Analysis of the complete genome of Tembusu virus, a flavivirus isolated from ducks in China.

During investigations into the outbreak of duck viral infection in 2010 in China, with a severe drop in egg production, a flavivirus was isolated from the affected ducks. It was characterized as a Tembusu virus (TMUV). In this study, we obtained a complete genome sequence of Tembusu virus using RT-PCR and RACE techniques. TMUV genome is a singled-stranded RNA, with 10,990 nucleotides in length, and contains a single open reading frame (3410 amino acids) encoding 11 viral proteins with 5'and 3'non-translated regions (NTRs) of 142 and 618 nt, respectively. We characterized the open reading frame (ORF) with respect to gene sizes, cleavage sites and potential glycosylation sites. The different genomic regions of the virus were also compared with those of six other flaviviruses including Japanese encephalitis virus, West Nile virus (WNV), dengue-2 virus, yellow fever virus, tick-borne encephalitis virus (TBEV) and Bagaza virus. TMUV demonstrated the highest similarity to Bagaza virus. The result of entire ORF scanning shows that TMUV was close to Bagaza viruses in genetic relatedness. These data demonstrate that TMUV is a unique virus among the mosquito-borne flaviviruses and also provide a useful reference for a critically important study to determine why TMUV is a serious pathogen for ducks.