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
JU.1
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-17500.9
South Korea
B.1.1.149
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-17502
China
B.1.594
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-17503.4
Japan
B.1.425
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-17503.4
Japan
B.1.426
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-17503.4
Japan
B.1.1.486
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-17506.3
Japan
B.1.351 (Beta)
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-17506.3
Japan
BT.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-17507.2
China
BA.5.2.62
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
LP.1
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
BE.6
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-17507.2
China
BA.5.2.1
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
BA.2.21
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-17507.2
China
B.1.1.378
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-17507.2
China
BQ.1.29
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-17507.2
China
BT.2
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-17507.2
China
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
JN.1.48.1
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
JN.1.48
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
N.8
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-17533.7
Singapore
AY.43.6 (Delta)
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-17551.5
China
AY.111 (Delta)
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
XBB.1.5.21
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
JN.1.47.2
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
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
A.21
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-17561.1
China
AY.112.3 (Delta)
S
NIID WH-1 Seq F24383R24865
AAGACTCACTTTCTTCCACAG
21
42.86
24366
24386
F
-17565.5
Japan
GW.2
S
NIID WH-1 Seq F24383R24865
AAGACTCACTTTCTTCCACAG
21
42.86
24366
24386
F
-17565.5
Japan
AY.56 (Delta)
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-17587.2
Japan
XBB.8.1
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
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.9
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.6.1
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17590
Japan
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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