Chapter 90 : Coronaviruses*

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Coronaviruses*, Page 1 of 2

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Coronaviruses (CoV) are enveloped viruses with large RNA genomes and are found in several animal species, including humans. Four coronaviruses HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1 are endemic in humans and associated with a range of upper and lower respiratory tract disease from the common cold to severe pneumonia. HCoVs make up a small but significant proportion of the viruses found in patients with acute respiratory illness (ARI), particularly in children and during the winter and spring months. The highly pathogenic CoVs responsible for severe acute respiratory syndrome (SARS-CoV) and Middle Eastern respiratory syndrome (MERS-CoV) have only recently emerged in the human population through zoonotic transmission. SARS-CoV has not been reported since early 2004 but caused significant morbidity and mortality during a global outbreak in 2002/2003. Since 2012, MERS-CoV has caused a number of cases of severe ARI linked to the Arabian Peninsula and transmission is still occurring. Isolation of CoVs is not effective as a routine diagnostic tool because many commonly used cell lines are not permissive for growth and cytopathic effect is generally nonspecific. Reagents for immunofluorescent detection are not widely available and serological testing is most useful for epidemiological studies and retrospective diagnosis. Direct detection of CoV nucleic acid in clinical specimens is the most common diagnostic method currently in use. A range of in-house RT-PCR methods have been developed for either pan-CoV or species-specific detection, and commercial nucleic acid amplification tests (NAATs) are also now available.

Citation: Gadsby N, Templeton K. 2015. Coronaviruses*, p 1565-1583. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch90
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Image of FIGURE 1

Electron micrograph of HCoV-OC43 showing pleomorphic shape and characteristic coronas made up of surrounding peplomers. doi:10.1128/9781555817381.ch90.f1

Citation: Gadsby N, Templeton K. 2015. Coronaviruses*, p 1565-1583. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch90
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Phylogenetic relationships among members of the subfamily . A rooted neighbor-joining tree was generated from amino acid sequence alignments of the replicase proteins encoded by polymerase ORF1b for 20 CoVs, each a representative of a currently recognized CoV species, and for the newly recognized MERS-CoV strain Hu/Jordan-N3/2012; bovine torovirus strain Breda served as an out-group. Only bootstrap values equal to or larger than 95% are indicated. Virus names are given with strain specifications between parentheses; species and genus names are in italics as per convention. The tree shows the four main monophyletic clusters, corresponding to genera , , -, and . Also indicated are lineages A through D (corresponding to former CoV subgroups 2A through D). (Modified from , kindly provided by RJ de Groot, and used with permission). doi:10.1128/9781555817381.ch90.f2

Citation: Gadsby N, Templeton K. 2015. Coronaviruses*, p 1565-1583. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch90
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HCoV cytopathic effect at 5 days postinfection. (A) Uninfected LLC-MK2 cells. (B) HCoV-NL63-infected LLC-MK2 cells. doi:10.1128/9781555817381.ch90.f3

Citation: Gadsby N, Templeton K. 2015. Coronaviruses*, p 1565-1583. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch90
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HCoV detection frequencies by month and age band over a 3-year period between 2006 and 2009 in Edinburgh, United Kingdom, using multiplex real-time RT-PCR. During this time, 11,661 specimens were tested, with 61 specimens positive for HCoV-HKU1, 99 for HCoV-OC43, 35 for HCoV-229E, and 75 for HCoV-NL63 (adapted from ). doi:10.1128/9781555817381.ch90.f4

Citation: Gadsby N, Templeton K. 2015. Coronaviruses*, p 1565-1583. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch90
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Examples of published real-time RT-PCR assays for the detection of endemic HCoVs using different target genes

Citation: Gadsby N, Templeton K. 2015. Coronaviruses*, p 1565-1583. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch90
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Examples of currently available commercial assays incorporating the detection of endemic HCoVs

Citation: Gadsby N, Templeton K. 2015. Coronaviruses*, p 1565-1583. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch90

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