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Diversity and independent evolutionary profiling of rodent-borne pathogens in tropical island, China
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  • Youyou Li,
  • Chuanning Tang,
  • Yun Zhang,
  • Zihan Li,
  • Gaoyu Wang,
  • Ruoyan Peng,
  • Yi Huang,
  • Xiaoyuan Hu,
  • Henan Xin,
  • Boxuan Feng,
  • Xuefang Cao,
  • Yongpeng He,
  • Tonglei Guo,
  • Yijun He,
  • Haoxiang Su,
  • Xiuji Cui,
  • Lina Niu,
  • Zhiqiang Wu,
  • Jian Yang,
  • Fan Yang,
  • Gang Lu,
  • Lei Gao,
  • Qi Jin,
  • Meifang Xiao,
  • Feifei Yin,
  • Jiang Du
Youyou Li
Hainan Medical University
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Chuanning Tang
Hainan Medical University
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Yun Zhang
Hainan Medical University
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Zihan Li
Hainan Medical University
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Gaoyu Wang
Hainan Medical University
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Ruoyan Peng
Hainan Medical University
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Yi Huang
Hainan Medical University
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Xiaoyuan Hu
Hainan Medical University
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Henan Xin
Chinese Academy of Medical Sciences & Peking Union Medical College
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Boxuan Feng
Chinese Academy of Medical Sciences & Peking Union Medical College
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Xuefang Cao
Chinese Academy of Medical Sciences & Peking Union Medical College
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Yongpeng He
Chinese Academy of Medical Sciences & Peking Union Medical College
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Tonglei Guo
Chinese Academy of Medical Sciences & Peking Union Medical College
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Yijun He
Chinese Academy of Medical Sciences & Peking Union Medical College
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Haoxiang Su
Chinese Academy of Medical Sciences & Peking Union Medical College
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Xiuji Cui
Hainan Medical University
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Lina Niu
Hainan Medical University
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Zhiqiang Wu
Chinese Academy of Medical Sciences & Peking Union Medical College
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Jian Yang
Chinese Academy of Medical Sciences & Peking Union Medical College
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Fan Yang
Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Pathogen Biology
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Gang Lu
Hainan Medical University
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Lei Gao
Chinese Academy of Medical Sciences & Peking Union Medical College
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Qi Jin
Chinese Academy of Medical Sciences & Peking Union Medical College
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Meifang Xiao
Hainan Women and Children's Medical Center
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Feifei Yin
Hainan Medical University
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Jiang Du

Corresponding Author:[email protected]

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Abstract

The risk of emerging infectious diseases (EID) is increasing globally. More than 60% of EIDs worldwide are caused by animal-borne pathogens, and most viral pathogens are rodent-borne. This study aimed to characterise the virome and analyse the phylogenetic evolution and diversity of rodent-borne viruses in Hainan Province, China. We collected 588 anal and throat samples from rodents, combined them into 28 pools according to their species and location, and processed them for next-generation sequencing and bioinformatics analysis. The diverse viral reads closely related to mammals were assigned to 15 viral families. Molecular clues of the important rodent-borne viruses were further identified by polymerase chain reaction for phylogenetic analysis and annotation of genetic characteristics such as coronavirus, arenavirus, picornavirus. We identified a pestivirus in Leopoldoms edwardsi and two bocaviruses in Rattus andamanensis and Leopoldoms edwardsi from the national nature reserves of Jianfengling and Bangxi with low amino acid identity to known pathogens are proposed as the novel species, and their rodent hosts have not been previously reported to carry these viruses. These results expand our knowledge of viral classification and host range and suggest that there are highly diverse, undiscovered viruses that have evolved independently in their unique wildlife hosts in inaccessible areas, which may cause zoonosis if they cross their host barrier. Our virome and phylogenetic analyses of rodent-borne viruses provide basic data for the prevention and control of human infectious diseases caused by rodent-borne viruses in the subtropical area of China.