RT Journal Article
SR Electronic
T1 assayM: a web application to monitor mutations in COVID-19 diagnostic assays
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.12.18.423467
DO 10.1101/2020.12.18.423467
A1 Raeece Naeem
A1 Arnab Pain
YR 2020
UL http://biorxiv.org/content/early/2020/12/18/2020.12.18.423467.abstract
AB Summary Reverse Transcriptase – Polymerase Chain Reaction (RT-PCR) is the gold standard as diagnostic assays for the detection of COVID-19 and the specificity and sensitivity of these assays depend on the complementarity of the RT-PCR primers to the genome of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the virus mutates over time during replication cycles, there is an urgent need to continuously monitor the virus genome for appearances of mutations and mismatches in the PCR primers used in these assays. Here we present assayM, a web application to explore and monitor mutations introduced in the primer and probe sequences published by the World Health Organisation (WHO) or in any custom-designed assay primers for SARS-CoV-2 detection assays in globally available SARS-CoV-2 genome datasets.Availability and implementation assayM is available on https://grafnet.kaust.edu.sa/assayM as a web application and also as an open-source R shiny application, downloadable from https://github.com/raeece/assayMContact arnab.pain{at}kaust.edu.saCompeting Interest StatementThe authors have declared no competing interest.