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
HK.16
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-9164.47
South Korea
EK.4
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-9164.47
South Korea
B.1.112
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-8964.71
South Korea
B.1.112
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-8919.23
Singapore
BM.4.1.1
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-8852.03
Hong Kong
BA.1.3
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-8852.03
Hong Kong
FL.13.4
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-8844.97
China
XBB.2
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-8796.37
Thailand
BA.5.2.44
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-8731.55
France
JR.1.1.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-8697.18
South Korea
BA.4.6.1
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-8653.14
Hong Kong
BA.2.58
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-8653.14
Hong Kong
DJ.1.1.1
ORF1ab
Charité-ORF1b
CARATGTTAAASACACTATTAGCATA
26
23.08
15530
15505
R
-8626.55
Germany
BA.5.2
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-8626.22
Germany
XBB.1.11.1
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-8626.22
Germany
BF.7.14.5
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-8567
China
B.1.112
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-8520.83
France
BW.1.2
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-8500.25
Japan
XBB.1.5.91
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-8429.46
France
BQ.1.1.76
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-8429.46
France
B.1.1.98
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-8411.27
Singapore
JB.1.1
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-8369.06
China
XBB.2.3.19
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-8369.06
China
AY.127.1 (Delta)
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-8301.01
China
XBB.1.38.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-8009.2
China
B.1.112
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
B.1.1.515
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
B.1.287
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
BA.1.17.1
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
B.1.1.516
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
B.1.177.71
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
B.1.1.445
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
AY.4.16 (Delta)
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
XBF.7.1
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
FL.20
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
EG.11
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
XCZ
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
FL.13.3
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
B.11
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
DV.7.1.4
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
XBB.1.14
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
XL
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
BA.4.6.1
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
FL.39.1
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
HK.18
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-7949.56
US
B.50
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-7941.22
France
CP.8
ORF1ab
Won-ORF1ab
CATGTGTGGCGGTTCACTAT
20
50
15441
15460
F
-7924.15
South Korea
B.19
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-7551.2
South Korea
EG.2.4
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-7537.46
Japan
BS.1
ORF1ab
Charité-ORF1b
CARATGTTAAASACACTATTAGCATA
26
23.08
15530
15505
R
-7459.53
Germany
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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