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-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 implementationThe 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 informationSupplementary data are available at Bioinformatics online.
- Research Organization:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Organization:
- Defense Threat Reduction Agency (DTRA); National Science Foundation (NSF); USDOE; USDOE Laboratory Directed Research and Development (LDRD) Program; USDOE Office of Science (SC). Biological and Environmental Research (BER)
- Grant/Contract Number:
- 89233218CNA000001
- OSTI ID:
- 1783364
- Alternate ID(s):
- OSTI ID: 1716526
OSTI ID: 1726201
OSTI ID: 1756812
- Report Number(s):
- LA-UR--20-23330; LA-UR--20-27750
- Journal Information:
- Bioinformatics, Journal Name: Bioinformatics Journal Issue: 7 Vol. 37; ISSN 1367-4803
- Publisher:
- Oxford University PressCopyright Statement
- Country of Publication:
- United Kingdom
- Language:
- English