2020/06/08 by Po‐E Li, Adán Myers y Gutiérrez, Li, Po-E +19
Medicine · #SARS-CoV-2 and COVID-19 Research #SARS-CoV-2 detection and testing #Viral gastroenteritis research and epidemiology
paper · pdf · doi:10.48550/arxiv.2006.04566
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])