Identification of the clades by single-variant specific PCRs
ARMS-based PCRs for single SNP variants (singleplex PCRs) were optimized at an annealing temperature of 57°C. The primer pairs for the variants 23403 A>G (p.D614G) and 28882 G>A (p.R203K) amplified the related mutant bands (208bp and 387bp, respectively). On the other hand, the primer pairs designed to denote the variants 25563 G>T (p.Q57H), 26144 G>T(p.G251V) and 28144 T>C (p.L84S) had wild type amplicons (279bp, 568bp and 496bp, respectively) (Fig.2 IA-IE ). Hence, the single-variant specific PCRs were able to identify the SARS-CoV-2 positive sample containing GR-clade of the virus.