Table 3.

Rates of recovery of inoculated PV1 from a sediment sample using direct methods^a

Method	Lysis buffer	Purification method	Total (flow 3)			Lysis, extraction, and concn recovery rate (%)b	Purification and RT-qPCR (flow 4)			No. of samples
			No. of copies detected/no. of inoculated copies	Recovery rate (%)			No. of copies detected/no. of inoculated copies	Recovery rate (%)
				GM	GSD			GM	GSD
F	SDS without EDTA	DEAE-cellulose	9.9 × 104/1.1 × 108	0.09	0.004	0.6	2.6 × 105/1.7 × 106	15	0.18	3
G	SDS without EDTA	Magnetic beads	8.2 × 105/1.1 × 108	0.77	0.03	1.5	8.9 × 105/1.7 × 106	52	0.04	3
H	SDS with EDTA	Magnetic beads	1.2 × 107/1.1 × 108	11	0.02	41	4.7 × 105/1.7 × 106	27	0.10	7
I	TRIzol reagent	Magnetic beads	1.0 × 105/1.1 × 108	0.10	0.24	6.7	2.5 × 104/1.7 × 106	1.5	0.11	3

^aGM, geometric mean; GSD, geometric standard deviation.

^bRecovery rates for the lysis, extraction, and concentration steps were calculated from those of flow 3 and flow 4.