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
BA.1.1.9
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.1.3
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.16.2
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
DT.2
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.6
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.1.17
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.5
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.14
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.1.4
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BD.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.13
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
HW.1.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.1 (Omicron)
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.23
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.3
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BC.2
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.15.3
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.16.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.4
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.8
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.12
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.7
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.1.12
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.1.13
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
XP
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.1.15
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.10
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BA.1.16
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-18441.9
South Korea
BQ.1.1.47
S
NIID WH-1 Seq F24383R24865
AAGACTCACTTTCTTCCACAG
21
42.86
24366
24386
F
-18462.8
Japan
DV.6.2
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-18465.4
China
BN.1.3.9
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-18467.4
China
B.1.525 (Eta)
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-18468.8
US
B.1.391
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-18468.8
US
FY.2.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-18468.8
US
AY.5.3 (Delta)
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-18472.8
Japan
XBB.2.3.21
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-18472.8
Japan
B.1.1.333
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-18472.8
Japan
B.50
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-18475.5
Japan
B.1.351 (Beta)
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-18475.6
China
B.1.36.33
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-18475.6
China
B.1.177.2
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-18479.4
China
B.1.263
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-18479.4
China
B.1.1.132
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-18479.4
China
AY.103 (Delta)
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-18479.4
China
B.1.1.486
S
NIID WH-1 Seq F24383R24865
AAGACTCACTTTCTTCCACAG
21
42.86
24366
24386
F
-18481
Japan
B.1.351 (Beta)
S
NIID WH-1 Seq F24383R24865
AAGACTCACTTTCTTCCACAG
21
42.86
24366
24386
F
-18481
Japan
B.1.1.423
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-18483.1
Japan
XBB.1.5.93
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-18483.6
Japan
GQ.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-18483.6
Japan
GA.4.1.2
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-18487.6
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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