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. 2025 May 31;17(6):803.
doi: 10.3390/v17060803.

Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer Fawns

Weiyang Wang  1 , Qilin Wang  1 , Runlai Cao  1 , Yacong Li  1 , Ziyu Liu  1 , Zhuqing Xue  1 , Xiaoxu Wang  1 , Zhijie Liu  1
Affiliations

Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer Fawns

Weiyang Wang et al. Viruses. .

Abstract

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 Siphoviridae, 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.

Keywords: rotavirus; sika deer; viral metagenomics; whole-genome sequencing.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
The pie chart shows the composition of fecal virus groups of diarrhea sika deer in different virus families.
Figure 2
Figure 2
Statistical map of relative abundance at the family level.
Figure 3
Figure 3
Relative abundance of viral communities in each group: (a) distribution of the Astroviri dae family; (b) distribution of the rotavirus genus; (c) distribution of the Coronaviridae family; (d) distribution of the Pestivirus genus.
Figure 4
Figure 4
Isolation, cultivation, and immunofluorescence identification of rotavirus: (a) CPE of fourth-passage Vero cells infected with the SY1 isolate for 36 h. (b) CPE of fifth-passage Vero cells infected with the SY1 isolates for 24 h. (c) Normal Vero cells. (d) SY1-infected Vero cells stained with the RVA antibody (green). (e) The stained nuclei (blue) of Vero cells. (f) Merged image of Vero cells.
Figure 5
Figure 5
Electron microscopy image of RVA/Sika deer-wt/CHN/SY1/2024 virus particles (25,000×).
Figure 6
Figure 6
Phylogenetic tree of the nucleotide sequences of the VP1, VP2, VP3, VP4, VP6, and VP7 genes of RVA strains. Phylogenetic trees were constructed based on the nucleotide sequences of different gene segments of SY1 and other reference strains using a proximity analysis with 1000 bootstrap repeats. The RVA strains are color-coded: human strains are shown in purple; pig breed strains are shown in green; herbivore strains are shown in green; and bat strains are shown in orange. Red triangles highlight the RVA strain SY1 identified in this study. The scale representing evolutionary distance represents the nucleotide replacement rate at each site. The bootstrap value is displayed in the branch to the left of the main node above.
Figure 6
Figure 6
Phylogenetic tree of the nucleotide sequences of the VP1, VP2, VP3, VP4, VP6, and VP7 genes of RVA strains. Phylogenetic trees were constructed based on the nucleotide sequences of different gene segments of SY1 and other reference strains using a proximity analysis with 1000 bootstrap repeats. The RVA strains are color-coded: human strains are shown in purple; pig breed strains are shown in green; herbivore strains are shown in green; and bat strains are shown in orange. Red triangles highlight the RVA strain SY1 identified in this study. The scale representing evolutionary distance represents the nucleotide replacement rate at each site. The bootstrap value is displayed in the branch to the left of the main node above.
Figure 7
Figure 7
Phylogenetic tree of the nucleotide sequences of the NSP1, NSP2, NSP3, NSP4, and NSP5 genes of RVA strains. Phylogenetic trees were constructed based on the nucleotide sequences of different gene segments of SY1 and other reference strains using a proximity analysis with 1000 bootstrap repeats. The RVA strains are color-coded: human strains are shown in purple; pig breed strains are shown in green; herbivore strains are shown in green; and bat strains are shown in orange. Red triangles highlight the RVA strain SY1 identified in this study. The scale representing evolutionary distance represents the nucleotide replacement rate at each site. The bootstrap value is displayed in the branch to the left of the main node above.
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