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.3.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-3872.72
Singapore
JN.3.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-2798.28
Singapore
GE.1.2.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-17071
Singapore
GE.1.2.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.58.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
JN.1.58.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.11.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
XBB.1.11.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
GJ.1.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
GJ.1.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HJ.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
HJ.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.5.101
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
XBB.1.5.101
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.31
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
XBB.1.31
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.5.28
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-3120.32
Singapore
XBB.1.5.28
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-2999.47
Singapore
XBB.1.5.84
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
XBB.1.5.84
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
EU.1.1.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-2999.47
Singapore
XBB.1.5.97
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
XBB.1.5.97
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
CH.1.1.14
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
CH.1.1.14
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
FE.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
FE.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
GB.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
GB.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
FY.2.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
FY.2.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.13
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
XBB.1.13
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
FL.11
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
FL.11
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
FL.4.1.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
FL.4.1.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
FD.2.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
FD.2.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
FP.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
FP.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
FD.3
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
FD.3
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
FG.3
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
FG.3
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.5.19
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
XBB.1.5.19
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BQ.1.1.56
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-2643.45
Singapore
BQ.1.1.56
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-2999.47
Singapore
XBB.1.5.31
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
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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