Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer Fawns
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethical Approval
2.2. Collection of Fecal Samples and Processing
2.3. RNA Isolation
2.4. Viral Metagenomic Library Construction and High-Throughput Sequencing
2.5. Bioinformatics Analysis
2.6. Real-Time PCR
2.7. Isolation and Identification of Rotavirus
2.8. Whole-Genome Sequencing and Assembly of the Rotavirus Genome
2.9. Phylogenetic Analysis
3. Results
3.1. Quality Control Analysis of Viral Metagenomic Data
3.2. Diversity Analysis of Enteric RNA Viruses in Fawns
3.3. Epidemiological Investigation of Enteric Pathogens in Fawns
3.4. In Vitro Identification of Rotavirus
3.5. Genetype Analysis of Rotavirus
3.6. Genetic Evolutionary Analysis
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Groups | Clean Reads | All Tran Num | Clean Bases | Error Rate | Q20 | Q30 | GC Content |
---|---|---|---|---|---|---|---|
A1 | 37,291,842 | 56,013 | 5.59 G | 0.02 | 98.56 | 95.57 | 40 |
A2 | 45,535,848 | 84,558 | 6.83 G | 0.02 | 98.63 | 95.75 | 44.53 |
A4 | 36,317,604 | 53,317 | 5.45 G | 0.02 | 98.47 | 95.34 | 47.47 |
A3 | 34,308,390 | 54,727 | 5.15 G | 0.02 | 98.43 | 95.22 | 39.22 |
A5 | 40,418,916 | 42,393 | 6.06 G | 0.02 | 98.42 | 95.15 | 37.46 |
Family/Groups | A1 | A2 | A3 | A4 | A5 | Total |
---|---|---|---|---|---|---|
Sedoreoviridae | 95.21% | 78.00% | 93.85% | 17.55% | 96.82% | 82.10% |
Astroviridae | 3.932% | 20.27% | 5.582% | 61.17% | 2.779% | 14.25% |
Coronaviridae | 0.007009% | 0.01029% | 0.004904% | 15.90% | 0.1652% | 2.279% |
Caliciviridae | 0 | 0 | 0.0007864% | 0.009401% | 0.00004804% | 0.001481% |
Retroviridae | 0.003899% | 0.01039% | 0.006507% | 0.02781% | 0.001106% | 0.007843% |
Nodaviridae | 0.001326% | 0 | 0 | 0 | 0 | 0.0003038% |
Hepeviridae | 0.001023% | 0.004980% | 0.0006945% | 0.0004869% | 0.0003797% | 0.001258% |
Flaviviridae | 0.0003907% | 0.01831% | 0.006307% | 0.01925% | 0.003013% | 0.007497% |
Picornaviridae | 0.8440% | 1.690% | 0.5484% | 5.318% | 0.2328% | 1.353% |
Pathogens | Positive Samples | Negative Samples | Positive Rate/% |
---|---|---|---|
BRV | 212 | 148 | 58.89 |
BCoV | 214 | 146 | 59.44 |
BVDV | 78 | 282 | 21.67 |
BRV and BCoV | 97 | 263 | 26.94 |
BRV and BVDV | 5 | 355 | 1.39 |
BCoV and BVDV | 13 | 347 | 3.61 |
BRV, BCoV and BVDV | 58 | 302 | 16.11 |
Gene | Length (bp) | Coding Region (bp) | Genotype | Virus with the Highest Identity | Identity (%) | GenBank ID |
---|---|---|---|---|---|---|
VP1 | 3302 | 3267 | R2 | Human-wt/HUN/BP1062 | 99.76 | PV158729 |
VP2 | 2690 | 2260 | C2 | Human-wt/MWI/MW2-181_B | 100 | PV158730 |
VP3 | 2508 | 2508 | M2 | Cow-tc/China/SCMY2 | 99.48 | PV158731 |
VP4 | 2362 | 2088 | P[1] | Cow-tc/CHN/SDA2/G6P[1] | 99.83 | PV158732 |
VP6 | 1352 | 1215 | I2 | RV/Bovine/HM26 | 96.60 | PV158733 |
VP7 | 1062 | 981 | G6 | Yak-tc/China/F8 | 96.81 | PV158734 |
NSP1 | 1579 | 1476 | A3 | Yak-tc/CHN/HY-1 | 100.00 | PV158735 |
NSP2 | 1055 | 996 | N2 | Bovine/C73 | 97.43 | PV158736 |
NSP3 | 1074 | 966 | T6 | Lamb/CHN/LLR | 98.24 | PV158737 |
NSP4 | 749 | 567 | E2 | Bovine/HM26 | 98.40 | PV158738 |
NSP5 | 597 | 597 | H3 | Cow-tc/JPN/GB12-22 | 98.32 | PV158739 |
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Wang, W.; Wang, Q.; Cao, R.; Li, Y.; Liu, Z.; Xue, Z.; Wang, X.; Liu, Z. Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer Fawns. Viruses 2025, 17, 803. https://doi.org/10.3390/v17060803
Wang W, Wang Q, Cao R, Li Y, Liu Z, Xue Z, Wang X, Liu Z. Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer Fawns. Viruses. 2025; 17(6):803. https://doi.org/10.3390/v17060803
Chicago/Turabian StyleWang, Weiyang, Qilin Wang, Runlai Cao, Yacong Li, Ziyu Liu, Zhuqing Xue, Xiaoxu Wang, and Zhijie Liu. 2025. "Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer Fawns" Viruses 17, no. 6: 803. https://doi.org/10.3390/v17060803
APA StyleWang, W., Wang, Q., Cao, R., Li, Y., Liu, Z., Xue, Z., Wang, X., & Liu, Z. (2025). Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer Fawns. Viruses, 17(6), 803. https://doi.org/10.3390/v17060803