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
FL.8
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
FL.8
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.1.5.71
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.1.5.71
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
FD.1.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
FD.1.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.2.3.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.2.3.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
GK.1.3
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
GK.1.3
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
EG.3
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
EG.3
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.1.5.8
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.1.5.8
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
EG.2.3
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
EG.2.3
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.1.5.37
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.1.5.37
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XAY.2
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XAY.2
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.1.16.5
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.1.16.5
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.1.5.60
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.1.5.60
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
FH.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
FH.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
CJ.1.3
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
CJ.1.3
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
AY.5.4 (Delta)
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
AY.5.4 (Delta)
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
B.1.1.323
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
B.1.1.323
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
B.15
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
B.15
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
AY.105 (Delta)
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
AY.105 (Delta)
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
AY.4.4 (Delta)
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
AY.4.4 (Delta)
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
AY.4.9 (Delta)
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
AY.4.9 (Delta)
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
B.1.250
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
B.1.250
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
B.1.177.63
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
B.1.177.63
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
B.27
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
B.27
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
B.23
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
B.23
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
B.1.1.130
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
B.1.1.130
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
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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