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

A total of eighty-seven fecal samples from two species of bat (E. helvum and E. gambianus) were collected from three localities of the South West Region of Cameroon: Limbe, Lysoka, and Muyuka ( Fig. 1) (Yinda et al. 2016b ). These samples were divided over twenty-five pools of one to five samples each, enriched for viral particles and then sequenced. Illumina sequencing yielded a total of 218 million reads and approximately half was trimmed out in the quality control and deduplication process. Out of the remaining 108 million reads, 14% could be assigned as viral while 86% was non-viral (bacterial, host, or dark matter). Most of the viral reads were assigned as phages (89%) and about 11% were eukaryotic viruses (as summarized in Table 1 ). Only a single pool was made from the samples from E. gambianus fruit bat, which generated mainly phage viral reads after sequencing. Therefore, all eukaryotic genomes described here were from E. helvum. Many of the eukaryotic viral reads belong to vertebrate infecting viral families/orders possessing known and potentially causative agents for gastroenteritis in humans. In particular, we identified members of the order Picornavirales and the families Caliciviridae, Reoviridae, Astroviridae, Picobirnaviridae, Circorviridae, and Parvoviridae. In addition, viruses with a high zoonotic potential belonging to the family Coronaviridae (Betacoronavirus), as well as viruses with a low potential of crossing the species barrier (Papillomaviridae) were detected (Fig. 2) . Strikingly, most of the rotavirus (RV) (family Reoviridae) positive samples were detected in adult pools (92%, Fig. 2B ). This is unlike in other animal (including humans) wherein RV mostly infect their young (Parashar et al. 2006) . Moreover, we observed geographical differences in the percentage of pools in which eukaryotic viral families were present (Fig. 2D ). These differences in the sampling sites (i.e. Limbe, Lysoka and Moyuka) maybe due to differences in the acute infections going on at the time of sampling or due to differences in the age of captured bats (all juvenile bats were from Limbe). A detailed analyses of the viruses belonging to the order Picornavirales and the families Papillomaviridae, Reoviridae (RVA) and Caliciviridae (Sapovirus) have been reported elsewhere (Yinda et al. 2016a (Yinda et al. , b, 2017a Here, we analyzed the remaining viral sequences belonging to double-stranded RNA (families Reoviridae, Picobirnaviridae, and Partitiviridae), single-stranded RNA (families Astroviridae and Coronaviridae) and single-stranded DNA (families Parvoviridae and Circoviridae) viral groups. All the sizes of the contig (genomes) described in this study, together with their sequence coverage and closest GenBank hit can be found on Supplementary Table S1. 3. Double-stranded RNA viral sequences 3.1 Identification of the first near complete bat rotavirus H genome