Making Sense of Respiratory Viral Panel Results

March 2, 2020

Viral culture, once the gold standard method for detection of respiratory viruses, is slow and labor-intensive and requires specialized expertise, while rapid antigen detection methods are faster but generally suffer from low sensitivity. Multiplex molecular assays, which rely on detection of viral nucleic acids, provide prompt results with high sensitivity and specificity, making them ideal tests when used in the context of a thoughtful clinical evaluation, but their ready availability can sometimes leave clinicians and clinical microbiologists with more information than they know what to do with.

Collecting a nasopharyngeal swab for testing via respiratory viral panel.

What Viruses do PCR-based Panels Detect?

While there is some variation among panels, most multiplex PCR-based respiratory viral panels test for influenza, respiratory syncytial virus (RSV), adenovirus, parainfluenza virus, adenovirus, coronavirus (not that coronavirus–see below), rhinovirus, enterovirus, and human metapneumovirus; some also include bocavirus and offer subtyping of influenza, parainfluenza, RSV, and coronavirus. (Of note, most panels cannot distinguish between rhinovirus and enterovirus.)

The “respiratory viral panel” (RVP) offered by a given hospital or clinic lab may refer to one of a number of different tests. The focus of this article is on commercial multiplex systems, in which a company produces both a testing platform and the associated consumables (cartridges to which the patient sample, usually a nasopharyngeal swab, is added), but some labs offer PCR-based tests that they have developed and validated in-house, known as laboratory-developed tests (LDTs). The LDT tests or test panels offered by a hospital laboratory are unlikely to be as extensive or comprehensive as the panels provided with commercial platforms and usually include a more limited list of pathogens – for example, influenza, RSV, and adenovirus.

How Long Does a Test Remain Positive after Infection?

The high sensitivity of RVPs is one of their main advantages, but it also means that tests may remain positive when the presence of virus is no longer clinically relevant (or may be positive in the complete absence of symptoms; see below). Viral shedding can continue after resolution of symptoms in respiratory infections; shedding for up to a week following symptom onset is not uncommon in influenza, for example. In children and immunocompromised people, shedding of respiratory viruses can last for weeks or longer. It is also important to note that RVPs detect nucleic acid from respiratory viruses, but the presence of nucleic acid does not necessarily imply the presence of viable virus–it may simply be “leftover” genetic material from a recent infection.

What is the Clinical Significance of Respiratory Viral Panel Results?

It is essential that RVP results be interpreted carefully in clinical context. This is true of every diagnostic test, of course, but this is a particularly pronounced issue in multiplex testing, where a clinician may have been concerned primarily with only a few of the viruses on the panel but still has to interpret results for all of them. Here are a few key considerations:
  • Not all positive results indicate current active infection. Indeed, a study of 108 adults and children who underwent weekly RVP testing for a year found that approximately half of all viral detection episodes were asymptomatic. Asymptomatic episodes were especially common for bocavirus and rhinovirus, so a clinical judgement must be made about whether the virus detected is causing the patient’s symptoms or whether the symptoms are incidentally occurring during a period of asymptomatic viral detection.
  • The likelihood of at least one false positive is inevitably increased in multiplex panels with many targets, despite the fact that the false positive rate for most individual viruses on RVPs is low.
  • Even a positive result that is indicative of a current active infection does not rule out the possibility of another concomitant infection or superinfection; influenza, in particular, is notorious for predisposing patients to severe bacterial pneumonia superinfection. Thus, while one of the major benefits of RVPs is the ability to limit unnecessary antibacterial therapy by identifying viral causes for respiratory illness, it is always important to consider whether the virus identified explains the patient’s entire clinical picture. This is also an important consideration for severely immunocompromised patients, who may have more than one simultaneous active infectious process.
  • RVPs do not test for every viral cause of respiratory tract infections, despite their extensive testing breadth; in nearly half of the symptomatic respiratory illness episodes reported in the year-long study described above, no virus was detected. Furthermore, false-negative results are possible with any test, and are more likely for RVPs if suboptimal sampling procedures are performed. If a patient has a negative RVP in the setting of what clearly appears to be viral respiratory infection, there’s probably a virus in there somewhere. If suspicion for a particular virus is high and results would influence management, then testing for that virus, by targeted PCR or another method such as viral culture, may be helpful. 
Transmission electron micrograph of two Adenovirus particles.

How can RVP Results Guide Patient Care?

Uncertainty remains about the utility of multiplex RVPs for otherwise healthy patients. Most results on a full RVP are unlikely to affect management in this population, so targeted testing (e.g. for influenza alone) may be preferable, although there is evidence that positive RVP results can help to reduce hospital admissions and unnecessary or prolonged antibiotic courses. (For immunocompromised patients, a full RVP is more likely to influence management.) In practice, most laboratories have a limited number of options for molecular viral respiratory testing, so clinicians may end up having to interpret the results of a full RVP even if they were only interested in testing for 1 or 2 of the viruses. Following are clinical considerations for some of the viruses on these panels; the clinical microbiology laboratory is also a valuable resource for clinicians seeking guidance on test interpretation.
  • Influenza: Influenza is the respiratory virus for which a positive test result is most likely to prompt an intervention, because of the severity of disease it can cause and because antiviral treatment is available; antiviral prophylaxis is also sometimes indicated for contacts of a person diagnosed with influenza. The CDC and IDSA have excellent resources to help clinicians decide which patients should be tested for influenza.
  • RSV: RSV can cause upper and lower respiratory tract disease in people of all ages, but its most characteristic manifestation is bronchiolitis, or inflammation of the small distal airways, in infants, especially those born prematurely, sometimes requiring hospitalization. The diagnosis of RSV is also important for infection control purposes in hospitalized patients and can play a role in assessing the likelihood of serious bacterial infection in febrile neonates.
  • Adenovirus: Respiratory tract infections are the most common manifestation of adenovirus infection, and may be severe. In the immunocompromised population, diagnosis is important in part because antiviral treatment with cidofovir is sometimes used. Antiviral treatment is rarely employed for immunologically normal hosts, but identification of adenovirus can still be useful in some circumstances in this population, for example in a child with fevers of unclear etiology who may be spared further diagnostic workup and empiric antibiotics once a diagnosis of adenovirus infection is made.
  • Other viruses: Most of the other viruses included in RVPs are useful primarily for hospitalized patients and people with immunocompromising conditions. For these populations, identification of a virus as a likely cause of respiratory tract symptoms and fever may support a decision to stop unnecessary antibiotics, a major goal of antimicrobial stewardship programs (although, as discussed above, the presence of a virus does not automatically rule out the possibility of other concomitant infections). On the other hand, some viruses on the panel that generally cause mild and self-limited disease in otherwise healthy hosts can be serious and prolonged in severely immunocompromised patients, and identification of one of these viruses may be an indication for interventions such as delaying a planned surgical procedure or reduction of immunosuppression. 

My Patient’s Panel is Positive for Coronavirus. Should I Panic?

No. The coronaviruses detected by commercial RVPs are common circulating strains that generally cause self-limited disease; these tests do not cross-react with SARS-CoV-2, the novel coronavirus first identified in late 2019 that causes COVID-19 disease. Molecular testing for SARS-CoV-2 is currently available at the CDC and is expected to be available soon at some state laboratories.

The above represent the views of the author and does not necessarily reflect the opinion of the American Society for Microbiology.

Author: Thea Brennan-Krohn

Thea Brennan-Krohn
Thea Brennan-Krohn is a diplomate of the American Board of Medical Microbiology at Beth Israel Deaconess Medical Center (BIDMC). She is an attending in Pediatric Infectious Diseases at Boston Children's Hospital and a postdoctoral fellow at Beth Israel Deaconess Medical Center,