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.1.160.26
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-389.525
Hong Kong
BN.1.3.4
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BA.1.3
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BC.2
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
XBB.2.3.10
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
AY.43.8 (Delta)
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BA.2.36
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BA.5.2
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
JN.1.4.6
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BA.5.1.17
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
JN.1.63
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
EG.6
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
XBB.1.5.90
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
XBB.1.5.60
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
C.13
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BA.1.1.3
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
XBB.1.5.28
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
GA.2
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
XBB.1.11.1
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BQ.1.1.70
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BQ.1.1.69
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BR.2.1
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BQ.1.1.13
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
XBB.1.5.80
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
GD.1
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BQ.1.1.10
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BQ.1.1.6
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
HN.1
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
LB.1.3.1
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
MH.1
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
JN.1.24.1
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
MF.2
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
JN.1.49
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
KR.1.1
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
JN.1.7.3
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
B.1.274
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BA.2.3.8
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
XAQ
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
GA.7.2
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
B.1.1.53
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BA.5.8
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BA.2.3.18
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BA.2.3.2
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BM.3
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BF.28
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
CH.1.1.24
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
CQ.2
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
ED.1
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BF.7.4.3
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BA.5.2.47
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
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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