A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays
Abstract
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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Aug 10, 2020
- Source ID
- 10.1093/bioinformatics/btaa710
Entities
People
- Adán Myers y Gutiérrez
- Bin Hu
- Chien-Chi Lo
- Elais Player Jackson
- Jason Gans
- Karen W Davenport
- Mark Flynn
- Migun Shakya
- Patrick S Chain
- Po‐E Li
- Yan Xu
Organizations
- Defense Threat Reduction Agency
- Los Alamos National Laboratory
- National Science Foundation
- United States Department of Energy