SARS-CoV-2 variant identification using a genome tiling array and genotyping probes

With over 5.5 million deaths worldwide attributed to the respiratory disease COVID-19 caused by the novel coronavirus SARS-CoV-2, it is essential that continued efforts be made to track the evolution and spread of the virus globally. The authors previously presented a rapid and cost-effective method to sequence the entire SARS-CoV-2 genome with 95% coverage and 99.9% accuracy. This method is advantageous for identifying and tracking variants in the SARS-CoV-2 genome compared with traditional short-read sequencing methods which can be time-consuming and costly. Herein, the addition of genotyping probes to a DNA chip that targets known SARS-CoV-2 variants is presented. The incorporation of genotyping probe sets along with the advent of a moving average filter improved the sequencing coverage and accuracy of the SARS-CoV-2 genome.