The virome investigation of the globally endangered Eld’s deer (Rucervus eldii) on Hainan Island, China
Abstract Eld’s deer (Rucervus eldii) is a rare and globally endangered tropical Southeast Asian deer species. There is no research on pathogens in Eld’s deer in Hainan, China. This study aimed to understand the virus diversity and novel viruses in Eld’s deer, and provided important epidemiological b...
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Nature Portfolio
2025-03-01
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| Online Access: | https://doi.org/10.1038/s41598-025-92781-4 |
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| author | Haoxiang Su Dandan Zheng Zihan Li Xuming Qi Yunxing Chang Guangxu Ren Qingqing Lu Jiaqi Li Yu Li Chuan Tian Ruoyan Peng Gaoyu Wang Xiaoyuan Hu Yi Huang Chuanning Tang Xiuji Cui Lina Niu Mingming Zhao Xianghui Tan Jie Dong Jian Yang Fan Yang Feifei Yin Youyou Li Gang Lu Yun Zhang |
| author_facet | Haoxiang Su Dandan Zheng Zihan Li Xuming Qi Yunxing Chang Guangxu Ren Qingqing Lu Jiaqi Li Yu Li Chuan Tian Ruoyan Peng Gaoyu Wang Xiaoyuan Hu Yi Huang Chuanning Tang Xiuji Cui Lina Niu Mingming Zhao Xianghui Tan Jie Dong Jian Yang Fan Yang Feifei Yin Youyou Li Gang Lu Yun Zhang |
| author_sort | Haoxiang Su |
| collection | DOAJ |
| description | Abstract Eld’s deer (Rucervus eldii) is a rare and globally endangered tropical Southeast Asian deer species. There is no research on pathogens in Eld’s deer in Hainan, China. This study aimed to understand the virus diversity and novel viruses in Eld’s deer, and provided important epidemiological baseline information for conservation of this endangered species. 33 nasal swabs, 33 anal swabs, and 9 wound (bitten by ticks) swabs were collected from 33 wild Eld’s deer in a nature reserve in Hainan, which constituted into 5 pools. Based on next-generation sequencing (NGS) and macrogenomic analysis, there were differences in the 5 pools of viral reads, while the overall viral reads were closely related to mammals. The novel papillomavirus (PsPV-HMU-1) and Circular Rep-encoding (replication-associated protein encoding) single-stranded DNA (CRESS DNA) virus (PsaCV-HMU-1) were identified in Eld’s deer, with amino acid homology of the less than 77.20% of the L1 and less than 45.43% of the rep, respectively. PsPV-HMU-1 and PsaCV-HMU-1 are relatively independent on their phylogenetic trees, and with the overall prevalence of 24.24% (8/33) and 3.03% (1/33) in Eld’s deer, respectively. Our results expanded the viral genomic information and host range, and implied that it is necessary for continued epidemiological surveillance in order to understand pathogenicity and the potential for cross-species transmission of viruses in wild Eld’s deer. |
| format | Article |
| id | doaj-art-698de320f2464b07a919bc7ff4dafcdf |
| institution | DOAJ |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-698de320f2464b07a919bc7ff4dafcdf2025-08-20T02:56:11ZengNature PortfolioScientific Reports2045-23222025-03-0115111110.1038/s41598-025-92781-4The virome investigation of the globally endangered Eld’s deer (Rucervus eldii) on Hainan Island, ChinaHaoxiang Su0Dandan Zheng1Zihan Li2Xuming Qi3Yunxing Chang4Guangxu Ren5Qingqing Lu6Jiaqi Li7Yu Li8Chuan Tian9Ruoyan Peng10Gaoyu Wang11Xiaoyuan Hu12Yi Huang13Chuanning Tang14Xiuji Cui15Lina Niu16Mingming Zhao17Xianghui Tan18Jie Dong19Jian Yang20Fan Yang21Feifei Yin22Youyou Li23Gang Lu24Yun Zhang25NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical CollegeNHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical CollegeNHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical CollegeBawangling Branch of Hainan Tropical Rainforest National Park AdministrationHainan Bangxi Provincial Nature Reserve AdministrationKey Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical UniversityKey Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical UniversityKey Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical UniversityDepartment of Nuclear Medicine, the 928th Hospital of PLA Joint Logistics ForceDepartment of Oncology, the Affiliated Hospital of Guizhou Medical UniversityKey Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical UniversityKey Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical UniversityKey Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical UniversityKey Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical UniversityKey Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical UniversityKey Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical UniversityKey Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical UniversityKey Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical UniversityKey Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical UniversityNHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical CollegeNHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical CollegeNHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical CollegeKey Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical UniversityDepartment of Blood Transfusion, the Affiliated Cancer Hospital of Guizhou Medical UniversityKey Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical UniversityKey Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical UniversityAbstract Eld’s deer (Rucervus eldii) is a rare and globally endangered tropical Southeast Asian deer species. There is no research on pathogens in Eld’s deer in Hainan, China. This study aimed to understand the virus diversity and novel viruses in Eld’s deer, and provided important epidemiological baseline information for conservation of this endangered species. 33 nasal swabs, 33 anal swabs, and 9 wound (bitten by ticks) swabs were collected from 33 wild Eld’s deer in a nature reserve in Hainan, which constituted into 5 pools. Based on next-generation sequencing (NGS) and macrogenomic analysis, there were differences in the 5 pools of viral reads, while the overall viral reads were closely related to mammals. The novel papillomavirus (PsPV-HMU-1) and Circular Rep-encoding (replication-associated protein encoding) single-stranded DNA (CRESS DNA) virus (PsaCV-HMU-1) were identified in Eld’s deer, with amino acid homology of the less than 77.20% of the L1 and less than 45.43% of the rep, respectively. PsPV-HMU-1 and PsaCV-HMU-1 are relatively independent on their phylogenetic trees, and with the overall prevalence of 24.24% (8/33) and 3.03% (1/33) in Eld’s deer, respectively. Our results expanded the viral genomic information and host range, and implied that it is necessary for continued epidemiological surveillance in order to understand pathogenicity and the potential for cross-species transmission of viruses in wild Eld’s deer.https://doi.org/10.1038/s41598-025-92781-4Eld’s deerPapillomaviridaeCRESS DNA virusCircoviridaeGenetic diversityPhylogenetic analysis |
| spellingShingle | Haoxiang Su Dandan Zheng Zihan Li Xuming Qi Yunxing Chang Guangxu Ren Qingqing Lu Jiaqi Li Yu Li Chuan Tian Ruoyan Peng Gaoyu Wang Xiaoyuan Hu Yi Huang Chuanning Tang Xiuji Cui Lina Niu Mingming Zhao Xianghui Tan Jie Dong Jian Yang Fan Yang Feifei Yin Youyou Li Gang Lu Yun Zhang The virome investigation of the globally endangered Eld’s deer (Rucervus eldii) on Hainan Island, China Scientific Reports Eld’s deer Papillomaviridae CRESS DNA virusCircoviridae Genetic diversity Phylogenetic analysis |
| title | The virome investigation of the globally endangered Eld’s deer (Rucervus eldii) on Hainan Island, China |
| title_full | The virome investigation of the globally endangered Eld’s deer (Rucervus eldii) on Hainan Island, China |
| title_fullStr | The virome investigation of the globally endangered Eld’s deer (Rucervus eldii) on Hainan Island, China |
| title_full_unstemmed | The virome investigation of the globally endangered Eld’s deer (Rucervus eldii) on Hainan Island, China |
| title_short | The virome investigation of the globally endangered Eld’s deer (Rucervus eldii) on Hainan Island, China |
| title_sort | virome investigation of the globally endangered eld s deer rucervus eldii on hainan island china |
| topic | Eld’s deer Papillomaviridae CRESS DNA virusCircoviridae Genetic diversity Phylogenetic analysis |
| url | https://doi.org/10.1038/s41598-025-92781-4 |
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