12/10/2013. Welcome. Welcome. Diagnostic Challenges and Molecular Solutions for Respiratory Viruses

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1 Diagnostic Challenges and Molecular Solutions for Respiratory Viruses The phone lines will open, 15 minutes prior to the start of the webinar. Toll Free: Entry Code: You may download a copy of the handout by clicking on the handout icon, located in the upper right hand corner of your screen. Welcome Your Host: Karen Riba Handout is available by clicking on the handout icon in the upper right hand corner of your screen For technical difficulties please kchandler@paml.com. For questions you have during the presentation use the Q & A link at the top of your screen Questions will be answered at the end of the presentation This webinar is being recorded and will be available in one week on paml.com. Welcome P.A.C.E. credit may be obtained by submitting your completed evaluation form at the end of the webinar CE credit may be obtained by downloading the Certificate of Completion PAML employees will be able to receive one hour of continuing education. 1

2 Peter M. Krein, PhD Director of Scientific Affairs Dr. Krein has a bachelor s degree in Microbiology and Immunology and completed his PhD in the molecular biology of sepsis and lung disease. Learning Objectives Understand the clinical value of comprehensive respiratory virus testing Describe the value of molecular methods for respiratory virus testing Understand the different test methods and commercial assays available for the diagnostic laboratory Agenda Review of Clinically Relevant Respiratory Viruses Clinical Value Patient Health Outcomes Infection control, co-infection Antibiotic Stewardship Methods & Limitations Traditional Tests Culture, DFA, Rapid Tests Molecular multiplex tests Impact of Testing Algorithms 2

3 Respiratory Infections Represent the most common cause of acute illness in the U.S million people infected with Influenza / year in U.S. 1 Most common reason for ED visit & hospitalization of children 2,3 Economic impact of viral infections in the US $40 billion 4 Medications: antibiotics, bronchodilators, corticosteroids Medical visits, supportive care, over-the-counter analgesics Intangible costs Loss of productivity & missed work Persistent dyspnea / wheeze Deterioration of airway function (e.g. COPD) 1. CDC (Season Influenza Q&A) Shay et al. JAMA 1999; 282: Fendrick et al. Arch Intern Med 2003; 163: Respiratory Viruses Causing Human Illness Orthomyxoviridae Influenza A H1, H2, H3, H5, H7, H9, H10 Influenza B FDA Approved Antivirals FDA Approved Antivirals Respiratory Syncytial Virus A, B Ribavirin/Palivizumab Vaccine in development Paramyxovirus Human Metapneumovirus A, B Vaccine in development Parainfluenza Virus 1,2,3,4 Vaccine in development Adenoviridae Human Adenovirus A, B, C, D, E, F Serious Illness: cidofovir Enterovirus Coronaviridae Human Rhinovirus A, B, C Enterovirus A, B, C, D Human Coronavirus Alpha, Beta Antiviral in development No therapeutic/vaccine No therapeutic/vaccine? Respiratory Viruses Causing Human Illness Enterovirus Coronavirus Adenovirus Influenza (A/B) PIV Metapneumovirus * Rhinovirus * RSV * New targets to PAML cdc.org 3

4 Respiratory Virus Prevalence Annually Influenza A Influenza B Respiratory Syncytial Virus Parainfluenza Virus 1,2 Parainfluenza Virus 3 Rhinovirus Adenovirus Metapneumovirus cdc.org Diagnosis of Acute Respiratory Infection Challenge: Difficult to distinguish based on clinical presentation Timely comprehensive test results often not available Poorly defined clinical action for many viruses Why test for Respiratory Viruses: Antivirals for Influenza Risk: High Risk Populations Infection Control nosocomial spread Antibiotic Stewardship Prognosis Epidemiology Comprehensive Viral Testing Diagnostic effectiveness in various clinical settings IDSA & CDC Recommendations: Nucleic Acid Test correctly placed in algorithm of other clinical-epidemiological criteria. Outpatients clinic mild ARI - Testing not cost effective - Test only for epidemiological purposes ICU Immunocompromised patients - Most sensitive and comprehensive testing algorithm - Empiric / prophylactic Abx Emergency Room Patients do not fulfill criteria for admission - Rapid testing good PPV, poor NPV - Exceptions: pregnancy, co-morbidities Need sensitive test to avoid unnecessary Rx Emergency Room Patients requiring hospitalization - Flu & RSV neg. reflex to comprehensive test Molecular testing recommended in certain patient populations and situations. 1. Harper, S.A. et al Seasonal Influenza in Adults and Children-Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management. Clinical Practice Guidelines of the Infectious Diseases Society of America

5 Boiling Recommendations Down Limited Testing Recommended Possible: Influenza test for antiviral Comprehensive Molecular Testing -improve patient outcome -limit nosocomial spread -high risk population risk Subsequent to the pandemic it became clear that over half of patients admitted for influenza-like illness actually had something other than influenza. That sold me on molecular panels for hospitalized patients - Kim Chapin, MD CAP Today April 2012 Respiratory Virus: Who is at Risk? High Risk Populations Infants/ young (<5 YO, preterm) Any chronic Lung Disease Crowding: Day care, barracks, nursing home, hospitals Elderly Any congenital heart disease Immune-compromised Respiratory Virus: What is the Risk? Immunocompromised / Elderly/ Very Young Prolonged Infection Prolonged Viral Shedding Increased risk of severe infection / pneumonia Higher nosocomial acquisition Higher risk of co-pathogen presence Higher rate of death Transplant Populations Perhaps Highest Risk Population Higher risk of Transplant rejection/ complications 5

6 Viruses have significant health effects Comprehensive and sensitive testing is key Respiratory Syncytial Virus Nosocomial infection accounts for <35% of all infection in immunosupporessed High mortality in HSCT population (37% one study) Human Metapneumovirus HSCT 50-80% fatality rate in PCR confirmed hmpv Adult care outbreaks with morbidity and mortality Parainfluenza Viruses Nosocomial outbreak in neonatal ward with morbidity and mortality Adenovirus Mortality rates of 50-70% in immunosuppressed populations Increased risk of mechanical ventilation in children Rhinovirus Exacerbation of Allergy, Asthma and COPD Lower Respiratory Tract ventilation risk Bottom Line: -Many viruses cause significant health risk -High sensitivity comprehensive molecular test best identifies respiratory viruses Infection Control Respiratory Viruses Patient cohorting when respiratory infection suspected Typical: cohort by Flu and RSV status Testing comprehensively creates opportunity to adjust: cohorting practices appropriate therapy de-escalation of non-infectious individuals minimize nosocomial viral transmission/co-infection Cost reduction- LOS & tests ordered Co-infection: Common in adults and more so in pediatric populations ~ 30% of pediatric patients have 2 or more viruses Associated with increased morbidity and hospital cost impact 1,2 Length of hospital stay > 3 days 3x Risk for PICU admission and increased risk of mechanical ventilation 2 1 Mansbach et. al Arch Ped Adol Med (8): Goka et. al Influenza and other Resp Viruses (6): High Risk Populations Comprehensive and Sensitive testing is key Lower respiratory tract infections Most common hospital acquired infection in the ICU Impact: Patient health / outcomes length of stay Financial burden for healthcare system 2013 Study 1 Germany (DRG system; cost structure may be different from US) ICU Patients with / without nosocomial lower respiratory tract infection: Increased Cost of Care: 17,015 Increased length of hospital stay: 9 days 2002 Study 2 Washington University, St. Louis Patients with pneumonia in the ICU: Increased ICU time: 26 vs 4 days Increased Hospital Stay: 38 vs 13 days Increased Cost: $70,568 vs. $21, $11,897 directly attributable to respiratory infection 1 Leistner et. al Antimicrob Resist Infect Control 2013(1);13 2 Warren et.al Crit Care Med (5);

7 Antibiotic Stewardship Acute Respiratory Infection: most common reason for antibiotic prescription 2001: Over ½ prescribed for viral infections $726 million! 2006: Outpatient Setting 65% of patients with respiratory symptoms resulted in antibiotic prescription Gonzales CID 2001;33: Gill Fam Med 2006; 38:349 Role of Respiratory Virus Testing in Antibiotic Stewardship CDC and NHS CDC Recent Report Antibiotic Resistance serious health threat 7

8 Antibiotic Stewardship Impact of inappropriate antibiotic use Emergence and spread of resistant organisms 1 Longer hospital stay by days $18k $71k per patient attributable medical cost Increased morbidity & mortality 6.5% Antibiotic Adverse Events 20% of drug adverse event ER visits due to Abx 2 Side effects such as abdominal pain, diarrhea, nausea/vomiting related to use of Macrolides (azithromycin) C. diff. due to Abx use Microbiome alteration 3 Abx in early life 84% increased relative risk of Inflammatory Bowel Disease 4 Trials: Antibiotic failed to demonstrate benefit in Acute Resp. Infection 5 Antibiotics should not be used to treat nonspecific upper respiratory tract infections in previously healthy adults 6 -American College of Physicians 1. CDC (A Public Health Action Plan to Antibiotic Resistance 2012) 2. Shehab Clin infect disease 2008: 47: Ubeda Trends in Immunology 2012; 33: Kronman Pediatrics 2012; 130:e Arroll Resp Medicine : Gonzales Ann intern Med : Published Nov. 18, 2013 Considering the frequency of upper respiratory infections {URI} and the large proportion of antibiotic prescribing attributable to URI visits, these conditions represent a high-impact target for guidelines and other interventions designated to optimize antibiotic prescribing. What can a clinician do with Viral Diagnostic Test Information? Provide patient anti-viral (Flu, RSV, Adenovirus) Rule out bacterial infection- withhold antibiotics In-patient infection control Better understand prognosis Reduce unnecessary testing CXR, CBC, Micro workup 8

9 Respiratory Virus Laboratory Testing Methods Common Diagnostic Methods Method Sensitivity Specificity Skill Level Time to result Challenges Viral Culture High 3-15 days Rapid Antigen +/- +/- Low <30 minutes Fluorescent Antibody (FA) High 2-5 hours Shell Vial + FA High 1-3 days Molecular High 4-10 hours Time Skill Performance Breadth Performance Skill Performance Skill Skill Cost Traditional Cell Culture Strength Gold Standard 30+ years Excellent Sensitivity Diverse (unexpected) virus detection Virus Mutation does not affect Differentiate viable from non-viable If specimen storage improper- test fail Virus available for subsequent study Susceptibility testing Characterization (serotype, molecular) Weakness Technical expertise Cell passage, sterile technique, QC Time to result Some virus difficult to propagate/detect: hmnv, Rhinovirus, Adenovirus Cost of maintaining culture Biosafety hood, equipment, supplies, lab space, FTE Identification is presumed Cytopathic changes expertise mimic cell death Hemadsorbtion Staining or DFA 9

10 Fluorescent Antibody Speed Low Cost Strength Less Expertise than Cytopathogenic Changes Required Weakness Technical expertise Fluorescent microscope Not all viruses/serotypes detected hmnv, Adenovirus Unable to differentiate related family virus (eg. Enteroviruses) Background- mucus, cell remnants Lower Sensitivity than Culture/Molecular Rapid Tests Strength Speed minutes Low Cost CLIA waived (*) Weakness Low Sensitivity Sensitivity across seasonal strains Flu / RSV only (*) FDA sub-committee has recommended re-classification of rapid tests FDA Submission Data for Rapid (within 30 min) Influenza Tests * Specimen Type Throat Swab Type Detected A Population % Sensitivity (95% CI) % Specificity (95% CI) Pediatric Adult Throat Swab A & B Not Specified NP Wash/Aspirate Nasal Nasal and Aspirate A A Pediatric Adult Pediatric Adult A Not Specified Nasal Swab A & B Not Specified * Culture was the comparative standard for FDA submission. Courtesy: Dr. Kim Chapin 10

11 Molecular Respiratory Testing Methods Sensitivity of DFA vs. PCR Education regarding ~40% gap in sensitivity of detection 1 for infection control and patient management in hospitalized patients, PCR is the preferred test due to its greater sensitivity 1 1. Yale University Virology Newsletter Nov

12 Nucleic Acid Tests: Increase Sensitivity Traditional Culture Compared to RT-PCR 668 pediatric patients Traditional Culture vs. PCR (RSV, PIV 1-3, Flu A &B) RT-PCR Culture Positive Negative Positive Negative positive samples missed by traditional culture 15.5% of samples Weinberg et. al JID ;706 Nucleic Acid Tests: Increase Sensitivity Culture-DFA Compared to FDA-multiplex PCR 294 NP specimens Culture-DFA Positive Negative Not Tested RVP Positive Negative positive samples missed by traditional culture-dfa 20% of samples Mahony et. al JCM ;2812 GenMark Respiratory Viral Panel (IVD) Comprehensive panel of viruses FDA cleared respiratory viral test Single tube test includes 14 clinically relevant targets with sub-typing Objective results automatically generated by GenMark s FDAcleared system 12

13 Alaska Department of Public Health Case Study 2012 Algorithm All Samples Influenza: PCR* RSV DFA *PCR includes Flu A subtyping and Flu B Report as Flu or RSV positive Perform traditional viral culture Report as Virus positive or Negative Alaska Department of Public Health 127 samples characterized using 2012 algorithm 2012 Algorithm GenMark RVP Parainfluenza 3 Parainfluenza 1 8% 1% Parainfluenza 2 HCoV OC43 Influenza A/H3 4% 9% 5% NVR 69% Parainfluenza 3 5% Rhino 3% RSV 1% Adenovirus B 3% Adenovirus C HMPV 2% 1% Influenza A/H3 Influenza A 5% 2009/H1N1 Influenza B 3% 3% NVR 17% Rhino 15% Dual Isolates 20% Parainfluenza 2 5% HMPV 4% HCoV HKU1 3% Influenza B RSV B 3% 3% Adenovirus B HCoV 1% Influenza A 2009/H1N1 229E HCoV 1% 1% NL63 RSV A Parainfluenza 1 1% 1% 1% Amongst no virus detected by 2012 algorithm GenMark detected virus in 39 samples: 29 positive one virus, 10 positive 2 viruses Data courtesy of Jayme Parker Public Health Microbiologist, Alaska State Virology Laboratory FDA Cleared Virus Panel Tests Comparison Study Compare four FDA-cleared multiplex PCR 300 NP specimens Popowitch J Clin Micro 2013; 51(5):

14 FDA Cleared Virus Panel Tests Comparison Study Overall Sensitivity Sensitivity <5 year old Sensitivity <18 year old Sensitivity >18 year old Co-infection Detection GenMark esensor RVP 99.6% - * - * - * 96.8% Luminex xtag RVP 92.7% 85.5% - * - * 71.0% Luminex xtag RVP Fast 84.4% - * 81.5% 89.8% 54.8% BioFire FilmArray RP 84.5% 80.2% 80.6% 91.9% 61.3% -* = No significant difference to overall sensitivity Conclusion: GenMark RVP delivers highest sensitivity across all age groups of all FDA-cleared multiplex tests Popowitch J Clin Micro 2013; 51(5): Laboratory Testing Algorithms Improved Testing Algorithm Patient Population RVP Test Consult Infection Control Follow hospital procedures Most Costly Patient Group 1 Follow Clinical Diagnostic Algorithm 1. Mahony et al. J Clin Micro (4)

15 Value of Comprehensive Respiratory Virus Test Accurate, clinically valuable information False Negative Rapid tests have low sensitivity Immunoassays: sensitivity 30-80% 1 Culture & DFA have low sensitivity compared to molecular tests 20% of positive patient samples missed by culture-dfa 2 Molecular test increased sensitivity of detection in children by 74% over DFA and viral culture 3 False Negative Results: Patient Health Risk- unknown etiology Unnecessary testing (CXR, CBC, microbiology) Inappropriate antibiotics Nosocomial spread Hospital Cost 1 False negative DFA and Culture results: 2x total cost to treat patients 1 1. Beck et al MMWR 61(43); Mahony et al. J Clin Micro (4) Gharabaghi et al. Clinical Microbiology and Infection 2011; 17(12): Mahony et al. J of Clin Micro 2009; 47 (9): Economics Benefit Utilizing Molecular Respiratory Virus Testing 500 bed hospital; viral diagnostic test resulted in: Overall 5 day reduction in Length of Stay Reduced mortality ~$5,000 cost savings per patient After costs; $145,000 annual savings to health system Benefits of viral diagnostic 50% reduction in hospital stays 30% reduced Abx use 20% reduction in Dx tests/ procedures ordered Relevant Sources Babcock 2008; Infect control and Hosp Epidemiology C Vanden Dool 2008; Infect control and Hosp Epidemiology Barenfanger J Cin Micro 2000; 38: Hendrickson Pediatr Ann 2005; 34:24 31 Doan Evidence-based Child Health, Cochrane Review 2010 Sensitivity Case Study 72-year old male with multiple myeloma Facing chemotherapy & autologous stem cell transplant practicefusion.com 1 week prior to admission: symptoms of respiratory infection Chest X-ray right lobe infiltrate given antibiotic Time of procedure continued cough X-ray showed improvement Three days post discharge Worsening respiratory symptoms 1 st Respiratory Virus Test (Luminex) negative Patient admitted bilateral infiltrates All bacterial/fungal tests negative 2 nd Respiratory virus test (Luminex) negative; rapid RSV antigen positive Treatment Ribavirin, antibacterial, antifungal agents, but developed C. diff and died Patient was part of nosocomial outbreak of RSV in HSCT ward; several patients died False negative respiratory results Luminex and Rapid tests delayed isolation and treatment GenMark RVP: RSV+ all five patients (retrospectively tested) Hawkison, D. Diag Micro and Infect Dis. 2013; 15

16 Comprehensive Molecular Respiratory Virus Test Accurate, clinically valuable information Comprehensive molecular respiratory viral panel: Value: result added to other clinical and pathological assessments Rule in / Rule out viral infection- infection control, antibiotic use Lower cost of treatment- unnecessary tests Efficient: Single tube: common viruses / subtypes in single test High sensitivity means less reflex testing Simplified testing algorithm; increased speed to result Performance: Detect more viruses than traditional tests 30-40% more viral infections detected with molecular vs traditional methods Increased sensitivity of detection in children by 74% over DFA and viral culture Highest sensitivity of FDA cleared molecular panels PAML RVP Test Information The test will be live at PAML on December 17, 2013 Test Code RVPCR Specimen Type NP swab in M6 media (see Test Change Alert #414) TAT one to three days Contact for questions Client Services or you Account Manager Questions 16

17 Thank You for Attending P.A.C.E. credit may be obtained by submitting your completed evaluation form. You will find the form by clicking on the handouts icon in the upper right hand corner of your screen CE credit may be obtained by downloading the Certificate of Completion under the handouts icon PAML employees will be able to receive one hour of continuing education credit by submitting your attendance through CE Manager. Thank You for Attending We will be leaving the webinar open for 15 minutes to allow you to download the handouts This webinar has been recorded and will be available by Tuesday, December 17 th, at Look for PAML s next webinar early next year Please send ideas for future webinar topics. 17