Multiplex Fragment Analysis Identifies SARS-CoV-2 Variants

Clark, A. E.; Wang, Z.; Cantarel, B. L.; Kanchwala, M.; Xing, C.; Chen, L.; Irwin, P.; Xu, Y.; Oliver, D.; Lee, F.; Gagan, J. R.; Park, J. Y.; Filkins, L.; Muthukumar, A.; Sarode, R.; SoRelle, J. A.

The rapid spread of SARS-CoV-2 variants are of critical concern, necessitating systematic efforts for epidemiological surveillance. The current method for identifying variants is viral genome sequencing. Sequencing has multiple limitations to broad clinical adoption including requirements for technical expertise, expense of equipment and bioinformatics, and time for implementation. Here we describe a scalable non-sequencing-based capillary electrophoresis assay to affordably screen variants of SARS-CoV-2. The assay has targets for N1 (CDC nucleocapsid target, internal control), spike gene 69_70 deletion, spike gene 144 deletion, and ORF1A 3675_3677 deletion, which are all present in the B.1.1.7 (UK) variant. ORF1A deletions alone are also present in the New York, Brazil, and South African variants. 648 specimens have been tested to date and the assay is able to detect the B.1.1.7 variant 32 times (n=23 specimens, n=9 positive control replicates). Additionally, the B.1.429 (California) variant can be detected when a 3bp insertion or drop out of the S144 target is present. 7/23 B.1.1.7 specimens have been confirmed by Whole Genome Sequencing (16 pending confirmation), and demonstrate the ability to rapidly track the progression of COVID-19 variants in the population.