Chapter 51 : Coronaviruses

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Coronaviruses have been classified as members of the order , positive-sense RNA viruses that replicate using a nested ("nido") set of mRNAs. On the basis of antigenic relationships and genetic homologies, the coronaviruses were divided into three groups. The first contains human coronaviruses (HCoVs) 229E and several animal strains; the second contains OC43, murine hepatitis viruses (MHV) and several other animal strains; and the third contains infectious bronchitis virus (IBV) and several other avian coronaviruses. Coronaviruses, along with rhinoviruses, influenza virus, and respiratory syncytial virus (RSV), are commonly associated with acute respiratory disease in the elderly. Most of the human respiratory coronaviruses that were isolated in the 1960s were originally recovered during upper respiratory illness. A study of acute lower tract viral infections in patients after lung transplantation found respiratory viruses in 66%, with coronaviruses (OC43, 229E, and NL63) being present in rank order right behind rhinoviruses and ahead of others, and a highly significant association of viral infection with a decline in one-second forced expiratory volume (FEV-1), acute rejection, and likely development of bronchiolitis obliterans syndrome. The major complications of respiratory coronavirus infections have been seen in children or adults with underlying cardiopulmonary disease. Respiratory coronaviruses are difficult to grow in tissue culture. Coronaviruses can be detected by immunofluorescence of cells shed from the respiratory tract using commercially available reagents or polyclonal or monoclonal reagents developed in individual laboratories. Interest in prevention of severe acute respiratory syndrome (SARS) was intense from the very beginning of the epidemic.

Citation: McIntosh K, Peiris J. 2009. Coronaviruses, p 1155-1171. In Richman D, Whitley R, Hayden F (ed), Clinical Virology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815981.ch51

Key Concept Ranking

Porcine epidemic diarrhea virus
Severe Acute Respiratory Syndrome
Acute Respiratory Distress Syndrome
Influenza C virus
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Image of FIGURE 1

Coronavirus OC16, viewed by EM and negatively stained. The characteristic round, or oval, shape is seen, along with the petal-shaped peplomers. Bar, 100 nm. (Reprinted from reference with permission.)

Citation: McIntosh K, Peiris J. 2009. Coronaviruses, p 1155-1171. In Richman D, Whitley R, Hayden F (ed), Clinical Virology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815981.ch51
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Image of FIGURE 2

Phylogenetic analysis of RNA sequences coding for the RNA-dependent RNA polymerase (ORF1b) (partial sequence, 1,176 bp). The phylogenetic tree was constructed by the neighbor-joining method, and bootstrap values were determined with 1,000 replicates. The virus sequences used were HCoV OC43 (GenBank accession no. AY585229), bovine coronavirus (BCoV) (GenBank accession no. AF391541), MHV A59 (GenBank accession no. NC_001846), HCoV HKU1 (GenBank accession no. NC_006577), bat SARS-CoV Rm1/2004 (Rm1) (GenBank accession no. NC_009696), bat SARS-CoV Rp3/2004 (Rp3) (GenBank accession no. NC_009693), SARS-CoV (GenBank accession no. AY278491), civet SARS-CoV SZ3 (GenBank accession no. AY304486), bat coronavirus (CoV) HKU4 (GenBank accession no. NC_009019), avian IBV (AIBV) (GenBank accession no. AY319651), feline infectious peritonitis virus (GenBank accession no. AY994055), transmissible gastroenteritis virus (TGEV) (GenBank accession NC_002306), porcine epidemic diarrhea virus (PEDV) (GenBank accession no. NC_003436), bat CoV 1A (unpublished data), HCoV NL63 (GenBank accession no. NC_005831), bat CoV HKU2 (GenBank accession no. DQ249235), and HCoV 229E (GenBank accession no. NC_002645).

Citation: McIntosh K, Peiris J. 2009. Coronaviruses, p 1155-1171. In Richman D, Whitley R, Hayden F (ed), Clinical Virology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815981.ch51
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Image of FIGURE 3

Coronavirus 229E in WI38 cells. Characteristic crescents (Cr) of budding particles (B) are seen, as well as particles which are free in cytoplasmic vesicles. (Reprinted from reference with permission.)

Citation: McIntosh K, Peiris J. 2009. Coronaviruses, p 1155-1171. In Richman D, Whitley R, Hayden F (ed), Clinical Virology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815981.ch51
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Image of FIGURE 4

Genomic organization of HCoVs. Strains 229E and NL63 belong to group 1, OC43 and HKU1 belong to group 2a, and SARS-CoV belongs to group 2b. ORF1 comprises ORF1a and ORF1b, which overlap. Translation of ORF1b depends on a ribosomal frameshift. ORF1 and ORF2 are translated into polyproteins that are cleaved into 16 nonstructural proteins, nsp1 to nsp16, by papain-like proteases (PL) encoded by ORF1a and a chymotrypsin-like protease (3CL). ORF1b encodes the viral RNA-dependent RNA polymerase (RdRp) and a multifunctional helicase (Hel) which has NTPase, dNTPase, and 5′-triphosphatase activities in addition to its helicase function. The main structural proteins present in all coronaviruses are the S, envelope (E), M, and N proteins. Some coronaviruses have an additional HE glycoprotein. Recently the ORF3a product has also been reported to be a structural protein in SARS-CoV. These genes are interspersed with ORFs encoding nonstructural proteins which differ markedly in their number and gene order between different coronavirus groups. nt, nucleotides.

Citation: McIntosh K, Peiris J. 2009. Coronaviruses, p 1155-1171. In Richman D, Whitley R, Hayden F (ed), Clinical Virology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815981.ch51
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Classification of coronaviruses

Citation: McIntosh K, Peiris J. 2009. Coronaviruses, p 1155-1171. In Richman D, Whitley R, Hayden F (ed), Clinical Virology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815981.ch51
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Published surveys of respiratory coronavirus infection in various pediatric populations and in relation to other respiratory viruses

Citation: McIntosh K, Peiris J. 2009. Coronaviruses, p 1155-1171. In Richman D, Whitley R, Hayden F (ed), Clinical Virology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815981.ch51

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