Table 2.

Representative results of the Pan-Flavi assay to detect different flaviviruses, and its comparison with flavivirus species-specific assays

Virus	Strain/ Acc. No.	Pan-flavi assay*,#			Virus-specific assay#
		Mean of Ct value	SD of Ct value	Mean of GC/ml	Mean of Ct value	SD of Ct value	Mean of GC/ml	Reference
Flavivirus
DENV-1	ATCC VR-344	15.64	0.02	2.0 × 109	15.93	0.03	4.6 × 109	[29]
DENV-2	ATCC VR-345	20.76	0.20	6.6 × 107	18.77	0.11	6.7 × 108
DENV-3	ATCC VR-1256	19.36	0.01	1.7 × 108	20.30	0.01	2.4 × 108
DENV-4	ATCC VR-1257	16.33	0.19	1.3 × 109	16.18	0.29	3.9 × 109
YFV 17D	X03700	19.17	0.17	1.9 × 108	20.51	0.17	5.6 × 108	[30]
YFV ASIBI	RKI reference strain	23.73	0.05	9.1 × 106	23.72	0.28	4.7 × 107
YFV Brazil	RKI reference strain	21.18	0.07	5.0 × 107	22.50	0.10	1.2 × 108
YFV Ivory Cost	RKI reference strain	21.44	0.21	4.2 × 107	21.29	0.05	3.1 × 108
WNV Uganda	AY532665, lineage 1	28.74	0.06	3.2 × 105	26.83	0.27	3.4 × 106	[31]
WNV Israel	lineage 2	19.81	0.15	1.2 × 108	19.86	0.01	4.0 × 108
TBEV K23	AF091010	16.33	0.03	1.3 × 109	16.78	0.14	2.1 × 108	[32]
RSSEV	RKI reference strain	24.20	0.32	6.7 × 106	19.35	0.01	4.1 × 106
TBEV Louping ill	RKI reference strain	20.59	0.22	7.4 × 107	20.43	0.06	2.0 × 107
JEV	ATCC SA14-14-2	19.36	0.01	2.4 × 108	16.73	0.01	7.7 × 108	In house assay

GC: genome copies, Ct: threshold cycle, SD: standard deviation.

DENV: Dengue virus, JEV: Japanese encephalitis virus, RSSEV: Russian spring-summer encephalitis virus, WNV: West Nile virus, TBEV: Tick-borne encephalitis virus, YFV: Yellow fever virus.

^*Pan-Flavi assay was performed using Flavi-all S, Flavi all AS2, DEN4 F primer and Flavi all probe3 mix.

^#The same amount of RNA (5 μl) was applied to both pan-Flavi assay and virus species-specific one-step qRT-PCR assays.