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
DG.1	N	Young-N	AGCACCATAGGGAAGTCC	18	55.56	28648	28631	R	-16939.3	Singapore
HK.2.1	N	Young-N	AGCACCATAGGGAAGTCC	18	55.56	28648	28631	R	-16939.3	Singapore
GK.1.6.1	N	Young-N	AGCACCATAGGGAAGTCC	18	55.56	28648	28631	R	-16939.3	Singapore
GA.4.1	N	Chan-N	GCGTTCTTCGGAATGTCG	18	55.56	29210	29227	F	-16933	China
BQ.1.12	N	Chan-N	GCGTTCTTCGGAATGTCG	18	55.56	29210	29227	F	-16933	China
JM.1	N	Chan-N	GCGTTCTTCGGAATGTCG	18	55.56	29210	29227	F	-16933	China
AD.1	N	Chan-N	GCGTTCTTCGGAATGTCG	18	55.56	29210	29227	F	-16933	China
HC.3	N	Chan-N	GCGTTCTTCGGAATGTCG	18	55.56	29210	29227	F	-16933	China
GW.5.2	N	Chan-N	GCGTTCTTCGGAATGTCG	18	55.56	29210	29227	F	-16933	China
B.1.1.315	N	Chan-N	GCGTTCTTCGGAATGTCG	18	55.56	29210	29227	F	-16933	China
B.1.36.8	N	Chan-N	GCGTTCTTCGGAATGTCG	18	55.56	29210	29227	F	-16933	China
AD.2	N	Chan-N	GCGTTCTTCGGAATGTCG	18	55.56	29210	29227	F	-16933	China
A.12	N	Chan-N	GCGTTCTTCGGAATGTCG	18	55.56	29210	29227	F	-16933	China
B.1.595.2	N	Chan-N	GCGTTCTTCGGAATGTCG	18	55.56	29210	29227	F	-16933	China
AY.21 (Delta)	N	Chan-N	GCGTTCTTCGGAATGTCG	18	55.56	29210	29227	F	-16933	China
AY.78 (Delta)	N	Chan-N	GCGTTCTTCGGAATGTCG	18	55.56	29210	29227	F	-16933	China
AY.66 (Delta)	N	CN-CDC-N	GGGGAACTTCTCCTGCTAGAAT	22	50	28881	28902	F	-16910.2	China
B.1.1.228	N	Young-N	AGCACCATAGGGAAGTCC	18	55.56	28648	28631	R	-16904	Singapore
BA.5.2.25	ORF1ab	CN-CDC-ORF1ab	CCCTGTGGGTTTTACACTTAA	21	42.86	13342	13362	F	-16902.6	China
FL.2.2.1	E	Niu-E	TTCTTGCTTTCGTGGTATTC	20	40	26303	26322	F	-16900.3	China
AY.39.1.4	E	Niu-E	TTCTTGCTTTCGTGGTATTC	20	40	26303	26322	F	-16900.3	China
B.1.177.46	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-16884.2	Singapore
JN.1.8.4	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-16879.6	Japan
B.1.1.517	N	CN-CDC-N	GGGGAACTTCTCCTGCTAGAAT	22	50	28881	28902	F	-16867.9	China
BA.1.13	ORF1ab	Yip-ORF1ab	TTGTTATAGCGGCCTTCTGT	20	45	1970	1951	R	-16848.5	China
BA.1.13.1	ORF1ab	Yip-ORF1ab	TTGTTATAGCGGCCTTCTGT	20	45	1970	1951	R	-16848.5	China
XBB.3.5	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-16841.5	Japan
XBB.5	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-16841.5	Japan
XBB.7	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-16841.5	Japan
XBB.6.1	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-16841.5	Japan
XBB.3.3	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-16841.5	Japan
XBB.3.4	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-16841.5	Japan
XBB.4	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-16841.5	Japan
XBB.6	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-16841.5	Japan
XBB.3.1	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-16841.5	Japan
XBB.8.1	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-16841.5	Japan
XBB.3	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-16841.5	Japan
KP.2.5	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-16841.5	Japan
XBB.9	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-16841.5	Japan
XBB.4.1	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-16841.5	Japan
XBB.3.2	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-16841.5	Japan
XBB.8	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-16841.5	Japan
KB.2	N	CN-CDC-N	GGGGAACTTCTCCTGCTAGAAT	22	50	28881	28902	F	-16824.6	China
BQ.1.2.3	E	Niu-E	TTCTTGCTTTCGTGGTATTC	20	40	26303	26322	F	-16811.6	China
B.1.1.304	N	CN-CDC-N	GGGGAACTTCTCCTGCTAGAAT	22	50	28881	28902	F	-16806.4	China
B.1.1.44	N	CN-CDC-N	GGGGAACTTCTCCTGCTAGAAT	22	50	28881	28902	F	-16806.4	China
B.1.321	N	Chan-N	TTGGATCTTTGTCATCCAATTTG	23	34.78	29306	29284	R	-16800.3	China
JN.11.1	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	-16797.4	Japan
JN.17	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	-16797.4	Japan
BM.1.1.2	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	-16797.4	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