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 |