  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_ADDRESS>and Patrick Chain<EMAIL_ADDRESS>