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

Table 3

Comparative detection of VOC classifying mutations with RT-qPCR and NGS-based approaches. Variant determined by NGS (see Appendix for method).

Evaluation of Q-PCR-based SARS-CoV-2 variant detection solutions					VOC (n = 67)		Non-VOC (n = 11)
					PCR	NGS	PCR	NGS
Manufacturer	Catalog #	Reaction	Targets	Variants (WHO label) harboring this mutation	0	0	0	0
GT molecular fort collins, CO, USA	100180	Reaction-1	N501Y	Alpha (B.1.1.7), beta (B.1.351), gamma (P.1)	0	0	0	0
			Del69-70	Alpha (UK, B.1.1.7)	0	0	0	0
		Reaction-2	N501Y	Alpha (B.1.1.7), Beta (B.1.351), gamma (P.1)	0	0	0	0
			E484K	Beta (B.1.351), gamma (P.1)	1	1	0	0
			K417N	Beta (B.1.351), Delta plus	0	0	0	0
			K417T	Gamma (P.1)	0	0	0	0
		Reaction - 3	L452R	Epsilon (B.1.427/B.1.429), Delta (B.1.617.2)	67	67	0	0
			T478K	Delta (B.1.617.2)	62	64	0	0
	100172	Reaction-1	L452R	Epsilon (B.1.427/B.1.429), Delta (B.1.617.2)	67	67	0	0
			T478K	Delta (B.1.617.2)	62	64	0	0
Thermo fisher scientific Inc., Waltham, MA, USA	A51819	Reaction-1	L452R	B.1.617, B.1.617.1, Delta (B.1.617.2), B.1.617.3, B.1.429	63	67	0	0
	A51822	Reaction-2	P681R	B.1.617.1, B.1.617.2, B.1.617.3	55	64	0	0