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
XCC
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-17603.1
China
GA.7
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-17603.1
China
JD.1.1.4
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-17597.6
Hong Kong
BA.2.51
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-17594
China
EG.5.1.7
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-17594
China
C.37.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-17590.1
China
CT.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-17590.1
China
XBB.8
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17590
Japan
XBB.3.2
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17590
Japan
XBB.3
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17590
Japan
XBB.6
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17590
Japan
XBB.3.1
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17590
Japan
XBB.8.1
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17590
Japan
XBB.4.1
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17590
Japan
XBB.9
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17590
Japan
XBB.3.3
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17590
Japan
XBB.4
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17590
Japan
XBB.3.5
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17590
Japan
XBB.5
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17590
Japan
XBB.7
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17590
Japan
XBB.6.1
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17590
Japan
AY.56 (Delta)
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-17587.2
Japan
GW.2
S
NIID WH-1 Seq F24383R24865
AAGACTCACTTTCTTCCACAG
21
42.86
24366
24386
F
-17565.5
Japan
AY.112.3 (Delta)
S
NIID WH-1 Seq F24383R24865
AAGACTCACTTTCTTCCACAG
21
42.86
24366
24386
F
-17565.5
Japan
A.21
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-17561.1
China
HR.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-17559.5
Hong Kong
HR.1.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-17559.5
Hong Kong
XBB.1.5.21
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-17554.7
Japan
BQ.1.1.23
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-17554.7
Japan
EG.4.5
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-17554.7
Japan
KP.3.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-17554.7
Japan
JN.1.47.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-17554.7
Japan
AY.111 (Delta)
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-17554.7
Japan
AY.43.6 (Delta)
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-17551.5
China
N.8
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-17533.7
Singapore
JN.1.48
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-17519.3
Japan
JN.1.48.3
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-17519.3
Japan
LD.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-17519.3
Japan
JN.1.48.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-17519.3
Japan
JN.1.48.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-17519.3
Japan
XBB.1.5.8
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-17512
US
B.1.415.1
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-17512
US
BA.5.2.62
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-17507.2
China
BT.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-17507.2
China
LP.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-17507.2
China
BE.6
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-17507.2
China
DE.2
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-17507.2
China
FL.21.2
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-17507.2
China
GJ.1.2.4
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-17507.2
China
BA.5.1.21
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-17507.2
China
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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