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

At the end of January 2015, PEDV was identified in a pooled diarrheic fecal sample of fattening pigs from a Belgian pig farm. Using an in house RT-qPCR assay, a low viral load of PEDV was detected, indicating that other viruses may have played a more important role in the pathogenesis of diarrhea in these pigs. Therefore, it was aimed to unravel the complete fecal virome of this pooled sample using an NGS approach. After trimming, a total of 57,164,223 NGS reads were assembled de novo into contigs (Bankevich et al. 2012; Bolger et al. 2014) . A total of 38,118,443 reads were assigned with DIAMOND (Buchfink et al. 2015) , of which 5,937,747 were assigned as viruses (16%). From these reads, 2,454,031 could be assigned to the order of the Caudovirales (41%) and 537,279 (9%) to the family Microviridae, which both contain exclusively bacteriophages. Only 2,780 NGS reads (0.1%) were obtained for PEDV, which corroborates the low viral load (Cq > 30) found by RT-qPCR. A total of 2,246,215 reads could be attributed to (near) complete mammalian porcine virus genomes (Table 2) . Of these, reads matching the porcine bocavirus (2,110,362 reads, 34%) were far most dominant, followed by 63,317 reads matching porcine enteroviruses. All viruses described hereafter were deposited in GenBank and accession numbers are provided in Table 2 .