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.5.1.7
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
DE.2
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BQ.2
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
B.1.333
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BQ.1.1.62
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
GA.7
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
FL.23
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
XBB.2.3.13
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
B.1.160
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
JV.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
XCY
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
HK.16
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-2477.92
Hong Kong
JN.1.1.4
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
EK.4
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
HV.1.10
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
HV.1.6.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
EF.1.2
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BU.3
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.5.1.38
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.5.2.34
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BF.7.12
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
CJ.1.2
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BQ.1.1.21
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.4.6.3
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
CM.7.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.5.3.3
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BQ.1.22
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BF.7.19
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
FA.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
EE.4
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BQ.1.1.72
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
XBJ.2
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BF.14
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
CK.2.1.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
KP.5
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
XDP.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
KP.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
JN.1.31
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
JN.1.11.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
JD.1.1.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
JN.1.13.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
JN.1.32.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
JN.1.4.7
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.2.86.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
JN.1.34
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
HK.3.2
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
JN.1.6
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
JG.3.2
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
JN.1.4
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
JN.1.22
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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