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.1.16.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
JN.1.16.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.57.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
JN.1.57.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.44.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
JN.1.44.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.2.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
JN.2.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XDP.3
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
XDP.3
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
KR.5
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
KR.5
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
KZ.1.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
KZ.1.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
KS.1.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
KS.1.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BA.1.19
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.19
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HN.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
HN.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
FL.9
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
FL.9
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HK.23.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
HK.23.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JE.1.1.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
JE.1.1.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.5.83
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
XBB.1.5.83
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.5.32
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
XBB.1.5.32
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XDD.3
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
XDD.3
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
KR.1.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
KR.1.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
MD.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
MD.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XDD.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-2798.28
Singapore
JN.1.64.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
JN.1.64.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XDQ.1.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
XDQ.1.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.18
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
JN.18
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
GJ.1.2.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
GJ.1.2.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HK.3.2.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
HK.3.2.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HK.2.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
HK.2.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
GW.5.3.1
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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