Update on laboratory testing of respiratory viruses with a focus on influenza

Aug. 24, 2016

Influenza virus testing remains the most common respiratory virus test requested by clinicians. In part, this is driven by estimates that 10 percent to 20 percent of the U.S. population is infected each year, of whom 50 percent are symptomatic. Not all patients need to be tested for influenza, as for most people, convalescing at home is the best treatment. However, there are patients who should be considered for testing, including those who are candidates for treatment with antivirals. These include but are not limited to the following groups: 1) patients who will be hospitalized; 2) children less than two years old; 3) adults older than 65 years; 4) pregnant women; and 5) patients with underlying medical conditions that place them at high risk for severe flu-like complications. CDC also recommends that patients suspected of having influenza who are at high risk of flu complications or who are very sick with flu-like illness should receive prompt treatment with influenza antiviral drugs without waiting for confirmatory testing.

Key points for clinicians are:

  • The emergence of variant strains and international travel has made influenza a year-round illness.
  • Influenza should be considered in patients with fever, cough, and myalgia (muscle pain).
    Exposure history is important, and patients should be asked about whether they have had for example, swine and/or bird exposure.
  • There are turnaround time (TAT) pressures for testing in these patients, in part because treatment is most effective when initiated within 48 hours of onset of symptoms, and hospitalized patients are placed in droplet isolation or contact precautions until influenza and respiratory syncytial virus (RSV) are ruled out.

Lab testing of respiratory viruses: what’s new

Since the authors published a previous review in MLO three years ago (“Testing for seasonal influenza viruses and beyond.” MLO. 2013;45(9)30-33), significant changes in clinical laboratory respiratory virus testing and reporting have emerged. Cleveland Clinic Clinical Virology Laboratories have adopted several strategies to keep up with the demands of clinicians.

During the last two years, laboratory testing for flu A, flu B, and RSV have gradually evolved from a batch testing format to random access rapid molecular testing. Since molecular tests have higher sensitivity and specificity when compared with the lateral flow rapid EIA tests, many laboratories are starting to adopt rapid molecular flu/RSV tests. These tests are gradually decentralized to the ED and the outpatient clinics.

Clinicians now request faster TAT for respiratory virus test results; a two hour TAT for results from Emergency Departments and intensive care units is desired. Recently patient-centered testing and reporting have become the standard practice in many clinics and hospitals. This has led to improved patient care, reduced TAT, and reduced bed utilization and overall cost saving.

In 2015, FDA approved the first molecular point-of-care test (POCT) for flu A/flu B—Alere’s i FluA and FluB Test. Later, the POCT Group A Strep test was also approved. These two tests were also approved as CLIA-waived tests. Since then, Roche’s Liat FluA/FluB and Liat Group A Strep were FDA approved and CLIA waived. These molecular POCTs take 15 to 20 minutes to complete and require no confirmatory test to follow. Patients and doctors can now have the results in 15 to 20 minutes instead of a few hours. Several studies evaluating these POCT molecular tests in ED and/or outpatient clinics have shown that these rapid molecular tests improve patient care, improve patient and doctor satisfaction, reduce unnecessary antibiotic usage, and produce cost saving.

The molecular POCTs can be performed in the outpatient clinic, the ED, and in a physician’s office. The tests do not require expensive instruments with annual service contracts. Less sample size and fewer reagents are needed, and no special training to perform the tests and QA/QC is required.

Strategies adopted to meet the demand

The 2015-2016 influenza season was less severe overall. The A(H1N1) virus was the predominant respiratory virus, but influenza A (H3N2) and influenza B viruses were also circulated. The season peaked around mid-March 2016. Testing for seasonal viruses is still continued throughout the year.

Nucleic acid test (NAT) panels are extensively used to detect and identify respiratory viral infections. The Cleveland Clinic Laboratory continues to offer flu A/flu B/RSV test (ProFlu+) for outpatients and the respiratory virus panel (RVP) test for hospitalized and immunocompromised patients year round. Several other multiplex respiratory virus tests, also known as “syndromic “tests, are FDA cleared for patient care. A symptom-driven approach on patient care and testing can reduce the time to make a comprehensive diagnosis, which can improve patient care and lower healthcare cost. In the era of better test utilization, this fits the credo: offer the right test, for the right patient, at the right time. Laboratory testing is valuable when its use is supported by clinicians, and it’s most effective when it’s decentralized and patient-centered.

In 2015, we evaluated the impact of rapid diagnosis of RVP tests on clinical management and outcome of patients during a five-month period (Dec 1, 2014 – April 30, 2014). A total of 2,073 tests were performed, with 777 (37 percent) positive for one or more viruses. Fifty-six (7.2 percent) of those 777 were from patients with two or more positive viruses. The most commonly detected virus was rhinovirus. Review of the medical history of patients with two or more co-infected respiratory viruses resulted in a change in clinical management in 20 percent (n=11) of patients, but antibiotics were continued in 38 percent of patients. In a total of 35 patients (63 percent), co-detection of respiratory viruses was beneficial in appropriately altering management or in reinforcing clinical suspicion and treatment of a viral etiology.

Vaccine: prevention is the cure

The best way to prevent the flu is with a flu vaccine. The Centers for Disease Control and Prevention (CDC) recommends that everyone six months of age and older get a seasonal flu vaccine each year soon after it becomes available, and by October if possible. Vaccination is especially important for people 65 years and older because they are at high risk for complications from flu. Flu vaccines are often updated to keep up with changing viruses, and immunity wanes over a year, so annual vaccination is needed to ensure the best possible protection.

Trivalent vaccines for use in the 2016-2017 influenza season (Northern Hemisphere winter) contain the following:

  • A/California/7/2009 (H1N1) pdm09-like virus
  • A/Hong Kong/4801/2014 (H3N2)-like virus
  • B/Brisbane/60/2008-like virus (B/Victoria lineage).

Quadrivalent vaccines containing two influenza B viruses contain the above three viruses and a B/Phuket/3073/2013-like virus (B/Yamagata lineage).

The vaccine viruses recommended for inclusion in the 2016-2017 Northern Hemisphere influenza vaccines are the same vaccine viruses that were chosen for inclusion in 2016 Southern Hemisphere seasonal flu vaccines.

The menu of influenza vaccines available continues to expand. People 65 years and older have two flu shots available to choose from, a regular dose flu vaccine and a newer flu vaccine designed specifically for people 65 and older with a higher dose. The “high dose vaccine” contains four times the amount of antigen as the regular flu shot and is associated with a stronger immune response following vaccination (higher antibody production).

Of note, on June 22, 2016, the Advisory Committee on Immunization Practices (ACIP) released a statement that live-attenuated vaccine (LAIV), or Flumist, should not be used for the upcoming flu season. This decision was made due to a lack of effectiveness in the previous seasons.

A new influenza product was approved by the U.S. Food and Drug Administration (FDA) in May 2016, The product is Flucelvax Quadrivalent from Seqirus. It is manufactured using cell culture technology and is egg-free, antibiotic-free, preservative/thimerosal-free, and latex-free. It is approved for ages >4 years.


Clinical laboratories need to be flexible and prepared to manage the demands of providing testing for viral pathogens during respiratory seasons. In addition, all clinical testing laboratories should be knowledgeable in handling any samples from patients suspected with potential exposure to newly reported respiratory viruses such as H7N9, MERS-CoV, and recurrence of the Swine Influenza A virus (H3N2v).

Steven M. Gordon, MD, serves as Chair of the Infectious Disease Department at the Cleveland Clinic. He has worked in the Hospital Infections Program at the CDC and has served as president of the Society for Healthcare Epidemiology of America.

Belinda Yen-Lieberman, PhD, is Contract Staff on Clinical and Molecular Virology in Pediatric Institute. She is formerly the medical director of Clinical and Molecular Virology in Laboratory Medicine at the Cleveland Clinic.