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
AY.133 (Delta)
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-16787.9
Japan
AY.42.1 (Delta)
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-16787.9
Japan
B.1.595.2
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-16787.9
Japan
AT.1
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-16787.9
Japan
B.1.1.345
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-16787.9
Japan
XBB.1.5.8
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-16787.9
Japan
B.1.601
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-16787.9
Japan
B.1.131
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-16787.9
Japan
A.11
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-16787.9
Japan
JG.2
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-16737.9
China
XBC.1.4
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-16734.9
China
CJ.1.1
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-16721.6
Japan
BQ.1.1.19
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-16721.6
Japan
XAY.2.3
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-16721.6
Japan
EA.1
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-16719.1
US
JN.3.2.1
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-16719.1
US
JN.3.2
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-16719.1
US
BF.7.3
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-16719.1
US
BN.6
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-16719.1
US
B.1.617
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-16719.1
US
JC.5
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-16719.1
US
JC.5.1
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-16719.1
US
CH.1.1.32
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-16719.1
US
AH.3
S
Chan-S
CCTACTAAATTAAATGATCTCTGCTTTACT
30
30
22712
22741
F
-16718.3
China
BA.2.29
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-16716.8
China
B.1.544
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-16716.8
China
B.1.366
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-16705.6
Thailand
B.1.487
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-16705.6
Thailand
B.1.422
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-16705.6
Thailand
N.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-16670.3
Hong Kong
N.4
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-16670.3
Hong Kong
N.6
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-16670.3
Hong Kong
B.1.1.393
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-16670.3
Hong Kong
BY.1.1.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-16670.3
Hong Kong
N.7
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-16670.3
Hong Kong
N.10
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-16670.3
Hong Kong
N.5
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-16670.3
Hong Kong
B.1.1.33
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-16670.3
Hong Kong
N.3
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-16670.3
Hong Kong
N.9
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-16670.3
Hong Kong
N.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-16670.3
Hong Kong
BN.1.4.4
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-16669.7
China
AY.37 (Delta)
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-16669.2
Singapore
JD.1.2
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-16669.2
Singapore
GP.2
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-16655.8
China
XBB.1.45
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-16655.8
China
BQ.1
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-16625.5
US
JN.1.63
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-16615.8
Germany
XBB.3
S
NIID WH-1 Seq F24383R24865
AAGACTCACTTTCTTCCACAG
21
42.86
24366
24386
F
-16614.7
Japan
AZ.2
S
NIID WH-1 Seq F24383R24865
AAGACTCACTTTCTTCCACAG
21
42.86
24366
24386
F
-16614.7
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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