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

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

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Molecular detection of viruses in Kenyan bats and discovery of novel astroviruses, caliciviruses and rotaviruses
Series Title:
Virologica Sinica
Waruhiu, Cecilia
Ommeh, Sheila
Obanda, Vincent
Agwanda, Bernard
Gakuya, Francis
Ge, Xing-Yi
Yang, Xing-Lou
Wu, Li-Jun
Zohaib, Ali
Hu, Ben
Shi, Zheng-Li
Publication Date:


Subjects / Keywords:
Astroviruses (Astvs) ( local )
Calicivirus (Calvs) ( local )
Rotavirus A ( local )
229-E-Like Bat Coronavirus ( local )
serial ( sobekcm )


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.
Original Version:
Virologica Sinica, Vol. 32 (2017-04-06).

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Source Institution:
University of South Florida Library
Holding Location:
University of South Florida
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This item is licensed with the Creative Commons Attribution License. This license lets others distribute, remix, tweak, and build upon this work, even commercially, as long as they credit the author for the original creation.
Resource Identifier:
K26-05209 ( USFLDC: LOCAL DOI )
k26.5209 ( USFLDC: LOCAL Handle )

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