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
BN.1.9
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-22388.1
South Korea
BN.1.9
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
BQ.1.28
ORF1ab
Won-ORF1ab
CATGTGTGGCGGTTCACTAT
20
50
15441
15460
F
-22753.7
South Korea
BQ.1.28
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
BQ.1.28
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-22142.8
South Korea
BQ.1.28
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-21965.9
South Korea
BQ.1.28
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-18253.7
South Korea
BQ.1.28
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-19261.4
South Korea
BQ.1.28
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-22388.1
South Korea
BQ.1.28
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
BA.5.1.7
ORF1ab
Won-ORF1ab
CATGTGTGGCGGTTCACTAT
20
50
15441
15460
F
-22753.7
South Korea
BA.5.1.7
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
BA.5.1.7
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-22142.8
South Korea
BA.5.1.7
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-21965.9
South Korea
BA.5.1.7
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-18253.7
South Korea
BA.5.1.7
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-19261.4
South Korea
BA.5.1.7
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-22388.1
South Korea
BA.5.1.7
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
DE.2
ORF1ab
Won-ORF1ab
CATGTGTGGCGGTTCACTAT
20
50
15441
15460
F
-22753.7
South Korea
DE.2
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
DE.2
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-22142.8
South Korea
DE.2
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-21965.9
South Korea
DE.2
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-18253.7
South Korea
DE.2
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-19261.4
South Korea
DE.2
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-22388.1
South Korea
DE.2
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
BQ.2
ORF1ab
Won-ORF1ab
CATGTGTGGCGGTTCACTAT
20
50
15441
15460
F
-22753.7
South Korea
BQ.2
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
BQ.2
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-20083.2
South Korea
BQ.2
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-21965.9
South Korea
BQ.2
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-18253.7
South Korea
BQ.2
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-19261.4
South Korea
BQ.2
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-22388.1
South Korea
BQ.2
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
B.1.333
ORF1ab
Won-ORF1ab
CATGTGTGGCGGTTCACTAT
20
50
15441
15460
F
-22753.7
South Korea
B.1.333
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
B.1.333
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-2729.83
South Korea
B.1.333
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-21965.9
South Korea
B.1.333
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
B.1.333
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-19261.4
South Korea
B.1.333
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-22388.1
South Korea
B.1.333
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-1923.32
South Korea
CM.6.1
ORF1ab
Won-ORF1ab
CATGTGTGGCGGTTCACTAT
20
50
15441
15460
F
-22753.7
South Korea
CM.6.1
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
CM.6.1
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-22142.8
South Korea
CM.6.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-21965.9
South Korea
CM.6.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-18253.7
South Korea
CM.6.1
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-19261.4
South Korea
CM.6.1
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-22388.1
South Korea
CM.6.1
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
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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