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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

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

Virus Virus abbreviation Strain/Reference Pan-flavi assay RT-PCR *
  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.
  1. 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.