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Chapter 87 : Coronaviruses

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Abstract:

The family includes the genera and in the order . Coronaviruses (CoVs) were first identified by electron microscopy (EM) of cultured samples and were named for the distinct crown-like morphology of the long surface spikes. Two types of spikes line the outside of the CoV virion. The majority of severe acute respiratory syndrome (SARS)-CoV isolates identified worldwide are genetically closely linked. In one study, human CoV (HCoV)-OC43 was the most commonly identified HCoV in bronchoalveolar lavage (BAL) samples from hospitalized adults. Nucleic acid extraction procedures have the advantage of inactivating viruses before analysis, making them the most likely front-line test in such circumstances. The most common diagnostic approach for identification of HCoVs is now amplification and detection of virus-specific RNA. Assays utilizing one-step or two-step reverse transcription-polymerase chain reaction (RT-PCR) procedures for the amplification stage have dominated most diagnostic formats. The majority of nucleic acid amplification tests (NAATs) for detection of HCoV-229E, HCoV-OC43, and HCoV-NL63 have targeted the N, M, and genes. Broad detection of respiratory viruses is particularly important in analyses of outbreaks, and recent studies have shown the added value of broad respiratory virus detection in such diagnostic situations.

Citation: Pabbaraju K, Fox J. 2011. Coronaviruses , p 1410-1422. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch87
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FIGURE 1

Electron micrograph of HCoV-OC43 showing pleomorphic shape and characteristic coronas made up of surrounding peplomers.

Citation: Pabbaraju K, Fox J. 2011. Coronaviruses , p 1410-1422. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch87
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Image of FIGURE 2
FIGURE 2

Phylogenetic analysis of the RNA-dependent RNA polymerase gene showing the grouping of CoVs. Analysis was undertaken by use of complete genome sequences available by the end of 2008. The tree was constructed by the neighbor-joining method, using Kimura's twoparameter correction and bootstrap values calculated from 1,000 trees. Nine hundred fifty-eight amino acid positions were included in the analysis. The scale bar indicates the estimated number of substitutions per 50 amino acids. The following viral sequences (GenBank accession number) were used: HCoV-229E, human coronavirus 229E (GenBank accession no. NC_002645); PEDV, porcine epidemic diarrhea virus (NC_003436); TGEV, porcine transmissible gastroenteritis virus (NC_002306); FCoV, feline coronavirus (AY994055); PRCV, porcine respiratory coronavirus (DQ811787); HCoV-NL63, human coronavirus NL63 (NC_005831); bat-CoV-HKU2 (EF203064), -HKU4 (NC_009019), -HKU5 (NC_009020), -HKU8 (NC_010438), -HKU9 (NC_009021), -1A (NC_010437), -1B (NC_010436), and -512/2005 (NC_009657); HCoV-HKU1, human coronavirus HKU1 (NC_006577), HCoV-OC43, human coronavirus OC43 (NC_005147); MHV, mouse hepatitis virus (NC_006852); BCoV, bovine coronavirus (NC_003045); PHEV, porcine hemagglutinating encephalomyelitis virus (NC_007732); ECoV, equine coronavirus (NC_010327); SARS-CoV, SARS coronavirus (NC_004718); bat-SARS-CoV-HKU3, bat SARS coronavirus HKU3 (NC_009694); IBV, infectious bronchitis virus (NC_001451); TCoV, turkey coronavirus (NC_010800); SW1, beluga whale coronavirus (NC_010646); BuCoV-HKU11, bulbul coronavirus HKU11 (NC_011548); ThCoV-HKU12, thrush coronavirus HKU12 (NC_011549); and MuCoV-HKU13, munia coronavirus HKU13 (NC_011550). (Reproduced from reference )

Citation: Pabbaraju K, Fox J. 2011. Coronaviruses , p 1410-1422. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch87
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FIGURE 3

HCoV CPE at 5 days postinfection. (A) Uninfected LLC-MK2 cells. (B) HCoV-NL63-infected LLC-MK2 cells.

Citation: Pabbaraju K, Fox J. 2011. Coronaviruses , p 1410-1422. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch87
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Image of FIGURE 4
FIGURE 4

Circulating HCoVs in respiratory samples. Samples received from community and hospitalized patients with respiratory symptoms were tested for HCoVs by use of a multiplex panel test as described previously ( ). The total number of samples tested was 25,799, with 437 HCoV-positive samples (overall, 1.7% of samples were positive for any HCoV).

Citation: Pabbaraju K, Fox J. 2011. Coronaviruses , p 1410-1422. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch87
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Tables

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TABLE 1

Comparison of diagnostic procedures for detection of HCoVs

Citation: Pabbaraju K, Fox J. 2011. Coronaviruses , p 1410-1422. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch87
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TABLE 2

Real-time RT-PCR methods for detection of currently-circulating HCoVs

Citation: Pabbaraju K, Fox J. 2011. Coronaviruses , p 1410-1422. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch87

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