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.1.424
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.1.61
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.264
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.581
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.330
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.1.205
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.1.177
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.301
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.308
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.1.210
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.1.325
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.590
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.116
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.496
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-4484.57
China
B.1.438.4
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
AY.49 (Delta)
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
BA.2.25
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.1.237
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
XBN
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
XBJ.1
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.356
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.462
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
A.29
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.147
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
P.1.6 (Gamma)
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
P.1.5 (Gamma)
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
P.1.4 (Gamma)
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.420
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-4484.57
China
XBB.2.12
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
BF.39.1
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
EK.1
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.233
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
XBB.1.24
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.1.320
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
C.33
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.635
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
C.21
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
C.14
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
AY.19 (Delta)
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
N.4
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
AM.2
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
AY.15 (Delta)
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.1.113
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
GA.10
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
BF.5.2
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.423
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
AP.1
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
AK.1
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
AY.98.1.1
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
BA.1.13.1
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
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
Page 3728 of 5293
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