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.

Viruses in bats and potential spillover to animals and humans

“…These bats were shown to harbor divergent viruses, including members of the families Astroviridae, Circoviruidae, Parvoviridae, Partitviridae, Coronaviridae, Picobirnavirdae, Adenoviridae, Herpesviridae, Papillomaviridae, Phenuiviridae, and Picornaviridae [98,99]. These recent studies build upon previous work [100][101][102][103] to further expand the diversity of the bat virome. Uniquely, the picobirnaviruses identified utilize an alternative genetic code [98].…”

Molecular characterization of a human G20P[28] rotavirus a strain with multiple genes related to bat rotaviruses

“…However, the genetically close relationships of the VP7, VP4, VP6, NSP3 and NSP5 gene segments of the study strain to bat strain 3081/BRA and/or bat-like human strain Ecu534, suggest that RVA/Human-wt/SUR/2014735512/2013/G20P[28] is of bat origin. A few investigators have reported the detection of human RVAs genes in bat RVA strains (Esona et al, 2010; Sasaki et al, 2016; Waruhiu et al, 2017), but this report represents only the second time bat RVAs gene segments have been found in a human RVA strain (Solberg et al, 2009). …”

“…Several improvements in viral detection and characterization methodologies such as high-throughput next generation sequencing have led to a successful discovery and characterization of several novel viruses in bats, including enteric pathogens such as RVA (Luis et al, 2013; Waruhiu et al, 2017). However, since the first detection and characterization of a human-bat reassortant RVA from a Straw-colored Fruit bat in 2010 (Esona et al, 2010), a few of other bat RVA strains, detected and characterized from different bat species and different geographic locations have been reported (Asano et al, 2016; He et al, 2013; Sasaki et al, 2016; Waruhiu et al, 2017; Xia et al, 2013; Yinda et al, 2016). Among the reported bat RVA strains, only bat RVA strain 3081/BRA from Brazil was closely related in the VP7, NSP3 and NSP5 gene segments with the study strain from Suriname.…”

“…The nucleotide sequences of these bat RVAs are typically distant from those of human and other mammalian RVAs and have been suggested to be bat specific (Esona et al, 2010; He et al, 2013; Xia et al, 2014; Yinda et al, 2016). However, the VP4 and NSP4 gene segments of bat RVA strain RVA/Bat-wt/KEN/KE4852/2007/G25P[6] detected in Kenya (Esona et al, 2010), gene segments VP7, VP4, VP3, NSP2 and NSP3 of bat RVA strain RVA/Bat-wt/ZMB/LUS12–14/2012/G3P[3] reported in Zambia (Sasaki et al, 2016) and VP6 gene segment of bat RVA strains 2980/BatRVA and 322/BatRVA detected in Kenya (Waruhiu et al, 2017) are highly similar to cognate gene sequences of human RVAs circulating in the same community. This suggests that single or multiple gene reassortment events have occurred between human and bat RVAs.…”

Full genome characterization of two novel Alpha-coronavirus species from Italian bats

“…During the last fifteen years, two Beta-CoVs, SARS-CoV and MERS-CoV, have jumped from bats to a mammalian intermediate host to humans (Field, 2009;Omrani et al, 2015). In addition, strains related to human Alpha-CoVs (HuCoV-229E, HuCoV-NL63) have been detected in bats, indicating the importance of the bat as a CoV reservoir (Pfefferle et al, 2009;Corman et al, 2015;Tao et al, 2017;Waruhiu et al, 2017). In this study, we characterized two Alpha-CoVs from Italian bats divergent from human CoVs strains and two new Alpha-CoV species.…”