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

Diarrhea is an important health problem affecting piglets, as well as an important cause of production losses in fattening pigs. Typical causes of clinical and subclinical enteric problems in the latter age group are bacteria such as Brachyspira spp., Lawsonia intracellularis and/or Salmonella spp., whereas viral causes at this age are generally less common (Stå hl et al. 2011; Collins and Barchia 2014; De Ridder et al. 2014) . In a minority of cases, fattening pigs and sows can be affected by porcine epidemic diarrhea virus (PEDV), a re-emerging enteric coronavirus (Stevenson et al. 2013; Pensaert and Martelli 2016) . Classical diagnostic methods such as specific antigen-, gene-, or antibodydetection assays are currently in use in veterinary practice in order to reach an etiological diagnosis and to put into practice targeted prophylactic and therapeutic measures. However, in recent years, a considerable progress has been made in the field of viral metagenomics, which makes it more affordable to apply next-generation sequencing (NGS) technologies to analyze the entire fecal viral content (the fecal virome) of a sample. Using this approach, the most frequently detected mammalian viruses in viral metagenomics studies were kobuviruses, rotaviruses, pig stool-associated ssDNA viruses, astroviruses, sapoviruses, and enteroviruses (Shan et al. 2011; Sachsenrö der et al. 2012; Zhang et al. 2013) .