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SARS-CoV-2 Molecular Diagnostics Testing Implementation PowerPoint Presentation

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Published on : Aug 06, 2021 | Views : 1254 | Downloads : 0

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SARS-CoV-2 Molecular Diagnostics Testing Implementation Hanna Rennert, PhD Director, Molecular Pathology March 11, 2020
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Policy for Diagnostics Testing in Laboratories Certified to Perform High Complexity Testing under CLIA Policy for Diagnostics Testing in Laboratories Certified to Perform High Complexity Testing under CLIA prior to Emergency Use Authorization for Coronavirus Disease-2019 during the Public Health Emergency Immediately in Effect Guidance for Clinical Laboratories and Food and Drug Administration Staff Document issued on the web on February 29, 2020. U.S. Department of Health and Human Services Food and Drug Administration Center for Devices and Radiological Health
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Policy The guidance includes recommendations regarding: Validation of newly developed SARS-CoV-2 tests prior to clinical use Notifying FDA when clinical use begins Confirming the first 5 positive and negative samples with an Emergency Use Authorization (EUA) authorized test Indicating in the report that testing has been validated but pending FDA review Submitting the Emergency Use Authorization (EUA) application to the FDA within 15 days of initiating testing Steps to take if the initial confirmatory testing fails or FDA unable to authorize the EUA
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Test Validation The guidance also includes recommendations regarding the minimal testing to be performed for validation: Limit of Detection (LoD) Clinical Evaluation (accuracy studies) Inclusivity (SARS-CoV-2 sequences that can be detected) Cross-Reactivity Requirements for RNA control material 4
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SARS-CoV-2 real-time RT-PCR Acceptable Performance 100% agreement at all LOD concentrations and clinical samples (Positive and Negative) tested S-Gene E-Gene
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Testing Work Flow (~90 patient samples in 6h-8h) Reporting LIS/EMR Timeline 2 Runs/day
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7 Reporting of Results
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8 SARS-CoV-2 Testing Instructions Effective March 11, SARS-CoV-2 testing will be available in house in limited capacity. All requests for this test must be screened by Infection Prevention and Control (IPC). Algorithm evolving. The lab will accept either nasopharyngeal or oropharyngeal swabs, or both in one container collected in viral transport media (VTM). Do not send sputum at this time; will be validated next. Results will be available in EMR. When results return please contact IPC for further instructions. All samples must be delivered to the Microbiology laboratory. The SARS-CoV-2 test will be performed twice a day. Samples must be in Molecular Pathology by 11am for same day results. Results for samples arriving after 11am, will be available the next day.
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Acknowledgment 9 Molecular Pathology Laboratory Microbiology Laboratory Clinical Pathology team
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10
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Interpretation of Results E (envelope) gene detects all members of the lineage B of the beta-CoVs which are all SARS, SARS-like and SARS-related viruses S (spike) gene specifically detects the SARS-CoV-2 *An S-gene neg/E-gene pos would indicate positivity for SARS (including but not necessarily limited to SARS-CoV-2). This result does not rule out SARS-Cov-2— Recommending repeating the test or follow up with another test method.
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Safety Sample Processing- Using biosafety cabinets Level 2 (Policy for diagnostic testing in laboratories certified to perform high complexity testing under CLIA- FDA) Aerosolization control- Extraction with Qiasymphony with off board lysis (OBL) protocol. Automated extraction using a closed system Protective equipment - Wearing gown, gloves, eye protection, respiratory protection Disinfection procedures Use EPA-registered hospital disinfectants effective against other respiratory pathogens (e.g., seasonal influenza, HuCoVs)
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13 Sequencing of SARS-CoV-2 Recovered from NP Specimens Genetic variation of circulating variants described (Phan et al., 2020 Infect Genet Evol PMID: 32092483) Sequence cDNA generated from RNA extracted from clinical NP specimens obtained at NYPH-WCMC In addition to in silico analyses, will demonstrate if circulating variants in NYC in our patient population are compatible with current diagnostic assays