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
GK.2.4
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-1981.59
Japan
JN.1.1.10
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-1981.59
Japan
JN.4
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-1981.59
Japan
BA.2.86
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-1981.59
Japan
GK.2
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-1981.59
Japan
HN.5
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-1981.59
Japan
XCR
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-1981.59
Japan
GW.5.3
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-1981.59
Japan
HN.6
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-1988.81
Singapore
FL.25
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-1988.81
Singapore
GN.4
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-1988.81
Singapore
B.1.595.3
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-1988.81
Singapore
B.1.2
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-1988.81
Singapore
GA.4.1
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-1988.81
Singapore
BQ.1.1.70
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-1988.81
Singapore
BC.1
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-1988.81
Singapore
B.1.1.53
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-1988.81
Singapore
BA.2.75.1
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-1988.81
Singapore
FF.1
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-1988.81
Singapore
XBB.1.5.90
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
FT.3
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
JN.1.4.1
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
BQ.1.1.10
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
BQ.1.1.56
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
JN.1.18.7
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
XBB.1.9
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
XBB.1.16.7
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
GW.4
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
HY.1
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
HC.4
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
HW.1
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
GS.3
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
HK.12
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
BA.2.86.2
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
DV.7.1.2
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
XDE
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
KH.1
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
XDD.1
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
XBV
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
BA.2.3.2
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-2005.91
Singapore
BA.2.3.8
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-2013.34
China
XDN
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-2013.34
China
BN.1.3.12
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-2013.34
China
XDK.2
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-2013.34
China
JN.1.4.6
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-2013.34
China
FL.32.1
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-2013.34
China
GA.8
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-2013.34
China
GE.1.2.1
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-2013.34
China
MD.3
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-2013.34
China
KR.4
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-2013.34
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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