Identification and molecular characterization of a novel duck Tembusu virus isolate from Southwest China

Tembusu virus (TMUV) has caused significant economic losses in the Chinese duck industry and may have been overlooked regarding its zoonotic transmission potential. A novel TMUV isolate (named CQW1) was separated from the liver tissue of a young duck in Southwest China. The CQW1 isolate proliferated in embryonated duck eggs and led to death within 3-4 days post-inoculation. Furthermore, CQW1 replicated in duck embryo fibroblast (DEF) cells and caused a cytopathic effect (CPE). The disease emerged on a duck farm in Southwest China and was reproduced by animal experiment. We found that CQW1 was detectable by RT-PCR in brain and liver tissues of dead ducklings within 5 days after inoculation. Most importantly, concentrated nuclei, neuronophagia and microglial nodules were observed in the brain tissue of the inoculated ducklings, and additionally, the liver tissue was affected, mainly by disordered lobular architecture, degeneration, necrosis and regenerated hepatocytes. Analysis of the complete genome sequence showed that CQW1 was 10,992 nt in length with two nucleotide insertions and shared 96.8% to 99.1% and 98.4% to 99.6% identity at nucleotide and amino acid level, respectively, with Chinese isolates. Phylogenetic analysis of the nucleotide sequences demonstrated that the CQW1 isolate was closely related to other members of the genus Flavivirus and formed a new clade together with the GX2013H isolate. Also, the CQW1 isolate demonstrated the highest average pairwise distance value among the Chinese isolates. In the present study, we obtained evidence that TMUV is present in Southwest China. Extensive pathological and epidemiological studies are urgently needed.