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

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

Discovery of novel DNA viruses in small mammals from Kenya

Griphin Ochieng Ochola ^a,b,c,d ,
Bei Li ^a ,
Vincent Obanda ^e ,
Sheila Ommeh ^f ,
Harold Ochieng ^c ,
Xing-Lou Yang ^a,b ,
Samson Omondi Onyuok ^a,c ,
Zheng-Li Shi ^a,b ,
Bernard Agwanda ^{c
,,} ,
Ben Hu ^{a,b
,,}

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
Available online: 06 June 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

Electronic Supplementary Material

10.1016j.virs.2022.06.001-ESM.docx
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