Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer Fawns
Diarrhea is a common disease in sika deer. The causes of diarrhea in sika deer are complex and involve a variety of pathogens. Additionally, new virulent pathogens are continuously emerging, which poses a serious threat to deer’s health and particularly affects fawns’ survival rate. In the present s...
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2025-05-01
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| author | Weiyang Wang Qilin Wang Runlai Cao Yacong Li Ziyu Liu Zhuqing Xue Xiaoxu Wang Zhijie Liu |
| author_facet | Weiyang Wang Qilin Wang Runlai Cao Yacong Li Ziyu Liu Zhuqing Xue Xiaoxu Wang Zhijie Liu |
| author_sort | Weiyang Wang |
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| description | Diarrhea is a common disease in sika deer. The causes of diarrhea in sika deer are complex and involve a variety of pathogens. Additionally, new virulent pathogens are continuously emerging, which poses a serious threat to deer’s health and particularly affects fawns’ survival rate. In the present study, feces samples were collected from fawns with diarrhea in Jilin Province, in the northeast of China. The viral communities were investigated using the metagenomic method. Viral metagenome data revealed that the viruses in the fecal samples were mainly from 21 families in 14 orders. The major viruses in high abundance were astrovirus, rotavirus, coronavirus, and bovine viral diarrhea virus. In addition, a large number of phages, which mainly belonged to the family <i>Siphoviridae</i>, were identified. Then, the known causative virus species were investigated via RT-qPCR. The results showed that the infection rates of bovine coronavirus, bovine rotavirus, and bovine viral diarrhea virus were 59.44%, 58.89%, and 21.67%, respectively, and mixed infections were commonly seen in the samples. A bovine rotavirus strain was successfully isolated from the positive samples. Whole-genome sequencing revealed that the genotype of the strain was G6-P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3, indicating the recombination of rotavirus. This study revealed the profiles and characteristics of viruses that cause sika deer diarrhea, which will be helpful for understanding diarrhea diseases in sika deer. |
| format | Article |
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| institution | OA Journals |
| issn | 1999-4915 |
| language | English |
| publishDate | 2025-05-01 |
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| record_format | Article |
| series | Viruses |
| spelling | doaj-art-792ed2c15e314bf1926690b9d54b653a2025-08-20T02:21:54ZengMDPI AGViruses1999-49152025-05-0117680310.3390/v17060803Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer FawnsWeiyang Wang0Qilin Wang1Runlai Cao2Yacong Li3Ziyu Liu4Zhuqing Xue5Xiaoxu Wang6Zhijie Liu7Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture and Rural Affairs, Jilin Provincial International Cooperation Key Laboratory for Science and Technology Innovation of Special Animal and Plants, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, ChinaKey Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture and Rural Affairs, Jilin Provincial International Cooperation Key Laboratory for Science and Technology Innovation of Special Animal and Plants, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, ChinaKey Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture and Rural Affairs, Jilin Provincial International Cooperation Key Laboratory for Science and Technology Innovation of Special Animal and Plants, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, ChinaKey Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture and Rural Affairs, Jilin Provincial International Cooperation Key Laboratory for Science and Technology Innovation of Special Animal and Plants, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, ChinaKey Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture and Rural Affairs, Jilin Provincial International Cooperation Key Laboratory for Science and Technology Innovation of Special Animal and Plants, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, ChinaKey Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture and Rural Affairs, Jilin Provincial International Cooperation Key Laboratory for Science and Technology Innovation of Special Animal and Plants, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, ChinaKey Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture and Rural Affairs, Jilin Provincial International Cooperation Key Laboratory for Science and Technology Innovation of Special Animal and Plants, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, ChinaKey Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture and Rural Affairs, Jilin Provincial International Cooperation Key Laboratory for Science and Technology Innovation of Special Animal and Plants, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, ChinaDiarrhea is a common disease in sika deer. The causes of diarrhea in sika deer are complex and involve a variety of pathogens. Additionally, new virulent pathogens are continuously emerging, which poses a serious threat to deer’s health and particularly affects fawns’ survival rate. In the present study, feces samples were collected from fawns with diarrhea in Jilin Province, in the northeast of China. The viral communities were investigated using the metagenomic method. Viral metagenome data revealed that the viruses in the fecal samples were mainly from 21 families in 14 orders. The major viruses in high abundance were astrovirus, rotavirus, coronavirus, and bovine viral diarrhea virus. In addition, a large number of phages, which mainly belonged to the family <i>Siphoviridae</i>, were identified. Then, the known causative virus species were investigated via RT-qPCR. The results showed that the infection rates of bovine coronavirus, bovine rotavirus, and bovine viral diarrhea virus were 59.44%, 58.89%, and 21.67%, respectively, and mixed infections were commonly seen in the samples. A bovine rotavirus strain was successfully isolated from the positive samples. Whole-genome sequencing revealed that the genotype of the strain was G6-P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3, indicating the recombination of rotavirus. This study revealed the profiles and characteristics of viruses that cause sika deer diarrhea, which will be helpful for understanding diarrhea diseases in sika deer.https://www.mdpi.com/1999-4915/17/6/803sika deerviral metagenomicswhole-genome sequencingrotavirus |
| spellingShingle | Weiyang Wang Qilin Wang Runlai Cao Yacong Li Ziyu Liu Zhuqing Xue Xiaoxu Wang Zhijie Liu Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer Fawns Viruses sika deer viral metagenomics whole-genome sequencing rotavirus |
| title | Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer Fawns |
| title_full | Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer Fawns |
| title_fullStr | Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer Fawns |
| title_full_unstemmed | Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer Fawns |
| title_short | Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer Fawns |
| title_sort | metagenomic investigation of pathogenic rna viruses causing diarrhea in sika deer fawns |
| topic | sika deer viral metagenomics whole-genome sequencing rotavirus |
| url | https://www.mdpi.com/1999-4915/17/6/803 |
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