Nidovirales

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Nidovirales

Mesoniviruses have no known disease association and host range analysis indicates that their replication is restricted to mosquitoes and that they are unable to replicate in vertebrate cells in culture.

From: Reference Module in Life Sciences, 2020

Related terms:

Protein

RNA

Nucleophosmin

Arteriviridae

Coronaviridae

Roniviridae

Arterivirus

Coronavirinae

SARS Coronavirus

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Nidovirales

L. Enjuanes, ... E.J. Snijder, in Encyclopedia of Virology (Third Edition), 2008

Taxonomy and Phylogeny

The order Nidovirales includes the families Coronaviridae, Roniviridae, and Arteriviridae (Figure 1). The Coronaviridae comprises two well-established genera, Coronavirus and Torovirus, and a tentative new genus, Bafinivirus. The Arteriviridae and Roniviridae include only one genus each, Arterivirus and Okavirus, respectively. All nidoviruses have single-stranded RNA genomes of positive polarity that, in the case of the Corona- and Roniviridae (26–32 kbp), are the largest presently known RNA virus genomes. In contrast, members of the Arteriviridae have a smaller genome ranging from about 13 to 16 kbp. The data available from phylogenetic analysis of the highly conserved RNA-dependent RNA polymerase (RdRp) domain of these viruses, and the collinearity of the array of functional domains in nidovirus replicase polyproteins, were the basis for clustering coronaviruses and toroviruses (Figure 2). The more distantly related roniviruses also group with corona- and toroviruses, thus forming a kind of supercluster of nidoviruses with large genomes. By contrast, arteriviruses must have diverged earlier during nidovirus evolution. The current taxonomic position of coronaviruses and toroviruses as two genera of the family Coronaviridae is currently being revised by elevating these virus groups to the taxonomic rank of either subfamily or family.



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Figure 1. Nidovirus classification and prototype members. The order Nidovirales containing the families Coronaviridae (including the established genera Coronavirus and Torovirus, and a new tentative genus Bafinivirus), Arteriviridae, and Roniviridae. Phylogenetic analysis (see Figure 2) has confirmed the division of coronaviruses into three groups. In arteriviruses, four comparably distant genetic clusters have been differentiated. To facilitate the taxonomy of the different virus isolates, the types Co, To, Ba, Ro, standing for coronavirus, torovirus, bafinivirus, or ronivirus, respectively, have been included. The following CoVs are shown: human coronaviruses (HCoV) 229E, HKU1, OC43 and NL63, transmissible gastroenteritis virus (TGEV), feline coronavirus (FCoV), porcine epidemic diarrhoea virus (PEDV), mouse hepatitis virus (MHV), bovine coronavirus (BCoV), bat coronaviruses (BtCoV) HKU3, HKU5, HKU9, 133 and 512 (the last two isolated in 2005), porcine hemagglutinating encephalomyelitis virus (PHEV), avian infectious bronchitis virus (IBV), and severe acute respiratory syndrome coronavirus (SARS-CoV); ToV: equine torovirus (EToV), bovine torovirus (BToV), human torovirus (HToV), and porcine torovirus (PToV); BaV: white bream virus (WBV); Arterivirus: equine arteritis virus (EAV), simian haemorrhagic fever virus (SHFV), lactate dehydrogenase-elevating virus (LDV), and three (Euro, HB1, and MLV) porcine reproductive and respiratory syndrome viruses (PRRSV); RoV: gill-associated virus (GAV) and yellow head virus (YHV). Human viruses are highlighted in red. Some nodes are formed by a pair of very closely related viruses (e.g., SARS-CoV and BtCoV-HKU3). Asterisk indicates tentative genus.



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Figure 2. Nidovirus phylogeny. Tree depicting the evolutionary relationships between the five major groups of nidoviruses as shown in Figure 1 (Coronavirus, Torovirus, Bafinivirus, Ronivirus, and Arterivirus). This unrooted maximum parsimonious tree was inferred using multiple nucleotide alignments of the RdRp-HEL region of a representative set of nidoviruses with the help of the PAUP*v.4.0b10 software (AEG, unpublished). Support for all bifurcations from 100 bootstraps performed is indicated. The phylogenetic distances shown are approximate. For acronyms, see Figure 1.

A comparative sequence analysis of coronaviruses reveals three phylogenetically compact clusters: groups 1, 2, and 3. Within group 1, two subsets can be distinguished: subgroup 1a that includes transmissible gastroenteritis virus (TGEV), canine coronavirus (CCoV), and feline coronavirus (FCoV), and subgroup 1b that includes the human coronaviruses (HCoV) 229E and NL63, porcine epidemic diarrhoea virus (PEDV), and bat coronavirus (BtCoV) 512 which was isolated in 2005. Within group 2 coronaviruses, two subsets have been recognized: subgroup 2a, including mouse hepatitis virus (MHV), bovine coronavirus (BCoV), HCoV-OC43, and HCoV-HKU1; and subgroup 2b, including severe acute respiratory syndrome coronavirus (SARS-CoV) and its closest circulating bat coronavirus relative, BtCoV-HKU3. A growing number of other bat viruses has been recently identified in groups 1 and 2. It is currently being debated whether some of these viruses (e.g., BtCoV-HKU5, BtCoV-133 (isolated in 2005), and BtCoV-HKU9) may in fact represent novel subgroups or groups. Avian infectious bronchitis virus (IBV) is the prototype of coronavirus group 3, which also includes several other bird coronaviruses. In arteriviruses, there are four comparably distant genetic clusters, the prototypes of which are equine arteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV) of mice, simian hemorrhagic fever virus (SHFV) infecting monkeys, and porcine reproductive and respiratory syndrome virus (PRRSV) which infects pigs and includes European and North American genotypes.

Roniviruses are the only members of the order Nidovirales that are known to infect invertebrates. The family Roniviridae includes the penaeid shrimp virus, gill-associated virus (GAV), and the closely related yellow head virus (YHV).

More than 100 full-length coronavirus genome sequences and around 30 arterivirus genome sequences have been documented so far, whereas only very few sequences have been reported for toroviruses, bafiniviruses, and roniviruses. Therefore, information on the genetic variability of these nidovirus taxa is limited.

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Nidovirales

In Virus Taxonomy, 2012

This chapter focuses on the Nidovirales order whose member families include Arteriviridae, Coronaviridae, and Roniviridae. The nidoviruses genome is an infectious, linear, positive sense RNA molecule, which is capped and polyadenylated. Based on the genome size, they are divided into two groups large and small nidoviruses. The genomes of the large nidoviruses are well over 25 kb in length with size differences in the 5 kb range. Based on the genome size, they can be distinguished into two groups, large and small nidoviruses. The genomes of the large nidoviruses are well over 25 kb in length with size differences in the 5 kb range. Although the structural proteins of the nidoviruses are generally functionally equivalent, there is no firm indication that any single protein species is evolutionary conserved across all of the families. Members of the family Coronaviridae generally possess three or four envelope proteins. The most abundant one is the membrane (M) protein. Though different in sequence, the M proteins of corona-, toro-, and bafiniviruses are alike in size, structure, and presumably also in function. Nidoviruses have lipid envelopes, which are commonly acquired by budding at membranes of the endoplasmic reticulum, intermediate compartment and/or Golgi complex. In coronaviruses, the S protein is an important target for T cell responses and is the major inducer of virus-neutralizing antibodies, which are elicited by epitopes located mostly in the N-terminal half of the molecule.

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Plus-Strand RNA Viruses

JAMES H. STRAUSS, ELLEN G. STRAUSS, in Viruses and Human Disease (Second Edition), 2008

Production of Subgenomic RNAs

The members of the Nidovirales produce a nested set of subgenomic mRNAs (Fig. 3.38), which are capped and polyadenylated. The number produced depends on the virus but is 5 to 8 for most. Each subgenomic RNA is a messenger that is translated into one to three proteins from the 5′ ORF(s) in the mRNA. The five subgenomic mRNAs of IBV and the proteins translated from them are illustrated in Fig. 3.38A. Four of the subgenomic mRNAs are translated into the structural proteins in the virion, S, E, M, and N, found in that order in the genomes of all coronaviruses. Four small accessory proteins of unknown function are also produced, two from the E mRNA and two from RNA 5. Coronaviruses encode variable numbers of such accessory proteins which are not conserved as to sequence or to number among the various members of the family and whose function in unknown. It is also not known how multiple proteins are translated from a single mRNAs in the case of the coronaviruses.

Two mechanisms have been proposed for the production of these subgenomic RNAs. The first mechanism proposed was primer-directed synthesis from the (−)RNA template (i.e., from the antigenome produced from the genomic RNA). In this model, a primer of about 60 nucleotides is transcribed from the 3′ end of the template, which is therefore identical to the 5′ end of the genomic RNA. The primer is proposed to dissociate from the template and to be used by the viral RNA synthetase to reinitiate synthesis at any of the several sub-genomic promoters in the (−)RNA template. Evidence for this model includes the fact that each subgenomic RNA has at its 5′ end the same 60 nucleotides that are present at the 5′ end of the genomic RNA, and that there is a short sequence element present at the beginning of each gene that could act as an acceptor for the primer (this sequence, e.g., is ACGAAC in the SARS CoV). A recent model proposes that the bulk of the subgenomic mRNAs are produced by independent replication of the subgenomic RNAs as replicons. Such replication is thought to be possible because the mRNAs contain both the 5′ and 3′ sequences present in the genomic RNA, and therefore possess the promoters required for replication. Evidence for this model includes the fact that both plus-sense and minus-sense subgenomic RNAs are present in infected cells. The model favored is that the subgenomic RNAs are first produced during synthesis of minus-strand RNA from the genomic RNA. In this model, synthesis initiates at the 3′ end of the genome and then jumps to the 5′ leader at one of the junctions between the genes. Once produced, the subgenomic RNAs begin independent replication.

Coronaviruses undergo high-frequency recombination in which up to 10% of the progeny may be recombinant. It is proposed that the mechanism for generation of the subgenomic RNAs, which requires the polymerase to stop at defined sites and then reinitiate synthesis at defined promoters, may allow the formation of perfect recombinants at high frequency.

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The middle east respiratory syndrome coronavirus respiratory infection: an emerging infection from the arabian peninsula

J.A. Al-Tawfiq, Z.A. Memish, in The Microbiology of Respiratory System Infections, 2016

2 The organism

Coronaviruses are parts of the Nidovirales order. The name stems from the presence of crown-like spikes on their surfaces. Coronaviruses were first identified as human pathogens in the mid-1960s. Coronaviruses are enveloped RNA viruses and there are four virus clusters within the Coronavirinae subfamily: alpha, beta, gamma, and delta coronaviruses. Pathogenic human coronaviruses are classified into the genera alpha-coronavirus (HCoV-229E and HCoV-NL63) and beta-coronavirus (HCoV-OC43, HCoV-HKU1, and SARS-CoV).1 MERS-CoV emerged as a significant pathogen after the initial identification in 2012 from a patient with rapidly fatal community acquired pneumonia and is the first human coronavirus in lineage C of the beta-coronavirus genus.1,8 The MERS-CoV virus is known to have multiple clades circulating in humans. In one study, four different phylogenetic MERS-CoV clades were circulating in Saudi Arabia in Sep. 2012 to May 2013.9 Only one clade persisted at the end of the observation period.9 The length of each clade was different: Al-Hasa clade from Apr. 21, 2013 to Jun. 22, 2013 (62 days), Riyadh_3 clade from Feb. 5, 2013 to Jul. 2, 2013 (147 days), Buraidah_1 clade from May 3, 2013 to Aug. 5, 2013 (84 days), and Hafr-Al-Batin_1 clade from Jun. 4, 2013 to Oct. 1, 2013 (119 days).9 Most of the cases in the 2014 Jeddah outbreak belong to a single clade indicating human-to-human transmission.10 The imported case into South Korea showed that the MERS-CoV is a recombinant of groups 3 and 5 elements and that the recombination event occurred in the second half of 2014.11

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Neurovirology

Philip E. Pellett, ... Thomas C. Holland, in Handbook of Clinical Neurology, 2014

Coronaviruses

Human coronaviruses belong to order Nidovirales, family Coronaviridae, subfamily Coronavirinae, and either genus Alphacoronavirus or Betacoronavirus. They typically cause transient respiratory or gastrointestinal illness. The rapidly emergent outbreak in 2003–2004 of severe disease caused by the severe acute respiratory syndrome (SARS)-related coronavirus was notable in many ways, including the presence of neurologic manifestations (Weiss and Leibowitz, 2011).

Coronavirus virions are spherical, 120–160 nm in diameter, with an outer envelope bearing 20-nm-long club-shaped projections that collectively resemble a crown or the solar corona. The ssRNA + genome is coiled inside a helical nucleocapsid of 9–11 nm diameter. At 27–32 kb, coronavirus genomes are the largest among RNA viruses. They are non-segmented, 5'capped, and 3' polyadenylated.

Coronaviruses attach to cell surface receptors and then enter the cell by fusion at the plasma membrane or after endocytosis (Fig. 2.2, paths A2 and A1, respectively) (Perlman and Netland, 2009). Replication occurs in the cytoplasm. After uncoating, genome replication possibly occurs on double-membrane vesicles that originate from the endoplasmic reticulum. A virus-specific RdRp is translated, which transcribes the viral genomic RNA to produce a full-length antigenome. New positive-strand RNA and nested set of subgenomic mRNAs are then transcribed from the antigenome template. Each capped and polyadenylated mRNA produces a single polypeptide. Newly synthesized genomic RNA is incorporated into virions that assemble on membranes between the endoplasmic reticulum and Golgi. Mature virions egress by exocytosis after vesicular transport to the cell membrane (Fig. 2.5, path A/C3).

Coronaviruses are transmitted by respiratory aerosols and usually produce mild upper respiratory infections (Weiss and Leibowitz, 2011). They have been suggested as possible etiologic agents of multiple sclerosis. Neurologic manifestations associated with SARS coronavirus infections include axonopathic polyneuropathy, myopathy, and ischemic stroke. No vaccine or antiviral is available for human coronavirus infections.

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Viruses Associated With Foodborne Infections

Helen O'Shea, ... Rose Fitzgerald, in Reference Module in Life Sciences, 2019

Classification and Biophysical Properties

The Coronaviridae belong to the order Nidovirales of single stranded, positive sense RNA viruses. Within the Coronaviridae there are 2 sub-families, of which the Coronavirinae contain 4 genera. Phylogenetically, SARS-CoV is within the betacoronavirus genus (ICTV, 2017). In older literature, SARS-like CoVs were assigned to group 2b coronaviruses (Lau et al., 2005). The viruses are roughly spherical (120–140 nm diameter), with an envelope that contains many surface glycoproteins that form a corona (crown) under electron microscopy (Masters and Perlman, 2013). Although enveloped, the virus is relatively stable especially in faeces and urine for 1–2 days (or longer) at room temperature, and up to 4 days if stool is from diarrhea patients (the pH is higher) (see "Relevant Websites section"). However, they are sensitive to heat, lipid solvents, oxidizing agents and non-ionic detergents (Markey et al., 2013a). Many coronaviruses are associated with respiratory and intestinal disease and can cause severe epidemic gastrointestinal disease in agriculturally important species such as porcine epidemic diarrhea virus in pigs (Masters and Perlman, 2013).

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Coronaviruses

R.J.G. Hulswit, ... B.-J. Bosch, in Advances in Virus Research, 2016

1 Introduction

Coronaviruses (CoVs) (order Nidovirales, family Coronaviridae, subfamily Coronavirinae) are enveloped, positive-sense RNA viruses that contain the largest known RNA genomes with a length of up to 32 kb. The subfamily Coronavirinae, which contains viruses of both medical and veterinary importance, can be divided into the four genera alpha-, beta-, gamma- and deltacoronavirus (α-, β-, γ- and δ-CoV). The coronavirus particle comprises at least the four canonical structural proteins E (envelope protein), M (membrane protein), N (nucleocapsid protein), and S (spike protein). In addition, viruses belonging to lineage A of the betacoronaviruses express the membrane-anchored HE (hemagglutinin–esterase) protein. The S glycoprotein contains both the receptor-binding domain (RBD) and the domains involved in fusion, rendering it the pivotal protein in the CoV entry process.

Coronaviruses primarily infect the respiratory and gastrointestinal tract of a wide range of animal species including many mammals and birds. Although individual virus species mostly appear to be restricted to a narrow host range comprising a single animal species, genome sequencing and phylogenetic analyses testify that CoVs have crossed the host species barrier frequently (Chan et al., 2013; Woo et al., 2012). In fact most if not all human coronaviruses seem to originate from bat CoVs (BtCoVs) that transmitted to humans directly or indirectly through an intermediate host. It therefore appears inevitable that similar zoonotic infections will occur in the future.

In the past 15 years, the world witnessed two such zoonotic events. In 2002–2003 cross-species transmissions from bats and civet cats were at the base of the SARS (severe acute respiratory syndrome)-CoV epidemic that found its origin in the Chinese Guangdong province (Li et al., 2006; Song et al., 2005). The SARS-CoV nearly became a pandemic and led to over 700 deaths, before it disappeared when the appropriate hygiene and quarantine precautions were taken. In 2012, the MERS (Middle East respiratory syndrome)-CoV emerged in the human population on the Arabian Peninsula and currently continues to make a serious impact on the local but also global health system with 1800 laboratory confirmed cases and 640 deaths as of September 1, 2016 (WHO | Middle East respiratory syndrome coronavirus (MERS-CoV) – Saudi Arabia, 2016). The natural reservoir of MERS-CoV is presumed to be in dromedary camels from which zoonotic transmissions repeatedly give rise to infections of the lower respiratory tract in humans (Alagaili et al., 2014; Azhar et al., 2014; Briese et al., 2014; Reusken et al., 2013; Widagdo et al., 2016). Besides these two novel CoVs, four other CoVs were previously identified in humans which are found in either the alphacoronavirus (HCoV-NL63 and HCoV-229E) or the betacoronavirus genera (HCoV-OC43 and HCoV-HKU1). Phylogenetic analysis has shown that the bovine CoV (BCoV) has been the origin for HCoV-OC43 following a relatively recent cross-species transmission event (Vijgen et al., 2006). Moreover, HCoV-NL63, HCoV-229E, SARS-CoV, and MERS-CoV also have been predicted to originate from bats (Annan et al., 2013; Bolles et al., 2011; Corman et al., 2015; Hu et al., 2015; Huynh et al., 2012).

In general, four major criteria determine cross-species transmission of a particular virus (Racaniello et al., 2015). The cellular tropism of a virus is determined by the susceptibility of host cells (i.e., presence of the receptor needed for entry) as well as by the permissiveness of these host cells to allow the virus to replicate and to complete its life cycle. A third determinant consists of the accessibility of susceptible and permissive cells in the host. Finally, the innate immune response may restrict viral replication in a host species-specific manner. The above-mentioned criteria may play a critical role in the success of a cross-species transmission event. However, for CoVs, it seems that host tropism and changes therein are particularly determined by the susceptibility of host cells to infection. While CoV accessory genes, including the HE proteins, are thought to play a role in host tropism and adaptation to a new host, the S glycoprotein appears to be the main determinant for the success of initial cross-species infection events. In this review, we focus on the molecular changes in the S protein that underlie tropism changes at the cellular, tissue, and host species level and put these in perspective of the recently published cryo-EM structures.

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Human Coronaviruses: General Features

Xin Li, ... Patrick C.Y. Woo, in Reference Module in Biomedical Sciences, 2019

Taxonomy and Classification

Coronaviruses form the largest group of viruses under the order Nidovirales, which includes the families Coronaviridae, Arteriviridae, Roniviridae and Mesoviridae, with highly conserved genomic organization and 3′ nested subgenomic mRNAs (nido, Latin word for "nest"). The Coronaviridae family consists of two subfamilies: Coronavirinae and Torovirinae. The Coronavirinae are classified into four genera, Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus. The genus Betacoronavirus was previously further subdivided into lineages A, B, C, and D. Recently, these four lineages have been reclassified as subgenera of Betacoronavirus, and renamed Embecovirus (previous lineage A), Sarbecovirus (previous lineage B), Merbecovirus (previous lineage C) and Nobecovirus (previous lineage D). In addition, a fifth subgenus, Hibecovirus, was also included (Table 1).

Table 1. Classification of coronavirus

GeneraSubgeneraSpeciesAlphacoronavirusColacovirusBat coronavirus CDPHE15DecacovirusBat coronavirus HKU10

Rhinolophus ferrumequinum alphacoronavirus HuB-2013DuvinacovirusHuman coronavirus 229ELuchacovirusLucheng Rn rat coronavirusMinacovirusFerret coronavirus

Mink coronavirus 1MinunacovirusMiniopterus bat coronavirus 1

Miniopterus bat coronavirus HKU8MyotacovirusMyotis ricketti alphacoronavirus Sax-2011NyctacovirusNyctalus velutinus alphacoronavirus SC-2013PedacovirusPorcine epidemic diarrhea virus

Scotophilus bat coronavirus 512RhinacovirusRhinolophus bat coronavirus HKU2SetracovirusHuman coronavirus NL63

NL63-related bat coronavirus strain BtKYNL63-9bTegacovirusAlphacoronavirus 1aBetacoronavirusEmbecovirus (lineage A)Betacoronavirus 1

China Rattus coronavirus HKU24

Human coronavirus HKU1

Murine coronavirusSarbecovirus (lineage B)Severe acute respiratory syndrome-related coronavirusMerbecovirus (lineage C)Hedgehog coronavirus 1

Middle East respiratory syndrome-related coronavirus

Pipistrellus bat coronavirus HKU5

Tylonycteris bat coronavirus HKU4Nobecovirus (lineage D)Rousettus bat coronavirus GCCDC1

Rousettus bat coronavirus HKU9HibecovirusBat Hp-betacoronavirus Zhejiang 2013GammacoronavirusCegacovirusBeluga whale coronavirus SW1IgacovirusAvian coronavirusDeltacoronavirusAndecovirusWigeon coronavirus HKU20BuldecovirusBulbul coronavirus HKU11

Coronavirus HKU15

Munia coronavirus HKU13

White-eye coronavirus HKU16HerdecovirusNight heron coronavirus HKU19MoordecovirusCommon moorhen coronavirus HKU21

aAlphacoronavirus 1 contains viruses with the historical names: Transmissible gastroenteritis virus of swine, Porcine transmissible gastroenteritis virus, Feline infectious peritonitis virus, Canine coronavirus, and Feline coronavirus.

Based on International Committee on Taxonomy of Viruses https://talk.ictvonline.org/taxonomy/.

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Coronaviruses

Christopher J. Burrell, ... Frederick A. Murphy, in Fenner and White's Medical Virology (Fifth Edition), 2017

Classification

The family Coronaviridae is one of three RNA virus families within the order Nidovirales, the other being the Arteriviridae and the Roniviridae containing pathogens of birds and insects, respectively. The family consists of two subfamilies, Coronavirinae and Torovirinae, the latter containing viruses causing mainly enteric infections of horses, cattle, pigs, cats, and goats. Although of economic importance, members of the Torovirinae subfamily are not as yet known to cause human infection, and thus are not dealt with further. All coronaviruses share a common morphology and possess a single-stranded RNA genome of up to 30 kb in length.

Members of the subfamily Coronavirinae are subdivided into four genera. The genus Alphacoronavirus contains the human virus HCoV-229E, one other human coronavirus (HCoV-NL63), and many animal viruses. The genus Betacoronavirus includes the prototype mouse hepatitis virus (MHV), the three human viruses HCoV-OC43, SARS-HCoV, and HCoV-HKU1, and the SARS-related coronavirus, Middle Eastern respiratory syndrome (MERS) coronavirus, together with a number of animal coronaviruses. The genus Gammacoronavirus contains viruses of cetaceans (whales) and birds, and the genus Deltacoronavirus contains viruses isolated from pigs and birds.

Since 2005, dozens of new coronaviruses have been isolated from bats, and there is evidence that human respiratory coronaviruses, SARS coronavirus, and MERS coronavirus, may each have originally emerged from ancestral bat viruses (Table 31.1, Fig. 31.1).

Table 31.1. Properties of Coronaviruses

●

Virion is pleomorphic spherical 80 to 220 nm (coronaviruses); or disc, kidney, or rod shaped 120 to 140 nm (toroviruses)

●

Envelope with large, widely spaced club-shaped peplomers

●

Tubular nucleocapsid with helical symmetry

●

Linear, plus sense ssRNA genome 27 to 33 kb, capped, polyadenylated, infectious; untranslated sequences at each end

●

Three or four structural proteins: nucleoprotein (N), peplomer glycoprotein (S), transmembrane glycoprotein (M), sometimes hemagglutinin-esterase (HE)

●

Genome encodes 3 to 10 further non-structural proteins, including the RNA-dependent RNA polymerase made up of subunits cleaved from two polyproteins translated from the 5′-end

●

Replicates in cytoplasm; genome is transcribed to full-length negative sense RNA, from which is transcribed a 3′-coterminaI nested set of mRNAs, only the unique 5′ sequences of which are translated

●

Virions are assembled and bud into the endoplasmic reticulum and Golgi cisternae; release is by exocytosis

●

Variant viruses arise readily, by mutation and recombination, and the use of different receptors influences the host range exhibited



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Figure 31.1. Phylogeny of coronaviruses. Phylogenetic tree of 50 coronaviruses constructed by the neighbor-joining method using MEGA 5.0 using partial nucleotide sequences of RNA-dependent RNA polymerase. The scale bar indicates the estimated number of substitutions per 20 nucleotides. Space does not permit providing full virus names, except for the human viruses, which are scattered among the viruses isolated from many other species (major pathogens shown in red): HCoV-229E, human coronavirus 229E; HCoV-HKU1, human coronavirus HKU1; HCoV-NL63, human coronavirus NL63; HCoV-OC43, human coronavirus OC43; KSA-CAMEL-363, KSA-CAMEL-363 isolate of Middle East respiratory syndrome coronavirus; MERS-CoV, Middle East respiratory syndrome coronavirus; MHV, murine hepatitis virus, the prototypic virus of the family; SARS-CoV, SARS coronavirus; SARSr-CiCoV, SARS-related palm civet coronavirus. A remarkable number of the viruses represented here are from bats, many different species of bats, and quite a few of these are rather closely related to SARS-CoV.

Modified from Chan, J.F., Lau, S.K., To, K.K., Cheng, V.C., Woo, P.C., Yuen, K.Y., 2015. Middle East respiratory syndrome coronavirus: another zoonotic betacoronavirus causing SARS-like disease. Clin. Microbiol. Rev. 28, 465–522, with permission.

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Coronaviruses

K. Nakagawa, ... S. Makino, in Advances in Virus Research, 2016

1.2 CoVs

CoVs are enveloped plus-strand RNA viruses that belong to the order Nidovirales in the subfamily Coronavirinae (family Coronaviridae) and are classified into four genera, Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus (de Groot et al., 2011; Gorbalenya et al., 2004; Snijder et al., 2003; Woo et al., 2010, 2012). CoVs cause primarily respiratory and/or enteric diseases and are found in many animal species, including wild animals, domestic animals, and humans (Weiss and Navas-Martin, 2005). While most human CoVs (HCoV) cause relatively mild upper respiratory tract infections (common cold), two zoonotic viruses called severe acute respiratory syndrome (SARS) CoV and Middle East respiratory syndrome (MERS) CoV are associated with severe lower respiratory tract infections and are major public health threats. SARS-CoV, MERS-CoV, and some HCoVs, including HCoV-OC43 and HCoV-HKU1, belong to the genus Betacoronavirus, while other HCoVs, HCoV-229E, and HCoV-NL63, belong to the genus Alphacoronavirus. Animal CoVs from the genera Alpha- and Betacoronavirus are mainly associated with infections in mammals, while viruses in the genera Gamma- and Deltacoronavirus primarily (but not exclusively) infect birds. There is now compelling evidence to suggest that bats are the natural reservoir involved in the evolution and spread of many mammalian CoVs, including SARS-CoV and MERS-CoV (Lau et al., 2005; Li et al., 2005; Memish et al., 2013).

The CoV particles have a spherical shape with a diameter of roughly 100 nm (Davies and Macnaughton, 1979; Wege et al., 1979). They carry three major structural proteins (S, M, and E) in the envelope and contain a helical nucleocapsid that is formed by the viral genomic RNA and the viral N protein. The viral S protein binds has receptor-binding and fusogenic functions (Heald-Sargent and Gallagher, 2012; Masters, 2006) and thus is essential for initiation of CoV infection.

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Virus Research

Volume 117, Issue 1, April 2006, Pages 17-37

Nidovirales: Evolving the largest RNA virus genome

Author links open overlay panelAlexander E.GorbalenyaaEric J.Snijdera

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Abstract

This review focuses on the monophyletic group of animal RNA viruses united in the order Nidovirales. The order includes the distantly related coronaviruses, toroviruses, and roniviruses, which possess the largest known RNA genomes (from 26 to 32 kb) and will therefore be called 'large' nidoviruses in this review. They are compared with their arterivirus cousins, which also belong to the Nidovirales despite having a much smaller genome (13–16 kb). Common and unique features that have been identified for either large or all nidoviruses are outlined. These include the nidovirus genetic plan and genome diversity, the composition of the replicase machinery and virus particles, virus-specific accessory genes, the mechanisms of RNA and protein synthesis, and the origin and evolution of nidoviruses with small and large genomes. Nidoviruses employ single-stranded, polycistronic RNA genomes of positive polarity that direct the synthesis of the subunits of the replicative complex, including the RNA-dependent RNA polymerase and helicase. Replicase gene expression is under the principal control of a ribosomal frameshifting signal and a chymotrypsin-like protease, which is assisted by one or more papain-like proteases. A nested set of subgenomic RNAs is synthesized to express the 3′-proximal ORFs that encode most conserved structural proteins and, in some large nidoviruses, also diverse accessory proteins that may promote virus adaptation to specific hosts. The replicase machinery includes a set of RNA-processing enzymes some of which are unique for either all or large nidoviruses. The acquisition of these enzymes may have improved the low fidelity of RNA replication to allow genome expansion and give rise to the ancestors of small and, subsequently, large nidoviruses.

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Keywords

RNA viruses

Nidoviruses

Coronaviruses

Arteriviruses

Roniviruses

Astroviruses

Virus evolution

RNA replication

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Copyright © 2006 Elsevier B.V. All rights reserved.



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