Table 1.

RT-PCR and whole genome sequencing assays and RNA extraction methods used during the weeks of 2021 according to the emergence of new variants of concern and reagents availability.

Week	RT-PCR			Whole genome sequencing
	Amplification reagents	Mutations detected	RNA extraction method	Reagents	RNA Extraction method
1–6	TaqPath COVID-19 assay (Thermo Fisher Scientific, Waltham, MA, USA)	H69-V70 deletion	EasyMag (bioMérieux Diagnostics, Marcy-l'Etoile, France)	Ion Torrent (Thermo Fisher Scientific, Waltham, MA, USA)	EasyMag (bioMérieux Diagnostics, Marcy-l'Etoile, France)
7–11	VirSNiP SARS-CoV-2 Spike N501Y, del H69/V70, E484K TIB Molbiol (Berlin, Germany)	H69-V70 deletion N501Y, E484K	EasyMag (bioMérieux Diagnostics, Marcy-l'Etoile, France)
12–24	Allplex SARS-CoV-2 Variants I Assay (Seegene, Seoul, South Korea)a	H69-V70 deletion N501Y, E484K	Microlab STARlet (Seegene, Seoul, South Korea)	Ion Torrent (Thermo Fisher Scientific, Waltham, MA, USA) and ABL SA Group (Luxembourg/Illumina, San Diego, CA, USA)b
25–32	VirSNiP SARS-CoV-2 Spike L452R TIB Molbiol (Berlin, Germany)	L452R	Microlab STARlet (Seegene, Seoul, South Korea)	ABL SA Group (Luxembourg/Illumina, San Diego, CA, USA)
33–52	Allplex SARS-CoV-2 Variants II Assay (Seegene, Seoul, South Korea)	K417N, K417T, L452R, W152C	Microlab STARlet (Seegene, Seoul, South Korea)

^aAllplex SARS-CoV-2 Variants I was performed from week 12 to 52, along with VirSNiP SARS-CoV-2 Spike L452R (during weeks 25–32) and Allplex SARS-CoV-2 Variants II (during weeks 33–52).

^bIon Torrent or ABL platforms were used during 12–24 weeks according to the reagents availability.