The accessory genes are specific for either a single virus species or a few viruses that form a compact phylogenetic cluster. Many proteins encoded by accessory genes may function in infected cells or in vivo to counteract host defenses and, when removed, may lead to attenuated virus phenotypes. Group 1 coronaviruses may have 2—3 accessory genes located between the S and E genes and up to two other genes downstream of N gene.
Viruses of group 2 form the most diverse coronavirus cluster, and they may have between three and eight accessory genes. In contrast, the most distant group 2 member, SARS-CoV, has seven or eight unique accessory genes, two between the S and E protein genes, four to five between the M and N protein genes, and ORF9b which entirely overlaps with the N protein gene in an alternative reading frame. In group 3 avian coronaviruses, of which IBV is the prototype, several accessory genes, which are expressed from functionally tri- or bicistronic mRNAs, have been identified in the region between the S and E protein genes gene 3 and between the M and N protein genes gene 5.
Some functionally dispensable ORF1a-encoded replicase domains may also be considered as accessory protein functions. Like in all other positive-stranded RNA viruses, nidovirus genome replication is mediated through the synthesis of a full-length, negative-strand RNA which, in turn, is the template for the synthesis of progeny virus genomes.
This process is mediated by the viral replication complex that includes all or most of the 14—16 nsps derived from the proteolytic processing of the pp1a and pp1ab replicase polyproteins of arteriviruses and coronaviruses. The replication complex, which is likely to include also cellular proteins, is associated with modified intracellular membranes, which may be important to create a microenvironment suitable for viral RNA synthesis as well as for recruitment of host factors. The origin of DMVs is under debate and different intracellular compartments including the Golgi, late endosomal membranes, autophagosomes, and the endoplasmic reticulum have been implicated in their formation.
Studies of cis -acting sequences required for nidovirus replication have mainly relied on coronavirus defective-interfering DI RNAs replicated by helper virus.
There is, however, some experimental evidence supporting protein-mediated cross-talk between both genome ends in the form of RNA—protein and protein—protein interactions. Several experimental approaches have implicated, in addition to the nsps encoded by the replicase gene, the N protein in coronavirus RNA synthesis.
Early in infection, the coronavirus N protein colocalizes with the site of viral RNA synthesis. In addition, the N protein can enhance the rescue of various coronaviruses from synthetic full-length RNA, transcribed in vitro or from cDNA clones. In contrast, arterivirus RNA synthesis does not require the N protein. Host factors that may participate in nidovirus RNA synthesis have been identified mainly from studies of coronaviruses and arteriviruses.
The functional relevance of hnRNP A1 in coronavirus replication was supported by experiments showing that its overexpression promotes MHV replication, whereas replication was reduced in cells expressing a dominant-negative mutant of hnRNP A1. Other cellular proteins found to bind to coronavirus genomic RNA, such as aconitase and the heat shock proteins HS40 and HS70, might be involved in modulating coronavirus replication.
Similarly, interactions of cellular proteins such as transcription cofactor p with the EAV nsp1, or of PTB or fructose bisphosphate aldolase A with SHFV genomic RNA, suggest that, in arterivirus replication also, a number of cellular proteins may be involved. RNA-dependent RNA transcription in some members of the Nidovirales coronaviruses, bafiniviruses, and arteriviruses , but not in others roniviruses , includes a discontinuous RNA-synthesis step.
Toroviruses are remarkable in that they employ a mixed transcription strategy to produce their mRNAs. Synthesis of torovirus mRNAs 3 through 5, and possibly of the two mRNAs in roniviruses, is thought to require the premature termination of negative-strand RNA synthesis at conserved, intergenic, TRS-like sequences to generate subgenome-length negative-strand RNAs that can be used directly as templates for sg mRNA synthesis. It is thought that during negative-strand synthesis, the hairpin structure may cause the transcriptase complex to detach, prompting a template switch similar to that seen in arteri- and coronaviruses.
In addition to regulatory RNA sequences, viral and host components involved in protein—RNA and protein—protein recognition are likely to be important in transcription.
For example, the arterivirus nsp1 protein has been identified as a factor that is dispensable for genome replication but absolutely required for sg RNA synthesis. The identification of host factors participating in nidovirus transcription is a field under development and specific binding assays have recently identified a limited number of cellular proteins that associate with cis -acting RNA regulatory sequences.
For example, differences in affinity of such factors for body TRSs might regulate transcription in nidoviruses by a mechanism similar to that of the DNA-dependent RNA-polymerase I termination system, in which specific proteins bind to termination sequences. The complex genetic plan and the replicase gene of nidoviruses must have evolved from simpler ones. Using this natural assumption, a speculative scenario of major events in nidovirus evolution has been proposed.
It has been speculated that the most recent common ancestor of the Nidovirales had a genome size close to that of the current arteriviruses. This ancestor may have evolved from a smaller RNA virus by acquiring the two nidovirus genetic marker domains represented by the helicase-associated zinc-binding domain ZBD and the NendoU function.
These two domains may have been used to improve the low fidelity of RdRp-mediated RNA replication, thus generating viruses capable of efficiently replicating genomes of about 14 kbp. The subsequent evolution of much larger nidovirus genomes may have been accompanied by the acquisition of the ExoN domain. Compared to other viruses, the interactions of nidoviruses with their hosts have not been studied in great detail. In many cases, information is based on relatively few studies performed on a limited number of viruses from the families Coronaviridae and Arteriviridae.
Also, most studies have been performed with viruses that have been adapted to cell culture and therefore may have properties that differ from those of field strains. Coronaviruses and arteriviruses are clearly the best-studied members of the Nidovirales in terms of their interactions with the host.
Coronavirus infection affects cellular gene expression at the level of both transcription and translation. Upon infection, host cell translation is significantly suppressed but not shut off, as is the case in several other positive-RNA viruses.
Another mechanism affecting host cell protein synthesis may be based on specific cleavage of the 28S rRNA subunit, which was observed in MHV-infected cells. Differences in cellular gene expression have been proposed to be linked to differences in the pathogenesis caused by these two human coronaviruses.
Apart from the downregulation of genes involved in translation and cytoskeleton maintenance, genes involved in stress response, proapoptotic, proinflammatory, and procoagulating pathways were significantly upregulated.
Nidoviruses have also been reported to interfere with cell cycle control. Many viruses encode proteins that modulate apoptosis and, more generally, cell death, which allows for highly efficient viral replication or the establishment of persistent infections. Infection by coronaviruses e. Apoptosis has also been reported in shrimp infected with the ronivirus YHV and is thought to be involved in pathogenesis. Both apoptotic and antiapoptotic molecules have been found to be upregulated, suggesting that a delicate counterbalance of pro- and antiapoptotic molecules is required to ensure cell survival during the early phase of infection, and rapid virus multiplication before cell lysis occurs.
Coronavirus-induced apoptosis appears to occur in a tissue-specific manner, which obviously has important implications for viral pathogenesis. For instance, SARS-CoV was shown to infect epithelial cells of the intestinal tract and induce an antiapoptotic response that may counteract a rapid destruction of infected enterocytes.
These findings are consistent with clinical observations of a relatively normal endoscopic and microscopic appearance of the intestine in SARS patients. Also the MHV E protein has been reported to induce apoptosis. The SARS-CoV 7a protein was found to induce apoptosis in cell lines derived from lung, kidney, and liver, by a caspase-dependent pathway. Apoptosis has also been associated with arterivirus infection but information on underlying mechanisms and functional implications is limited.
Coronavirus and arterivirus infections trigger proinflammatory responses that often are associated with the clinical outcome of the infection. Thus, for example, there seems to be a direct link between the IL-8 plasma levels of SARS patients and disease severity, similar to what has been described for pulmonary infections caused by respiratory syncytial virus. In contrast, despite the upregulation of IL-8 in intestinal epithelial cells, biopsy specimens taken from the colon and terminal ileum of SARS patients failed to demonstrate any inflammatory infiltrates, which may be the consequence of a virus-induced suppression of specific cytokines and chemokines, including IL, in the intestinal environment.
Innate immunity is essential to control vertebrate nidovirus infection in vivo. Type I interferon is a key player in innate immunity and in the activation of effective adaptive immune responses.
Like many other viruses, coronaviruses have developed strategies to escape IFN responses. This is a reproduction of L. Enjuanes, A. Gorbalenya, R. Mahy and Marc H. Van Regenmortel, Elsevier Ltd. National Center for Biotechnology Information , U. Encyclopedia of Virology. Published online Mar 1. Raoul J. Jeff A. Eric J. Guest Editor s : Dennis H. Bamford and Mark Zuckerman. Copyright and License information Disclaimer. All rights reserved. Elsevier hereby grants permission to make all its COVIDrelated research that is available on the COVID resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source.
Abstract Nidoviruses form a phylogenetically compact but diverse group of enveloped positive-stranded RNA viruses with the largest RNA genome known. Glossary 3CL pro or M pro 3C-like proteinase, or main proteinase. NendoU Nidovirus endoribonuclease. PL pro Papain-like cysteine proteinase. TRS Transcription-regulating sequence. Open in a separate window. Diseases Associated with Nidoviruses Coronavirus infections are mainly associated with respiratory, enteric, hepatic, and central nervous system diseases.
Virus Structure In addition to the significant variations in genome size among the three nidovirus families mentioned above, there are also major differences in virion morphology Fig. Different images were reproduced with permission from different authors: arterivirus, E. Snijder Leiden, The Netherlands ; ronivirus, P. Enjuanes CNB, Spain. Structural and Accessory Protein Genes In contrast to the large genome of Coronaviridae , which can accommodate genes encoding accessory proteins i.
NCRs may have specific, critical nucleotide sequences but in some cases they are regions of the genome that fold into conserved structures, and structure may be more critical than a specific sequence. Of course a source of RdRp must be supplied. RdRp may be encoded in the minigenome or may be supplied in trans by using a cell line stably expressing the viral RdRp, for example.
The sequences required to direct RNA replication are often fairly simple and can be linked to virtually any RNA sequence to drive its replication. These promoter sequences can be rather short but provide a means to direct the RdRp to internal sites on the genome. There may also be specific RNA sequences that signal polyadenylation. There are a variety of different strategies that RNA viruses use to regulate transcription and genome replication, but all involve RNA sequences found in the genome.
The RNA genomes of some viruses are highly structured and extensively base paired. The IRES serves as a platform for ribosome assembly. Promoters can be quite long and complex and promoter regions themselves are not transcribed. It is particularly important, in the case of genome synthesis, that genetic information not be lost or modified; however, mRNAs are often capped and polyadenylated.
Are the methods for priming viral mRNA synthesis the same or different from the methods of priming genome replication? The RNA viruses seem to have experimented widely. For example, the picornaviruses use poly A tracts encoded in the genome. Among the negative-strand RNA viruses, those in the order Mononegavirales use a stuttering mechanism to synthesize long poly A tracts from short poly U tracts Fig.
A strategy to regulate mRNA synthesis. This figure shows the organization of a paramyxovirus genome paramyxoviruses are members of the order Mononegavirales ; negative-strand RNA viruses with unsegmented genomes. Each protein-coding region is flanked by regulatory sequences that control capping and polyadenylation.
The order of the genes on the genome regulates the relative quantities of mRNAs synthesized. Because RdRp does often dissociate from the genome during transcription, the downstream genes are produced in lower quantities. Even with fairly simple genomes, RNA viruses must, and do, regulate the amounts of genome, copy genome, and mRNAs that are synthesized during an infection.
It is much more efficient to synthesize many genomes from each copy genome. Internal promoters for mRNA synthesis can vary in sequence, controlling the relative affinity of the transcription complex for each mRNA. An important feature of RNA viruses is that many exist in nature as quasispecies. The term quasispecies is used to describe a group of closely related, but nonidentical genomes Fig.
A Positive-strand RNA viruses exist as quasispecies, complex mixtures of related genomes. The mixture is more fit than any individual genome; fitness is maintained by generation of new variants in response to selective pressures.
B Potential for safer vaccines. If the fidelity of RdRp is increased the population remains more homogeneous. Therefore an attenuated virus with a high-fidelity RdRp is more likely to remain attenuated. Poliovirus PV is a good example of a virus that forms a quasispecies. If one examines genome sequences from a mouse experimentally infected with PV serotype 1, we find that the genomes are not identical, although they are all clearly related to one another.
To the surprise of many virologists, it turns out that the population quasispecies may be more fit than any individual genome. Or put another way, we cannot find any single genome in the population that replicates better than the group as a whole and in fact, most individual genomes replicate more poorly than the group.
Why this occurs is not always clear, but an animal is a very complex ecosystem. Different members of the quasispecies may be better adapted to different niches in the animal. How does a quasispecies form? But as the cloned virus replicates, mutations accumulate generating a quasispecies. Measurable levels of mutation occur because the fidelity of PV RdRp is low. RdRps do not have proof-reading activities as do many DNA polymerases.
If a mistake occurs, there are only two possibilities: RNA synthesis can stop, or RNA synthesis can continue beyond the mistake to generate a point mutation. A rate of one mutation per 10 5 nucleotides synthesized ensures that during an infection, many progeny will contain a mutation. The population is fitter than the individual Box A well-studied example is polio virus PV a picornavirus. Vignuzzi et al. While the mutant replicated as well as the wild-type virus produced equivalent numbers of virions , there was measurably less diversity in the population.
The less diverse population performed poorly, when compared to the wild-type virus, when exposed to adverse growth conditions. Adverse conditions included exposure to an antiviral drug in cultured cells and inoculation into mice. The process and its consequences, for example the generation of viruses with novel phenotypes, has historically been studied by analysis of the end products.
More recently, with an appreciation that there are both replicative and non-replicative mechanisms at work, and with new approaches and techniques to analyse intermediate products, the viral and cellular factors that influence the process are becoming understood. The major influence on replicative recombination is the fidelity of viral polymerase, although RNA structures and sequences may also have an impact.
In replicative recombination the viral polymerase is necessary and sufficient, although roles for other viral or cellular proteins may exist.
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