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.1.371
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
B.4.4
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
FY.6.1
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
HU.2
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
EG.1.4.1
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
KJ.1
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
JC.6
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
B.1.1.148
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
B.1.382
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
B.1.1.356
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
B.1.1.376
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
B.1.607
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
B.1.163
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
B.1.337
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
B.1.1.158
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
B.1.602
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
B.1.289
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
DV.7.1.6
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
XBB.1.5.4
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
EG.1.7
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
GS.2
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
B.1.258.17
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-2242.74
Japan
BA.1.21.1
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
BA.5.1.37
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
XBB.1.39
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
EE.3
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
DV.4
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
ES.1
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
XBB.1.5.41
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
XBB.2.3.18
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
XBC.1.6.5
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
FL.39
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
B.1.1.141
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
B.1.591
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
B.1.468
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
AY.131 (Delta)
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
B.1.586
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
B.1.366
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
B.1.1.380
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
BF.37
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
CK.3
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
CM.5
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
XBC.1.3.1
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
JN.11.1
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
XDL
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
JN.17
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
AY.29.1 (Delta)
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
AY.29.2 (Delta)
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
BC.1
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
BA.2.10.1
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
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 4940 of 5293
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