Diversity and independent evolutionary profiling of rodent-borne viruses in Hainan, a tropical island of China

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

doi:10.1016/j.virs.2023.08.003

October 2023

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 and Jiang Du. Diversity and independent evolutionary profiling of rodent-borne viruses in Hainan, a tropical island of China[J]. Virologica Sinica, 2023, 38(5): 651-662. doi: 10.1016/j.virs.2023.08.003

Citation: 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. Diversity and independent evolutionary profiling of rodent-borne viruses in Hainan, a tropical island of China .VIROLOGICA SINICA, 2023, 38(5) : 651-662. http://dx.doi.org/10.1016/j.virs.2023.08.003

海南鼠类携带病毒的系统进化分析及多样性

黎优优 ^c,d,e ,
唐川宁 ^c,d,e ,
张云 ^c,d,e ,
李子涵 ^c,d,e ,
王高玉 ^c,d,e ,
彭箬岩 ^c,d,e ,
黄艺 ^c,d,e ,
胡小媛 ^c,d,e ,
辛赫男 ^a ,
冯博轩 ^a ,
曹雪芳 ^a ,
何勇鹏 ^a ,
郭同磊 ^a ,
何翼君 ^a ,
苏浩翔 ^a ,
崔秀吉 ^c,d,e ,
牛丽娜 ^c,d,e ,
吴志强 ^a ,
杨剑 ^a ,
杨帆 ^a ,
吕刚 ^c,d,e ,
高磊 ^a ,
金奇 ^a ,
肖美芳 ^b,, ,
尹飞飞 ^b,c,d,e,, ,
杜江 ^a,c,d,,

a 国家卫生健康委员会病原系统生物学重点实验室, 病原生物学研究所, 中国医学科学院&北京协和医院, 北京, 100005, 中国;
b 临床检验科, 医学检验中心, 海南妇女儿童医学中心, 海口, 571199, 中国;
c 海南医学院热带病转化医学教育部重点实验室, 海南医学院, 海口, 571199, 中国;
d 海南医学院-香港大学热带传染病联合实验室, 海南医学院, 海口, 571199, 中国;
e 海南医学院病原教研室, 海南医学院, 海口, 571199, 中国

通讯作者： 肖美芳, xiaomeifang2006@hotmail.com; 尹飞飞, yinfeifeiff@163.com; 杜江, dujiangemail@163.com
收稿日期： 2023-03-21
录用日期： 2023-08-08

摘要

全球范围内新发传染病（Emerging infectious diseases，EID）的风险不断增加，60%以上的EIDs是由动物源性病原体引起的。本研究旨在鉴定海南省鼠传病毒组，并分析其系统发育进化和确定鼠类携带病毒多样性。我们从啮齿动物身上收集了682份肛门和喉咙拭子样本，根据采集地理位置和物种将样本进行分类混合得到28个混合样本。混合样本通过过滤、超离和磁珠分选的前处理，接着进行新一代测序和生物信息学分析。高通量测序结果显示病毒重叠群（contig）与22个哺乳动物病毒科相关，根据鼠类携带重要病毒的分子线索，利用聚合酶链式反应技术进一步鉴定并进行遗传特征注释和系统发育分析，如沙粒病毒、冠状病毒、星状病毒、瘟病毒、细小病毒和乳头瘤病毒。我们在白沙县黄猄角岭的小泡巨鼠中鉴定瘟病毒和细小病毒，在邦溪国家级自然保护区的黑缘齿鼠中鉴定到细小病毒，它们与已知病原体的氨基酸同源性较低，建议为新种，而它们的啮齿动物宿主此前尚未报道携带这些病毒。这些结果扩展了海南鼠类携带病毒的宿主种类和地域范围，新种或新属病毒的发现扩展了病毒学分类，并表明在人迹罕至的地区有高度多样、未被发现的病毒在其独特的野生动物宿主中独立进化。
- 鼠类
- , 病毒组
- , 进化分析
- , 新病毒
- , 野生动物

Diversity and independent evolutionary profiling of rodent-borne viruses in Hainan, a tropical island of China

Youyou Li ^c,d,e ,
Chuanning Tang ^c,d,e ,
Yun Zhang ^c,d,e ,
Zihan Li ^c,d,e ,
Gaoyu Wang ^c,d,e ,
Ruoyan Peng ^c,d,e ,
Yi Huang ^c,d,e ,
Xiaoyuan Hu ^c,d,e ,
Henan Xin ^a ,
Boxuan Feng ^a ,
Xuefang Cao ^a ,
Yongpeng He ^a ,
Tonglei Guo ^a ,
Yijun He ^a ,
Haoxiang Su ^a ,
Xiuji Cui ^c,d,e ,
Lina Niu ^c,d,e ,
Zhiqiang Wu ^a ,
Jian Yang ^a ,
Fan Yang ^a ,
Gang Lu ^c,d,e ,
Lei Gao ^a ,
Qi Jin ^a ,
Meifang Xiao ^b,, ,
Feifei Yin ^b,c,d,e,, ,
Jiang Du ^a,c,d,,

a. NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China;
b. Department of Clinical Laboratory, Center for Laboratory Medicine, Hainan Women and Children's Medical Center, Haikou, 571199, China;
c. Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China;
d. Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, 571199, China;
e. Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China

Corresponding author: Meifang Xiao, xiaomeifang2006@hotmail.com Feifei Yin, yinfeifeiff@163.com Jiang Du, dujiangemail@163.com
Received Date: 21 March 2023
Accepted Date: 08 August 2023

Abstract

The risk of emerging infectious diseases (EID) is increasing globally. More than 60% of EIDs worldwide are caused by animal-borne pathogens. This study aimed to characterize the virome, analyze the phylogenetic evolution, and determine the diversity of rodent-borne viruses in Hainan Province, China. We collected 682 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 contigs closely related to mammals were assigned to 22 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 arenavirus, coronavirus, astrovirus, pestivirus, parvovirus, and papillomavirus. We identified pestivirus and bocavirus in Leopoldoms edwardsi from Huangjinjiaoling, and bocavirus in Rattus andamanensis from the national nature reserves of 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.
- Rodents
- , Virome
- , Phylogenetic analysis
- , Novel viruses
- , Wildlife

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