Authoritative guidance on respiratory virus testing

Coming off a tough winter for respiratory viruses, with high rates of flu, SARS-CoV-2, and respiratory syncytial virus (RSV), it might seem particularly timely that the Association for Diagnostics & Laboratory Medicine (ADLM, formerly AACC) released its first guidance document on laboratory diagnosis of respiratory viruses (J Appl Lab Med 2024; doi: 10.1093/jalm/jfae010).

But the idea for the work dates back a couple of years, the authors said. Respiratory testing “was a particularly hot topic after the COVID-19 pandemic,” said coauthor Heba Mostafa, MBBCh, PhD, director of the molecular virology laboratory at The Johns Hopkins Hospital in Baltimore. Additionally, she said, there is increasing diversity in testing modalities and types of samples used, along with some confusion about the clinical utility of testing for a broader range of molecular targets. “It was time to take a dive into the literature and what is known … and form a guideline.”

Testing had been evolving even before the pandemic, said coauthor Esther Babady, PhD, D(ABMM), FIDSA, FAAM, chief of the clinical microbiology service at Memorial Sloan Kettering Cancer Center in New York City. “But as you can imagine, with COVID, that really was accelerated” to include at-home testing for the first time, she said.

As the methodology became more simple and some tests became CLIA-waived, point-of-care tests for viruses such as SARS-CoV-2 could be offered in expanded settings like physician offices and emergency rooms. “There are so many more people that not only have access to the tests but are in charge of selecting which tests to use for different indications,” Babady said. “We thought this was a great opportunity … to share our clinical microbiology expertise.”

The guidance, compiled by clinical microbiologists and infectious disease clinicians, covers everything from which tests should be used to detect respiratory viruses, to the sample types and methods used for detection of these viruses, to how test results should be interpreted and who should be tested in the first place. Extensive tables list common viral pathogens and their associated clinical syndromes, testing methods for routine detection of respiratory viruses, and examples of molecular respiratory viral testing by level of complexity. A suggested testing algorithm for respiratory viruses can help clinicians determine when and how to test patients for these viruses.

The document should be helpful as a guide “on what people need to order, for which population, and in which clinical settings,” Mostafa said. “However, I’m sure that each practice and each provider will modify their testing based on the population of patients they have, along with other factors like insurance and billing.”

What’s In the Guidance

The document starts with an overview of the most common viruses causing respiratory illness, their signs and symptoms, and complications that can occur. Although healthy, immunocompetent individuals usually recover from acute respiratory infections without the need for laboratory diagnosis or treatment, laboratory testing generally is necessary for immunosuppressed patients and those with underlying conditions in order to implement appropriate, targeted therapy when available, or isolate the patient if necessary, the authors said. The accuracy of clinical diagnosis alone may be limited.

In the testing section, the authors note that nasopharyngeal swabs are the preferred specimen type for upper respiratory infections. When this is not practical, alternatives include nasal or throat swabs, saliva, or bronchoalveolar lavage fluids (for lower respiratory tract infections). Nucleic acid amplification tests (NAATs) are the gold standard for viruses, but when that is not readily available, antigen tests provide a less sensitive alternative. Direct fluorescent antibody assays, serology, and viral culture are not recommended for routine diagnosis.

Specimen collections should match the particular test used for diagnosis, Mostafa emphasized: “We consider nasopharyngeal swabs as the gold standard, but we also started to see nasal specimens collected, and saliva. It’s really important for providers to understand the test requirements and assemble the proper specimen, because this is the key for accurate results.” 

In the interpretation section, authors note that viral load test results should be interpreted in light of clinical symptoms. For example, a positive molecular or antigen test result in someone without symptoms may reflect asymptomatic carriage, presymptomatic infection, or shedding following a resolved infection. Conversely, negative test results in symptomatic patients may be false-negative, and repeat testing is recommended.

The high sensitivity of NAATs “provides a great opportunity to detect infection when it’s there,” Babady said. “However, we also know that you can have a positive molecular NAAT once you’ve resolved the infection, because it’s so sensitive it’s picking up minute amounts of RNA or DNA left by a virus that’s already gone and not replicating. How you interpret that is important. You have to take into consideration when the patient presented and how long they’ve had the infection.”

Laboratory medicine professionals can provide interpretation using data including seasonality, positivity rates, and a patient’s clinical presentation, Mostafa added.

Testing should be performed only if there is a high pretest probability of respiratory viral infection based on clinical presentation and local prevalence, the authors said, and in cases where results will change clinical management. Testing should be limited to children who are hospitalized or who have underlying conditions, as well as aging, ill, and immunocompromised patients. Immunocompetent adults should be tested only if results will impact management, primarily for influenza and SARS-CoV-2.

Diagnostic Stewardship Is Essential

One section is dedicated to diagnostic stewardship. Much like antimicrobial stewardship efforts that advocate for judicious prescribing of antibiotics, diagnostic stewardship aims to select the right test at the right time for the right patient, thereby generating accurate, relevant results to guide clinical management. In this area, the guidance recommends educational material be made available for clinicians to guide respiratory test selection, that electronic health record algorithms help drive appropriate test selection, and that clinicians generally opt for small, multiplexed panels or targeted NAATs unless patients are immunocompromised.

“Better utilization of tests in the correct scenarios is very important, particularly when it comes to a molecular test that can detect multiple targets,” Mostafa says. Individual labs should work with hospital infection control departments to define stewardship and the best clinical utility of tests. “If you’re ordering a test and you’re not planning to use the result for clinical management, you shouldn’t consider ordering the test.” Practices may differ based on location and type, “but the overall rule is the test has to generate a result that will be acted on,” she said.

With a plethora of testing options, it can be tempting “to just test everybody all the time for everything,” Babady added, but patient-centric care is important, as is recognizing there is a limit to payor reimbursement for testing. “The importance here is really to think about what the ultimate goal of the test is going to be.”

Lessons From COVID-19

Since the pandemic, clinicians have learned that testing can be possible in many more types of samples — including at home — and how whole genome sequencing can provide information on different types of viruses present in a clinical sample, Babady said.

“I don’t want to say that there was a good side of the pandemic, because there’s no good side to the pandemic, but the explosion of testing options has been incredible,” she said. “We’ve learned a lot.” Tenets that used to be dogma, such as not using saliva for respiratory virus testing, were dismissed in some SARS-CoV-2 tests, and now laboratorians are considering how it could be used for other types of testing, she said.

Scientific developments, such as CRISPR-based diagnostics and next-generation sequencing, also continue, Mostafa said. “It’s interesting to see the CRISPR modalities making it into diagnostic methods and reaching point-of-care testing and testing modalities,”
she said.

What might the future portend? Things will continue to evolve, Babady said. When the authors began writing the document, for example, the RSV vaccine Abrysvo had not yet been FDA-approved. “As things like that become a reality — not just vaccines but treatments for the viruses that we can detect right now — all of that information is really going to guide how, who, when, and why we should be testing,” Babady said. “It will be interesting to see how all of that evolves and connects with respiratory testing.”

Many testing platforms used for SARS-CoV-2 might eventually expand to other viruses such as influenza and RSV, the authors said. As such, “laboratorians should remain alert and involved to provide guidance on managing testing and the information obtained from a wider range of testing settings.”

Karen Blum is a freelance medical/science writer in Owings Mills, Maryland. +Email: karen_blum@verizon.net