Cameroonian fruit bats harbor divergent viruses, including rotavirus H, bastroviruses, and picobirnaviruses using an alternative genetic code

Yinda, Claude Kwe; Ghogomu, Stephen Mbigha; Conceição-Neto, Nádia; Beller, Leen; Deboutte, Ward; Vanhulle, Emiel; Maes, Piet; Van Ranst, Marc; Matthijnssens, Jelle

CoVs are enveloped single-stranded, positive sense RNA viruses that belong to the Order Nidovirales, Family Coronaviridae and Subfamily Coronavirinae. This subfamily is made up of four genera: Alphacoronavirus, Betacoronavirus, Deltacoronavirus, and Gammacoronavirus (Adams and Carstens 2012). Gamma-CoV and Delta-CoV mainly contain bird viruses as well as a few mammalian viruses, whereas Alpha-and Beta-CoV infect mainly mammalian species (Drexler et al. 2014) . Since bats were implicated as reservoir hosts for SARS-related CoVs, subsequent studies in bats have identified a great diversity of Alpha-CoV and Beta-CoV (Lau et al. 2005; Li et al. 2005) . Furthermore, it has also been established that bats are potential reservoir host for the human CoV 229E and MERS-CoV, although it is now more plausible that the intermediate host of human MERS-CoV is dromedary camel (Annan et al. 2013; Chan et al. 2015; Corman et al. 2015; Sabir et al. 2015) . The genus Beta-CoV is further classified into lineages A-D, and has been identified in a wide variety of hosts including humans, numerous domestic and peridomestic animals, and multiple bat species (41, 42). Infection of E. helvum with lineage D Beta-CoV has been reported at high frequency in Kenya and recently in Nigeria (Tong et al. 2009; Tao et al. 2012; Leopardi et al. 2016 ). Here we identified five near complete CoV genomes from E. helvum fruit bats in Cameroon. All the strains identified here belong to the lineage Beta-D. Phylogenetic analysis of at least 700 nt of the representative sequences of the subfamily Coronovirinae showed that in the Beta-D lineage, all strains (including four novel strains from this study) are generally clustered by host species (Supplementary Fig. S3 ). One exception was the Cameroonian strain CMR66, which clustered with Rousettus spp, D Beta-CoV strains, indicating that despite the existence of bat host-CoV co-evolution, there have been occasional interspecies events either within the Chiropteran order or to other orders (Tao et al. 2017 ).