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Nature of Genome: |
positive-stranded ssRNA
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Order |
03. Nidovirales |
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Taxonomic Structure of the Family |
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Family 03.019. Coronaviridae |
03.019.0.01. Coronavirus |
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03.019.0.01.001. Infectious bronchitis virus |
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Practically, species in the Coronavirus genus have been differentiated using four parameters: (i) the position and variety of the non-essential non-structural proteins in the 3'-part of genome, (ii) antigenic properties, (iii) the processing of the S protein into two halves (S1 and S2), and (iv) the host range. No rigorous guidelines have been developed to apply the above criteria for defining new coronavirus species or differentiating between existing species. A brief posteriori analysis of the coronavirus species diversity in respect to these criteria is summarized below.
The number, type and location of the non-essential genes (encoding non-structural proteins) significantly vary. Some of these genes are common for a set of closely related viruses, e.g. CPD and HE genes in MHV, BCoV and HCoV-043, and others may be specific for a virus species, e.g. all unique ORFs in SARS-CoV. Importantly, different isolates of the same coronavirus may also differ in respect to certain 3'-located ORFs, e.g. ORF8a and ORF8b are fused in a single ORF in some human vs. animal isolates of SARSCoV. Serological characterization allows placing a virus within an antigenic cluster and nucleic (amino) acid similarity within a genetic cluster or group; the characterized coronaviruses form at least 3 genetic clusters or groups (see below). All coronaviruses fall in one of two divisions depending whether the S protein is processed into S1 and S2 subunits or not. Those with uncleaved S protein include Group 1 coronaviruses (CCoV, FCoV, HCoV229E, PEDV and TGEV) and Group 2, SARS-CoV, and those with the cleaved S protein include species of Groups 2 (BCoV, MHV and HCoV-OC43) and 3 (IBV). Coronaviruses infect a wide range of mammals and distantly related coronaviruses may infect the same host, e.g. HCoV-229E, HCoV-043 and SARS-CoV, from different groups of coronaviruses, all infect humans. The group 3 consists exclusively of avian coronaviruses. Future revision of the taxonomy of the family Coronaviridae may propose a quantitative measure of genome similarity or other criterion to discriminate coronavirus species rigorously
The ICTVdB virus code and the viruses. Official virus species names are in italics. Tentative virus species
names, alternative names ( ), isolates, strains, serotypes, subspecies, or rejected names are not italicized.
Virus codes, virus names, genome sequence accession numbers [ ] and assigned abbreviations ( ), are:
| Group 1 species | |||
(CCOV) | |||
(FCoV) | |||
(FIPV) | |||
(HCoV-229E) | |||
(PEDV) | |||
(PRCoV) | |||
(TGEV) | |||
(TGEV) | |||
(TGEV) | |||
(TGEV) | |||
| Group 2 species | |||
(BCoV) | |||
(HCoV-OC43) | |||
(HECoV) | |||
(MHV) | |||
(HEV) | |||
(PCOV) | |||
(RtCoV) | |||
(SDAV) | |||
| Group 3 species | |||
(IBV) | |||
(PhCoV) | |||
(TCoV) |
(RbCoV) |
03.019.0.02. Torovirus |
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03.019.0.02.001. Equine torovirus |
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So far, only limited molecular genetic information is available for toroviruses. Comparative sequence analysis of the structural protein genes of a set torovirus field variants identified three distinct genotypes, displaying 20 to 40% divergence. These are exemplified by BToV Breda strain, PToV Markelo strain and EToV Berne strain. Human torovirus, for which only the HE gene has been characterized, may represent a fourth genotype.
The bovine and porcine toroviruses apparently display host species preference. In phylogenetic analyses, all PToV variants cluster, while the extant European BToVs mostly resemble the New World BToV variant Breda, identified 19 years ago. However, there is evidence for recurring intergenotypic recombination. All newly characterized European BToV variants seem to have arisen from a genetic exchange, during which the 3'-end of the HE gene, the N gene, and the 3' -UTR of a Breda virus-like parent had been swapped for those of PToV. Moreover, some PToV and BToV variants carried chimeric HE genes, which apparently resulted from recombination events involving hitherto unknown toroviruses. From these observations, the existence of two additional torovirus genotypes can be inferred.
Sequencing of C-terminus of the N gene and the 3'-UTR have shown > 93% identity between HToV, BToV and EToV. Nevertheless, small but consistent sequence differences were noted among five HToV isolated and EToV. The published HToV HE sequence is most related to that of BToV variant Breda (83%), and more distantly related to those of the European BToV strains (-73%) and PToV strain (-56%).
BToV, PToV and HToV cause gastroenteritis and the BToV sporadically infects the respiratory system, in contrast to EToV that has remained as a virus in search of a disease.
The ICTVdB virus code and the viruses. Official virus species names are in italics. Tentative virus species
names, alternative names ( ), isolates, strains, serotypes, subspecies, or rejected names are not italicized.
Virus codes, virus names, genome sequence accession numbers [ ] and assigned abbreviations ( ), are:
(BToV) | |||
(BRV) | |||
(BEV) | |||
(EToV) | |||
(HToV) | |||
(PToV) |
None reported.
None reported.
Coronavirus mRNAs contain a 5' leader sequence, which is acquired via discontinuous RNA transcription, most likely during (-)strand RNA synthesis. In contrast, the torovirus mRNAs seem to be produced mainly via a non-discontinuous transcription mechanism: subgenomic mRNAs 3 through 5 of EToV strain Berne do not possess a leader. EToV mRNA2, however, contains a short 15-18 nt sequence at its 5'end, which apparently is derived from the 5'-end of the genome. Coronaviruses have a loosely wound helical nucleocapsid protected by a core shell while the toroviruses have a more rigid tubular nucleocapsid. All torovirus field strains studied so far express an HE protein; of the coronaviruses only those belonging to group 2 encode an HE protein. The N protein is much larger in coronaviruses than in toroviruses. The M protein is glycosylated only in coronaviruses. Toroviruses do not have a counterpart to the E protein and direct the synthesis of fewer subgenomic mRNAs than any coronavirus. A putative CPD was mapped to the very C-terminus of ppla in a torovirus but it is encoded immediately downstream of ORF1b in some coronaviruses. Upon comparison of every pair of homologous protein, toroviruses and coronaviruses do not interleaved and form separate groups.
Table 3: Features of coronaviruses and toroviruses.
Corona, from the Latin corona for "crown", representing the appearance of surface projections in negatively-stained electron micrographs of members of the Coronavirus genus.
Toro, from the Latin torus, "lowest convex moulding in the base of a column", representing the toroviruses nucleocapsid shape.
Collated from VIIIth ICTV Report
Spaan, W.J.M., Brian, D., Cavanagh, D., de Groot, R.J., Enjuanes, L., Gorbalenya, A.E., Holmes, K.V., Masters, P., Rottier, P., Taguchi, F. and Talbot, P.
Version 4 is based on Virus Taxonomy, Classification and Nomenclature of Viruses, 8th ICTV Report of the International Committee on Taxonomy of Viruses. Fauquet, CM, Mayo, MA, Maniloff, J, Desselberger, U, and Ball, LA (EDS) (2005) Elsevier/Academic Press, pp. 1259.
Comments to ICTVdB
Management
by Cornelia
Büchen-Osmond
Copyright © 2002 International Committee on Taxonomy of Viruses. All rights reserved.
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