Flexible upscaling of laboratory PCR testing capacity at the Robert Koch Institute during the SARS-CoV-2 pandemic

Table 8 PCR positivity comparison between individual testing, two-sample pools and four-sample pools

Performance parameter	Duplex PCRs			Quadruplex PCR			AllFAM Quadruplex PCR
Performance parameter	Indiv. testing	Pools of 2	Pools of 4	Indiv. testing	Pools of 2	Pools of 4	Indiv. testing	Pools of 2	Pools of 4
Number of detected samples	20/24	17/24	14/24	22/24	19/24	16/24	19/24	21/24	19/24
E-Gene and orf1ab detected	18/24	11/24	10/24	17/24	16/24	11/24	n.a	n.a	n.a
Only E-Gene detected	0/24	2/24	2/24	4/24	2/24	5/25	n.a	n.a	n.a
Only orf1ab detected	2/24	4/24	2/24	1/24	1/24	0/24	n.a	n.a	n.a
E-Gene mean Ct value	34.03	35.62	35.24	33.55	34.43	34.80	32.73*	35.11*	35.24*
E-Gene range of Ct values	28.94–37.97	28.44–41.69	29.19–40.04	27.67–38.70	27.06–39.69	27.99–39.26	27.81–36.28*	26.85–42.17*	27.97–41.69*
orf1ab mean Ct value	35.37	36.41	36.32	34.02	35.25	33.95	n.a	n.a	n.a
orf1ab range of Ct values	29.47–43.41	28.86–42.89	30.00–41.06	28.63–41.58	27.75–41.24	28.49–37.54	n.a	n.a	n.a

24 weakly positive patient samples were extracted individually and in a pool with either one or three negative patient samples. PCR analyses were performed by using the SARS-CoV-2 duplex PCRs, the standard quadruplex PCR and the pooling-specific allFAM quadruplex PCR
n.a.: not applicable
*The Ct values of the allFAM quadruplex PCR refer to the combined signals of the E-Gene and orf1ab assays as they are both detected in the same fluorescence channel in this assay

ISSN: 1743-422X