Table 2.

Primers designed for this study and corresponding targeted regions.

	Primer sequence	Targeted region of reference genome GX-P5L*	Amplicon size
RdRp gene region 1 [corresponding to the region amplified in Watanabe et al. (26)]
Primer set 1		15,237–15,691	455 bp
R1-Set1-Fw	5′-AAT-ATG-TTR-AAA-ACT-GTT-TAC-A-3′
R1-Set1-Rev	5′-AAA-GCA-MAC-AAC-AGC-ATC-ATC-AGA-3′
Primer set 2		15,286–15,678	393 bp
R1-Set2-Fw	5′-GGT-TGG-GAT-TAY-CCW-AAA-TGT-GA-3′
R1-Set2-Rev	5′-GCA-TCA-TCA-GAR-AGT-ATC-ATC-ATT-3′
Primer set 3		15,292–15,678	387 bp
R1-Set3-Fw	5′-GAT-TAY-CCW-AAA-TGT-GAY-AGA-GC-3′
R1-Set2-Rev	5′-GCA-TCA-TCA-GAR-AGT-ATC-ATC-ATT-3′ (same as set 2)
RdRp gene region 2 [corresponding to the region amplified in Quan et al. (27)]
Primer set 1		18,361–18,799	439 bp
R2-Set1-Fw	5′-TTA-CAG-YTA-GGC-TTT-TCW-ACA-GGT-GT-3′
R2-Set1-Rev	5′-CAT-GTG-CAT-TAC-CRT-GTA-CTT-G-3′
Primer set 2		18,418–18,760	343 bp
R2-Set2-Fw	5′-YGT-TGA-YAC-AYC-TAA-TRM-WAC-AGA-KTT-YWC-3′
R2-Set2-Rev	5′-RGT-CAT-GGT-TAC-TYT-GWA-RGT-TAC-CWG-TAA-A-3′
Primer set 3		18,454–18,742	289 bp
R2-Set3-Fw	5′-RCC-ACC-ACC-TGG-WGA-CCA-RTT-3′
R2-Set3-Rev	5′-TAA-AAC-CCC-ATT-GYT-GAA-CAT-C-3′

^*Reference genome is the Pangolin CoV isolate PCoV_GX-P5L, GenBank accession number MT040335.