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.1.367
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-19600.9
Germany
B.1.597
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-19600.9
Germany
AY.134
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-19590.4
Germany
XAA
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-19568.4
US
BN.1.4
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19563.7
Singapore
AY.108 (Delta)
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-19557.5
Japan
BM.5
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-19557.5
Japan
HQ.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-19557.5
Japan
JN.1.18.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-19557.5
Japan
B.1.444
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-19557.5
Japan
B.1.258.17
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-19557.5
Japan
B.1.308
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-19557.5
Japan
AA.2
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-19557.5
Japan
B.1.258.11
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-19557.5
Japan
B.1.35
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-19557.5
Japan
B.1.1.285
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-19557.5
Japan
HK.13.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-19557.5
Japan
JN.1.53
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-19557.5
Japan
FL.2.2.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-19557.5
Japan
LL.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-19557.5
Japan
XDP.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-19548.1
Japan
B.1.258.2
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-19543.5
Thailand
G.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-19543.5
Thailand
AY.112.3 (Delta)
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19531.1
Japan
GW.2
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19531.1
Japan
A.2.5
S
Chan-S
CCTACTAAATTAAATGATCTCTGCTTTACT
30
30
22712
22741
F
-19530.5
China
AY.23.1 (Delta)
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-19493.8
Japan
B.1.1.421
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-19493.8
Japan
B.1.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-19493.8
Japan
AY.103 (Delta)
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-19493.8
Japan
HH.2.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-19477.7
Singapore
B.1.619.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-19477.7
Singapore
BA.2.31
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-19431.6
Japan
B.1.1.420
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19429.6
Japan
JV.2
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19429.6
Japan
JV.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19429.6
Japan
DV.7.1.2
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19429.6
Japan
XCM
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19429.6
Japan
BN.3.1
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-19429.5
South Korea
AY.4.16 (Delta)
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-19429.5
South Korea
AY.75.3 (Delta)
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-19409.6
Hong Kong
B.1.385
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-19409.6
Hong Kong
BA.5.8
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-19409.6
Hong Kong
B.1.408
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-19409.6
Hong Kong
B.1.588
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-19409.6
Hong Kong
EG.5.1.13
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-19409.6
Hong Kong
B.1.1.517
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-19409.6
Hong Kong
B.1.587
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-19409.6
Hong Kong
AY.64 (Delta)
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-19409.6
Hong Kong
LE.1.3.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-19409.6
Hong Kong
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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