Browse

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.1.160.27	N	CN-CDC-N	CAGACATTTTGCTCTCAAGCTG	22	45.45	28979	28958	R	-18066.2	China
B.1.160.7	N	CN-CDC-N	CAGACATTTTGCTCTCAAGCTG	22	45.45	28979	28958	R	-18066.2	China
B.1.160.30	N	CN-CDC-N	CAGACATTTTGCTCTCAAGCTG	22	45.45	28979	28958	R	-18066.2	China
B.1.160.23	N	CN-CDC-N	CAGACATTTTGCTCTCAAGCTG	22	45.45	28979	28958	R	-18066.2	China
B.1.160.17	N	CN-CDC-N	CAGACATTTTGCTCTCAAGCTG	22	45.45	28979	28958	R	-18066.2	China
B.1.160.13	N	CN-CDC-N	CAGACATTTTGCTCTCAAGCTG	22	45.45	28979	28958	R	-18066.2	China
B.1.160.8	N	CN-CDC-N	CAGACATTTTGCTCTCAAGCTG	22	45.45	28979	28958	R	-18066.2	China
B.1.160.28	N	CN-CDC-N	CAGACATTTTGCTCTCAAGCTG	22	45.45	28979	28958	R	-18066.2	China
B.1.160	N	CN-CDC-N	CAGACATTTTGCTCTCAAGCTG	22	45.45	28979	28958	R	-18066.2	China
AY.14 (Delta)	ORF1ab	Yip-ORF1ab	ATGCATTTGCATCAGAGGCT	20	45	1866	1885	F	-18073.3	China
BQ.1.4	N	US-CDC-N-2	TTACAAACATTGGCCGCAAA	20	40	29164	29183	F	-18073.5	US
P.1 (Gamma)	S	NIID WH-1 F24381R24873	TCAAGACTCACTTTCTTCCAC	21	42.86	24364	24384	F	-18074.7	Japan
B.1.489	S	NIID WH-1 F24381R24873	TCAAGACTCACTTTCTTCCAC	21	42.86	24364	24384	F	-18074.7	Japan
B.1.607	S	NIID WH-1 F24381R24873	TCAAGACTCACTTTCTTCCAC	21	42.86	24364	24384	F	-18074.7	Japan
B.1.44	S	NIID WH-1 F24381R24873	TCAAGACTCACTTTCTTCCAC	21	42.86	24364	24384	F	-18074.7	Japan
B.1.177.62	S	NIID WH-1 F24381R24873	TCAAGACTCACTTTCTTCCAC	21	42.86	24364	24384	F	-18074.7	Japan
B.1.639	S	NIID WH-1 F24381R24873	TCAAGACTCACTTTCTTCCAC	21	42.86	24364	24384	F	-18074.7	Japan
B.1.372	S	NIID WH-1 F24381R24873	TCAAGACTCACTTTCTTCCAC	21	42.86	24364	24384	F	-18074.7	Japan
BA.2.13	S	NIID WH-1 F24381R24873	TCAAGACTCACTTTCTTCCAC	21	42.86	24364	24384	F	-18074.7	Japan
B.1.177.61	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-18075.7	Singapore
AY.91 (Delta)	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-18075.7	Singapore
LQ.1.1	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-18075.7	Singapore
XDV	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-18075.7	Singapore
LQ.1	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-18075.7	Singapore
B.1.1.333	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-18075.7	Singapore
B.1.9.2	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-18075.7	Singapore
B.1.487	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-18075.7	Singapore
KP.3.4.1	ORF1ab	Pasteur-ORF1ab-1	ATGAGCTTAGTCCTGTTG	18	44.44	12690	12707	F	-18076.1	France
B.1.596	ORF1ab	Pasteur-ORF1ab-1	ATGAGCTTAGTCCTGTTG	18	44.44	12690	12707	F	-18076.1	France
XBS	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
XAY.1.1.2	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
B.1.523	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
XBE	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
FW.2	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
JN.2.2.1	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
XAY.2	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
XBB.1.5.71	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
CH.1.1.12	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
CZ.2	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
EW.2	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
CH.1.1.23	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
AY.127.1 (Delta)	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
XBC.1.6.5	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
HN.1	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
CM.7	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
CM.6.1	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
B.1.413	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
HS.1.1	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
BG.1	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-18076.7	Japan
AY.103.1 (Delta)	N	CN-CDC-N	GGGGAACTTCTCCTGCTAGAAT	22	50	28881	28902	F	-18076.8	China
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