Table 5. Validation of 5-SSG primers target mutations sequence using clinical samples.

Grades of concern	Lineage	Sample	Sequence analysis method		Final Determination
			NGS	Sanger sequencing
VOC	B.1.1.7	Sample A	ΔH69/V70, ΔY144, N501Y, A570D, D614G, P681H, T716I	ΔH69/V70, ΔY144, N501Y, A570D, D614G, P681H, T716I	Match
		Sample B	ΔH69/V70, ΔY144, N501Y, A570D, D614G, P681H, T716I	ΔH69/V70, ΔY144, N501Y, A570D, D614G, P681H, T716I	Match
	B.1.351	Sample C	D80A, D215G, ΔLAL242-244, K417N, E484K, N501Y, D614G, A701V	D80A, D215G, ΔLAL242-244, K417N, E484K, N501Y, D614G, A701V	Match
	P.1	Sample D	D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y	D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y	Match
	B.1.617.2	Sample E	G142D, ΔE156/F157, R158G, L452R, T478K, D614G, P681R	G142D, ΔE156/F157, R158G, L452R, T478K, D614G, P681R	Match
		Sample F	G142D, ΔE156/F157, R158G, L452R, T478K, D614G, P681R	G142D, ΔE156/F157, R158G, L452R, T478K, D614G, P681R	Match
		Sample G	T95I, G142D, ΔE156/F157, R158G, L452R, T478K, D614G, P681R	T95I, G142D, ΔE156/F157, R158G, L452R, T478K, D614G, P681R	Match
VOI	B.1.429	Sample H	ΔLGVY141-144, W152C, G252V, S256L, L452R, D614G	ΔLGVY141-144, W152C, G252V, S256L, L452R, D614G	Match
	B.1.525	Sample I	Q52R, A67V, ΔH69/V70, ΔY144, E484K, D614G, Q677H	Q52R, A67V, ΔH69/V70, ΔY144, E484K, D614G, Q677H	Match
	B.1.617.1	Sample J	G142D, E154K, L452R, E484Q, D614G, P681R	G142D, E154K, L452R, E484Q, D614G, P681R	Match
		Sample K	T95I, G142D, E154K, L452R, E484Q, D614G, P681R	T95I, G142D, E154K, L452R, E484Q, D614G, P681R	Match
Not included	B.1.497	Sample L	D614G	D614G	Match
		Sample M	D614G	D614G	Match
		Sample N	D614G	D614G	Match
	B.1.619	Sample O	I210T, N440K, E484K, D614G	I210T, N440K, E484K, D614G	Match
		Sample P	I210T, N440K, E484K, D614G	I210T, N440K, E484K, D614G	Match
		Sample Q	I210T, N440K, E484K, D614G	I210T, N440K, E484K, D614G	Match

Abbreviations: VOC, Variant of concern; VOI, variant of interest; Δ, deletion. Low-coverage NGS data are marked in underline.