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
DV.7
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
DV.7
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13317.5
China
DV.7
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
DV.7
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
DV.7
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-25148.4
US
DV.7
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
CH.1.1.3
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-20695.4
Singapore
CH.1.1.3
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
CH.1.1.3
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13317.5
China
CH.1.1.3
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
CH.1.1.3
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
CH.1.1.3
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-25148.4
US
CH.1.1.3
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
XBB.2.3.9
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
XBB.2.3.9
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13317.5
China
XBB.2.3.9
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-18611
Singapore
XBB.2.3.9
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
XBB.2.3.9
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-25148.4
US
XBB.2.3.9
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
XBB.1.5.47
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-20695.4
Singapore
XBB.1.5.47
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
XBB.1.5.47
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-17292.3
China
XBB.1.5.47
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.5.47
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
XBB.1.5.47
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-25148.4
US
XBB.1.5.47
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
BQ.1.1.13
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-20695.4
Singapore
BQ.1.1.13
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
BQ.1.1.13
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13317.5
China
BQ.1.1.13
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BQ.1.1.13
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
BQ.1.1.13
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-25148.4
US
BQ.1.1.13
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
BN.1.10
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-20695.4
Singapore
BN.1.10
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
BN.1.10
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13317.5
China
BN.1.10
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BN.1.10
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
BN.1.10
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-25148.4
US
BN.1.10
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
XBB.1.5.23
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-20695.4
Singapore
XBB.1.5.23
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
XBB.1.5.23
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-17292.3
China
XBB.1.5.23
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.5.23
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
XBB.1.5.23
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-25148.4
US
XBB.1.5.23
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
GA.3
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-20695.4
Singapore
GA.3
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
GA.3
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-17292.3
China
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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