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
LK.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
LK.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
XDS
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XDS
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
LY.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
LY.2
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
XDQ.1.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XDQ.1.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
JN.18
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.18
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
GJ.1.2.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
GJ.1.2.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
HK.3.2.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HK.3.2.2
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
HK.2.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HK.2.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
GW.5.3.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
GW.5.3.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
FL.9
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
FL.9
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
HK.23.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HK.23.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
JE.1.1.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JE.1.1.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
XBB.1.5.83
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.5.83
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
XBB.1.5.32
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.5.32
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
HN.3
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HN.3
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
HK.13
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HK.13
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
JN.1.29.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.29.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
KP.2.8
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
KP.2.8
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
JN.1.11
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.11
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
JN.1.24.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.24.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
JN.1.18.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.18.2
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
LU.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
LU.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
JN.1.40
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.40
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
MG.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
MG.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
JN.1.59
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.59
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
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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