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
FL.5
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
FU.3
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.16
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BN.1.3.6
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BN.1.3.8
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.57
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BN.1.2.3
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BN.1.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BN.1.1.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
FL.10.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.16.4
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.9.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.16.22
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.5.76
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.5.39
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.5.43
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.121 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-18863.5
Singapore
AY.14 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.119 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.46.2 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.114 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.54 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.64 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.46.4 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.107 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.81 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.117 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.118 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.27 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
B.1.617.2 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.67 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.110 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.39.1 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.20 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.42 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.62 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.113 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.4 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.43 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.98.1 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.127 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.83 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.4.2 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.1 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BA.1.1.16
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.16.18
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.2.3.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
FL.2.3
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.5.15
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.2.3.6
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
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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