Researchers from Washington University School of Medicine, St. Louis, have identified a mutation that reduces the ability of reverse transcriptase PCR (RT-PCR) a commonly used diagnostic assay, to identify SARS-CoV-2. They then discovered that this mutation was present in SARS-CoV-2 samples from all over the world. The research is published in the Journal of Clinical Microbiology, a publication of the American Society for Microbiology.
Diagnostic reverse transcriptase PCR (RT-PCR) is used widely during public health emergencies to identify infectious viral agents, as these assays can effectively measure a virus' abundance and spread within the community. But SARS-CoV-2 mutates frequently, and some of these mutations occur in genome regions that diagnostic assays use to identify the virus.
As part of their research, the investigators examined all clinical samples that had been tested using an FDA-authorized RT-PCR platform that assays 2 regions of the genome. Some samples gave strong signals from one target region, but much weaker signals from the other region. Sequencing of whole genomes of the virus in these samples revealed a single mutation in the latter target region that resulted in the weaker signal.
The reliability of these tests is paramount, as false negatives can delay the response of public health officials, reducing the speed with which an afflicted community can enact protective measures such as mandating masks, and closing bars and restaurants said corresponding author David Wang, who is professor of Molecular Microbiology, and Pathology & Immunology. Such delays result in a faster spread of infections. False negatives likely hastened the spread of the naturally highly transmissible B.1.1.7 variant, due to a 6 nucleotide deletion within the S gene.
"Using diagnostic assays that target more than one region can help improve the accuracy of SARS-CoV-2 testing," said Dr. Wang.
