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
ML.1
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-16362.7
Japan
AY.43.7 (Delta)
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-16362.7
Japan
BA.2.86.7
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-16362.7
Japan
FY.6.1
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-16362.7
Japan
BA.5.1.19
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-16369.3
Germany
BA.1.9
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-16389.6
China
XDK.2
S
WuhanCoV-spk1
TGTGGTTCATAAAAATTCCTTTGTG
25
32
24900
24876
R
-16394.6
Japan
BF.7.20
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-16402.8
South Korea
KJ.1
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-16402.8
South Korea
XAY.1
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-16402.8
South Korea
B.1.177.38
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-16402.8
South Korea
A.24
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-16402.8
South Korea
KP.3.3.1
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-16402.8
South Korea
BQ.1.25.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-16428.4
South Korea
B.1.274
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-16439.6
Japan
JB.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-16441.2
France
BN.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-16441.2
France
FL.15.2
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-16445.1
Hong Kong
GP.3
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-16445.1
Hong Kong
DS.3
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-16448.7
China
AY.125 (Delta)
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-16453.1
Hong Kong
BA.2.41
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-16453.1
Hong Kong
B.1.1.480
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-16453.1
Hong Kong
AY.125.1 (Delta)
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-16453.1
Hong Kong
BA.2.80
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-16454.1
Singapore
B.1.1.466
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-16466.5
China
BA.5.2.58
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-16472.1
China
B.1.1.7 (Alpha)
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-16507.7
China
XBB.1.5.51
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-16519.7
China
B.1.341
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-16519.7
China
KE.2
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-16535.3
Japan
B.1.1.12
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-16535.3
Japan
JN.1.7.7
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-16535.3
Japan
BA.5.2.30
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-16572.3
France
EU.1.1.3
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-16572.3
France
GA.8
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-16572.4
China
XBB.1.22
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-16572.4
China
XBB.1.5.39
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-16581
China
CH.1.1.27
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-16581
China
BA.4.6.2
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-16581
China
FT.2
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-16581
China
B.1.1.318
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-16581
China
FT.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-16581
China
AY.11 (Delta)
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-16581
China
AY.8 (Delta)
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-16587
France
B.1.1.49
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-16598.1
China
B.1.177.67
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-16604.2
China
B.1.1.421
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-16604.2
China
B.1.471
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-16604.2
China
AZ.1
S
NIID WH-1 Seq F24383R24865
AAGACTCACTTTCTTCCACAG
21
42.86
24366
24386
F
-16614.7
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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