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
B.1.570
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-22844.7
China
B.1.570
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17028.5
South Korea
B.1.633
ORF1ab
Won-ORF1ab
CATGTGTGGCGGTTCACTAT
20
50
15441
15460
F
-22753.7
South Korea
B.1.633
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.633
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-12026.7
South Korea
B.1.633
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-21965.9
South Korea
B.1.633
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-19261.4
South Korea
B.1.633
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-18666.6
China
B.1.633
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-22388.1
South Korea
DD.1
ORF1ab
Won-ORF1ab
CATGTGTGGCGGTTCACTAT
20
50
15441
15460
F
-22753.7
South Korea
DD.1
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
DD.1
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-22142.8
South Korea
DD.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-21965.9
South Korea
DD.1
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-19261.4
South Korea
DD.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
DD.1
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-22388.1
South Korea
B.1.1.136
ORF1ab
Won-ORF1ab
CATGTGTGGCGGTTCACTAT
20
50
15441
15460
F
-22753.7
South Korea
B.1.1.136
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.1.136
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-22142.8
South Korea
B.1.1.136
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-21965.9
South Korea
B.1.1.136
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-19261.4
South Korea
B.1.1.136
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.1.136
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-22388.1
South Korea
XAY
ORF1ab
Won-ORF1ab
CATGTGTGGCGGTTCACTAT
20
50
15441
15460
F
-19758.2
South Korea
XAY
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
XAY
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-22142.8
South Korea
XAY
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-21965.9
South Korea
XAY
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-19261.4
South Korea
XAY
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XAY
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-22388.1
South Korea
DJ.1
ORF1ab
Won-ORF1ab
CATGTGTGGCGGTTCACTAT
20
50
15441
15460
F
-22753.7
South Korea
DJ.1
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
DJ.1
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-22142.8
South Korea
DJ.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-21965.9
South Korea
DJ.1
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-19261.4
South Korea
DJ.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
DJ.1
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-22388.1
South Korea
XAE
ORF1ab
Won-ORF1ab
CATGTGTGGCGGTTCACTAT
20
50
15441
15460
F
-22753.7
South Korea
XAE
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
XAE
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-22142.8
South Korea
XAE
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-21965.9
South Korea
XAE
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-19261.4
South Korea
XAE
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XAE
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-22388.1
South Korea
B.1.467
ORF1ab
Won-ORF1ab
CATGTGTGGCGGTTCACTAT
20
50
15441
15460
F
-22753.7
South Korea
B.1.467
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
B.1.467
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-22142.8
South Korea
B.1.467
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-21965.9
South Korea
B.1.467
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-19261.4
South Korea
B.1.467
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-22844.7
China
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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