Coronavirus Detection in the Clinical Microbiology Laboratory: Are We Ready for Identifying and Diagnosing a Novel Virus?

Katharine Uhteg; Karen C Carroll; Heba H Mostafa

doi:10.1016/j.cll.2020.08.004

Coronavirus Detection in the Clinical Microbiology Laboratory: Are We Ready for Identifying and Diagnosing a Novel Virus?

Clin Lab Med. 2020 Dec;40(4):459-472. doi: 10.1016/j.cll.2020.08.004. Epub 2020 Aug 8.

Authors

Katharine Uhteg¹, Karen C Carroll¹, Heba H Mostafa²

Affiliations

¹ Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD 21287-7093, USA.
² Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD 21287-7093, USA. Electronic address: hmostaf2@jhmi.edu.

Abstract

Endemic species of coronavirus (HCoV-OC43, HCoV-229E, HCoV-NL63, and HCoV-HKU1) are frequent causes of upper respiratory tract infections. Three highly pathogenic coronaviruses have been associated with outbreaks and epidemics and have challenged clinical microbiology laboratories to quickly develop assays for diagnosis. Their initial characterization was achieved by molecular methods. With the great advance in metagenomic whole-genome sequencing directly from clinical specimens, diagnosis of novel coronaviruses could be quickly implemented into the workflow of managing cases of pneumonia of unknown cause, which will markedly affect the time of the initial characterization and accelerate the initiation of outbreak control measures.

Keywords: COVID-19; Coronaviruses; MERS; Molecular diagnosis; SARS; SARS-CoV-2 (2019-nCoV); Sequencing.

Publication types

Review

MeSH terms

Clinical Laboratory Services
Communicable Disease Control / methods*
Coronavirus* / classification
Coronavirus* / genetics
Coronavirus* / isolation & purification
Coronavirus* / pathogenicity
Disease Outbreaks / prevention & control*
Humans
Microbiological Techniques / methods*
Respiratory Tract Infections* / epidemiology
Respiratory Tract Infections* / virology
Whole Genome Sequencing