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
GA.2
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
GA.2
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.1.5.6
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.1.5.6
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.1.5.67
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.1.5.67
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
FL.2.6
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
DV.8
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
DV.8
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.1.11.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.1.11.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
GJ.1.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
GJ.1.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
HJ.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
HJ.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.1.5.101
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.1.5.101
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.1.31
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.1.31
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
EF.1.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
EF.1.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.1.5.84
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.1.5.84
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
EU.1.1.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
EU.1.1.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.1.5.97
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.1.5.97
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
CH.1.1.14
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
CH.1.1.14
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-18660.1
China
FE.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
FE.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.1.5.31
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.1.5.31
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.1.5.22
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.1.5.22
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
EN.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
EN.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.2.3.14
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.2.3.14
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
FL.13
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
FL.13
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
FD.2.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
FD.2.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
FP.2
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
FP.2
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
FD.3
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
FD.3
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
FG.3
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
FG.3
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.1.5.19
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
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
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