assayM COVID-19: track sensitivity of RT-PCR primers on COVID-19 Variants

* The data is last updated on 10th February, 2023 from GISAID, based on 2379 variants from (14.9 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 2379 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.19	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	4395.36	Japan
B.1.1.56	N	US-CDC-N-3	GGGAGCCTTGAATACACCAAAA	22	45.45	28681	28702	F	3497.73	US
AY.91.1 (Delta)	N	US-CDC-N-3	GGGAGCCTTGAATACACCAAAA	22	45.45	28681	28702	F	3497.73	US
BA.1.1.6	N	US-CDC-N-3	GGGAGCCTTGAATACACCAAAA	22	45.45	28681	28702	F	3497.73	US
BQ.1.9	N	US-CDC-N-3	GGGAGCCTTGAATACACCAAAA	22	45.45	28681	28702	F	3497.73	US
BM.1	N	US-CDC-N-3	GGGAGCCTTGAATACACCAAAA	22	45.45	28681	28702	F	3497.73	US
AT.1	N	US-CDC-N-3	GGGAGCCTTGAATACACCAAAA	22	45.45	28681	28702	F	3497.73	US
AY.7.2 (Delta)	N	US-CDC-N-3	GGGAGCCTTGAATACACCAAAA	22	45.45	28681	28702	F	3497.73	US
BF.4	N	US-CDC-N-3	GGGAGCCTTGAATACACCAAAA	22	45.45	28681	28702	F	3497.73	US
AZ.5	N	US-CDC-N-3	GGGAGCCTTGAATACACCAAAA	22	45.45	28681	28702	F	3497.73	US
BA.2.64	N	US-CDC-N-3	GGGAGCCTTGAATACACCAAAA	22	45.45	28681	28702	F	3497.73	US
B.1.1.263	N	US-CDC-N-3	GGGAGCCTTGAATACACCAAAA	22	45.45	28681	28702	F	3497.73	US
XQ	N	US-CDC-N-3	GGGAGCCTTGAATACACCAAAA	22	45.45	28681	28702	F	3497.73	US
BQ.2	N	US-CDC-N-3	GGGAGCCTTGAATACACCAAAA	22	45.45	28681	28702	F	3176.87	US
B.1.1.305	S	WuhanCoV-spk1	TGTGGTTCATAAAAATTCCTTTGTG	25	32	24900	24876	R	3010.7	Japan
AU.1	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	2623.78	Japan
B.1.1.132	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	2623.78	Japan
B.1.1.243	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	2623.78	Japan
B.1.619.1	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	2623.78	Japan
B.1.258.3	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	2623.78	Japan
B.1.1.193	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	2623.78	Japan
B.1.105	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	2623.78	Japan
B.18	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	2623.78	Japan
B.1.2	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	2623.78	Japan
B.1.1.48	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	2623.78	Japan
B.1.619	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	2623.78	Japan
AA.6	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	2623.78	Japan
B.1.1.300	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	2623.78	Japan
B.1.1.425	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	2623.78	Japan
AY.39 (Delta)	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
B.1.1.519	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
AY.49 (Delta)	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
B.1.1.197	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
BA.5.1.25	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
B.1.2	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
B.18	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
B.1.1.377	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
B.1.1.263	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
B.1.105	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
AV.1	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
B.1.1.525	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
B.1.1.243	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
B.1.258.3	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
AY.82 (Delta)	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
N.8	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
B.29	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
BA.1.15.2	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
AU.1	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
B.1.1.48	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	Japan
B.1.1.132	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	2588.09	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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