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
C.13
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
BC.2
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
BN.1.3.12
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
XDK.2
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
XDN
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
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
BA.5.2.21
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
BA.5.2.9
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
BF.41
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
BF.7.4.3
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
BF.28
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
B.1.1.53
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
B.1.504
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
AY.29.2 (Delta)
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
B.1.1.74
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
AY.39.3 (Delta)
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
AT.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
B.1.160.10
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
B.1.177.71
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
B.1.1.445
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
B.1.1.391
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
BA.2.3.8
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
GA.7.2
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
CM.11
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-3387.47
China
CM.6
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-3387.47
China
CM.8.1.5
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-3387.47
China
CM.9
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-3387.47
China
CM.5.2
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-3387.47
China
CM.8.1.3
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-3387.47
China
BA.5.2.13
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-3406.8
South Korea
HK.3.7
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-3418.08
Japan
FY.4.1
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-3418.08
Japan
HK.32
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-3418.08
Japan
GN.2
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-3418.08
Japan
FY.1.2.1
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-3418.08
Japan
BA.2.9.7
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-3418.08
Japan
EN.1.1
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-3418.08
Japan
B.1.287
S
WuhanCoV-spk1
TGTGGTTCATAAAAATTCCTTTGTG
25
32
24900
24876
R
-3421.45
Japan
XBB.1.16.17
S
WuhanCoV-spk1
TGTGGTTCATAAAAATTCCTTTGTG
25
32
24900
24876
R
-3421.45
Japan
GK.2
S
WuhanCoV-spk1
TGTGGTTCATAAAAATTCCTTTGTG
25
32
24900
24876
R
-3421.45
Japan
JN.1.1.9
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-3469.33
Japan
B.1.6
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-3484.59
South Korea
B.1.444
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-3484.59
South Korea
B.1.537
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-3484.59
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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