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 AND IMPLEMENTATION: The assay evaluation website and supporting software are Open Source and freely available at https://covid19.edgebioinformatics.org/#/assayValidation, https://github.com/jgans/thermonucleotideBLAST, and https://github.com/LANL-Bioinformatics/assay_validation. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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Validation Automated INFORMATION Assessment Website

Flynn, Mark,Li, Po-E, Lo, Chien-Chi, Myers y Gutiérrez, Adán, Chain, Patrick S G, Xu, Yan, Gans, Jason, Shakya, Migun, Davenport, Karen, Hu, Bin, Jackson, Elais Player,.A Public Website for the Automated Assessment and Validation of SARS-CoV-2 Diagnostic PCR Assays. (),.

Flynn, Mark, et al."A Public Website for the Automated Assessment and Validation of SARS-CoV-2 Diagnostic PCR Assays"

Flynn, Mark,Li, Po-E, Lo, Chien-Chi, Myers y Gutiérrez, Adán, Chain, Patrick S G, Xu, Yan, Gans, Jason, Shakya, Migun, Davenport, Karen, Hu, Bin, Jackson, Elais Player,"A Public Website for the Automated Assessment and Validation of SARS-CoV-2 Diagnostic PCR Assays"