A Public Website for the Automated Assessment and Validation of SARS-CoV-2 Diagnostic PCR Assays

Li, Po-E; Myers y Gutiérrez, Adán; Davenport, Karen; Flynn, Mark; Hu, Bin; Lo, Chien-Chi; Player Jackson, Elais; Shakya, Migun; Xu, Yan; Gans, Jason; Chain, Patrick S G

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.