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
BQ.1.1.31
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
GA.6
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
GA.6
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.5.12
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
XBB.1.5.12
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.2.3.9
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
XBB.2.3.9
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-18611
Singapore
XBB.1.5.47
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
XBB.1.5.47
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BQ.1.1.13
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
BQ.1.1.13
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XCY
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
XCY
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HK.16
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
HK.16
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.1.4
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
JN.1.1.4
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
EK.4
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
EK.4
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HV.1.10
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
HV.1.10
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HV.1.6.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
HV.1.6.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HK.7
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
HK.7
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HS.1.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
HS.1.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HH.5
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
HH.5
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HU.1.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
HU.1.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HV.1.5
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
HV.1.5
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BA.5.11
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
BA.5.11
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
HV.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
HV.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
KK.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
KK.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
FY.1.4.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
FY.1.4.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.5
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
JN.5
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JG.3.4
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
JG.3.4
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XCV
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
XCV
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BA.2.31.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-18860.4
Singapore
BA.2.31.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BA.2.50
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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