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
JN.1.58.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
KP.1.1.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
JN.1.4.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
KP.2.5
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
KP.3.1.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
BQ.1.1.16
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
BA.5.2.38
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
DA.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
BQ.1.1.14
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
DN.1.1.4
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
Q.8 (Alpha)
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
CT.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
FF.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
DN.1.1.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
BQ.1.19
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
BA.5.1.19
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
JN.12
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
JN.3.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
JN.1.57
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
B.1.258.24
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-12306.8
Singapore
B.19
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-12250.3
Germany
C.38
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-12216.7
Japan
KW.1.1.1
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-12184.5
Japan
JN.1.28.1
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-12184.5
Japan
JN.1.7.6
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-12184.5
Japan
KW.1
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-12184.5
Japan
LG.1
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-12184.5
Japan
KW.1.1
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-12184.5
Japan
BA.5 (Omicron)
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-12135.1
Singapore
JF.1.1
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-12100.6
China
B.1.36.36
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-12070.6
US
B.1.633
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-12026.7
South Korea
BN.1.5.1
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-11919.9
China
BF.39.1
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-11900
Japan
P.1.9 (Gamma)
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-11852.8
US
BN.1.4.4
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-11852.8
US
B.1.636
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-11852.8
US
B.30
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-11836.9
South Korea
AY.39.3 (Delta)
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-11836.9
South Korea
BA.1.1.3
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-11828.8
US
B.19
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-11794
Hong Kong
B.50
ORF1ab
Won-ORF1ab
CATGTGTGGCGGTTCACTAT
20
50
15441
15460
F
-11766.4
South Korea
EG.5.1.8
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-11752.2
Japan
BA.1.23
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-11746.4
China
W.3
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-11712.3
China
B.1.1.253
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-11712.3
China
B.1.165
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-11666.3
China
CM.5.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-11629.5
South Korea
XR
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-11629.5
South Korea
JN.1.1.4
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-11629.5
South Korea
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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