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
BF.11.5
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
XBF.7.1
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
FY.5.3
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
FP.2.1.1
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
XBB.2.9
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
FL.2.2
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
JW.1
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
JL.1
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
B.1.571
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
AY.55 (Delta)
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
XAM
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
B.1.1.239
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
B.1.574
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
B.1.493
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
B.1.351.2 (Beta)
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
B.1.640.2
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
B.1.1.352
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
B.1.1.251
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
HC.1
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
XCJ
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
FT.2
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
FZ.2
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
FY.4
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
B.1.497
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
B.1.355
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
GA.7.2
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
B.1.403
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
A.27
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
BQ.1.1.30
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
BQ.1.9
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
GW.2
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
XBB.1.40
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
FY.7
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
BQ.1.2.2
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
B.1.1.367
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
GK.1.9
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
BN.1.3.13
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
B.1.385
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
XBB.1.5.45
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-1313
China
B.1.1.244
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
JD.2.1
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
EP.1
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
FL.17.2
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
EG.12
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
CM.7.1.1
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
FL.10.2
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
FD.1
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
KG.2
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
XBB.1.5.13
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
HA.2
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
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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