Objective      To establish a rapid and accurate method to detect Zaire ebola virus (ZEBOV).       Methods      According to the 3 new strains of ZEBOV genome-wide reference sequences separated from West Africa in 2014 and the Zaire ebola virus strain isolated from Mayinga (NC_002549) in 1976

specific sequence signature of ZEBOV was calculated out based on Insignia system algorithm comparison with GenBank Nt library. Primers and TaqMan probe were designed

and the reaction conditions were optimized. Ten-fold series dilution positive plasmid were used as the standard samples to do amplification plots and standard curve. Also the repeatability and accuracy of the method were tested. The rest of the 4 types of ebola virus

marburg virus

west Nile virus

eastern equine encephalitis virus

and Western equine encephalitis virus

and the 48 clinical comparison samples were employed to contrast for specificity test.       Results      The specific sequence (KJ660348

11331-11514) design probe and primers were designed. Standard curve’s correlation coefficient was greater than 0.99 and the sensitivity was up to 5×101 copies. Repeatability and accuracy test’s results showed that the coefficient of variation (CV) of the intra assay reproducibility was 0.88% to 2.50%

and the CV of the inter assay reproducibility was 1.75% to 3.31%. Eight strains of viruses and 19 clinical comparison samples were all negative.       Conclusion      The specific sequence signature of Zaire ebola virus in the non-coding regions (KJ660348

11331-11514)

was verified to be specific. Our established fluorescence quantitative PCR is a rapid

sensitive and reproducible method for ZEBOV detection.