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
BA.1.14.1	S	NIID WH-1 F24381R24873	ATTTGAAACAAAGACACCTTCAC	23	34.78	24856	24834	R	-22193.2	Japan
BA.1 (Omicron)	N	Chan-N	TTGGATCTTTGTCATCCAATTTG	23	34.78	29306	29284	R	-21867.4	China
BA.1 (Omicron)	N	SC2	CTGCAGATTTGGATGATTTCTCC	23	43.48	29463	29485	F	-23117.2	US
BA.1 (Omicron)	ORF1ab	NIID WH-1 F501R913	CTTTACCAGCACGTGCTAGAAGG	23	52.17	896	874	R	-25657.5	Japan
BA.1 (Omicron)	S	NIID WH-1 F24381R24873	ATTTGAAACAAAGACACCTTCAC	23	34.78	24856	24834	R	-22193.2	Japan
BA.1.17.2	N	Chan-N	TTGGATCTTTGTCATCCAATTTG	23	34.78	29306	29284	R	-21867.4	China
BA.1.17.2	N	SC2	CTGCAGATTTGGATGATTTCTCC	23	43.48	29463	29485	F	-23117.2	US
BA.1.17.2	ORF1ab	NIID WH-1 F501R913	CTTTACCAGCACGTGCTAGAAGG	23	52.17	896	874	R	-25657.5	Japan
BA.1.17.2	S	NIID WH-1 F24381R24873	ATTTGAAACAAAGACACCTTCAC	23	34.78	24856	24834	R	-22193.2	Japan
AY.99.2 (Delta)	N	Chan-N	TTGGATCTTTGTCATCCAATTTG	23	34.78	29306	29284	R	-21867.4	China
AY.99.2 (Delta)	N	SC2	CTGCAGATTTGGATGATTTCTCC	23	43.48	29463	29485	F	-23117.2	US
AY.99.2 (Delta)	ORF1ab	NIID WH-1 F501R913	CTTTACCAGCACGTGCTAGAAGG	23	52.17	896	874	R	-25657.5	Japan
AY.99.2 (Delta)	S	NIID WH-1 F24381R24873	ATTTGAAACAAAGACACCTTCAC	23	34.78	24856	24834	R	-22193.2	Japan
JN.1.52	N	Chan-N	TTGGATCTTTGTCATCCAATTTG	23	34.78	29306	29284	R	-21867.4	China
JN.1.52	N	SC2	CTGCAGATTTGGATGATTTCTCC	23	43.48	29463	29485	F	-23117.2	US
JN.1.52	ORF1ab	NIID WH-1 F501R913	CTTTACCAGCACGTGCTAGAAGG	23	52.17	896	874	R	-26378.9	Japan
JN.1.52	S	NIID WH-1 F24381R24873	ATTTGAAACAAAGACACCTTCAC	23	34.78	24856	24834	R	-22193.2	Japan
JN.1.42	N	Chan-N	TTGGATCTTTGTCATCCAATTTG	23	34.78	29306	29284	R	-21867.4	China
JN.1.42	N	SC2	CTGCAGATTTGGATGATTTCTCC	23	43.48	29463	29485	F	-23117.2	US
JN.1.42	ORF1ab	NIID WH-1 F501R913	CTTTACCAGCACGTGCTAGAAGG	23	52.17	896	874	R	-26378.9	Japan
JN.1.42	S	NIID WH-1 F24381R24873	ATTTGAAACAAAGACACCTTCAC	23	34.78	24856	24834	R	-22193.2	Japan
KB.1	N	Chan-N	TTGGATCTTTGTCATCCAATTTG	23	34.78	29306	29284	R	-21867.4	China
KB.1	N	SC2	CTGCAGATTTGGATGATTTCTCC	23	43.48	29463	29485	F	-23117.2	US
KB.1	ORF1ab	NIID WH-1 F501R913	CTTTACCAGCACGTGCTAGAAGG	23	52.17	896	874	R	-25657.5	Japan
KB.1	S	NIID WH-1 F24381R24873	ATTTGAAACAAAGACACCTTCAC	23	34.78	24856	24834	R	-22193.2	Japan
JN.1.14	N	Chan-N	TTGGATCTTTGTCATCCAATTTG	23	34.78	29306	29284	R	-21867.4	China
JN.1.14	N	SC2	CTGCAGATTTGGATGATTTCTCC	23	43.48	29463	29485	F	-23117.2	US
JN.1.14	ORF1ab	NIID WH-1 F501R913	CTTTACCAGCACGTGCTAGAAGG	23	52.17	896	874	R	-26378.9	Japan
JN.1.14	S	NIID WH-1 F24381R24873	ATTTGAAACAAAGACACCTTCAC	23	34.78	24856	24834	R	-22193.2	Japan
MJ.1	N	Chan-N	TTGGATCTTTGTCATCCAATTTG	23	34.78	29306	29284	R	-21867.4	China
MJ.1	N	SC2	CTGCAGATTTGGATGATTTCTCC	23	43.48	29463	29485	F	-23117.2	US
MJ.1	ORF1ab	NIID WH-1 F501R913	CTTTACCAGCACGTGCTAGAAGG	23	52.17	896	874	R	-26378.9	Japan
MJ.1	S	NIID WH-1 F24381R24873	ATTTGAAACAAAGACACCTTCAC	23	34.78	24856	24834	R	-22193.2	Japan
JN.1.1.6	N	Chan-N	TTGGATCTTTGTCATCCAATTTG	23	34.78	29306	29284	R	-21867.4	China
JN.1.1.6	N	SC2	CTGCAGATTTGGATGATTTCTCC	23	43.48	29463	29485	F	-19772	US
JN.1.1.6	ORF1ab	NIID WH-1 F501R913	CTTTACCAGCACGTGCTAGAAGG	23	52.17	896	874	R	-26378.9	Japan
JN.1.1.6	S	NIID WH-1 F24381R24873	ATTTGAAACAAAGACACCTTCAC	23	34.78	24856	24834	R	-22193.2	Japan
JN.1.39.2	N	Chan-N	TTGGATCTTTGTCATCCAATTTG	23	34.78	29306	29284	R	-21867.4	China
JN.1.39.2	N	SC2	CTGCAGATTTGGATGATTTCTCC	23	43.48	29463	29485	F	-23117.2	US
JN.1.39.2	ORF1ab	NIID WH-1 F501R913	CTTTACCAGCACGTGCTAGAAGG	23	52.17	896	874	R	-26378.9	Japan
JN.1.39.2	S	NIID WH-1 F24381R24873	ATTTGAAACAAAGACACCTTCAC	23	34.78	24856	24834	R	-22193.2	Japan
JN.1.58.2	N	Chan-N	TTGGATCTTTGTCATCCAATTTG	23	34.78	29306	29284	R	-21867.4	China
JN.1.58.2	N	SC2	CTGCAGATTTGGATGATTTCTCC	23	43.48	29463	29485	F	-23117.2	US
JN.1.58.2	ORF1ab	NIID WH-1 F501R913	CTTTACCAGCACGTGCTAGAAGG	23	52.17	896	874	R	-26378.9	Japan
JN.1.58.2	S	NIID WH-1 F24381R24873	ATTTGAAACAAAGACACCTTCAC	23	34.78	24856	24834	R	-22193.2	Japan
JN.1.18.3	N	Chan-N	TTGGATCTTTGTCATCCAATTTG	23	34.78	29306	29284	R	-21867.4	China
JN.1.18.3	N	SC2	CTGCAGATTTGGATGATTTCTCC	23	43.48	29463	29485	F	-23117.2	US
JN.1.18.3	ORF1ab	NIID WH-1 F501R913	CTTTACCAGCACGTGCTAGAAGG	23	52.17	896	874	R	-26378.9	Japan
JN.1.18.3	S	NIID WH-1 F24381R24873	ATTTGAAACAAAGACACCTTCAC	23	34.78	24856	24834	R	-22193.2	Japan
LF.4.1	N	Chan-N	TTGGATCTTTGTCATCCAATTTG	23	34.78	29306	29284	R	-21867.4	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