Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections

• Published in: Clinical microbiology reviews 2019-01, Vol.32 (1)
• Main Authors: Charlton, Carmen L, Babady, Esther, Ginocchio, Christine C, Hatchette, Todd F, Jerris, Robert C, Li, Yan, Loeffelholz, Mike, McCarter, Yvette S, Miller, Melissa B, Novak-Weekley, Susan, Schuetz, Audrey N, Tang, Yi-Wei, Widen, Ray, Drews, Steven J
• Format: Article
• Language: English
• Subjects: Acute Disease; Clinical Laboratory Techniques - methods; Clinical Laboratory Techniques - standards; Humans; Microbiological Techniques - methods; Microbiological Techniques - standards; Molecular Diagnostic Techniques - standards; Molecular Diagnostic Techniques - trends; Practical Guidance for Clinical Microbiology; Respiratory Tract Infections - diagnosis; Respiratory Tract Infections - virology; Virology - methods; Virology - standards; Virus Diseases - diagnosis; Virus Diseases - virology
• ISSN: 0893-8512; 1098-6618
• DOI: 10.1128/CMR.00042-18

Respiratory viral infections are associated with a wide range of acute syndromes and infectious disease processes in children and adults worldwide. Many viruses are implicated in these infections, and these viruses are spread largely via respiratory means between humans but also occasionally from animals to humans. This article is an American Society for Microbiology (ASM)-sponsored Practical Guidance for Clinical Microbiology (PGCM) document identifying best practices for diagnosis and characterization of viruses that cause acute respiratory infections and replaces the most recent prior version of the ASM-sponsored Cumitech 21 document, , published in 1986. The scope of the original document was quite broad, with an emphasis on clinical diagnosis of a wide variety of infectious agents and laboratory focus on antigen detection and viral culture. The new PGCM document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. The article provides guidance to a rapidly changing field of diagnostics and outlines the epidemiology and clinical impact of acute respiratory viral infections, including preferred methods of specimen collection and current methods for diagnosis and characterization of viral pathogens causing acute respiratory tract infections. Compared to the case in 1986, molecular techniques are now the preferred diagnostic approaches for the detection of acute respiratory viruses, and they allow for automation, high-throughput workflows, and near-patient testing. These changes require quality assurance programs to prevent laboratory contamination as well as strong preanalytical screening approaches to utilize laboratory resources appropriately. Appropriate guidance from laboratorians to stakeholders will allow for appropriate specimen collection, as well as correct test ordering that will quickly identify highly transmissible emerging pathogens.