoparticles.
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Affiliation(s)
- Maria Kalamvoki
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Vic Norris
- Laboratory of Microbiology Signals and Microenvironment, University of Rouen, 76821 Mont Saint Aignan, France;
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23
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Emrani J, Ahmed M, Jeffers-Francis L, Teleha JC, Mowa N, Newman RH, Thomas MD. SARS-COV-2, infection, transmission, transcription, translation, proteins, and treatment: A review. Int J Biol Macromol 2021; 193:1249-1273. [PMID: 34756970 PMCID: PMC8552795 DOI: 10.1016/j.ijbiomac.2021.10.172] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/21/2021] [Indexed: 01/18/2023]
Abstract
In this review, we describe the key molecular entities involved in the process of infection by SARS-CoV-2, while also detailing how those key entities influence the spread of the disease. We further introduce the molecular mechanisms of preventive and treatment strategies including drugs, antibodies, and vaccines.
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Affiliation(s)
- Jahangir Emrani
- Department of Chemistry, North Carolina A&T State University, Greensboro, NC 27411, United States of America.
| | - Maryam Ahmed
- Department of Biology, Appalachian State University, Boone, NC 28608, United States of America
| | - Liesl Jeffers-Francis
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, United States of America
| | - John C Teleha
- Department of Reference and Instruction, North Carolina A&T State University, Greensboro, NC 27411, United States of America
| | - Nathan Mowa
- Department of Biology, Appalachian State University, Boone, NC 28608, United States of America
| | - Robert H Newman
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, United States of America
| | - Misty D Thomas
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, United States of America
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24
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de O Araújo J, Pinheiro S, Zamora WJ, Alves CN, Lameira J, Lima AH. Structural, energetic and lipophilic analysis of SARS-CoV-2 non-structural protein 9 (NSP9). Sci Rep 2021; 11:23003. [PMID: 34837010 PMCID: PMC8626507 DOI: 10.1038/s41598-021-02366-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/08/2021] [Indexed: 12/02/2022] Open
Abstract
In SARS-CoV-2 replication complex, the Non-structural protein 9 (Nsp9) is an important RNA binding subunit in the RNA-synthesizing machinery. The dimeric forms of coronavirus Nsp9 increase their nucleic acid binding affinity and the N-finger motif appears to play a critical role in dimerization. Here, we present a structural, lipophilic and energetic study about the Nsp9 dimer of SARS-CoV-2 through computational methods that complement hydrophobicity scales of amino acids with molecular dynamics simulations. Additionally, we presented a virtual N-finger mutation to investigate whether this motif contributes to dimer stability. The results reveal for the native dimer that the N-finger contributes favorably through hydrogen bond interactions and two amino acids bellowing to the hydrophobic region, Leu45 and Leu106, are crucial in the formation of the cavity for potential drug binding. On the other hand, Gly100 and Gly104, are responsible for stabilizing the α-helices and making the dimer interface remain stable in both, native and mutant (without N-finger motif) systems. Besides, clustering results for the native dimer showed accessible cavities to drugs. In addition, the energetic and lipophilic analysis reveal that the higher binding energy in the native dimer can be deduced since it is more lipophilic than the mutant one, increasing non-polar interactions, which is in line with the result of MM-GBSA and SIE approaches where the van der Waals energy term has the greatest weight in the stability of the native dimer. Overall, we provide a detailed study on the Nsp9 dimer of SARS-CoV-2 that may aid in the development of new strategies for the treatment and prevention of COVID-19.
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Affiliation(s)
- Jéssica de O Araújo
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil
| | - Silvana Pinheiro
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil
| | - William J Zamora
- School of Chemistry & Faculty of Pharmacy, University of Costa Rica, San Pedro, San José, Costa Rica
- Advanced Computing Lab (CNCA), National High Technology Center (CeNAT-CONARE), Pavas, San José, Costa Rica
| | - Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil
| | - Anderson H Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil.
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25
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Buratto D, Saxena A, Ji Q, Yang G, Pantano S, Zonta F. Rapid Assessment of Binding Affinity of SARS-COV-2 Spike Protein to the Human Angiotensin-Converting Enzyme 2 Receptor and to Neutralizing Biomolecules Based on Computer Simulations. Front Immunol 2021; 12:730099. [PMID: 34858396 PMCID: PMC8632240 DOI: 10.3389/fimmu.2021.730099] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/25/2021] [Indexed: 12/17/2022] Open
Abstract
SARS-CoV-2 infects humans and causes Coronavirus disease 2019 (COVID-19). The S1 domain of the spike glycoprotein of SARS-CoV-2 binds to human angiotensin-converting enzyme 2 (hACE2) via its receptor-binding domain, while the S2 domain facilitates fusion between the virus and the host cell membrane for entry. The spike glycoprotein of circulating SARS-CoV-2 genomes is a mutation hotspot. Some mutations may affect the binding affinity for hACE2, while others may modulate S-glycoprotein expression, or they could result in a virus that can escape from antibodies generated by infection with the original variant or by vaccination. Since a large number of variants are emerging, it is of vital importance to be able to rapidly assess their characteristics: while changes of binding affinity alone do not always cause direct advantages for the virus, they still can provide important insights on where the evolutionary pressure is directed. Here, we propose a simple and cost-effective computational protocol based on Molecular Dynamics simulations to rapidly screen the ability of mutated spike protein to bind to the hACE2 receptor and selected neutralizing biomolecules. Our results show that it is possible to achieve rapid and reliable predictions of binding affinities. A similar approach can be used to perform preliminary screenings of the potential effects of S-RBD mutations, helping to prioritize the more time-consuming and expensive experimental work.
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Affiliation(s)
- Damiano Buratto
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Abhishek Saxena
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Qun Ji
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Sergio Pantano
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Francesco Zonta
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
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26
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Muruato A, Vu MN, Johnson BA, Davis-Gardner ME, Vanderheiden A, Lokugamage K, Schindewolf C, Crocquet-Valdes PA, Langsjoen RM, Plante JA, Plante KS, Weaver SC, Debbink K, Routh AL, Walker D, Suthar MS, Shi PY, Xie X, Menachery VD. Mouse-adapted SARS-CoV-2 protects animals from lethal SARS-CoV challenge. PLoS Biol 2021; 19:e3001284. [PMID: 34735434 PMCID: PMC8594810 DOI: 10.1371/journal.pbio.3001284] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 11/16/2021] [Accepted: 10/17/2021] [Indexed: 01/16/2023] Open
Abstract
The emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has resulted in a pandemic causing significant damage to public health and the economy. Efforts to understand the mechanisms of Coronavirus Disease 2019 (COVID-19) have been hampered by the lack of robust mouse models. To overcome this barrier, we used a reverse genetic system to generate a mouse-adapted strain of SARS-CoV-2. Incorporating key mutations found in SARS-CoV-2 variants, this model recapitulates critical elements of human infection including viral replication in the lung, immune cell infiltration, and significant in vivo disease. Importantly, mouse adaptation of SARS-CoV-2 does not impair replication in human airway cells and maintains antigenicity similar to human SARS-CoV-2 strains. Coupled with the incorporation of mutations found in variants of concern, CMA3p20 offers several advantages over other mouse-adapted SARS-CoV-2 strains. Using this model, we demonstrate that SARS-CoV-2-infected mice are protected from lethal challenge with the original Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), suggesting immunity from heterologous Coronavirus (CoV) strains. Together, the results highlight the use of this mouse model for further study of SARS-CoV-2 infection and disease.
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Affiliation(s)
- Antonio Muruato
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Michelle N. Vu
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Bryan A. Johnson
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Meredith E. Davis-Gardner
- Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Abigail Vanderheiden
- Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Kumari Lokugamage
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Craig Schindewolf
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | | | - Rose M. Langsjoen
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jessica A. Plante
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kenneth S. Plante
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Scott C. Weaver
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kari Debbink
- Department of Natural Science, Bowie State University, Bowie, Maryland, United States of America
| | - Andrew L. Routh
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - David Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Mehul S. Suthar
- Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
| | - Pei-Yong Shi
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Xuping Xie
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Vineet D. Menachery
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
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27
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Boras B, Jones RM, Anson BJ, Arenson D, Aschenbrenner L, Bakowski MA, Beutler N, Binder J, Chen E, Eng H, Hammond H, Hammond J, Haupt RE, Hoffman R, Kadar EP, Kania R, Kimoto E, Kirkpatrick MG, Lanyon L, Lendy EK, Lillis JR, Logue J, Luthra SA, Ma C, Mason SW, McGrath ME, Noell S, Obach RS, O' Brien MN, O'Connor R, Ogilvie K, Owen D, Pettersson M, Reese MR, Rogers TF, Rosales R, Rossulek MI, Sathish JG, Shirai N, Steppan C, Ticehurst M, Updyke LW, Weston S, Zhu Y, White KM, García-Sastre A, Wang J, Chatterjee AK, Mesecar AD, Frieman MB, Anderson AS, Allerton C. Preclinical characterization of an intravenous coronavirus 3CL protease inhibitor for the potential treatment of COVID19. Nat Commun 2021; 12:6055. [PMID: 34663813 PMCID: PMC8523698 DOI: 10.1038/s41467-021-26239-2] [Citation(s) in RCA: 171] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 09/23/2021] [Indexed: 01/27/2023] Open
Abstract
COVID-19 caused by the SARS-CoV-2 virus has become a global pandemic. 3CL protease is a virally encoded protein that is essential across a broad spectrum of coronaviruses with no close human analogs. PF-00835231, a 3CL protease inhibitor, has exhibited potent in vitro antiviral activity against SARS-CoV-2 as a single agent. Here we report, the design and characterization of a phosphate prodrug PF-07304814 to enable the delivery and projected sustained systemic exposure in human of PF-00835231 to inhibit coronavirus family 3CL protease activity with selectivity over human host protease targets. Furthermore, we show that PF-00835231 has additive/synergistic activity in combination with remdesivir. We present the ADME, safety, in vitro, and in vivo antiviral activity data that supports the clinical evaluation of PF-07304814 as a potential COVID-19 treatment.
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Affiliation(s)
- Britton Boras
- Worldwide Research and Development, Pfizer Inc, La Jolla, CA, 92121, USA
| | - Rhys M Jones
- Worldwide Research and Development, Pfizer Inc, La Jolla, CA, 92121, USA.
| | - Brandon J Anson
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Dan Arenson
- Worldwide Research and Development, Pfizer Inc, Groton, CT, 06340, USA
| | | | - Malina A Bakowski
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Joseph Binder
- Worldwide Research and Development, Pfizer Inc, La Jolla, CA, 92121, USA
| | - Emily Chen
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Heather Eng
- Worldwide Research and Development, Pfizer Inc, Groton, CT, 06340, USA
| | - Holly Hammond
- Department of Microbiology and Immunology University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Jennifer Hammond
- Worldwide Research and Development, Pfizer Inc., Collegeville, PA, 19426, USA
| | - Robert E Haupt
- Department of Microbiology and Immunology University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Robert Hoffman
- Worldwide Research and Development, Pfizer Inc, La Jolla, CA, 92121, USA
| | - Eugene P Kadar
- Worldwide Research and Development, Pfizer Inc, Groton, CT, 06340, USA
| | - Rob Kania
- Worldwide Research and Development, Pfizer Inc, La Jolla, CA, 92121, USA
| | - Emi Kimoto
- Worldwide Research and Development, Pfizer Inc, Groton, CT, 06340, USA
| | | | - Lorraine Lanyon
- Worldwide Research and Development, Pfizer Inc, Groton, CT, 06340, USA
| | - Emma K Lendy
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Jonathan R Lillis
- Worldwide Research and Development, Pfizer Inc, Sandwich, CT13 9ND, UK
| | - James Logue
- Department of Microbiology and Immunology University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Suman A Luthra
- Worldwide Research and Development, Pfizer Inc, Cambridge, MA, 02139, USA
| | - Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Stephen W Mason
- Worldwide Research and Development, Pfizer Inc, Groton, CT, 06340, USA
- Worldwide Research and Development, Pfizer Inc., Pearl River, NY, 10965, USA
| | - Marisa E McGrath
- Department of Microbiology and Immunology University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Stephen Noell
- Worldwide Research and Development, Pfizer Inc, Groton, CT, 06340, USA
| | - R Scott Obach
- Worldwide Research and Development, Pfizer Inc, Groton, CT, 06340, USA
| | - Matthew N O' Brien
- Worldwide Research and Development, Pfizer Inc, Lake Forest, IL, 60045, USA
| | - Rebecca O'Connor
- Worldwide Research and Development, Pfizer Inc, Groton, CT, 06340, USA
| | - Kevin Ogilvie
- Worldwide Research and Development, Pfizer Inc, Groton, CT, 06340, USA
| | - Dafydd Owen
- Worldwide Research and Development, Pfizer Inc, Cambridge, MA, 02139, USA
| | - Martin Pettersson
- Worldwide Research and Development, Pfizer Inc, Cambridge, MA, 02139, USA
| | - Matthew R Reese
- Worldwide Research and Development, Pfizer Inc, Groton, CT, 06340, USA
| | - Thomas F Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- UC San Diego Division of Infectious Diseases and Global Public Health, UC San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Jean G Sathish
- Worldwide Research and Development, Pfizer Inc., Pearl River, NY, 10965, USA
| | - Norimitsu Shirai
- Worldwide Research and Development, Pfizer Inc, Groton, CT, 06340, USA
| | - Claire Steppan
- Worldwide Research and Development, Pfizer Inc, Groton, CT, 06340, USA
| | - Martyn Ticehurst
- Worldwide Research and Development, Pfizer Inc, Sandwich, CT13 9ND, UK
| | - Lawrence W Updyke
- Worldwide Research and Development, Pfizer Inc, Cambridge, MA, 02139, USA
| | - Stuart Weston
- Department of Microbiology and Immunology University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Yuao Zhu
- Worldwide Research and Development, Pfizer Inc., Pearl River, NY, 10965, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Arnab K Chatterjee
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Andrew D Mesecar
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Matthew B Frieman
- Department of Microbiology and Immunology University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | | | - Charlotte Allerton
- Worldwide Research and Development, Pfizer Inc, Cambridge, MA, 02139, USA
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28
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F Dudás E, Puglisi R, Korn SM, Alfano C, Bellone ML, Piaz FD, Kelly G, Monaca E, Schlundt A, Schwalbe H, Pastore A. Backbone chemical shift spectral assignments of SARS coronavirus-2 non-structural protein nsp9. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:235-241. [PMID: 33755914 PMCID: PMC7985572 DOI: 10.1007/s12104-021-10011-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
As part of an International consortium aiming at the characterization by NMR of the proteins of the SARS-CoV-2 virus, we have obtained the virtually complete assignment of the backbone atoms of the non-structural protein nsp9. This small (12 kDa) protein is encoded by ORF1a, binds to RNA and seems to be essential for viral RNA synthesis. The crystal structures of the SARS-CoV-2 protein and other homologues suggest that the protein is dimeric as also confirmed by analytical ultracentrifugation and dynamic light scattering. Our data constitute the prerequisite for further NMR-based characterization, and provide the starting point for the identification of small molecule lead compounds that could interfere with RNA binding and prevent viral replication.
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Affiliation(s)
- Erika F Dudás
- Department of Basic and Clinical Neuroscience, Maurice Wohl Institute, UK-DRI at King's College London, 5 Cutcombe Rd, London, SE59RT, UK
| | - Rita Puglisi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Institute, UK-DRI at King's College London, 5 Cutcombe Rd, London, SE59RT, UK
| | - Sophie Marianne Korn
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | | | - Maria Laura Bellone
- Department of Medicine and Surgery, University of Salerno, Via Giovanni Paolo II, 84081, Baronissi, SA, Italy
| | - Fabrizio Dal Piaz
- Department of Medicine and Surgery, University of Salerno, Via Giovanni Paolo II, 84081, Baronissi, SA, Italy
| | - Geoff Kelly
- Francis Crick Institute, MRC Biomedical NMR Centre, 1 Midland Rd, London, NW1 1AT, UK
| | | | - Andreas Schlundt
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - Harald Schwalbe
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - Annalisa Pastore
- Department of Basic and Clinical Neuroscience, Maurice Wohl Institute, UK-DRI at King's College London, 5 Cutcombe Rd, London, SE59RT, UK.
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29
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Knight AC, Montgomery SA, Fletcher CA, Baxter VK. Mouse Models for the Study of SARS-CoV-2 Infection. Comp Med 2021; 71:383-397. [PMID: 34610856 PMCID: PMC8594264 DOI: 10.30802/aalas-cm-21-000031] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/19/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023]
Abstract
Mice are an invaluable resource for studying virus-induced disease. They are a small, genetically modifiable animal for which a large arsenal of genetic and immunologic tools is available for evaluation of pathogenesis and potential vaccines and therapeutics. SARS-CoV-2, the betacoronavirus responsible for the COVID-19 pandemic, does not naturally replicate in wild-type mice, due to structural differences between human and mouse ACE2, the primary receptor for SARS-CoV-2 entry into cells. However, several mouse strains have been developed that allow for SARS-CoV-2 replication and clinical disease. Two broad strategies have primarily been deployed for developing mouse strains susceptible to COVID-19-like disease: adding in the human ACE2 gene and adapting the virus to the mouse ACE2 receptor. Both approaches result in mice that develop several of the clinical and pathologic hallmarks of COVID-19, including acute respiratory distress syndrome and acute lung injury. In this review, we describe key acute pulmonary and extrapulmonary pathologic changes seen in COVID-19 patients that mouse models of SARS-CoV-2 infection ideally replicate, the essential development of mouse models for the study of Severe Acute Respiratory Syndrome and Middle Eastern Respiratory Syndrome and the basis of many of the models of COVID-19, and key clinical and pathologic features of currently available mouse models of SARS-CoV-2 infection.
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Key Words
- aav, adeno-associated virus
- ace2, angiotensin-converting enzyme 2
- ali, acute lung injury
- ards, acute respiratory distress syndrome
- covid-19, coronavirus disease 19
- dad, diffuse alveolar damage
- dpi, days postinfection
- dpp4, dipeptidyl peptidase 4
- hace2, human angiotensin-converting enzyme 2
- mace2, mouse angiotensin-converting enzyme 2
- mers, middle eastern respiratory syndrome
- mers-cov, middle eastern respiratory syndrome coronavirus
- sars, severe acute respiratory syndrome
- sars-cov, severe acute respiratory syndrome coronavirus
- sars-cov-2, severe acute respiratory syndrome coronavirus 2
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Affiliation(s)
- Audrey C Knight
- Department of Pathology and Laboratory Medicine
- Institute for Global Health and Infectious Diseases, and
| | - Stephanie A Montgomery
- Department of Pathology and Laboratory Medicine
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Craig A Fletcher
- Department of Pathology and Laboratory Medicine
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Victoria K Baxter
- Department of Pathology and Laboratory Medicine
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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30
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Sonkar C, Doharey PK, Rathore AS, Singh V, Kashyap D, Sahoo AK, Mittal N, Sharma B, Jha HC. Repurposing of gastric cancer drugs against COVID-19. Comput Biol Med 2021; 137:104826. [PMID: 34537409 PMCID: PMC8420180 DOI: 10.1016/j.compbiomed.2021.104826] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 12/19/2022]
Abstract
Corona Virus Disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has become a global pandemic. Additionally, the SARS-CoV-2 infection in the patients of Gastric Cancer (GC; the third leading cause of death in the world) pose a great challenge for the health management of the patients. Since there have been uncertainties to develop a new drug against COVID-19, there is an urgent need for repurposing drugs that can target key proteins of both SARS-CoV-2 and GC. The SARS-CoV-2-RdRp protein contains the NiRAN domain, which is known to have kinase-like folds. A docking study of the FDA approved drugs against GC was performed using AutoDock 4.2 and Glide Schrodinger suite 2019 against SARS-CoV-2-RdRp protein. MMGBSA and MD simulation studies were performed to investigate the binding and stability of the inhibitors with the target protein. In this study, we have found 12 kinase inhibitors with high binding energies namely Baricitinib, Brepocitinib, Decernotinib, Fasudil, Filgotinib, GSK2606414, Peficitinib, Ruxolitinib, Tofacitinib, Upadacitinib, Pamapimod and Ibrutinib. These FDA approved drugs against GC can play a key role in the treatment of COVID-19 patients along with GC as comorbidity. We also hypothesize that JAK, ITK, Rho-associated kinases, FGFR2, FYN, PERK, TYK2, p38-MAPK and SYK kinases can be considered as key therapeutic targets in COVID-19 treatment. Taken altogether, we have proposed the SARS-CoV-2-RdRp as a potential therapeutic target through in-silico studies. However, further in-vitro and in-vivo studies are required for the validation of the proposed targets and drugs for the treatment of COVID-19 patients already suffering from GC.
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Affiliation(s)
- Charu Sonkar
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Pawan Kumar Doharey
- Department of Biochemistry, University of Allahabad, Allahabad, 211002, U.P., India
| | - Anuranjan Singh Rathore
- SASTRA Deemed to Be University, Trichy-Tanjore Road, Thirumalaisamudram, Thanjavur, Tamil Nadu, 613401, India
| | - Vishal Singh
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, 211015, U.P., India
| | - Dharmendra Kashyap
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Amaresh Kumar Sahoo
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, 211015, U.P., India
| | - Nitish Mittal
- Computational and Systems Biology, Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056, Basel, Switzerland
| | - Bechan Sharma
- Department of Biochemistry, University of Allahabad, Allahabad, 211002, U.P., India
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India.
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31
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Littler DR, Mohanty B, Lowery SA, Colson RN, Gully BS, Perlman S, Scanlon MJ, Rossjohn J. Binding of a pyrimidine RNA base-mimic to SARS-CoV-2 nonstructural protein 9. J Biol Chem 2021; 297:101018. [PMID: 34331944 PMCID: PMC8317483 DOI: 10.1016/j.jbc.2021.101018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 01/18/2023] Open
Abstract
The coronaviral nonstructural protein 9 (Nsp9) is essential for viral replication; it is the primary substrate of Nsp12's pseudokinase domain within the viral replication transcription complex, an association that also recruits other components during different stages of RNA reproduction. In the unmodified state, Nsp9 forms an obligate homodimer via an essential GxxxG protein-interaction motif, but its ssRNA-binding mechanism remains unknown. Using structural biological techniques, here we show that a base-mimicking compound identified from a small molecule fragment screen engages Nsp9 via a tetrameric Pi-Pi stacking interaction that induces the formation of a parallel trimer-of-dimers. This oligomerization mechanism allows an interchange of "latching" N-termini, the charges of which contribute to a series of electropositive channels that suggests a potential interface for viral RNA. The identified pyrrolo-pyrimidine compound may also serve as a potential starting point for the development of compounds seeking to probe Nsp9's role within SARS-CoV-2 replication.
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Affiliation(s)
- Dene R Littler
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| | - Biswaranjan Mohanty
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia; Sydney Analytical Core Research Facility, The University of Sydney, Sydney, New South Wales, Australia; ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Shea A Lowery
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Rhys N Colson
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Benjamin S Gully
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Martin J Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia; ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.
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32
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Niu S, Wang J, Bai B, Wu L, Zheng A, Chen Q, Du P, Han P, Zhang Y, Jia Y, Qiao C, Qi J, Tian W, Wang H, Wang Q, Gao GF. Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. EMBO J 2021; 40:e107786. [PMID: 34018203 PMCID: PMC8209949 DOI: 10.15252/embj.2021107786] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/08/2021] [Accepted: 05/14/2021] [Indexed: 12/02/2022] Open
Abstract
Pangolins have been suggested as potential reservoir of zoonotic viruses, including SARS-CoV-2 causing the global COVID-19 outbreak. Here, we study the binding of two SARS-CoV-2-like viruses isolated from pangolins, GX/P2V/2017 and GD/1/2019, to human angiotensin-converting enzyme 2 (hACE2), the receptor of SARS-CoV-2. We find that the spike protein receptor-binding domain (RBD) of pangolin CoVs binds to hACE2 as efficiently as the SARS-CoV-2 RBD in vitro. Furthermore, incorporation of pangolin CoV RBDs allows entry of pseudotyped VSV particles into hACE2-expressing cells. A screen for binding of pangolin CoV RBDs to ACE2 orthologs from various species suggests a broader host range than that of SARS-CoV-2. Additionally, cryo-EM structures of GX/P2V/2017 and GD/1/2019 RBDs in complex with hACE2 show their molecular binding in modes similar to SARS-CoV-2 RBD. Introducing the Q498H substitution found in pangolin CoVs into the SARS-CoV-2 RBD expands its binding capacity to ACE2 homologs of mouse, rat, and European hedgehog. These findings suggest that these two pangolin CoVs may infect humans, highlighting the necessity of further surveillance of pangolin CoVs.
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Affiliation(s)
- Sheng Niu
- College of Veterinary MedicineShanxi Agricultural UniversityJinzhongChina
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Jia Wang
- Ministry of Education Key Laboratory of Protein SciencesTsinghua‐Peking Joint Center for Life SciencesBeijing Advanced Innovation Center for Structural BiologyBeijing Frontier Research Center of Biological StructuresSchool of Life SciencesTsinghua UniversityBeijingChina
| | - Bin Bai
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Lili Wu
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Anqi Zheng
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Qian Chen
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- Institute of Physical Science and InformationAnhui UniversityHefeiChina
| | - Pei Du
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Pengcheng Han
- Department of biomedical engineeringEmory UniversityAtlantaGAUSA
| | - Yanfang Zhang
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- Laboratory of Protein Engineering and VaccinesTianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
| | - Yunfei Jia
- College of Veterinary MedicineShanxi Agricultural UniversityJinzhongChina
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Chengpeng Qiao
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Wen‐xia Tian
- College of Veterinary MedicineShanxi Agricultural UniversityJinzhongChina
| | - Hong‐Wei Wang
- Ministry of Education Key Laboratory of Protein SciencesTsinghua‐Peking Joint Center for Life SciencesBeijing Advanced Innovation Center for Structural BiologyBeijing Frontier Research Center of Biological StructuresSchool of Life SciencesTsinghua UniversityBeijingChina
| | - Qihui Wang
- College of Veterinary MedicineShanxi Agricultural UniversityJinzhongChina
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- Institute of Physical Science and InformationAnhui UniversityHefeiChina
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - George Fu Gao
- College of Veterinary MedicineShanxi Agricultural UniversityJinzhongChina
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
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Pascual-Iglesias A, Canton J, Ortega-Prieto AM, Jimenez-Guardeño JM, Regla-Nava JA. An Overview of Vaccines against SARS-CoV-2 in the COVID-19 Pandemic Era. Pathogens 2021; 10:1030. [PMID: 34451494 PMCID: PMC8402174 DOI: 10.3390/pathogens10081030] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/01/2021] [Accepted: 08/11/2021] [Indexed: 12/14/2022] Open
Abstract
The emergence of SARS-CoV-2 in late 2019 led to the COVID-19 pandemic all over the world. When the virus was first isolated and its genome was sequenced in the early months of 2020, the efforts to develop a vaccine began. Based on prior well-known knowledge about coronavirus, the SARS-CoV-2 spike (S) protein was selected as the main target. Currently, more than one hundred vaccines are being investigated and several of them are already authorized by medical agencies. This review summarizes and compares the current knowledge about main approaches for vaccine development, focusing on those authorized and specifically their immunogenicity, efficacy preventing severe disease, adverse side effects, protection, and ability to cope with emergent SARS-CoV-2 variants.
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Affiliation(s)
- Alejandro Pascual-Iglesias
- The Innate Immune Response Group, IdiPAZ, La Paz University Hospital, 28046 Madrid, Spain;
- Tumor Immunology Laboratory, IdiPAZ, La Paz University Hospital, 28046 Madrid, Spain
| | - Javier Canton
- International Institute for Defense and Security (CISDE), 41007 Sevilla, Spain;
| | - Ana Maria Ortega-Prieto
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London SE1 9RT, UK;
| | - Jose M. Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London SE1 9RT, UK;
| | - Jose Angel Regla-Nava
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Microbiology and Pathology, University Center for Health Science (CUCS), University of Guadalajara, Guadalajara 44340, Mexico
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34
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Brill SA, Guerrero-Martin SM, Metcalf Pate KA. The Symbiotic Relationship Between Scientific Quality and Animal Research Ethics. ILAR J 2021; 60:334-340. [PMID: 34352091 DOI: 10.1093/ilar/ilab023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 05/10/2021] [Accepted: 06/02/2021] [Indexed: 11/13/2022] Open
Abstract
Researchers have worked with animals as models for decades to expand our knowledge of basic biological processes and to systematically study the physiology of disease. In general, the public has an expectation that work with animals has a purpose and will ultimately reap benefits. The likelihood of such an outcome is directly dependent on the quality of the science being conducted with those animals. However, not all frameworks for consideration of the ethics around animal research overtly consider scientific quality. In the following review, we explore the complex relationship between scientific quality and animal research ethics. We advocate for the development of a detailed "Harm-Yield Analysis" for the evaluation of biomedical animal research that emphasizes scientific quality along with societal benefit in the ethical justification of the research. We reflect on the lost opportunity to establish best practices in animal research early in the career of scientists by introducing in the curriculum and encouraging the use of a paradigm of the iterative consideration of the ethics of animal research alongside other aspects of experimental design.
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Affiliation(s)
- Samuel A Brill
- College of Veterinary Medicine and Biomedical Sciences Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Selena M Guerrero-Martin
- School of Medicine Department of Molecular and Comparative Pathobiology, Johns Hopkins University, Baltimore, Maryland, USA.,Division of Comparative Medicine and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kelly A Metcalf Pate
- Division of Comparative Medicine and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Francis ME, Richardson B, Goncin U, McNeil M, Rioux M, Foley MK, Ge A, Pechous RD, Kindrachuk J, Cameron CM, Richardson C, Lew J, Machtaler S, Cameron MJ, Gerdts V, Falzarano D, Kelvin AA. Sex and age bias viral burden and interferon responses during SARS-CoV-2 infection in ferrets. Sci Rep 2021; 11:14536. [PMID: 34267262 PMCID: PMC8282673 DOI: 10.1038/s41598-021-93855-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/17/2021] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) hospitalizations and deaths disportionally affect males and older ages. Here we investigated the impact of male sex and age comparing sex-matched or age-matched ferrets infected with SARS-CoV-2. Differences in temperature regulation was identified for male ferrets which was accompanied by prolonged viral replication in the upper respiratory tract after infection. Gene expression analysis of the nasal turbinates indicated that 1-year-old female ferrets had significant increases in interferon response genes post infection which were delayed in males. These results provide insight into COVID-19 and suggests that older males may play a role in viral transmission due to decreased antiviral responses.
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Affiliation(s)
- Magen E Francis
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, B3H 4R2, Canada
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, S7N 5E3, Canada
| | - Brian Richardson
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Una Goncin
- Department of Medical Imaging, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada
| | - Mara McNeil
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Melissa Rioux
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Mary K Foley
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Anni Ge
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Roger D Pechous
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AK, 72205, USA
| | - Jason Kindrachuk
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, S7N 5E3, Canada
- Laboratory of Emerging and Re-emerging Viruses, Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
| | - Cheryl M Cameron
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Christopher Richardson
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Jocelyne Lew
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, S7N 5E3, Canada
| | - Steven Machtaler
- Department of Medical Imaging, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada
| | - Mark J Cameron
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Volker Gerdts
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - Alyson A Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, S7N 5E3, Canada.
- Department of Pediatrics, Division of Infectious Disease, Faculty of Medicine, Dalhousie University, Halifax, NS, B3K 6R8, Canada.
- Canadian Centre for Vaccinology, IWK Health Centre, 5980 University Ave, 4th Floor, R4020, Halifax, NS, B3K 6R8, Canada.
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De Sanctis JB, García AH, Moreno D, Hajduch M. Coronavirus infection: An immunologists' perspective. Scand J Immunol 2021; 93:e13043. [PMID: 33783027 PMCID: PMC8250184 DOI: 10.1111/sji.13043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/15/2021] [Accepted: 03/25/2021] [Indexed: 02/06/2023]
Abstract
Coronavirus infections are frequent viral infections in several species. As soon as the severe acute respiratory syndrome (SARS) appeared in the early 2000s, most of the research focused on pulmonary disease. However, disorders in immune response and organ dysfunctions have been documented. Elderly individuals with comorbidities exhibit worse outcomes in all the coronavirus that cause SARS. Disease severity in SARS-CoV-2 infection is related to severe inflammation and tissue injury, and effective immune response against the virus is still under analysis. ACE2 receptor expression and polymorphism, age, gender and immune genetics are factors that also play an essential role in patients' clinical features and immune responses and have been partially discussed. The present report aims to review the physiopathology of SARS-CoV-2 infection and propose new research topics to understand the complex mechanisms of viral infection and viral clearance.
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Affiliation(s)
- Juan Bautista De Sanctis
- Institute of Molecular and Translational MedicineFaculty of Medicine and DentistryPalacky UniversityOlomoucCzech Republic
- Institute of ImmunologyFaculty of MedicineUniversidad Central de VenezuelaCaracasVenezuela
| | - Alexis Hipólito García
- Institute of ImmunologyFaculty of MedicineUniversidad Central de VenezuelaCaracasVenezuela
| | - Dolores Moreno
- Chair of General Pathology and PathophysiologyFaculty of MedicineCentral University of VenezuelaCaracasVenezuela
| | - Marián Hajduch
- Institute of Molecular and Translational MedicineFaculty of Medicine and DentistryPalacky UniversityOlomoucCzech Republic
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Huang K, Zhang Y, Hui X, Zhao Y, Gong W, Wang T, Zhang S, Yang Y, Deng F, Zhang Q, Chen X, Yang Y, Sun X, Chen H, Tao YJ, Zou Z, Jin M. Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. EBioMedicine 2021; 67:103381. [PMID: 33993052 PMCID: PMC8118724 DOI: 10.1016/j.ebiom.2021.103381] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 01/24/2023] Open
Abstract
Background An ideal animal model to study SARS-coronavirus 2 (SARS-CoV-2) pathogenesis and evaluate therapies and vaccines should reproduce SARS-CoV-2 infection and recapitulate lung disease like those seen in humans. The angiotensin-converting enzyme 2 (ACE2) is a functional receptor for SARS-CoV-2, but mice are resistant to the infection because their ACE2 is incompatible with the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein . Methods SARS-CoV-2 was passaged in BALB/c mice to obtain mouse-adapted virus strain. Complete genome deep sequencing of different generations of viruses was performed to characterize the dynamics of the adaptive mutations in SARS-CoV-2. Indirect immunofluorescence analysis and Biolayer interferometry experiments determined the binding affinity of mouse-adapted SARS-CoV-2 WBP-1 RBD to mouse ACE2 and human ACE2. Finally, we tested whether TLR7/8 agonist Resiquimod (R848) could also inhibit the replication of WBP-1 in the mouse model. Findings The mouse-adapted strain WBP-1 showed increased infectivity in BALB/c mice and led to severe interstitial pneumonia. We characterized the dynamics of the adaptive mutations in SARS-CoV-2 and demonstrated that Q493K and Q498H in RBD significantly increased its binding affinity towards mouse ACE2. Additionally, the study tentatively found that the TLR7/8 agonist Resiquimod was able to protect mice against WBP-1 challenge. Therefore, this mouse-adapted strain is a useful tool to investigate COVID-19 and develop new therapies. Interpretation We found for the first time that the Q493K and Q498H mutations in the RBD of WBP-1 enhanced its interactive affinities with mACE2. The mouse-adapted SARS-CoV-2 provides a valuable tool for the evaluation of novel antiviral and vaccine strategies. This study also tentatively verified the antiviral activity of TLR7/8 agonist Resiquimod against SARS-CoV-2 in vitro and in vivo. Funding This research was funded by the National Key Research and Development Program of China (2020YFC0845600) and Emergency Science and Technology Project of Hubei Province (2020FCA046) and Robert A. Welch Foundation (C-1565).
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Affiliation(s)
- Kun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; Key Laboratory of development of veterinary diagnostic products, Ministry of Agriculture, Wuhan, 430070, PR China
| | - Yufei Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; Key Laboratory of development of veterinary diagnostic products, Ministry of Agriculture, Wuhan, 430070, PR China
| | - Xianfeng Hui
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; Key Laboratory of development of veterinary diagnostic products, Ministry of Agriculture, Wuhan, 430070, PR China
| | - Ya Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; Key Laboratory of development of veterinary diagnostic products, Ministry of Agriculture, Wuhan, 430070, PR China
| | - Wenxiao Gong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; Key Laboratory of development of veterinary diagnostic products, Ministry of Agriculture, Wuhan, 430070, PR China
| | - Ting Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; Key Laboratory of development of veterinary diagnostic products, Ministry of Agriculture, Wuhan, 430070, PR China
| | - Shaoran Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yong Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; Key Laboratory of development of veterinary diagnostic products, Ministry of Agriculture, Wuhan, 430070, PR China
| | - Fei Deng
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Qiang Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; Key Laboratory of development of veterinary diagnostic products, Ministry of Agriculture, Wuhan, 430070, PR China
| | - Xi Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Ying Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; Key Laboratory of development of veterinary diagnostic products, Ministry of Agriculture, Wuhan, 430070, PR China
| | - Xiaomei Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; Key Laboratory of development of veterinary diagnostic products, Ministry of Agriculture, Wuhan, 430070, PR China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Yizhi J Tao
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Zhong Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; Key Laboratory of development of veterinary diagnostic products, Ministry of Agriculture, Wuhan, 430070, PR China.
| | - Meilin Jin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; Key Laboratory of development of veterinary diagnostic products, Ministry of Agriculture, Wuhan, 430070, PR China.
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Muruato A, Vu MN, Johnson BA, Davis-Gardner ME, Vanderheiden A, Lokugmage K, Schindewolf C, Crocquet-Valdes PA, Langsjoen RM, Plante JA, Plante KS, Weaver SC, Debbink K, Routh AL, Walker D, Suthar MS, Xie X, Shi PY, Xie X, Menachery VD. Mouse Adapted SARS-CoV-2 protects animals from lethal SARS-CoV challenge. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.05.03.442357. [PMID: 33972939 PMCID: PMC8109199 DOI: 10.1101/2021.05.03.442357] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The emergence of SARS-CoV-2 has resulted in a worldwide pandemic causing significant damage to public health and the economy. Efforts to understand the mechanisms of COVID-19 disease have been hampered by the lack of robust mouse models. To overcome this barrier, we utilized a reverse genetic system to generate a mouse-adapted strain of SARS-CoV-2. Incorporating key mutations found in SARSCoV-2 variants, this model recapitulates critical elements of human infection including viral replication in the lung, immune cell infiltration, and significant in vivo disease. Importantly, mouse-adaptation of SARS-CoV-2 does not impair replication in human airway cells and maintains antigenicity similar to human SARS-CoV-2 strains. Utilizing this model, we demonstrate that SARS-CoV-2 infected mice are protected from lethal challenge with the original SARS-CoV, suggesting immunity from heterologous CoV strains. Together, the results highlight the utility of this mouse model for further study of SARS-CoV-2 infection and disease.
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Affiliation(s)
- Antonio Muruato
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
- Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Michelle N. Vu
- Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Bryan A. Johnson
- Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Meredith E. Davis-Gardner
- Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Abigail Vanderheiden
- Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Kumari Lokugmage
- Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Craig Schindewolf
- Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Rose M. Langsjoen
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jessica A. Plante
- Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Kenneth S. Plante
- Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Scott C. Weaver
- Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Kari Debbink
- Department of Natural Science, Bowie State University, Bowie, MD, USA
| | - Andrew L. Routh
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - David Walker
- Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Mehul S. Suthar
- Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Xuping Xie
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D. Menachery
- Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
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Hillen HS. Structure and function of SARS-CoV-2 polymerase. Curr Opin Virol 2021; 48:82-90. [PMID: 33945951 PMCID: PMC8023233 DOI: 10.1016/j.coviro.2021.03.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/18/2021] [Accepted: 03/30/2021] [Indexed: 01/18/2023]
Abstract
Coronaviruses use an RNA-dependent RNA polymerase (RdRp) to replicate and express their genome. The RdRp associates with additional non-structural proteins (nsps) to form a replication–transcription complex (RTC) that carries out RNA synthesis, capping and proofreading. However, the structure of the RdRp long remained elusive, thus limiting our understanding of coronavirus genome expression and replication. Recently, the cryo-electron microscopy structure of SARS-CoV-1 RdRp was reported. Driven by the ongoing COVID-19 pandemic, structural data on the SARS-CoV-2 polymerase and associated factors has since emerged at an unprecedented pace, with more than twenty structures released to date. This review provides an overview of the currently available coronavirus RdRp structures and outlines how they have, together with functional studies, led to a molecular understanding of the viral polymerase, its interactions with accessory factors and the mechanisms by which promising antivirals may inhibit coronavirus replication.
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Affiliation(s)
- Hauke S Hillen
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany; Research Group Structure and Function of Molecular Machines, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, D-37075 Göttingen, Germany.
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40
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Buchko GW, Zhou M, Craig JK, Van Voorhis WC, Myler PJ. Backbone chemical shift assignments for the SARS-CoV-2 non-structural protein Nsp9: intermediate (ms - μs) dynamics in the C-terminal helix at the dimer interface. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:107-116. [PMID: 33392924 PMCID: PMC7779335 DOI: 10.1007/s12104-020-09992-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 11/24/2020] [Indexed: 05/28/2023]
Abstract
The Betacoronavirus SARS-CoV-2 non-structural protein Nsp9 is a 113-residue protein that is essential for viral replication, and consequently, a potential target for the development of therapeutics against COVID19 infections. To capture insights into the dynamics of the protein's backbone in solution and accelerate the identification and mapping of ligand-binding surfaces through chemical shift perturbation studies, the backbone 1H, 13C, and 15N NMR chemical shifts for Nsp9 have been extensively assigned. These assignments were assisted by the preparation of an ~ 70% deuterated sample and residue-specific, 15N-labelled samples (V, L, M, F, and K). A major feature of the assignments was the "missing" amide resonances for N96-L106 in the 1H-15N HSQC spectrum, a region that comprises almost the complete C-terminal α-helix that forms a major part of the homodimer interface in the crystal structure of SARS-CoV-2 Nsp9, suggesting this region either undergoes intermediate motion in the ms to μs timescale and/or is heterogenous. These "missing" amide resonances do not unambiguously appear in the 1H-15N HSQC spectrum of SARS-CoV-2 Nsp9 collected at a concentration of 0.0007 mM. At this concentration, at the detection limit, native mass spectrometry indicates the protein is exclusively in the monomeric state, suggesting the intermediate motion in the C-terminal of Nsp9 may be due to intramolecular dynamics. Perhaps this intermediate ms to μs timescale dynamics is the physical basis for a previously suggested "fluidity" of the C-terminal helix that may be responsible for homophilic (Nsp9-Nsp9) and postulated heterophilic (Nsp9-Unknown) protein-protein interactions.
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Affiliation(s)
- Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA.
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
- School of Molecular Biosciences, Washington State University, Pullman, Washington, USA.
| | - Mowei Zhou
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Justin K Craig
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease, University of Washington, Seattle, Washington, USA
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease, University of Washington, Seattle, Washington, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, Department of Medical Education and Biomedical Informatics, Department of Global Health, University of Washington, Seattle, Washington, USA
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41
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Muhammad M, Ibrahim SA, Yarube IU, Bello B. A REVIEW ON EMERGING PATHOGENESIS OF COVID-19 AND POINTS OF CONCERN FOR RESEARCH COMMUNITIES IN NIGERIA. Afr J Infect Dis 2021; 15:36-43. [PMID: 33889801 PMCID: PMC8052969 DOI: 10.21010/ajid.v15i2.7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND COVID-19 remains an emerging pandemic that continuously poses an alarming threat and challenge to economic, social and well-being of the people throughout the world. It also remains an evolving disease which complete pathogenesis that translates into clinical features is only just emerging by each second of the day. There have been observations about the emerging trends of the disease in Nigeria like in any other country in the world where there is outbreak. This study examined from evidence-based literature the emerging pathogenesis of COVID-19 and important points of concern of the disease in Nigeria. MATERIALS AND METHODS The paper reviewed published articles in PubMed and Google Scholar using search terms 'COVID-19" and "SARS-CoV-2", as well as searched for general COVID-19 information on internet. RESULTS The result summarized literature on emerging pathogenesis of COVID-19 and important points of concern as well as research questions as to the peculiar trends of the disease in Nigeria. CONCLUSION Pathogenesis of COVID-19 remains an emerging knowledge and there are many important research questions that need to be scientifically answered for a successful containment of COVID-19 in Nigeria. It is recommended that all members of intellectual research communities should join the fight against COVID-19 pandemic.
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Affiliation(s)
- Mubarak Muhammad
- Department of Physiology, College of Medicine, University of Ibadan, Nigeria
| | - Salisu Ahmed Ibrahim
- Department of Human Physiology, College of Health Sciences, Bayero University Kano, Nigeria
| | - Isyaku Umar Yarube
- Department of Human Physiology, College of Health Sciences, Bayero University Kano, Nigeria
| | - Bashir Bello
- Department of Physiotherapy, College of Health Sciences, Bayero University Kano, Nigeria
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42
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Kadam SB, Sukhramani GS, Bishnoi P, Pable AA, Barvkar VT. SARS-CoV-2, the pandemic coronavirus: Molecular and structural insights. J Basic Microbiol 2021; 61:180-202. [PMID: 33460172 PMCID: PMC8013332 DOI: 10.1002/jobm.202000537] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 12/12/2022]
Abstract
The outbreak of a novel coronavirus associated with acute respiratory disease, called COVID-19, marked the introduction of the third spillover of an animal coronavirus (CoV) to humans in the last two decades. The genome analysis with various bioinformatics tools revealed that the causative pathogen (SARS-CoV-2) belongs to the subgenus Sarbecovirus of the genus Betacoronavirus, with highly similar genome as bat coronavirus and receptor-binding domain (RBD) of spike glycoprotein as Malayan pangolin coronavirus. Based on its genetic proximity, SARS-CoV-2 is likely to have originated from bat-derived CoV and transmitted to humans via an unknown intermediate mammalian host, probably Malayan pangolin. Further, spike protein S1/S2 cleavage site of SARS-CoV-2 has acquired polybasic furin cleavage site which is absent in bat and pangolin suggesting natural selection either in an animal host before zoonotic transfer or in humans following zoonotic transfer. In the current review, we recapitulate a preliminary opinion about the disease, origin and life cycle of SARS-CoV-2, roles of virus proteins in pathogenesis, commonalities, and differences between different corona viruses. Moreover, the crystal structures of SARS-CoV-2 proteins with unique characteristics differentiating it from other CoVs are discussed. Our review also provides comprehensive information on the molecular aspects of SARS-CoV-2 including secondary structures in the genome and protein-protein interactions which can be useful to understand the aggressive spread of the SARS-CoV-2. The mutations and the haplotypes reported in the SARS-CoV-2 genome are summarized to understand the virus evolution.
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Affiliation(s)
| | | | | | - Anupama A. Pable
- Department of MicrobiologySavitribai Phule Pune UniversityPuneIndia
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43
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Rosa RB, Dantas WM, do Nascimento JCF, da Silva MV, de Oliveira RN, Pena LJ. In Vitro and In Vivo Models for Studying SARS-CoV-2, the Etiological Agent Responsible for COVID-19 Pandemic. Viruses 2021; 13:379. [PMID: 33673614 PMCID: PMC7997194 DOI: 10.3390/v13030379] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/19/2021] [Accepted: 01/31/2021] [Indexed: 02/07/2023] Open
Abstract
The emergence and rapid worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has prompted the scientific community to rapidly develop in vitro and in vivo models that could be applied in COVID-19 research. In vitro models include two-dimensional (2D) cultures of immortalized cell lines or primary cells and three-dimensional (3D) cultures derived from lung, alveoli, bronchi, and other organs. Although cell-based systems are economic and allow strict control of experimental variables, they do not always resemble physiological conditions. Thus, several in vivo models are being developed, including different strains of mice, hamsters, ferrets, dogs, cats, and non-human primates. In this review, we summarize the main models of SARS-CoV-2 infection developed so far and discuss their advantages, drawbacks and main uses.
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Affiliation(s)
- Rafael B. Rosa
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife 50740-465, Brazil; (R.B.R.); (J.C.F.d.N.)
- Rodents Animal Facilities Complex, Federal University of Uberlandia, Uberlandia 38400-902, Brazil;
| | - Willyenne M. Dantas
- Department of Chemistry, Federal Rural University of Pernambuco (UFRPE), Recife 52171-900, Brazil; (W.M.D.); (R.N.d.O.)
| | - Jessica C. F. do Nascimento
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife 50740-465, Brazil; (R.B.R.); (J.C.F.d.N.)
| | - Murilo V. da Silva
- Rodents Animal Facilities Complex, Federal University of Uberlandia, Uberlandia 38400-902, Brazil;
| | - Ronaldo N. de Oliveira
- Department of Chemistry, Federal Rural University of Pernambuco (UFRPE), Recife 52171-900, Brazil; (W.M.D.); (R.N.d.O.)
| | - Lindomar J. Pena
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife 50740-465, Brazil; (R.B.R.); (J.C.F.d.N.)
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44
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Gorgulla C, Padmanabha Das KM, Leigh KE, Cespugli M, Fischer PD, Wang ZF, Tesseyre G, Pandita S, Shnapir A, Calderaio A, Gechev M, Rose A, Lewis N, Hutcheson C, Yaffe E, Luxenburg R, Herce HD, Durmaz V, Halazonetis TD, Fackeldey K, Patten J, Chuprina A, Dziuba I, Plekhova A, Moroz Y, Radchenko D, Tarkhanova O, Yavnyuk I, Gruber C, Yust R, Payne D, Näär AM, Namchuk MN, Davey RA, Wagner G, Kinney J, Arthanari H. A multi-pronged approach targeting SARS-CoV-2 proteins using ultra-large virtual screening. iScience 2021; 24:102021. [PMID: 33426509 PMCID: PMC7783459 DOI: 10.1016/j.isci.2020.102021] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/28/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023] Open
Abstract
The unparalleled global effort to combat the continuing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic over the last year has resulted in promising prophylactic measures. However, a need still exists for cheap, effective therapeutics, and targeting multiple points in the viral life cycle could help tackle the current, as well as future, coronaviruses. Here, we leverage our recently developed, ultra-large-scale in silico screening platform, VirtualFlow, to search for inhibitors that target SARS-CoV-2. In this unprecedented structure-based virtual campaign, we screened roughly 1 billion molecules against each of 40 different target sites on 17 different potential viral and host targets. In addition to targeting the active sites of viral enzymes, we also targeted critical auxiliary sites such as functionally important protein-protein interactions.
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Affiliation(s)
- Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Krishna M. Padmanabha Das
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kendra E. Leigh
- Max Planck Institute of Biophysics, Frankfurt am Main, Hessen 60438, Germany
| | | | - Patrick D. Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Saarland 66123, Germany
| | - Zi-Fu Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | | | | | | | - Anthony Calderaio
- VirtualFlow Organization, https://virtual-flow.org/, Boston, MA 02115, USA
| | | | - Alexander Rose
- Mol∗ Consortium, https://molstar.org, San Diego, CA 92109, USA
| | | | | | | | | | - Henry D. Herce
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | | | - Konstantin Fackeldey
- Zuse Institute Berlin (ZIB), Berlin 14195, Germany
- Institute of Mathematics, Technical University Berlin, Berlin 10587, Germany
| | - J.J. Patten
- Department of Microbiology, Boston University Medical School, Boston University, Boston, MA 02118, USA
| | | | | | | | - Yurii Moroz
- Chemspace, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Kyiv 01601, Ukraine
| | - Dmytro Radchenko
- Enamine, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Kyiv 01601, Ukraine
| | | | | | - Christian Gruber
- Innophore GmbH, Graz 8010, Austria
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria
| | - Ryan Yust
- Google, Mountain View, CA 94043, USA
| | | | - Anders M. Näär
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Mark N. Namchuk
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Robert A. Davey
- Department of Microbiology, Boston University Medical School, Boston University, Boston, MA 02118, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | | | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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45
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Koff WC, Schenkelberg T, Williams T, Baric RS, McDermott A, Cameron CM, Cameron MJ, Friemann MB, Neumann G, Kawaoka Y, Kelvin AA, Ross TM, Schultz-Cherry S, Mastro TD, Priddy FH, Moore KA, Ostrowsky JT, Osterholm MT, Goudsmit J. Development and deployment of COVID-19 vaccines for those most vulnerable. Sci Transl Med 2021; 13:13/579/eabd1525. [PMID: 33536277 DOI: 10.1126/scitranslmed.abd1525] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 01/15/2021] [Indexed: 12/20/2022]
Abstract
Development of safe and effective COVID-19 vaccines is a global priority and the best hope for ending the COVID-19 pandemic. Remarkably, in less than 1 year, vaccines have been developed and shown to be efficacious and are already being deployed worldwide. Yet, many challenges remain. Immune senescence and comorbidities in aging populations and immune dysregulation in populations living in low-resource settings may impede vaccine effectiveness. Distribution of vaccines among these populations where vaccine access is historically low remains challenging. In this Review, we address these challenges and provide strategies for ensuring that vaccines are developed and deployed for those most vulnerable.
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Affiliation(s)
- Wayne C Koff
- Human Vaccines Project, New York, NY 10119, USA. .,Human Immunomics Initiative, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Theodore Schenkelberg
- Human Vaccines Project, New York, NY 10119, USA.,Human Immunomics Initiative, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Tere Williams
- Department of Pathology, Albert Einstein College of Medicine Bronx, NY 10461, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Adrian McDermott
- Vaccine Immunology Program, Vaccine Research Center, National Institutes of Health, Bethesda, MD 20814, USA
| | - Cheryl M Cameron
- School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Mark J Cameron
- School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Matthew B Friemann
- Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, MD School of Medicine, Baltimore, MD 21201, USA
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA.,Institute of Medical Science, University of Tokyo, Bunkyo City, Tokyo 113-8654, Japan
| | - Alyson A Kelvin
- Departments of Pediatrics, Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Ted M Ross
- Animal Health Research Center, Center for Vaccines, Immunology and Infectious Disease, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Stacey Schultz-Cherry
- Infectious Diseases Research, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | | | - Frances H Priddy
- Vaccine Alliance Aotearoa New Zealand, Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Kristine A Moore
- Center for Infectious Disease Research and Policy (CIDRAP), University of Minnesota, Minneapolis MN 55455, USA
| | - Julia T Ostrowsky
- Center for Infectious Disease Research and Policy (CIDRAP), University of Minnesota, Minneapolis MN 55455, USA
| | - Michael T Osterholm
- Center for Infectious Disease Research and Policy (CIDRAP), University of Minnesota, Minneapolis MN 55455, USA
| | - Jaap Goudsmit
- Human Vaccines Project, New York, NY 10119, USA.,Human Immunomics Initiative, Departments of Epidemiology, Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
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46
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Boras B, Jones RM, Anson BJ, Arenson D, Aschenbrenner L, Bakowski MA, Beutler N, Binder J, Chen E, Eng H, Hammond H, Hammond J, Haupt RE, Hoffman R, Kadar EP, Kania R, Kimoto E, Kirkpatrick MG, Lanyon L, Lendy EK, Lillis JR, Logue J, Luthra SA, Ma C, Mason SW, McGrath ME, Noell S, Obach RS, O'Brien MN, O'Connor R, Ogilvie K, Owen D, Pettersson M, Reese MR, Rogers TF, Rossulek MI, Sathish JG, Shirai N, Steppan C, Ticehurst M, Updyke LW, Weston S, Zhu Y, Wang J, Chatterjee AK, Mesecar AD, Frieman MB, Anderson AS, Allerton C. Discovery of a Novel Inhibitor of Coronavirus 3CL Protease for the Potential Treatment of COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 32935104 DOI: 10.1101/2020.09.12.293498] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
COVID-19 caused by the SARS-CoV-2 virus has become a global pandemic. 3CL protease is a virally encoded protein that is essential across a broad spectrum of coronaviruses with no close human analogs. The designed phosphate prodrug PF-07304814 is metabolized to PF-00835321 which is a potent inhibitor in vitro of the coronavirus family 3CL pro, with selectivity over human host protease targets. Furthermore, PF-00835231 exhibits potent in vitro antiviral activity against SARS-CoV-2 as a single agent and it is additive/synergistic in combination with remdesivir. We present the ADME, safety, in vitro , and in vivo antiviral activity data that supports the clinical evaluation of this compound as a potential COVID-19 treatment.
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47
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Parida PK, Paul D, Chakravorty D. Nature's therapy for COVID-19: Targeting the vital non-structural proteins (NSP) from SARS-CoV-2 with phytochemicals from Indian medicinal plants. PHYTOMEDICINE PLUS : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2021; 1:100002. [PMID: 35403083 PMCID: PMC7691168 DOI: 10.1016/j.phyplu.2020.100002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/06/2020] [Accepted: 11/24/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Containing COVID-19 is still a global challenge. It has affected the "normal" world by targeting its economy and health sector. The effect is shifting of focus of research from life threatening diseases like cancer. Thus, we need to develop a medical solution at the earliest. The purpose of this present work was to understand the efficacy of 22 rationally screened phytochemicals from Indian medicinal plants obtained from our previous work, following drug-likeness properties, against 6 non-structural-proteins (NSP) from SARS-CoV-2. METHODS 100 ns molecular dynamics simulations were performed, and relative binding free energies were computed by MM/PBSA. Further, principal component analysis, dynamic cross correlation and hydrogen bond occupancy were analyzed to characterize protein-ligand interactions. Biological pathway enrichment analysis was also carried out to elucidate the therapeutic targets of the phytochemicals in comparison to SARS-CoV-2. RESULTS The potential binding modes and favourable molecular interaction profile of 9 phytochemicals, majorly from Withania somnifera with lowest free binding energies, against the SARS-CoV-2 NSP targets were identified. It was understood that phytochemicals and 2 repurposed drugs with steroidal moieties in their chemical structures formed stable interactions with the NSPs. Additionally, human target pathway analysis for SARS-CoV-2 and phytochemicals showed that cytokine mediated pathway and phosphorylation pathways were with the most significant p-value. CONCLUSIONS To summarize this work, we suggest a global approach of targeting multiple proteins of SARS-CoV-2 with phytochemicals as a natural alternative therapy for COVID-19. We also suggest that these phytochemicals need to be tested experimentally to confirm their efficacy.
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Key Words
- ACPYPE, AnteChamberPYthon Parser interface
- ATP, Adenosine tri phosphate
- Binding energy
- COVID-19, Corona Virus Disease 2019
- DCCM, Dynamic Cross Correlation Matrix
- GO, Gene Ontology enrichment
- H-bond, Hydrogen Bond
- HIV, Human Immuno Deficiency Virus
- India
- JAK-STAT, The Janus kinase (JAK)-signal transducer and activator of transcription (STAT)
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MAPK, Mitogen-activated protein kinase
- MD, Molecular dynamics
- MM/PBSA, Molecular Mechanics/Poisson–Boltzmann (Generalized Born) surface area
- Molecular dynamics simulation
- NSP, Non Structural Proteins
- PCA, Principal Component Analysis
- PME, Particle-Mesh-Ewald summation
- Pathway enrichment
- Phytochemicals
- RMSD, Root mean square deviation
- RMSF, Root mean square fluctuations
- RNA, Ribonucleic Acid
- RdRp, RNA-dependent RNA polymerase
- Rg, Radius of gyration (Rg)
- SARS-CoV, Severe acute respiratory syndrome/coronavirus
- SARS-CoV-2
- SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2
- vdW, van der Waal's energy.
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Affiliation(s)
| | - Dipak Paul
- Noor Enzymes Private Limited, 37-B, Darga Road, Kolkata 700 017, India
| | - Debamitra Chakravorty
- Novel Techsciences (OPC) Private Limited, 37-B, Darga Road, 1st Floor, Kolkata 700 017, India
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48
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Junior NN, Santos IA, Meireles BA, Nicolau MSP, Lapa IR, Aguiar RS, Jardim ACG, José DP. In silico evaluation of lapachol derivatives binding to the Nsp9 of SARS-CoV-2. J Biomol Struct Dyn 2021; 40:5917-5931. [PMID: 33478342 PMCID: PMC7832454 DOI: 10.1080/07391102.2021.1875050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
SARS-CoV-2 is the etiological agent of COVID-19, which represents a global health emergency that was rapidly declared a pandemic by the World Health Organization. Currently, there is a dearth of effective targeted therapies against viruses. Natural products isolated from traditional herbal plants have had a huge impact on drug development aimed at various diseases. Lapachol is a 1,4- naphthoquinone compound that has been demonstrated to have therapeutic effects against several diseases. SARS-CoV-2 non-structural proteins (nsps) play an important role in the viral replication cycle. Nsp9 seems to play a key role in transcription of the RNA genome of SARS-CoV-2. Virtual screening by docking and molecular dynamics suggests that lapachol derivatives can interact with Nsp9 from SARS-CoV-2. Complexes of lapachol derivatives V, VI, VIII, IX, and XI with the Nsp9 RNA binding site were subjected to molecular dynamics assays, to assess the stability of the complexes via RMSD. All complexes were stable over the course of 100 ns dynamics assays. Analyses of the hydrogen bonds in the complexes showed that lapachol derivatives VI and IX demonstrated strongest binding, with a stable or increasing number of hydrogen bonds over time. Our results demonstrate that Nsp9 from SARS-CoV-2 could be an important target in prospecting for ligands with antiviral potential. In addition, we showed that lapachol derivatives are potential ligands for SARS-CoV-2 Nsp9. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Nilson Nicolau Junior
- Laboratory of Molecular Modeling, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Brazil
| | - Igor Andrade Santos
- Laboratory of Virology, Institute of Biomedical Science, ICBIM, Federal University of Uberlândia, Uberlândia, Brazil
| | - Bruno Amaral Meireles
- Campus Universitário de Iturama, Federal University of Triângulo Mineiro, Iturama, MG, Brazil
| | | | - Igor Rodrigues Lapa
- Campus Universitário de Iturama, Federal University of Triângulo Mineiro, Iturama, MG, Brazil
| | - Renato Santana Aguiar
- Laboratory of Integrative Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Ana Carolina Gomes Jardim
- Laboratory of Virology, Institute of Biomedical Science, ICBIM, Federal University of Uberlândia, Uberlândia, Brazil
| | - Diego Pandeló José
- Campus Universitário de Iturama, Federal University of Triângulo Mineiro, Iturama, MG, Brazil
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49
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Khan MT, Irfan M, Ahsan H, Ahmed A, Kaushik AC, Khan AS, Chinnasamy S, Ali A, Wei DQ. Structures of SARS-CoV-2 RNA-Binding Proteins and Therapeutic Targets. Intervirology 2021; 64:55-68. [PMID: 33454715 PMCID: PMC7900486 DOI: 10.1159/000513686] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/10/2020] [Indexed: 11/19/2022] Open
Abstract
Background The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) epidemic has resulted in thousands of infections and deaths worldwide. Several therapies are currently undergoing clinical trials for the treatment of SARS-CoV-2 infection. However, the development of new drugs and the repositioning of existing drugs can only be achieved after the identification of potential therapeutic targets within structures, as this strategy provides the most precise solution for developing treatments for sudden epidemic infectious diseases. Summary In the current investigation, crystal and cryo-electron microscopy structures encoded by the SARS-CoV-2 genome were systematically examined for the identification of potential drug targets. These structures include nonstructural proteins (Nsp-9; Nsp-12; and Nsp-15), nucleocapsid (N) proteins, and the main protease (Mpro). Key Message The structural information reveals the presence of many potential alternative therapeutic targets, primarily involved in interaction between N protein and Nsp3, forming replication-transcription complexes (RTCs) which might be a potential drug target for effective control of current SARS-CoV-2 pandemic. RTCs consist of 16 nonstructural proteins (Nsp1-16) that play the most essential role in the synthesis of viral RNA. Targeting the physical linkage between the envelope and single-stranded positive RNA, a process facilitated by matrix proteins may provide a good alternative strategy. Our current study provides useful information for the development of new lead compounds against SARS-CoV-2 infections.
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Affiliation(s)
- Muhammad Tahir Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan.,School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Hina Ahsan
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Abrar Ahmed
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | | | - Anwar Sheed Khan
- Department of Microbiology, University of Science and Technology, Kohat, Pakistan
| | - Sathishkumar Chinnasamy
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Arif Ali
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China, .,Peng Cheng Laboratory, Shenzhen, China,
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Francis ME, Richardson B, McNeil M, Rioux M, Foley MK, Ge A, Pechous RD, Kindrachuk J, Cameron CM, Richardson C, Lew J, Cameron MJ, Gerdts V, Falzarano D, Kelvin AA. Male sex and age biases viral burden, viral shedding, and type 1 and 2 interferon responses during SARS-CoV-2 infection in ferrets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.12.426381. [PMID: 33469587 PMCID: PMC7814824 DOI: 10.1101/2021.01.12.426381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) hospitalizations and deaths disportionally affect males and the elderly. Here we investigated the impact of male sex and age by infecting adult male, aged male, and adult female ferrets with SARS-CoV-2. Aged male ferrets had a decrease in temperature which was accompanied by prolonged viral replication with increased pathology in the upper respiratory tract after infection. Transcriptome analysis of the nasal turbinates and lungs indicated that female ferrets had significant increases in interferon response genes (OASL, MX1, ISG15, etc.) on day 2 post infection which was delayed in aged males. In addition, genes associated with taste and smell such as RTP1, CHGA, and CHGA1 at later time points were upregulated in males but not in females. These results provide insight into COVID-19 and suggests that older males may play a role in viral transmission due to decreased antiviral responses.
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Affiliation(s)
- Magen E. Francis
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Vaccine and Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
| | - Brian Richardson
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA44106
| | - Mara McNeil
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Melissa Rioux
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Mary K. Foley
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Anni Ge
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Roger D. Pechous
- University of Arkansas for Medical Sciences, Department of Microbiology and Immunology, Little Rock, AK, USA
| | - Jason Kindrachuk
- Vaccine and Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
- Laboratory of Emerging and Re-Emerging Viruses, Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Cheryl M. Cameron
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - Christopher Richardson
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Jocelyne Lew
- Vaccine and Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
| | - Mark J. Cameron
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA44106
| | - Volker Gerdts
- Vaccine and Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Alyson A. Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Vaccine and Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
- Department of Pediatrics, Division of Infectious Disease, Faculty of Medicine, Dalhousie University, Halifax, NS B3K 6R8, Canada
- Canadian Centre for Vaccinology, IWK Health Centre, Halifax, NS B3K 6R8, Canada
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