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.5.2.41
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
BF.7.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
BF.7.13.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
BF.7.9
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
CP.1.2
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
BF.3.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
BA.5.2.4
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
BF.7.3
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
BF.19
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
BA.5.2.51
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
BA.5.2.11
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
CY.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
XBT
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
XBM
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
BF.34
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
CP.4
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
CP.8
ORF1ab
Charité-ORF1b
CARATGTTAAASACACTATTAGCATA
26
23.08
15530
15505
R
-4260.71
Germany
MB.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-4251.49
China
EG.2.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-4251.49
China
GK.1.10
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-4251.49
China
EG.10.1.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-4251.49
China
GJ.1.2.4
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-4251.49
China
BF.5
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-4251.49
China
BA.2.58
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-4251.49
China
A.27
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-4251.49
China
BT.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.2.76
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.4.6
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.5.6.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.5.1.10
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BS.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.5.1.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BQ.1.18
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BN.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.5.9
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BL.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
CQ.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.2.51
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.2.3.18
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.2.3.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.2.65
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BG.5
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.2.61
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.5.1.23
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.2.74
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BM.3
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.5.8
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.2.13.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.5.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BE.1.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
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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