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
B.1.420
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-941.915
South Korea
B.1.167
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-941.915
South Korea
B.1.444
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-941.915
South Korea
B.1.274
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-941.915
South Korea
B.1.515
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-941.915
South Korea
B.1.258.23
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-941.915
South Korea
GJ.1.2.4
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-937.283
Japan
B.11
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-937.283
Japan
MB.1
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-937.283
Japan
EG.2.1
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-937.283
Japan
XCZ
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-937.283
Japan
XBB.1.5.11
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-937.283
Japan
JN.1.4.6
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-937.283
Japan
BQ.1.2
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-937.283
Japan
FL.39.1
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-937.283
Japan
BA.1.17.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-903.077
Singapore
B.1.277
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-896.59
Singapore
B.1.1.412
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-896.59
Singapore
JN.1.55
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-896.59
Singapore
GW.5
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
JN.1.1.9
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
JR.1.1.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
XDE
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
FL.20.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
JN.1.30
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
GJ.1.2.4
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
DV.7.1.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
BQ.1.1.70
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
GK.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
HN.6
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
JY.1.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
P.7
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
XBB.1.5.11
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
XBB.1.5.42
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
JN.1.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
GW.4
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
HY.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
GK.2.4
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
B.1.444
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
B.1.160.27
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
B.1.177.68
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
B.1.1.74
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
AY.29.2 (Delta)
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
B.1.1.371
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
GK.1.11.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
B.1.160.26
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
Q.6 (Alpha)
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
B.1.177.26
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
AY.121.1 (Delta)
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
BA.2.53
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-837.986
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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