Recent reports of potentially more dangerous SARS-CoV-2 variants highlights the need for surveillance to quickly identify changes in the viral genome and contain the spread. These variants are of particular concern because they may spread faster and/or may cause more severe disease. Additionally, variants may impact the performance of current diagnostic approaches or the effectiveness of vaccines.
RT-PCR is the gold standard tool for the detection of COVID-19, due to the inherent benefits of accuracy, sensitivity, speed, and scalability. However, these first-tier detection assays provide limited information about SARS-CoV-2 variants in the sample. Second tier NGS assays can provide information on variants by using a portion of the sample determined to be positive using the first-tier assay.