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.1.1.412
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-1579.08
China
BA.2.75.10
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-1580.06
Japan
BN.1.5.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-1580.06
Japan
BQ.1.26
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-1580.06
Japan
ER.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-1580.06
Japan
BN.1.3.9
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-1580.06
Japan
BA.5 (Omicron)
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-1580.06
Japan
FY.4.1
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-1587.14
China
Q.6 (Alpha)
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-1590.7
Japan
BA.2.58
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-1591.5
Hong Kong
B.1.1.74
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-1591.5
Hong Kong
CM.8.1.2
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-1591.5
Hong Kong
JN.1.49
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-1633.38
China
GW.5
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-1638.08
US
GK.1.11.1
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-1638.08
US
B.1.277
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-1638.08
US
B.1.1.74
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-1638.08
US
B.1.177.49
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
B.1.1.74
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
B.1.491
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
B.1.1.516
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
BF.1.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
AP.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
B.1.267
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
B.1.444
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
B.1.537
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
BA.1.17.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
B.1.1.515
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
B.1.287
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
MK.2
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
GK.1.11.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
HC.2
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
BE.1.3
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
BF.7.4.2
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
AY.105 (Delta)
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
B.1.610
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-1648.07
Singapore
FL.32.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-1649.2
South Korea
BA.2.75
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-1649.2
South Korea
CH.1.1.6
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-1649.2
South Korea
XDN
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-1649.2
South Korea
B.1.277
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-1649.2
South Korea
GA.8
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-1649.2
South Korea
AY.121.1 (Delta)
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-1649.2
South Korea
B.1.1.391
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-1649.2
South Korea
XBF.7.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-1649.2
South Korea
FD.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-1649.2
South Korea
XDQ
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-1649.2
South Korea
JG.3.4
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-1649.2
South Korea
FL.2.2.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-1649.2
South Korea
CM.8.1.2
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-1668.53
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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