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Table 2 Representative results of the Pan-Flavi assay to detect different flaviviruses, and its comparison with flavivirus species-specific assays

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

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
  1. GC: genome copies, Ct: threshold cycle, SD: standard deviation.
  2. 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.
  3. *Pan-Flavi assay was performed using Flavi-all S, Flavi all AS2, DEN4 F primer and Flavi all probe3 mix.
  4. #The same amount of RNA (5 μl) was applied to both pan-Flavi assay and virus species-specific one-step qRT-PCR assays.