PCR Amplicon | Primer Type | Start | End | Sequence 5’-3’ | Size (bp) |
N gene Co4/Co3 Nested | Co1 primary F. | 28707 | 28727 | ACATTGGCACCCGCAATCCTG | 416 |
Co8 primary R. | 29102 | 29122 | TTGGGTTTGTTCTGGACCACG | ||
Co4 nested F. | 28720 | 28740 | CAATCCTGCTAACAATGCTGC | 398 | |
Co3 nested R. | 29097 | 29117 | TTTGTTCTGGACCACGTCTGC | ||
S geneRBD S9/S10 Nested | SS1 primary F. | 22643 | 22663 | TGTGTTGCTGATTATTCTGTC | 460 |
SS2 primary R. | 23082 | 23102 | AAAGTACTACTACTCTGTATG | ||
S9 nested F. | 22652 | 22672 | GATTATTCTGTCCTATATAAT | 445 | |
S10 nested R. | 23076 | 23096 | CTACTACTCTGTATGGTTGGT | ||
S gene NTD SB12/SB8 Nested | SB11 primary F. | 21594 | 21614 | TCTCTAGTCAGTGTGTTAATC | 530 |
SB6 primary R. | 22103 | 22123 | TTTGAAATTACCCTGTTTTCC | ||
SB12 nested F. | 21609 | 22629 | TTAATCTTACAACCAGAACTC | 509 | |
SB8 nested R. | 22097 | 22117 | ATTACCCTGTTTTCCTTCAAG | ||
S gene NTD SB7/SB8 Nested | SB5 primary F. | 21619 | 21639 | AACCAGAACTCAATTACCCCC | 505 |
SB6 primary R. | 22103 | 22123 | TTTGAAATTACCCTGTTTTCC | ||
SB7 nested F. | 21628 | 21648 | TCAATTACCCCCTGCATACAC | 490 | |
SB8 nested R. | 22097 | 22117 | ATTACCCTGTTTTCCTTCAAG | ||
S gene RBD NF3/NR4 Nested | PF1 primary F. | 22357 | 22377 | TTATGTGGGTTATCTTCAACC | 451 |
PR2 primary R. | 22787 | 22807 | AGTTTGCCCTGGAGCGATTTG | ||
NF3 nested F. | 22361 | 22381 | GTGGGTTATCTTCAACCTAGG | 445 | |
NR4 nested R. | 22785 | 22805 | TTTGCCCTGGAGCGATTTGTC | ||
S gene NTD/RBD Junction for Omicron BA.1 & BA.2 SB13/NR4 Nested | SB14 primary F. | 22107 | 22127 | AACAGGGTAATTTCAAAAATC | 707(BA.1) 701(BA.2) |
PR2 primary R. | 22787 | 22807 | AGTTTGCCCTGGAGCGATTTG | ||
SB13 nested F. | 22112 | 22132 | GGTAATTTCAAAAATCTTAGG | 700 (BA.1) 694 (BA.2) | |
NR4 nested R. | 22785 | 22805 | TTTGCCCTGGAGCGATTTGTC | ||
S gene NTD/RBD Junction for Omicron BA.1 only.EF2/NR4 Nested | EF1 primary F. | 22184 | EPEins | ACGCCTATTATAGTGCGTGAG | 630 (BA.1) |
PR2 primary R. | 22787 | 22807 | AGTTTGCCCTGGAGCGATTTG | ||
EF2 nested F. | 22189 | EPEins | TATTATAGTGCGTGAGCCAGA | 623 (BA.1) | |
NR4 nestedR. | 22785 | 22805 | TTTGCCCTGGAGCGATTTGTC |