title: Molecular detection of viruses in Kenyan bats and discovery of novel astroviruses, caliciviruses and rotaviruses.
abstract: 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.
authors.affiliation: 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.
authors.forename: Cecilia
authors.initials: C
authors.lastname: Waruhiu
authors.affiliation: Institute of Biotechnology Research, Jomo Kenyatta University of Science and Technology, Nairobi, 00200, Kenya. sommeh@jkuat.ac.ke.
authors.forename: Sheila
authors.initials: S
authors.lastname: Ommeh
authors.affiliation: Veterinary Services Department, Kenya Wildlife Service, Nairobi, 00100, Kenya.
authors.forename: Vincent
authors.initials: V
authors.lastname: Obanda
authors.affiliation: Mammalogy Section, National Museum of Kenya, Nairobi, 00100, Kenya.
authors.forename: Bernard
authors.initials: B
authors.lastname: Agwanda
authors.affiliation: Veterinary Services Department, Kenya Wildlife Service, Nairobi, 00100, Kenya.
authors.forename: Francis
authors.initials: F
authors.lastname: Gakuya
authors.affiliation: 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.
authors.forename: Xing-Yi
authors.initials: XY
authors.lastname: Ge
authors.affiliation: 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.
authors.forename: Xing-Lou
authors.initials: XL
authors.lastname: Yang
authors.affiliation: Key Lab of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
authors.forename: Li-Jun
authors.initials: LJ
authors.lastname: Wu
authors.affiliation: Key Lab of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
authors.forename: Ali
authors.initials: A
authors.lastname: Zohaib
authors.affiliation: 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.
authors.forename: Ben
authors.initials: B
authors.lastname: Hu
authors.affiliation: Key Lab of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China. zlshi@wh.iov.cn.|Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430071, China. zlshi@wh.iov.cn.
authors.forename: Zheng-Li
authors.initials: ZL
authors.lastname: Shi
mesh_terms: D000818:Animals; D002685:Chiroptera / Q000821:virology*; D004266:DNA Virus Infections / Q000662:veterinary* / Q000821:virology; D004267:DNA Viruses / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D005243:Feces / Q000821:virology*; D007630:Kenya; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012327:RNA Virus Infections / Q000662:veterinary* / Q000821:virology; D012328:RNA Viruses / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA
keywords: 229-E-like bat coronavirus; Rotavirus A; astroviruses (AstVs); calicivirus (CalVs)