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