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:Bioinformatics (Oxford, England) England), 2020-08, Vol.37 (7)
Main Authors: 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 D., Chain, Patrick S. G., Elofsson, ed., Arne
Format: Article
Language:English
Subjects:
BASIC BIOLOGICAL SCIENCES
Biological science
SARS-CoV-2, PCR
SARS2, COVID-19, assay validation, PCR
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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.
ISSN:1367-4803
1367-4811