Author: Li, Po-E; Guti'errez, Ad'an Myers y; Davenport, Karen; Flynn, Mark; Hu, Bin; Lo, Chien-Chi; Jackson, Elais Player; Shakya, Migun; Xu, Yan; Gans, Jason; Chain, Patrick S. G.
Title: A Public Website for the Automated Assessment and Validation of SARS-CoV-2 Diagnostic PCR Assays Cord-id: 5m50ql15 Document date: 2020_6_8
ID: 5m50ql15
Snippet: Summary: Polymerase chain reaction-based assays are the current gold standard for detecting and diagnosing SARS-CoV-2. However, as SARS-CoV-2 mutates, we need to constantly assess whether existing PCR-based assays will continue to detect all known viral strains. To enable the continuous monitoring of SARS-CoV-2 assays, we have developed a web-based assay validation algorithm that checks existing PCR-based assays against the ever-expanding genome databases for SARS-CoV-2 using both thermodynamic
Document: Summary: Polymerase chain reaction-based assays are the current gold standard for detecting and diagnosing SARS-CoV-2. However, as SARS-CoV-2 mutates, we need to constantly assess whether existing PCR-based assays will continue to detect all known viral strains. To enable the continuous monitoring of SARS-CoV-2 assays, we have developed a web-based assay validation algorithm that checks existing PCR-based assays against the ever-expanding genome databases for SARS-CoV-2 using both thermodynamic and edit-distance metrics. The assay screening results are displayed as a heatmap, showing the number of mismatches between each detection and each SARS-CoV-2 genome sequence. Using a mismatch threshold to define detection failure, assay performance is summarized with the true positive rate (recall) to simplify assay comparisons. Availability: https://covid19.edgebioinformatics.org/#/assayValidation. Contact: Jason Gans ([email protected]) and Patrick Chain ([email protected])
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