Virologica Sinica

, Volume 32, Issue 2, pp 101–114 | Cite as

Molecular detection of viruses in Kenyan bats and discovery of novel astroviruses, caliciviruses and rotaviruses

  • Cecilia Waruhiu
  • Sheila OmmehEmail author
  • Vincent Obanda
  • Bernard Agwanda
  • Francis Gakuya
  • Xing-Yi Ge
  • Xing-Lou Yang
  • Li-Jun Wu
  • Ali Zohaib
  • Ben Hu
  • Zheng-Li ShiEmail author
Research Article


This is the first country-wide surveillance of bat-borne viruses in Kenya spanning from 2012–2015 covering sites perceived to have medium to high level bat-human interaction. The objective of this surveillance study was to apply a non-invasive approach using fresh feces to detect viruses circulating within the diverse species of Kenyan bats. We screened for both DNA and RNA viruses; specifically, astroviruses (AstVs), adenoviruses (ADVs), caliciviruses (CalVs), coronaviruses (CoVs), flaviviruses, filoviruses, paramyxoviruses (PMVs), polyomaviruses (PYVs) and rotaviruses. We used family-specific primers, amplicon sequencing and further characterization by phylogenetic analysis. Except for filoviruses, eight virus families were detected with varying distributions and positive rates across the five regions (former provinces) studied. AstVs (12.83%), CoVs (3.97%), PMV (2.4%), ADV (2.26%), PYV (1.65%), CalVs (0.29%), rotavirus (0.19%) and flavivirus (0.19%). Novel CalVs were detected in Rousettus aegyptiacus and Mops condylurus while novel Rotavirus-A-related viruses were detected in Taphozous bats and R. aegyptiacus. The two Rotavirus A (RVA) strains detected were highly related to human strains with VP6 genotypes I2 and I16. Genotype I16 has previously been assigned to human RVA-strain B10 from Kenya only, which raises public health concern, particularly considering increased human-bat interaction. Additionally, 229E-like bat CoVs were detected in samples originating from Hipposideros bats roosting in sites with high human activity. Our findings confirm the presence of diverse viruses in Kenyan bats while providing extended knowledge on bat virus distribution. The detection of viruses highly related to human strains and hence of public health concern, underscores the importance of continuous surveillance.


astroviruses (AstVs) calicivirus (CalVs) Rotavirus A 229-E-like bat coronavirus 



We are grateful for the Government of Kenya who permitted this study, specifically the Directors of Kenya Wildlife Service and National Museums of Kenya. We also appreciate the field and laboratory teams in Kenya and China who assisted in many different ways towards the success of this work. This work was funded by Sino-Africa Joint Research Center (SAJC201313 and SAJC 201605).

Author Contributions

Z-LS, SO and CW designed the study. Z-LS, SO, BA and VO coordinated the study. Z-LS, SO, VO, BA, FG, XYG, XLY, LJW and CW participated and supported in field sampling. CW and AZ carried out molecular studies under the supervision of HB. CW analyzed the data. CW and Z-LS drafted the manuscript. All authors read and approved the final manuscript

Compliance with Ethics and Guidelines

The authors declare they have no conflicts of interest. The study was approved by the Kenya Wildlife Service, research permit, KWS/BRM/5001. All institutional and National guidelines for care and handling use of animals were followed.

Supplementary material

12250_2016_3930_MOESM1_ESM.pdf (4.9 mb)
Molecular detection of viruses in Kenyan bats and discovery of novel astroviruses, caliciviruses and rotaviruses


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© The Author(s) 2017

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Authors and Affiliations

  • Cecilia Waruhiu
    • 1
    • 2
  • Sheila Ommeh
    • 3
    Email author
  • Vincent Obanda
    • 4
  • Bernard Agwanda
    • 5
  • Francis Gakuya
    • 4
  • Xing-Yi Ge
    • 1
    • 2
  • Xing-Lou Yang
    • 1
    • 2
  • Li-Jun Wu
    • 1
  • Ali Zohaib
    • 1
  • Ben Hu
    • 1
    • 2
  • Zheng-Li Shi
    • 1
    • 2
    Email author
  1. 1.Key Lab of Special Pathogens, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
  2. 2.Sino-Africa Joint Research CenterChinese Academy of SciencesWuhanChina
  3. 3.Institute of Biotechnology ResearchJomo Kenyatta University of Science and TechnologyNairobiKenya
  4. 4.Veterinary Services DepartmentKenya Wildlife ServiceNairobiKenya
  5. 5.Mammalogy SectionNational Museum of KenyaNairobiKenya

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