Metagenomic Investigation on RNA Viral Pathogens Causing Fawn Sika Deer Diarrhoea

Diarrhea is a common disease in Sika deer breeding. The etiology is intricate, with several disease types and the continuous emergence of novel viruses, posing a significant threat to the health of Sika deer, particularly the survival rate of fawns. In order to master the virus spectrum causing diarrhea in Sika deer. In this study, fecal samples of Sika deer from different regions of Jilin Province were collected for viral metagenome sequencing. The main viruses were investigated by RT-qPCR, and the positive samples were isolated and identified. Finally, whole genome sequencing and genetic evolution analysis were performed for the isolated strains. The results showed that nine RNA viruses caused diarrhea in Sika deer, among which the infection rates of BCoV, BRV, and BVDV were 59.72%, 58.89%, and 21.67%, respectively. There was also apparent mixed infection. A strain exhibiting a characteristic cytopathic effect was successfully isolated from BRV - positive samples. The investigation of whole genome sequencing revealed that the genotype of the strain was G6-P[1]-I2-R2-C2- M2-A3-N2-T6 -E2-H3. This study enriched the pathogen spectrum and epidemiologi-cal survey data of side diarrhea. It confirmed the recombination characteristics of ro-tavirus, providing a new perspective for understanding its genetic diversity and evo-lution.