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
AA.3
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
AA.8
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
B.1.163
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
B.1.497
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
AA.5
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
C.14
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
AY.43.5 (Delta)
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
AA.6
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
AA.7
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
B.1.177.15
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
AA.1
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
AA.4
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
B.1.402
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
A.30
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
DL.1
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
BA.5.1.15
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
BF.41.1
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
BF.39
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
BA.2.3.20
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
BE.10
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
HK.13
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17121.6
US
AY.117 (Delta)
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-17128.2
France
AY.46.3 (Delta)
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-17128.2
France
GW.2
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-17130.7
Japan
AY.112.3 (Delta)
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-17130.7
Japan
HH.8
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-17131.6
South Korea
HG.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-17135.3
Japan
XBB.1.5.56
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-17139.2
China
GA.7.2
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17139.9
Singapore
JW.1
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17147.9
Japan
BF.39.1
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17147.9
Japan
D.3
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17147.9
Japan
AY.120.1 (Delta)
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17147.9
Japan
BE.10
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17147.9
Japan
B.1.623
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-17161.5
China
JN.1.61
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-17161.5
China
BQ.1.1.24
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-17161.5
China
HK.3.7
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-17161.5
China
HW.1.1
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-17161.5
China
XBB.1.16.16
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-17161.5
China
B.1.273
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-17161.5
China
B.1.415.1
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-17161.5
China
B.1.177.21
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-17161.5
China
AM.3
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17162.5
Japan
EE.4
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17162.5
Japan
EZ.1
E
Charité-E
ACAGGTACGTTAATAGTTAATAGCGT
26
34.62
26269
26294
F
-17195.6
Germany
BQ.1.1.43
E
Charité-E
ACAGGTACGTTAATAGTTAATAGCGT
26
34.62
26269
26294
F
-17195.6
Germany
BE.7
E
Charité-E
ACAGGTACGTTAATAGTTAATAGCGT
26
34.62
26269
26294
F
-17195.6
Germany
CM.9
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-17205
US
KP.2.13
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-17205
US
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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