Laboratory guidance for respiratory viruses

Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections. Charlton CL, Babady E, Ginocchio CC, Hatchette TF, Jerris RC, Li Y*, Loeffelholz M, McCarter YS, Miller MB, Novak-Weekley S, Schuetz AN, Tang Y, Widen R, Drews SJ. Clin Microbiol Rev 2018 Dec 12; 32(1):e00042-18. doi: https://doi.org/10.1128/CMR.00042-18


This science story discusses the development of a guidance document for clinical microbiology laboratories regarding their investigation of viruses that cause acute respiratory tract infections (ARIs). ARIs are among the most common infections reported in Canada and worldwide. Guidance on how to best address these highly infectious pathogens (e.g., how to collect and test infectious disease specimens) contributes to a consistent approach across the global public health laboratory community that can help address these public health priority pathogens.

What was known about this area prior to your work, and why was the research done?

In the World Health Organization’s 2013 global disease burden study, respiratory infections were listed as the leading cause of infectious disease worldwide and the most common reason that people seek medical care in the United States of America. Until now, the latest guidance document to address respiratory virus testing was published in 1986 (Cumitech 21, Laboratory Diagnosis of Viral Respiratory Disease). Since that time, the practice of clinical microbiology and the landscape of respiratory virus testing has changed significantly. Most notably, the development of new molecular approaches are increasingly replacing traditional methods for testing and diagnosis of respiratory viruses. Also, the continual emergence of new respiratory pathogens poses challenges as laboratorians are required to understand the limitations of primary laboratory tests, and recognize when to refer samples to more specialised reference laboratories for analysis. This new guidance document outlines consistent and standard steps and actions for public health laboratorians/laboratories to take when dealing with samples of these pathogens.

What are your most significant findings from this work?

This consensus-based document provides up-to-date guidance to a rapidly changing field of diagnostics. It outlines: the epidemiology and clinical impact of acute respiratory viral infections; step-wise instructions including preferred methods of specimen collection; and recommended methods for diagnosis and characterisation of viral pathogens causing ARIs. The guidance document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. It also notes the importance of aligning processes across public health laboratories to enable consistent virus characterisation and antiviral resistance testing.

What are the implications or impact of the research?

Respiratory viruses are a global problem with varied temporal and geographic patterns of circulation. Laboratorians and clinicians need to be able to identify and differentiate samples as precisely as possible to best understand progression, transmission, and risks to populations. Multiple viruses can cause similar symptoms when infecting the upper or lower respiratory tract, and this is important to identify as it can limit clinical diagnosis. Clear guidance, as found in this document, can help enable appropriate specimen collection and correct test ordering to quickly identify these highly transmissible pathogens. Further, timely and accurate identification of these pathogens can help generate the evidence needed to inform public health intervention and prevention strategies.

Additional References of Significance:

  • US Centers for Disease Control and Prevention. 14 September 2017. Interim guidelines for collecting, handling, and testing clinical specimens from patients under investigation (PUIs) for Middle East respiratory syndrome coronavirus (MERS-CoV)—version 2.1. https://www.cdc.gov/coronavirus/mers/guidelines-clinical-specimens.html
  • US Centers for Disease Control and Prevention. 8 May 2018. Interim guidance on testing, specimen collection, and processing for patients with suspected infection with novel influenza A viruses with the potential to cause severe disease in humans. https://www.cdc.gov/flu/avianflu/severe-potential.htm



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