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.32.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
C.13
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
XDN
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
BN.1.3.12
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
JN.1.4.6
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
XDK.2
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
AY.43.8 (Delta)
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
AY.4.9 (Delta)
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
GE.1.2.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
B.1.277
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
B.1.160.17
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
BA.1.1.3
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
B.1.160.8
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
BA.1.23
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
BA.1.3
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
GA.8
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
BC.2
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
BF.7.4
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
BQ.1.1.5
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
BQ.1.1.69
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
GD.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
MD.3
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
LF.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
KR.4
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
JN.1.7.3
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
KR.1.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
MF.2
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
B.1.637
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
JN.1.24.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
JN.1.29.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
KP.2.8
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
JN.1.11
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
JN.1.24.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
JN.1.18.2
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
LU.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
JN.1.40
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
MG.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
JN.1.59
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
LG.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
KP.2.10
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
LK.2.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
LB.1.7.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
KP.2.9
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
KP.2.7
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
LD.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
KP.1.2
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
KW.1.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
KR.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
JN.1.15.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
JN.1.50.2
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
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
Page 5182 of 5293
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