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
CJ.1.2
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
BA.5.3.3
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
GK.1.6
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
HN.8
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
BA.5.11
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
XBB.1.5.54
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
BA.5.3
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
BA.5.1.18
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
BA.5.6.3
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
CQ.1.1
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
XAD
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
XAY.1.1.1
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
CH.1.1.21
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
BN.1.3.9
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
BA.5 (Omicron)
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
CH.1.1.28
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
BF.5
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
JN.7
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
BM.2
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
XDV
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-17732.3
China
B.1.617.2 (Delta)
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-17730
US
GJ.1.1
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-17730
US
B.1.115
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-17729.2
Hong Kong
B.1.177.74
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-17729.2
Hong Kong
BA.2.12.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-17729.2
Hong Kong
FM.2
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-17729.2
Hong Kong
A.24
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17727.2
South Korea
CM.8.1.5
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17723.5
South Korea
XBB.1.16.6
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17723.5
South Korea
B.1.1.517
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17723.5
South Korea
B.1.397
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17723.5
South Korea
BF.32
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17723.5
South Korea
FK.1
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17723.5
South Korea
CH.1.1.18
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17723.5
South Korea
B.1.1.228
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17723.5
South Korea
B.1.1.174
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17723.5
South Korea
BA.2.55
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-17718.1
Japan
BA.2.13.1
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-17718.1
Japan
XBB.1.5.97
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-17718.1
Japan
KB.1
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-17718.1
Japan
A.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-17715.7
South Korea
B.1.597
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-17713.6
Hong Kong
FK.1.4.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-17713.6
Hong Kong
N.4
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-17710.7
China
FY.8.1.1
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-17683
South Korea
EG.5.1.19
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-17683
South Korea
XBB.1.37
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17676.7
Japan
BN.1.4.2
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17676.7
Japan
BA.5.5.2
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-17667.3
South Korea
AY.61 (Delta)
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-17667.3
South Korea
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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