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
HN.8
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-20419.5
China
BA.5.3.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-20419.5
China
MK.2
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-20419.5
China
A.12
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-20419.5
China
XBB.1.5.39
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-20413.7
South Korea
BN.3.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-20407.1
China
AY.4.16 (Delta)
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-20407.1
China
AY.4.16 (Delta)
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-20394.2
Germany
BN.3.1
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-20394.2
Germany
KP.4.2.2
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-20389.3
US
JN.1.42.2
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-20387.2
Germany
BN.1.1.1
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-20385.1
US
B.1.177.42
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-20376.5
Thailand
HW.1.1
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-20362.3
US
BR.2
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-20351.8
US
B.1.441
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-20347.6
China
XBB.1.5.109
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-20346.1
Japan
JN.1.35
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-20341.7
Singapore
HK.3.10
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-20338.9
South Korea
JN.1.39.1
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-20338.9
South Korea
XBB.1.18.1
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-20338.9
South Korea
FY.9
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-20338.9
South Korea
BA.4.1.4
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-20338.9
South Korea
KP.2.14
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-20338.9
South Korea
B.1.438.3
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-20338.9
South Korea
B.1.1.273
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-20338.9
South Korea
CM.8.1.5
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-20331.1
US
XBB.1.16.6
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-20331.1
US
B.1.397
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-20331.1
US
BF.32
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-20331.1
US
B.1.1.517
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-20331.1
US
FK.1
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-20331.1
US
CH.1.1.18
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-20331.1
US
B.1.1.228
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-20331.1
US
B.1.1.174
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-20331.1
US
B.4.8
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-20326.9
US
B.4
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-20326.9
US
B.4.7
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-20326.9
US
B.4.4
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-20326.9
US
B.4.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-20326.9
US
B.4.5
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-20326.9
US
B.1.1.299
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-20316.5
South Korea
R.2
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-20316.5
South Korea
AY.130
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-20311.7
China
B.1.36.23
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-20306.8
China
B.1.1.213
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-20306.2
China
B.1.1.12
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-20306.2
China
B.1.1.341
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-20306.2
China
B.1.1.89
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-20306.2
China
B.1.36.23
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-20306.2
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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