Discovery of novel DNA viruses in small mammals from Kenya

Griphin Ochieng Ochola; Bei Li; Vincent Obanda; Sheila Ommeh; Harold Ochieng; Xing-Lou Yang; Samson Omondi Onyuok; Zheng-Li Shi; Bernard Agwanda; Ben Hu

doi:10.1016/j.virs.2022.06.001

August 2022

Griphin Ochieng Ochola, Bei Li, Vincent Obanda, Sheila Ommeh, Harold Ochieng, Xing-Lou Yang, Samson Omondi Onyuok, Zheng-Li Shi, Bernard Agwanda and Ben Hu. Discovery of novel DNA viruses in small mammals from Kenya[J]. Virologica Sinica, 2022, 37(4): 491-502. doi: 10.1016/j.virs.2022.06.001

Citation: Griphin Ochieng Ochola, Bei Li, Vincent Obanda, Sheila Ommeh, Harold Ochieng, Xing-Lou Yang, Samson Omondi Onyuok, Zheng-Li Shi, Bernard Agwanda, Ben Hu. Discovery of novel DNA viruses in small mammals from Kenya .VIROLOGICA SINICA, 2022, 37(4) : 491-502. http://dx.doi.org/10.1016/j.virs.2022.06.001

肯尼亚小型哺乳动物中新型DNA病毒的发现

a 中国科学院武汉病毒研究所, 中国科学院高致病性病原生物学与生物安全重点实验室;
b 中国科学院中-非联合研究中心;
c 肯尼亚国家博物馆哺乳动物学部;
d 中国科学院大学;
e 肯尼亚野生动物保护局兽医事务部;
f 乔莫肯雅塔农业技术大学生物技术研究所

通讯作者： Bernard Agwanda, benrisky@gmail.com; 胡犇, huben@wh.iov.cn
收稿日期： 2021-11-18
录用日期： 2022-05-17

摘要

野生动物来源的新发和再发传染病频繁出现，因此针对动物宿主进行主动、先发式的病原监测成为公共卫生领域需要优先开展的工作。啮齿动物和鼩鼱是两类数量丰富的脊椎动物，也是许多重要的人兽共患病毒的自然宿主。许多病原监测项目聚焦于RNA病毒，相比之下，有关啮齿动物和鼩鼱等小型哺乳动物携带DNA病毒的信息要少的多。为了填补这项知识缺口，本研究在肯尼亚的5个郡采集了232只动物的样本，包括226只啮齿动物、5只鼩鼱和一只刺猬，通过PCR进行了7个DNA病毒科的核酸检测，检测到了丰富多样的腺病毒、腺相关病毒、疱疹病毒和多瘤病毒DNA序列。系统发育分析显示本研究所发现的大部分病毒和此前已报道的病毒存在明显差异，在进化树上形成了多个新簇。此外，本研究首次报道了在草鼠属的鼠种中发现的多瘤病毒，并对一株病毒进行了全长基因组测序和鉴定。该毒株命名为条纹草鼠多瘤病毒KY187株。将其和目前已知的与其亲缘关系最近的睡鼠多瘤病毒1、灰松鼠多瘤病毒1两种多瘤病毒相比较，它们大T抗原蛋白和小T抗原蛋白的氨基酸序列相似度均低于60%，因此这一病毒可被推定为β多瘤病毒属的一个新种。本研究有助于我们更好地了解肯尼亚啮齿动物和鼩鼱种群中DNA病毒的遗传多样性，为认识这些DNA病毒在小型哺乳动物储存宿主中的演化提供了新见解，研究结果也说明了在东非地区针对啮齿动物传播病毒持续开展病原发现研究的必要性。
- 肯尼亚
- , DNA病毒
- , 啮齿动物
- , 鼩鼱
- , 多瘤病毒

Discovery of novel DNA viruses in small mammals from Kenya

a CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China;
b Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China;
c Mammalogy Section, National Museums of Kenya, Nairobi, 40658-00100, Kenya;
d University of Chinese Academy of Sciences, Beijing, 100049, China;
e Veterinary Services Department, Kenya Wildlife Service, Nairobi, 40241-00100, Kenya;
f Institute of Biotechnology Research, Jomo Kenyatta University of Science and Technology, Nairobi, 62000-00200, Kenya

Corresponding author: Bernard Agwanda, benrisky@gmail.com Ben Hu, huben@wh.iov.cn
Received Date: 18 November 2021
Accepted Date: 17 May 2022

Abstract

Emergence and re-emergence of infectious diseases of wildlife origin have led pre-emptive pathogen surveillances in animals to be a public health priority. Rodents and shrews are among the most numerically abundant vertebrate taxa and are known as natural hosts of important zoonotic viruses. Many surveillance programs focused more on RNA viruses. In comparison, much less is known about DNA viruses harbored by these small mammals. To fill this knowledge gap, tissue specimens of 232 animals including 226 rodents, five shrews and one hedgehog were collected from 5 counties in Kenya and tested for the presence of DNA viruses belonging to 7 viral families by PCR. Diverse DNA sequences of adenoviruses, adeno-associated viruses, herpesviruses and polyomaviruses were detected. Phylogenetic analyses revealed that most of these viruses showed distinction from previously described viruses and formed new clusters. Furthermore, this is the first report of the discovery and full-length genome characterization of a polyomavirus in Lemniscomys species. This novel polyomavirus, named LsPyV KY187, has less than 60% amino acid sequence identity to the most related Glis glis polyomavirus 1 and Sciurus carolinensis polyomavirus 1 in both large and small T-antigen proteins and thus can be putatively allocated to a novel species within Betapolyomavirus. Our findings help us better understand the genetic diversity of DNA viruses in rodent and shrew populations in Kenya and provide new insights into the evolution of those DNA viruses in their small mammal reservoirs. It demonstrates the necessity of ongoing pathogen discovery studies targeting rodent-borne viruses in East Africa.
- Kenya
- , DNA viruses
- , Rodents
- , Shrews
- , Polyomavirus

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