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
BA.4.1.11
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
CQ.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.5.2.13
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
XM
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.1.1.4
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.2.70
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.2.63
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.4.1.4
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BQ.1.8.2
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
EC.1.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BM.1.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
XL
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BD.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
AY.87 (Delta)
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.2.23.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
XN
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
AY.111 (Delta)
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BM.5
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.5.1.31
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.5.2.30
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
CG.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.5.2.16
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BQ.1.20
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
CH.1.1.30
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.2.8
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BF.7.11
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
CE.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.2.6
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-17626
Hong Kong
EA.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.2.22
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
DH.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
XG
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BF.6
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.2.9.5
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.5.6.4
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.2.34
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
CH.1.1.12
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.2.9.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BN.1.4.4
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.5.2.58
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
XAY.2.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.2.71
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
XBC.1.2.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
CP.6
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.5.3
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
DN.1.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
CL.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
XBB.3.2
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BN.1.2.4
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
CH.1.1.25
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
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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