Clade SNP position Primer* direction Sequence (5’-3’) Position in CDS# Amplicon size (bp) Tm (°C)
S 28144 NS8_28144_F Forward AAGTTCAAGAACTTTACTCTCC ORF7a_275-296 496 58.1
NS8_28144_wR Reverse TGGCAATTAATTGTAAAAGGTA ORF8_251-272 58
NS8_28144_mR TGGCAATTAATTGTAAAAGGTG ORF8_251-272 57.8
V 26144 NS3_26144_F Forward TGGCAACTAGCACTCTCC ORF3a_205-222 568 60.9
NS3_26144_wR Reverse GATTAACAACTCCGGATGAAC ORF3a_752-772 58.7
NS3_26144_mR GATTAACAACTCCGGATGAAA ORF3a_752-772 58.3
G 23403 S_23403_wF Forward GTTGCTGTTCTTTATCAGGA Spike_1822-1841 208 58
S_23403_mF GTTGCTGTTCTTTATCAGGG Spike_1822-1841 58
S_23404_R Reverse TGAGTCTGATAACTAGCGC Spike_2012-2030 58
GH 25563 NS3_25563_wF Forward CACTTCTTGCTGTTTTTCAG ORF3a_152-171 279 58
NS3_25563_mF CACTTCTTGCTGTTTTTCAT ORF3a_152-171 57
NS3_25563_R Reverse TGGCATCATAAAGTAATGGG ORF3a_411-430 57.8
GR 28881-28883 N_28882_F Forward CCAGATGACCAAATTGGC N protein_238-255 387 58
N_28882_wR Reverse TAGCAGGAGAAGTTCCCC N protein_608-625 60
N_28882_mR TAGCAGGAGAAGTTCGTT N protein_608-625 58