New Tests Detect Novel Coronavirus and Influenza in a Single Sample

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As influenza (flu) season nears and COVID-19 continues to spread in many parts of the United States, the Food and Drug Administration (FDA) has authorized new molecular-based tests that use a single sample and can distinguish between influenza, SARS-CoV-2 (the virus that causes COVID-19), and other respiratory pathogens.

COVID-19, influenza, and other common respiratory infections can cause similar symptoms early on. They include fever, chills, cough, difficulty breathing, fatigue, body aches, headache, sore throat, runny nose, nausea, vomiting, and diarrhea. Testing is the only way to correctly identify the pathogens causing these symptoms.

Both influenza and COVID-19 can cause illnesses that range from mild to severe, and in some cases, can lead to death. Although these infections can affect all ages, the very young, the elderly, and people with weakened immune systems, chronic kidney disease, lung disease, cancer or obesity are at particular risk of severe disease. Also at risk of infection are people in close contact with one another or in confined spaces, such as hospitals, nursing homes, schools, and military facilities.

The ability to test for multiple respiratory pathogens from a single sample means less discomfort for the patient compared to collecting a separate sample for each test. Testing a single sample for multiple pathogens also uses fewer resources as compared to running several individual tests on multiple samples to detect different pathogens.

“If there is COVID-19 and flu activity at the same time, this could place a tremendous burden on the healthcare system related to bed occupancy, laboratory testing needs, personal protective equipment and healthcare worker safety,” Centers for Disease Control and Prevention (CDC) Director Robert Redfield said in prepared remarks to a House of Representatives committee in June. Many lab supplies—such as swabs and reagents (the chemicals needed to run tests)—have often been in short supply during the COVID-19 pandemic.

“With just one swab or sample, combination tests can be used to get answers to Americans faster. This efficiency can go a long way to providing timely information for those sick with an unknown respiratory ailment,” FDA Commissioner Stephen M. Hahn, M.D. said in a press release.

The Tests
As of August 18, 2020, the FDA has granted emergency use authorization (EUA) to combination tests manufactured by the CDC and two commercial companies. All three tests detect genetic material from infectious pathogens, and the preferred sample is a swab of the back of the nose (nasopharyngeal or NP swab). Additionally, the CDC test can use other respiratory samples, such as nasal and throat swabs.

The CDC’s test detects two types of influenza viruses—influenza A and B—and differentiates them from SARS-CoV-2, the virus that causes COVID-19. The CDC’s test is intended for state and local public health labs and takes four hours to perform.

The combination tests developed by the two commercial manufacturers detect numerous respiratory pathogens. In addition to SARS-CoV-2, influenza B and three distinct strains of the influenza A virus, the tests detect four other coronaviruses, human metapneumovirus, human rhinovirus/enterovirus, parainfluenza virus and respiratory syncytial virus (RSV). Besides viruses, these tests can also identify a few types of bacteria that cause respiratory illnesses, such as Bordetella pertussis, which causes whooping cough, Chlamydia pneumoniae, and Mycoplasma pneumoniae. These commercial tests take about one hour to complete.

Although the FDA has granted EUA for these combination tests, they may not be immediately available for patients in all areas. Before offering the new combination tests or other existing influenza and COVID-19 tests, labs must consider several factors. Their decisions may be influenced by local prevalence of influenza and COVID-19, availability of reagents and other supplies needed to run specific tests, their turnaround times, and whether lab staff has appropriate expertise.

Likewise, healthcare professionals also take several considerations into account when choosing testing for their patients. Not everyone with symptoms of a respiratory infection is tested with a comprehensive panel. Healthcare practitioners consider how quickly they need a diagnosis, whether an individual test is more appropriate based on signs and symptoms and medical history, and whether specific treatment is available.

Some healthcare practitioners or health facilities may reserve the new combination tests for people who need a quick diagnosis and appropriate treatment because they are seriously ill and/or hospitalized, have an increased risk for a severe infection with complications, have multiple infections, compromised immune systems, or other pre-existing chronic diseases. (For additional details, read the Respiratory Pathogens Panel article.)

View Sources

Press release. Coronavirus (COVID-19) Update: FDA Authorizes Additional COVID-19 Combination Diagnostic Test Ahead of Flu Season. Food and Drug Administration. Available online at Released July 2, 2020. Accessed August 10, 2020.

Centers for Disease Control and Prevention. CDC’s Diagnostic Multiplex Assay for Flu and COVID-19 and Supplies. Available online at Updated August 2, 2020. Accessed August 10, 2020.

U.S. Centers for Disease Control and Prevention. Table 4. Multiplex Assays Authorized for Simultaneous Detection of Influenza Viruses and SARS-CoV-2 by FDA Emergency Use Authorization. Available online at Page last reviewed August 6, 2020. Accessed August 10, 2020.

News story. CDC Gets FDA Nod for Coronavirus-Flu combination Diagnostic. MedTech Dive. Available online at Published July 6, 2020. Accessed August 10, 2020.

(September 1, 2020) Deborah Levenson. Flu Season and COVID-19 Pandemic Require Complicated Decisions About Test Choices, Algorithms, and Utilization. Clinical Laboratory News. Accessed September 2020.

Transcript. June 23, 2020 Hearing on Oversight of the Trump Administration’s Response to the COVID-19 Pandemic. Available at Accessed August 12, 2020.

(May 1, 2020) Fact Sheet for Healthcare Providers. BioFire® Respiratory Panel 2.1 (RP2.1). Available online at Accessed August 18, 2020.

© QIAGEN 2020. QIAstat-Dx Respiratory SARS-CoV-2 Panel. Available online at Accessed August 18, 2020.