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
BN.1.3.12
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-2620.39
Japan
BA.2.9
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-2620.39
Japan
BN.1.3.1
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-2620.39
Japan
B.1.1.149
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-2620.39
Japan
A.23
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-2620.39
Japan
B.1.596.1
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-2620.39
Japan
B.1.267
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-2620.39
Japan
B.1.177.35
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-2620.39
Japan
B.55
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-2620.39
Japan
XBB.1.11.1
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-2620.39
Japan
GD.1
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-2620.39
Japan
XBB.1.5.78
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-2620.39
Japan
BA.1.21
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-2620.39
Japan
JN.1.51.1
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-2620.39
Japan
JN.1.49
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-2620.39
Japan
MK.2
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-2619.71
Germany
GK.1.11.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-2619.71
Germany
HC.2
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-2619.71
Germany
B.1.160.26
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-2619.71
Germany
B.1.177.49
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-2619.71
Germany
B.1.537
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-2619.71
Germany
B.1.1.74
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-2601.1
Japan
BQ.1.1.6
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-2595.92
Singapore
B.1.444
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-2586.25
US
GK.1.11.1
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-2586.25
US
GS.5
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-2584.54
Japan
BA.2.36
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-2584.54
Japan
BQ.1.2
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-2584.54
Japan
KP.2.14
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-2584.54
Japan
GE.1.2.2
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-2584.54
Japan
KP.1.1.4
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-2584.54
Japan
CM.8.1.2
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-2584.54
Japan
XBB.1.16.7
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-2584.54
Japan
XBB.1.9
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-2584.54
Japan
HK.16
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-2584.54
Japan
FL.4.11
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-2584.54
Japan
FL.13.3.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-2584.54
Japan
FR.2
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-2584.54
Japan
B.1.287
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-2582.97
Singapore
A.2
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-2575.96
South Korea
HK.24.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-2575.96
South Korea
CM.4
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-2556.23
Japan
B.1.1.291
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-2556.23
Japan
FL.2.5
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-2556.23
Japan
BQ.1.1.1
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-2556.23
Japan
BG.2
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-2556.23
Japan
JN.1.25
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-2556.23
Japan
CM.8.1.2
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-2556.23
Japan
JN.1.56
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-2556.23
Japan
GD.1
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-2556.23
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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