SARS-CoV-2: from its discovery to genome structure, transcription, and replication

AbstractSARS-CoV-2 is an extremely contagious respiratory virus causing adult atypical pneumonia COVID-19 with severe acute respiratory syndrome (SARS). SARS-CoV-2 has a single-stranded, positive-sense RNA (+RNA) genome of ~ 29.9 kb and exhibits significant genetic shift from different isolates. After entering the susceptible cells expressing both ACE2 and TMPRSS2, the SARS-CoV-2 genome directly functions as an mRNA to translate two polyproteins from the ORF1a and ORF1b region, which are cleaved by two viral proteases into sixteen non-structural proteins (nsp1-16) to initiate viral genome replication and transcription. The SARS-CoV-2 genome also encodes four structural (S, E, M and N) and up to six accessory (3a, 6, 7a, 7b, 8, and 9b) proteins, but their translation requires newly synthesized individual subgenomic RNAs (sgRNA) in the infected cells. Synthesis of the full-length viral genomic RNA (gRNA) and sgRNAs are conducted inside double-membrane vesicles (DMVs) by the viral replication and transcription complex (RTC), which comprises nsp7, nsp8, nsp9, nsp12, nsp13 and a short RNA primer. To produce sgRNAs, RTC starts RNA synthesis from the highly structured gRNA 3' end and switches template at various transcription regulatory sequence (TRSB) sites along the gRNA body probably mediated by a long-distance RNA–RNA interaction. The TRS motif in the gRNA 5' leader (TRSL) is responsible for the RNA–RNA interaction with the TRSB upstream of each ORF and skipping of the viral genome in between them to produce individual sgRNAs. Abundance of individual sgRNAs and viral gRNA synthesized in the infected cells depend on the location and read-through efficiency of each TRSB. Although more studies are needed, the unprecedented COVID-19 pandemic has taught the world a painful lesson that is to invest and proactively prepare future emergence of other types of coronaviruses and any other possible biological horrors.

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Analysis of the Replication Mechanisms of the Human Papillomavirus Genomes

Frontiers in Microbiology ◽

10.3389/fmicb.2021.738125 ◽

2021 ◽

Vol 12 ◽

Author(s):

Lisett Liblekas ◽

Alla Piirsoo ◽

Annika Laanemets ◽

Eva-Maria Tombak ◽

Airiin Laaneväli ◽

...

Keyword(s):

Life Cycle ◽

Viral Genome ◽

Maintenance Phase ◽

Viral Life Cycle ◽

Human Papillomaviruses ◽

Genome Replication ◽

Viral Genomes ◽

Viral Genome Replication ◽

Infected Cells ◽

Cell Genome

The life-cycle of human papillomaviruses (HPVs) includes three distinct phases of the viral genome replication. First, the viral genome is amplified in the infected cells, and this amplification is often accompanied by the oligomerization of the viral genomes. Second stage includes the replication of viral genomes in concert with the host cell genome. The viral genome is further amplified during the third stage of the viral-life cycle, which takes place only in the differentiated keratinocytes. We have previously shown that the HPV18 genomes utilize at least two distinct replication mechanisms during the initial amplification. One of these mechanisms is a well-described bidirectional replication via theta type of replication intermediates. The nature of another replication mechanism utilized by HPV18 involves most likely recombination-dependent replication. In this paper, we show that the usage of different replication mechanisms is a property shared also by other HPV types, namely HPV11 and HPV5. We further show that the emergence of the recombination dependent replication coincides with the oligomerization of the viral genomes and is dependent on the replicative DNA polymerases. We also show that the oligomeric genomes of HPV18 replicate almost exclusively using recombination dependent mechanism, whereas monomeric HPV31 genomes replicate bi-directionally during the maintenance phase of the viral life-cycle.

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Migration of Influenza Virus Nucleoprotein into the Nucleolus Is Essential for Ribonucleoprotein Complex Formation

mBio ◽

10.1128/mbio.03315-21 ◽

2022 ◽

Author(s):

Sho Miyamoto ◽

Masahiro Nakano ◽

Takeshi Morikawa ◽

Ai Hirabayashi ◽

Ryoma Tamura ◽

...

Keyword(s):

Influenza Virus ◽

Life Cycle ◽

Viral Genome ◽

Influenza A ◽

Genome Replication ◽

Ribonucleoprotein Complex ◽

Virus Life Cycle ◽

Viral Genome Replication ◽

Infected Cells ◽

Nuclear Domains

Influenza A virus ribonucleoprotein complex (RNP) is responsible for viral genome replication, thus playing essential roles in the virus life cycle. RNP formation occurs in the nuclei of infected cells; however, little is known about the nuclear domains involved in this process.

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Alternative translation and alternative RNA processing mechanism in parvovirus RNA processing

10.32469/10355/45905 ◽

2014 ◽

Author(s):

◽

Olufemi Fasina

Keyword(s):

Gene Expression ◽

Rna Processing ◽

Viral Genome ◽

Transcription Initiation ◽

Alternative Polyadenylation ◽

Open Reading Frames ◽

Genome Replication ◽

University Of Missouri ◽

Diverse Range ◽

Viral Genome Replication

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Viruses as obligate intracellular metabolic parasite require the capacity to orchestrate and modulate the host environment either in the nucleus or cytoplasm for their efficient reproductive life cycle. This warrants the use of diverse range of proteins expressed from the viral genome with the ability of regulating viral genome replication, transcription and translation, in addition antagonizing host factors inhibitory to the virus. Therefore, in order to achieve these goals, viruses utilizes gene expression strategies to expand their coding capacity. Gene expression mechanism such as transcription initiation, capping, splicing and 3ï¿½-end processing afford viruses the opportunities to utilize the eukaryotic metabolic machineries for generating proteome diversity. Parvoviruses and other DNA viruses effectively capitalize on their use of nuclear eukaryotic metabolic machineries to co-opt host cell factors for optimal replication and gene expression. Parvoviruses with small genome size and overlapping open reading frames utilize alternative transcription initiation, alternative splicing and alternative polyadenylation to co-ordinate the expression of its non-structural and structural proteins. In this work, we have characterized how two parvoviruses; Dependovirus AAV5 and Bocavirus Minute virus of canine (MVC) utilize alternative gene expression mechanisms and strategies to optimize expression of viral proteins from their genome.

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Dimerisation of the influenza virus RNA polymerase during viral genome replication

Access Microbiology ◽

10.1099/acmi.ac2019.po0145 ◽

2019 ◽

Vol 1 (1A) ◽

Author(s):

Alexander Walker ◽

Haitian Fan ◽

Loic Carrique ◽

Jeremy Keown ◽

David Bauer ◽

...

Keyword(s):

Influenza Virus ◽

Rna Polymerase ◽

Viral Genome ◽

Genome Replication ◽

Virus Rna ◽

Viral Genome Replication

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The formation and modification of chromatin-like structure of human parvovirus B19 regulate viral genome replication and RNA processing

Virus Research ◽

10.1016/j.virusres.2017.03.001 ◽

2017 ◽

Vol 232 ◽

pp. 134-138 ◽

Cited By ~ 1

Author(s):

Huanzhou Xu ◽

Sujuan Hao ◽

Junmei Zhang ◽

Zhen Chen ◽

Hanzhong Wang ◽

...

Keyword(s):

Rna Processing ◽

Viral Genome ◽

Parvovirus B19 ◽

Genome Replication ◽

Human Parvovirus B19 ◽

Viral Genome Replication

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Pharmacotherapy for SARS-CoV-2 and Seizures for drug repurposing presumed on Mechanistic Targets

Current Molecular Pharmacology ◽

10.2174/1874467214666211013122528 ◽

2021 ◽

Vol 14 ◽

Author(s):

Divya Goel ◽

Ankit Srivastava ◽

Ángel Aledo-Serrano ◽

Anuja Krishnan ◽

Divya Vohora

Keyword(s):

Valproic Acid ◽

Viral Genome ◽

Drug Targeting ◽

Literature Search ◽

Genome Structure ◽

Drug Repurposing ◽

Drug Candidate ◽

Atypical Pneumonia ◽

Comparative Toxicogenomics Database ◽

Indirect Association

Background: The currently circulating novel SARS-CoV-2 coronavirus disease (COVID-19) has brought the whole world to a standstill. Recent studies have deciphered the viral genome structure, epidemiology and are in the process of unveiling multiple mechanisms of pathogenesis. Apart from atypical pneumonia and lung disease manifestations, this disease has also been found to be associated with neurological symptoms, which include dizziness, headache, stroke, or seizures, among others. However, a possible direct or indirect association between SARS-CoV-2 and seizures is still not clear. In any manner, it may be of interest to analyze the drugs being used for viral infection in the background of epilepsy or vice versa. Objective: To identify the most credible drug candidate for COVID-19 in persons with epilepsy or COVID-19 patients experiencing seizures. Methods: A literature search for original and review articles was performed, and further, the Comparative Toxicogenomics Database was used to unearth the most credible drug candidate. Results: Our search based on common mechanistic targets affecting SARS-CoV-2 and seizures revealed ivermectin, dexamethasone, anakinra, and tocilizumab for protection against both COVID-19 and seizures. Amongst the antiseizure medications, we found valproic acid as the most probable pharmacotherapy for COVID-19 patients experiencing seizures. Conclusion: These findings would hopefully provide the basis for initiating further studies on the pathogenesis and drug targeting strategies for this emerging infection accompanied with seizures or in people with epilepsy.

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Mosquito metabolomics reveal that dengue virus replication requires phospholipid reconfiguration via the remodeling cycle

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2015095117 ◽

2020 ◽

Vol 117 (44) ◽

pp. 27627-27636

Author(s):

Thomas Vial ◽

Wei-Lian Tan ◽

Eric Deharo ◽

Dorothée Missé ◽

Guillaume Marti ◽

...

Keyword(s):

Dengue Virus ◽

Viral Genome ◽

De Novo ◽

Genome Replication ◽

Mosquito Vector ◽

Phospholipid Biosynthesis ◽

Replication Complex ◽

Mosquito Cells ◽

Viral Genome Replication ◽

Blood Meals

Dengue virus (DENV) subdues cell membranes for its cellular cycle by reconfiguring phospholipids in humans and mosquitoes. Here, we determined how and why DENV reconfigures phospholipids in the mosquito vector. By inhibiting and activating the de novo phospholipid biosynthesis, we demonstrated the antiviral impact of de novo–produced phospholipids. In line with the virus hijacking lipids for its benefit, metabolomics analyses indicated that DENV actively inhibited the de novo phospholipid pathway and instead triggered phospholipid remodeling. We demonstrated the early induction of remodeling during infection by using isotope tracing in mosquito cells. We then confirmed in mosquitoes the antiviral impact of de novo phospholipids by supplementing infectious blood meals with a de novo phospholipid precursor. Eventually, we determined that phospholipid reconfiguration was required for viral genome replication but not for the other steps of the virus cellular cycle. Overall, we now propose that DENV reconfigures phospholipids through the remodeling cycle to modify the endomembrane and facilitate formation of the replication complex. Furthermore, our study identified de novo phospholipid precursor as a blood determinant of DENV human-to-mosquito transmission.

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Function, Architecture, and Biogenesis of Reovirus Replication Neoorganelles

Viruses ◽

10.3390/v11030288 ◽

2019 ◽

Vol 11 (3) ◽

pp. 288 ◽

Cited By ~ 7

Author(s):

Raquel Tenorio ◽

Isabel Fernández de Castro ◽

Jonathan J. Knowlton ◽

Paula F. Zamora ◽

Danica M. Sutherland ◽

...

Keyword(s):

Protein Complexes ◽

Host Cells ◽

Genome Replication ◽

Nonstructural Proteins ◽

Particle Assembly ◽

The Matrix ◽

Viral Genome Replication ◽

Pathogenic Viruses ◽

Infected Cells ◽

Reovirus Replication

Most viruses that replicate in the cytoplasm of host cells form neoorganelles that serve as sites of viral genome replication and particle assembly. These highly specialized structures concentrate viral proteins and nucleic acids, prevent the activation of cell-intrinsic defenses, and coordinate the release of progeny particles. Reoviruses are common pathogens of mammals that have been linked to celiac disease and show promise for oncolytic applications. These viruses form nonenveloped, double-shelled virions that contain ten segments of double-stranded RNA. Replication organelles in reovirus-infected cells are nucleated by viral nonstructural proteins µNS and σNS. Both proteins partition the endoplasmic reticulum to form the matrix of these structures. The resultant membranous webs likely serve to anchor viral RNA–protein complexes for the replication of the reovirus genome and the assembly of progeny virions. Ongoing studies of reovirus replication organelles will advance our knowledge about the strategies used by viruses to commandeer host biosynthetic pathways and may expose new targets for therapeutic intervention against diverse families of pathogenic viruses.

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Dual Role of a Viral Polymerase in Viral Genome Replication and Particle Self-Assembly

mBio ◽

10.1128/mbio.01242-18 ◽

2018 ◽

Vol 9 (5) ◽

Cited By ~ 2

Author(s):

Xiaoyu Sun ◽

Serban L. Ilca ◽

Juha T. Huiskonen ◽

Minna M. Poranen

Keyword(s):

Self Assembly ◽

Viral Genome ◽

Rna Viruses ◽

The Self ◽

Genome Replication ◽

Double Stranded Rna ◽

Polymerase Complex ◽

Viral Genome Replication ◽

Dsrna Viruses

ABSTRACTDouble-stranded RNA (dsRNA) viruses package several RNA-dependent RNA polymerases (RdRp) together with their dsRNA genome into an icosahedral protein capsid known as the polymerase complex. This structure is highly conserved among dsRNA viruses but is not found in any other virus group. RdRp subunits typically interact directly with the main capsid proteins, close to the 5-fold symmetric axes, and perform viral genome replication and transcription within the icosahedral protein shell. In this study, we utilizedPseudomonasphage Φ6, a well-established virus self-assembly model, to probe the potential roles of the RdRp in dsRNA virus assembly. We demonstrated that Φ6 RdRp accelerates the polymerase complex self-assembly process and contributes to its conformational stability and integrity. We highlight the role of specific amino acid residues on the surface of the RdRp in its incorporation during the self-assembly reaction. Substitutions of these residues reduce RdRp incorporation into the polymerase complex during the self-assembly reaction. Furthermore, we determined that the overall transcription efficiency of the Φ6 polymerase complex increased when the number of RdRp subunits exceeded the number of genome segments. These results suggest a mechanism for RdRp recruitment in the polymerase complex and highlight its novel role in virion assembly, in addition to the canonical RNA transcription and replication functions.IMPORTANCEDouble-stranded RNA viruses infect a wide spectrum of hosts, including animals, plants, fungi, and bacteria. Yet genome replication mechanisms of these viruses are conserved. During the infection cycle, a proteinaceous capsid, the polymerase complex, is formed. An essential component of this capsid is the viral RNA polymerase that replicates and transcribes the enclosed viral genome. The polymerase complex structure is well characterized for many double-stranded RNA viruses. However, much less is known about the hierarchical molecular interactions that take place in building up such complexes. Using the bacteriophage Φ6 self-assembly system, we obtained novel insights into the processes that mediate polymerase subunit incorporation into the polymerase complex for generation of functional structures. The results presented pave the way for the exploitation and engineering of viral self-assembly processes for biomedical and synthetic biology applications. An understanding of viral assembly processes at the molecular level may also facilitate the development of antivirals that target viral capsid assembly.

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Reovirus Nonstructural Protein σNS Acts as an RNA Stability Factor Promoting Viral Genome Replication

Journal of Virology ◽

10.1128/jvi.00563-18 ◽

2018 ◽

Vol 92 (15) ◽

Cited By ~ 3

Author(s):

Paula F. Zamora ◽

Liya Hu ◽

Jonathan J. Knowlton ◽

Roni M. Lahr ◽

Rodolfo A. Moreno ◽

...

Keyword(s):

Virus Replication ◽

Viral Genome ◽

Nonstructural Protein ◽

Dsrna Virus ◽

Genome Replication ◽

Nonstructural Proteins ◽

Content Type ◽

The Family ◽

Viral Genome Replication

ABSTRACTViral nonstructural proteins, which are not packaged into virions, are essential for the replication of most viruses. Reovirus, a nonenveloped, double-stranded RNA (dsRNA) virus, encodes three nonstructural proteins that are required for viral replication and dissemination in the host. The reovirus nonstructural protein σNS is a single-stranded RNA (ssRNA)-binding protein that must be expressed in infected cells for production of viral progeny. However, the activities of σNS during individual steps of the reovirus replication cycle are poorly understood. We explored the function of σNS by disrupting its expression during infection using cells expressing a small interfering RNA (siRNA) targeting the σNS-encoding S3 gene and found that σNS is required for viral genome replication. Using complementary biochemical assays, we determined that σNS forms complexes with viral and nonviral RNAs. We also discovered, usingin vitroand cell-based RNA degradation experiments, that σNS increases the RNA half-life. Cryo-electron microscopy revealed that σNS and ssRNAs organize into long, filamentous structures. Collectively, our findings indicate that σNS functions as an RNA-binding protein that increases the viral RNA half-life. These results suggest that σNS forms RNA-protein complexes in preparation for genome replication.IMPORTANCEFollowing infection, viruses synthesize nonstructural proteins that mediate viral replication and promote dissemination. Viruses from the familyReoviridaeencode nonstructural proteins that are required for the formation of progeny viruses. Although nonstructural proteins of different viruses in the familyReoviridaediverge in primary sequence, they are functionally homologous and appear to facilitate conserved mechanisms of dsRNA virus replication. Usingin vitroand cell culture approaches, we found that the mammalian reovirus nonstructural protein σNS binds and stabilizes viral RNA and is required for genome synthesis. This work contributes new knowledge about basic mechanisms of dsRNA virus replication and provides a foundation for future studies to determine how viruses in the familyReoviridaeassort and replicate their genomes.

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