A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays

• Published in: Bioinformatics 2021-05, Vol.37 (7), p.1024-1025
• 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
• Format: Article
• Language: English
• Subjects: Applications Notes; Biological Science; COVID-19; COVID-19 Testing; Humans; Polymerase Chain Reaction; SARS-CoV-2; SARS2, COVID-19, assay validation, PCR; Sensitivity and Specificity
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btaa710

Abstract 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/thermonucleotide BLAST and https://github.com/LANL-Bioinformatics/assay_validation. Supplementary information Supplementary data are available at Bioinformatics online.