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
JV.1
S
NIID WH-1 Seq F24383R24865
AAGACTCACTTTCTTCCACAG
21
42.86
24366
24386
F
-17464
Japan
JV.2
S
NIID WH-1 Seq F24383R24865
AAGACTCACTTTCTTCCACAG
21
42.86
24366
24386
F
-17464
Japan
B.1.1.420
S
NIID WH-1 Seq F24383R24865
AAGACTCACTTTCTTCCACAG
21
42.86
24366
24386
F
-17464
Japan
BQ.1.1.47
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-17467.1
Japan
BA.2.32
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-17471.2
Singapore
B.1.1.518
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-17471.2
Singapore
JN.1.4.6
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-17471.7
China
JN.1.4.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
C.36
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
CC.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
BQ.1.6
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
BA.2.70
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
P.1.17.1 (Gamma)
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
C.1.2
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
B.1.606
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
AY.94 (Delta)
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
AY.4.3 (Delta)
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
B.1.1.50
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
FL.19
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
N.4
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
FY.7
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
XBB.1.19.2
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
BA.5.9
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
B.1.243.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
B.1.1.429
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
B.1.1.299
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
BF.7.21
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
B.1.1.347
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
B.1.390
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
XBB.1.9.4
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
XBB.1.22.3
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
XBB.1.41.2
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
B.1.563
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
XBB.1.5.96
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
XBC.1.4
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
XBB.1.5.12
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
P.1.17 (Gamma)
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-17480.9
Singapore
AY.43 (Delta)
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-17487.9
Hong Kong
B.1.1.279
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-17489.1
Japan
B.1.1.348
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-17498
France
BY.1.2
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-17498
France
BY.1.2.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-17498
France
GJ.1.2.3
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-17500.9
South Korea
GS.2
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-17500.9
South Korea
XBB.1.19.2
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-17500.9
South Korea
HH.6
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-17500.9
South Korea
XBB.2.3.18
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-17500.9
South Korea
HA.2
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-17500.9
South Korea
EU.1.1.3
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-17500.9
South Korea
XBB.2.3.2
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-17500.9
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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