Identification of an enterovirus recombinant with a torovirus-like gene insertion during a diarrhea outbreak in fattening pigs

Conceição-Neto, Nádia; Theuns, Sebastiaan; Cui, Tingting; Zeller, Mark; Yinda, Claude Kwe; Christiaens, Isaura; Heylen, Elisabeth; Van Ranst, Marc; Carpentier, Sebastien; Nauwynck, Hans J.; Matthijnssens, Jelle

Furthermore, we identified 4 picobirnavirus capsid segments (Fig. 3E ) and 3 RdRp segments (Fig. 3D) . Picobirnaviruses are bisegmented double-stranded RNA viruses, belonging to the Picobirnaviridae family. Segment 1 encodes for a capsid protein and ORF1 with unknown function, while segment 2 encodes for the RdRp gene (Ganesh et al. 2012) . Up to date, only seven complete sequences for porcine picobirnaviruses are available in (Fig. 3B) . Figure 3B shows the genome organization of the novel gemycircularvirus and the phylogenetic analysis of known gemycircularviruses based on the amino acid level of the Rep gene. The porcine gemycircularvirus BEL15V015 presented the typical nonanucleotide stem loop motif (TATAAATAG) and rolling circle replication motifs I (LFTYS), II (HLHVFAD), III (YATKD), GRS (RKFDVEGFHPNIVPSL) and helicase motifs Walker-A (GRSRTGKT) and Walker-B (VFDDI). The novel porcine gemycircularvirus replicase shares its highest similarity on the amino-acid level (76%) with Mongoose fecesassociated gemycircularvirus b (Conceição-Neto et al. 2015) (Fig. 3B) . The divergent ssDNA circular virus (Fig. 3C ) encodes for two ORFs, bidirectionally transcribed: porcine stool associated circular virus BEL/15V010. The complete genome of the virus identified showed its highest similarity with porcine stool associated circular virus 5 isolate CP3 (82.9% nt). Interestingly, the capsid gene of the virus shows 91.3% nt similarity with isolate CP3 but only 65.2% similarity with the replicase. However, these two viruses did not cluster closely with other circular single-stranded DNA viruses and seem to belong to a new isolated clade (Fig. 3C) (Cheung et al. 2014) . Even though only two viruses from this clade were described so far, both were isolated from diarrheic porcine feces.