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An outbreak of rabies affected domestic raccoon dogs on an animal farm in Inner Mongolia, China in 2007. A study was conducted to characterize the aetiological agent and clarify the origin of the rabies virus. Brain tissues were obtained from five rabid raccoon dogs. Viral nucleoprotein antigen was detected in the brain tissues and five rabies viruses were isolated from these rabid animals. Phylogenetic analysis of the N and G gene sequences showed that these isolates were closely related to Arctic-like rabies viruses isolated from the far-eastern region of Russia and South Korea, but distinct from the rabies viruses that are widely distributed in endemic areas in China. Epidemiological data suggested that the likely source of infection was from one wild raccoon dog that was captured and placed in the same type of pen used for domestic raccoon dogs.

Background Previous investigations of phylogeny in Cervus recovered many clades without whole genomic support. Methods In this study, the genetic diversity and phylogeny of 5 species (21 subspecies/populations from C. unicolor , C. albirostris , C. nippon , C. elaphus and C. eldii ) in the genus Cervus were analyzed using reduced-representation genome sequencing. Results A total of 197,543 SNPs were identified with an average sequencing depth of 16 x. A total of 21 SNP matrices for each subspecies/population and 1 matrix for individual analysis were constructed, respectively. Nucleotide diversity and heterozygosity analysis showed that all 21 subspecies/populations had different degrees of genetic diversity. C. eldii , C. unicolor and C. albirostris showed relatively high expected and observed heterozygosity, while observed heterozygosity in C. nippon was the lowest, indicating there was a certain degree of inbreeding rate in these subspecies/populations. Phylogenetic ML tree of all Cervus based on the 21 SNP matrices showed 5 robustly supported clades that clearly separate C. eldii , C. unicolor , C. albirostris , C. elaphus and C. nippon . Within C. elaphus clade, 4 subclades were well differentiated and statistically highly supported: C. elaphus (New Zealand), C. e. yarkandensis , C. c. canadensis and the other grouping the rest of C. canadensis from China. In the C. nippon clade, 2 well-distinct subclades corresponding to C. n. aplodontus and other C. nippon populations were separated. Phylogenetic reconstruction indicated that the first evolutionary event of the genus Cervus occurred approximately 7.4 millions of years ago. The split between C. elaphus and C. nippon could be estimated at around 3.6 millions of years ago. Phylogenetic ML tree of all samples based on individual SNP matrices, together with geographic distribution, have shown that there were 3 major subclades of C. elaphus and C. canadensis in China, namely C. e. yarkandensis (distributed in Tarim Basin), C. c. macneilli/C. c. kansuensis / C. c. alashanicus (distributed in middle west of China), ...

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