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
KP.3.3.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
KP.3.3.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
ML.2
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
ML.2
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
KP.2.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
KP.2.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
KP.3.1.6
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
KP.3.1.6
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
KP.3.3
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
KP.3.3
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
KP.3.1.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
KP.3.1.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
LB.1.4
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
LB.1.4
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XDY
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XDY
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
JN.1.18.4
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
JN.1.18.4
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
KP.4.1.3
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
KP.4.1.3
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
KS.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
KS.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
MM.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
MM.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
JN.1.48.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
JN.1.48.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
LB.1.7
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
LB.1.7
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
JN.1.16.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
JN.1.16.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
LW.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
LW.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
LP.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
LP.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-17507.2
China
LB.1.2.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
LB.1.2.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
KP.3.3.3
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
KP.3.3.3
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBL.3.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBL.3.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.2.4
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.2.4
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.1.28.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.1.28.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
GA.6.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
GA.6.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.1.5.61
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.1.5.61
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
FR.1.2
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
FR.1.2
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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