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

Cecilia Waruhiu,Vincent Obanda,Ali Zohaib,Xing-Lou Yang,Bernard Agwanda,Sheila Ommeh,Li-Jun Wu,Francis Gakuya,Xing-Yi Ge,Zheng-Li Shi,Ben Hu

doi:10.1007/s12250-016-3930-2

Abstract

This is the first country-wide surveillance of bat-borne viruses in Kenya spanningfrom 2012–2015 covering sites perceived to have medium to high level bat-humaninteraction. The objective of this surveillance study was to apply a non-invasiveapproach using fresh feces to detect viruses circulating within the diverse speciesof 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) androtaviruses. We used family-specific primers, amplicon sequencing and furthercharacterization by phylogenetic analysis. Except for filoviruses, eight virusfamilies were detected with varying distributions and positive rates across the fiveregions (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%). NovelCalVs were detected in Rousettus aegyptiacus andMops condylurus while novelRotavirus-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-batinteraction. Additionally, 229E-like bat CoVs were detected in samples originatingfrom Hipposideros bats roosting in sites withhigh human activity. Our findings confirm the presence of diverse viruses in Kenyanbats while providing extended knowledge on bat virus distribution. The detection ofviruses highly related to human strains and hence of public health concern,underscores the importance of continuous surveillance.

Highlights

Bats (Order Chiroptera) are a group of highly diverse mammalian species that occurs throughout the world and accounts for more than 25% of mammals (Olival, 2016)
Some of the viruses harbored in bats such as; Nipah virus, severe acute respiratory syndrome coronavirus (SARS-CoV), multiple strains of lyssavirus, Marburg virus and Ebola virus have spilled over to humans and livestock causing severe disease in different parts of the world (Chua et al, 2000; Leroy et al, 2005; Wang et al, 2005)
For the first time in Kenya, AstVs and CalVs were detected in bats, while new genotypes of Rotavirus A (RVA) are reported in R. aegyptiacus and T. mauritianus

Summary

Introduction

Bats (Order Chiroptera) are a group of highly diverse mammalian species that occurs throughout the world and accounts for more than 25% of mammals (Olival, 2016). Virus prevalence and diversity in Kenyan Bats have extended their roost sites from forested areas, caves and other isolated sites to habitats with substantial human activity. This can be attributed to anthropogenic activities such as urbanization and deforestation that have resulted in destruction of natural bat habitats (Plowright et al, 2015). Bats have been recognized as an important natural reservoir for zoonotic viruses affecting both humans and livestock (Plowright et al, 2015). Some of the viruses harbored in bats such as; Nipah virus, severe acute respiratory syndrome coronavirus (SARS-CoV), multiple strains of lyssavirus, Marburg virus and Ebola virus have spilled over to humans and livestock causing severe disease in different parts of the world (Chua et al, 2000; Leroy et al, 2005; Wang et al, 2005)

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