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Ujike M, Suzuki T. Progress of research on coronaviruses and toroviruses in large domestic animals using reverse genetics systems. Vet J 2024; 305:106122. [PMID: 38641200 DOI: 10.1016/j.tvjl.2024.106122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/24/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
Abstract
The generation of genetically engineered recombinant viruses from modified DNA/RNA is commonly referred to as reverse genetics, which allows the introduction of desired mutations into the viral genome. Reverse genetics systems (RGSs) are powerful tools for studying fundamental viral processes, mechanisms of infection, pathogenesis and vaccine development. However, establishing RGS for coronaviruses (CoVs) and toroviruses (ToVs), which have the largest genomes among vertebrate RNA viruses, is laborious and hampered by technical constraints. Hence, little research has focused on animal CoVs and ToVs using RGSs, especially in large domestic animals such as pigs and cattle. In the last decade, however, studies of porcine CoVs and bovine ToVs using RGSs have been reported. In addition, the coronavirus disease-2019 pandemic has prompted the development of new and simple CoV RGSs, which will accelerate RGS-based research on animal CoVs and ToVs. In this review, we summarise the general characteristics of CoVs and ToVs, the RGSs available for CoVs and ToVs and the progress made in the last decade in RGS-based research on porcine CoVs and bovine ToVs.
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Affiliation(s)
- Makoto Ujike
- Laboratory of Veterinary Infectious Diseases, Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan; Research Center for Animal Life Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan.
| | - Tohru Suzuki
- Division of Zoonosis Research, Sapporo Research Station, National Institute of Animal Health, NARO, Sapporo, Hokkaido 062-0045, Japan
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2
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Martiáñez-Vendrell X, Bloeme-ter Horst J, Hutchinson R, Guy C, Bowie AG, Kikkert M. Human Coronavirus 229E Infection Inactivates Pyroptosis Executioner Gasdermin D but Ultimately Leads to Lytic Cell Death Partly Mediated by Gasdermin E. Viruses 2024; 16:898. [PMID: 38932190 PMCID: PMC11209299 DOI: 10.3390/v16060898] [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: 03/29/2024] [Revised: 05/15/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Human coronavirus 229E (HCoV-229E) is associated with upper respiratory tract infections and generally causes mild respiratory symptoms. HCoV-229E infection can cause cell death, but the molecular pathways that lead to virus-induced cell death as well as the interplay between viral proteins and cellular cell death effectors remain poorly characterized for HCoV-229E. Studying how HCoV-229E and other common cold coronaviruses interact with and affect cell death pathways may help to understand its pathogenesis and compare it to that of highly pathogenic coronaviruses. Here, we report that the main protease (Mpro) of HCoV-229E can cleave gasdermin D (GSDMD) at two different sites (Q29 and Q193) within its active N-terminal domain to generate fragments that are now unable to cause pyroptosis, a form of lytic cell death normally executed by this protein. Despite GSDMD cleavage by HCoV-229E Mpro, we show that HCoV-229E infection still leads to lytic cell death. We demonstrate that during virus infection caspase-3 cleaves and activates gasdermin E (GSDME), another key executioner of pyroptosis. Accordingly, GSDME knockout cells show a significant decrease in lytic cell death upon virus infection. Finally, we show that HCoV-229E infection leads to increased lytic cell death levels in cells expressing a GSDMD mutant uncleavable by Mpro (GSDMD Q29A+Q193A). We conclude that GSDMD is inactivated by Mpro during HCoV-229E infection, preventing GSDMD-mediated cell death, and point to the caspase-3/GSDME axis as an important player in the execution of virus-induced cell death. In the context of similar reported findings for highly pathogenic coronaviruses, our results suggest that these mechanisms do not contribute to differences in pathogenicity among coronaviruses. Nonetheless, understanding the interactions of common cold-associated coronaviruses and their proteins with the programmed cell death machineries may lead to new clues for coronavirus control strategies.
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Affiliation(s)
- Xavier Martiáñez-Vendrell
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (X.M.-V.)
| | - Jonna Bloeme-ter Horst
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (X.M.-V.)
| | - Roy Hutchinson
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (X.M.-V.)
| | - Coralie Guy
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin 2, Ireland (A.G.B.)
| | - Andrew G. Bowie
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin 2, Ireland (A.G.B.)
| | - Marjolein Kikkert
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin 2, Ireland (A.G.B.)
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3
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Park JY, Lee HM, Jun SH, Kamitani W, Kim O, Shin HJ. Insights into the Pathogenesis and Development of Recombinant Japanese Encephalitis Virus Genotype 3 as a Vaccine. Vaccines (Basel) 2024; 12:597. [PMID: 38932326 PMCID: PMC11209496 DOI: 10.3390/vaccines12060597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Japanese encephalitis virus (JEV), a flavivirus transmitted by mosquitoes, has caused epidemics and severe neurological diseases in Asian countries. In this study, we developed a cDNA infectious clone, pBAC JYJEV3, of the JEV genotype 3 strain (EF571853.1) using a bacterial artificial chromosome (BAC) vector. The constructed infectious clone was transfected into Vero cells, where it exhibited infectivity and induced cytopathic effects akin to those of the parent virus. Confocal microscopy confirmed the expression of the JEV envelope protein. Comparative analysis of growth kinetics revealed similar replication dynamics between the parental and recombinant viruses, with peak titers observed 72 h post-infection (hpi). Furthermore, plaque assays demonstrated comparable plaque sizes and morphologies between the viruses. Cryo-electron microscopy confirmed the production of recombinant virus particles with a morphology identical to that of the parent virus. Immunization studies in mice using inactivated parental and recombinant viruses revealed robust IgG responses, with neutralizing antibody production increasing over time. These results showcase the successful generation and characterization of a recombinant JEV3 virus and provide a platform for further investigations into JEV pathogenesis and vaccine development.
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Affiliation(s)
- Jae-Yeon Park
- College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.P.); (H.-M.L.); (O.K.)
| | - Hye-Mi Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.P.); (H.-M.L.); (O.K.)
| | - Sung-Hoon Jun
- Electron Microscopy & Spectroscopy Team, Korea Basic Science Institute, Cheongju 28119, Republic of Korea;
| | - Wataru Kamitani
- Department of Infectious Diseases and Host Defense, Gunma University Graduate School of Medicine, Maebashi 371-0034, Japan;
| | - Onnuri Kim
- College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.P.); (H.-M.L.); (O.K.)
| | - Hyun-Jin Shin
- College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.P.); (H.-M.L.); (O.K.)
- Research Institute of Veterinary Medicine, Chungnam National University, Daejeon 34134, Republic of Korea
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4
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Khan S, Uddin I, Khan M, Iqbal N, Alshanbari HM, Ahmad B, Khan DM. Sequence based model using deep neural network and hybrid features for identification of 5-hydroxymethylcytosine modification. Sci Rep 2024; 14:9116. [PMID: 38643305 DOI: 10.1038/s41598-024-59777-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/15/2024] [Indexed: 04/22/2024] Open
Abstract
RNA modifications are pivotal in the development of newly synthesized structures, showcasing a vast array of alterations across various RNA classes. Among these, 5-hydroxymethylcytosine (5HMC) stands out, playing a crucial role in gene regulation and epigenetic changes, yet its detection through conventional methods proves cumbersome and costly. To address this, we propose Deep5HMC, a robust learning model leveraging machine learning algorithms and discriminative feature extraction techniques for accurate 5HMC sample identification. Our approach integrates seven feature extraction methods and various machine learning algorithms, including Random Forest, Naive Bayes, Decision Tree, and Support Vector Machine. Through K-fold cross-validation, our model achieved a notable 84.07% accuracy rate, surpassing previous models by 7.59%, signifying its potential in early cancer and cardiovascular disease diagnosis. This study underscores the promise of Deep5HMC in offering insights for improved medical assessment and treatment protocols, marking a significant advancement in RNA modification analysis.
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Affiliation(s)
- Salman Khan
- Department of Computer Science, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Islam Uddin
- Department of Computer Science, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Mukhtaj Khan
- Department of Information Technology, The University of Haripur, Haripur, Pakistan
| | - Nadeem Iqbal
- Department of Computer Science, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Huda M Alshanbari
- Department of Mathematical Sciences, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, 11671, Riyadh, Saudi Arabia
| | - Bakhtiyar Ahmad
- Higher Education Department Afghanistan, Kabul, Afghanistan.
| | - Dost Muhammad Khan
- Department of Statistics, Abdul Wali Khan University Mardan, Mardan, 23200, KP, Pakistan
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5
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Schmied K, Ehmann R, Kristen-Burmann C, Ebert N, Barut GT, Almeida L, Kelly JN, Thomann L, Stalder H, Lang R, Tekes G, Thiel V. An RNA replicon system to investigate promising inhibitors of feline coronavirus. J Virol 2024; 98:e0121623. [PMID: 38236006 PMCID: PMC10878086 DOI: 10.1128/jvi.01216-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024] Open
Abstract
Feline infectious peritonitis (FIP) is a fatal feline disease, caused by a feline coronavirus (FCoV), namely feline infectious peritonitis virus (FIPV). We produced a baby hamster kidney 21 (BHK) cell line expressing a serotype I FCoV replicon RNA with a green fluorescent protein (GFP) reporter gene (BHK-F-Rep) and used it as an in vitro screening system to test different antiviral compounds. Two inhibitors of the FCoV main protease (Mpro), namely GC376 and Nirmatrelvir, as well as the nucleoside analog Remdesivir proved to be effective in inhibiting the replicon system. Different combinations of these compounds also proved to be potent inhibitors, having an additive effect when combined. Remdesivir, GC376, and Nirmatrelvir all have a 50% cytotoxic concentration (CC50) more than 200 times higher than their half-maximal inhibitory concentrations (IC50), making them important candidates for future in vivo studies as well as clinically implemented drug candidates. In addition, results were acquired with a virus infection system, where Felis catus whole fetus 4 (Fcwf-4) cells were infected with a previously described recombinant GFP-expressing FIPV (based on the laboratory-adapted serotype I FIPV strain Black) and treated with the most promising compounds. Results acquired with the replicon system were comparable to the results acquired with the virus infection system, demonstrating that we successfully implemented the FCoV replicon system for antiviral screening. We expect that this system will greatly facilitate future screens for anti-FIPV compounds and provide a non-infectious system to study and evaluate drug-resistant mutations that may emerge in the FIPV genome.IMPORTANCEFIPV is of great significance in the cat population around the world, causing 0.3%-1.4% of feline deaths in veterinary practices (2). As there are neither effective preventive measures nor approved treatment options available, there is an urgent need to identify antiviral drugs against FIPV. Our FCoV replicon system provides a valuable tool for drug discovery in vitro. Due to the lack of cell culture systems for serotype I FCoVs (the serotype most prevalent in the feline population) (2), a different system is needed to study these viruses. A viral replicon system is a valuable tool for studying FCoVs. Overall, our results demonstrate the utility of the serotype I feline coronavirus replicon system for antiviral screening as well as to study this virus in general. We propose several compounds representing promising candidates for future clinical trials and ultimately with the potential to save cats suffering from FIP.
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Affiliation(s)
- Kimberly Schmied
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Rosina Ehmann
- Institute of Virology, Justus Liebig University Giessen, Giessen, Germany
| | | | - Nadine Ebert
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Güliz Tuba Barut
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lea Almeida
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna N. Kelly
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases (MCID), University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center (EVBC), Jena, Germany
| | - Lisa Thomann
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Hanspeter Stalder
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Reto Lang
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Gergely Tekes
- Institute of Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases (MCID), University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center (EVBC), Jena, Germany
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6
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Kipfer ET, Hauser D, Lett MJ, Otte F, Urda L, Zhang Y, Lang CMR, Chami M, Mittelholzer C, Klimkait T. Rapid cloning-free mutagenesis of new SARS-CoV-2 variants using a novel reverse genetics platform. eLife 2023; 12:RP89035. [PMID: 37988285 PMCID: PMC10662946 DOI: 10.7554/elife.89035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Reverse genetic systems enable the engineering of RNA virus genomes and are instrumental in studying RNA virus biology. With the recent outbreak of the coronavirus disease 2019 pandemic, already established methods were challenged by the large genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein we present an elaborated strategy for the rapid and straightforward rescue of recombinant plus-stranded RNA viruses with high sequence fidelity using the example of SARS-CoV-2. The strategy called CLEVER (CLoning-free and Exchangeable system for Virus Engineering and Rescue) is based on the intracellular recombination of transfected overlapping DNA fragments allowing the direct mutagenesis within the initial PCR-amplification step. Furthermore, by introducing a linker fragment - harboring all heterologous sequences - viral RNA can directly serve as a template for manipulating and rescuing recombinant mutant virus, without any cloning step. Overall, this strategy will facilitate recombinant SARS-CoV-2 rescue and accelerate its manipulation. Using our protocol, newly emerging variants can quickly be engineered to further elucidate their biology. To demonstrate its potential as a reverse genetics platform for plus-stranded RNA viruses, the protocol has been successfully applied for the cloning-free rescue of recombinant Chikungunya and Dengue virus.
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Affiliation(s)
- Enja Tatjana Kipfer
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - David Hauser
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Martin J Lett
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Fabian Otte
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Lorena Urda
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Yuepeng Zhang
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Christopher MR Lang
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Mohamed Chami
- BioEM Lab, Biozentrum, University of Basel, MattenstrasseBaselSwitzerland
| | | | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
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7
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Benčić P, Keppler M, Kuge M, Qiu D, Schütte LM, Häner M, Strack K, Jessen HJ, Andexer JN, Loenarz C. Non-canonical nucleosides: Biomimetic triphosphorylation, incorporation into mRNA and effects on translation and structure. FEBS J 2023; 290:4899-4920. [PMID: 37329249 DOI: 10.1111/febs.16889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/24/2023] [Accepted: 06/14/2023] [Indexed: 06/18/2023]
Abstract
Recent advances in mRNA therapeutics demand efficient toolkits for the incorporation of nucleoside analogues into mRNA suitable for downstream applications. Herein, we report the application of a versatile enzyme cascade for the triphosphorylation of a broad range of nucleoside analogues, including unprotected nucleobases containing chemically labile moieties. Our biomimetic system was suitable for the preparation of nucleoside triphosphates containing adenosine, cytidine, guanosine, uridine and non-canonical core structures, as determined by capillary electrophoresis coupled to mass spectrometry. This enabled us to establish an efficient workflow for transcribing and purifying functional mRNA containing these nucleoside analogues, combined with mass spectrometric verification of analogue incorporation. Our combined methodology allows for analyses of how incorporation of nucleoside analogues that are commercially unavailable as triphosphates affect mRNA properties: The translational fidelity of the produced mRNA was demonstrated in analyses of how incorporated adenosine analogues impact translational recoding. For the SARS-CoV-2 frameshifting site, analyses of the mRNA pseudoknot structure using circular dichroism spectroscopy allowed insight into how the pharmacologically active 7-deazaadenosine destabilises RNA secondary structure, consistent with observed changes in recoding efficiency.
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Affiliation(s)
- Patricia Benčić
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
| | - Michael Keppler
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
| | - Marco Kuge
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
| | - Danye Qiu
- Institute of Organic Chemistry, University of Freiburg, Germany
| | - Lena M Schütte
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
| | - Markus Häner
- Institute of Organic Chemistry, University of Freiburg, Germany
| | - Katharina Strack
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
| | | | | | - Christoph Loenarz
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
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8
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Gilbertson B, Subbarao K. What Have We Learned by Resurrecting the 1918 Influenza Virus? Annu Rev Virol 2023; 10:25-47. [PMID: 37774132 DOI: 10.1146/annurev-virology-111821-104408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
The 1918 Spanish influenza pandemic was one of the deadliest infectious disease events in recorded history, resulting in approximately 50-100 million deaths worldwide. The origins of the 1918 virus and the molecular basis for its exceptional virulence remained a mystery for much of the 20th century because the pandemic predated virologic techniques to isolate, passage, and store influenza viruses. In the late 1990s, overlapping fragments of influenza viral RNA preserved in the tissues of several 1918 victims were amplified and sequenced. The use of influenza reverse genetics then permitted scientists to reconstruct the 1918 virus entirely from cloned complementary DNA, leading to new insights into the origin of the virus and its pathogenicity. Here, we discuss some of the advances made by resurrection of the 1918 virus, including the rise of innovative molecular research, which is a topic in the dual use debate.
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Affiliation(s)
- Brad Gilbertson
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia;
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9
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Kipfer E, Hauser D, Lett MJ, Otte F, Urda L, Zhang Y, Lang CMR, Chami M, Mittelholzer C, Klimkait T. Rapid cloning-free mutagenesis of new SARS-CoV-2 variants using a novel reverse genetics platform. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540343. [PMID: 37292682 PMCID: PMC10245781 DOI: 10.1101/2023.05.11.540343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Reverse genetic systems enable the engineering of RNA virus genomes and are instrumental in studying RNA virus biology. With the recent outbreak of the COVID-19 pandemic, already established methods were challenged by the large genome of SARS-CoV-2. Herein we present an elaborated strategy for the rapid and straightforward rescue of recombinant plus-stranded RNA viruses with high sequence fidelity, using the example of SARS-CoV-2. The strategy called CLEVER (CLoning-free and Exchangeable system for Virus Engineering and Rescue) is based on the intracellular recombination of transfected overlapping DNA fragments allowing the direct mutagenesis within the initial PCR-amplification step. Furthermore, by introducing a linker fragment - harboring all heterologous sequences - viral RNA can directly serve as a template for manipulating and rescuing recombinant mutant virus, without any cloning step. Overall, this strategy will facilitate recombinant SARS-CoV-2 rescue and accelerate its manipulation. Using our protocol, newly emerging variants can quickly be engineered to further elucidate their biology. To demonstrate its potential as a reverse genetics platform for plus-stranded RNA viruses, the protocol has been successfully applied for the cloning-free rescue of recombinant Chikungunya and Dengue virus.
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Affiliation(s)
- Enja Kipfer
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - David Hauser
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Martin J. Lett
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Fabian Otte
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Lorena Urda
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Yuepeng Zhang
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Christopher M. R. Lang
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Mohamed Chami
- BioEM Lab, Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Christian Mittelholzer
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
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10
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Mueller S. Recombination between coronaviruses and synthetic RNAs and biorisk implications motivated by a SARS-CoV-2 FCS origin controversy. Front Bioeng Biotechnol 2023; 11:1209054. [PMID: 37600318 PMCID: PMC10436746 DOI: 10.3389/fbioe.2023.1209054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/12/2023] [Indexed: 08/22/2023] Open
Abstract
The urgent need for improved policy, regulation, and oversight of research with potential pandemic pathogens (PPPs) has been widely acknowledged. A 2022 article in Frontiers in Virology raises questions, reporting on a 100% sequence homology between the SARS-CoV-2 furin cleavage site (FCS) and the negative strand of a 2017 patented sequence. Even though Ambati and collaborators suspect a possible inadvertent or intentional cause leading to the FCS insert, the related underpinnings have not been studied from the perspective of potential biorisk policy gaps. A commentary on their article contests the low coincidence likelihood that was calculated by Ambati et al., arguing that the sequence match could have been a chance occurrence alone. Additionally, it has been suggested that the odds of the recombination event may be low. These considerations seem to have put many speculations related to any implied viral beginnings, notably from a research setting likely outside the Wuhan Institute of Virology, to rest. However, potential implications for future disasters in terms of biosafety and biosecurity have not been addressed. To demonstrate the feasibility of the Ambati et al. postulate, a theoretical framework is developed that substantially extends the research orientations implicated by these authors and the related patent. It is argued that specific experimental conditions, in combination, could significantly increase the implied recombination profile between coronaviruses and synthetic RNAs. Consequently, this article scrutinizes these largely unrecognized vulnerabilities to discuss implications across the spectrum of the biological risk landscape, with special attention to a potential "crime harvest." Focusing on insufficiently understood features of interaction between the natural and man-made world, vulnerabilities related to contaminants, camouflaging, and various misuse potentials fostered by the digitization and computerization of synthetic biology, it highlights novel biorisk gaps not covered by existing PPP policy. Even though this work does not aim to provide proof of the viral origin, it will make the point that, in theory, a convergence of under-appreciated lab experiments and technologies could have led to the SARS-CoV-2 FCS insert, which analogously could be exploited by various threat actors for the clandestine genesis of similar or even worse pathogens.
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Affiliation(s)
- Siguna Mueller
- Independent Transdisciplinary Researcher, Kaernten, Austria
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11
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Kang DD, Li H, Dong Y. Advancements of in vitro transcribed mRNA (IVT mRNA) to enable translation into the clinics. Adv Drug Deliv Rev 2023; 199:114961. [PMID: 37321375 PMCID: PMC10264168 DOI: 10.1016/j.addr.2023.114961] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023]
Abstract
The accelerated progress and approval of two mRNA-based vaccines to address the SARS-CoV-2 virus were unprecedented. This record-setting feat was made possible through the solid foundation of research on in vitro transcribed mRNA (IVT mRNA) which could be utilized as a therapeutic modality. Through decades of thorough research to overcome barriers to implementation, mRNA-based vaccines or therapeutics offer many advantages to rapidly address a broad range of applications including infectious diseases, cancers, and gene editing. Here, we describe the advances that have supported the adoption of IVT mRNA in the clinics, including optimization of the IVT mRNA structural components, synthesis, and lastly concluding with different classes of IVT RNA. Continuing interest in driving IVT mRNA technology will enable a safer and more efficacious therapeutic modality to address emerging and existing diseases.
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Affiliation(s)
- Diana D Kang
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Haoyuan Li
- Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Yizhou Dong
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Department of Biomedical Engineering, The Center for Clinical and Translational Science, The Comprehensive Cancer Center; Dorothy M. Davis Heart & Lung Research Institute, Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, United States; Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
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12
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Marzaman ANF, Roska TP, Sartini S, Utami RN, Sulistiawati S, Enggi CK, Manggau MA, Rahman L, Shastri VP, Permana AD. Recent Advances in Pharmaceutical Approaches of Antimicrobial Agents for Selective Delivery in Various Administration Routes. Antibiotics (Basel) 2023; 12:antibiotics12050822. [PMID: 37237725 DOI: 10.3390/antibiotics12050822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/15/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Globally, the increase of pathogenic bacteria with antibiotic-resistant characteristics has become a critical challenge in medical treatment. The misuse of conventional antibiotics to treat an infectious disease often results in increased resistance and a scarcity of effective antimicrobials to be used in the future against the organisms. Here, we discuss the rise of antimicrobial resistance (AMR) and the need to combat it through the discovery of new synthetic or naturally occurring antibacterial compounds, as well as insights into the application of various drug delivery approaches delivered via various routes compared to conventional delivery systems. AMR-related infectious diseases are also discussed, as is the efficiency of various delivery systems. Future considerations in developing highly effective antimicrobial delivery devices to address antibiotic resistance are also presented here, especially on the smart delivery system of antibiotics.
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Affiliation(s)
| | - Tri Puspita Roska
- Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
| | - Sartini Sartini
- Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
| | - Rifka Nurul Utami
- Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
| | | | | | | | - Latifah Rahman
- Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
| | - Venkatram Prasad Shastri
- Institute for Macromolecular Chemistry, Albert Ludwigs Universitat Freiburg, 79085 Freiburg, Germany
| | - Andi Dian Permana
- Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
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13
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Radzikowska U, Eljaszewicz A, Tan G, Stocker N, Heider A, Westermann P, Steiner S, Dreher A, Wawrzyniak P, Rückert B, Rodriguez-Coira J, Zhakparov D, Huang M, Jakiela B, Sanak M, Moniuszko M, O'Mahony L, Jutel M, Kebadze T, Jackson JD, Edwards RM, Thiel V, Johnston LS, Akdis AC, Sokolowska M. Rhinovirus-induced epithelial RIG-I inflammasome suppresses antiviral immunity and promotes inflammation in asthma and COVID-19. Nat Commun 2023; 14:2329. [PMID: 37087523 PMCID: PMC10122208 DOI: 10.1038/s41467-023-37470-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/16/2023] [Indexed: 04/24/2023] Open
Abstract
Rhinoviruses and allergens, such as house dust mite are major agents responsible for asthma exacerbations. The influence of pre-existing airway inflammation on the infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is largely unknown. We analyse mechanisms of response to viral infection in experimental in vivo rhinovirus infection in healthy controls and patients with asthma, and in in vitro experiments with house dust mite, rhinovirus and SARS-CoV-2 in human primary airway epithelium. Here, we show that rhinovirus infection in patients with asthma leads to an excessive RIG-I inflammasome activation, which diminishes its accessibility for type I/III interferon responses, leading to their early functional impairment, delayed resolution, prolonged viral clearance and unresolved inflammation in vitro and in vivo. Pre-exposure to house dust mite augments this phenomenon by inflammasome priming and auxiliary inhibition of early type I/III interferon responses. Prior infection with rhinovirus followed by SARS-CoV-2 infection augments RIG-I inflammasome activation and epithelial inflammation. Timely inhibition of the epithelial RIG-I inflammasome may lead to more efficient viral clearance and lower the burden of rhinovirus and SARS-CoV-2 infections.
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Affiliation(s)
- Urszula Radzikowska
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
- Christine Kühne - Center for Allergy Research and Education (CK-CARE), Herman-Burchard-Strasse 1, 7265, Davos Wolfgang, Switzerland
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Waszyngtona 13 Str., 15-269, Bialystok, Poland
| | - Andrzej Eljaszewicz
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
- Christine Kühne - Center for Allergy Research and Education (CK-CARE), Herman-Burchard-Strasse 1, 7265, Davos Wolfgang, Switzerland
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Waszyngtona 13 Str., 15-269, Bialystok, Poland
| | - Ge Tan
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Nino Stocker
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
| | - Anja Heider
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
| | - Patrick Westermann
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
| | - Silvio Steiner
- Institute of Virology and Immunology (IVI), Laenggassstrasse 122, 3012, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, 3012, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland
| | - Anita Dreher
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
- Christine Kühne - Center for Allergy Research and Education (CK-CARE), Herman-Burchard-Strasse 1, 7265, Davos Wolfgang, Switzerland
| | - Paulina Wawrzyniak
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
- Christine Kühne - Center for Allergy Research and Education (CK-CARE), Herman-Burchard-Strasse 1, 7265, Davos Wolfgang, Switzerland
- Division of Clinical Chemistry and Biochemistry, University Children's Hospital Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
- Children's Research Center, University Children's Hospital Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Beate Rückert
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
| | - Juan Rodriguez-Coira
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
- IMMA, Department of Basic Medical Sciences, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities Madrid, C. de Julian Romea 23, 28003, Madrid, Spain
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities Madrid, Urb. Monteprincipe 28925, Alcorcon, Madrid, Spain
| | - Damir Zhakparov
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
| | - Mengting Huang
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
| | - Bogdan Jakiela
- Department of Internal Medicine, Jagiellonian University Medical College, M. Skawinska 8 Str., 31-066, Krakow, Poland
| | - Marek Sanak
- Department of Internal Medicine, Jagiellonian University Medical College, M. Skawinska 8 Str., 31-066, Krakow, Poland
| | - Marcin Moniuszko
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Waszyngtona 13 Str., 15-269, Bialystok, Poland
- Department of Allergology and Internal Medicine, Medical University of Bialystok, M. Sklodowskiej-Curie 24A Str., 15-276, Bialystok, Poland
| | - Liam O'Mahony
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
- Department of Medicine and School of Microbiology, APC Microbiome Ireland, University College Cork, College Rd, T12 E138, Cork, Ireland
| | - Marek Jutel
- Department of Clinical Immunology, Wroclaw Medical University, wyb. Lidwika Pasteura 1 Str, 50-367, Wroclaw, Poland
- ALL-MED Medical Research Institute, Gen. Jozefa Hallera 95 Str., 53-201, Wroclaw, Poland
| | - Tatiana Kebadze
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Cale Street, London, SW3 6LY, UK
- Department of Infectious Diseases, Imperial College London, School of Medicine, St Mary's Hospital, Praed Street, London, W21NY, UK
| | - J David Jackson
- Guy's Severe Asthma Centre, School of Immunology & Microbial Sciences, King's College London, Strand, London, WC2R 2LS, UK
- Guy's & St Thomas' NHS Trust, St Thomas' Hospital, Westminster Bridge Rd, London, SE1 7EH, UK
| | - R Michael Edwards
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Cale Street, London, SW3 6LY, UK
- Asthma UK Centre in Allergic Mechanisms of Asthma, Norfolk Place, London, W2 1PG, UK
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Laenggassstrasse 122, 3012, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Hallerstrasse 6, 3012, Bern, Switzerland
| | - L Sebastian Johnston
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Cale Street, London, SW3 6LY, UK
- Asthma UK Centre in Allergic Mechanisms of Asthma, Norfolk Place, London, W2 1PG, UK
- Imperial College Healthcare HNS Trust, The Bays, S Wharf Rd, London, W2 1NY, UK
| | - A Cezmi Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
- Christine Kühne - Center for Allergy Research and Education (CK-CARE), Herman-Burchard-Strasse 1, 7265, Davos Wolfgang, Switzerland
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland.
- Christine Kühne - Center for Allergy Research and Education (CK-CARE), Herman-Burchard-Strasse 1, 7265, Davos Wolfgang, Switzerland.
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14
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Whittle L, Chapman R, Douglass N, Jaffer M, Margolin E, Rybicki E, Williamson AL. Development of a dual vaccine against East Coast fever and lumpy skin disease. Front Immunol 2023; 14:1143034. [PMID: 37063887 PMCID: PMC10098110 DOI: 10.3389/fimmu.2023.1143034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/21/2023] [Indexed: 03/31/2023] Open
Abstract
East Coast fever is an acute bovine disease caused by the apicomplexan parasite Theileria parva and is regarded as one of the most important tick-vectored diseases in Africa. The current vaccination procedure has many drawbacks, as it involves the use of live T. parva sporozoites. As a novel vaccination strategy, we have constructed the recombinant lumpy skin disease virus (LSDV) named LSDV-SODis-p67HA-BLV-Gag, encoding a modified form of the T. parva p67 surface antigen (p67HA), as well as the bovine leukemia virus (BLV) gag gene for the formation of virus-like particles (VLPs) to potentially enhance p67 immunogenicity. In place of the native sequence, the chimeric p67HA antigen has the human tissue plasminogen activator signal sequence and the influenza hemagglutinin A2 transmembrane domain and cytoplasmic tail. p67HA was detected on the surface of infected cells, and VLPs comprising BLV Gag and p67HA were produced. We also show that higher multiple bands observed in western blot analysis are due to glycosylation of p67. The two vaccines, pMExT-p67HA (DNA) and LSDV-SODis-p67HA-BLV-Gag, were tested for immunogenicity in mice. p67-binding antibodies were produced by vaccinated animals, with higher titers detected in mice vaccinated with the recombinant LSDV. This candidate dual vaccine warrants further testing in cattle.
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Affiliation(s)
- Leah Whittle
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ros Chapman
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- *Correspondence: Ros Chapman,
| | - Nicola Douglass
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mohamed Jaffer
- Electron Microscope Unit, University of Cape Town, Cape Town, South Africa
| | - Emmanuel Margolin
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
| | - Edward Rybicki
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
| | - Anna-Lise Williamson
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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15
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Lumpy Skin Disease—An Emerging Cattle Disease in Europe and Asia. Vaccines (Basel) 2023; 11:vaccines11030578. [PMID: 36992162 DOI: 10.3390/vaccines11030578] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
Lumpy skin disease virus (LSDV) is a member of the Capripoxvirus genus, mainly infecting cattle and buffalo, which until relatively recently was only endemic in parts of Africa and then spread to the Middle East and lately Europe and Asia. Lumpy skin disease (LSD) is a notifiable disease with a serious impact on the beef industry as it causes mortality of up to 10% and has impacts on milk and meat production, as well as fertility. The close serological relationship between LSDV, goat poxvirus (GTPV) and sheep poxvirus (SPPV) has led to live attenuated GTPV and SPPV vaccines being used to protect against LSD in some countries. There is evidence that the SPPV vaccine does not protect from LSD as well as the GTPV and LSDV vaccines. One of the LSD vaccines used in Eastern Europe was found to be a combination of different Capripoxviruses, and a series of recombination events in the manufacturing process resulted in cattle being vaccinated with a range of recombinant LSDVs resulting in virulent LSDV which spread throughout Asia. It is likely that LSD will become endemic throughout Asia as it will be very challenging to control the spread of the virus without widespread vaccination.
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16
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Fuertes MA, Alonso C. New Short RNA Motifs Potentially Relevant in the SARS-CoV-2 Genome. Curr Genomics 2023; 23:424-440. [PMID: 37920558 PMCID: PMC10173420 DOI: 10.2174/1389202924666230202152351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 01/16/2023] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Background The coronavirus disease has led to an exhaustive exploration of the SARS-CoV-2 genome. Despite the amount of information accumulated, the prediction of short RNA motifs encoding peptides mediating protein-protein or protein-drug interactions has received limited attention. Objective The study aims to predict short RNA motifs that are interspersed in the SARS-CoV-2 genome. Methods A method in which 14 trinucleotide families, each characterized by being composed of triplets with identical nucleotides in all possible configurations, was used to find short peptides with biological relevance. The novelty of the approach lies in using these families to search how they are distributed across genomes of different CoV genera and then to compare the distributions of these families with each other. Results We identified distributions of trinucleotide families in different CoV genera and also how they are related, using a selection criterion that identified short RNA motifs. The motifs were reported to be conserved in SARS-CoVs; in the remaining CoV genomes analysed, motifs contained, exclusively, different configurations of the trinucleotides A, T, G and A, C, G. Eighty-eight short RNA motifs, ranging in length from 12 to 49 nucleotides, were found: 50 motifs in the 1a polyprotein-encoding orf, 27 in the 1b polyprotein-encoding orf, 5 in the spike-encoding orf, and 6 in the nucleocapsid-encoding orf. Although some motifs (~27%) were found to be intercalated or attached to functional peptides, most of them have not yet been associated with any known functions. Conclusion Some of the trinucleotide family distributions in different CoV genera are not random; they are present in short peptides that, in many cases, are intercalated or attached to functional sites of the proteome.
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Affiliation(s)
- Miguel Angel Fuertes
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, Madrid, 28049, Spain
| | - Carlos Alonso
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, Madrid, 28049, Spain
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17
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Zhang Q, Zhu S, Zhang X, Su L, Ni J, Zhang Y, Fang L. Recent insights into reverse genetics of norovirus. Virus Res 2023; 325:199046. [PMID: 36657615 DOI: 10.1016/j.virusres.2023.199046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 12/23/2022] [Accepted: 01/15/2023] [Indexed: 01/18/2023]
Abstract
Norovirus is the leading cause of viral gastroenteritis globally, and poses substantial threats to public health. Despite substantial progress made in preventing norovirus diseases, the lack of a robust virus culture system has hampered biological research and effective strategies to combat this pathogen. Reverse genetic system is the technique to generate infectious viruses from cloned genetic constructs, which is a powerful tool for the investigation of viral pathogenesis and for the development of novel drugs and vaccines. The strategies of reverse genetics include bacterial artificial chromosomes, vaccinia virus vectors, and entirely plasmid-based systems. Since each strategy has its pros and cons, choosing appropriate approaches will greatly improve the efficiency of virus rescue. Reverse genetic systems that have been employed for norovirus greatly extend its life cycle and facilitate the development of medical countermeasures. In this review, we summarize the current knowledge on the structure, transmission, genetic evolution and clinical manifestations of norovirus, and describe recent advances in the studies of norovirus reverse genetics as well as its future prospects for therapeutics and vaccine development.
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Affiliation(s)
- Qinyi Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, China; Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Shuirong Zhu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | | | - Lingxuan Su
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jun Ni
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yanjun Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China.
| | - Lei Fang
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China.
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18
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Kurhade C, Xie X, Shi PY. Reverse genetic systems of SARS-CoV-2 for antiviral research. Antiviral Res 2023; 210:105486. [PMID: 36657881 PMCID: PMC9776485 DOI: 10.1016/j.antiviral.2022.105486] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
Reverse genetic systems are widely used to engineer recombinant viruses with desired mutations. In response to the COVID-19 pandemic, four types of reverse genetic systems have been developed for SARS-CoV-2: (i) a full-length infectious clone that can be used to prepare recombinant SARS-CoV-2 at biosafety level 3 (BSL3), (ii) a trans-complementation system that can be used to produce single-round infectious SARS-CoV-2 at BSL2, (iii) an attenuated SARS-CoV-2 vaccine candidate (with deletions of viral accessory genes) that may be developed for veterinary use as well as for antiviral screening at BSL2, and (iv) replicon systems with deletions of viral structural genes that can be used at BSL2. Each of these genetic systems has its advantages and disadvantages that can be used to address different questions for basic and translational research. Due to the long genomic size and bacteria-toxic sequences of SARS-CoV-2, several experimental approaches have been established to rescue recombinant viruses and replicons, including (i) in vitro DNA ligation, (ii) bacterial artificial chromosome (BAC) system, (iii) yeast artificial chromosome (YAC) system, and (iv) circular polymerase extension reaction (CPER). This review summarizes the current status of SARS-CoV-2 genetic systems and their applications for studying viral replication, pathogenesis, vaccines, and therapeutics.
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Affiliation(s)
- Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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19
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Mengiste AA, Wilson RH, Weissman RF, Papa Iii LJ, Hendel SJ, Moore CL, Butty VL, Shoulders MD. Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria. Nucleic Acids Res 2023; 51:e31. [PMID: 36715334 PMCID: PMC10085711 DOI: 10.1093/nar/gkad003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 11/16/2022] [Accepted: 01/03/2023] [Indexed: 01/31/2023] Open
Abstract
Targeted mutagenesis mediated by nucleotide base deaminase-T7 RNA polymerase fusions has recently emerged as a novel and broadly useful strategy to power genetic diversification in the context of in vivo directed evolution campaigns. Here, we expand the utility of this approach by introducing a highly active adenosine deaminase-T7 RNA polymerase fusion protein (eMutaT7A→G), resulting in higher mutation frequencies to enable more rapid directed evolution. We also assess the benefits and potential downsides of using this more active mutator. We go on to show in Escherichia coli that adenosine deaminase-bearing mutators (MutaT7A→G or eMutaT7A→G) can be employed in tandem with a cytidine deaminase-bearing mutator (MutaT7C→T) to introduce all possible transition mutations simultaneously. We illustrate the efficacy of this in vivo mutagenesis approach by exploring mutational routes to antibacterial drug resistance. This work sets the stage for general application of optimized MutaT7 tools able to induce all types of transition mutations during in vivo directed evolution campaigns across diverse organisms.
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Affiliation(s)
- Amanuella A Mengiste
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert H Wilson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rachel F Weissman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Louis J Papa Iii
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Samuel J Hendel
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher L Moore
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Vincent L Butty
- BioMicroCenter, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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20
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Väisänen E, Jiang M, Laine L, Waris M, Julkunen I, Österlund P. Infectious viruses from transfected SARS-CoV-2 genomic RNA. Front Bioeng Biotechnol 2023; 11:1129111. [PMID: 37064222 PMCID: PMC10098207 DOI: 10.3389/fbioe.2023.1129111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/22/2023] [Indexed: 04/18/2023] Open
Abstract
SARS-CoV-2 emerged at the end of 2019, and like other novel pathogens causing severe symptoms, WHO recommended heightened biosafety measures for laboratories working with the virus. The positive-stranded genomic RNA of coronaviruses has been known to be infectious since the 1970s, and overall, all experiments with the possibility of SARS-CoV-2 propagation are carried out in higher containment level laboratories. However, as SARS-CoV-2 RNA has been routinely handled in BSL-2 laboratories, the question of the true nature of RNA infectiousness has risen along with discussion of appropriate biosafety measures. Here, we studied the ability of native SARS-CoV-2 genomic RNA to produce infectious viruses when transfected into permissive cells and discussed the biosafety control measures related to these assays. In transfection assays large quantities of genomic vRNA of SARS-CoV-2 was required for a successful production of infectious viruses. However, the quantity of vRNA alone was not the only factor, and especially when the transfected RNA was derived from infected cells, even small amounts of genomic vRNA was enough for an infection. Virus replication was found to start rapidly after transfection, and infectious viruses were detected in the cell culture media at 24 h post-transfection. In addition, silica membrane-based kits were shown to be as good as traditional TRI-reagent based methods in extracting high-quality, 30 kb-long genomic vRNA. Taken together, our data indicates that all transfection experiments with samples containing genomic SARS-CoV-2 RNA should be categorized as a propagative work and the work should be conducted only in a higher containment BSL-3 laboratory.
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Affiliation(s)
- Elina Väisänen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
- *Correspondence: Elina Väisänen,
| | - Miao Jiang
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Larissa Laine
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Matti Waris
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Ilkka Julkunen
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Pamela Österlund
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
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21
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Advances in Molecular Genetics Enabling Studies of Highly Pathogenic RNA Viruses. Viruses 2022; 14:v14122682. [PMID: 36560685 PMCID: PMC9784166 DOI: 10.3390/v14122682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
Experimental work with viruses that are highly pathogenic for humans and animals requires specialized Biosafety Level 3 or 4 facilities. Such pathogens include some spectacular but also rather seldomly studied examples such as Ebola virus (requiring BSL-4), more wide-spread and commonly studied viruses such as HIV, and the most recent example, SARS-CoV-2, which causes COVID-19. A common characteristic of these virus examples is that their genomes consist of single-stranded RNA, which requires the conversion of their genomes into a DNA copy for easy manipulation; this can be performed to study the viral life cycle in detail, develop novel therapies and vaccines, and monitor the disease course over time for chronic virus infections. We summarize the recent advances in such new genetic applications for RNA viruses in Switzerland over the last 25 years, from the early days of the HIV/AIDS epidemic to the most recent developments in research on the SARS-CoV-2 coronavirus. We highlight game-changing collaborative efforts between clinical and molecular disciplines in HIV research on the path to optimal clinical disease management. Moreover, we summarize how the modern technical evolution enabled the molecular studies of emerging RNA viruses, confirming that Switzerland is at the forefront of SARS-CoV-2 research and potentially other newly emerging viruses.
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22
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Reverse genetics in virology: A double edged sword. BIOSAFETY AND HEALTH 2022. [DOI: 10.1016/j.bsheal.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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23
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Engineering and Characterization of Avian Coronavirus Mutants Expressing Fluorescent Reporter Proteins from the Replicase Gene. J Virol 2022; 96:e0065322. [PMID: 35862676 PMCID: PMC9327687 DOI: 10.1128/jvi.00653-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Infectious bronchitis virus (IBV) is an avian coronavirus that causes infectious bronchitis, an acute and highly contagious respiratory disease of chickens. IBV evolution under the pressure of comprehensive and widespread vaccination requires surveillance for vaccine resistance, as well as periodic vaccine updates. Reverse genetics systems are very valuable tools in virology, as they facilitate rapid genetic manipulation of viral genomes, thereby advancing basic and applied research. We report here the construction of an infectious clone of IBV strain Beaudette as a bacterial artificial chromosome (BAC). The engineered full-length IBV clone allowed the rescue of an infectious virus that was phenotypically indistinguishable from the parental virus. We used the infectious IBV clone and examined whether an enhanced green fluorescent protein (EGFP) can be produced by the replicase gene ORF1 and autocatalytically released from the replicase polyprotein through cleavage by the main coronavirus protease. We show that IBV tolerates insertion of the EGFP ORF at the 3' end of the replicase gene, between the sequences encoding nsp13 and nsp16 (helicase, RNA exonuclease, RNA endonuclease, and RNA methyltransferase). We further show that EGFP is efficiently cleaved from the replicase polyprotein and can be localized in double-membrane vesicles along with viral RNA polymerase and double-stranded RNA, an intermediate of IBV genome replication. One of the engineered reporter EGFP viruses were genetically stable during passage in cultured cells. We demonstrate that the reporter EGFP viruses can be used to study virus replication in host cells and for antiviral drug discovery and development of diagnostic assays. IMPORTANCE Reverse genetics systems based on bacterial artificial chromosomes (BACs) are the most valuable systems in coronavirus research. Here, we describe the establishment of a reverse genetics system for the avian coronavirus strain Beaudette, the most intensively studied strain. We cloned a copy of the avian coronavirus genome into a BAC vector and recovered infectious virus in permissive cells. We used the new system to construct reporter viruses that produce enhanced green fluorescent protein (EGFP). The EGFP coding sequence was inserted into 11 known cleavage sites of the major coronavirus protease in the replicase gene ORF1. Avian coronavirus tolerated the insertion of the EGFP coding sequence at three sites. The engineered reporter viruses replicated with parental efficiency in cultured cells and were sufficiently genetically stable. The new system facilitates functional genomics of the avian coronavirus genome but can also be used for the development of novel vaccines and anticoronaviral drugs.
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24
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Mélade J, Piorkowski G, Touret F, Fourié T, Driouich JS, Cochin M, Bouzidi HS, Coutard B, Nougairède A, de Lamballerie X. A simple reverse genetics method to generate recombinant coronaviruses. EMBO Rep 2022; 23:e53820. [PMID: 35239997 PMCID: PMC9066064 DOI: 10.15252/embr.202153820] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 12/11/2022] Open
Abstract
Engineering recombinant viruses is a pre‐eminent tool for deciphering the biology of emerging viral pathogens such as the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). However, the large size of coronavirus genomes renders the current reverse genetics methods challenging. Here, we describe a simple method based on “infectious subgenomic amplicons” (ISA) technology to generate recombinant infectious coronaviruses with no need for reconstruction of the complete genomic cDNA and apply this method to SARS‐CoV‐2 and also to the feline enteric coronavirus. In both cases we rescue wild‐type viruses with biological characteristics similar to original strains. Specific mutations and fluorescent red reporter genes can be readily incorporated into the SARS‐CoV‐2 genome enabling the generation of a genomic variants and fluorescent reporter strains for in vivo experiments, serological diagnosis, and antiviral assays. The swiftness and simplicity of the ISA method has the potential to facilitate the advance of coronavirus reverse genetics studies, to explore the molecular biological properties of the SARS‐CoV‐2 variants, and to accelerate the development of effective therapeutic reagents.
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Affiliation(s)
- Julien Mélade
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Géraldine Piorkowski
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Franck Touret
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Toscane Fourié
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Jean-Sélim Driouich
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Maxime Cochin
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Hawa Sophia Bouzidi
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Bruno Coutard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Antoine Nougairède
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
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25
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Choi S, Kim KW, Ku KB, Kim SJ, Park C, Park D, Kim S, Yi H. Human Alphacoronavirus Universal Primers for Genome Amplification and Sequencing. Front Microbiol 2022; 13:789665. [PMID: 35401489 PMCID: PMC8990890 DOI: 10.3389/fmicb.2022.789665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
Rapid and accurate sequencing covering the entire genome is essential to identify genetic variations of viral pathogens. However, due to the low viral titers in clinical samples, certain amplification steps are required for viral genome sequencing. At present, there are no universal primers available for alphacoronaviruses and that, since these viruses have diverse strains, new primers specific to the target strain must be continuously developed for sequencing. Thus, in this study, we aimed to develop a universal primer set valid for all human alphacoronaviruses and applicable to samples containing trace amounts of the virus. To this aim, we designed overlapping primer pairs capable of amplifying the entire genome of all known human alphacoronaviruses. The selected primers, named the AC primer set, were composed of 10 primer pairs stretching over the entire genome of alphacoronaviruses, and produced PCR products of the expected size (3-5 kb) from both the HCoV-229E and HCoV-NL63 strains. After genome amplification, an evaluation using various sequencing platforms was carried out. The amplicon library sequencing data were assembled into complete genome sequences in all sequencing strategies examined in this study. The sequencing accuracy varied depending on the sequencing technology, but all sequencing methods showed a sequencing error of less than 0.01%. In the mock clinical specimen, the detection limit was 10-3 PFU/ml (102 copies/ml). The AC primer set and experimental procedure optimized in this study may enable the fast diagnosis of mutant alphacoronaviruses in future epidemics.
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Affiliation(s)
- Sungmi Choi
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, South Korea
| | - Kwan Woo Kim
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, South Korea
| | - Keun Bon Ku
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | - Seong-Jun Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | - Changwoo Park
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Dongju Park
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, South Korea.,Department of Biological Science, Chungnam National University, Daejeon, South Korea
| | - Seil Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, South Korea.,Department of Bio-Analysis Science, University of Science and Technology, Daejeon, South Korea
| | - Hana Yi
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, South Korea.,School of Biosystems and Biomedical Sciences, Korea University, Seoul, South Korea
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26
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Wang W, Peng X, Jin Y, Pan JA, Guo D. Reverse genetics systems for SARS-CoV-2. J Med Virol 2022; 94:3017-3031. [PMID: 35324008 PMCID: PMC9088479 DOI: 10.1002/jmv.27738] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/18/2022] [Indexed: 11/29/2022]
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID‐19) has caused severe public health crises and heavy economic losses. Limited knowledge about this deadly virus impairs our capacity to set up a toolkit against it. Thus, more studies on severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) biology are urgently needed. Reverse genetics systems, including viral infectious clones and replicons, are powerful platforms for viral research projects, spanning many aspects such as the rescues of wild‐type or mutant viral particles, the investigation of viral replication mechanism, the characterization of viral protein functions, and the studies on viral pathogenesis and antiviral drug development. The operations on viral infectious clones are strictly limited in the Biosafety Level 3 (BSL3) facilities, which are insufficient, especially during the pandemic. In contrast, the operation on the noninfectious replicon can be performed in Biosafety Level 2 (BSL2) facilities, which are widely available. After the outbreak of COVID‐19, many reverse genetics systems for SARS‐CoV‐2, including infectious clones and replicons are developed and given plenty of options for researchers to pick up according to the requirement of their research works. In this review, we summarize the available reverse genetics systems for SARS‐CoV‐2, by highlighting the features of these systems, and provide a quick guide for researchers, especially those without ample experience in operating viral reverse genetics systems.
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Affiliation(s)
- Wenhao Wang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong, 518107, China
| | - Xiaoxue Peng
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong, 518107, China
| | - Yunyun Jin
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong, 518107, China
| | - Ji-An Pan
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong, 518107, China
| | - Deyin Guo
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong, 518107, China
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27
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Persaud AT, Burnie J, Thaya L, DSouza L, Martin S, Guzzo C. A UV-LED module that is highly effective at inactivating human coronaviruses and HIV-1. Virol J 2022; 19:29. [PMID: 35144624 PMCID: PMC8829982 DOI: 10.1186/s12985-022-01754-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/24/2022] [Indexed: 11/10/2022] Open
Abstract
Ultraviolet (UV) light has previously been established as useful method of disinfection, with demonstrated efficacy to inactivate a broad range of microorganisms. The advent of ultraviolet light-emitting diodes provides advantages in ease of disinfection, in that there can be delivery of germicidal UV with the same light unit that delivers standard white light to illuminate a room. Herein we demonstrate the efficacy and feasibility of ultraviolet light-emitting diodes as a means of decontamination by inactivating two distinct virus models, human coronavirus 229E and human immunodeficiency virus. Importantly, the same dose of ultraviolet light that inactivated human viruses also elicited complete inactivation of ultraviolet-resistant bacterial spores (Bacillus pumilus), a gold standard for demonstrating ultraviolet-mediated disinfection. This work demonstrates that seconds of ultraviolet light-emitting diodes (UV-LED) exposure can inactivate viruses and bacteria, highlighting that UV-LED could be a useful and practical tool for broad sanitization of public spaces.
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Affiliation(s)
- Arvin T Persaud
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Room SW560, Toronto, ON, M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Jonathan Burnie
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Room SW560, Toronto, ON, M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Laxshaginee Thaya
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Room SW560, Toronto, ON, M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Liann DSouza
- Safe Antiviral Technologies Inc, 822 Manning Ave, Toronto, ON, M6G 2W8, Canada
| | - Steven Martin
- Safe Antiviral Technologies Inc, 822 Manning Ave, Toronto, ON, M6G 2W8, Canada
| | - Christina Guzzo
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Room SW560, Toronto, ON, M1C 1A4, Canada.
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada.
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28
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Zhou Y, Li C, Ren C, Hu J, Song C, Wang X, Li Y. One-Step Assembly of a Porcine Epidemic Diarrhea Virus Infectious cDNA Clone by Homologous Recombination in Yeast: Rapid Manipulation of Viral Genome With CRISPR/Cas9 Gene-Editing Technology. Front Microbiol 2022; 13:787739. [PMID: 35222326 PMCID: PMC8870625 DOI: 10.3389/fmicb.2022.787739] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV), a swine enteric coronavirus causing acute diarrhea in piglets, is one of the major threatens to the pork industry globally. Reverse genetics is a valuable tool for the virological study and vaccine development for coronaviruses. Due to the large size and unstable problem in Escherichia coli of coronavirus genome, construction and manipulation of reverse genetics system for coronaviruses remain laborious and time-consuming. In this study, a reverse genetics system of the genotype II PEDV strain HM was generated using the transformation-associated recombination (TAR) technology in yeast within 1 week. The rescued virus (rPEDV) exhibited similar growth properties to the wild-type virus in vitro. With this PEDV infectious cDNA clone, CRISPR/Cas9 technology and homologous recombination were combined to generate a recombinant virus rPEDV-EGFP in which the ORF3 gene was swapped with an EGFP gene. The reporter virus displayed similar growth properties to the parental virus rPEDV and remained stable during serial passage in vitro. Of note, the strategies of construction and manipulation of PEDV infectious cDNA clone are extremely simple and efficient, which could be applied for other RNA viruses and DNA viruses.
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Affiliation(s)
- Yanyang Zhou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Chenxi Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, China
| | - Cicheng Ren
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Jingbo Hu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Changxu Song
- College of Animal Science & National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou, China
| | - Xinjie Wang
- Guangdong Key Laboratory of Mental Health and Cognitive Science, Center for Studies of Psychological Application, Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China
| | - Yanhua Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, China
- *Correspondence: Yanhua Li,
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29
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Vanderheijden N, Stevaert A, Xie J, Ren X, Barbezange C, Noppen S, Desombere I, Verhasselt B, Geldhof P, Vereecke N, Stroobants V, Oh D, Vanhee M, Naesens LMJ, Nauwynck HJ. Functional Analysis of Human and Feline Coronavirus Cross-Reactive Antibodies Directed Against the SARS-CoV-2 Fusion Peptide. Front Immunol 2022; 12:790415. [PMID: 35069571 PMCID: PMC8766817 DOI: 10.3389/fimmu.2021.790415] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/15/2021] [Indexed: 12/11/2022] Open
Abstract
To face the continuous emergence of SARS-CoV-2 variants, broadly protective therapeutic antibodies are highly needed. We here focused on the fusion peptide (FP) region of the viral spike antigen since it is highly conserved among alpha- and betacoronaviruses. First, we found that coronavirus cross-reactive antibodies are commonly formed during infection, being omnipresent in sera from COVID-19 patients, in ~50% of pre-pandemic human sera (rich in antibodies against endemic human coronaviruses), and even in feline coronavirus-infected cats. Pepscan analyses demonstrated that a confined N-terminal region of the FP is strongly immunogenic across diverse coronaviruses. Peptide-purified human antibodies targeting this conserved FP epitope exhibited broad binding of alpha- and betacoronaviruses, besides weak and transient SARS-CoV-2 neutralizing activity. Being frequently elicited by coronavirus infection, these FP-binding antibodies might potentially exhibit Fc-mediated effector functions and influence the kinetics or severity of coronavirus infection and disease.
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Affiliation(s)
- Nathalie Vanderheijden
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Annelies Stevaert
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven – University of Leuven, Leuven, Belgium
| | - Jiexiong Xie
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Xiaolei Ren
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Cyril Barbezange
- National Influenza Centre and Epidemiology of Infectious Diseases, Sciensano, Brussels, Belgium
| | - Sam Noppen
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven – University of Leuven, Leuven, Belgium
| | | | - Bruno Verhasselt
- Laboratory for Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | - Peter Geldhof
- Laboratory of Parasitology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Nick Vereecke
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
- PathoSense BV, Lier, Belgium
| | - Veerle Stroobants
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Dayoung Oh
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Merijn Vanhee
- Department of Laboratory Medicine, AZ Sint-Jan Brugge-Oostende, Bruges, Belgium
| | - Lieve M. J. Naesens
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven – University of Leuven, Leuven, Belgium
| | - Hans J. Nauwynck
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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30
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Inayoshi Y, Oguro S, Tanahashi E, Lin Z, Kawaguchi Y, Kodama T, Sasakawa C. Bacterial artificial chromosome-based reverse genetics system for cloning and manipulation of the full-length genome of infectious bronchitis virus. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100155. [PMID: 35909616 PMCID: PMC9325906 DOI: 10.1016/j.crmicr.2022.100155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Reverse genetics system to clone attenuated IBV C-78 full-length genome in a BAC. Rescued virus from BAC-cloned C-78 show parental virus properties. Genetic manipulation of BAC-cloned C-78 using Red-mediated recombination in E. coli. Construction of S gene recombinant C-78 by swapping with the S gene of virulent IBV. S gene determines neutralization specificity but not virulence and tissue-tropism.
Avian infectious bronchitis virus (IBV) causes highly contagious respiratory reproductive and renal system diseases in chickens, and emergence of serotypic variants resulting from mutations in the viral S gene hampers vaccine management for IBV infection. In this study, to facilitate the molecular analysis of IBV pathogenesis and the development of a new-generation IBV vaccine, we established a reverse genetics system (RGS) for cloning the full-length cDNA of the IBV C-78E128 attenuated strain in a bacterial artificial chromosome (BAC). The BAC-cloned C-78E128 cDNA generated infectious viruses with biological properties of the parental C-78E128 strain with regard to an avirulent phenotype, tissue tropism and induction of virus neutralizing (VN) antibody in vivo. To assess the feasibility of genetic manipulation of the IBV genome using the BAC-based RGS, the S gene of the BAC-cloned C-78E128 cDNA was replaced with that of the IBV S95E4 virulent strain, which differs from the C-78E128 strain in serotype and tissue tropism, by bacteriophage lambda Red-mediated homologous recombination in Escherichia coli (E. coli). The resultant S gene recombinant virus was found to be avirulent and fully competent to induce a serotype-specific VN antibody against the S95 strain; however, the S gene recombinant virus did not fully recapitulate the tissue tropism of the S95E4 strain. These data imply that serotype-specific VN immunogenicity, but not tissue-tropism and pathogenicity, of IBV is determined by the viral S gene. The IBV BAC-based RGS that enables cloning and manipulation of the IBV virus genome entirely in E. coli provides a useful platform for the molecular analyses of IBV pathogenesis and the development of rationally designed IBV recombinant vaccines.
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31
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Lindenbach BD. Reinventing positive-strand RNA virus reverse genetics. Adv Virus Res 2022; 112:1-29. [PMID: 35840179 PMCID: PMC9273853 DOI: 10.1016/bs.aivir.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Reverse genetics is the prospective analysis of how genotype determines phenotype. In a typical experiment, a researcher alters a viral genome, then observes the phenotypic outcome. Among RNA viruses, this approach was first applied to positive-strand RNA viruses in the mid-1970s and over nearly 50 years has become a powerful and widely used approach for dissecting the mechanisms of viral replication and pathogenesis. During this time the global health importance of two virus groups, flaviviruses (genus Flavivirus, family Flaviviridae) and betacoronaviruses (genus Betacoronavirus, subfamily Orthocoronavirinae, family Coronaviridae), have dramatically increased, yet these viruses have genomes that are technically challenging to manipulate. As a result, several new techniques have been developed to overcome these challenges. Here I briefly review key historical aspects of positive-strand RNA virus reverse genetics, describe some recent reverse genetic innovations, particularly as applied to flaviviruses and coronaviruses, and discuss their benefits and limitations within the larger context of rigorous genetic analysis.
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Roberts A, Chouhan RS, Shahdeo D, Shrikrishna NS, Kesarwani V, Horvat M, Gandhi S. A Recent Update on Advanced Molecular Diagnostic Techniques for COVID-19 Pandemic: An Overview. Front Immunol 2021; 12:732756. [PMID: 34970254 PMCID: PMC8712736 DOI: 10.3389/fimmu.2021.732756] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/23/2021] [Indexed: 12/11/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), which started out as an outbreak of pneumonia, has now turned into a pandemic due to its rapid transmission. Besides developing a vaccine, rapid, accurate, and cost-effective diagnosis is essential for monitoring and combating the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its related variants on time with precision and accuracy. Currently, the gold standard for detection of SARS-CoV-2 is Reverse Transcription Polymerase Chain Reaction (RT-PCR), but it lacks accuracy, is time-consuming and cumbersome, and fails to detect multi-variant forms of the virus. Herein, we have summarized conventional diagnostic methods such as Chest-CT (Computed Tomography), RT-PCR, Loop Mediated Isothermal Amplification (LAMP), Reverse Transcription-LAMP (RT-LAMP), as well new modern diagnostics such as CRISPR-Cas-based assays, Surface Enhanced Raman Spectroscopy (SERS), Lateral Flow Assays (LFA), Graphene-Field Effect Transistor (GraFET), electrochemical sensors, immunosensors, antisense oligonucleotides (ASOs)-based assays, and microarrays for SARS-CoV-2 detection. This review will also provide an insight into an ongoing research and the possibility of developing more economical tools to tackle the COVID-19 pandemic.
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Affiliation(s)
- Akanksha Roberts
- Department of Biotechnology (DBT)-National Institute of Animal Biotechnology (NIAB), Hyderabad, India
| | | | - Deepshikha Shahdeo
- Department of Biotechnology (DBT)-National Institute of Animal Biotechnology (NIAB), Hyderabad, India
| | | | - Veerbhan Kesarwani
- Department of Biotechnology (DBT)-National Institute of Animal Biotechnology (NIAB), Hyderabad, India
| | - Milena Horvat
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Sonu Gandhi
- Department of Biotechnology (DBT)-National Institute of Animal Biotechnology (NIAB), Hyderabad, India
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Klemm C, Wood H, Thomas GH, Ólafsson G, Torres MT, Thorpe PH. Forced association of SARS-CoV-2 proteins with the yeast proteome perturb vesicle trafficking. MICROBIAL CELL (GRAZ, AUSTRIA) 2021; 8:280-296. [PMID: 34909432 PMCID: PMC8642885 DOI: 10.15698/mic2021.12.766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/07/2021] [Accepted: 10/15/2021] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the highly infectious coronavirus disease COVID-19. Extensive research has been performed in recent months to better understand how SARS-CoV-2 infects and manipulates its host to identify potential drug targets and support patient recovery from COVID-19. However, the function of many SARS-CoV-2 proteins remains uncharacterised. Here we used the Synthetic Physical Interactions (SPI) method to recruit SARS-CoV-2 proteins to most of the budding yeast proteome to identify conserved pathways which are affected by SARS-CoV-2 proteins. The set of yeast proteins that result in growth defects when associated with the viral proteins have homologous functions that overlap those identified in studies performed in mammalian cells. Specifically, we were able to show that recruiting the SARS-CoV-2 NSP1 protein to HOPS, a vesicle-docking complex, is sufficient to perturb membrane trafficking in yeast consistent with the hijacking of the endoplasmic-reticulum-Golgi intermediate compartment trafficking pathway during viral infection of mammalian cells. These data demonstrate that the yeast SPI method is a rapid way to identify potential functions of ectopic viral proteins.
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Affiliation(s)
- Cinzia Klemm
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS, UK
| | - Henry Wood
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS, UK
| | - Grace Heredge Thomas
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS, UK
| | - Guðjón Ólafsson
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS, UK
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Mara Teixeira Torres
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS, UK
| | - Peter H. Thorpe
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS, UK
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Abstract
Historically part of the coronavirus (CoV) family, torovirus (ToV) was recently classified into the new family Tobaniviridae. While reverse genetics systems have been established for various CoVs, none exist for ToVs. Herein, we developed a reverse genetics system using an infectious full-length cDNA clone of bovine ToV (BToV) in a bacterial artificial chromosome (BAC). Recombinant BToV harboring genetic markers had the same phenotype as wild-type (wt) BToV. To generate two types of recombinant virus, the hemagglutinin-esterase (HE) gene was edited, as cell-adapted wtBToV generally loses full-length HE (HEf), resulting in soluble HE (HEs). First, recombinant viruses with HEf and HA-tagged HEf or HEs genes were rescued. These exhibited no significant differences in their effect on virus growth in HRT18 cells, suggesting that HE is not essential for viral replication in these cells. Thereafter, we generated recombinant virus (rEGFP), wherein HE was replaced by the enhanced green fluorescent protein (EGFP) gene. The rEGFP expressed EGFP in infected cells, but showed significantly lower viral growth compared to wtBToV. Moreover, the rEGFP readily deleted the EGFP gene after one passage. Interestingly, rEGFP variants with two mutations (C1442F and I3562T) in non-structural proteins (NSPs) that emerged during passages exhibited improved EGFP expression, EGFP gene retention, and viral replication. An rEGFP into which both mutations were introduced displayed a similar phenotype to these variants, suggesting that the mutations contributed to EGFP gene acceptance. The current findings provide new insights into BToV, and reverse genetics will help advance the current understanding of this neglected pathogen. Importance ToVs are diarrhea-causing pathogens detected in various species, including humans. Through the development of a BAC-based BToV, we introduced the first reverse genetics system for Tobaniviridae. Utilizing this system, recombinant BToVs with a full-length HE gene were generated. Remarkably, although clinical BToVs generally lose the HE gene after a few passages, some recombinant viruses generated in the current study retained the HE gene for up to 20 passages while accumulating mutations in NSPs, which suggested that these mutations may be involved in HE gene retention. The EGFP gene of recombinant viruses was unstable, but rEGFP into which two NSP mutations were introduced exhibited improved EGFP expression, gene retention, and viral replication. These data suggested the existence of an NSP-based acceptance or retention mechanism for exogenous RNA or HE genes. Recombinant BToVs and reverse genetics are powerful tools for understanding fundamental viral processes, infection pathogenesis, and BToV vaccine development.
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Khalid S, Siddique R, Shaheen S, Shahid MN, Shamim Z, Khan MKA, Serçe ÇU. Current understanding of an Emerging Coronavirus using in silico approach: Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2). BRAZ J BIOL 2021; 83:e247237. [PMID: 34495154 DOI: 10.1590/1519-6984.247237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/09/2021] [Indexed: 11/22/2022] Open
Abstract
Novel coronavirus (nCoV) namely "SARS-CoV-2" is being found responsible for current PANDEMIC commenced from Wuhan (China) since December 2019 and has been described with epidemiological linkage to China in about 221 countries and territories until now. In this study we have characterized the genetic lineage of SARS-CoV-2 and report the recombination within the genus and subgenus of coronaviruses. Phylogenetic relationship of thirty nine coronaviruses belonging to its four genera and five subgenera was analyzed by using the Neighbor-joining method using MEGA 6.0. Phylogenetic trees of full length genome, various proteins (spike, envelope, membrane and nucleocapsid) nucleotide sequences were constructed separately. Putative recombination was probed via RDP4. Our analysis describes that the "SARS-CoV-2" although shows great similarity to Bat-SARS-CoVs sequences through whole genome (giving sequence similarity 89%), exhibits conflicting grouping with the Bat-SARS-like coronavirus sequences (MG772933 and MG772934). Furthermore, seven recombination events were observed in SARS-CoV-2 (NC_045512) by RDP4. But not a single recombination event fulfills the high level of certainty. Recombination mostly housed in spike protein genes than rest of the genome indicating breakpoint cluster arises beyond the 95% and 99% breakpoint density intervals. Genetic similarity levels observed among "SARS-CoV-2" and Bat-SARS-CoVs advocated that the latter did not exhibit the specific variant that cause outbreak in humans, proposing a suggestion that "SARS-CoV-2" has originated possibly from bats. These genomic features and their probable association with virus characteristics along with virulence in humans require further consideration.
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Affiliation(s)
- S Khalid
- Lahore College for Women University, Department of Botany, Jail Road, Lahore, Pakistan
| | - R Siddique
- Lahore College for Women University, Department of Botany, Jail Road, Lahore, Pakistan
| | - S Shaheen
- Lahore College for Women University, Department of Botany, Jail Road, Lahore, Pakistan
| | - M N Shahid
- University of Education, Township, Department of Botany, Division of Science and Technology, Lahore, Pakistan
| | - Z Shamim
- Mirpur University of Science and Technology, Department of Biotechnology, Mirpur, Azad Kashmir, Pakistan
| | - M K A Khan
- University of Okara, Department of Zoology, Okara, Pakistan
| | - Ç Ulubaş Serçe
- Niğde Ömer Halisdemir Üniversitesi, Tarım Bilimleri ve Teknolojileri Fakültesi, Bitkisel Üretim ve Teknolojileri Bölümü, Niğde, Turkey
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Low ZY, Yip AJW, Sharma A, Lal SK. SARS coronavirus outbreaks past and present-a comparative analysis of SARS-CoV-2 and its predecessors. Virus Genes 2021; 57:307-317. [PMID: 34061288 PMCID: PMC8167830 DOI: 10.1007/s11262-021-01846-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/10/2021] [Indexed: 02/08/2023]
Abstract
The Coronavirus Disease 2019 (COVID-19), a pneumonic disease caused by the SARS Coronavirus 2 (SARS-CoV-2), is the 7th Coronavirus to have successfully infected and caused an outbreak in humans. Genome comparisons have shown that previous isolates, the SARS-related coronavirus (SARSr-CoV), including the SARS-CoV are closely related, yet different in disease manifestation. Several explanations were suggested for the undetermined origin of SARS-CoV-2, in particular, bats, avian and Malayan pangolins as reservoir hosts, owing to the high genetic similarity. The general morphology and structure of all these viral isolates overlap with analogous disease symptoms such as fever, dry cough, fatigue, dyspnoea and headache, very similar to the current SARS-CoV-2. Chest CT scans for SARS-CoV-2, SARS-CoV and MERS-CoV reveal pulmonary lesions, bilateral ground-glass opacities, and segmental consolidation in the lungs, a common pathological trait. With greatly overlapping similarities among the previous coronavirus, the SARS-CoV, it becomes interesting to observe marked differences in disease severity of the SARS-CoV-2 thereby imparting it the ability to rapidly transmit, exhibit greater stability, bypass innate host defences, and increasingly adapt to their new host thereby resulting in the current pandemic. The most recent B.1.1.7, B.1.351 and P.1 variants of SARS-CoV-2, highlight the fact that changes in amino acids in the Spike protein can contribute to enhanced infection and transmission efficiency. This review covers a comparative analysis of previous coronavirus outbreaks and highlights the differences and similarities among different coronaviruses, including the most recent isolates that have evolved to become easily transmissible with higher replication efficiency in humans.
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Affiliation(s)
- Zheng Yao Low
- School of Science, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia
| | - Ashley Jia Wen Yip
- School of Science, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia
| | - Anshika Sharma
- School of Science, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia
| | - Sunil K Lal
- School of Science, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia.
- Tropical Medicine and Biology Platform, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia.
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37
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Low ZY, Yip AJW, Sharma A, Lal SK. SARS coronavirus outbreaks past and present-a comparative analysis of SARS-CoV-2 and its predecessors. Virus Genes 2021. [PMID: 34061288 DOI: 10.1007/s11262‐021‐01846‐9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The Coronavirus Disease 2019 (COVID-19), a pneumonic disease caused by the SARS Coronavirus 2 (SARS-CoV-2), is the 7th Coronavirus to have successfully infected and caused an outbreak in humans. Genome comparisons have shown that previous isolates, the SARS-related coronavirus (SARSr-CoV), including the SARS-CoV are closely related, yet different in disease manifestation. Several explanations were suggested for the undetermined origin of SARS-CoV-2, in particular, bats, avian and Malayan pangolins as reservoir hosts, owing to the high genetic similarity. The general morphology and structure of all these viral isolates overlap with analogous disease symptoms such as fever, dry cough, fatigue, dyspnoea and headache, very similar to the current SARS-CoV-2. Chest CT scans for SARS-CoV-2, SARS-CoV and MERS-CoV reveal pulmonary lesions, bilateral ground-glass opacities, and segmental consolidation in the lungs, a common pathological trait. With greatly overlapping similarities among the previous coronavirus, the SARS-CoV, it becomes interesting to observe marked differences in disease severity of the SARS-CoV-2 thereby imparting it the ability to rapidly transmit, exhibit greater stability, bypass innate host defences, and increasingly adapt to their new host thereby resulting in the current pandemic. The most recent B.1.1.7, B.1.351 and P.1 variants of SARS-CoV-2, highlight the fact that changes in amino acids in the Spike protein can contribute to enhanced infection and transmission efficiency. This review covers a comparative analysis of previous coronavirus outbreaks and highlights the differences and similarities among different coronaviruses, including the most recent isolates that have evolved to become easily transmissible with higher replication efficiency in humans.
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Affiliation(s)
- Zheng Yao Low
- School of Science, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia
| | - Ashley Jia Wen Yip
- School of Science, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia
| | - Anshika Sharma
- School of Science, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia
| | - Sunil K Lal
- School of Science, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia. .,Tropical Medicine and Biology Platform, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia.
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38
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Pasquier C, Robichon A. Computational search of hybrid human/SARS-CoV-2 dsRNA reveals unique viral sequences that diverge from those of other coronavirus strains. Heliyon 2021; 7:e07284. [PMID: 34179538 PMCID: PMC8219292 DOI: 10.1016/j.heliyon.2021.e07284] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/14/2021] [Accepted: 06/08/2021] [Indexed: 12/16/2022] Open
Abstract
The role of the RNAi/Dicer/Ago system in degrading RNA viruses has been elusive in mammals in the past, which has prompted authors to think that interferon (IFN) synthesis is essential in this clade, relegating the RNAi defense strategy against viral infection as an accessory function. However, recent publications highlight the existence of abundant viral small interference and micro RNAs (VsiRNAs and VmiRNAs) in both cell-line and whole organism based experiments, indicating a contribution of these molecules in host responses and/or viral replication. We explore the theoretical possibility that RNAi triggered by SARS-CoV-2 might degrade some host transcripts in the opposite direction, although this hypothesis seems counterintuitive. The SARS-CoV-2 genome was therefore computationally searched for exact intrapairing within the viral RNA and exact hybrid pairing with the human transcriptome over a minimum of 20 bases in length. Minimal segments of 20-base lengths of SARS-CoV-2 RNA were found based on the theoretical matching with existing complementary strands in the human host transcriptome. Few human genes potentially annealing with SARS-CoV-2 RNA, including mitochondrial deubiquitinase USP30, the subunit of ubiquitin protein ligase complex FBXO21 and two long noncoding RNAs, were retrieved. The hypothesis that viral-originated RNAi might mediate degradation of host transcriptome messages was corroborated by published high throughput sequencing of RNA from infected tissues and cultured cells, clinical observation and phylogenetic comparative analysis, indicating a strong specificity of these SARS-CoV-2 hybrid pairing sequences for human genomes.
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Beeraka NM, Tulimilli SV, Karnik M, Sadhu SP, Pragada RR, Aliev G, Madhunapantula SV. The Current Status and Challenges in the Development of Vaccines and Drugs against Severe Acute Respiratory Syndrome-Corona Virus-2 (SARS-CoV-2). BIOMED RESEARCH INTERNATIONAL 2021; 2021:8160860. [PMID: 34159203 PMCID: PMC8168478 DOI: 10.1155/2021/8160860] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 04/16/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection causes coronavirus disease-19 (COVID-19), which is characterized by clinical manifestations such as pneumonia, lymphopenia, severe acute respiratory distress, and cytokine storm. S glycoprotein of SARS-CoV-2 binds to angiotensin-converting enzyme II (ACE-II) to enter into the lungs through membrane proteases consequently inflicting the extensive viral load through rapid replication mechanisms. Despite several research efforts, challenges in COVID-19 management still persist at various levels that include (a) availability of a low cost and rapid self-screening test, (b) lack of an effective vaccine which works against multiple variants of SARS-CoV-2, and (c) lack of a potent drug that can reduce the complications of COVID-19. The development of vaccines against SARS-CoV-2 is a complicated process due to the emergence of mutant variants with greater virulence and their ability to invoke intricate lung pathophysiology. Moreover, the lack of a thorough understanding about the virus transmission mechanisms and complete pathogenesis of SARS-CoV-2 is making it hard for medical scientists to develop a better strategy to prevent the spread of the virus and design a clinically viable vaccine to protect individuals from being infected. A recent report has tested the hypothesis of T cell immunity and found effective when compared to the antibody response in agammaglobulinemic patients. Understanding SARS-CoV-2-induced changes such as "Th-2 immunopathological variations, mononuclear cell & eosinophil infiltration of the lung and antibody-dependent enhancement (ADE)" in COVID-19 patients provides key insights to develop potential therapeutic interventions for immediate clinical management. Therefore, in this review, we have described the details of rapid detection methods of SARS-CoV-2 using molecular and serological tests and addressed different therapeutic modalities used for the treatment of COVID-19 patients. In addition, the current challenges against the development of vaccines for SARS-CoV-2 are also briefly described in this article.
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Affiliation(s)
- Narasimha M. Beeraka
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Academy of Higher Education & Research (JSS AHER), Mysore, 570015 Karnataka, India
- Sechenov First Moscow State Medical University (Sechenov University), St. Trubetskaya, 8, Bld. 2, Moscow 119991, Russia
| | - SubbaRao V. Tulimilli
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Academy of Higher Education & Research (JSS AHER), Mysore, 570015 Karnataka, India
| | - Medha Karnik
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Academy of Higher Education & Research (JSS AHER), Mysore, 570015 Karnataka, India
| | - Surya P. Sadhu
- AU College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, 530003 Andhra Pradesh, India
| | - Rajeswara Rao Pragada
- AU College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, 530003 Andhra Pradesh, India
| | - Gjumrakch Aliev
- Sechenov First Moscow State Medical University (Sechenov University), St. Trubetskaya, 8, Bld. 2, Moscow 119991, Russia
- Institute of Physiologically Active Compounds, Russian Academy of Sciences, Chernogolovka, Moscow Region 142432, Russia
- Research Institute of Human Morphology, 3Tsyurupy Street, Moscow 117418, Russia
- GALLY International Research Institute, 7733 Louis Pasteur Drive, #330, San Antonio, TX 78229, USA
| | - SubbaRao V. Madhunapantula
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Academy of Higher Education & Research (JSS AHER), Mysore, 570015 Karnataka, India
- Special Interest Group in Cancer Biology and Cancer Stem Cells (SIG-CBCSC), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysore, 570015 Karnataka, India
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Shang J, Han N, Chen Z, Peng Y, Li L, Zhou H, Ji C, Meng J, Jiang T, Wu A. Compositional diversity and evolutionary pattern of coronavirus accessory proteins. Brief Bioinform 2021; 22:1267-1278. [PMID: 33126244 PMCID: PMC7665327 DOI: 10.1093/bib/bbaa262] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/29/2020] [Indexed: 12/11/2022] Open
Abstract
Accessory proteins play important roles in the interaction between coronaviruses and their hosts. Accordingly, a comprehensive study of the compositional diversity and evolutionary patterns of accessory proteins is critical to understanding the host adaptation and epidemic variation of coronaviruses. Here, we developed a standardized genome annotation tool for coronavirus (CoroAnnoter) by combining open reading frame prediction, transcription regulatory sequence recognition and homologous alignment. Using CoroAnnoter, we annotated 39 representative coronavirus strains to form a compositional profile for all of the accessary proteins. Large variations were observed in the number of accessory proteins of 1–10 for different coronaviruses, with SARS-CoV-2 and SARS-CoV having the most (9 and 10, respectively). The variation between SARS-CoV and SARS-CoV-2 accessory proteins could be traced back to related coronaviruses in other hosts. The genomic distribution of accessory proteins had significant intra-genus conservation and inter-genus diversity and could be grouped into 1, 4, 2 and 1 types for alpha-, beta-, gamma-, and delta-coronaviruses, respectively. Evolutionary analysis suggested that accessory proteins are more conservative locating before the N-terminal of proteins E and M (E-M), while they are more diverse after these proteins. Furthermore, comparison of virus-host interaction networks of SARS-CoV-2 and SARS-CoV accessory proteins showed that they share multiple antiviral signaling pathways, those involved in the apoptotic process, viral life cycle and response to oxidative stress. In summary, our study provides a tool for coronavirus genome annotation and builds a comprehensive profile for coronavirus accessory proteins covering their composition, classification, evolutionary pattern and host interaction.
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Affiliation(s)
- Jingzhe Shang
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Jiangsu, Suzhou, China
| | - Na Han
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Jiangsu, Suzhou, China
| | - Ziyi Chen
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Jiangsu, Suzhou, China
| | | | - Liang Li
- Linyi people's hospital, Shandong, China
| | - Hangyu Zhou
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Jiangsu, Suzhou, China
| | - Chengyang Ji
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Jiangsu, Suzhou, China
| | - Jing Meng
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Jiangsu, Suzhou, China
| | - Taijiao Jiang
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Aiping Wu
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Jiangsu, Suzhou, China
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Ullah A, Ullah K. Inhibition of SARS-CoV-2 3CL M pro by Natural and Synthetic Inhibitors: Potential Implication for Vaccine Production Against COVID-19. Front Mol Biosci 2021; 8:640819. [PMID: 33912587 PMCID: PMC8072276 DOI: 10.3389/fmolb.2021.640819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/10/2021] [Indexed: 12/24/2022] Open
Abstract
COVID-19 has created a pandemic situation all over the world. It has spread in nearly every continent. Researchers all over the world are trying to produce an effective vaccine against this virus, however; no specific treatment for COVID-19 has been discovered -so far. The current work describes the inhibition study of the SARS-CoV-2 main proteinase or 3CL Mpro by natural and synthetic inhibitors, which include 2S albumin and flocculating protein from Moringa oleifera (M. oleifera) and Suramin. Molecular Docking study was carried out using the programs like AutoDock 4.0, HADDOCK2.4, patchdock, pardock, and firedock. The global binding energy of Suramin, 2S albumin, and flocculating proteins were −41.96, −9.12, and −14.78 kJ/mol, respectively. The docking analysis indicates that all three inhibitors bind at the junction of domains II and III. The catalytic function of 3CL Mpro is dependent on its dimeric form, and the flexibility of domain III is considered important for this dimerization. Our study showed that all three inhibitors reduce this flexibility and restrict their motion. The decrease in flexibility of domain III was further confirmed by analysis coming from Molecular dynamic simulation. The analysis results indicate that the temperature B-factor of the enzyme decreases tremendously when the inhibitors bind to it. This study will further explore the possibility of producing an effective treatment against COVID-19.
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Affiliation(s)
- Anwar Ullah
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Kifayat Ullah
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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García-Nicolás O, V'kovski P, Zettl F, Zimmer G, Thiel V, Summerfield A. No Evidence for Human Monocyte-Derived Macrophage Infection and Antibody-Mediated Enhancement of SARS-CoV-2 Infection. Front Cell Infect Microbiol 2021; 11:644574. [PMID: 33912475 PMCID: PMC8072125 DOI: 10.3389/fcimb.2021.644574] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/11/2021] [Indexed: 12/16/2022] Open
Abstract
Vaccines are essential to control the spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and to protect the vulnerable population. However, one safety concern of vaccination is the possible development of antibody-dependent enhancement (ADE) of SARS-CoV-2 infection. The potential infection of Fc receptor bearing cells such as macrophages, would support continued virus replication and inflammatory responses, and thereby potentially worsen the clinical outcome of COVID-19. Here we demonstrate that SARS-CoV-2 and SARS-CoV neither infect human monocyte-derived macrophages (hMDM) nor induce inflammatory cytokines in these cells, in sharp contrast to Middle East respiratory syndrome (MERS) coronavirus and the common cold human coronavirus 229E. Furthermore, serum from convalescent COVID-19 patients neither induced enhancement of SARS-CoV-2 infection nor innate immune response in hMDM. Although, hMDM expressed angiotensin-converting enzyme 2, no or very low levels of transmembrane protease serine 2 were found. These results support the view that ADE may not be involved in the immunopathological processes associated with COVID-19, however, more studies are necessary to understand the potential contribution of antibodies-virus complexes with other cells expressing FcR receptors.
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Affiliation(s)
- Obdulio García-Nicolás
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Philip V'kovski
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Ferdinand Zettl
- Institute of Virology and Immunology (IVI), Bern, Switzerland
| | - Gert Zimmer
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Artur Summerfield
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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43
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Hendel SJ, Shoulders MD. Directed evolution in mammalian cells. Nat Methods 2021; 18:346-357. [PMID: 33828274 DOI: 10.1038/s41592-021-01090-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 02/01/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023]
Abstract
Directed evolution experiments are typically carried out using in vitro systems, bacteria, or yeast-even when the goal is to probe or modulate mammalian biology. Performing directed evolution in systems that do not match the intended mammalian environment severely constrains the scope and functionality of the targets that can be evolved. We review new platforms that are now making it possible to use the mammalian cell itself as the setting for directed evolution and present an overview of frontier challenges and high-impact targets for this approach.
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Affiliation(s)
- Samuel J Hendel
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
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44
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Dijkstra JM, Frenette AP, Dixon B. Most Japanese individuals are genetically predisposed to recognize an immunogenic protein fragment shared between COVID-19 and common cold coronaviruses. F1000Res 2021; 10:196. [PMID: 34026045 PMCID: PMC8108557 DOI: 10.12688/f1000research.51479.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/25/2021] [Indexed: 12/15/2022] Open
Abstract
In the spring of 2020, we and others hypothesized that T cells in COVID-19 patients may recognize identical protein fragments shared between the coronaviruses of the common cold and COVID-19 and thereby confer cross-virus immune memory. Here, we look at this issue by screening studies that, since that time, have experimentally addressed COVID-19 associated T cell specificities. Currently, the identical T cell epitope shared between COVID-19 and common cold coronaviruses most convincingly identified as immunogenic is the CD8 + T cell epitope VYIGDPAQL if presented by the MHC class I allele HLA-A*24:02. The HLA-A*24:02 allele is found in the majority of Japanese individuals and several indigenous populations in Asia, Oceania, and the Americas. In combination with histories of common cold infections, HLA-A*24:02 may affect their protection from COVID-19.
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Affiliation(s)
- Johannes M. Dijkstra
- Institute for Comprehensive Medical Science, Fujita Health Universit, Toyoake-shi, 470-1192, Japan
| | - Aaron P. Frenette
- Department of Biology, University of Waterlo, Waterloo, ON, N2L 3G1, Canada
| | - Brian Dixon
- Department of Biology, University of Waterlo, Waterloo, ON, N2L 3G1, Canada
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45
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Ujike M, Taguchi F. Recent Progress in Torovirus Molecular Biology. Viruses 2021; 13:435. [PMID: 33800523 PMCID: PMC7998386 DOI: 10.3390/v13030435] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 11/16/2022] Open
Abstract
Torovirus (ToV) has recently been classified into the new family Tobaniviridae, although it belonged to the Coronavirus (CoV) family historically. ToVs are associated with enteric diseases in animals and humans. In contrast to CoVs, which are recognised as pathogens of veterinary and medical importance, little attention has been paid to ToVs because their infections are usually asymptomatic or not severe; for a long time, only one equine ToV could be propagated in cultured cells. However, bovine ToVs, which predominantly cause diarrhoea in calves, have been detected worldwide, leading to economic losses. Porcine ToVs have also spread globally; although they have not caused serious economic losses, coinfections with other pathogens can exacerbate their symptoms. In addition, frequent inter- or intra-recombination among ToVs can increase pathogenesis or unpredicted host adaptation. These findings have highlighted the importance of ToVs as pathogens and the need for basic ToV research. Here, we review recent progress in the study of ToV molecular biology including reverse genetics, focusing on the similarities and differences between ToVs and CoVs.
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Affiliation(s)
- Makoto Ujike
- Laboratory of Veterinary Infectious Diseases, Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan;
- Research Center for Animal Life Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan
| | - Fumihiro Taguchi
- Laboratory of Veterinary Infectious Diseases, Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan;
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46
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V'kovski P, Kratzel A, Steiner S, Stalder H, Thiel V. Coronavirus biology and replication: implications for SARS-CoV-2. Nat Rev Microbiol 2021; 19:155-170. [PMID: 33116300 PMCID: PMC7592455 DOI: 10.1038/s41579-020-00468-6] [Citation(s) in RCA: 1706] [Impact Index Per Article: 568.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2020] [Indexed: 02/06/2023]
Abstract
The SARS-CoV-2 pandemic and its unprecedented global societal and economic disruptive impact has marked the third zoonotic introduction of a highly pathogenic coronavirus into the human population. Although the previous coronavirus SARS-CoV and MERS-CoV epidemics raised awareness of the need for clinically available therapeutic or preventive interventions, to date, no treatments with proven efficacy are available. The development of effective intervention strategies relies on the knowledge of molecular and cellular mechanisms of coronavirus infections, which highlights the significance of studying virus-host interactions at the molecular level to identify targets for antiviral intervention and to elucidate critical viral and host determinants that are decisive for the development of severe disease. In this Review, we summarize the first discoveries that shape our current understanding of SARS-CoV-2 infection throughout the intracellular viral life cycle and relate that to our knowledge of coronavirus biology. The elucidation of similarities and differences between SARS-CoV-2 and other coronaviruses will support future preparedness and strategies to combat coronavirus infections.
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Affiliation(s)
- Philip V'kovski
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Silvio Steiner
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Hanspeter Stalder
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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47
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Zhou B, Thao TTN, Hoffmann D, Taddeo A, Ebert N, Labroussaa F, Pohlmann A, King J, Steiner S, Kelly JN, Portmann J, Halwe NJ, Ulrich L, Trüeb BS, Fan X, Hoffmann B, Wang L, Thomann L, Lin X, Stalder H, Pozzi B, de Brot S, Jiang N, Cui D, Hossain J, Wilson MM, Keller MW, Stark TJ, Barnes JR, Dijkman R, Jores J, Benarafa C, Wentworth DE, Thiel V, Beer M. SARS-CoV-2 spike D614G change enhances replication and transmission. Nature 2021; 592:122-127. [PMID: 33636719 DOI: 10.1038/s41586-021-03361-1] [Citation(s) in RCA: 344] [Impact Index Per Article: 114.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/16/2021] [Indexed: 12/18/2022]
Abstract
During the evolution of SARS-CoV-2 in humans, a D614G substitution in the spike glycoprotein (S) has emerged; virus containing this substitution has become the predominant circulating variant in the COVID-19 pandemic1. However, whether the increasing prevalence of this variant reflects a fitness advantage that improves replication and/or transmission in humans or is merely due to founder effects remains unknown. Here we use isogenic SARS-CoV-2 variants to demonstrate that the variant that contains S(D614G) has enhanced binding to the human cell-surface receptor angiotensin-converting enzyme 2 (ACE2), increased replication in primary human bronchial and nasal airway epithelial cultures as well as in a human ACE2 knock-in mouse model, and markedly increased replication and transmissibility in hamster and ferret models of SARS-CoV-2 infection. Our data show that the D614G substitution in S results in subtle increases in binding and replication in vitro, and provides a real competitive advantage in vivo-particularly during the transmission bottleneck. Our data therefore provide an explanation for the global predominance of the variant that contains S(D614G) among the SARS-CoV-2 viruses that are currently circulating.
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Affiliation(s)
- Bin Zhou
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tran Thi Nhu Thao
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Adriano Taddeo
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Fabien Labroussaa
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Jacqueline King
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Silvio Steiner
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jasmine Portmann
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nico Joel Halwe
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Lorenz Ulrich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Bettina Salome Trüeb
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Xiaoyu Fan
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Li Wang
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lisa Thomann
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Xudong Lin
- Battelle Memorial Institute, Atlanta, GA, USA
| | - Hanspeter Stalder
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Berta Pozzi
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Simone de Brot
- COMPATH, Institute of Animal Pathology, University of Bern, Bern, Switzerland
| | - Nannan Jiang
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Dan Cui
- Battelle Memorial Institute, Atlanta, GA, USA
| | - Jaber Hossain
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Malania M Wilson
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Matthew W Keller
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Thomas J Stark
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John R Barnes
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ronald Dijkman
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Joerg Jores
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Charaf Benarafa
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland. .,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
| | - David E Wentworth
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland. .,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.
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48
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Hakim MS. SARS-CoV-2, Covid-19, and the debunking of conspiracy theories. Rev Med Virol 2021; 31:e2222. [PMID: 33586302 PMCID: PMC7995093 DOI: 10.1002/rmv.2222] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/16/2021] [Accepted: 01/19/2021] [Indexed: 12/25/2022]
Abstract
The emergence of a novel human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), has engaged considerable awareness and attention around the world. The associated disease, coronavirus disease 2019 (Covid‐19), has now involved virtually all 200 countries. The total number of confirmed cases has been much more than in the two previous outbreaks of human coronaviruses, that is, SARS‐CoV and Middle East respiratory syndrome coronavirus. In line with the outbreak escalation, false information about SARS‐CoV‐2 and its associated disease disseminated globally, particularly through online and social media. Believers in conspiracy theories promote misinformation that the virus is not contagious, is the result of laboratory manipulation or is created to gain profit by distributing new vaccines. The most dangerous effect of this widely disseminated misinformation is it will negatively influence the attitudes and behaviours for preventive measures to contain the outbreak. In this review, I discuss common conspiracy theories associated with SARS‐CoV‐2 and Covid‐19 and consider how we can address and counterbalance these issues based on scientific information and studies.
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Affiliation(s)
- Mohamad S Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Center for Child Health-PRO, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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49
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Molecular Evolution of Human Coronavirus 229E in Hong Kong and a Fatal COVID-19 Case Involving Coinfection with a Novel Human Coronavirus 229E Genogroup. mSphere 2021; 6:6/1/e00819-20. [PMID: 33568452 PMCID: PMC8544887 DOI: 10.1128/msphere.00819-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Compared to other human coronaviruses, the genetic diversity and evolution of human coronavirus 229E (HCoV-229E) are relatively understudied. We report a fatal case of COVID-19 pneumonia coinfected with HCoV-229E in Hong Kong. Genome sequencing of SARS-CoV-2 and HCoV-229E from a nasopharyngeal sample of the patient showed that the SARS-CoV-2 strain HK13 was most closely related to SARS-CoV-2 type strain Wuhan-Hu-1 (99.99% nucleotide identity), compatible with his recent history of travel to Wuhan. The HCoV-229E strain HK20-42 was most closely related to HCoV-229E strain SC0865 from the United States (99.86% nucleotide identity). To investigate if it may represent a newly emerged HCoV-229E genotype in Hong Kong, we retrieved 41 archived respiratory samples that tested positive for HCoV-229E from 2004 to 2019. Pneumonia and exacerbations of chronic airway diseases were common among infected patients. Complete RdRp, S, and N gene sequencing of the 41 HCoV-229E strains revealed that our contemporary HCoV-229E strains have undergone significant genetic drift with clustering of strains in chronological order. Two novel genogroups were identified, in addition to previously described genogroups 1 to 4, with recent circulating strains including strain HK20-42 belonging to novel genogroup 6. Positive selection was detected in the spike protein and receptor-binding domain, which may be important for viral evolution at the receptor-binding interphase. Molecular dating analysis showed that HCoV-229E shared the most recent common ancestor with bat and camel/alpaca 229E-related viruses at ∼1884, while camel/alpaca viruses had a relatively recent common ancestor at ∼1999. Further studies are required to ascertain the evolutionary origin and path of HCoV-229E.IMPORTANCE Since its first appearance in the 1960s, the genetic diversity and evolution of human coronavirus 229E (HCoV-229E) have been relatively understudied. In this study, we report a fatal case of COVID-19 coinfected with HCoV-229E in Hong Kong. Genome sequencing revealed that our SARS-CoV-2 strain is highly identical to the SARS-CoV-2 strain from Wuhan, compatible with the patient's recent travel history, whereas our HCoV-229E strain in this study is highly identical to a recent strain in the United States. We also retrieved 41 archived HCoV-229E strains from 2004 to 2019 in Hong Kong for sequence analysis. Pneumonia and exacerbations of chronic airway diseases were common diagnoses among the 41 patients. The results showed that HCoV-229E was evolving in chronological order. Two novel genogroups were identified in addition to the four preexisting HCoV-229E genogroups, with recent circulating strains belonging to novel genogroup 6. Molecular clock analysis dated bat-to-human and bat-to-camelid transmission to as early as 1884.
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50
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Coronavirus replication-transcription complex: Vital and selective NMPylation of a conserved site in nsp9 by the NiRAN-RdRp subunit. Proc Natl Acad Sci U S A 2021; 118:2022310118. [PMID: 33472860 PMCID: PMC8017715 DOI: 10.1073/pnas.2022310118] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
RNA-dependent RNA polymerases (RdRps) of the Nidovirales (Coronaviridae, Arteriviridae, and 12 other families) are linked to an amino-terminal (N-terminal) domain, called NiRAN, in a nonstructural protein (nsp) that is released from polyprotein 1ab by the viral main protease (Mpro). Previously, self-GMPylation/UMPylation activities were reported for an arterivirus NiRAN-RdRp nsp and suggested to generate a transient state primed for transferring nucleoside monophosphate (NMP) to (currently unknown) viral and/or cellular biopolymers. Here, we show that the coronavirus (human coronavirus [HCoV]-229E and severe acute respiratory syndrome coronavirus 2) nsp12 (NiRAN-RdRp) has Mn2+-dependent NMPylation activity that catalyzes the transfer of a single NMP to the cognate nsp9 by forming a phosphoramidate bond with the primary amine at the nsp9 N terminus (N3825) following Mpro-mediated proteolytic release of nsp9 from N-terminally flanking nsps. Uridine triphosphate was the preferred nucleotide in this reaction, but also adenosine triphosphate, guanosine triphosphate, and cytidine triphosphate were suitable cosubstrates. Mutational studies using recombinant coronavirus nsp9 and nsp12 proteins and genetically engineered HCoV-229E mutants identified residues essential for NiRAN-mediated nsp9 NMPylation and virus replication in cell culture. The data corroborate predictions on NiRAN active-site residues and establish an essential role for the nsp9 N3826 residue in both nsp9 NMPylation in vitro and virus replication. This residue is part of a conserved N-terminal NNE tripeptide sequence and shown to be the only invariant residue in nsp9 and its homologs in viruses of the family Coronaviridae The study provides a solid basis for functional studies of other nidovirus NMPylation activities and suggests a possible target for antiviral drug development.
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