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

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-Co...

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Bibliographic Details
Published in:arXiv.org 2020-06
Main Authors: Po-E Li, Adán Myers y Gutiérrez, Davenport, Karen, Flynn, Mark, Hu, Bin, Chien-Chi Lo, Elais Player Jackson, Shakya, Migun, Xu, Yan, Gans, Jason, Chain, Patrick S G
Format: Article
Language:English
Subjects:
Algorithms
Assaying
Diagnostic systems
Genomes
Polymerase chain reaction
Severe acute respiratory syndrome coronavirus 2
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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 (jgans@lanl.gov) and Patrick Chain (pchain@lanl.gov)
ISSN:2331-8422