Universal probe assays for severe acute respiratory syndrome coronavirus 2

(a) Map of SARS-CoV-2 and the Universal probe target region. The target region shows little or no significant homology with SARS-CoV-1, MERS-CoV, 229E, HKU, HL63, and OC43. Discrimination between SARS-CoV-2 and SARS-CoV-1 was favored by selecting primer and linker-primer sites with high dissimilarity (6–15 mismatches per oligo). Two SARS-CoV-2  templates with 2-3 Universal probe sites were tested. (b) Detection of template 1 (left), template 2 (middle), or both templates (right) in multiplex reactions with two Universal probe assays. (c) Duplex detection of SARS-CoV-2 w/various probe combinations