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
C.4
S
Chan-S
CCTACTAAATTAAATGATCTCTGCTTTACT
30
30
22712
22741
F
-613.77
China
HK.18
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-604.348
US
JN.3.1
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-604.348
US
FL.39.1
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-604.348
US
BA.4.6.1
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-604.348
US
XL
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-604.348
US
XBB.1.14
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-604.348
US
B.1.177.71
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-604.348
US
B.1.177.71
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-552.006
Thailand
B.1.112
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-552.006
Thailand
AY.4.13 (Delta)
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-552.006
Thailand
B.11
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-552.006
Thailand
GW.5
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-552.006
Thailand
DV.7.1.4
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-552.006
Thailand
FL.13.3
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-552.006
Thailand
XCZ
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-552.006
Thailand
FL.20
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-552.006
Thailand
XBB.1.5.11
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-552.006
Thailand
XBB.1.14
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-552.006
Thailand
FL.39.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-552.006
Thailand
HK.18
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-552.006
Thailand
XL
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-552.006
Thailand
BA.4.6.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-552.006
Thailand
B.1.177.49
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-546.196
US
GJ.1.2.4
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-538.925
Japan
HV.1.4
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-538.925
Japan
XBB.1.5.90
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-524.276
France
GW.5
S
NIID WH-1 Seq F24383R24865
AAGACTCACTTTCTTCCACAG
21
42.86
24366
24386
F
-519.126
Japan
JG.3.3
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-495.687
Japan
JN.1.23
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-495.687
Japan
GK.1.10
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-495.687
Japan
FL.20
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-495.687
Japan
JN.1.48.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-495.687
Japan
FL.2.5
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-495.687
Japan
BQ.1.1.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-495.687
Japan
BG.2
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-495.687
Japan
LF.5
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-495.687
Japan
LB.1.4.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-495.687
Japan
B.1.1.482
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-495.687
Japan
CH.1.1.12
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-495.687
Japan
XAY.2.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-495.687
Japan
B.1.1.516
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-495.687
Japan
B.1.1.515
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-495.687
Japan
BA.1.17.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-495.687
Japan
B.1.274
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
XAQ
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
BA.2.3.8
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
B.1.1.74
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
B.1.160.10
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
South Korea
B.1.177.71
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-463.749
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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