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
AY.131 (Delta)
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.586
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.366
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.1.380
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.1.148
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XBB.1.5.100
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XBB.1.16.19
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XBB.1.43.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
EU.1.1.3
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XBB.1.5.18
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XBB.1.5.48
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XBB.1.5.10
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
EK.2.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XBB.1.5.2
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XBB.1.5.66
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XBB.1.5.4
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XDH
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
FL.15.2
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
EG.2.2
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XBB.1.16.32
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.1.273
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
AY.4.13 (Delta)
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.1.358
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
C.28
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.177.60
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.1.159
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.29
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
HD.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
GY.4
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
HH.6
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
KN.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
AY.43.1 (Delta)
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.1.332
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
JB.2.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
BA.2.86.7
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.12
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
JW.1.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.1.133
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.18
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.1.466
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-19104
China
B.1.489
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.1.363
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.1.95
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.36.26
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.531
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.1.45
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.1.200
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
BF.35
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
CY.2
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
FR.2
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
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 4194 of 5293
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