Testing for seasonal influenza viruses and beyond

Sept. 22, 2013

At the time of this report, the Centers for Disease Control and Prevention (CDC) continues to work closely with the World Health Organization (WHO) and other global partners to understand the latest new and emerging infectious disease, the Middle East Respiratory Syndrome (MERS-CoV), which used to be called the “novel coronavirus.” As of August 1, 2013, the WHO had confirmed a total of 94 cases, with 46 fatalities. Most cases have been identified in the Middle East, particularly the kingdom of Saudi Arabia.

MERS-CoV: what we know

To date, the source of MERS-CoV remains poorly understood. The virus does have many characteristics similar to the cluster of severe acute respiratory syndrome (SARS) caused by another coronavirus which emerged in November 2002. While the mortality from SARS was relatively low (approximately 813 deaths) compared to other infectious diseases, its impact in regard to response and global surveillance for new and emerging diseases was profound and resonates today. MERS-CoV and SARS are examples of emerging infectious diseases that have appeared in the population. In both cases, clusters of a severe acute respiratory illness of unknown etiology were the heralding presentation.

The difficulty of managing a non-specific syndrome-like illness such as SARS or MERS-CoV is especially anxiety-provoking when no rapid point-of-care test is available for the pathogen. In our global environment, where a diaspora of people is constantly engaged in international air travel, diseases are unlikely to be contained geographically. SARS has taught us that the capacity to identify all types of potential pathogens in a timely fashion, which includes sequencing and the rapid development of diagnostic testing, is one important aspect of the response and control of emerging and new infectious diseases.

 It is anticipated that diagnostic labs will soon have available a test for MERS-CoV. On June 5, 2013, the FDA issued an Emergency Use Authorization (EUA) for the CDC Novel Coronavirus 2012 Real-time PCR Assay. This test is for the presumptive detection of MERS-CoV in patients. With signs and symptoms of MERS-CoV infection in conjunction with clinical and epidemiological risk factors, this device will be distributed by CDC only to qualified laboratories.

2013 H7N9 influenza

Earlier this year, an outbreak of human infections with a new avian influenza A (H7N9) virus was first reported in China by the WHO. The virus was detected in poultry in China as well. During the outbreak, which was centered in Shanghai, more than 130 human infections with H7N9 were reported and 43 people died. Many of the people infected with H7N9 reported contact with poultry. No evidence of sustained person-to-person spread of the H7N9 virus was found. CDC has issued guidance for isolating, testing, and treating such patients. However, since this virus does not seem to be spreading easily from person to person, a few cases in the United States with travel links to China would not change the risk of infection for the general public in the United States. No cases of H7N9 outside of China have been reported, and the new H7N9 virus has not been detected in people or birds in the United States. Most concerning is the pandemic potential of this virus.

There are currently no readily available tests that can quickly detect and distinguish between the H7N9 virus and other flu viruses. However, a sophisticated test that specifically detects H7N9 virus has been developed by CDC for use by qualified public health laboratories in the United States and internationally. This test involves collecting a respiratory tract (i.e., nose, throat, and lung) sample from a sick patient. The sample is then sent to a public health laboratory where rRT-PCR (real-time reverse transcriptase polymerase chain reaction) is conducted. This procedure typically provides results within four hours of receipt of specimen.

Emerging testing strategies

Influenza virus testing remains the most common respiratory virus test requested by clinicians. In part, this is driven by estimates that 10% to 20% of the U.S. population is infected each year. (Approximately 50% 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 to be tested, including those who are candidates for treatment with antivirals (osetamivir or zanamir). These include but are not limited to the following groups: 1) patients who will be hospitalized; 2) children less than 2 years old; 3) adults older than 65 years; 4) pregnant women; 5) patients with underlying medical conditions that place them at high risk for severe flu-like complications. There are turnaround time 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.

Cleveland Clinic Clinical Virology Laboratories have adopted several strategies to keep up with the demands of clinicians.

The major platform the Cleveland Clinic laboratory employs for centralized testing clinical specimens for influenza and respiratory syncytial virus is rRT-PCR as a 3-plexed PCR test. There are significant advantages to rRT-PCR: it is very accurate and sensitive at detecting flu viruses; it has a turnaround time of six hours (from receipt of specimen); and it enables a lab to run hundreds of specimens a day during flu season in four runs. However, the importance of collecting an appropriate specimen in an appropriate way cannot be overstated. In obtaining a nasopharyngeal swab for testing for influenza, the nasal passage should be clear of mucus, the swab should be inserted until resistance is met, and it should then be rotated two or three times to obtain mucosal cells.

The clinical lab also provides platforms to test for additional various respiratory viruses: para-influenza 1, 2, 3; adenovirus and hMPV by DFA; together with the 3-plexed rtPCR as the combo panel test. This respiratory panel is targeted for immunocompromised patients (e.g., solid organ transplant or bone marrow transplant patients). In 2013-14 Cleveland Clinic will offer the newly FDA approved RVP test, which is a PCR test for the detection of an expanded panel of 12 respiratory viruses for hospitalized and immunocompromised patients.

Decentralized testing for influenza and RSV is also utilized for the Emergency Departments and outpatient clinics. Currently, several rapid FluA/FluB tests with high sensitivity and specificity can be performed as point-of-care testing in the outpatient setting. The lab evaluated two rapid FluA/FluB tests which provided results in 15 to 20 minutes. Both rapid tests demonstrated >80% to 87% sensitivity and 95% to 97% specificity. All negative point-of-care samples are transported to the main hospital laboratory and confirmed with a real-time PCR test.

The lab has many platforms available to provide the correct test, which is determined by volume, clinical situation, and suspected pathogens. With a volume in the tens of thousands of tests per year, throughput is a major consideration. The lab has embraced value-based testing and is actively assessing opportunities to improve services and reduce cost. Clinicians, administrators, and information technology and laboratory personnel have been included in a Test Utilization Committee to identify opportunities and challenges.

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, is Chair of the Infectious Disease Department at the Cleveland Clinic. He has worked in the Hospital Infections Program at the Centers for Disease Control and Prevention and served as president of the Society for Healthcare Epidemiology of America. Belinda Yen-Lieberman, PhD, is medical director of Clinical and Molecular Virology at the Cleveland Clinic.

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