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
B.1.580
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
B.1.306
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
B.1.280
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
B.1.1.329
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
B.1.396
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
B.1.595.3
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
B.1.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
B.1.311
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
B.1.369
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
B.1.367
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
B.1.595
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
B.1.240
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
DL.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BA.5.1.15
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
B.1.1.529 (Omicron)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BF.41.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BF.39
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BA.2.3.20
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.33 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BE.10
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BA.1.15
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BA.1.14.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BA.1.14.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BA.1 (Omicron)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
BA.1.17.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
AY.99.2 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.52
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.42
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-3736.39
Singapore
KB.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.14
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
MJ.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.1.6
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.39.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-3736.39
Singapore
JN.1.58.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.18.3
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
LF.4.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XDK.1.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XBB.1.5.20
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
LB.1.7.3
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.18.5
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.16.3
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
KP.3.2.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
KP.4.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
KP.3.2.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
JN.1.65.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
LF.1.1.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
XDV
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
KS.1.3
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
MK.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
KP.4.1.2
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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