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
FY.4.1.2
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18353.2
South Korea
P.1 (Gamma)
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-18356.8
Japan
B.1.1.300
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-18362.1
US
XD
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-18417.7
China
B.19
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-18418.6
Thailand
B.1.1.352
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-18427.7
US
B.1.428.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-18427.7
US
XBJ.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-18427.7
US
B.1.177.74
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-18427.7
US
HK.13
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-18427.7
US
BF.19
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-18427.7
US
HV.1.10
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-18436.1
Japan
B.1.118
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-18439.3
China
BA.1.17.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
XF
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.13.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.1.7
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
XS
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
CU.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BC.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.22
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.2
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
XD
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.21.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.1.11
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.1.6
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.19
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
KP.3.3.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.1.16
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
HZ.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.18
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.21
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.1.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.15.2
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.15.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.1.18
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.1.2
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.1.14
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.20
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.17
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.1.8
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.1.10
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.9
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
LK.2.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.15
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.14.2
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.14.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1 (Omicron)
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.17.2
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BF.19
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
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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