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
EG.5.2.3
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
B.11
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-552.006
Thailand
B.11
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-2082.55
Thailand
DV.7.1.5
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
DV.7.1.5
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
XBB.1.16.23
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
XBB.1.16.23
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
GN.1.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
GN.1.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
JH.2
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
JH.2
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
HK.3.9
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
HK.3.9
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
EG.6.1.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
EG.6.1.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
FD.5.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
FD.5.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
DV.7.1.2
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
DV.7.1.2
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
DV.7.1.4
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-552.006
Thailand
DV.7.1.4
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-2082.55
Thailand
XCL
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
XCL
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
XCH.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
XCH.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
XCT
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
XCT
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
KB.4
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
KB.4
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
HF.1.2
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
HF.1.2
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
BG.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BG.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
JN.1.42.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
JN.1.42.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
BQ.1.1.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BQ.1.1.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
B.1.1.517
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
B.1.1.517
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-22126.5
Thailand
B.1.427 (Epsilon)
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
B.1.427 (Epsilon)
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-22126.5
Thailand
B.1.429 (Epsilon)
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
B.1.429 (Epsilon)
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-22126.5
Thailand
HV.1.10
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
HV.1.10
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
HV.1.6.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
HV.1.6.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
EF.1.2
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
EF.1.2
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
BU.3
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-18184
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
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