Confirming Multiplex RT-qPCR Use in COVID-19 with Next-Generation Sequencing: Strategies for Epidemiological Advantage

Table 2

Data of representative samples (n = 21) sequenced and classified into Delta and non-VOC variants using NGS and RT-qPCR assays.

Sample	COVID-PCR (Ct values)		% of non-N bases (coverage≥10x)	Median coverage	COVID lineage by NGS		Variant-specific PCR (Ct values)				Lineage by RT-qPCR
							(GT molecular)		(Thermo fisher scientific)
	N1	N2			Next clade	Pango	L452R	T478K	L452R	P681R
NTC	Negative	Negative			N/A	N/A	Neg	Neg	Neg	Neg	N/A
665588	12.99	11.9	88.15	58	21A (elta)	AY.25	18.5	Neg	20.88	25.97	Delta
664789	28.72	27.78	99.40	221	21A (Delta)	AY.3	31.81	32.6	33.97	34.37	Delta
665660	16.71	15.64	98.45	116	21A (Delta)	AY.3	20.18	24.98	24.49	26.58	Delta
664822	26.3	25.24	93.87	103	21A (Delta)	AY.3	20.55	Neg	22.18	24.87	Delta
666013	14.5	13.98	99.36	217	21A (Delta)	B.1.617.2	22.72	33.27	27.8	28.78	Delta
665426	15.98	14.44	98.14	128	21A (Delta)	AY.3	18.69	25.39	23.92	25.52	Delta
21	21.41	21.71	100.0	1340	20C	B.1.243	Neg	Neg	Neg	Neg	Non-VOC
22	25.3	26.82	100.0	2380	19A	B.1.574	Neg	Neg	Neg	Neg	Non-VOC
23	25.35	25.04	100.0	1276	20C	B.1.574	Neg	Neg	Neg	Neg	Non-VOC
24	28.74	29.52	100.0	2618	20A	B.1.2	Neg	Neg	Neg	Neg	Non-VOC
25	19.86	20.43	100.0	229	20A	B.1	Neg	Neg	Neg	Neg	Non-VOC
26	17.33	17.64	100.0	1477	20C	B.1.234	Neg	Neg	Neg	Neg	Non-VOC
27	20.77	21.68	100.0	1092	20A	B.1.126	Neg	Neg	Neg	Neg	Non-VOC
28	19.98	20.58	100.0	1614	20C	B.1.602	Neg	Neg	Neg	Neg	Non-VOC
29	26.99	27.61	100.0	3734	20A	B.1	Neg	Neg	Neg	Neg	Non-VOC
210	33.9	32.64	100.0	1531	20C	B.1	Neg	Neg	Neg	Neg	Non-VOC
211	32.66	31.53	100.0	2485	20C	B.1.564	Neg	Neg	Neg	Neg	Non-VOC
212	33.19	35.37	100.0	2019	21A (Delta)	B.1.617.2	33.27	27.8	29.99	26.72	Delta
213	32.29	32.86	100.0	1888	21A (Delta)	AY.3	25.39	23.92	22.25	29.92	Delta
214	25.13	25.77	100.0	2618	21A (Delta)	B.1.617.2	32.32	33.12	24.93	31.56	Delta
Wuhan-hu1	25.26	25.89	100.00	3236	19B	A	Neg	Neg	Neg	Neg	Non-VOC