Emerging Concepts in the Diagnosis of Respiratory Viruses

1. Emerging Concepts in the Diagnosis of Respiratory Viruses Short Presentation on Emerging Concept (SPEC)

2. Respiratory Viral Infections • Respiratory infections account for ~4 million deaths per year, about half of which are due to viruses • Common viruses can cause serious respiratory infections • New viruses are also being identified • Metapneumovirus (MPV) • Severe acute respiratory syndrome coronavirus (SARS-CoV) • Avian influenza viruses H5N1, H7N9 • Coronaviruses NL63 and HKU1 • Human bocavirus • Middle East respiratory syndrome coronavirus (MERS-CoV)

3. Why Identify the Virus? • Many viruses have similar initial symptoms • Some patients will quickly deteriorate, while others could be sent home to recuperate with reassurance • Different viruses may require different isolation practices; allows hospital to utilize infection control practices where patients are separated into wards by virus type • Important to distinguish viral from bacterial causes • Avoid unnecessary antibiotics • Select specific antiviral agents, if available • By utilizing epidemiologic data from lab, can prescribe appropriate prophylactic treatments (influenza and RSV) when necessary for at risk patients

4. Source: Kiechle, et al. Clin Chim Acta. 2013 May 31. pii: S0009-8981(13)00238-6.

5. Why Identify the Virus? • As new pathogens emerge, the ability to exclude known viruses may help to more rapidly recognize and identify the presence of a new pathogen • Possible cost savings: • Shorter ER times for diagnosis/triage • Quicker access to treatment • Shorter hospital stays • Ability to “cohort” patients to prevent sick patient from catching a second virus

6. Traditional Identification of Viral Pathogens • Direct fluorescent-antibody assay and culture • Time consuming (slow turn-around-time) • Labor intensive/require expertise to interpret • Require monoclonal antibodies for viruses (for rapid cell culture) • Virus must be viable • Direct antigen testing • Quick results • Sensitivity and specificity vary widely, usually less sensitive than culture • Some are simple to use point-of-care tests

7. Molecular-Based Viral Identification • PCR (DNA/RNA)-based assays are gaining popularity • Quicker turn-around-time • Increased sensitivity • Quick development for emerging pathogens (does not rely on development of monoclonal antibody) • Ability to multiplex

8. Respiratory Virus Panels • Can multiplex relatively easily, with minimal increase in cost • More readily identify co-infections • Identify virus more quickly than ordering tests sequentially, particularly when there isn’t a prevalent virus “in season” • Sometimes a new virus may “cross-react” with an existing panel virus, aiding in identification until a specific test is available • Ability to exclude many viruses simultaneously

9. When should a viral panel be used vs. a single virus test? Single Virus Test Viral Panel When there isn’t a single prevalent virus Follow CDC data In hospital setting when infection control measures must be implemented To rule out many viruses at once when a new virus is suspected • During epidemic when there is one (or few) major virus(es) circulating • When a new/prevalent pathogen suspected is not on a panel, but has a specific test • When demand for test is too high for throughput available with panel

10. Good time to use panel Good time to use single virus test Source: http://www.cdc.gov/flu/weekly/

11. Biofire FilmArray RP • FDA-cleared • Detection Methodology: Melting Curve Analysis • Viruses Reported: Adenovirus; Coronavirus HKU1, NL63; Influenza A (H1/2009, H1, H3); Influenza B; Human metapneumovirus; Parainfluenza virus 1, 2, 3, 4; RSV; Rhinovirus/enterovirus • Overall Sensitivity: 89.4% • Overall Specificity: 99.6% • Hands-on Time: 0.05 hour • Time to Result: 1.2 hours • # of samples per instrument in 8 hrs: 7 Source: Popowitch, et al. 2013. J. Clin. Microbiol. 51(5): 1528-1533

12. Biofire FilmArray RP • Pros: • Quick turn-around time • Great specificity (~100% for all targets) • Extended FDA-cleared panel including several bacteria • Chlamydophila pneumoniae • Mycoplasma pneumoniae • Bordetella pertussis • Cons: • Limited capacity (1 sample at a time) Source: Popowitch, et al. 2013. J. Clin. Microbiol. 51(5): 1528-1533

13. Source: Biofire (http://www.biofiredx.com/pdfs/FilmArray/InfoSheet,%20FilmArray%20Respiratory%20Panel-0229.pdf)

14. Genmark eSensor RVP • FDA-cleared • Detection Method: Voltammetry • Viruses Reported: Adenovirus (C, B/E); Influenza A (H1/2009, H1, H3); Influenza B; Human Metapneumovirus; Parainfluenza viruses 1, 2, 3; RSV (A, B); Human Rhinovirus • Overall Sensitivity: 95.4% • Overall Specificity: 99.7% • Hands-on Time: 0.92 hour • Time to Result: 7.2 hours • # of Samples per Instrument in 8 hours: 21 Source: Popowitch, et al. 2013. J. Clin. Microbiol. 51(5): 1528-1533

15. Genmark eSensor RVP • Pros: • Very sensitive • Can report adenovirus species (C vs. B/E) • Cons: • Does not detect enterovirus • Time to result >7 hours Source: Popowitch, et al. 2013. J. Clin. Microbiol. 51(5): 1528-1533

16. Luminex xTAG RVPv1 • FDA-cleared • Detection Methodology: Fluroescence-labeled Bead Array • Viruses Detected: Adenovirus; Influenza A (H1, H3); Influenza B; Human Metapneumovirus; Parainfluenza virus 1, 2, 3; RSV (A/B); Rhinovirus/enterovirus • Sensitivity: 91.2% • Specificity: 99.7% • Hands-on time: 1.2 hours • Time to Result: 7.8 hours • # of Samples on Instrument in 8 hours: 21 Source: Popowitch, et al. 2013. J. Clin. Microbiol. 51(5): 1528-1533

17. Luminex xTAG RVPv1 Source: Popowitch, et al. 2013. J. Clin. Microbiol. 51(5): 1528-1533

18. Luminex xTAG RVPv1 Source: Luminex (http://www.xtagrvp.com/public/userfiles/MLD-019-KPI-001.pdf)

19. Luminex xTAG RVP Fast • FDA-cleared • Detection Methodology: Fluroescence-labeled Bead Array • Viruses Detected: Adenovirus; Influenza A (H1, H3); Influenza B; Human metapneumovirus; RSV; Rhinovirus/enterovirus • Sensitivity: 78.8% • Specificity: 99.6% • Hands-on Time: 0.75 hour • Time to Result: 4.8 hours • # of Samples per Instrument in 8 hours: 21 Source: Popowitch, et al. 2013. J. Clin. Microbiol. 51(5): 1528-1533

20. Luminex xTAG RVP Fast • Pros • Quick time-to-result • High throughput • Cons • No parainfluenza coverage • Lower sensitivity Source: Popowitch, et al. 2013. J. Clin. Microbiol. 51(5): 1528-1533

21. Respiratory Panel Considerations • Negative results do not exclude the possibility of infection with a respiratory virus as the virus could be below the assay limit of detection • Positive results do not exclude the possibility of co-infection with other viruses or bacteria, or concurrent underlying pulmonary pathology

22. Respiratory Panel Considerations • Specificity and sensitivity for each virus, throughput, and turn-around-time vary greatly among commercially available panels • Unique characteristics of the patient population being treated must be considered in selecting a panel • What viruses are my patients at risk for contracting? • How timely does the result need to be received to clinically impact patient care? • When multiple testing options are available, good communication between the laboratory and treating physicians is essential for optimal patient care

23. Selected Resources • Popowitch, et al. Comparison of the Biofire FilmArray RP, Genmark eSensor RVP, Luminex xTAG RVPv1, and Luminex xTAG RVP Fast Multiplex Assays for Detection of Respiratory Viruses. J. Clin. Microbiol. 2013, 51(5): 1528. • Mahony, et al. Development of a Respiratory Virus Panel Test for Detection of Twenty Human Respiratory Viruses by Use of Multiplex PCR and a Fluid Microbead-Based Assay. J. Clin. Microbiol. 2007, 45(9): 2965. • Griswold. Sizing up ‘mega’ multiplex panels for respiratory viruses. Cap Today. May 1, 2013.