Is Your Laboratory Following the Best Practices for Respiratory Virus Testing?
Background
The Academy of Diagnostics & Laboratory Medicine (ADLM) published a Guidance Document on Laboratory Diagnosis of Respiratory Virus testing in May 2024. The guidance document provides expert opinion related to laboratory diagnosis of respiratory viral infections as to who to test, specimens to test, and what tests to use. As we enter the Fall and Winter respiratory viral infection season, this blog will summarize those key elements from this guidance document.
Introduction1
The common respiratory viruses causing infection are rhinoviruses, enteroviruses, influenza viruses, SARS-CoV-2 (COVID), other coronaviruses, respiratory syncytial virus (RSV), parainfluenza viruses, adenoviruses, and human metapneumovirus. Respiratory infections caused by viruses are among the most common reasons for healthcare visits.
Signs and symptoms of respiratory illness, whether caused by bacteria or viruses, are similar and span presentations from the common cold to bronchitis to severe pneumonia. Certain populations such as pediatrics, the elderly, and those patients with underlying disease, are susceptible to developing severe respiratory disease and identification of the causative agent may be warranted.
Rapid identification of the causative agent impacts the therapeutic and prognostic evaluation of the illness. Most people will recover from a respiratory illness without obtaining a laboratory diagnosis or treatment. However, in the populations where severe illness could develop, laboratory diagnosis may be necessary and targeted therapy may be required.
Sample Types1
Sample types are dictated by the specific assay that the laboratory uses. Each assay provides an Instructions for Use (IFU) document that dictates the sample type requirements. Common sample types for respiratory viral testing are nasal swabs, throat swabs, nasopharyngeal swabs, and bronchoalveolar lavage fluids.
Current Test Methodologies1
Viral target detection is accomplished by these methodologies:
Viral Culture
Viral Culture testing was the only methodology in use until antigen and nucleic acid amplification assays became available. Viral culture testing requires specialized laboratory facilities. Many respiratory viruses are difficult to isolate and may be slow growing such that the turnaround time to a result could be as long as 14 days which limits the clinical usefulness of the test. Most U.S. laboratories have replaced viral culture with newer methodologies.
Lateral flow immunoassay
Lateral flow immunoassay tests provide rapid results using immunochromatographic methods and visual interpretation of the result. These assays have rapid turnaround time, are inexpensive, are readily available over the counter, and do not require an instrument. However, they have lower sensitivity and may have limited viral targets that are available. The regulatory status of assays are classified as CLIA-waived, Point-of-Care or a home test.
Direct fluorescent antibody
Direct fluorescent antibody assays have multiple steps, can be performed manually or by an instrument, and some can test for multiple infectious targets at the same time. However, these assays require trained staff and provide a moderate level of sensitivity. The regulatory status of these assays is Moderate Complex or Highly Complex.
Nucleic Acid Amplification Tests
(NAAT) assays provide the highest level of sensitivity and can be multiplexed to detect multiple targets at once. However, some of these assays are considered to be expensive. Assays are available for multiple testing environments such as home testing, point-of-care testing, or testing in a highly skilled laboratory. The regulatory status of assays ranges from CLIA-waived to Highly Complex and every level in between. NAATs are recognized as the “Gold Standard” for the diagnosis of respiratory viruses as they are easily modified to detect new strains or mutations. Several methodologies are available to detect viral nucleic acids:
- LAMP: Loop-mediated isothermal amplification
- TMA: Transcription-mediated amplification
- RT-PCR: Real time polymerase chain reaction
NAATs are extremely sensitive to detect the presence of viral nucleic acids; however, the presence of nucleic acids in the absence of signs and symptoms could be residual RNA or DNA from a past infection.
Population Testing1
Pediatrics:
Testing is more clearly demonstrated in children who are hospitalized or have an underlying health condition so that treatment decisions can be determined. Healthy children in an outpatient setting should only be tested if the test results are used by the clinician for clinical decision making.
Aging Population or Immunocompromised Patients:
In the aging population and in immunocompromised patients, respiratory viral infections lead to significant morbidity and mortality underscoring the need for rapid testing to influence patient management. Influenza, RSV, and recently SARS-CoV-2 are all major causes of morbidity and mortality in the elderly and immunocompromised populations. In some studies, for oncology patients diagnosed with influenza, parainfluenza, RSV and adenovirus, antivirals when available and administered early have been shown to improve outcomes. Therefore, testing for influenza, RSV, parainfluenza, and other prevalent community-circulating viruses in all symptomatic patients with malignancies is recommended since these results may be used to guide antiviral treatment decisions. Similarly, transplant recipients may also be an appropriate patient population for multiplex testing.
Inpatient setting:
The clinical utility of testing for viral respiratory pathogens is important for guiding treatment and infection control decisions. It is also clear from the literature that cases of respiratory infections are underestimated. One study looking at a period from 2003 to 2014 found that a quarter of influenza-attributable hospitalizations did not have a definitive acute respiratory infection diagnosis. Another study performed in the United States estimated that only 1 in 10 influenza-associated critical illnesses in intensive care unit patients included a formal diagnosis of influenza.
Outpatient setting:
In the outpatient setting, viruses are the most common pathogens identified in severe cases of community-acquired respiratory infections. It is also clear that in the outpatient population, the burden of respiratory viral infection is also significantly underestimated. The CDC published testing guidance for when SARS-CoV-2 and influenza viruses are co-circulating. In cases where a patient presents to the outpatient clinic or the ED with symptoms of acute respiratory illness that require hospitalization, the recommendation is to minimally test for influenza A, influenza B, and SARS-CoV-2. If the patient does not require hospitalization, the recommendation is to test for SARS-CoV-2 and influenza if the result will have an impact on clinical management or infection control. In immunocompetent adult patients, RSV causes a mild illness that often resolves within 5 days. For patients presenting in an outpatient setting with more severe diseases or with underlying chronic infections, testing for RSV may be warranted, similar to recommendations for immunocompromised patients.
Diagnostic Stewardship1
Diagnostic stewardship aims to select the right test for the right patient at the right time to generate accurate and clinically relevant results to guide appropriate clinical behavior and prevent overutilization of resources such as antibiotics. Clinician education that includes guidance in the form of algorithms can be useful tools to help with stewardship.
Conclusion1
The recent COVID-19 pandemic and prior to that the 2009 H1N1 influenza pandemic highlight the need for laboratories to be alert and prepared for the diagnosis of emerging respiratory infections. It is important for laboratories to monitor patterns of detection of respiratory pathogens targeted by current methods for unusual results that may suggest an emerging or changing viral environment. Additionally, new therapies including the recent FDA-approved Pfizer RSV vaccine (ABRYSVO™) for older adults and pregnant individuals will likely impact the epidemiology of RSV in the future. As antiviral therapeutic options eventually expand beyond influenza and RSV, the need for rapid testing will expand and recommendations for testing will need to be revised accordingly.
DTPM Solutions
DTPM’s mission is to provide solutions to help your laboratory improve efficiency and reduce costs so that your team can focus on what matters most.
The DTPM COVID-19 RT-PCR Test kit is authorized for use under Emergency Use Authorization1 for the detection of the SARS-CoV-2 virus in upper respiratory samples2.
DTPM offers an expanding portfolio of more than 130 molecular assays3 in addition to laboratory consumables which support your laboratory’s entire workflow including:
- DNA/RNA Purification Kits
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Contact us today to learn how DTPM can help your laboratory achieve successful and efficient operations.
1 The DTPM COVID-19 RT-PCR Test is Authorized for Use under Emergency Use Authorization (EUA). https://www.fda.gov/media/168321/download For Research Use Only.
2 Nasopharyngeal swab, oropharyngeal swab, anterior nasal swab, mid-turbinate nasal swab, nasal aspirate, and nasal wash specimens collected from individuals suspected of COVID-19 by their healthcare provider.
3 For Research Use Only. Not for use in diagnostic procedures.
