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Madhugiri R, Nguyen HV, Slanina H, Ziebuhr J. Alpha- and betacoronavirus cis-acting RNA elements. Curr Opin Microbiol 2024; 79:102483. [PMID: 38723345 DOI: 10.1016/j.mib.2024.102483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 06/11/2024]
Abstract
Coronaviruses have exceptionally large RNA genomes and employ multiprotein replication/transcription complexes to orchestrate specific steps of viral RNA genome replication and expression. Most of these processes involve viral cis-acting RNA elements that are engaged in vital RNA-RNA and/or RNA-protein interactions. Over the past years, a large number of studies provided interesting new insight into the structures and, to a lesser extent, functions of specific RNA elements for representative coronaviruses, and there is evidence to suggest that (a majority of) these RNA elements are conserved across genetically divergent coronavirus genera. It is becoming increasingly clear that at least some of these elements do not function in isolation but operate through complex and highly dynamic RNA-RNA interactions. This article reviews structural and functional aspects of cis-acting RNA elements conserved in alpha- and betacoronavirus 5'- and 3'-terminal genome regions, focusing on their critical roles in viral RNA synthesis and gene expression.
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Affiliation(s)
- Ramakanth Madhugiri
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Hoang Viet Nguyen
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Heiko Slanina
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany.
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2
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Bloom JD, Neher RA. Fitness effects of mutations to SARS-CoV-2 proteins. Virus Evol 2023; 9:vead055. [PMID: 37727875 PMCID: PMC10506532 DOI: 10.1093/ve/vead055] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/08/2023] [Accepted: 08/22/2023] [Indexed: 09/21/2023] Open
Abstract
Knowledge of the fitness effects of mutations to SARS-CoV-2 can inform assessment of new variants, design of therapeutics resistant to escape, and understanding of the functions of viral proteins. However, experimentally measuring effects of mutations is challenging: we lack tractable lab assays for many SARS-CoV-2 proteins, and comprehensive deep mutational scanning has been applied to only two SARS-CoV-2 proteins. Here, we develop an approach that leverages millions of publicly available SARS-CoV-2 sequences to estimate effects of mutations. We first calculate how many independent occurrences of each mutation are expected to be observed along the SARS-CoV-2 phylogeny in the absence of selection. We then compare these expected observations to the actual observations to estimate the effect of each mutation. These estimates correlate well with deep mutational scanning measurements. For most genes, synonymous mutations are nearly neutral, stop-codon mutations are deleterious, and amino acid mutations have a range of effects. However, some viral accessory proteins are under little to no selection. We provide interactive visualizations of effects of mutations to all SARS-CoV-2 proteins (https://jbloomlab.github.io/SARS2-mut-fitness/). The framework we describe is applicable to any virus for which the number of available sequences is sufficiently large that many independent occurrences of each neutral mutation are observed.
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Affiliation(s)
- Jesse D Bloom
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Richard A Neher
- Biozentrum, University of Basel, Spitalstrasse 41, Basel 4056, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerl
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3
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Skittrall JP, Irigoyen N, Brierley I, Gog JR. A novel approach to finding conserved features in low-variability gene alignments characterises RNA motifs in SARS-CoV and SARS-CoV-2. Sci Rep 2023; 13:12079. [PMID: 37495730 PMCID: PMC10372003 DOI: 10.1038/s41598-023-39207-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/21/2023] [Indexed: 07/28/2023] Open
Abstract
Collections of genetic sequences belonging to related organisms contain information on the evolutionary constraints to which the organisms have been subjected. Heavily constrained regions can be investigated to understand their roles in an organism's life cycle, and drugs can be sought to disrupt these roles. In organisms with low genetic diversity, such as newly-emerged pathogens, it is key to obtain this information early to develop new treatments. Here, we present methods that ensure we can leverage all the information available in a low-signal, low-noise set of sequences, to find contiguous regions of relatively conserved nucleic acid. We demonstrate the application of these methods by analysing over 5 million genome sequences of the recently-emerged RNA virus SARS-CoV-2 and correlating these results with an analysis of 119 genome sequences of SARS-CoV. We propose the precise location of a previously described packaging signal, and discuss explanations for other regions of high conservation.
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Affiliation(s)
- Jordan P Skittrall
- Department of Pathology, Division of Virology, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK.
| | - Nerea Irigoyen
- Department of Pathology, Division of Virology, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK
| | - Ian Brierley
- Department of Pathology, Division of Virology, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK
| | - Julia R Gog
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge, CB3 0WA, UK
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Terasaki K, Narayanan K, Makino S. Identification of a 1.4-kb-Long Sequence Located in the nsp12 and nsp13 Coding Regions of SARS-CoV-2 Genomic RNA That Mediates Efficient Viral RNA Packaging. J Virol 2023:e0065923. [PMID: 37367225 PMCID: PMC10373556 DOI: 10.1128/jvi.00659-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023] Open
Abstract
The specific packaging of the viral RNA genome into virus particles is an essential step in the replication cycle of coronaviruses (CoVs). Using a single-cycle, replicable severe acute respiratory syndrome CoV-2 (SARS-CoV-2) mutant, we demonstrated the preferential packaging of the SARS-CoV-2 genomic RNA into purified virus particles. Furthermore, based on the sequence of an efficiently packaged defective interfering RNA of SARS-CoV, a closely related CoV, that was generated after serial passages of SARS-CoV in cell culture, we designed a series of replication-competent SARS-CoV-2 minigenome RNAs to identify the specific viral RNA region that is important for SARS-CoV-2 RNA packaging into virus particles. We showed that a 1.4-kb-long sequence, derived from the nsp12 and nsp13 coding regions of the SARS-CoV-2 genomic RNA, is required for the efficient packaging of SARS-CoV-2 minigenome RNA into SARS-CoV-2 particles. In addition, we also showed that the presence of possibly the entire 1.4-kb-long sequence is important for the efficient packaging of SARS-CoV-2 RNA. Our findings highlight the differences between the RNA packaging sequence identified in SARS-CoV-2, a Sarbecovirus, and the packaging signal of mouse hepatitis virus (MHV), an Embecovirus, which is a 95-nt-long sequence located at the nsp15 coding region of MHV genomic RNA. Collectively, our data imply that both the location and the sequence/structural features of the RNA element(s) that drives the selective and efficient packaging of viral genomic RNA are not conserved among the subgenera Embecovirus and Sarbecovirus within the Betacoronavirus genus. IMPORTANCE Elucidating the mechanism of SARS-CoV-2 RNA packaging into virus particles is important for the rational design of antiviral drugs that inhibit this vital step in the replication cycle of CoVs. However, our knowledge about the RNA packaging mechanism in SARS-CoV-2, including the identification of the viral RNA region important for SARS-CoV-2 RNA packaging, is limited, primarily due to the logistical challenges of handing SARS-CoV-2 in biosafety level 3 (BSL3) facilities. Our study, using a single-cycle, replicable SARS-CoV-2 mutant, which can be handled in a BSL2 lab, demonstrated the preferential packaging of full-length SARS-CoV-2 genomic RNA into virus particles and identified a specific 1.4-kb-long RNA region in SARS-CoV-2 genomic RNA that is required for the efficient packaging of SARS-CoV-2 RNA into virus particles. The information generated in our study could be valuable for clarifying the mechanisms of SARS-CoV-2 RNA packaging and for the development of targeted therapeutics against SARS-CoV-2 and other related CoVs.
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Affiliation(s)
- Kaori Terasaki
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Krishna Narayanan
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Shinji Makino
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Diseases, The University of Texas Medical Branch, Galveston, Texas, USA
- UTMB Center for Tropical Diseases, The University of Texas Medical Branch, Galveston, Texas, USA
- The Sealy Institute for Vaccine Sciences, The University of Texas Medical Branch, Galveston, Texas, USA
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5
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Bloom JD, Neher RA. Fitness effects of mutations to SARS-CoV-2 proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526314. [PMID: 36778462 PMCID: PMC9915511 DOI: 10.1101/2023.01.30.526314] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Knowledge of the fitness effects of mutations to SARS-CoV-2 can inform assessment of new variants, design of therapeutics resistant to escape, and understanding of the functions of viral proteins. However, experimentally measuring effects of mutations is challenging: we lack tractable lab assays for many SARS-CoV-2 proteins, and comprehensive deep mutational scanning has been applied to only two SARS-CoV-2 proteins. Here we develop an approach that leverages millions of publicly available SARS-CoV-2 sequences to estimate effects of mutations. We first calculate how many independent occurrences of each mutation are expected to be observed along the SARS-CoV-2 phylogeny in the absence of selection. We then compare these expected observations to the actual observations to estimate the effect of each mutation. These estimates correlate well with deep mutational scanning measurements. For most genes, synonymous mutations are nearly neutral, stop-codon mutations are deleterious, and amino-acid mutations have a range of effects. However, some viral accessory proteins are under little to no selection. We provide interactive visualizations of effects of mutations to all SARS-CoV-2 proteins (https://jbloomlab.github.io/SARS2-mut-fitness/). The framework we describe is applicable to any virus for which the number of available sequences is sufficiently large that many independent occurrences of each neutral mutation are observed.
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Affiliation(s)
- Jesse D. Bloom
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Center
- Department of Genome Sciences, University of Washington
- Howard Hughes Medical Institute
| | - Richard A. Neher
- Biozentrum, University of Basel
- Swiss Institute of Bioinformatics
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6
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Bloom JD, Beichman AC, Neher RA, Harris K. Evolution of the SARS-CoV-2 Mutational Spectrum. Mol Biol Evol 2023; 40:msad085. [PMID: 37039557 PMCID: PMC10124870 DOI: 10.1093/molbev/msad085] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/07/2023] [Accepted: 04/06/2023] [Indexed: 04/12/2023] Open
Abstract
SARS-CoV-2 evolves rapidly in part because of its high mutation rate. Here, we examine whether this mutational process itself has changed during viral evolution. To do this, we quantify the relative rates of different types of single-nucleotide mutations at 4-fold degenerate sites in the viral genome across millions of human SARS-CoV-2 sequences. We find clear shifts in the relative rates of several types of mutations during SARS-CoV-2 evolution. The most striking trend is a roughly 2-fold decrease in the relative rate of G→T mutations in Omicron versus early clades, as was recently noted by Ruis et al. (2022. Mutational spectra distinguish SARS-CoV-2 replication niches. bioRxiv, doi:10.1101/2022.09.27.509649). There is also a decrease in the relative rate of C→T mutations in Delta, and other subtle changes in the mutation spectrum along the phylogeny. We speculate that these changes in the mutation spectrum could arise from viral mutations that affect genome replication, packaging, and antagonization of host innate-immune factors, although environmental factors could also play a role. Interestingly, the mutation spectrum of Omicron is more similar than that of earlier SARS-CoV-2 clades to the spectrum that shaped the long-term evolution of sarbecoviruses. Overall, our work shows that the mutation process is itself a dynamic variable during SARS-CoV-2 evolution and suggests that human SARS-CoV-2 may be trending toward a mutation spectrum more similar to that of other animal sarbecoviruses.
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Affiliation(s)
- Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
- Howard Hughes Medical Institute, Seattle, WA
| | | | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, Seattle, WA
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7
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Abstract
The existence of coronaviruses has been known for many years. These viruses cause significant disease that primarily seems to affect agricultural species. Human coronavirus disease due to the 2002 outbreak of Severe Acute Respiratory Syndrome and the 2012 outbreak of Middle East Respiratory Syndrome made headlines; however, these outbreaks were controlled, and public concern quickly faded. This complacency ended in late 2019 when alarms were raised about a mysterious virus responsible for numerous illnesses and deaths in China. As we now know, this novel disease called Coronavirus Disease 2019 (COVID-19) was caused by Severe acute respiratory syndrome-related-coronavirus-2 (SARS-CoV-2) and rapidly became a worldwide pandemic. Luckily, decades of research into animal coronaviruses hastened our understanding of the genetics, structure, transmission, and pathogenesis of these viruses. Coronaviruses infect a wide range of wild and domestic animals, with significant economic impact in several agricultural species. Their large genome, low dependency on host cellular proteins, and frequent recombination allow coronaviruses to successfully cross species barriers and adapt to different hosts including humans. The study of the animal diseases provides an understanding of the virus biology and pathogenesis and has assisted in the rapid development of the SARS-CoV-2 vaccines. Here, we briefly review the classification, origin, etiology, transmission mechanisms, pathogenesis, clinical signs, diagnosis, treatment, and prevention strategies, including available vaccines, for coronaviruses that affect domestic, farm, laboratory, and wild animal species. We also briefly describe the coronaviruses that affect humans. Expanding our knowledge of this complex group of viruses will better prepare us to design strategies to prevent and/or minimize the impact of future coronavirus outbreaks.
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Key Words
- bcov, bovine coronavirus
- ccov, canine coronavirus
- cov(s), coronavirus(es)
- covid-19, coronavirus disease 2019
- crcov, canine respiratory coronavirus
- e, coronaviral envelope protein
- ecov, equine coronavirus
- fcov, feline coronavirus
- fipv, feline infectious peritonitis virus
- gfcov, guinea fowl coronavirus
- hcov, human coronavirus
- ibv, infectious bronchitis virus
- m, coronaviral membrane protein
- mers, middle east respiratory syndrome-coronavirus
- mhv, mouse hepatitis virus
- pedv, porcine epidemic diarrhea virus
- pdcov, porcine deltacoronavirus
- phcov, pheasant coronavirus
- phev, porcine hemagglutinating encephalomyelitis virus
- prcov, porcine respiratory coronavirus
- rt-pcr, reverse transcriptase polymerase chain reaction
- s, coronaviral spike protein
- sads-cov, swine acute diarrhea syndrome-coronavirus
- sars-cov, severe acute respiratory syndrome-coronavirus
- sars-cov-2, severe acute respiratory syndrome–coronavirus–2
- tcov, turkey coronavirus
- tgev, transmissible gastroenteritis virus
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Affiliation(s)
- Alfonso S Gozalo
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland;,
| | - Tannia S Clark
- Office of Laboratory Animal Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - David M Kurtz
- Comparative Medicine Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, North Carolina
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Wang Y, Zhou Z, Wu X, Li T, Wu J, Cai M, Nie J, Wang W, Cui Z. Pseudotyped Viruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1407:1-27. [PMID: 36920689 DOI: 10.1007/978-981-99-0113-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Pseudotyped viruses have been constructed for many viruses. They can mimic the authentic virus and have many advantages compared to authentic viruses. Thus, they have been widely used as a surrogate of authentic virus for viral function analysis, detection of neutralizing antibodies, screening viral entry inhibitors, and others. This chapter reviewed the progress in the field of pseudotyped viruses in general, including the definition and the advantages of pseudotyped viruses, their potential usage, different strategies or vectors used for the construction of pseudotyped viruses, and factors that affect the construction of pseudotyped viruses.
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Affiliation(s)
- Youchun Wang
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Kunming, China.
| | - Zehua Zhou
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China
| | - Xi Wu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China
| | - Tao Li
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China
| | - Jiajing Wu
- Beijing Yunling Biotechnology Co., Ltd., Beijing, China
| | - Meina Cai
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China
| | - Jianhui Nie
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China
| | - Wenbo Wang
- Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China
| | - Zhimin Cui
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China
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9
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Chechetkin VR, Lobzin VV. Evolving ribonucleocapsid assembly/packaging signals in the genomes of the human and animal coronaviruses: targeting, transmission and evolution. J Biomol Struct Dyn 2022; 40:11239-11263. [PMID: 34338591 DOI: 10.1080/07391102.2021.1958061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A world-wide COVID-19 pandemic intensified strongly the studies of molecular mechanisms related to the coronaviruses. The origin of coronaviruses and the risks of human-to-human, animal-to-human and human-to-animal transmission of coronaviral infections can be understood only on a broader evolutionary level by detailed comparative studies. In this paper, we studied ribonucleocapsid assembly-packaging signals (RNAPS) in the genomes of all seven known pathogenic human coronaviruses, SARS-CoV, SARS-CoV-2, MERS-CoV, HCoV-OC43, HCoV-HKU1, HCoV-229E and HCoV-NL63 and compared them with RNAPS in the genomes of the related animal coronaviruses including SARS-Bat-CoV, MERS-Camel-CoV, MHV, Bat-CoV MOP1, TGEV and one of camel alphacoronaviruses. RNAPS in the genomes of coronaviruses were evolved due to weakly specific interactions between genomic RNA and N proteins in helical nucleocapsids. Combining transitional genome mapping and Jaccard correlation coefficients allows us to perform the analysis directly in terms of underlying motifs distributed over the genome. In all coronaviruses, RNAPS were distributed quasi-periodically over the genome with the period about 54 nt biased to 57 nt and to 51 nt for the genomes longer and shorter than that of SARS-CoV, respectively. The comparison with the experimentally verified packaging signals for MERS-CoV, MHV and TGEV proved that the distribution of particular motifs is strongly correlated with the packaging signals. We also found that many motifs were highly conserved in both characters and positioning on the genomes throughout the lineages that make them promising therapeutic targets. The mechanisms of encapsidation can affect the recombination and co-infection as well.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vladimir R Chechetkin
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, Russia
| | - Vasily V Lobzin
- School of Physics, University of Sydney, Sydney, NSW, Australia
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10
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Carlson CR, Adly AN, Bi M, Howard CJ, Frost A, Cheng Y, Morgan DO. Reconstitution of the SARS-CoV-2 ribonucleosome provides insights into genomic RNA packaging and regulation by phosphorylation. J Biol Chem 2022; 298:102560. [PMID: 36202211 PMCID: PMC9529352 DOI: 10.1016/j.jbc.2022.102560] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/06/2022] Open
Abstract
The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 is responsible for compaction of the ∼30-kb RNA genome in the ∼90-nm virion. Previous studies suggest that each virion contains 35 to 40 viral ribonucleoprotein (vRNP) complexes, or ribonucleosomes, arrayed along the genome. There is, however, little mechanistic understanding of the vRNP complex. Here, we show that N protein, when combined in vitro with short fragments of the viral genome, forms 15-nm particles similar to the vRNP structures observed within virions. These vRNPs depend on regions of N protein that promote protein-RNA and protein-protein interactions. Phosphorylation of N protein in its disordered serine/arginine region weakens these interactions to generate less compact vRNPs. We propose that unmodified N protein binds structurally diverse regions in genomic RNA to form compact vRNPs within the nucleocapsid, while phosphorylation alters vRNP structure to support other N protein functions in viral transcription.
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Affiliation(s)
| | - Armin N Adly
- Department of Physiology, University of California, San Francisco, California, USA
| | - Maxine Bi
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - Conor J Howard
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - Adam Frost
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, California, USA.
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11
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Lama L, Ryan K. Starting and stopping RNA polymerase III transcription on single-stranded DNA oligonucleotides. RNA (NEW YORK, N.Y.) 2022; 28:1315-1324. [PMID: 35853667 PMCID: PMC9479740 DOI: 10.1261/rna.078981.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Circularized single-stranded DNA oligonucleotides, or coligos, show promise as promoter-independent RNA polymerase III (Pol III) transcription templates for generating small RNA in human cells. Using a modified small RNA-seq method, we studied the sequence and secondary structure characteristics that determine Pol III initiation and termination on six coligo templates. The coligos each consisted of an imperfectly base-paired stem flanked by one larger and one smaller loop and were unrelated in sequence. Small RNA-seq data from Pol III coligo transcripts revealed a strong preference for initiating transcription within a 5-nucleotide (nt) window spanning the stem-larger loop junction (loop size 11-24 nt). Transcription in all cases proceeded into the stem rather than into the larger loop, indicating the junction is a site-specific, secondary structure-based Pol III transcription initiator. On average, 81% of sequencing reads showed initiation within this 5 nt junction region, with a template start site nucleotide preference of C > T >> A > G, and a requirement for a template purine at Tss-1. Termination was less precise than initiation and occurred in the larger loop at the same end of the stem where transcription initiated. Termination efficiency was on average 82% and was distributed among the first 11 single-stranded larger loop nt following the stem. The size heterogeneity of Pol III coligo transcripts is thus mainly due to 3' end heterogeneity, whereas the RNA 5' ends were more predictable and homogeneous. Transcription termination did not require an oligo dA template sequence, indicating that termination in this context may be mechanistically different than Pol III's normal gene-context termination. A stepwise model for coligo transcription by Pol III is proposed.
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Affiliation(s)
- Lodoe Lama
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, USA
- Biochemistry and Chemistry Ph.D. Programs, The City University of New York Graduate Center, New York, New York 10016, USA
| | - Kevin Ryan
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, USA
- Biochemistry and Chemistry Ph.D. Programs, The City University of New York Graduate Center, New York, New York 10016, USA
- Chemistry Ph.D. Programs, The City University of New York Graduate Center, New York, New York 10016, USA
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12
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Zhao H, Zhang C, Lam H, Meng X, Peng Z, Yeung ML, Chan JFW, Kai-Wang To K, Yuen KY. Peptidic defective interfering gene nanoparticles against Omicron, Delta SARS-CoV-2 variants and influenza A virus in vivo. Signal Transduct Target Ther 2022; 7:266. [PMID: 35922403 PMCID: PMC9349215 DOI: 10.1038/s41392-022-01138-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 07/11/2022] [Accepted: 07/25/2022] [Indexed: 11/24/2022] Open
Abstract
Defective interfering genes (DIGs) are short viral genomes and interfere with wild-type viral replication. Here, we demonstrate that the new designed SARS-CoV-2 DIG (CD3600) can significantly inhibit the replication of SARS-CoV-2 including Alpha, Delta, Kappa and Omicron variants in human HK-2 cells and influenza DIG (PAD4) can significantly inhibit influenza virus replication in human A549 cells. One dose of influenza DIGs prophylactically protects 90% mice from lethal challenge of A(H1N1)pdm09 virus and CD3600 inhibits SARS-CoV-2 replication in hamster lungs when DIGs are administrated to lungs one day before viral challenge. To further investigate the gene delivery vector in the respiratory tract, a peptidic TAT2-P1&LAH4, which can package genes to form small spherical nanoparticles with high endosomal escape ability, is demonstrated to dramatically increase gene expression in the lung airway. TAT2-P1&LAH4, with the dual-functional TAT2-P1 (gene-delivery and antiviral), can deliver CD3600 to significantly inhibit the replication of Delta and Omicron SARS-CoV-2 in hamster lungs. This peptide-based nanoparticle system can effectively transfect genes in lungs and deliver DIGs to inhibit SARS-CoV-2 variants and influenza virus in vivo, which provides the new insight into the drug delivery system for gene therapy against respiratory viruses.
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Affiliation(s)
- Hanjun Zhao
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China.
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China.
| | - Chuyuan Zhang
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hoiyan Lam
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Xinjie Meng
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Zheng Peng
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Man Lung Yeung
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Guangzhou Laboratory, Guangzhou, Guangdong Province, China
| | - Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Guangzhou Laboratory, Guangzhou, Guangdong Province, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China.
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China.
- Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
- Guangzhou Laboratory, Guangzhou, Guangdong Province, China.
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13
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Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication. Microbiol Mol Biol Rev 2022; 86:e0005721. [PMID: 35862724 PMCID: PMC9491204 DOI: 10.1128/mmbr.00057-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
SARS-CoV-2, the etiological agent responsible for the COVID-19 pandemic, is a member of the virus family Coronaviridae, known for relatively extensive (~30-kb) RNA genomes that not only encode for numerous proteins but are also capable of forming elaborate structures. As highlighted in this review, these structures perform critical functions in various steps of the viral life cycle, ultimately impacting pathogenesis and transmissibility. We examine these elements in the context of coronavirus evolutionary history and future directions for curbing the spread of SARS-CoV-2 and other potential human coronaviruses. While we focus on structures supported by a variety of biochemical, biophysical, and/or computational methods, we also touch here on recent evidence for novel structures in both protein-coding and noncoding regions of the genome, including an assessment of the potential role for RNA structure in the controversial finding of SARS-CoV-2 integration in “long COVID” patients. This review aims to serve as a consolidation of previous works on coronavirus and more recent investigation of SARS-CoV-2, emphasizing the need for improved understanding of the role of RNA structure in the evolution and adaptation of these human viruses.
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14
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Calvo-Alvarez E, Dolci M, Perego F, Signorini L, Parapini S, D’Alessandro S, Denti L, Basilico N, Taramelli D, Ferrante P, Delbue S. Antiparasitic Drugs against SARS-CoV-2: A Comprehensive Literature Survey. Microorganisms 2022; 10:microorganisms10071284. [PMID: 35889004 PMCID: PMC9320270 DOI: 10.3390/microorganisms10071284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 01/09/2023] Open
Abstract
More than two years have passed since the viral outbreak that led to the novel infectious respiratory disease COVID-19, caused by the SARS-CoV-2 coronavirus. Since then, the urgency for effective treatments resulted in unprecedented efforts to develop new vaccines and to accelerate the drug discovery pipeline, mainly through the repurposing of well-known compounds with broad antiviral effects. In particular, antiparasitic drugs historically used against human infections due to protozoa or helminth parasites have entered the main stage as a miracle cure in the fight against SARS-CoV-2. Despite having demonstrated promising anti-SARS-CoV-2 activities in vitro, conflicting results have made their translation into clinical practice more difficult than expected. Since many studies involving antiparasitic drugs are currently under investigation, the window of opportunity might be not closed yet. Here, we will review the (controversial) journey of these old antiparasitic drugs to combat the human infection caused by the novel coronavirus SARS-CoV-2.
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Affiliation(s)
- Estefanía Calvo-Alvarez
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
- Correspondence:
| | - Maria Dolci
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| | - Federica Perego
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| | - Lucia Signorini
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| | - Silvia Parapini
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy;
| | - Sarah D’Alessandro
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milan, Italy; (S.D.); (D.T.)
| | - Luca Denti
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| | - Nicoletta Basilico
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| | - Donatella Taramelli
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milan, Italy; (S.D.); (D.T.)
| | - Pasquale Ferrante
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| | - Serena Delbue
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
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15
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Carlson CR, Adly AN, Bi M, Cheng Y, Morgan DO. Reconstitution of the SARS-CoV-2 ribonucleosome provides insights into genomic RNA packaging and regulation by phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.05.23.493138. [PMID: 35664996 PMCID: PMC9164447 DOI: 10.1101/2022.05.23.493138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The nucleocapsid (N) protein of coronaviruses is responsible for compaction of the ∼30-kb RNA genome in the ∼100-nm virion. Cryo-electron tomography suggests that each virion contains 35-40 viral ribonucleoprotein (vRNP) complexes, or ribonucleosomes, arrayed along the genome. There is, however, little mechanistic understanding of the vRNP complex. Here, we show that N protein, when combined with viral RNA fragments in vitro, forms cylindrical 15-nm particles similar to the vRNP structures observed within coronavirus virions. These vRNPs form in the presence of stem-loop-containing RNA and depend on regions of N protein that promote protein-RNA and protein-protein interactions. Phosphorylation of N protein in its disordered serine/arginine (SR) region weakens these interactions and disrupts vRNP assembly. We propose that unmodified N binds stem-loop-rich regions in genomic RNA to form compact vRNP complexes within the nucleocapsid, while phosphorylated N maintains uncompacted viral RNA to promote the protein's transcriptional function.
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Affiliation(s)
| | - Armin N. Adly
- Department of Physiology, University of California, San Francisco CA 94143
| | - Maxine Bi
- Department of Biochemistry & Biophysics, University of California, San Francisco CA 94143
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco CA 94143
| | - David O. Morgan
- Department of Physiology, University of California, San Francisco CA 94143
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16
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Lu W, Zhao Z, Huang YW, Wang B. Review: A systematic review of virus-like particles of coronavirus: Assembly, generation, chimerism and their application in basic research and in the clinic. Int J Biol Macromol 2022; 200:487-497. [PMID: 35065135 PMCID: PMC8769907 DOI: 10.1016/j.ijbiomac.2022.01.108] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/27/2022]
Abstract
Virus-like particles (VLPs) are nano-scale particles that are morphologically similar to a live virus but which lack a genetic component. Since the pandemic spread of COVID-19, much focus has been placed on coronavirus (CoV)-related VLPs. CoVs contain four structural proteins, though the minimum requirement for VLP formation differs among virus species. CoV VLPs are commonly produced in mammalian and insect cell systems, sometimes in the form of chimeric VLPs that enable surface display of CoV epitopes. VLPs are an ideal model for virological research and have been applied as vaccines and diagnostic reagents to aid in clinical disease control. This review summarizes and updates the research progress on the characteristics of VLPs from different known CoVs, mainly focusing on assembly, in vitro expression systems for VLP generation, VLP chimerism, protein-based nanoparticles and their applications in basic research and clinical settings, which may aid in development of novel VLP vaccines against emerging coronavirus diseases such as SARS-CoV-2.
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Affiliation(s)
- Wan Lu
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Zhuangzhuang Zhao
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yao-Wei Huang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
| | - Bin Wang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China.
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17
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Detection of the ORF1 Gene Is an Indicator of the Possible Isolation of Severe Acute Respiratory Syndrome Coronavirus 2. Pathogens 2022; 11:pathogens11030302. [PMID: 35335626 PMCID: PMC8953321 DOI: 10.3390/pathogens11030302] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 02/06/2023] Open
Abstract
In the ongoing coronavirus diseases 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), real-time RT-PCR based diagnostic assays have been used for the detection of infection, but the positive signal of real-time RT-PCR does not necessarily indicate the infectivity of the patient. Due to the unique replication system of the coronavirus, primer/probe sets targeted nucleocapsid (N) and spike (S) protein detect the abundantly synthesized subgenomic RNAs as well as the virus genome, possibly making the assay unsuitable for estimation of the infectivity of the specimen, although it has an advantage for the diagnostic tests. In this study, the primer/probe set targeting the open reading frame 1a (ORF1a) gene was developed to specifically detect viral genomic RNA. Then the relation between the ORF1a signal and infectivity of the clinical specimens was validated by virus isolation using VeroE6 cells, which constitutively express transmembrane protease, serine 2, (VeroE6/TMPRSS2). The analytical sensitivity of developed ORF1a set was similar to that of previously developed N and S sets. Nevertheless, in the assay of the clinical specimen, detection rate of the ORF1a gene was lower than that of the N and S genes. These data indicated that clinical specimens contain a significant amount of subgenomic RNAs. However, as expected, the isolation-succeeded specimen always showed an RT-PCR-positive signal for the ORF1a gene, suggesting ORF1a detection in combination with N and S sets could be a more rational indicator for the possible infectivity of the clinical specimens.
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18
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Clayton E, Rohaim MA, Bayoumi M, Munir M. The Molecular Virology of Coronaviruses with Special Reference to SARS-CoV-2. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1352:15-31. [PMID: 35132592 DOI: 10.1007/978-3-030-85109-5_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Coronaviruses (CoVs) are large, enveloped and positive-sense RNA viruses which are responsible for a range of upper respiratory and digestive tract infections. Interest in coronaviruses has recently escalated due to the identification of a newly emerged coronavirus named severe acute respiratory syndrome 2 (SARS-CoV-2), which is the causative agent of the COVID-19 pandemic. In this chapter, we summarise molecular virological features of coronaviruses and understand their molecular mechanisms of replication in guiding the control of the global COVID-19 pandemic. METHODS We applied a holistic and comparative approach to assess the current understanding of coronavirus molecular virology and identify research gaps among different human coronaviruses. RESULTS Coronaviruses can utilise unique strategies that aid in their pathogenicity, replication and survival in multiple hosts. Replication of coronaviruses involves novel mechanisms such as ribosomal frameshifting and the synthesis of both genomic and sub-genomic RNAs. We summarised the key components in coronavirus molecular biology and molecular determinants of pathogenesis. Focusing largely on SARS-CoV-2 due to its current importance, this review explores the virology of recently emerged coronaviruses to gain an in-depth understanding of these infectious diseases. CONCLUSIONS The presented information provides fundamental bottlenecks to devise future disease control and management strategies to curtail the impact of coronaviruses in human populations.
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Affiliation(s)
- Emily Clayton
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, UK
| | - Mohammed A Rohaim
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, UK
| | - Mahmoud Bayoumi
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, UK
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, UK.
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19
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Bruce EA, Mills MG, Sampoleo R, Perchetti GA, Huang M, Despres HW, Schmidt MM, Roychoudhury P, Shirley DJ, Jerome KR, Greninger AL, Botten JW. Predicting infectivity: comparing four PCR-based assays to detect culturable SARS-CoV-2 in clinical samples. EMBO Mol Med 2022; 14:e15290. [PMID: 34862752 PMCID: PMC8819313 DOI: 10.15252/emmm.202115290] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 01/04/2023] Open
Abstract
With the COVID-19 pandemic caused by SARS-CoV-2 now in its second year, there remains an urgent need for diagnostic testing that can identify infected individuals, particularly those who harbor infectious virus. Various RT-PCR strategies have been proposed to identify specific viral RNA species that may predict the presence of infectious virus, including detection of transcriptional intermediates (e.g., subgenomic RNA [sgRNA]) and replicative intermediates (e.g., negative-strand RNA species). Using a novel primer/probe set for detection of subgenomic (sg)E transcripts, we successfully identified 100% of specimens containing culturable SARS-CoV-2 from a set of 126 clinical samples (total sgE CT values ranging from 12.3 to 37.5). This assay showed superior performance compared to a previously published sgRNA assay and to a negative-strand RNA assay, both of which failed to detect target RNA in a subset of samples from which we isolated live virus. In addition, total levels of viral RNA (genome, negative-strand, and sgE) detected with the WHO/Charité primer-probe set correlated closely with levels of infectious virus. Specifically, infectious virus was not detected in samples with a CT above 31.0. Clinical samples with higher levels of viral RNA also displayed cytopathic effect (CPE) more quickly than those with lower levels of viral RNA. Finally, we found that the infectivity of SARS-CoV-2 samples is significantly dependent on the cell type used for viral isolation, as Vero E6 cells expressing TMRPSS2 extended the analytical sensitivity of isolation by more than 3 CT compared to parental Vero E6 cells and resulted in faster isolation. Our work shows that using a total viral RNA Ct cutoff of > 31 or specifically testing for sgRNA can serve as an effective rule-out test for the presence of culturable virus.
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Affiliation(s)
- Emily A Bruce
- Division of ImmunobiologyDepartment of MedicineRobert Larner, M.D. College of MedicineUniversity of VermontBurlingtonVTUSA
- Present address:
Department of Microbiology and Molecular GeneticsRobert Larner, M.D. College of MedicineUniversity of VermontBurlingtonVTUSA
| | - Margaret G Mills
- Virology DivisionDepartment of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWAUSA
| | - Reigran Sampoleo
- Virology DivisionDepartment of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWAUSA
| | - Garrett A Perchetti
- Virology DivisionDepartment of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWAUSA
| | - Meei‐Li Huang
- Virology DivisionDepartment of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWAUSA
| | - Hannah W Despres
- Department of Microbiology and Molecular GeneticsRobert Larner, M.D. College of MedicineUniversity of VermontBurlingtonVTUSA
| | - Madaline M Schmidt
- Department of Microbiology and Molecular GeneticsRobert Larner, M.D. College of MedicineUniversity of VermontBurlingtonVTUSA
| | - Pavitra Roychoudhury
- Virology DivisionDepartment of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWAUSA
- Vaccine and Infectious Disease DivisionFred Hutchinson Cancer Research CenterSeattleWAUSA
| | | | - Keith R Jerome
- Virology DivisionDepartment of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWAUSA
- Vaccine and Infectious Disease DivisionFred Hutchinson Cancer Research CenterSeattleWAUSA
| | - Alexander L Greninger
- Virology DivisionDepartment of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWAUSA
- Vaccine and Infectious Disease DivisionFred Hutchinson Cancer Research CenterSeattleWAUSA
| | - Jason W Botten
- Division of ImmunobiologyDepartment of MedicineRobert Larner, M.D. College of MedicineUniversity of VermontBurlingtonVTUSA
- Department of Microbiology and Molecular GeneticsRobert Larner, M.D. College of MedicineUniversity of VermontBurlingtonVTUSA
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20
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Syed AM, Taha TY, Tabata T, Chen IP, Ciling A, Khalid MM, Sreekumar B, Chen PY, Hayashi JM, Soczek KM, Ott M, Doudna JA. Rapid assessment of SARS-CoV-2-evolved variants using virus-like particles. Science 2021; 374:1626-1632. [PMID: 34735219 PMCID: PMC9005165 DOI: 10.1126/science.abl6184] [Citation(s) in RCA: 180] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/29/2021] [Indexed: 01/16/2023]
Abstract
Efforts to determine why new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants demonstrate improved fitness have been limited to analyzing mutations in the spike (S) protein with the use of S-pseudotyped particles. In this study, we show that SARS-CoV-2 virus-like particles (SC2-VLPs) can package and deliver exogenous transcripts, enabling analysis of mutations within all structural proteins and at multiple steps in the viral life cycle. In SC2-VLPs, four nucleocapsid (N) mutations found universally in more-transmissible variants independently increased messenger RNA delivery and expression ~10-fold, and in a reverse genetics model, the serine-202→arginine (S202R) and arginine-203→methionine (R203M) mutations each produced >50 times as much virus. SC2-VLPs provide a platform for rapid testing of viral variants outside of a biosafety level 3 setting and demonstrate N mutations and particle assembly to be mechanisms that could explain the increased spread of variants, including B.1.617.2 (Delta, which contains the R203M mutation).
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Affiliation(s)
- Abdullah M. Syed
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Taha Y. Taha
- Gladstone Institute of Virology, San Francisco, CA, USA
| | - Takako Tabata
- Gladstone Institute of Virology, San Francisco, CA, USA
| | - Irene P. Chen
- Gladstone Institute of Virology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
| | - Alison Ciling
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Mir M. Khalid
- Gladstone Institute of Virology, San Francisco, CA, USA
| | | | - Pei-Yi Chen
- Gladstone Institute of Virology, San Francisco, CA, USA
| | | | - Katarzyna M. Soczek
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Melanie Ott
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Gladstone Institute of Virology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, CA, USA
| | - Jennifer A. Doudna
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
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21
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Alshammary AF, Al-Sulaiman AM. The journey of SARS-CoV-2 in human hosts: a review of immune responses, immunosuppression, and their consequences. Virulence 2021; 12:1771-1794. [PMID: 34251989 PMCID: PMC8276660 DOI: 10.1080/21505594.2021.1929800] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/13/2021] [Accepted: 05/10/2021] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a highly infectious viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Laboratory findings from a significant number of patients with COVID-19 indicate the occurrence of leukocytopenia, specifically lymphocytopenia. Moreover, infected patients can experience contrasting outcomes depending on lymphocytopenia status. Patients with resolved lymphocytopenia are more likely to recover, whereas critically ill patients with signs of unresolved lymphocytopenia develop severe complications, sometimes culminating in death. Why immunodepression manifests in patients with COVID-19 remains unclear. Therefore, the evaluation of clinical symptoms and laboratory findings from infected patients is critical for understanding the disease course and its consequences. In this review, we take a logical approach to unravel the reasons for immunodepression in patients with COVID-19. Following the footprints of the virus within host tissues, from entry to exit, we extrapolate the mechanisms underlying the phenomenon of immunodepression.
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Affiliation(s)
- Amal F. Alshammary
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
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22
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Krishnan S, Thirunavukarasu A, Jha NK, Gahtori R, Roy AS, Dholpuria S, Kesari KK, Singh SK, Dua K, Gupta PK. Nanotechnology-based therapeutic formulations in the battle against animal coronaviruses: an update. JOURNAL OF NANOPARTICLE RESEARCH : AN INTERDISCIPLINARY FORUM FOR NANOSCALE SCIENCE AND TECHNOLOGY 2021; 23:229. [PMID: 34690535 PMCID: PMC8520458 DOI: 10.1007/s11051-021-05341-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 10/03/2021] [Indexed: 06/13/2023]
Abstract
Outbreak of infectious diseases imposes a serious threat to human population and also causes a catastrophic impact on global economy. Animal coronaviruses remain as one of the intriguing problems, known to cause deadly viral diseases on economically important animal population, and also these infections may spread to other animals and humans. Through isolation of the infected animals from others and providing appropriate treatment using antiviral drugs, it is possible to prevent the virus transmission from animals to other species. In recent times, antiviral drug-resistant strains are being emerged as a deadly virus which are known to cause pandemic. To overcome this, nanoparticles-based formulations are developed as antiviral agent which attacks the animal coronaviruses at multiple sites in the virus replication cycle. Nanovaccines are also being formulated to protect the animals from coronaviruses. Nanoformulations contain particles of one or more dimensions in nano-scale (few nanometers to 1000 nm), which could be inorganic or organic in nature. This review presents the comprehensive outline of the nanotechnology-based therapeutics formulated against animal coronaviruses, which includes the nanoparticles-based antiviral formulations and nanoparticles-based adjuvant vaccines. The mechanism of action of these nanoparticles-based antivirals against animal coronavirus is also discussed using relevant examples. In addition, the scope of repurposing the existing nano-enabled antivirals and vaccines to combat the coronavirus infections in animals is elaborated.
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Affiliation(s)
| | | | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering and Technology (SET), Sharda University, Plot no. 32 – 34, Knowledge Park III, Greater Noida, 201310 Uttar Pradesh India
| | - Rekha Gahtori
- Department of Biotechnology, Sir J. C. Bose Technical Campus, Kumaun University, Nainital, 263136 Uttarakhand India
| | - Ayush Singha Roy
- Department of Biotechnology, Amity School of Biotechnology, Amity University, Mumbai-Pune Expressway, Mumbai, Maharashtra 410206 India
| | - Sunny Dholpuria
- Department of Life Sciences, J.C. Bose University of Science and Technology, YMCA, Faridabad, 121006 Haryana India
| | | | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab India
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW 2007 Australia
| | - Piyush Kumar Gupta
- Department of Life Sciences, School of Basic Sciences and Research (SBSR), Sharda University, Plot no. 32 – 34, Knowledge Park III, Greater Noida, 201310 Uttar Pradesh India
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23
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Yao S, Narayanan A, Majowicz SA, Jose J, Archetti M. A synthetic defective interfering SARS-CoV-2. PeerJ 2021; 9:e11686. [PMID: 34249513 PMCID: PMC8255065 DOI: 10.7717/peerj.11686] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/07/2021] [Indexed: 11/20/2022] Open
Abstract
Viruses thrive by exploiting the cells they infect, but in order to replicate and infect other cells they must produce viral proteins. As a result, viruses are also susceptible to exploitation by defective versions of themselves that do not produce such proteins. A defective viral genome with deletions in protein-coding genes could still replicate in cells coinfected with full-length viruses. Such a defective genome could even replicate faster due to its shorter size, interfering with the replication of the virus. We have created a synthetic defective interfering version of SARS-CoV-2, the virus causing the Covid-19 pandemic, assembling parts of the viral genome that do not code for any functional protein but enable the genome to be replicated and packaged. This synthetic defective genome replicates three times faster than SARS-CoV-2 in coinfected cells, and interferes with it, reducing the viral load of infected cells by half in 24 hours. The synthetic genome is transmitted as efficiently as the full-length genome, suggesting the location of the putative packaging signal of SARS-CoV-2. A version of such a synthetic construct could be used as a self-promoting antiviral therapy: by enabling replication of the synthetic genome, the virus would promote its own demise.
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Affiliation(s)
- Shun Yao
- Department of Biology, Pennsylvania State University, University Park, United States of America
| | - Anoop Narayanan
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, United States of America
| | - Sydney A Majowicz
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, United States of America
| | - Joyce Jose
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, United States of America.,The Huck Institutes for the Life Sciences, Pennsylvania State University, University Park, United States of America
| | - Marco Archetti
- Department of Biology, Pennsylvania State University, University Park, United States of America.,The Huck Institutes for the Life Sciences, Pennsylvania State University, University Park, United States of America
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24
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Chen SC, Olsthoorn RCL, Yu CH. Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2. Virus Evol 2021; 7:veab021. [PMID: 34141447 PMCID: PMC8206606 DOI: 10.1093/ve/veab021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In many single-stranded (ss) RNA viruses, the cis-acting packaging signal that confers selectivity genome packaging usually encompasses short structured RNA repeats. These structural units, termed repetitive structural motifs (RSMs), potentially mediate capsid assembly by specific RNA–protein interactions. However, general knowledge of the conservation and/or the diversity of RSMs in the positive-sense ssRNA coronaviruses (CoVs) is limited. By performing structural phylogenetic analysis, we identified a variety of RSMs in nearly all CoV genomic RNAs, which are exclusively located in the 5′-untranslated regions (UTRs) and/or in the inter-domain regions of poly-protein 1ab coding sequences in a lineage-specific manner. In all alpha- and beta-CoVs, except for Embecovirus spp, two to four copies of 5′-gUUYCGUc-3′ RSMs displaying conserved hexa-loop sequences were generally identified in Stem-loop 5 (SL5) located in the 5′-UTRs of genomic RNAs. In Embecovirus spp., however, two to eight copies of 5′-agc-3′/guAAu RSMs were found in the coding regions of non-structural protein (NSP) 3 and/or NSP15 in open reading frame (ORF) 1ab. In gamma- and delta-CoVs, other types of RSMs were found in several clustered structural elements in 5′-UTRs and/or ORF1ab. The identification of RSM-encompassing structural elements in all CoVs suggests that these RNA elements play fundamental roles in the life cycle of CoVs. In the recently emerged SARS-CoV-2, beta-CoV-specific RSMs are also found in its SL5, displaying two copies of 5′-gUUUCGUc-3′ motifs. However, multiple sequence alignment reveals that the majority of SARS-CoV-2 possesses a variant RSM harboring SL5b C241U, and intriguingly, several variations in the coding sequences of viral proteins, such as Nsp12 P323L, S protein D614G, and N protein R203K-G204R, are concurrently found with such variant RSM. In conclusion, the comprehensive exploration for RSMs reveals phylogenetic insights into the RNA structural elements in CoVs as a whole and provides a new perspective on variations currently found in SARS-CoV-2.
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Affiliation(s)
- Shih-Cheng Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng-Kung University, No.1, University Road, Tainan City 701, Taiwan
| | - René C L Olsthoorn
- Department of Supramolecular Biomaterials Chemistry, Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC, Leiden,The Netherlands
| | - Chien-Hung Yu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng-Kung University, No.1, University Road, Tainan City 701, Taiwan
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25
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de Melo IS, Sabino-Silva R, Cunha TM, Goulart LR, Reis WL, Jardim ACG, Shetty AK, de Castro OW. Hydroelectrolytic Disorder in COVID-19 patients: Evidence Supporting the Involvement of Subfornical Organ and Paraventricular Nucleus of the Hypothalamus. Neurosci Biobehav Rev 2021; 124:216-223. [PMID: 33577841 PMCID: PMC7872848 DOI: 10.1016/j.neubiorev.2021.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 02/07/2023]
Abstract
Multiple neurological problems have been reported in coronavirus disease-2019 (COVID-19) patients because severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) likely spreads to the central nervous system (CNS) via olfactory nerves or through the subarachnoid space along olfactory nerves into the brain's cerebrospinal fluid and then into the brain's interstitial space. We hypothesize that SARS-CoV-2 enters the subfornical organ (SFO) through the above routes and the circulating blood since circumventricular organs (CVOs) such as the SFO lack the blood-brain barrier, and infection of the SFO causes dysfunction of the hypothalamic paraventricular nucleus (PVN) and supraoptic nucleus (SON), leading to hydroelectrolytic disorder. SARS-CoV-2 can readily enter SFO-PVN-SON neurons because these neurons express angiotensin-converting enzyme-2 receptors and proteolytic viral activators, which likely leads to neurodegeneration or neuroinflammation in these regions. Considering the pivotal role of SFO-PVN-SON circuitry in modulating hydroelectrolyte balance, SARS-CoV-2 infection in these regions could disrupt the neuroendocrine control of hydromineral homeostasis. This review proposes mechanisms by which SARS-CoV-2 infection of the SFO-PVN-SON pathway leads to hydroelectrolytic disorder in COVID-19 patients.
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Affiliation(s)
- Igor Santana de Melo
- Department of Physiology, Institute of Biological Sciences and Health, Federal University of Alagoas (UFAL), Maceio, Brazil
| | - Robinson Sabino-Silva
- Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia (UFU), Uberlândia, MG, Brazil.
| | - Thúlio Marquez Cunha
- Department of Pulmonology, School of Medicine, Federal University of Uberlandia, Minas Gerais, Brazil
| | - Luiz Ricardo Goulart
- Institute of Biotechnology, Federal University of Uberlandia, Minas Gerais, Brazil
| | - Wagner Luis Reis
- Department of Physiological, Sciences Biological Sciences Centre Federal University of Santa Catarina (UFSC) Florianopolis, Santa Catarina, Brazil
| | - Ana Carolina Gomes Jardim
- Laboratory of Virology, Institute of Biomedical Sciences, Federal University of Uberlandia, Minas Gerais, Brazil
| | - Ashok K Shetty
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University College of Medicine, College Station, TX, 77843, USA.
| | - Olagide Wagner de Castro
- Department of Physiology, Institute of Biological Sciences and Health, Federal University of Alagoas (UFAL), Maceio, Brazil.
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26
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El-Sayed A, Kamel M. Coronaviruses in humans and animals: the role of bats in viral evolution. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:19589-19600. [PMID: 33655480 PMCID: PMC7924989 DOI: 10.1007/s11356-021-12553-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/14/2021] [Indexed: 04/15/2023]
Abstract
Bats act as a natural reservoir for many viruses, including coronaviruses, and have played a crucial epidemiological role in the emergence of many viral diseases. Coronaviruses have been known for 60 years. They are usually responsible for the induction of mild respiratory signs in humans. However, since 2002, the bat-borne virus started to induce fatal epidemics according to WHO reports. In this year, the first serious human coronavirus epidemic (severe acute respiratory syndrome; SARS) occurred (China, 8098 cases, 774 deaths [9.5% of the cases] in 17 countries). The case fatality was higher in elderly patients above 60 years and reached 50% of the cases. SARS epidemic was followed 10 years later by the emergence of the middle east respiratory syndrome (MERS) in Saudi Arabia (in 2012, 2260 cases, 803 deaths [35.5% of the cases] in 27 countries). Finally, in December 2019, a new epidemic in Wuhan, China, (corona virus disease 2019, COVID-19) emerged and could spread to 217 countries infecting more than 86,255,226 cases and killing 1,863,973 people by the end of 2020. There are many reasons why bats are ideal reservoir hosts for viral diseases such as the tolerance of their immune system to the invading viruses for several months. They can actively shed the viruses, although they develop no clinical signs (will be discussed in details later in the review). Bats were directly or indirectly involved in the three previous coronavirus epidemics. The indirect transmission takes place via intermediate hosts including civet cats for SARS and dromedary camels in the case of MERS. Although bats are believed to be the source of COVID-19 pandemic, direct pieces of evidence are still lacking. Therefore, coronaviruses' role in epidemics induction and the epidemiological role of bats are discussed. The current work also presents different evidence (phylogenetic data, animal experiments, bats artificial infection studies, and computerized models of SARS-CoV2 evolution) that underline the involvement of bats in the epidemiology of the pandemic.
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Affiliation(s)
- Amr El-Sayed
- Department of Medicine and Infectious Diseases, Faculty of Medicine and Infectious Diseases, Cairo University, Giza, 12211, Egypt
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Medicine and Infectious Diseases, Cairo University, Giza, 12211, Egypt.
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27
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Sahu AK, Sreepadmanabh M, Rai M, Chande A. SARS-CoV-2: phylogenetic origins, pathogenesis, modes of transmission, and the potential role of nanotechnology. Virusdisease 2021; 32:1-12. [PMID: 33644261 PMCID: PMC7897733 DOI: 10.1007/s13337-021-00653-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic has elicited a rapid response from the scientific community with significant advances in understanding the causative pathogen (SARS-CoV-2). Mechanisms of viral transmission and pathogenesis, as well as structural and genomic details, have been reported, which are essential in guiding containment, treatment, and vaccine development efforts. Here, we present a concise review of the recent research in these domains and an exhaustive analysis of the genomic origins of SARS-CoV-2. Particular emphasis has been placed on the pathology and disease progression of COVID-19 as documented by recent clinical studies, in addition to the characteristic immune responses involved therein. Furthermore, we explore the potential of nanomaterials and nanotechnology to develop diagnostic tools, drug delivery systems, and personal protective equipment design within the ongoing pandemic context. We present this as a ready resource for researchers to gain succinct, up-to-date insights on SARS-CoV-2.
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Affiliation(s)
- Amit Kumar Sahu
- Molecular Virology Laboratory, Indian Institute of Science Education and Research (IISER) Bhopal, Indore By-Pass Road, Bhopal, 462066 India
| | - M. Sreepadmanabh
- Molecular Virology Laboratory, Indian Institute of Science Education and Research (IISER) Bhopal, Indore By-Pass Road, Bhopal, 462066 India
| | - Mahendra Rai
- Department of Biotechnology, SGB Amravati University, Amravati, Maharashtra 444602 India
| | - Ajit Chande
- Molecular Virology Laboratory, Indian Institute of Science Education and Research (IISER) Bhopal, Indore By-Pass Road, Bhopal, 462066 India
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28
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Zhang Y, Tang LV. Overview of Targets and Potential Drugs of SARS-CoV-2 According to the Viral Replication. J Proteome Res 2021; 20:49-59. [PMID: 33347311 PMCID: PMC7770889 DOI: 10.1021/acs.jproteome.0c00526] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Indexed: 01/18/2023]
Abstract
Since the novel coronavirus pandemic, people around the world have been touched in varying degrees, and this pandemic has raised a major global health concern. As there is no effective drug or vaccine, it is urgent to find therapeutic drugs that can serve to deal with the current epidemic situation in all countries and regions. We searched drugs and response measures for SARS-CoV-2 in the PubMed database, and then updated the potential targets and therapeutic drugs from the perspective of the viral replication cycle. The drug research studies of the viral replication cycle are predominantly focused on the process of the virus entering cells, proteases, and RdRp. The inhibitors of the virus entry to cells and RdRp, such as Arbidol, remdesivir, favipiravir, EIDD-2081, and ribavirin, are in clinical trials, while most of the protease inhibitors are mainly calculated by molecular docking technology, which needs in vivo and in vitro experiments to prove the effect for SARS-CoV-2. This review summarizes the drugs targeting the viral replication process and provides a basis and directions for future drug development and reuse on the protein level of COVID-19.
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Affiliation(s)
- Yi Zhang
- Institute
of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Liang V. Tang
- Institute
of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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29
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Iserman C, Roden CA, Boerneke MA, Sealfon RSG, McLaughlin GA, Jungreis I, Fritch EJ, Hou YJ, Ekena J, Weidmann CA, Theesfeld CL, Kellis M, Troyanskaya OG, Baric RS, Sheahan TP, Weeks KM, Gladfelter AS. Genomic RNA Elements Drive Phase Separation of the SARS-CoV-2 Nucleocapsid. Mol Cell 2020; 80:1078-1091.e6. [PMID: 33290746 PMCID: PMC7691212 DOI: 10.1016/j.molcel.2020.11.041] [Citation(s) in RCA: 212] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/28/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023]
Abstract
We report that the SARS-CoV-2 nucleocapsid protein (N-protein) undergoes liquid-liquid phase separation (LLPS) with viral RNA. N-protein condenses with specific RNA genomic elements under physiological buffer conditions and condensation is enhanced at human body temperatures (33°C and 37°C) and reduced at room temperature (22°C). RNA sequence and structure in specific genomic regions regulate N-protein condensation while other genomic regions promote condensate dissolution, potentially preventing aggregation of the large genome. At low concentrations, N-protein preferentially crosslinks to specific regions characterized by single-stranded RNA flanked by structured elements and these features specify the location, number, and strength of N-protein binding sites (valency). Liquid-like N-protein condensates form in mammalian cells in a concentration-dependent manner and can be altered by small molecules. Condensation of N-protein is RNA sequence and structure specific, sensitive to human body temperature, and manipulatable with small molecules, and therefore presents a screenable process for identifying antiviral compounds effective against SARS-CoV-2.
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Affiliation(s)
- Christiane Iserman
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christine A Roden
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark A Boerneke
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Grace A McLaughlin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ethan J Fritch
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joanne Ekena
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chase A Weidmann
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chandra L Theesfeld
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Olga G Troyanskaya
- Center for Computational Biology, Flatiron Institute, New York, NY, USA; Department of Computer Science, Princeton University, Princeton, NJ, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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30
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Oliveira TL, Melo IS, Cardoso-Sousa L, Santos IA, El Zoghbi MB, Shimoura CG, Georjutti RP, Castro OW, Goulart LR, Jardim ACG, Cunha TM, Sabino-Silva R. Pathophysiology of SARS-CoV-2 in Lung of Diabetic Patients. Front Physiol 2020; 11:587013. [PMID: 33362575 PMCID: PMC7758507 DOI: 10.3389/fphys.2020.587013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/27/2020] [Indexed: 12/11/2022] Open
Abstract
Novel coronavirus disease (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Its impact on patients with comorbidities is clearly related to fatality cases, and diabetes has been linked to one of the most important causes of severity and mortality in SARS-CoV-2 infected patients. Substantial research progress has been made on COVID-19 therapeutics; however, effective treatments remain unsatisfactory. This unmet clinical need is robustly associated with the complexity of pathophysiological mechanisms described for COVID-19. Several key lung pathophysiological mechanisms promoted by SARS-CoV-2 have driven the response in normoglycemic and hyperglycemic subjects. There is sufficient evidence that glucose metabolism pathways in the lung are closely tied to bacterial proliferation, inflammation, oxidative stress, and pro-thrombotic responses, which lead to severe clinical outcomes. It is also likely that SARS-CoV-2 proliferation is affected by glucose metabolism of type I and type II cells. This review summarizes the current understanding of pathophysiology of SARS-CoV-2 in the lung of diabetic patients and highlights the changes in clinical outcomes of COVID-19 in normoglycemic and hyperglycemic conditions.
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Affiliation(s)
- Tales Lyra Oliveira
- Heart Institute, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.,Medical School, Municipal University of São Caetano do Sul, São Paulo, Brazil
| | - Igor Santana Melo
- Institute of Biological Sciences and Health, Federal University of Alagoas, Alagoas, Brazil
| | - Léia Cardoso-Sousa
- Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, Brazil
| | - Igor Andrade Santos
- Laboratory of Virology, Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, Brazil
| | | | - Caroline Gusson Shimoura
- Department of Physiology and Anatomy, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Renata Pereira Georjutti
- Department of Physiology and Anatomy, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Olagide Wagner Castro
- Institute of Biological Sciences and Health, Federal University of Alagoas, Alagoas, Brazil
| | - Luiz Ricardo Goulart
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Brazil.,Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, United States
| | - Ana Carolina Gomes Jardim
- Laboratory of Virology, Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, Brazil
| | - Thúlio Marquez Cunha
- Department of Pulmonology, School of Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Robinson Sabino-Silva
- Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, Brazil
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31
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Wang Y, Grunewald M, Perlman S. Coronaviruses: An Updated Overview of Their Replication and Pathogenesis. Methods Mol Biol 2020; 2203:1-29. [PMID: 32833200 DOI: 10.1007/978-1-0716-0900-2_1] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Coronaviruses (CoVs), enveloped positive-sense RNA viruses, are characterized by club-like spikes that project from their surface, an unusually large RNA genome, and a unique replication strategy. CoVs cause a variety of diseases in mammals and birds ranging from enteritis in cows and pigs, and upper respiratory tract and kidney disease in chickens to lethal human respiratory infections. Most recently, the novel coronavirus, SARS-CoV-2, which was first identified in Wuhan, China in December 2019, is the cause of a catastrophic pandemic, COVID-19, with more than 8 million infections diagnosed worldwide by mid-June 2020. Here we provide a brief introduction to CoVs discussing their replication, pathogenicity, and current prevention and treatment strategies. We will also discuss the outbreaks of the highly pathogenic Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV), which are relevant for understanding COVID-19.
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Affiliation(s)
- Yuhang Wang
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Matthew Grunewald
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA.
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32
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Hartenian E, Nandakumar D, Lari A, Ly M, Tucker JM, Glaunsinger BA. The molecular virology of coronaviruses. J Biol Chem 2020; 295:12910-12934. [PMID: 32661197 PMCID: PMC7489918 DOI: 10.1074/jbc.rev120.013930] [Citation(s) in RCA: 302] [Impact Index Per Article: 75.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/13/2020] [Indexed: 12/14/2022] Open
Abstract
Few human pathogens have been the focus of as much concentrated worldwide attention as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of COVID-19. Its emergence into the human population and ensuing pandemic came on the heels of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), two other highly pathogenic coronavirus spillovers, which collectively have reshaped our view of a virus family previously associated primarily with the common cold. It has placed intense pressure on the collective scientific community to develop therapeutics and vaccines, whose engineering relies on a detailed understanding of coronavirus biology. Here, we present the molecular virology of coronavirus infection, including its entry into cells, its remarkably sophisticated gene expression and replication mechanisms, its extensive remodeling of the intracellular environment, and its multifaceted immune evasion strategies. We highlight aspects of the viral life cycle that may be amenable to antiviral targeting as well as key features of its biology that await discovery.
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Affiliation(s)
- Ella Hartenian
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Divya Nandakumar
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Azra Lari
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Michael Ly
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Jessica M Tucker
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Britt A Glaunsinger
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; Department of Plant and Microbial Biology, University of California, Berkeley, California, USA; Howard Hughes Medical Institute, University of California, Berkeley, California, USA.
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33
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Artika IM, Dewantari AK, Wiyatno A. Molecular biology of coronaviruses: current knowledge. Heliyon 2020; 6:e04743. [PMID: 32835122 PMCID: PMC7430346 DOI: 10.1016/j.heliyon.2020.e04743] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023] Open
Abstract
The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) late December 2019 in Wuhan, China, marked the third introduction of a highly pathogenic coronavirus into the human population in the twenty-first century. The constant spillover of coronaviruses from natural hosts to humans has been linked to human activities and other factors. The seriousness of this infection and the lack of effective, licensed countermeasures clearly underscore the need of more detailed and comprehensive understanding of coronavirus molecular biology. Coronaviruses are large, enveloped viruses with a positive sense single-stranded RNA genome. Currently, coronaviruses are recognized as one of the most rapidly evolving viruses due to their high genomic nucleotide substitution rates and recombination. At the molecular level, the coronaviruses employ complex strategies to successfully accomplish genome expression, virus particle assembly and virion progeny release. As the health threats from coronaviruses are constant and long-term, understanding the molecular biology of coronaviruses and controlling their spread has significant implications for global health and economic stability. This review is intended to provide an overview of our current basic knowledge of the molecular biology of coronaviruses, which is important as basic knowledge for the development of coronavirus countermeasures.
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Affiliation(s)
- I. Made Artika
- Biosafety Level 3 Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor, 16680, Indonesia
| | - Aghnianditya Kresno Dewantari
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
| | - Ageng Wiyatno
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
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34
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Sood S, Aggarwal V, Aggarwal D, Upadhyay SK, Sak K, Tuli HS, Kumar M, Kumar J, Talwar S. COVID-19 Pandemic: from Molecular Biology, Pathogenesis, Detection, and Treatment to Global Societal Impact. CURRENT PHARMACOLOGY REPORTS 2020; 6:212-227. [PMID: 32837855 PMCID: PMC7382994 DOI: 10.1007/s40495-020-00229-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
PURPOSE OF REVIEW In December 2019, there was an outbreak of viral disease in Wuhan, China which raised the concern across the whole world. The viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or novel coronavirus or COVID-19 (CoV-19) is known as a pandemic. After SARS-CoV and Middle East respiratory syndrome (MERS)-related CoV, COVID-19 is the third most pathogenic virus, hazardous to humans which have raised worries concerning the capacity of current security measures and the human services framework to deal with such danger. RECENT FINDINGS According to WHO, the mortality rate of COVID-19 exceeded that of SARS and MERS in view of which COVID-19 was declared as public health emergency of international concern. Coronaviruses are positive-sense RNA viruses with single stranded RNA and non-segmented envelopes. Recently, genome sequencing confirmed that COVID-19 is similar to SARS-CoV and bat coronavirus, but the major source of this pandemic outbreak, its transmission, and mechanisms related to its pathogenicity to humans are not yet known. SUMMARY In order to prevent the further pandemic and loss to humanity, scientists are studying the development of therapeutic drugs, vaccines, and strategies to cure the infections. In this review, we present a brief introduction to emerging and re-emerging pathogens, i.e., coronavirus in humans and animals, its taxonomic classification, genome organization, its replication, pathogenicity, impact on socioeconomic growth, and drugs associated with COVID-19.
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Affiliation(s)
- Shivani Sood
- Department of Biotechnology, Mukand Lal National College, Yamuna Nagar, India
| | - Vaishali Aggarwal
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA USA
| | - Diwakar Aggarwal
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 India
| | - Sushil K Upadhyay
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 India
| | | | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 India
| | - Manoj Kumar
- Department of Chemistry, Maharishi Markandeshwar University, Sadopur, 134007 India
| | - Jayant Kumar
- Department of Biotechnology, Mukand Lal National College, Yamuna Nagar, India
| | - Shivangi Talwar
- Amity Institute of Biotechnology, Amity University, Noida, India
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Abstract
Currently, pandemic coronavirus disease 2019 (COVID-19) is the biggest threat to all human beings globally. Till June 8, 2020, it has infected 6,931,000 people and caused 400,857 deaths worldwide. The first case was identified in a patient with influenza-like symptoms along with severe acute respiratory syndrome in Wuhan, China, in December 2019 and now it has spread in more than 200 countries. Since there is no approved cure for this disease until now, there is a lot of mass fear, apprehensions, and questions globally regarding (i) genetic origin and history of the novel coronavirus, (ii) what are the first-line therapies for those who contract this disease, and (iii) what could be the potential vaccine targets. In this short review, we have tried to address these queries in the simplest manner and compiled the history of previous coronaviruses, recent developments in the COVID-19 research, potential future therapeutics, and possible targets to cure the disease.
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Abstract
Initially recognized of COVID-19 within the world in 2019, the World Health Organization situational report from May 22nd, 2020, globally, there is a complete of 5,204,508 confirmed cases, with 212 countries being affected by the novel coronavirus. 2019 novel coronavirus (SARS-CoV-2) is that the seventh member of the family of coronaviruses is enveloped viruses with a positive sense, single-stranded RNA genome. The SARS-CoV-2 may be a �-CoV of group 2B there is 70% comparability in genetic sequence to SARS-CoV. The source of the new coronavirus infection has been resolved as bats. With whole-genome sequences of SARS-CoV-2 is 96% comparatively at the whole-genome level to a bat coronavirus. Mechanisms of transmission are concluded to incorporate contact, droplet, and possibly airborne under certain circumstances supported ancient experiences associated with SARS-CoV outbreaks. Although antiretroviral therapy is being widely used everywhere the globe for such patents, effects at finding a SARS-CoV vaccine haven�t succeeded so far.
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Iserman C, Roden C, Boerneke M, Sealfon R, McLaughlin G, Jungreis I, Park C, Boppana A, Fritch E, Hou YJ, Theesfeld C, Troyanskaya OG, Baric RS, Sheahan TP, Weeks K, Gladfelter AS. Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.11.147199. [PMID: 32587965 PMCID: PMC7310621 DOI: 10.1101/2020.06.11.147199] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A mechanistic understanding of the SARS-CoV-2 viral replication cycle is essential to develop new therapies for the COVID-19 global health crisis. In this study, we show that the SARS-CoV-2 nucleocapsid protein (N-protein) undergoes liquid-liquid phase separation (LLPS) with the viral genome, and propose a model of viral packaging through LLPS. N-protein condenses with specific RNA sequences in the first 1000 nts (5'-End) under physiological conditions and is enhanced at human upper airway temperatures. N-protein condensates exclude non-packaged RNA sequences. We comprehensively map sites bound by N-protein in the 5'-End and find preferences for single-stranded RNA flanked by stable structured elements. Liquid-like N-protein condensates form in mammalian cells in a concentration-dependent manner and can be altered by small molecules. Condensation of N-protein is sequence and structure specific, sensitive to human body temperature, and manipulatable with small molecules thus presenting screenable processes for identifying antiviral compounds effective against SARS-CoV-2.
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Affiliation(s)
- Christiane Iserman
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christine Roden
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark Boerneke
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rachel Sealfon
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Grace McLaughlin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Chris Park
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Avinash Boppana
- Department of Computer Science, Princeton University, Princeton, NJ USA
| | - Ethan Fritch
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chandra Theesfeld
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA
| | - Olga G Troyanskaya
- Flatiron Institute, Simons Foundation, New York, NY, USA
- Department of Computer Science, Princeton University, Princeton, NJ USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kevin Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Lundstrom K. Coronavirus Pandemic-Therapy and Vaccines. Biomedicines 2020; 8:E109. [PMID: 32375268 PMCID: PMC7277397 DOI: 10.3390/biomedicines8050109] [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] [Received: 03/31/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 12/13/2022] Open
Abstract
The current coronavirus COVID-19 pandemic, which originated in Wuhan, China, has raised significant social, psychological and economic concerns in addition to direct medical issues. The rapid spread of severe acute respiratory syndrome-coronavirus (SARS-CoV)-2 to almost every country on the globe and the failure to contain the infections have contributed to fear and panic worldwide. The lack of available and efficient antiviral drugs or vaccines has further worsened the situation. For these reasons, it cannot be overstated that an accelerated effort for the development of novel drugs and vaccines is needed. In this context, novel approaches in both gene therapy and vaccine development are essential. Previous experience from SARS- and MERS-coronavirus vaccine and drug development projects have targeted glycoprotein epitopes, monoclonal antibodies, angiotensin receptor blockers and gene silencing technologies, which may be useful for COVID-19 too. Moreover, existing antivirals used for other types of viral infections have been considered as urgent action is necessary. This review aims at providing a background of coronavirus genetics and biology, examples of therapeutic and vaccine strategies taken and potential innovative novel approaches in progress.
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Bommanavar S, Smitha T. ABO blood grouping and COVID 19: Is there any correlation in suspectibility? J Oral Maxillofac Pathol 2020; 24:212-216. [PMID: 33456226 PMCID: PMC7802878 DOI: 10.4103/jomfp.jomfp_240_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 06/09/2020] [Indexed: 12/01/2022] Open
Affiliation(s)
- Sushma Bommanavar
- Department of Oral Pathology and Microbiology and Forensic Odontology, School of Dental Sciences, Krishna Institute of Medical Sciences, Karad, Maharashtra, India
| | - T Smitha
- Department of Oral and Maxillofacial Pathology, V S Dental College and Hospital, Bengaluru, Karnataka, India
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An in vivo cell-based assay for investigating the specific interaction between the SARS-CoV N-protein and its viral RNA packaging sequence. Biochem Biophys Res Commun 2019; 520:499-506. [PMID: 31594639 PMCID: PMC7092827 DOI: 10.1016/j.bbrc.2019.09.115] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 09/26/2019] [Indexed: 01/25/2023]
Abstract
The SARS-CoV nucleocapsid (N) protein serves multiple functions in viral replication, transcription, and assembly of the viral genome complex. Coronaviruses specifically package genomic RNA into assembled virions, and in SARS-CoV, it is reported that this process is driven by an interaction between the N-protein and a packaging signal encoded within the viral RNA. While recent studies have uncovered the sequence of this packaging signal, little is known about the specific interaction between the N-protein and the packaging signal sequence, and the mechanisms by which this interaction drives viral genome packaging. In this study, we developed a novel in vivo cell-based assay for examining this interaction between the N-protein and packaging signal RNA for SARS-CoV, as well as other viruses within the coronaviridae family. Our results demonstrate that the N-protein specifically recognizes the SARS-CoV packaging signal with greater affinity compared to signals from other coronaviruses or non-coronavirus species. We also use deletion mapping to identify a 151-nt region within the packaging signal sequence that is critical for N-protein-RNA binding, and conversely, we show that both the N-terminal and C-terminal domains of the N protein are necessary for recognizing the packaging RNA. These results describe, for the first time, in vivo evidence for an interaction between the SARS-CoV N-protein and its packaging signal RNA, and demonstrate the feasibility of using this cell-based assay to further probe viral RNA-protein interactions in future studies.
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Dinan AM, Keep S, Bickerton E, Britton P, Firth AE, Brierley I. Comparative Analysis of Gene Expression in Virulent and Attenuated Strains of Infectious Bronchitis Virus at Subcodon Resolution. J Virol 2019; 93:e00714-19. [PMID: 31243124 PMCID: PMC6714804 DOI: 10.1128/jvi.00714-19] [Citation(s) in RCA: 20] [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: 04/30/2019] [Accepted: 06/17/2019] [Indexed: 12/27/2022] Open
Abstract
Like all coronaviruses, avian infectious bronchitis virus (IBV) possesses a long, single-stranded, positive-sense RNA genome (∼27 kb) and has a complex replication strategy that includes the production of a nested set of subgenomic mRNAs (sgmRNAs). Here, we used whole-transcriptome sequencing (RNASeq) and ribosome profiling (RiboSeq) to delineate gene expression in the IBV M41-CK and Beau-R strains at subcodon resolution. RNASeq facilitated a comparative analysis of viral RNA synthesis and revealed two novel transcription junction sites in the attenuated Beau-R strain, one of which would generate a sgmRNA encoding a ribosomally occupied open reading frame (dORF) located downstream of the nucleocapsid coding region. RiboSeq permitted quantification of the translational efficiency of virus gene expression and identified, for the first time, sites of ribosomal pausing on the genome. Quantification of reads flanking the programmed ribosomal frameshifting (PRF) signal at the genomic RNA ORF1a/ORF1b junction revealed that PRF in IBV is highly efficient (33 to 40%). Triplet phasing of RiboSeq data allowed precise determination of reading frames and revealed the translation of two ORFs (ORF4b and ORF4c on sgmRNA IR), which are widely conserved across IBV isolates. Analysis of differential gene expression in infected primary chick kidney cells indicated that the host cell response to IBV occurs primarily at the level of transcription, with global upregulation of immune-related mRNA transcripts following infection and comparatively modest changes in the translation efficiencies of host genes. Cellular genes and gene networks differentially expressed during virus infection were also identified, giving insights into the host cell response to IBV infection.IMPORTANCE IBV is a major avian pathogen and presents a substantial economic burden to the poultry industry. Improved vaccination strategies are urgently needed to curb the global spread of this virus, and the development of suitable vaccine candidates will be aided by an improved understanding of IBV molecular biology. Our high-resolution data have enabled a precise study of transcription and translation in cells infected with both pathogenic and attenuated forms of IBV and expand our understanding of gammacoronaviral gene expression. We demonstrate that gene expression shows considerable intraspecies variation, with single nucleotide polymorphisms being associated with altered production of sgmRNA transcripts, and our RiboSeq data sets enabled us to uncover novel ribosomally occupied ORFs in both strains. The numerous cellular genes and gene networks found to be differentially expressed during virus infection provide insights into the host cell response to IBV infection.
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Affiliation(s)
- Adam M Dinan
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Sarah Keep
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | | | - Paul Britton
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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Abstract
RNA viruses carry out selective packaging of their genomes in a variety of ways, many involving a genomic packaging signal. The first coronavirus packaging signal was discovered nearly thirty years ago, but how it functions remains incompletely understood. This review addresses the current state of knowledge of coronavirus genome packaging, which has mainly been studied in two prototype species, mouse hepatitis virus and transmissible gastroenteritis virus. Despite the progress that has been made in the mapping and characterization of some packaging signals, there is conflicting evidence as to whether the viral nucleocapsid protein or the membrane protein plays the primary role in packaging signal recognition. The different models for the mechanism of genomic RNA packaging that have been prompted by these competing views are described. Also discussed is the recent exciting discovery that selective coronavirus genome packaging is critical for in vivo evasion of the host innate immune response. Selective incorporation of the coronavirus genome into virions is mediated by a cis-acting RNA packaging signal. Packaging signals vary across different coronavirus genera and lineages. Different lines of evidence attribute packaging signal recognition to either the nucleocapsid or the membrane protein. Selective coronavirus genome packaging plays a role in evasion of host innate immunity.
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Affiliation(s)
- Paul S Masters
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, United States.
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43
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Hsin WC, Chang CH, Chang CY, Peng WH, Chien CL, Chang MF, Chang SC. Nucleocapsid protein-dependent assembly of the RNA packaging signal of Middle East respiratory syndrome coronavirus. J Biomed Sci 2018; 25:47. [PMID: 29793506 PMCID: PMC5966903 DOI: 10.1186/s12929-018-0449-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 05/15/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Middle East respiratory syndrome coronavirus (MERS-CoV) consists of a positive-sense, single-stranded RNA genome and four structural proteins: the spike, envelope, membrane, and nucleocapsid protein. The assembly of the viral genome into virus particles involves viral structural proteins and is believed to be mediated through recognition of specific sequences and RNA structures of the viral genome. METHODS AND RESULTS A culture system for the production of MERS coronavirus-like particles (MERS VLPs) was determined and established by electron microscopy and the detection of coexpressed viral structural proteins. Using the VLP system, a 258-nucleotide RNA fragment, which spans nucleotides 19,712 to 19,969 of the MERS-CoV genome (designated PS258(19712-19969)ME), was identified to function as a packaging signal. Assembly of the RNA packaging signal into MERS VLPs is dependent on the viral nucleocapsid protein. In addition, a 45-nucleotide stable stem-loop substructure of the PS258(19712-19969)ME interacted with both the N-terminal domain and the C-terminal domain of the viral nucleocapsid protein. Furthermore, a functional SARS-CoV RNA packaging signal failed to assemble into the MERS VLPs, which indicated virus-specific assembly of the RNA genome. CONCLUSIONS A MERS-oV RNA packaging signal was identified by the detection of GFP expression following an incubation of MERS VLPs carrying the heterologous mRNA GFP-PS258(19712-19969)ME with virus permissive Huh7 cells. The MERS VLP system could help us in understanding virus infection and morphogenesis.
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Affiliation(s)
- Wei-Chen Hsin
- Institute of Microbiology, College of Medicine, National Taiwan University, No. 1, Jen-Ai Road, First Section, Taipei, 100, Taiwan
| | - Chan-Hua Chang
- Institute of Microbiology, College of Medicine, National Taiwan University, No. 1, Jen-Ai Road, First Section, Taipei, 100, Taiwan
| | - Chi-You Chang
- Institute of Microbiology, College of Medicine, National Taiwan University, No. 1, Jen-Ai Road, First Section, Taipei, 100, Taiwan
| | - Wei-Hao Peng
- Institute of Anatomy and Cell Biology, College of Medicine, National Taiwan University, No. 1, Jen-Ai Road, First Section, Taipei, 100, Taiwan
| | - Chung-Liang Chien
- Institute of Anatomy and Cell Biology, College of Medicine, National Taiwan University, No. 1, Jen-Ai Road, First Section, Taipei, 100, Taiwan
| | - Ming-Fu Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, No. 1, Jen-Ai Road, First Section, Taipei, 100, Taiwan.
| | - Shin C Chang
- Institute of Microbiology, College of Medicine, National Taiwan University, No. 1, Jen-Ai Road, First Section, Taipei, 100, Taiwan.
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Abstract
Selective packaging is a mechanism used by multiple virus families to specifically incorporate genomic RNA (gRNA) into virions and exclude other types of RNA. Lineage A betacoronaviruses incorporate a 95-bp stem-loop structure, the packaging signal (PS), into the nsp15 locus of ORF1b that is both necessary and sufficient for the packaging of RNAs. However, unlike other viral PSs, where mutations generally resulted in viral replication defects, mutation of the coronavirus (CoV) PS results in large increases in subgenomic RNA packaging with minimal effects on gRNA packaging in vitro and on viral titers. Here, we show that selective packaging is also required for viral evasion of the innate immune response and optimal pathogenicity. We engineered two distinct PS mutants in two different strains of murine hepatitis virus (MHV) that packaged increased levels of subgenomic RNAs, negative-sense genomic RNA, and even cellular RNAs. All PS mutant viruses replicated normally in vitro but caused dramatically reduced lethality and weight loss in vivo. PS mutant virus infection of bone marrow-derived macrophages resulted in increased interferon (IFN) production, indicating that the innate immune system limited the replication and/or pathogenesis of PS mutant viruses in vivo. PS mutant viruses remained attenuated in MAVS−/− and Toll-like receptor 7-knockout (TLR7−/−) mice, two well-known RNA sensors for CoVs, but virulence was restored in interferon alpha/beta receptor-knockout (IFNAR−/−) mice or in MAVS−/− mice treated with IFNAR-blocking antibodies. Together, these data indicate that coronaviruses promote virulence by utilizing selective packaging to avoid innate immune detection. Coronaviruses (CoVs) produce many types of RNA molecules during their replication cycle, including both positive- and negative-sense genomic and subgenomic RNAs. Despite this, coronaviruses selectively package only positive-sense genomic RNA into their virions. Why CoVs selectively package their genomic RNA is not clear, as disruption of the packaging signal in MHV, which leads to loss of selective packaging, does not affect genomic RNA packaging or virus replication in cultured cells. This contrasts with other viruses, where disruption of selective packaging generally leads to altered replication. Here, we demonstrate that in the absence of selective packaging, the virulence of MHV was significantly reduced. Importantly, virulence was restored in the absence of interferon signaling, indicating that selective packaging is a mechanism used by CoVs to escape innate immune detection.
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An "Old" protein with a new story: Coronavirus endoribonuclease is important for evading host antiviral defenses. Virology 2018; 517:157-163. [PMID: 29307596 PMCID: PMC5869138 DOI: 10.1016/j.virol.2017.12.024] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 12/21/2017] [Accepted: 12/22/2017] [Indexed: 12/19/2022]
Abstract
Here we review the evolving story of the coronavirus endoribonuclease (EndoU). Coronavirus EndoU is encoded within the sequence of nonstructural protein (nsp) 15, which was initially identified as a component of the viral replication complex. Biochemical and structural studies revealed the enzymatic nature of nsp15/EndoU, which was postulated to be essential for the unique replication cycle of viruses in the order Nidovirales. However, the role of nsp15 in coronavirus replication was enigmatic as EndoU-deficient coronaviruses were viable and replicated to near wild-type virus levels in fibroblast cells. A breakthrough in our understanding of the role of EndoU was revealed in recent studies, which showed that EndoU mediates the evasion of viral double-stranded RNA recognition by host sensors in macrophages. This new discovery of nsp15/EndoU function leads to new opportunities for investigating how a viral EndoU contributes to pathogenesis and exploiting this enzyme for therapeutics and vaccine design against pathogenic coronaviruses.
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Madhugiri R, Karl N, Petersen D, Lamkiewicz K, Fricke M, Wend U, Scheuer R, Marz M, Ziebuhr J. Structural and functional conservation of cis-acting RNA elements in coronavirus 5'-terminal genome regions. Virology 2017; 517:44-55. [PMID: 29223446 PMCID: PMC7112051 DOI: 10.1016/j.virol.2017.11.025] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 01/09/2023]
Abstract
Structure predictions suggest a partial conservation of RNA structure elements in coronavirus terminal genome regions. Here, we determined the structures of stem-loops (SL) 1 and 2 of two alphacoronaviruses, human coronavirus (HCoV) 229E and NL63, by RNA structure probing and studied the functional relevance of these putative cis-acting elements. HCoV-229E SL1 and SL2 mutants generated by reverse genetics were used to study the effects on viral replication of single-nucleotide substitutions predicted to destabilize the SL1 and SL2 structures. The data provide conclusive evidence for the critical role of SL1 and SL2 in HCoV-229E replication and, in some cases, revealed parallels with previously characterized betacoronavirus SL1 and SL2 elements. Also, we were able to rescue viable HCoV-229E mutants carrying replacements of SL2 with equivalent betacoronavirus structural elements. The data obtained in this study reveal a remarkable degree of structural and functional conservation of 5′-terminal RNA structural elements across coronavirus genus boundaries. Conservation of 5'-terminal SL1 and SL2 elements in alpha- and betacoronaviruses. HCoV-229E reverse genetics data suggest critical role for SL1/2 in viral replication. Replacement of SL2 in HCoV-229E with betacoronavirus equivalents is tolerated.
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Affiliation(s)
| | - Nadja Karl
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Daniel Petersen
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Kevin Lamkiewicz
- Faculty of Mathematics and Computer Science, Friedrich Schiller University, Jena, Germany; European Virus Bioinformatics Center, Jena, Germany
| | - Markus Fricke
- Faculty of Mathematics and Computer Science, Friedrich Schiller University, Jena, Germany; European Virus Bioinformatics Center, Jena, Germany
| | - Ulrike Wend
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Robina Scheuer
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Manja Marz
- Faculty of Mathematics and Computer Science, Friedrich Schiller University, Jena, Germany; FLI Leibniz Institute for Age Research, Jena, Germany; European Virus Bioinformatics Center, Jena, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany; European Virus Bioinformatics Center, Jena, Germany.
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In Situ Tagged nsp15 Reveals Interactions with Coronavirus Replication/Transcription Complex-Associated Proteins. mBio 2017; 8:mBio.02320-16. [PMID: 28143984 PMCID: PMC5285509 DOI: 10.1128/mbio.02320-16] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Coronavirus (CoV) replication and transcription are carried out in close proximity to restructured endoplasmic reticulum (ER) membranes in replication/transcription complexes (RTC). Many of the CoV nonstructural proteins (nsps) are required for RTC function; however, not all of their functions are known. nsp15 contains an endoribonuclease domain that is conserved in the CoV family. While the enzymatic activity and crystal structure of nsp15 are well defined, its role in replication remains elusive. nsp15 localizes to sites of RNA replication, but whether it acts independently or requires additional interactions for its function remains unknown. To begin to address these questions, we created an in situ tagged form of nsp15 using the prototypic CoV, mouse hepatitis virus (MHV). In MHV, nsp15 contains the genomic RNA packaging signal (P/S), a 95-bp RNA stem-loop structure that is not required for viral replication or nsp15 function. Utilizing this knowledge, we constructed an internal hemagglutinin (HA) tag that replaced the P/S. We found that nsp15-HA was localized to discrete perinuclear puncta and strongly colocalized with nsp8 and nsp12, both well-defined members of the RTC, but not the membrane (M) protein, involved in virus assembly. Finally, we found that nsp15 interacted with RTC-associated proteins nsp8 and nsp12 during infection, and this interaction was RNA independent. From this, we conclude that nsp15 localizes and interacts with CoV proteins in the RTC, suggesting it plays a direct or indirect role in virus replication. Furthermore, the use of in situ epitope tags could be used to determine novel nsp-nsp interactions in coronaviruses. IMPORTANCE Despite structural and biochemical data demonstrating that the coronavirus nsp15 protein contains an endoribonuclease domain, its precise function during coronavirus infection remains unknown. In this work, we created a novel in situ tagged form of nsp15 to study interactions and localization during infection. This in situ tag was tolerated by MHV and did not affect viral replication. Utilizing this tag, we established that nsp15 localized to sites of replication but not sites of assembly throughout infection. Furthermore, we found that nsp15 interacted with the putative viral primase nsp8 and polymerase nsp12 during CoV infection. The strong association of nsp15 with replication complexes and interactions with replicative CoV enzymes suggest nsp15 is involved in CoV replication. These data and tools developed in this study help elucidate the function of nsp15 during infection and may be used to uncover other novel viral protein interactions.
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Fuchs M, Schmitt-Keichinger C, Sanfaçon H. A Renaissance in Nepovirus Research Provides New Insights Into Their Molecular Interface With Hosts and Vectors. Adv Virus Res 2016; 97:61-105. [PMID: 28057260 DOI: 10.1016/bs.aivir.2016.08.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nepoviruses supplied seminal landmarks to the historical trail of plant virology. Among the first agriculturally relevant viruses recognized in the late 1920s and among the first plant viruses officially classified in the early 1970s, nepoviruses also comprise the first species for which a soil-borne ectoparasitic nematode vector was identified. Early research on nepoviruses shed light on the genome structure and expression, biological properties of the two genomic RNAs, and mode of transmission. In recent years, research on nepoviruses enjoyed an extraordinary renaissance. This resurgence provided new insights into the molecular interface between viruses and their plant hosts, and between viruses and dagger nematode vectors to advance our understanding of some of the major steps of the infectious cycle. Here we examine these recent findings, highlight ongoing work, and offer some perspectives for future research.
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Affiliation(s)
- M Fuchs
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, United States.
| | - C Schmitt-Keichinger
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
| | - H Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, Canada
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Abstract
Coronaviruses have exceptionally large RNA genomes of approximately 30 kilobases. Genome replication and transcription is mediated by a multisubunit protein complex comprised of more than a dozen virus-encoded proteins. The protein complex is thought to bind specific cis-acting RNA elements primarily located in the 5'- and 3'-terminal genome regions and upstream of the open reading frames located in the 3'-proximal one-third of the genome. Here, we review our current understanding of coronavirus cis-acting RNA elements, focusing on elements required for genome replication and packaging. Recent bioinformatic, biochemical, and genetic studies suggest a previously unknown level of conservation of cis-acting RNA structures among different coronavirus genera and, in some cases, even beyond genus boundaries. Also, there is increasing evidence to suggest that individual cis-acting elements may be part of higher-order RNA structures involving long-range and dynamic RNA-RNA interactions between RNA structural elements separated by thousands of nucleotides in the viral genome. We discuss the structural and functional features of these cis-acting RNA elements and their specific functions in coronavirus RNA synthesis.
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Affiliation(s)
- R Madhugiri
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - M Fricke
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany
| | - M Marz
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany; FLI Leibniz Institute for Age Research, Jena, Germany
| | - J Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany.
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Kuo L, Koetzner CA, Masters PS. A key role for the carboxy-terminal tail of the murine coronavirus nucleocapsid protein in coordination of genome packaging. Virology 2016; 494:100-7. [PMID: 27105451 PMCID: PMC4884538 DOI: 10.1016/j.virol.2016.04.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/04/2016] [Accepted: 04/06/2016] [Indexed: 12/31/2022]
Abstract
The prototype coronavirus mouse hepatitis virus (MHV) exhibits highly selective packaging of its genomic positive-stranded RNA into assembled virions, despite the presence in infected cells of a large excess of subgenomic viral mRNAs. One component of this selectivity is the MHV packaging signal (PS), an RNA structure found only in genomic RNA and not in subgenomic RNAs. It was previously shown that a major determinant of PS recognition is the second of the two RNA-binding domains of the viral nucleocapsid (N) protein. We have now found that PS recognition additionally depends upon a segment of the carboxy-terminal tail (domain N3) of the N protein. Since domain N3 is also the region of N protein that interacts with the membrane (M) protein, this finding suggests a mechanism by which selective genome packaging is accomplished, through the coupling of genome encapsidation to virion assembly.
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Affiliation(s)
- Lili Kuo
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States
| | - Cheri A Koetzner
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States
| | - Paul S Masters
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States.
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