Enabled by data from
assayM COVID-19: track sensitivity of RT-PCR primers on COVID-19 Variants
#last Updated:
Sunday, 15 September 2024 05:10:01 GMT+3 (Arabian Standard Time)
, based on 3892 variants (from 8.94 million sequences) and 34 primer sets.
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Prediction results retrieved after performance evaluation of WHO approved 34 primers to estimate their binding affinities for 3892 SARS-CoV-2 variants.
Lineage
(WHO label)
Target Gene
Primer Name
Primer Sequence
Primer Length
Primer GC Content (%)
Start Position
End Position
Primer Direction
ΔG (cal)
Primer first used
BA.2.75.8
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
CH.1
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
CH.1
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-17655.9
Hong Kong
CH.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
CH.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
B.1.570
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
B.1.570
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-17655.9
Hong Kong
B.1.570
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
B.1.570
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
B.1.633
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
B.1.633
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-17655.9
Hong Kong
B.1.633
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
B.1.633
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
DD.1
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
DD.1
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-17655.9
Hong Kong
DD.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
DD.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
B.1.1.136
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
B.1.1.136
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-17655.9
Hong Kong
B.1.1.136
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
B.1.1.136
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
XAY
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
XAY
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-17655.9
Hong Kong
XAY
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XAY
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.2.3.8
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
BA.2.3.8
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
B.1.569
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
B.1.569
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-17655.9
Hong Kong
B.1.569
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
B.1.569
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
B.1.524
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
B.1.524
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-17655.9
Hong Kong
B.1.524
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
B.1.524
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
A.23
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
A.23
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-17655.9
Hong Kong
A.23
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
A.23
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
B.1.596.1
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
B.1.596.1
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-17655.9
Hong Kong
B.1.596.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
B.1.596.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
B.1.473
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-4768.1
Hong Kong
B.1.473
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-17655.9
Hong Kong
B.1.473
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
B.1.473
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
B.1.595.2
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7228.39
Hong Kong
B.1.595.2
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-17655.9
Hong Kong
B.1.595.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
Lineage
(WHO label)
Target Gene
Primer Name
Primer Sequence
Primer Length
Primer GC Content (%)
Start Position
End Position
Primer Direction
ΔG (cal)
Primer first used
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