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
BA.2.71
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
XBC.1.2.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.5.3
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
DN.1.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
CL.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BN.1.2.4
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
CH.1.1.25
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
CH.1.1.16
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
CZ.2
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.5.1.18
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BQ.1.1.29
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.4.1.2
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.2.47
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
FK.1.2.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
XBC.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BQ.1.26.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
DS.3
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.5.1.11
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.5.3.2
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BE.2
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BQ.1.1.9
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BF.11.3
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
XBF.3
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BQ.1.10.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.5.10
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.2.44
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BE.1.4
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.5.5.2
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.2.37
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.4.5
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.2.54
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.2.52
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BL.3
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.2.48
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
JQ.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.5.10.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BL.5
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BL.2
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BE.7
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
FS.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
XBB.1.5.54
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
N.5
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
P.1.15 (Gamma)
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
B.1.1.348
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
B.1.575
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
C.26
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
Q.4 (Alpha)
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
B.1.1.442
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
P.1.1 (Gamma)
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
A.2.5.2
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
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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