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
JN.1.1.9
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13317.5
China
JN.1.1.9
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.1.9
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
JN.1.1.9
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-25148.4
US
JN.1.1.9
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-22762.7
Japan
JN.19
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-20695.4
Singapore
JN.19
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
JN.19
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13317.5
China
JN.19
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.19
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
JN.19
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-25148.4
US
JN.19
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-22762.7
Japan
KU.1
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-20695.4
Singapore
KU.1
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
KU.1
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13317.5
China
KU.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
KU.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
KU.1
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-25148.4
US
KU.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-22762.7
Japan
KZ.1
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-20695.4
Singapore
KZ.1
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
KZ.1
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13317.5
China
KZ.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
KZ.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
KZ.1
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-25148.4
US
KZ.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-22762.7
Japan
JN.1.36
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-20695.4
Singapore
JN.1.36
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
JN.1.36
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13317.5
China
JN.1.36
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.36
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
JN.1.36
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-25148.4
US
JN.1.36
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-22762.7
Japan
JQ.2.1
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-20695.4
Singapore
JQ.2.1
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
JQ.2.1
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13317.5
China
JQ.2.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JQ.2.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
JQ.2.1
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-25148.4
US
JQ.2.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-22762.7
Japan
KT.1
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-20695.4
Singapore
KT.1
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
KT.1
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13317.5
China
KT.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
KT.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
KT.1
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-25148.4
US
KT.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
LA.2
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-20695.4
Singapore
LA.2
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
LA.2
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13317.5
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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