Molecular characterization of a duck Tembusu virus from China XiaoFei Bai • Rang Lv • ChunGuo Liu • Na Qiu • Yilong He • XiuChen Yin • XiaoJun Li • Ming Liu • Yun Zhang Received: 27 April 2013 / Accepted: 26 July 2013 / Published online: 15 August 2013 Ó Springer Science+Business Media New York 2013 Abstract A new emerging flavivirus caused severe egg- drop in poultry and spread quickly across most duck-pro- ducing regions of China in 2010. Complete genome sequencing indicated that the virus genome is 10,989 nucleotides in length and possesses typical flavivirus genome organization, 5 0 untranslated region (UTR)-Cv-Ci- prM-M-E-NS1-NS2A-NS2B-NS3-NS4A-2K-NS4B-NS5- 3 0 -UTR. The long open reading frame (ORF) encodes 3,425 amino acids (95–10,372 nt). The 94-nucleotide 5 0 -UTR is of intermediate size and the 617-nucleotide 3 0 -UTR is quite long relative to those of other flaviviruses. The polyprotein cleavage sites, potential glycosylation sites, distribution of cysteine residues, and 3 0 -UTR secondary structure were characterized. Phylogenetic analysis of the polyprotein sequences indicates that the HN isolate is closely related to Tembusu viruses of the Ntaya virus group. Keywords Flavivirus Á Tembusu virus Á Cleavage sites Á Secondary structure Introduction Flaviviruses are arthropod-transmitted viruses that belong to the Flaviviridae family. The flavivirus genome consists of single-stranded, positive-sense RNA, approximately 10.5 kb in length, encoding three structural and seven non-structural proteins in one open reading frame (ORF) [1]. The genome lacks a poly-A segment at the 3 0 -end. Virions consist of capsid proteins (C), envelope proteins (E), small non-gly- cosylated proteins (M), and seven non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5). The E protein, which is glycosylated in most flaviviruses, is located on the virion surface and plays an important role in virus receptor-binding, entry, and fusion. In 2010, an outbreak of unknown infectious severe egg-drop disease spread across most poultry farming regions in China [2–4]. The pathogen caused high morbidity, up to 100 %, and less than 5 % mortality. Egg production rates dropped drasti- cally to 10 % within 5 days. Postmortem examinations showed severe ovarian hemorrhage, ovaritis, and regression. The disease has caused a serious economic loss because of complete elimination of reproduction for some farms. Here, virus from a sick Muscovy duck from this out- break was isolated and designated HN strain. To better understand the properties of this causative pathogen, to expand the available flavivirus sequences in public dat- abases, and to establish phylogenetic relationships between the duck flavivirus and others, the full genomic sequence of the HN strain was determined. Features of the HN strain genome, polyprotein cleavage sites, 3 0 -UTR secondary structure, and 3 0 -sequence analysis were also characterized. Materials and methods Virus propagation The duck flavivirus HN strain was isolated from the liver of duck with egg-drop symptoms in China in 2010. Briefly, X. Bai Á R. Lv Á C. Liu Á N. Qiu Á Y. He Á X. Yin Á X. Li Á M. Liu (&) Á Y. Zhang (&) State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Harbin 150001, People’s Republic of China e-mail: liuming04@126.com Y. Zhang e-mail: yunzhang03@yahoo.com 123 Virus Genes (2013) 47:478–482 DOI 10.1007/s11262-013-0966-3