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
CH.1.1.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
BA.2.75.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BA.2.75.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
BQ.1.1.66
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BQ.1.1.66
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
BN.1.3.12
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BN.1.3.12
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
CH.1.1.19
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
CH.1.1.19
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
BM.4.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BM.4.1.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
BA.5.2.35
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BA.5.2.35
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
BA.4.6.5
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BA.4.6.5
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
BA.2.18
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BA.2.18
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
BA.2.12.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BA.2.12.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
KP.2.3.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KP.2.3.2
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
LQ.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LQ.1.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
LY.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LY.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
MD.3.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
MD.3.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
MK.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
MK.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
LZ.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LZ.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
MB.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
MB.1.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
KP.3.2.4
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KP.3.2.4
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JN.1.50
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.50
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
KP.2.14
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KP.2.14
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-2584.54
Japan
unclassifiable
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
unclassifiable
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
KS.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KS.1.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
FL.1.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
FL.1.2
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
FY.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
FY.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
HH.2.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
HH.2.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
XCE
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
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
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