Development of one-step quantitative reverse transcription PCR for the rapid detection of flaviviruses

Table 3 Performance of the Pan-Flavi assay to detect different flaviviruses. Five μl of viral RNA extracted from virus cell culture supernatant were applied to both pan-Flavi assay and RT-PCR

Virus	Virus abbreviation	Strain/Reference	Pan-flavi assay	RT-PCR *
Virus	Virus abbreviation		Ct value	Confirmation by gel
*Flaviviridae*
St. Louis Encephalitis virus	SLEV	ATCC VR-1265	22.19	N.d.
Usutu virus	USUV	AY453411	22.48	N.d.
Kunjin virus	KUNV	PI.France	24.97	N.d.
Kedougou virus	KEDV	ArD 14701	29.62	Positive
Koutango virus	KOUV	AnD 5443	30.29	Positive
Spondweni virus	SPOV	SA Ar 94	26.02	Negative
Uganda S virus	UGSV	ArD 109325	29.48	Positive
Wesselsbron	WESSV	ArB 4177	24.73	Positive
Zika virus	ZIKV	PI, Senegal	22.45	Positive
Sepik virus	SEPV	MK 7148	16.77	Positive
Dakar bat virus	DBV	AnD 249	32.57	Positive
Yaounade virus	YAOV	ArY 276/68	17.52	Positive
Bouboui virus	BOUV	ArB 490	31.88	Negative
Saboya virus	SABV	AnD 4600	27.50	Negative
Nounane virus^#	NOUV	B3 isolate	No ct	N.d.
*Bunya viridae*
Rift valley fever virus	RVFV	RKI	No ct	N.d.
*Togaviridae*
Chikungunya virus		LR 2006	No ct	N.d.
Chikungunya virus		ST05,African isolate	No ct	N.d.
Sindbis virus		RKI	No ct	N.d.
*Influneza virus*
H1N1 Hamburg		A/Hamburg/04/2009 H1N1	No ct	N.d.
H1N1 California		A/California/04/2009 H1N1	No ct	N.d.
H5N1		A/dk/Germany R603/06 H5N1	No ct	N.d.

N.d.: not done, Ct: threshold cycle, * RNA of African flaviviruses were detected using reference method described previously [33].^# Nounane virus was detected using final optimized primer sets Flavi all S/Flavi all S2/Flavi all AS4 and Flavi all probe 3 mix.

ISSN: 1743-422X