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.1.177.64
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-17039.2
Germany
B.1.1.163
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-17039.2
Germany
JV.2
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-17029.2
Japan
B.1.1.420
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-17029.2
Japan
XCM
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-17029.2
Japan
DV.7.1.2
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-17029.2
Japan
JV.1
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-17029.2
Japan
KP.4.2
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17028.5
South Korea
JN.1.59
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17028.5
South Korea
JN.1.4.4
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17028.5
South Korea
FL.3
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17028.5
South Korea
BL.5
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17028.5
South Korea
BF.4
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17028.5
South Korea
B.1.177.75
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17028.5
South Korea
XBB.1.24
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17028.5
South Korea
BF.31.1
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17028.5
South Korea
B.1.570
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-17028.5
South Korea
B.1.1.225
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-17020.5
Japan
B.1.629
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-17020.5
Japan
BK.1
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-17009
France
BA.2.79
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-17007.8
US
B.1.366
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-17007.8
US
AY.70 (Delta)
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-16999.4
Singapore
B.1.233
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-16998.3
Japan
XBB.1.16.10
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-16994.8
Japan
FB.2
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-16988.9
US
BQ.1.2.1
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-16988.9
US
FB.1
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-16988.9
US
B.1.1.243
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-16987.7
Thailand
AY.11 (Delta)
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-16987.7
Thailand
BA.5.3.1
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-16984.7
China
JC.1
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-16984.7
China
HN.8
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-16984.7
China
MK.2
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-16984.7
China
B.1.1.101
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-16984.7
China
B.1.525 (Eta)
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-16984.7
China
BA.2.77
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-16984.7
China
B.1.443
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-16978.6
China
B.1.570
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-16978.6
China
B.1.554
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-16974.6
China
B.1.1.315
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-16970.4
Singapore
B.1.389
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-16962.5
China
GU.1
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-16962.5
China
EG.11
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-16962.5
China
FY.1.2.1
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-16960.9
China
B.1.39
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-16957.3
China
CH.1.1.6
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-16954
Germany
XBB.1.16.25
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-16953.8
China
XCS
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-16953.8
China
XBB.1.9.4
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-16947.8
Singapore
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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