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

Virologica Sinica 2017年第2期32卷 101-114页

作者： Cecilia Waruhiu Sheila Ommeh Vincent Obanda Bernard Agwanda Francis Gakuya Xing-Yi Ge Xing-Lou Yang Li-Jun Wu Ali Zohaib Ben Hu Zheng-Li Shi Key Lab of Special Pathogens Wuhan Institute of Virology Chinese Academy of Sciences Wuhan 430071 China Sino-Africa Joint Research Center Chinese Academy of Sciences Wuhan 430071 China Institute of Biotechnology Research Jomo Kenyatta University of Science and Technology Nairobi 00200 Kenya Veterinary Services Department Kenya Wildlife Service Nairobi 00100 Kenya Mammalogy Section National Museum of Kenya Nairobi 00100 Kenya Mammalogy Section National Museum of Kenya Nairobi 00100 Kenya

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 phyloge- netic 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 12 and 116. Genotype 116 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.

关键词： astroviruses (AstVs) calicivirus (CalVs) Rotavirus A 229-e-like bat coronavirus

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