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Wang X, Chen Y, Qi C, Li F, Zhang Y, Zhou J, Wu H, Zhang T, Qi A, Ouyang H, Xie Z, Pang D. Mechanism, structural and functional insights into nidovirus-induced double-membrane vesicles. Front Immunol 2024; 15:1340332. [PMID: 38919631 PMCID: PMC11196420 DOI: 10.3389/fimmu.2024.1340332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/22/2024] [Indexed: 06/27/2024] Open
Abstract
During infection, positive-stranded RNA causes a rearrangement of the host cell membrane, resulting in specialized membrane structure formation aiding viral genome replication. Double-membrane vesicles (DMVs), typical structures produced by virus-induced membrane rearrangements, are platforms for viral replication. Nidoviruses, one of the most complex positive-strand RNA viruses, have the ability to infect not only mammals and a few birds but also invertebrates. Nidoviruses possess a distinctive replication mechanism, wherein their nonstructural proteins (nsps) play a crucial role in DMV biogenesis. With the participation of host factors related to autophagy and lipid synthesis pathways, several viral nsps hijack the membrane rearrangement process of host endoplasmic reticulum (ER), Golgi apparatus, and other organelles to induce DMV formation. An understanding of the mechanisms of DMV formation and its structure and function in the infectious cycle of nidovirus may be essential for the development of new and effective antiviral strategies in the future.
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Affiliation(s)
- Xi Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Yiwu Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Chunyun Qi
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Feng Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Yuanzhu Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Jian Zhou
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Heyong Wu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Tianyi Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Aosi Qi
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Hongsheng Ouyang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
- Chongqing Research Institute, Jilin University, Chongqing, China
- Center for Animal Science and Technology Research, Chongqing Jitang Biotechnology Research Institute Co., Ltd, Chongqing, China
| | - Zicong Xie
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
- Chongqing Research Institute, Jilin University, Chongqing, China
| | - Daxin Pang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
- Chongqing Research Institute, Jilin University, Chongqing, China
- Center for Animal Science and Technology Research, Chongqing Jitang Biotechnology Research Institute Co., Ltd, Chongqing, China
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2
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Lauber C, Zhang X, Vaas J, Klingler F, Mutz P, Dubin A, Pietschmann T, Roth O, Neuman BW, Gorbalenya AE, Bartenschlager R, Seitz S. Deep mining of the Sequence Read Archive reveals major genetic innovations in coronaviruses and other nidoviruses of aquatic vertebrates. PLoS Pathog 2024; 20:e1012163. [PMID: 38648214 PMCID: PMC11065284 DOI: 10.1371/journal.ppat.1012163] [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: 08/25/2023] [Revised: 05/02/2024] [Accepted: 03/31/2024] [Indexed: 04/25/2024] Open
Abstract
Virus discovery by genomics and metagenomics empowered studies of viromes, facilitated characterization of pathogen epidemiology, and redefined our understanding of the natural genetic diversity of viruses with profound functional and structural implications. Here we employed a data-driven virus discovery approach that directly queries unprocessed sequencing data in a highly parallelized way and involves a targeted viral genome assembly strategy in a wide range of sequence similarity. By screening more than 269,000 datasets of numerous authors from the Sequence Read Archive and using two metrics that quantitatively assess assembly quality, we discovered 40 nidoviruses from six virus families whose members infect vertebrate hosts. They form 13 and 32 putative viral subfamilies and genera, respectively, and include 11 coronaviruses with bisegmented genomes from fishes and amphibians, a giant 36.1 kilobase coronavirus genome with a duplicated spike glycoprotein (S) gene, 11 tobaniviruses and 17 additional corona-, arteri-, cremega-, nanhypo- and nangoshaviruses. Genome segmentation emerged in a single evolutionary event in the monophyletic lineage encompassing the subfamily Pitovirinae. We recovered the bisegmented genome sequences of two coronaviruses from RNA samples of 69 infected fishes and validated the presence of poly(A) tails at both segments using 3'RACE PCR and subsequent Sanger sequencing. We report a genetic linkage between accessory and structural proteins whose phylogenetic relationships and evolutionary distances are incongruent with the phylogeny of replicase proteins. We rationalize these observations in a model of inter-family S recombination involving at least five ancestral corona- and tobaniviruses of aquatic hosts. In support of this model, we describe an individual fish co-infected with members from the families Coronaviridae and Tobaniviridae. Our results expand the scale of the known extraordinary evolutionary plasticity in nidoviral genome architecture and call for revisiting fundamentals of genome expression, virus particle biology, host range and ecology of vertebrate nidoviruses.
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Affiliation(s)
- Chris Lauber
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence 2155 RESIST, Hannover, Germany
| | - Xiaoyu Zhang
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Josef Vaas
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
| | - Franziska Klingler
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
| | - Pascal Mutz
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Arseny Dubin
- Marine Evolutionary Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Thomas Pietschmann
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence 2155 RESIST, Hannover, Germany
| | - Olivia Roth
- Marine Evolutionary Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Benjamin W. Neuman
- Department of Biology and Texas A&M Global Health Research Complex, Texas A&M University, College Station, Texas, United States
| | - Alexander E. Gorbalenya
- Leiden University Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
- Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ralf Bartenschlager
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
| | - Stefan Seitz
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
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3
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Schindewolf C, Menachery VD. Coronavirus 2'-O-methyltransferase: A promising therapeutic target. Virus Res 2023; 336:199211. [PMID: 37634741 PMCID: PMC10485632 DOI: 10.1016/j.virusres.2023.199211] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 08/29/2023]
Abstract
Coronaviruses (CoVs) have been the source of multiple epidemics and a global pandemic since the start of century, and there is an urgent need to understand CoV biology and develop better therapeutics. Here, we review the role of NSP16 in CoV replication, specifically its importance to 2'-O-methylation and CoV RNA capping. We describe the attenuation phenotypes of NSP16-mutant CoVs, the roles of MDA5 and IFITs in sensing and antagonizing viral RNA lacking 2'O methylation, and the dependence on 2'-O-methylation in other virus families. We also detail the growing body of research into targeting 2'-O-methylation for therapeutics or as a platform for live attenuated vaccines. Beyond its role in RNA capping, NSP16 may have yet uncharacterized importance to CoV replication, highlighting the need for continued studies into NSP16 functions. Understanding the full contribution of NSP16 to the replicative fitness of CoVs will better inform the development of treatments against future CoV outbreaks.
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Affiliation(s)
- Craig Schindewolf
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
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4
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Chen C, Liang J, Hu H, Li X, Wang L, Wang Z. Research progress in methods for detecting neutralizing antibodies against SARS-CoV-2. Anal Biochem 2023:115199. [PMID: 37257735 DOI: 10.1016/j.ab.2023.115199] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/13/2023] [Accepted: 05/27/2023] [Indexed: 06/02/2023]
Abstract
The emergence of SARS-CoV-2 has seriously affected the lives of people worldwide. Clarifying the attenuation rule of SARS-CoV-2 neutralizing antibody (NAb) in vivo is the key to prevent reinfection and recurrence of virus. Currently, the commonly used methods for detecting NAb include virus neutralization tests, pseudovirus neutralization assays, lateral flow immunochromatography and enzyme-linked immunosorbent assays. The detection of NAb not only can be used to evaluate the level of immunity after vaccination or infection but also can provide important theoretical support for virus reinfection, recurrence and vaccine iteration. In this research, the related technologies of SARS-CoV-2 NAb detection were reviewed, aiming to provide better research ideas for SARS-CoV-2 epidemic prevention and control.
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Affiliation(s)
- Chunxia Chen
- Joint National Laboratory for Antibody Drug Engineering, Clinical Laboratory of the First Affiliated Hospital, Henan University, Kaifeng, 475004, China
| | - Jiahui Liang
- Joint National Laboratory for Antibody Drug Engineering, Clinical Laboratory of the First Affiliated Hospital, Henan University, Kaifeng, 475004, China
| | - Hangzhan Hu
- Joint National Laboratory for Antibody Drug Engineering, Clinical Laboratory of the First Affiliated Hospital, Henan University, Kaifeng, 475004, China; Heze Municipal Hospital, Heze, 274000, China
| | - Xiaoquan Li
- Heze Municipal Hospital, Heze, 274000, China
| | - Li Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Henan University, Kaifeng, 475004, China.
| | - Zhizeng Wang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, China; Joint National Laboratory for Antibody Drug Engineering, Clinical Laboratory of the First Affiliated Hospital, Henan University, Kaifeng, 475004, China.
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5
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Intragenomic rearrangements involving 5'-untranslated region segments in SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses. Virol J 2023; 20:36. [PMID: 36829234 PMCID: PMC9957694 DOI: 10.1186/s12985-023-01998-0] [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: 05/08/2022] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Variation of the betacoronavirus SARS-CoV-2 has been the bane of COVID-19 control. Documented variation includes point mutations, deletions, insertions, and recombination among closely or distantly related coronaviruses. Here, we describe yet another aspect of genome variation by beta- and alphacoronaviruses that was first documented in an infectious isolate of the betacoronavirus SARS-CoV-2, obtained from 3 patients in Hong Kong that had a 5'-untranslated region segment at the end of the ORF6 gene that in its new location translated into an ORF6 protein with a predicted modified carboxyl terminus. While comparing the amino acid sequences of translated ORF8 genes in the GenBank database, we found a subsegment of the same 5'-UTR-derived amino acid sequence modifying the distal end of ORF8 of an isolate from the United States and decided to carry out a systematic search. METHODS Using the nucleotide and in the case of SARS-CoV-2 also the translated amino acid sequence in three reading frames of the genomic termini of coronaviruses as query sequences, we searched for 5'-UTR sequences in regions other than the 5'-UTR in SARS-CoV-2 and reference strains of alpha-, beta-, gamma-, and delta-coronaviruses. RESULTS We here report numerous genomic insertions of 5'-untranslated region sequences into coding regions of SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses, but not delta- or gammacoronaviruses. To our knowledge this is the first systematic description of such insertions. In many cases, these insertions would change viral protein sequences and further foster genomic flexibility and viral adaptability through insertion of transcription regulatory sequences in novel positions within the genome. Among human Embecorivus betacoronaviruses, for instance, from 65% to all of the surveyed sequences in publicly available databases contain inserted 5'-UTR sequences. CONCLUSION The intragenomic rearrangements involving 5'-untranslated region sequences described here, which in several cases affect highly conserved genes with a low propensity for recombination, may underlie the generation of variants homotypic with those of concern or interest and with potentially differing pathogenic profiles. Intragenomic rearrangements thus add to our appreciation of how variants of SARS-CoV-2 and other beta- and alphacoronaviruses may arise.
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6
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Mötz M, Stadler J, Kreutzmann H, Ladinig A, Lamp B, Auer A, Riedel C, Rümenapf T. A Conserved Stem-Loop Structure within ORF5 Is a Frequent Recombination Hotspot for Porcine Reproductive and Respiratory Syndrome Virus 1 (PRRSV-1) with a Particular Modified Live Virus (MLV) Strain. Viruses 2023; 15:258. [PMID: 36680298 PMCID: PMC9867337 DOI: 10.3390/v15010258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/09/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
The emergence of recombinant PRRSV strains has been observed for more than a decade. These recombinant viruses are characterized by a genome that contains genetic material from at least two different parental strains. Due to the advanced sequencing techniques and a growing number of data bank entries, the role of PRRSV recombinants has become increasingly important since they are sometimes associated with clinical outbreaks. Chimeric viruses observed more recently are products of PRRSV wild-type and vaccine strains. Here, we report on three PRRSV-1 isolates from geographically distant farms with differing clinical manifestations. A sequencing and recombination analysis revealed that these strains are crossovers between different wild-type strains and the same modified live virus vaccine strain. Interestingly, the recombination breakpoint of all analyzed isolates appears at the beginning of open reading frame 5 (ORF5). RNA structure predictions indicate a conserved stem loop in close proximity to the recombination hotspot, which is a plausible cause of a polymerase template switch during RNA replication. Further research into the mechanisms of the stem loop is needed to help understand the PRRSV recombination process and the role of MLVs as parental strains.
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Affiliation(s)
- Marlene Mötz
- Institute of Virology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Julia Stadler
- Clinic for Swine, Center for Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstrasse 16, 85764 Oberschleissenheim, Germany
| | - Heinrich Kreutzmann
- Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Andrea Ladinig
- Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Benjamin Lamp
- Institute of Virology, Department of Veterinary Medicine, Justus-Liebig-University Giessen, Schubertstraße 81, 35392 Giessen, Germany
| | - Angelika Auer
- Institute of Virology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Christiane Riedel
- Département de Biologie, École Nationale Supérieure de Lyon, 46 Allée d’Italie, 69364 Lyon, France
- Centre International de Recherche en Infectiologie (CIRI), 46 Allée d’Italie, 69364 Lyon, France
| | - Till Rümenapf
- Institute of Virology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
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7
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Benazraf A, Arkin IT. Exhaustive mutational analysis of severe acute respiratory syndrome coronavirus 2 ORF3a: An essential component in the pathogen's infectivity cycle. Protein Sci 2023; 32:e4528. [PMID: 36468608 PMCID: PMC9795539 DOI: 10.1002/pro.4528] [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: 09/08/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 12/07/2022]
Abstract
Detailed knowledge of a protein's key residues may assist in understanding its function and designing inhibitors against it. Consequently, such knowledge of one of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)'s proteins is advantageous since the virus is the etiological agent behind one of the biggest health crises of recent times. To that end, we constructed an exhaustive library of bacteria differing from each other by the mutated version of the virus's ORF3a viroporin they harbor. Since the protein is harmful to bacterial growth due to its channel activity, genetic selection followed by deep sequencing could readily identify mutations that abolish the protein's function. Our results have yielded numerous mutations dispersed throughout the sequence that counteract ORF3a's ability to slow bacterial growth. Comparing these data with the conservation pattern of ORF3a within the coronavirinae provided interesting insights: Deleterious mutations obtained in our study corresponded to conserved residues in the protein. However, despite the comprehensive nature of our mutagenesis coverage (108 average mutations per site), we could not reveal all of the protein's conserved residues. Therefore, it is tempting to speculate that our study unearthed positions in the protein pertinent to channel activity, while other conserved residues may correspond to different functionalities of ORF3a. In conclusion, our study provides important information on a key component of SARS-CoV-2 and establishes a procedure to analyze other viroporins comprehensively.
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Affiliation(s)
- Amit Benazraf
- Department of Biological ChemistryThe Alexander Silberman Institute of Life Sciences, The Hebrew University of JerusalemJerusalemIsrael
| | - Isaiah T. Arkin
- Department of Biological ChemistryThe Alexander Silberman Institute of Life Sciences, The Hebrew University of JerusalemJerusalemIsrael
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8
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Ahmed JQ, Maulud SQ. Complete Genomic Characterisation and Mutation Patterns of Iraqi SARS-CoV-2 Isolates. Diagnostics (Basel) 2022; 13:diagnostics13010008. [PMID: 36611300 PMCID: PMC9818665 DOI: 10.3390/diagnostics13010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
This study was performed for molecular characterisation of the SARS-CoV-2 strains in Iraq and reveal their variants, lineages, clades, and mutation patterns. A total of 912 Iraqi sequences were retrieved from GISAID, which had been submitted from the beginning of the SARS-CoV-2 pandemic to 26 September 2022, along with 12 samples that were collected during the third and fifth waves of the SARS-CoV-2 pandemic. Next-generation sequencing was performed using an Illumina MiSeq system, and phylogenetic analysis was performed for all the Iraqi sequences retrieved from GISAID. Three established global platforms GISAID, Nextstrain, and PANGO were used for the classification of isolates into distinct clades, variants, and lineages. Analysis of the isolates of this study showed that all the sequences from the third wave were clustered in the GK clades and the 21J (Delta) clade according to the GISAID and Nextclade systems, while the PANGO system revealed that six sequences were B.1.617.2 and four sequences were of the AY.33 lineage. Furthermore, the latest e wave in the summer of 2022 was due to thpredominance of the BA.5.2 lineage of the 22B (Omicron) clade in Iraq. Our study revealed patterns of circulation and dominance of SARS-CoV-2 clades and their lineages in the subsequent pandemic waves in the country.
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Affiliation(s)
- Jivan Qasim Ahmed
- Department of Pathology and Microbiology, University of Duhok, Duhok 42001, Iraq
- Correspondence: ; Tel.: +964-7504907280
| | - Sazan Qadir Maulud
- Department of Biology, College of Education, Salahaddin University-Erbil, Erbil 44001, Iraq
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9
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Shannon A, Sama B, Gauffre P, Guez T, Debart F, Vasseur JJ, Decroly E, Canard B, Ferron F. A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome. Nucleic Acids Res 2022; 50:11186-11198. [PMID: 36265859 DOI: 10.1093/nar/gkac876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 09/29/2022] [Indexed: 11/12/2022] Open
Abstract
The order Nidovirales is a diverse group of (+)RNA viruses, with a common genome organization and conserved set of replicative and editing enzymes. In particular, RNA methyltransferases play a central role in mRNA stability and immune escape. However, their presence and distribution in different Nidovirales families is not homogeneous. In Coronaviridae, the best characterized family, two distinct methytransferases perform methylation of the N7-guanine and 2'-OH of the RNA-cap to generate a cap-1 structure (m7GpppNm). The genes of both of these enzymes are located in the ORF1b genomic region. While 2'-O-MTases can be identified for most other families based on conservation of both sequence motifs and genetic loci, identification of the N7-guanine methyltransferase has proved more challenging. Recently, we identified a putative N7-MTase domain in the ORF1a region (N7-MT-1a) of certain members of the large genome Tobaniviridae family. Here, we demonstrate that this domain indeed harbors N7-specific methyltransferase activity. We present its structure as the first N7-specific Rossmann-fold (RF) MTase identified for (+)RNA viruses, making it remarkably different from that of the known Coronaviridae ORF1b N7-MTase gene. We discuss the evolutionary implications of such an appearance in this unexpected location in the genome, which introduces a split-off in the classification of Tobaniviridae.
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Affiliation(s)
- Ashleigh Shannon
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France
| | - Bhawna Sama
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France
| | - Pierre Gauffre
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France
| | - Théo Guez
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Françoise Debart
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | | | - Etienne Decroly
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France
| | - Bruno Canard
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France.,European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - François Ferron
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France.,European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
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10
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Walter M, Chen IP, Vallejo-Gracia A, Kim IJ, Bielska O, Lam VL, Hayashi JM, Cruz A, Shah S, Soveg FW, Gross JD, Krogan NJ, Jerome KR, Schilling B, Ott M, Verdin E. SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein. PLoS Pathog 2022; 18:e1010811. [PMID: 36095012 PMCID: PMC9499238 DOI: 10.1371/journal.ppat.1010811] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 09/22/2022] [Accepted: 08/18/2022] [Indexed: 12/27/2022] Open
Abstract
SARS-CoV-2 non-structural protein Nsp14 is a highly conserved enzyme necessary for viral replication. Nsp14 forms a stable complex with non-structural protein Nsp10 and exhibits exoribonuclease and N7-methyltransferase activities. Protein-interactome studies identified human sirtuin 5 (SIRT5) as a putative binding partner of Nsp14. SIRT5 is an NAD-dependent protein deacylase critical for cellular metabolism that removes succinyl and malonyl groups from lysine residues. Here we investigated the nature of this interaction and the role of SIRT5 during SARS-CoV-2 infection. We showed that SIRT5 interacts with Nsp14, but not with Nsp10, suggesting that SIRT5 and Nsp10 are parts of separate complexes. We found that SIRT5 catalytic domain is necessary for the interaction with Nsp14, but that Nsp14 does not appear to be directly deacylated by SIRT5. Furthermore, knock-out of SIRT5 or treatment with specific SIRT5 inhibitors reduced SARS-CoV-2 viral levels in cell-culture experiments. SIRT5 knock-out cells expressed higher basal levels of innate immunity markers and mounted a stronger antiviral response, independently of the Mitochondrial Antiviral Signaling Protein MAVS. Our results indicate that SIRT5 is a proviral factor necessary for efficient viral replication, which opens novel avenues for therapeutic interventions.
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Affiliation(s)
- Marius Walter
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Irene P. Chen
- Gladstone Institutes, San Francisco, California, United States of America
- University of California San Francisco, San Francisco, California, United States of America
- QBI COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Albert Vallejo-Gracia
- Gladstone Institutes, San Francisco, California, United States of America
- University of California San Francisco, San Francisco, California, United States of America
- QBI COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Ik-Jung Kim
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Olga Bielska
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Victor L. Lam
- University of California San Francisco, San Francisco, California, United States of America
| | - Jennifer M. Hayashi
- Gladstone Institutes, San Francisco, California, United States of America
- University of California San Francisco, San Francisco, California, United States of America
- QBI COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Andrew Cruz
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Samah Shah
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Frank W. Soveg
- Gladstone Institutes, San Francisco, California, United States of America
- University of California San Francisco, San Francisco, California, United States of America
- QBI COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - John D. Gross
- University of California San Francisco, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, United States of America
| | - Nevan J. Krogan
- Gladstone Institutes, San Francisco, California, United States of America
- University of California San Francisco, San Francisco, California, United States of America
- QBI COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, United States of America
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Melanie Ott
- Gladstone Institutes, San Francisco, California, United States of America
- University of California San Francisco, San Francisco, California, United States of America
- QBI COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California, United States of America
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11
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Sequencing and mutations analysis of the first recorded SARS-CoV-2 Omicron variant during the fourth wave of pandemic in Iraq. Braz J Infect Dis 2022; 26:102677. [PMID: 35970304 PMCID: PMC9359486 DOI: 10.1016/j.bjid.2022.102677] [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] [Received: 05/05/2022] [Revised: 07/08/2022] [Accepted: 07/25/2022] [Indexed: 11/29/2022] Open
Abstract
Despite vaccine development and vaccination programs underway around the globe, the coronavirus disease 2019 (COVID-19) pandemic has not been controlled as the SARS-CoV-2 virus is evolving and new variants are emerging. This study was conducted to sequence and molecularly characterize the representing samples from the early fourth SARS-CoV-2 wave in Iraq. Here, we have performed next-generation sequencing of whole-genome sequencing of two representing samples from the country's early beginning of the fourth pandemic wave. The samples were sequenced using Illumina Miseq system, and the reference sequences were retrieved from GISAID database. Phylogenetic analysis was performed through Mega software. This study provides an initial sequence analysis and molecular characterization of the first Omicron variant cases recorded in the country. Our analysis revealed many mutations on the spike glycoprotein, especially on the receptor binding domain, with potential impact on immune escape and infectivity. The study findings suggest considering the highly mutated immunogenic epitope of the Omicron variant as a reference for developing a new vaccine for combating the ongoing pandemic.
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12
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Mötz M, Stas MR, Hammer SE, Duckova T, Fontaine F, Kiesler A, Seitz K, Ladinig A, Müller AC, Riedel C, Saalmüller A, Rümenapf T. Identification of MHC-I-Presented Porcine Respiratory and Reproductive Syndrome Virus (PRRSV) Peptides Reveals Immunogenic Epitopes within Several Non-Structural Proteins Recognized by CD8+ T Cells. Viruses 2022; 14:v14091891. [PMID: 36146698 PMCID: PMC9502253 DOI: 10.3390/v14091891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most relevant porcine pathogens worldwide. Active control of the disease relies on modified live virus vaccines (MLVs), as most inactivated vaccines provide very limited protection. Neutralizing antibodies occur late in infection; therefore, CD8+ T cells are considered important correlates of protection and are a frequent focus of investigation. Our aim was to identify viral peptides naturally bound by the class I major histocompatibility complex (MHC-I) and to confirm their ability to stimulate CD8+ T cells. For this purpose, we immunoprecipitated MHC-I/peptide complexes of PRRSV (strain AUT15-33) -infected cells (SLA-I Lr-Hp 35.0/24 mod) to isolate the viral epitopes and analyzed them with liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Furthermore, we employed these identified peptides to stimulate peripheral blood mononuclear cells (PBMCs) of previously PRRSV-infected pigs and measured the PRRSV-specific CD8+ T-cell response with an intracellular cytokine staining (ICS). Our data revealed that PRRSV non-structural proteins (NSPs), encoded in open reading frame 1a and 1b (ORF1), present the major source of MHC-I-presented peptides. Additionally, we show that our identified epitopes are able to trigger IFNγ responses in vitro. These findings are a basis for understanding the proteasomal degradation of PRRSV proteins, the cellular ability to display them via MHC-I, and their potential to restimulate CD8+ T cells.
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Affiliation(s)
- Marlene Mötz
- Institute of Virology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
- Correspondence: (M.M.); (T.R.)
| | - Melissa R. Stas
- Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Sabine E. Hammer
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Tereza Duckova
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Frederic Fontaine
- CeMM Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Alexandra Kiesler
- Institute of Virology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Kerstin Seitz
- Institute of Virology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Andrea Ladinig
- Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - André C. Müller
- CeMM Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Christiane Riedel
- Institute of Virology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Armin Saalmüller
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Till Rümenapf
- Institute of Virology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
- Correspondence: (M.M.); (T.R.)
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13
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Campagnola G, Govindarajan V, Pelletier A, Canard B, Peersen OB. The SARS-CoV nsp12 Polymerase Active Site Is Tuned for Large-Genome Replication. J Virol 2022; 96:e0067122. [PMID: 35924919 PMCID: PMC9400494 DOI: 10.1128/jvi.00671-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/06/2022] [Indexed: 01/18/2023] Open
Abstract
Positive-strand RNA viruses replicate their genomes using virally encoded RNA-dependent RNA polymerases (RdRP) with a common active-site structure and closure mechanism upon which replication speed and fidelity can evolve to optimize virus fitness. Coronaviruses (CoV) form large multicomponent RNA replication-transcription complexes containing a core RNA synthesis machine made of the nsp12 RdRP protein with one nsp7 and two nsp8 proteins as essential subunits required for activity. We show that assembly of this complex can be accelerated 5-fold by preincubation of nsp12 with nsp8 and further optimized with the use of a novel nsp8L7 heterodimer fusion protein construct. Using rapid kinetics methods, we measure elongation rates of up to 260 nucleotides (nt)/s for the core replicase, a rate that is unusually fast for a viral polymerase. To address the origin of this fast rate, we examined the roles of two CoV-specific residues in the RdRP active site: Ala547, which replaces a conserved glutamate above the bound NTP, and Ser759, which mutates the palm domain GDD sequence to SDD. Our data show that Ala547 allows for a doubling of replication rate, but this comes at a fidelity cost that is mitigated by using a SDD sequence in the palm domain. Our biochemical data suggest that fixation of mutations in polymerase motifs F and C played a key role in nidovirus evolution by tuning replication rate and fidelity to accommodate their large genomes. IMPORTANCE Replicating large genomes represents a challenge for RNA viruses because fast RNA synthesis is needed to escape innate immunity defenses, but faster polymerases are inherently low-fidelity enzymes. Nonetheless, the coronaviruses replicate their ≈30-kb genomes using the core polymerase structure and mechanism common to all positive-strand RNA viruses. The classic explanation for their success is that the large-genome nidoviruses have acquired an exonuclease-based repair system that compensates for the high polymerase mutation rate. In this work, we establish that the nidoviral polymerases themselves also play a key role in maintaining genome integrity via mutations at two key active-site residues that enable very fast replication rates while maintaining typical mutation rates. Our findings further demonstrate the evolutionary plasticity of the core polymerase platform by showing how it has adapted during the expansion from short-genome picornaviruses to long-genome nidoviruses.
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Affiliation(s)
- Grace Campagnola
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Vishnu Govindarajan
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Annelise Pelletier
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Bruno Canard
- Centre National de la Recherche Scientifique, Aix-Marseille Université CNRS UMR 7257, AFMB, Marseille, France
| | - Olve B. Peersen
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
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14
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Kawashima IY, Lopez MCN, Cunha MDP, Hashimoto RF. SARS-CoV-2 host prediction based on virus-host genetic features. Sci Rep 2022; 12:4576. [PMID: 35301337 PMCID: PMC8930995 DOI: 10.1038/s41598-022-08350-6] [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] [Received: 09/30/2021] [Accepted: 02/28/2022] [Indexed: 11/25/2022] Open
Abstract
The genetic diversity of the Coronaviruses gives them different biological abilities, such as infect different cells and/or organisms, a wide spectrum of clinical manifestations, their different routes of dispersion, and viral transmission in a specific host. In recent decades, different Coronaviruses have emerged that are highly adapted for humans and causing serious diseases, leaving their host of unknown origin. The viral genome information is particularly important to enable the recognition of patterns linked to their biological characteristics, such as the specificity in the host-parasite relationship. Here, based on a previously computational tool, the Seq2Hosts, we developed a novel approach which uses new variables obtained from the frequency of spike-Coronaviruses codons, the Relative Synonymous Codon Usage (RSCU) to shed new light on the molecular mechanisms involved in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) host specificity. By using the RSCU obtained from nucleotide sequences before the SARS-CoV-2 pandemic, we assessed the possibility of know the hosts capable to be infected by these new emerging species, which was first identified infecting humans during 2019 in Wuhan, China. According to the model trained and validated using sequences available before the pandemic, bats are the most likely the natural host to the SARS-CoV-2 infection, as previously suggested in other studies that searched for the host viral origin.
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Affiliation(s)
- Irina Yuri Kawashima
- Institute of Mathematics and Statistics, University of Sao Paulo, São Paulo, 05508-090, Brazil
| | | | | | - Ronaldo Fumio Hashimoto
- Institute of Mathematics and Statistics, University of Sao Paulo, São Paulo, 05508-090, Brazil.
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15
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Morais P, Trovão N, Abecasis A, Parreira R. Readdressing the genetic diversity and taxonomy of the Mesoniviridae family, as well as its relationships with other nidoviruses and putative mesonivirus-like viral sequences. Virus Res 2022; 313:198727. [DOI: 10.1016/j.virusres.2022.198727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 10/18/2022]
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16
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Nikolaidis M, Markoulatos P, Van de Peer Y, Oliver SG, Amoutzias GD. The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes. Mol Biol Evol 2022; 39:msab292. [PMID: 34638137 PMCID: PMC8549283 DOI: 10.1093/molbev/msab292] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Coronaviruses (CoVs) have very large RNA viral genomes with a distinct genomic architecture of core and accessory open reading frames (ORFs). It is of utmost importance to understand their patterns and limits of homologous and nonhomologous recombination, because such events may affect the emergence of novel CoV strains, alter their host range, infection rate, tissue tropism pathogenicity, and their ability to escape vaccination programs. Intratypic recombination among closely related CoVs of the same subgenus has often been reported; however, the patterns and limits of genomic exchange between more distantly related CoV lineages (intertypic recombination) need further investigation. Here, we report computational/evolutionary analyses that clearly demonstrate a substantial ability for CoVs of different subgenera to recombine. Furthermore, we show that CoVs can obtain-through nonhomologous recombination-accessory ORFs from core ORFs, exchange accessory ORFs with different CoV genera, with other viruses (i.e., toroviruses, influenza C/D, reoviruses, rotaviruses, astroviruses) and even with hosts. Intriguingly, most of these radical events result from double crossovers surrounding the Spike ORF, thus highlighting both the instability and mobile nature of this genomic region. Although many such events have often occurred during the evolution of various CoVs, the genomic architecture of the relatively young SARS-CoV/SARS-CoV-2 lineage so far appears to be stable.
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Affiliation(s)
- Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Panayotis Markoulatos
- Microbial Biotechnology-Molecular Bacteriology-Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Stephen G Oliver
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Grigorios D Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
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17
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Walter M, Chen IP, Vallejo-Gracia A, Kim IJ, Bielska O, Lam VL, Hayashi JM, Cruz A, Shah S, Gross JD, Krogan NJ, Schilling B, Ott M, Verdin E. SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.01.04.474979. [PMID: 35018374 PMCID: PMC8750649 DOI: 10.1101/2022.01.04.474979] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
SARS-CoV-2 non-structural protein Nsp14 is a highly conserved enzyme necessary for viral replication. Nsp14 forms a stable complex with non-structural protein Nsp10 and exhibits exoribonuclease and N7-methyltransferase activities. Protein-interactome studies identified human sirtuin 5 (SIRT5) as a putative binding partner of Nsp14. SIRT5 is an NAD-dependent protein deacylase critical for cellular metabolism that removes succinyl and malonyl groups from lysine residues. Here we investigated the nature of this interaction and the role of SIRT5 during SARS-CoV-2 infection. We showed that SIRT5 stably interacts with Nsp14, but not with Nsp10, suggesting that SIRT5 and Nsp10 are parts of separate complexes. We found that SIRT5 catalytic domain is necessary for the interaction with Nsp14, but that Nsp14 does not appear to be directly deacylated by SIRT5. Furthermore, knock-out of SIRT5 or treatment with specific SIRT5 inhibitors reduced SARS-CoV-2 viral levels in cell-culture experiments. SIRT5 knock-out cells expressed higher basal levels of innate immunity markers and mounted a stronger antiviral response. Our results indicate that SIRT5 is a proviral factor necessary for efficient viral replication, which opens novel avenues for therapeutic interventions.
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Affiliation(s)
- Marius Walter
- Buck Institute for Research on Aging, Novato, CA, United States
| | - Irene P Chen
- Gladstone Institutes, San Francisco, CA, United States
- University of California San Francisco, San Francisco, CA, United States
| | - Albert Vallejo-Gracia
- Gladstone Institutes, San Francisco, CA, United States
- University of California San Francisco, San Francisco, CA, United States
| | - Ik-Jung Kim
- Buck Institute for Research on Aging, Novato, CA, United States
| | - Olga Bielska
- Buck Institute for Research on Aging, Novato, CA, United States
| | - Victor L Lam
- University of California San Francisco, San Francisco, CA, United States
| | - Jennifer M Hayashi
- Gladstone Institutes, San Francisco, CA, United States
- University of California San Francisco, San Francisco, CA, United States
| | - Andrew Cruz
- Buck Institute for Research on Aging, Novato, CA, United States
| | - Samah Shah
- Buck Institute for Research on Aging, Novato, CA, United States
| | - John D Gross
- University of California San Francisco, San Francisco, CA, United States
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, United States
| | - Nevan J Krogan
- Gladstone Institutes, San Francisco, CA, United States
- University of California San Francisco, San Francisco, CA, United States
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, United States
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, United States
| | | | - Melanie Ott
- Gladstone Institutes, San Francisco, CA, United States
- University of California San Francisco, San Francisco, CA, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA, United States
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18
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Amoutzias GD, Nikolaidis M, Tryfonopoulou E, Chlichlia K, Markoulatos P, Oliver SG. The Remarkable Evolutionary Plasticity of Coronaviruses by Mutation and Recombination: Insights for the COVID-19 Pandemic and the Future Evolutionary Paths of SARS-CoV-2. Viruses 2022; 14:78. [PMID: 35062282 PMCID: PMC8778387 DOI: 10.3390/v14010078] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/22/2021] [Accepted: 12/31/2021] [Indexed: 12/13/2022] Open
Abstract
Coronaviruses (CoVs) constitute a large and diverse subfamily of positive-sense single-stranded RNA viruses. They are found in many mammals and birds and have great importance for the health of humans and farm animals. The current SARS-CoV-2 pandemic, as well as many previous epidemics in humans that were of zoonotic origin, highlights the importance of studying the evolution of the entire CoV subfamily in order to understand how novel strains emerge and which molecular processes affect their adaptation, transmissibility, host/tissue tropism, and patho non-homologous genicity. In this review, we focus on studies over the last two years that reveal the impact of point mutations, insertions/deletions, and intratypic/intertypic homologous and non-homologous recombination events on the evolution of CoVs. We discuss whether the next generations of CoV vaccines should be directed against other CoV proteins in addition to or instead of spike. Based on the observed patterns of molecular evolution for the entire subfamily, we discuss five scenarios for the future evolutionary path of SARS-CoV-2 and the COVID-19 pandemic. Finally, within this evolutionary context, we discuss the recently emerged Omicron (B.1.1.529) VoC.
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Affiliation(s)
- Grigorios D. Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Eleni Tryfonopoulou
- Laboratory of Molecular Immunology, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus-Dragana, 68100 Alexandroupolis, Greece; (E.T.); (K.C.)
| | - Katerina Chlichlia
- Laboratory of Molecular Immunology, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus-Dragana, 68100 Alexandroupolis, Greece; (E.T.); (K.C.)
| | - Panayotis Markoulatos
- Microbial Biotechnology-Molecular Bacteriology-Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Stephen G. Oliver
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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19
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Caetano-Anollés K, Hernandez N, Mughal F, Tomaszewski T, Caetano-Anollés G. The seasonal behaviour of COVID-19 and its galectin-like culprit of the viral spike. METHODS IN MICROBIOLOGY 2021; 50:27-81. [PMID: 38620818 PMCID: PMC8590929 DOI: 10.1016/bs.mim.2021.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Seasonal behaviour is an attribute of many viral diseases. Like other 'winter' RNA viruses, infections caused by the causative agent of COVID-19, SARS-CoV-2, appear to exhibit significant seasonal changes. Here we discuss the seasonal behaviour of COVID-19, emerging viral phenotypes, viral evolution, and how the mutational landscape of the virus affects the seasonal attributes of the disease. We propose that the multiple seasonal drivers behind infectious disease spread (and the spread of COVID-19 specifically) are in 'trade-off' relationships and can be better described within a framework of a 'triangle of viral persistence' modulated by the environment, physiology, and behaviour. This 'trade-off' exists as one trait cannot increase without a decrease in another. We also propose that molecular components of the virus can act as sensors of environment and physiology, and could represent molecular culprits of seasonality. We searched for flexible protein structures capable of being modulated by the environment and identified a galectin-like fold within the N-terminal domain of the spike protein of SARS-CoV-2 as a potential candidate. Tracking the prevalence of mutations in this structure resulted in the identification of a hemisphere-dependent seasonal pattern driven by mutational bursts. We propose that the galectin-like structure is a frequent target of mutations because it helps the virus evade or modulate the physiological responses of the host to further its spread and survival. The flexible regions of the N-terminal domain should now become a focus for mitigation through vaccines and therapeutics and for prediction and informed public health decision making.
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Affiliation(s)
| | - Nicolas Hernandez
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Tre Tomaszewski
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
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20
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Tan CCS, Owen CJ, Tham CYL, Bertoletti A, van Dorp L, Balloux F. Pre-existing T cell-mediated cross-reactivity to SARS-CoV-2 cannot solely be explained by prior exposure to endemic human coronaviruses. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 95:105075. [PMID: 34509646 PMCID: PMC8428999 DOI: 10.1016/j.meegid.2021.105075] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 02/07/2023]
Abstract
T-cell-mediated immunity to SARS-CoV-2-derived peptides in individuals unexposed to SARS-CoV-2 has been previously reported. This pre-existing immunity was suggested to largely derive from prior exposure to 'common cold' endemic human coronaviruses (HCoVs). To test this, we characterised the sequence homology of SARS-CoV-2-derived T-cell epitopes reported in the literature across the full proteome of the Coronaviridae family. 54.8% of these epitopes had no homology to any of the HCoVs. Further, the proportion of SARS-CoV-2-derived epitopes with any level of sequence homology to the proteins encoded by any of the coronaviruses tested is well-predicted by their alignment-free phylogenetic distance to SARS-CoV-2 (Pearson's r = -0.958). No coronavirus in our dataset showed a significant excess of T-cell epitope homology relative to the proportion of expected random matches, given their genetic similarity to SARS-CoV-2. Our findings suggest that prior exposure to human or animal-associated coronaviruses cannot completely explain the T-cell repertoire in unexposed individuals that recognise SARS-CoV-2 cross-reactive epitopes.
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Affiliation(s)
- Cedric C S Tan
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, United Kingdom.
| | - Christopher J Owen
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Christine Y L Tham
- Emerging Infectious Diseases Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Antonio Bertoletti
- Emerging Infectious Diseases Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Francois Balloux
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, United Kingdom
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21
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Wang B, Svetlov D, Artsimovitch I. NMPylation and de-NMPylation of SARS-CoV-2 nsp9 by the NiRAN domain. Nucleic Acids Res 2021; 49:8822-8835. [PMID: 34352100 PMCID: PMC8385902 DOI: 10.1093/nar/gkab677] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/15/2021] [Accepted: 07/26/2021] [Indexed: 12/11/2022] Open
Abstract
The catalytic subunit of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) contains two active sites that catalyze nucleotidyl-monophosphate transfer (NMPylation). Mechanistic studies and drug discovery have focused on RNA synthesis by the highly conserved RdRp. The second active site, which resides in a Nidovirus RdRp-Associated Nucleotidyl transferase (NiRAN) domain, is poorly characterized, but both catalytic reactions are essential for viral replication. One study showed that NiRAN transfers NMP to the first residue of RNA-binding protein nsp9; another reported a structure of nsp9 containing two additional N-terminal residues bound to the NiRAN active site but observed NMP transfer to RNA instead. We show that SARS-CoV-2 RdRp NMPylates the native but not the extended nsp9. Substitutions of the invariant NiRAN residues abolish NMPylation, whereas substitution of a catalytic RdRp Asp residue does not. NMPylation can utilize diverse nucleotide triphosphates, including remdesivir triphosphate, is reversible in the presence of pyrophosphate, and is inhibited by nucleotide analogs and bisphosphonates, suggesting a path for rational design of NiRAN inhibitors. We reconcile these and existing findings using a new model in which nsp9 remodels both active sites to alternately support initiation of RNA synthesis by RdRp or subsequent capping of the product RNA by the NiRAN domain.
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Affiliation(s)
- Bing Wang
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | | | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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22
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Bhavaniramya S, Ramar V, Vishnupriya S, Palaniappan R, Sibiya A, Baskaralingam V. Comprehensive analysis of SARS-COV-2 drug targets and pharmacological aspects in treating the COVID-19. Curr Mol Pharmacol 2021; 15:393-417. [PMID: 34382513 DOI: 10.2174/1874467214666210811120635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/27/2021] [Accepted: 02/22/2021] [Indexed: 11/22/2022]
Abstract
Corona viruses are enveloped, single-stranded RNA (Ribonucleic acid) viruses and they cause pandemic diseases having a devastating effect on both human healthcare and the global economy. To date, six corona viruses have been identified as pathogenic organisms which are significantly responsible for the infection and also cause severe respiratory diseases. Among them, the novel SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) caused a major outbreak of corona virus diseases 2019 (COVID-19). Coronaviridae family members can affects both humans and animals. In human, corona viruses cause severe acute respiratory syndrome with mild to severe outcomes. Several structural and genomics have been investigated, and the genome encodes about 28 proteins most of them with unknown function though it shares remarkable sequence identity with other proteins. There is no potent and licensed vaccine against SARS-CoV-2 and several trials are underway to investigate the possible therapeutic agents against viral infection. However, some of the antiviral drugs that have been investigated against SARS-CoV-2 are under clinical trials. In the current review we comparatively emphasize the emergence and pathogenicity of the SARS-CoV-2 and their infection and discuss the various putative drug targets of both viral and host receptors for developing effective vaccines and therapeutic combinations to overcome the viral outbreak.
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Affiliation(s)
- Sundaresan Bhavaniramya
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
| | - Vanajothi Ramar
- Department of Biomedical Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024. India
| | - Selvaraju Vishnupriya
- College of Food and Dairy Technology, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600052. India
| | - Ramasamy Palaniappan
- Research and Development Wing, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education (BIHER), Chennai-600044, Tamilnadu. India
| | - Ashokkumar Sibiya
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
| | - Vaseeharan Baskaralingam
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
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23
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Ferron F, Sama B, Decroly E, Canard B. The enzymes for genome size increase and maintenance of large (+)RNA viruses. Trends Biochem Sci 2021; 46:866-877. [PMID: 34172362 DOI: 10.1016/j.tibs.2021.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/05/2021] [Accepted: 05/18/2021] [Indexed: 02/08/2023]
Abstract
With sizes <50 kb, viral RNA genomes are at the crossroads of genetic, biophysical, and biochemical stability in their host cell. Here, we analyze the enzymatic assets accompanying large RNA genome viruses, mostly based on recent scientific advances in Coronaviridae. We argue that, in addition to the presence of an RNA exonuclease (ExoN), two markers for the large size of viral RNA genomes are (i) the presence of one or more RNA methyltransferases (MTases) and (ii) a specific architecture of the RNA-dependent RNA polymerase active site. We propose that RNA genome expansion and maintenance are driven by an evolutionary ménage-à-trois made of fast and processive RNA polymerases, RNA repair ExoNs, and RNA MTases that relates to the transition between RNA- to DNA-based life.
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Affiliation(s)
- François Ferron
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, Case 925, 163, Avenue de Luminy, 13009 Marseille, France; European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Bhawna Sama
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, Case 925, 163, Avenue de Luminy, 13009 Marseille, France
| | - Etienne Decroly
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, Case 925, 163, Avenue de Luminy, 13009 Marseille, France
| | - Bruno Canard
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, Case 925, 163, Avenue de Luminy, 13009 Marseille, France; European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany.
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24
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The Role of Coronavirus RNA-Processing Enzymes in Innate Immune Evasion. Life (Basel) 2021; 11:life11060571. [PMID: 34204549 PMCID: PMC8235370 DOI: 10.3390/life11060571] [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: 05/31/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 01/21/2023] Open
Abstract
Viral RNA sensing triggers innate antiviral responses in humans by stimulating signaling pathways that include crucial antiviral genes such as interferon. RNA viruses have evolved strategies to inhibit or escape these mechanisms. Coronaviruses use multiple enzymes to synthesize, modify, and process their genomic RNA and sub-genomic RNAs. These include Nsp15 and Nsp16, whose respective roles in RNA capping and dsRNA degradation play a crucial role in coronavirus escape from immune surveillance. Evolutionary studies on coronaviruses demonstrate that genome expansion in Nidoviruses was promoted by the emergence of Nsp14-ExoN activity and led to the acquisition of Nsp15- and Nsp16-RNA-processing activities. In this review, we discuss the main RNA-sensing mechanisms in humans as well as recent structural, functional, and evolutionary insights into coronavirus Nsp15 and Nsp16 with a view to potential antiviral strategies.
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25
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Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition. J Virol 2021; 95:JVI.02274-20. [PMID: 33568513 PMCID: PMC8104106 DOI: 10.1128/jvi.02274-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/01/2021] [Indexed: 12/14/2022] Open
Abstract
Negative-sense RNA viruses (NSVs) rely on prepackaged viral RNA-dependent RNA polymerases (RdRp) to replicate and transcribe their viral genomes. Their replication machinery consists of an RdRp bound to viral RNA which is wound around a nucleoprotein (NP) scaffold, forming a viral ribonucleoprotein complex. NSV NP is known to regulate transcription and replication of genomic RNA; however, its role in maintaining and protecting the viral genetic material is unknown. Here, we exploited host microRNA expression to target NP of influenza A virus and Sendai virus to ascertain how this would impact genomic levels and the host response to infection. We find that in addition to inducing a drastic decrease in genome replication, the antiviral host response in the absence of NP is dramatically enhanced. Additionally, our data show that insufficient levels of NP prevent the replication machinery of these NSVs to process full-length genomes, resulting in aberrant replication products which form pathogen-associated molecular patterns in the process. These dynamics facilitate immune recognition by cellular pattern recognition receptors leading to a strong host antiviral response. Moreover, we observe that the consequences of limiting NP levels are universal among NSVs, including Ebola virus, Lassa virus, and measles virus. Overall, these results provide new insights into viral genome replication of negative-sense RNA viruses and highlight novel avenues for developing effective antiviral strategies, adjuvants, and/or live-attenuated vaccines.IMPORTANCE Negative-sense RNA viruses comprise some of the most important known human pathogens, including influenza A virus, measles virus, and Ebola virus. These viruses possess RNA genomes that are unreadable to the host, as they require specific viral RNA-dependent RNA polymerases in conjunction with other viral proteins, such as nucleoprotein, to be replicated and transcribed. As this process generates a significant amount of pathogen-associated molecular patterns, this phylum of viruses can result in a robust induction of the intrinsic host cellular response. To circumvent these defenses, these viruses form tightly regulated ribonucleoprotein replication complexes in order to protect their genomes from detection and to prevent excessive aberrant replication. Here, we demonstrate the balance that negative-sense RNA viruses must achieve both to replicate efficiently and to avoid induction of the host defenses.
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26
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Kaur N, Singh R, Dar Z, Bijarnia RK, Dhingra N, Kaur T. Genetic comparison among various coronavirus strains for the identification of potential vaccine targets of SARS-CoV2. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 89:104490. [PMID: 32745811 PMCID: PMC7395230 DOI: 10.1016/j.meegid.2020.104490] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/10/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023]
Abstract
On-going pandemic pneumonia outbreak COVID-19 has raised an urgent public health issue worldwide impacting millions of people with a continuous increase in both morbidity and mortality. The causative agent of this disease is identified and named as SARS-CoV2 because of its genetic relatedness to SARS-CoV species that was responsible for the 2003 coronavirus outbreak. The immense spread of the disease in a very small period demands urgent development of therapeutic and prophylactic interventions for the treatment of SARS-CoV2 infected patients. A plethora of research is being conducted globally on this novel coronavirus strain to gain knowledge about its origin, evolutionary history, and phylogeny. This review is an effort to compare genetic similarities and diversifications among coronavirus strains, which can hint towards the susceptible antigen targets of SARS-CoV2 to come up with the potential therapeutic and prophylactic interventions for the prevention of this public threat.
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Affiliation(s)
- Navpreet Kaur
- Department of Biophysics, Panjab University, Chandigarh, India
| | - Rimaljot Singh
- Department of Biophysics, Panjab University, Chandigarh, India
| | - Zahid Dar
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | | | - Neelima Dhingra
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Tanzeer Kaur
- Department of Biophysics, Panjab University, Chandigarh, India.
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27
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Vlasova AN, Saif LJ. Bovine Coronavirus and the Associated Diseases. Front Vet Sci 2021; 8:643220. [PMID: 33869323 PMCID: PMC8044316 DOI: 10.3389/fvets.2021.643220] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/08/2021] [Indexed: 12/17/2022] Open
Abstract
Coronaviruses (CoVs) possess the largest and most complex RNA genome (up to 32 kb) that encodes for 16 non-structural proteins regulating RNA synthesis and modification. Coronaviruses are known to infect a wide range of mammalian and avian species causing remarkably diverse disease syndromes. Variable tissue tropism and the ability to easily cross interspecies barriers are the well-known characteristics of certain CoVs. The 21st century epidemics of severe acute respiratory CoV (SARS-CoV), Middle East respiratory CoV and the ongoing SARS-CoV-2 pandemic further highlight these characteristics and emphasize the relevance of CoVs to the global public health. Bovine CoVs (BCoVs) are betacoronaviruses associated with neonatal calf diarrhea, and with winter dysentery and shipping fever in older cattle. Of interest, no distinct genetic or antigenic markers have been identified in BCoVs associated with these distinct clinical syndromes. In contrast, like other CoVs, BCoVs exist as quasispecies. Besides cattle, BCoVs and bovine-like CoVs were identified in various domestic and wild ruminant species (water buffalo, sheep, goat, dromedary camel, llama, alpaca, deer, wild cattle, antelopes, giraffes, and wild goats), dogs and humans. Surprisingly, bovine-like CoVs also cannot be reliably distinguished from BCoVs using comparative genomics. Additionally, there are historical examples of zoonotic transmission of BCoVs. This article will discuss BCoV pathogenesis, epidemiology, interspecies transmission, immune responses, vaccines, and diagnostics.
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Affiliation(s)
- Anastasia N Vlasova
- Center for Food Animal Health Research, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH, United States
| | - Linda J Saif
- Center for Food Animal Health Research, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH, United States
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28
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Dabbish AM, Yonis N, Salama M, Essa MM, Qoronfleh MW. Inflammatory pathways and potential therapies for COVID-19: A mini review. EUR J INFLAMM 2021. [DOI: 10.1177/20587392211002986] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The public health crisis of the novel coronavirus disease (COVID-19) is alarming since January 2020. COVID-19 genome (SARS-CoV-2) is related to other highly pathogenic coronaviruses SARS-CoV (severe acute respiratory syndrome coronavirus) and MERS-CoV (Middle East respiratory syndrome coronavirus). Amino acid substitutions in some of SARS-CoV-2 proteins resulted in mutations proposing more virulent and contagious properties for this novel virus. Coronavirus penetrates the host cell via endocytosis and once infected, immune responses are triggered to fight against the pathogen. Innate immune response activates major transcription factors to secrete proinflammatory cytokines and type 1 interferon response (T1INF) to induce antiviral immunity. While adaptive immunity initiates cascade of B-cells antibody mediated and T-cells cellular mediate immunities, several mechanisms are raised by SARS-CoV-2 to evade host immune response. Consequently, a surge of proinflammatory cytokines, known as cytokine storm (CS) are released. Failure to manage CS results in several pathological complications as acute respiratory distress syndrome (ARDS). Although researches have not discovered an effective treatment against SARS-CoV-2, recent therapeutic approaches recommending the use of anti-inflammatories in combination with antivirals and some repurposed drugs for COVID-19 patients. Future medications should be designed to target essential hallmarks in the CS to improve clinical outcomes.
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Affiliation(s)
- Areeg M Dabbish
- Biotechnology Graduate Program, School of Science and Engineering, The American University in Cairo, New Cairo, Egypt
| | - Nouran Yonis
- Institute of Global Health and Human Ecology (IGHHE) Graduate Program, The American University in Cairo, New Cairo, Egypt
| | - Mohamed Salama
- Institute of Global Health and Human Ecology (IGHHE), The American University in Cairo, New Cairo, Egypt
| | - Musthafa M Essa
- Department of Food Science and Nutrition, CAMS, Sultan Qaboos University, Muscat, Oman
- Ageing and Dementia Research Group, Sultan Qaboos University, Muscat, Oman
| | - M Walid Qoronfleh
- Research & Policy Department, World Innovation Summit for Health (WISH), Qatar Foundation, Doha, Qatar
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29
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Colina SE, Serena MS, Echeverría MG, Metz GE. Clinical and molecular aspects of veterinary coronaviruses. Virus Res 2021; 297:198382. [PMID: 33705799 PMCID: PMC7938195 DOI: 10.1016/j.virusres.2021.198382] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/20/2020] [Accepted: 03/04/2021] [Indexed: 12/12/2022]
Abstract
Coronaviruses are a large group of RNA viruses that infect a wide range of animal species. The replication strategy of coronaviruses involves recombination and mutation events that lead to the possibility of cross-species transmission. The high plasticity of the viral receptor due to a continuous modification of the host species habitat may be the cause of cross-species transmission that can turn into a threat to other species including the human population. The successive emergence of highly pathogenic coronaviruses such as the Severe Acute Respiratory Syndrome (SARS) in 2003, the Middle East Respiratory Syndrome Coronavirus in 2012, and the recent SARS-CoV-2 has incentivized a number of studies on the molecular basis of the coronavirus and its pathogenesis. The high degree of interrelatedness between humans and wild and domestic animals and the modification of animal habitats by human urbanization, has favored new viral spreads. Hence, knowledge on the main clinical signs of coronavirus infection in the different hosts and the distinctive molecular characteristics of each coronavirus is essential to prevent the emergence of new coronavirus diseases. The coronavirus infections routinely studied in veterinary medicine must be properly recognized and diagnosed not only to prevent animal disease but also to promote public health.
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Affiliation(s)
- Santiago Emanuel Colina
- Virology, Faculty of Veterinary Sciences, National University of La Plata, La Plata, Argentina; CONICET (National Scientific and Technical Research Council), CCT La Plata, Argentina
| | - María Soledad Serena
- Virology, Faculty of Veterinary Sciences, National University of La Plata, La Plata, Argentina; CONICET (National Scientific and Technical Research Council), CCT La Plata, Argentina
| | - María Gabriela Echeverría
- Virology, Faculty of Veterinary Sciences, National University of La Plata, La Plata, Argentina; CONICET (National Scientific and Technical Research Council), CCT La Plata, Argentina
| | - Germán Ernesto Metz
- Virology, Faculty of Veterinary Sciences, National University of La Plata, La Plata, Argentina; CONICET (National Scientific and Technical Research Council), CCT La Plata, Argentina.
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30
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Manfredonia I, Incarnato D. Structure and regulation of coronavirus genomes: state-of-the-art and novel insights from SARS-CoV-2 studies. Biochem Soc Trans 2021; 49:341-352. [PMID: 33367597 PMCID: PMC7925004 DOI: 10.1042/bst20200670] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 12/13/2022]
Abstract
Coronaviruses (CoV) are positive-sense single-stranded RNA viruses, harboring the largest viral RNA genomes known to date. Apart from the primary sequence encoding for all the viral proteins needed for the generation of new viral particles, certain regions of CoV genomes are known to fold into stable structures, controlling several aspects of CoV life cycle, from the regulation of the discontinuous transcription of subgenomic mRNAs, to the packaging of the genome into new virions. Here we review the current knowledge on CoV RNA structures, discussing it in light of the most recent discoveries made possible by analyses of the SARS-CoV-2 genome.
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Affiliation(s)
- Ilaria Manfredonia
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
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31
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Morandi E, Manfredonia I, Simon LM, Anselmi F, van Hemert MJ, Oliviero S, Incarnato D. Genome-scale deconvolution of RNA structure ensembles. Nat Methods 2021; 18:249-252. [PMID: 33619392 DOI: 10.1038/s41592-021-01075-w] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/19/2021] [Indexed: 12/27/2022]
Abstract
RNA structure heterogeneity is a major challenge when querying RNA structures with chemical probing. We introduce DRACO, an algorithm for the deconvolution of coexisting RNA conformations from mutational profiling experiments. Analysis of the SARS-CoV-2 genome using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and DRACO, identifies multiple regions that fold into two mutually exclusive conformations, including a conserved structural switch in the 3' untranslated region. This work may open the way to dissecting the heterogeneity of the RNA structurome.
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Affiliation(s)
- Edoardo Morandi
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands.,Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Torino, Italy
| | - Ilaria Manfredonia
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
| | - Lisa M Simon
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Torino, Italy
| | - Francesca Anselmi
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Torino, Italy
| | - Martijn J van Hemert
- Department of Medical Microbiology, Molecular Virology Laboratory, Leiden University Medical Center, Leiden, the Netherlands
| | - Salvatore Oliviero
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Torino, Italy. .,Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy.
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands.
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32
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Wang L, Ahn M, Anderson DE. Bats and Coronaviruses in the Context of COVID-19. China CDC Wkly 2021; 3:153-155. [PMID: 34595031 PMCID: PMC8392920 DOI: 10.46234/ccdcw2021.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 12/24/2022] Open
Affiliation(s)
- Linfa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
| | - Matae Ahn
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
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33
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Manfredonia I, Nithin C, Ponce-Salvatierra A, Ghosh P, Wirecki TK, Marinus T, Ogando NS, Snijder E, van Hemert MJ, Bujnicki JM, Incarnato D. Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements. Nucleic Acids Res 2020; 48:12436-12452. [PMID: 33166999 PMCID: PMC7736786 DOI: 10.1093/nar/gkaa1053] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/13/2020] [Accepted: 10/22/2020] [Indexed: 01/25/2023] Open
Abstract
SARS-CoV-2 is a betacoronavirus with a linear single-stranded, positive-sense RNA genome, whose outbreak caused the ongoing COVID-19 pandemic. The ability of coronaviruses to rapidly evolve, adapt, and cross species barriers makes the development of effective and durable therapeutic strategies a challenging and urgent need. As for other RNA viruses, genomic RNA structures are expected to play crucial roles in several steps of the coronavirus replication cycle. Despite this, only a handful of functionally-conserved coronavirus structural RNA elements have been identified to date. Here, we performed RNA structure probing to obtain single-base resolution secondary structure maps of the full SARS-CoV-2 coronavirus genome both in vitro and in living infected cells. Probing data recapitulate the previously described coronavirus RNA elements (5' UTR and s2m), and reveal new structures. Of these, ∼10.2% show significant covariation among SARS-CoV-2 and other coronaviruses, hinting at their functionally-conserved role. Secondary structure-restrained 3D modeling of these segments further allowed for the identification of putative druggable pockets. In addition, we identify a set of single-stranded segments in vivo, showing high sequence conservation, suitable for the development of antisense oligonucleotide therapeutics. Collectively, our work lays the foundation for the development of innovative RNA-targeted therapeutic strategies to fight SARS-related infections.
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Affiliation(s)
- Ilaria Manfredonia
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
| | - Chandran Nithin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Almudena Ponce-Salvatierra
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Pritha Ghosh
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Tomasz K Wirecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Tycho Marinus
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
| | - Natacha S Ogando
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Martijn J van Hemert
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
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34
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Structural and functional insights into non-structural proteins of coronaviruses. Microb Pathog 2020; 150:104641. [PMID: 33242646 PMCID: PMC7682334 DOI: 10.1016/j.micpath.2020.104641] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 12/15/2022]
Abstract
Coronaviruses (CoVs) are causing a number of human and animal diseases because of their zoonotic nature such as Middle East respiratory syndrome (MERS), severe acute respiratory syndrome (SARS) and coronavirus disease 2019 (COVID-19). These viruses can infect respiratory, gastrointestinal, hepatic and central nervous systems of human, livestock, birds, bat, mouse, and many wild animals. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly emerging respiratory virus and is causing CoVID-19 with high morbidity and considerable mortality. All CoVs belong to the order Nidovirales, family Coronaviridae, are enveloped positive-sense RNA viruses, characterised by club-like spikes on their surfaces and large RNA genome with a distinctive replication strategy. Coronavirus have the largest RNA genomes (~26–32 kilobases) and their expansion was likely enabled by acquiring enzyme functions that counter the commonly high error frequency of viral RNA polymerases. Non-structural proteins (nsp) 7–16 are cleaved from two large replicase polyproteins and guide the replication and processing of coronavirus RNA. Coronavirus replicase has more or less universal activities, such as RNA polymerase (nsp 12) and helicase (nsp 13), as well as a variety of unusual or even special mRNA capping (nsp 14, nsp 16) and fidelity regulation (nsp 14) domains. Besides that, several smaller subunits (nsp 7– nsp 10) serve as essential cofactors for these enzymes and contribute to the emerging “nsp interactome.” In spite of the significant progress in studying coronaviruses structural and functional properties, there is an urgent need to understand the coronaviruses evolutionary success that will be helpful to develop enhanced control strategies. Therefore, it is crucial to understand the structure, function, and interactions of coronaviruses RNA synthesizing machinery and their replication strategies.
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Gulyaeva AA, Gorbalenya AE. A nidovirus perspective on SARS-CoV-2. Biochem Biophys Res Commun 2020; 538:24-34. [PMID: 33413979 PMCID: PMC7664520 DOI: 10.1016/j.bbrc.2020.11.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023]
Abstract
Two pandemics of respiratory distress diseases associated with zoonotic introductions of the species Severe acute respiratory syndrome-related coronavirus in the human population during 21st century raised unprecedented interest in coronavirus research and assigned it unseen urgency. The two viruses responsible for the outbreaks, SARS-CoV and SARS-CoV-2, respectively, are in the spotlight, and SARS-CoV-2 is the focus of the current fast-paced research. Its foundation was laid down by studies of many corona- and related viruses that collectively form the vast order Nidovirales. Comparative genomics of nidoviruses played a key role in this advancement over more than 30 years. It facilitated the transfer of knowledge from characterized to newly identified viruses, including SARS-CoV and SARS-CoV-2, as well as contributed to the dissection of the nidovirus proteome and identification of patterns of variations between different taxonomic groups, from species to families. This review revisits selected cases of protein conservation and variation that define nidoviruses, illustrates the remarkable plasticity of the proteome during nidovirus adaptation, and asks questions at the interface of the proteome and processes that are vital for nidovirus reproduction and could inform the ongoing research of SARS-CoV-2.
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Affiliation(s)
- Anastasia A Gulyaeva
- Department of Medical Microbiology, Leiden University Medical Center, 2300 RC, Leiden, the Netherlands
| | - Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, 2300 RC, Leiden, the Netherlands; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119899, Moscow, Russia.
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Ogando NS, Zevenhoven-Dobbe JC, van der Meer Y, Bredenbeek PJ, Posthuma CC, Snijder EJ. The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. J Virol 2020; 94:e01246-20. [PMID: 32938769 PMCID: PMC7654266 DOI: 10.1128/jvi.01246-20] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/09/2020] [Indexed: 02/08/2023] Open
Abstract
Coronaviruses (CoVs) stand out for their large RNA genome and complex RNA-synthesizing machinery comprising 16 nonstructural proteins (nsps). The bifunctional nsp14 contains 3'-to-5' exoribonuclease (ExoN) and guanine-N7-methyltransferase (N7-MTase) domains. While the latter presumably supports mRNA capping, ExoN is thought to mediate proofreading during genome replication. In line with such a role, ExoN knockout mutants of mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SARS-CoV) were previously reported to have crippled but viable hypermutation phenotypes. Remarkably, using reverse genetics, a large set of corresponding ExoN knockout mutations has now been found to be lethal for another betacoronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV). For 13 mutants, viral progeny could not be recovered, unless-as happened occasionally-reversion had first occurred. Only a single mutant was viable, likely because its E191D substitution is highly conservative. Remarkably, a SARS-CoV-2 ExoN knockout mutant was found to be unable to replicate, resembling observations previously made for alpha- and gammacoronaviruses, but starkly contrasting with the documented phenotype of ExoN knockout mutants of the closely related SARS-CoV. Subsequently, we established in vitro assays with purified recombinant MERS-CoV nsp14 to monitor its ExoN and N7-MTase activities. All ExoN knockout mutations that proved lethal in reverse genetics were found to severely decrease ExoN activity while not affecting N7-MTase activity. Our study strongly suggests that CoV nsp14 ExoN has an additional function, which apparently is critical for primary viral RNA synthesis and thus differs from the proofreading function that, based on previous MHV and SARS-CoV studies, was proposed to boost longer-term replication fidelity.IMPORTANCE The bifunctional nsp14 subunit of the coronavirus replicase contains 3'-to-5' exoribonuclease (ExoN) and guanine-N7-methyltransferase domains. For the betacoronaviruses MHV and SARS-CoV, ExoN was reported to promote the fidelity of genome replication, presumably by mediating a form of proofreading. For these viruses, ExoN knockout mutants are viable while displaying an increased mutation frequency. Strikingly, we have now established that the equivalent ExoN knockout mutants of two other betacoronaviruses, MERS-CoV and SARS-CoV-2, are nonviable, suggesting an additional and critical ExoN function in their replication. This is remarkable in light of the very limited genetic distance between SARS-CoV and SARS-CoV-2, which is highlighted, for example, by 95% amino acid sequence identity in their nsp14 sequences. For (recombinant) MERS-CoV nsp14, both its enzymatic activities were evaluated using newly developed in vitro assays that can be used to characterize these key replicative enzymes in more detail and explore their potential as target for antiviral drug development.
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Affiliation(s)
- Natacha S Ogando
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jessika C Zevenhoven-Dobbe
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Yvonne van der Meer
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter J Bredenbeek
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Clara C Posthuma
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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Genetic, Morphological and Antigenic Relationships between Mesonivirus Isolates from Australian Mosquitoes and Evidence for Their Horizontal Transmission. Viruses 2020; 12:v12101159. [PMID: 33066222 PMCID: PMC7602028 DOI: 10.3390/v12101159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/08/2020] [Accepted: 10/08/2020] [Indexed: 12/26/2022] Open
Abstract
The Mesoniviridae are a newly assigned family of viruses in the order Nidovirales. Unlike other nidoviruses, which include the Coronaviridae, mesoniviruses are restricted to mosquito hosts and do not infect vertebrate cells. To date there is little information on the morphological and antigenic characteristics of this new group of viruses and a dearth of mesonivirus-specific research tools. In this study we determined the genetic relationships of recent Australian isolates of Alphamesonivirus 4 (Casuarina virus—CASV) and Alphamesonivirus 1 (Nam Dinh virus—NDiV), obtained from multiple mosquito species. Australian isolates of NDiV showed high-level similarity to the prototype NDiV isolate from Vietnam (99% nucleotide (nt) and amino acid (aa) identity). Isolates of CASV from Central Queensland were genetically very similar to the prototype virus from Darwin (95–96% nt and 91–92% aa identity). Electron microscopy studies demonstrated that virion diameter (≈80 nm) and spike length (≈10 nm) were similar for both viruses. Monoclonal antibodies specific to CASV and NDiV revealed a close antigenic relationship between the two viruses with 13/34 mAbs recognising both viruses. We also detected NDiV RNA on honey-soaked nucleic acid preservation cards fed on by wild mosquitoes supporting a possible mechanism of horizontal transmission between insects in nature.
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Abstract
RNA virus encodes a helicase essential for viral RNA transcription and replication when the genome size is larger than 7 kb. Coronavirus (CoV) has an exceptionally large RNA genome (~30 kb) and it encodes an essential replicase, the nonstructural protein 13 (nsp13), a member of superfamily 1 helicases. Nsp13 is among the evolutionary most conserved proteins not only in CoVs but also in nidovirales. Thus, it is considered as an important drug target. However, the high-resolution structure of CoV nsp13 remained unavailable even until more than a decade after the outbreak of the severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003, which hindered the structure-based drug design. This is in part due to the intrinsic flexibility of nsp13. Here, we describe protocols of deducing the crystal structure of Middle East respiratory syndrome coronavirus (MERS-CoV) helicase in detail, which include protein expression, purification, crystallization, enzymatic characterization, and structure determination. With these methods, catalytically active recombinant MERS-CoV nsp13 protein can be prepared and crystallized and the crystal structure can be solved.
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Krupanidhi S, Abraham Peele K, Venkateswarulu TC, Ayyagari VS, Nazneen Bobby M, John Babu D, Venkata Narayana A, Aishwarya G. Screening of phytochemical compounds of Tinospora cordifolia for their inhibitory activity on SARS-CoV-2: an in silico study. J Biomol Struct Dyn 2020; 39:5799-5803. [PMID: 32627715 PMCID: PMC7441789 DOI: 10.1080/07391102.2020.1787226] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In the present study, we explored phytochemical constituents of Tinospora cordifolia in terms of its binding affinity targeting the active site pocket of the main protease (3CL pro) of SARS-CoV-2 using molecular docking study and assessed the stability of top docking complex of tinosponone and 3CL pro using molecular dynamics simulations with GROMACS 2020.2 version. Out of 11 curated screened compounds, we found the significant docking score for tinosponone, xanosporic acid, cardiofolioside B, tembetarine and berberine in Tinospora cordifolia. Based on the findings of the docking study, it was confirmed that tinosponone is the potent inhibitor of main protease of SARS-CoV-2 with the best binding affinity of −7.7 kcal/mol. Further, ADME along with toxicity analysis was studied to predict the pharmacokinetics and drug-likeness properties of five top hits compounds. The molecular dynamics simulation analysis confirmed the stability of tinosponone and 3CL pro complex with a random mean square deviation (RMSD) value of 0.1 nm. The computer-aided drug design approach proved that the compound tinosponone from T. cordifolia is a potent inhibitor of 3CL main protease of SARS-CoV-2. Further, the in vitro and in vivo-based testing will be required to confirm its inhibitory effect on SARS-CoV-2. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- S Krupanidhi
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - K Abraham Peele
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - T C Venkateswarulu
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - Vijaya Sai Ayyagari
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - Md Nazneen Bobby
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - D John Babu
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - A Venkata Narayana
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - G Aishwarya
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
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Ferron F, Debat HJ, Shannon A, Decroly E, Canard B. A N7-guanine RNA cap methyltransferase signature-sequence as a genetic marker of large genome, non-mammalian Tobaniviridae. NAR Genom Bioinform 2019; 2:lqz022. [PMID: 32289120 PMCID: PMC7107822 DOI: 10.1093/nargab/lqz022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/22/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022] Open
Abstract
The order Nidovirales is a diverse group of (+)RNA viruses, classified together based on their common genome organisation and conserved replicative enzymes, despite drastic differences in size and complexity. One such difference pertains to the mechanisms and enzymes responsible for generation of the proposed viral 5′ RNA cap. Within the Coronaviridae family, two separate methytransferases (MTase), nsp14 and nsp16, perform the RNA-cap N7-guanine and 2′-OH methylation respectively for generation of the proposed m7GpppNm type I cap structure. For the majority of other families within the Nidovirales order, the presence, structure and key enzymes involved in 5′ capping are far less clear. These viruses either lack completely an RNA MTase signature sequence, or lack an N7-guanine methyltransferase signature sequence, obscuring our understanding about how RNA-caps are N7-methylated for these families. Here, we report the discovery of a putative Rossmann fold RNA methyltransferase in 10 Tobaniviridae members in Orf1a, an unusual genome locus for this gene. Multiple sequence alignments and structural analyses lead us to propose this novel gene as a typical RNA-cap N7-guanine MTase with substrate specificity and active-site organization similar to the canonical eukaryotic RNA-cap N7-guanine MTase.
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Affiliation(s)
- François Ferron
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France.,European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Humberto J Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, X5119 Córdoba, Argentina
| | - Ashleigh Shannon
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| | - Etienne Decroly
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France.,European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
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41
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Ogando NS, Ferron F, Decroly E, Canard B, Posthuma CC, Snijder EJ. The Curious Case of the Nidovirus Exoribonuclease: Its Role in RNA Synthesis and Replication Fidelity. Front Microbiol 2019; 10:1813. [PMID: 31440227 PMCID: PMC6693484 DOI: 10.3389/fmicb.2019.01813] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/23/2019] [Indexed: 12/20/2022] Open
Abstract
Among RNA viruses, the order Nidovirales stands out for including viruses with the largest RNA genomes currently known. Nidoviruses employ a complex RNA-synthesizing machinery comprising a variety of non-structural proteins (nsps). One of the postulated drivers of the expansion of nidovirus genomes is the presence of a proofreading 3′-to-5′ exoribonuclease (ExoN) belonging to the DEDDh family. ExoN may enhance the fidelity of RNA synthesis by correcting nucleotide incorporation errors made by the RNA-dependent RNA polymerase. Here, we review our current understanding of ExoN evolution, structure, and function. Most experimental data are derived from studies of the ExoN domain of coronaviruses (CoVs), which were triggered by the bioinformatics-based identification of ExoN in the genome of severe acute respiratory syndrome coronavirus (SARS-CoV) and its relatives in 2003. Although convincing data supporting the proofreading hypothesis have been obtained, from biochemical assays and studies with CoV mutants lacking ExoN functionality, the features of ExoN from most other nidovirus families remain to be characterized. Remarkably, viable ExoN knockout mutants were obtained only for two CoVs, mouse hepatitis virus (MHV) and SARS-CoV, whose RNA synthesis and replication kinetics were mildly affected by the lack of ExoN function. In several other CoV species, ExoN inactivation was not tolerated, and knockout mutants could not be rescued when launched using a reverse genetics system. This suggests that ExoN is also critical for primary viral RNA synthesis, a property that poorly matches the profile of an enzyme that would merely boost long-term replication fidelity. In CoVs, ExoN resides in a bifunctional replicase subunit (nsp14) whose C-terminal part has (N7-guanine)-methyltransferase activity. The crystal structure of SARS-CoV nsp14 has shed light on the interplay between these two domains, and on nsp14’s interactions with nsp10, a co-factor that strongly enhances ExoN activity in vitro assays. Further elucidation of the structure-function relationships of ExoN and its interactions with other (viral and/or host) members of the CoV replication machinery will be key to understanding the enzyme’s role in viral RNA synthesis and pathogenesis, and may contribute to the design of new approaches to combat emerging nidoviruses.
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Affiliation(s)
- Natacha S Ogando
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Francois Ferron
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France.,European Virus Bioinformatics Center, Jena, Germany
| | - Etienne Decroly
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Clara C Posthuma
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Eric J Snijder
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
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42
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TaqMan real-time and conventional nested PCR tests specific to yellow head virus genotype 7 (YHV7) identified in giant tiger shrimp in Australia. J Virol Methods 2019; 273:113689. [PMID: 31276700 DOI: 10.1016/j.jviromet.2019.113689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/01/2019] [Accepted: 07/01/2019] [Indexed: 12/11/2022]
Abstract
In 2013, a unique seventh yellow head virus genotype (YHV7) was detected in Black Tiger shrimp (Penaeus monodon) broodstock that suffered high mortality following their capture from Joseph Bonaparte Gulf (JBG) in northern Australia. To assist with its diagnosis and assessment of its distribution, prevalence and pathogenicity, YHV7-specific TaqMan real-time qPCR and conventional nested PCR primer sets were designed to ORF1b gene sequences divergent from the other YHV genotypes. Using high (≥108) copies of plasmid (p)DNA controls containing ORF1b gene inserts of representative strains of YHV genotypes 1-7, both PCR tests displayed specificity for YHV7. Amplifications of serial 10-fold dilutions of quantified YHV7 pDNA and synthetic ssRNA showed that both tests could reliably detect 10 genome copies. Pleopods/gills from wild P. monodon sourced from locations in geographically disparate regions across northern Australia as well as 96 juveniles (48 either appearing normal or displaying signs of morbidity) from a commercial pond experiencing mortalities were screened to partially validate the diagnostic capacity of the qPCR test. Based on these data and PCR primer/probe sequence mismatches with other newly identified YHV genotypes, both YHV7-specific PCR tests should prove useful in the sensitive detection and discrimination of this genotype from YHV 2 (gill-associated virus) and YHV6 that can occur in Australian P. monodon, as well as from YHV genotypes currently listed as exotic to Australia.
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Kanitz M, Blanck S, Heine A, Gulyaeva AA, Gorbalenya AE, Ziebuhr J, Diederich WE. Structural basis for catalysis and substrate specificity of a 3C-like cysteine protease from a mosquito mesonivirus. Virology 2019; 533:21-33. [PMID: 31078932 PMCID: PMC7111312 DOI: 10.1016/j.virol.2019.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 01/05/2023]
Abstract
Cavally virus (CavV) is a mosquito-borne plus-strand RNA virus in the family Mesoniviridae (order Nidovirales). We present X-ray structures for the CavV 3C-like protease (3CLpro), as a free enzyme and in complex with a peptide aldehyde inhibitor mimicking the P4-to-P1 residues of a natural substrate. The 3CLpro structure (refined to 1.94 Å) shows that the protein forms dimers. The monomers are comprised of N-terminal domains I and II, which adopt a chymotrypsin-like fold, and a C-terminal α-helical domain III. The catalytic Cys-His dyad is assisted by a complex network of interactions involving a water molecule that mediates polar contacts between the catalytic His and a conserved Asp located in the domain II-III junction and is suitably positioned to stabilize the developing positive charge of the catalytic His in the transition state during catalysis. The study also reveals the structural basis for the distinct P2 Asn-specific substrate-binding pocket of mesonivirus 3CLpros. First structure of a 3CLpro of an invertebrate RNA virus. Structural basis of the unique substrate specificity defined by Asn at the P2 position of mesonivirus 3CLpro substrates. Emerging role of a conserved Asp residue that assists the Cys-His catalytic dyad in vertebrate and invertebrate 3CLpros.
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Affiliation(s)
- Manuel Kanitz
- Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany; Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Sandra Blanck
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Anastasia A Gulyaeva
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany.
| | - Wibke E Diederich
- Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany; Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany.
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Abstract
RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically. Here, we review the insights that these two approaches have provided over the last 40 years. We show that experimental approaches using in vitro and in vivo laboratory models are largely focused on short-term intrahost evolutionary mechanisms, and may not always be relevant to natural systems. In contrast, the comparative approach relies on the phylogenetic analysis of natural virus populations, usually considering data collected over multiple cycles of virus-host transmission, but is divorced from the causative evolutionary processes. To truly understand RNA virus evolution it is necessary to meld experimental and comparative approaches within a single evolutionary genetic framework, and to link viral evolution at the intrahost scale with that which occurs over both epidemiological and geological timescales. We suggest that the impetus for this new synthesis may come from methodological advances in next-generation sequencing and metagenomics.
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Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Sydney Medical School, The University of Sydney, New South Wales 2006, Australia
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45
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Saberi A, Gulyaeva AA, Brubacher JL, Newmark PA, Gorbalenya AE. A planarian nidovirus expands the limits of RNA genome size. PLoS Pathog 2018; 14:e1007314. [PMID: 30383829 PMCID: PMC6211748 DOI: 10.1371/journal.ppat.1007314] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/02/2018] [Indexed: 12/28/2022] Open
Abstract
RNA viruses are the only known RNA-protein (RNP) entities capable of autonomous replication (albeit within a permissive host environment). A 33.5 kilobase (kb) nidovirus has been considered close to the upper size limit for such entities; conversely, the minimal cellular DNA genome is in the 100–300 kb range. This large difference presents a daunting gap for the transition from primordial RNP to contemporary DNA-RNP-based life. Whether or not RNA viruses represent transitional steps towards DNA-based life, studies of larger RNA viruses advance our understanding of the size constraints on RNP entities and the role of genome size in virus adaptation. For example, emergence of the largest previously known RNA genomes (20–34 kb in positive-stranded nidoviruses, including coronaviruses) is associated with the acquisition of a proofreading exoribonuclease (ExoN) encoded in the open reading frame 1b (ORF1b) in a monophyletic subset of nidoviruses. However, apparent constraints on the size of ORF1b, which encodes this and other key replicative enzymes, have been hypothesized to limit further expansion of these viral RNA genomes. Here, we characterize a novel nidovirus (planarian secretory cell nidovirus; PSCNV) whose disproportionately large ORF1b-like region including unannotated domains, and overall 41.1-kb genome, substantially extend the presumed limits on RNA genome size. This genome encodes a predicted 13,556-aa polyprotein in an unconventional single ORF, yet retains canonical nidoviral genome organization and expression, as well as key replicative domains. These domains may include functionally relevant substitutions rarely or never before observed in highly conserved sites of RdRp, NiRAN, ExoN and 3CLpro. Our evolutionary analysis suggests that PSCNV diverged early from multi-ORF nidoviruses, and acquired additional genes, including those typical of large DNA viruses or hosts, e.g. Ankyrin and Fibronectin type II, which might modulate virus-host interactions. PSCNV's greatly expanded genome, proteomic complexity, and unique features–impressive in themselves–attest to the likelihood of still-larger RNA genomes awaiting discovery. RNA viruses are the only known RNA-protein (RNP) entities capable of autonomous replication. The upper genome size for such entities was assumed to be <35 kb; conversely, the minimal cellular DNA genome is in the 100–300 kilobase (kb) range. This large difference presents a daunting gap for the proposed evolution of contemporary DNA-RNP-based life from primordial RNP entities. Here, we describe a nidovirus from planarians, named planarian secretory cell nidovirus (PSCNV), whose 41.1 kb genome is 23% larger than any riboviral genome yet discovered. This increase is nearly equivalent in size to the entire poliovirus genome, and it equips PSCNV with an unprecedented extra coding capacity to adapt. PSCNV has broken apparent constraints on the size of the genomic subregion that encodes core replication machinery in other nidoviruses, including coronaviruses, and has acquired genes not previously observed in RNA viruses. This virus challenges and advances our understanding of the limits to RNA genome size.
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Affiliation(s)
- Amir Saberi
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Anastasia A. Gulyaeva
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - John L. Brubacher
- Department of Biology, Canadian Mennonite University, Winnipeg, Canada
| | - Phillip A. Newmark
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
- * E-mail: (PAN); (AEG)
| | - Alexander E. Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- * E-mail: (PAN); (AEG)
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Bukhari K, Mulley G, Gulyaeva AA, Zhao L, Shu G, Jiang J, Neuman BW. Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae, and from a sister group to the Coronavirinae, the proposed genus Alphaletovirus. Virology 2018; 524:160-171. [PMID: 30199753 PMCID: PMC7112036 DOI: 10.1016/j.virol.2018.08.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/11/2018] [Accepted: 08/11/2018] [Indexed: 01/12/2023]
Abstract
Transcriptomics has the potential to discover new RNA virus genomes by sequencing total intracellular RNA pools. In this study, we have searched publicly available transcriptomes for sequences similar to viruses of the Nidovirales order. We report two potential nidovirus genomes, a highly divergent 35.9 kb likely complete genome from the California sea hare Aplysia californica, which we assign to a nidovirus named Aplysia abyssovirus 1 (AAbV), and a coronavirus-like 22.3 kb partial genome from the ornamented pygmy frog Microhyla fissipes, which we assign to a nidovirus named Microhyla alphaletovirus 1 (MLeV). AAbV was shown to encode a functional main proteinase, and a translational readthrough signal. Phylogenetic analysis suggested that AAbV represents a new family, proposed here as Abyssoviridae. MLeV represents a sister group to the other known coronaviruses. The importance of MLeV and AAbV for understanding nidovirus evolution, and the origin of terrestrial nidoviruses are discussed.
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Affiliation(s)
| | | | - Anastasia A Gulyaeva
- Dept. Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Lanying Zhao
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Guocheng Shu
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Benjamin W Neuman
- Texas A&M University-Texarkana, 7101 University Ave, Texarkana, TX 75503, United States.
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Durzynska I, Sauerwald M, Karl N, Madhugiri R, Ziebuhr J. Characterization of a bafinivirus exoribonuclease activity. J Gen Virol 2018; 99:1253-1260. [PMID: 30058998 DOI: 10.1099/jgv.0.001120] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
White bream virus (WBV), a poorly characterized plus-strand RNA virus infecting freshwater fish of the Cyprinidae family, is the prototype species of the genus Bafinivirus in the subfamily Torovirinae (family Coronaviridae, order Nidovirales). In common with other nidoviruses featuring >20 kilobase genomes, bafiniviruses have been predicted to encode an exoribonuclease (ExoN) in their replicase gene. Here, we used information on the substrate specificity of bafinivirus 3C-like proteases to express WBV ExoN in an active form in Escherichia coli. The 374-residue protein displayed robust 3'-to-5' exoribonuclease activity in the presence of Mg2+ ions and, unlike its coronavirus homologues, did not require a protein cofactor for activity. Characterization of mutant forms of ExoN provided support for predictions on putative active-site and conserved zinc-binding residues. WBV ExoN was revealed to be most active on double-stranded RNA substrates containing one or two non-paired 3'-terminal nucleotides, supporting its presumed role in increasing the fidelity of the bafinivirus RNA-dependent RNA polymerase.
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Affiliation(s)
- Izabela Durzynska
- 1Centre for Infection and Immunity, Queen's University, Belfast, UK.,†Present address: Department of Cancer Biology, Dana Farber Cancer Institute, Boston, USA.,‡Present address: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, USA
| | - Marc Sauerwald
- 2Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Nadja Karl
- 1Centre for Infection and Immunity, Queen's University, Belfast, UK.,2Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | | | - John Ziebuhr
- 2Institute of Medical Virology, Justus Liebig University, Giessen, Germany.,1Centre for Infection and Immunity, Queen's University, Belfast, UK
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Mahmoudabadi G, Phillips R. A comprehensive and quantitative exploration of thousands of viral genomes. eLife 2018; 7:31955. [PMID: 29624169 PMCID: PMC5908442 DOI: 10.7554/elife.31955] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 03/30/2018] [Indexed: 01/27/2023] Open
Abstract
The complete assembly of viral genomes from metagenomic datasets (short genomic sequences gathered from environmental samples) has proven to be challenging, so there are significant blind spots when we view viral genomes through the lens of metagenomics. One approach to overcoming this problem is to leverage the thousands of complete viral genomes that are publicly available. Here we describe our efforts to assemble a comprehensive resource that provides a quantitative snapshot of viral genomic trends – such as gene density, noncoding percentage, and abundances of functional gene categories – across thousands of viral genomes. We have also developed a coarse-grained method for visualizing viral genome organization for hundreds of genomes at once, and have explored the extent of the overlap between bacterial and bacteriophage gene pools. Existing viral classification systems were developed prior to the sequencing era, so we present our analysis in a way that allows us to assess the utility of the different classification systems for capturing genomic trends.
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Affiliation(s)
- Gita Mahmoudabadi
- Department of Bioengineering, California Institute of Technology, Pasadena, United States
| | - Rob Phillips
- Department of Bioengineering, California Institute of Technology, Pasadena, United States.,Department of Applied Physics, California Institute of Technology, Pasadena, United States
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Rappe JCF, de Wilde A, Di H, Müller C, Stalder H, V'kovski P, Snijder E, Brinton MA, Ziebuhr J, Ruggli N, Thiel V. Antiviral activity of K22 against members of the order Nidovirales. Virus Res 2018; 246:28-34. [PMID: 29337162 PMCID: PMC7114538 DOI: 10.1016/j.virusres.2018.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/10/2018] [Accepted: 01/10/2018] [Indexed: 01/31/2023]
Abstract
Recently, a novel antiviral compound (K22) that inhibits replication of a broad range of animal and human coronaviruses was reported to interfere with viral RNA synthesis by impairing double-membrane vesicle (DMV) formation (Lundin et al., 2014). Here we assessed potential antiviral activities of K22 against a range of viruses representing two (sub)families of the order Nidovirales, the Arteriviridae (porcine reproductive and respiratory syndrome virus [PRRSV], equine arteritis virus [EAV] and simian hemorrhagic fever virus [SHFV]), and the Torovirinae (equine torovirus [EToV] and White Bream virus [WBV]). Possible effects of K22 on nidovirus replication were studied in suitable cell lines. K22 concentrations significantly decreasing infectious titres of the viruses included in this study ranged from 25 to 50 μM. Reduction of double-stranded RNA intermediates of viral replication in nidovirus-infected cells treated with K22 confirmed the anti-viral potential of K22. Collectively, the data show that K22 has antiviral activity against diverse lineages of nidoviruses, suggesting that the inhibitor targets a critical and conserved step during nidovirus replication.
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Affiliation(s)
- Julie Christiane Françoise Rappe
- Institute for Virology and Immunology IVI, Mittelhäusern and Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland; Department of Infectious Diseases and Pathobiology, University of Bern, Switzerland.
| | - Adriaan de Wilde
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Han Di
- Department of Biology, 623 Petit Science Center, Georgia State University, 161 Jesse Hill Jr Drive, Atlanta, GA 30303, United States.
| | - Christin Müller
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany.
| | - Hanspeter Stalder
- Institute for Virology and Immunology IVI, Mittelhäusern and Bern, Switzerland; Department of Infectious Diseases and Pathobiology, University of Bern, Switzerland.
| | - Philip V'kovski
- Institute for Virology and Immunology IVI, Mittelhäusern and Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland; Department of Infectious Diseases and Pathobiology, University of Bern, Switzerland.
| | - Eric Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Margo A Brinton
- Department of Biology, 623 Petit Science Center, Georgia State University, 161 Jesse Hill Jr Drive, Atlanta, GA 30303, United States.
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany.
| | - Nicolas Ruggli
- Institute for Virology and Immunology IVI, Mittelhäusern and Bern, Switzerland; Department of Infectious Diseases and Pathobiology, University of Bern, Switzerland.
| | - Volker Thiel
- Institute for Virology and Immunology IVI, Mittelhäusern and Bern, Switzerland; Department of Infectious Diseases and Pathobiology, University of Bern, Switzerland.
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50
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Abstract
The human coronaviruses have been shown to be a major player in clinical microbiology and frequently occur as pathogens responsible for mild to severe respiratory infections. Moreover, two of the most dangerous viral respiratory infections are caused by novel coronaviruses, namely, the SARS and the MERS coronavirus. This chapter briefly summarizes the most important facts and knowledge required for the appropriate laboratory diagnostics of infections caused by the human coronaviruses.
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Affiliation(s)
- Yi-Wei Tang
- Departments of Laboratory Medicine and Internal Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Charles W. Stratton
- Department of Pathology, Microbiology and Immunology and Medicine, Vanderbilt University Medical Center, Nashville, TN USA
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