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

In January 2015, a case of diarrhea in fattening pigs occurred on a Belgian pig farm. Diarrhea emerged 2 days upon arrival after transport and clinical signs in the herd (1,000 fattening pigs) lasted for 21 days, affecting a total of 20 fattening pigs. The veterinarian suspected an infection with the re-emerging PEDV. This virus belongs to the genus Alphacoronavirus within the family of Coronaviridae. The virus replicates in enterocytes and leads to sloughing of the gut villi, which causes diarrhea. It was widely spread across Europe between the 1970s and 1990s, causing epidemics of diarrhea on pig farms. However, since then it has only sporadically been detected (Pensaert and de Bouck 1978) . In 2010, this virus was detected during severe outbreaks in Asia, and for the first time in the US swine population during spring 2013, causing mortality and severe economic losses (Song et al. 2015) . In 2014, a milder variant of the virus (OH 855) was detected in the US swine herds (Wang et al. 2014 ). These strains were later also detected in German swineherds in 2014, as well as in other European countries (Grasland et al. 2015; Mesquita et al. 2015; Stadler et al. 2015) . However, it is unclear if these genomic changes are correlating with an increased virulence of PEDV (Pensaert and Martelli 2016) . At the beginning of 2015 and following the outbreaks of PEDV in USA, there was an increased awareness in Europe, including Belgium, as this virus could also emerge in the local swine population at any given moment. Therefore, when the outbreak of diarrhea occurred on the above-mentioned farm, a mixed fecal sample (n ¼ 12 pigs) was sent to the Laboratory of Virology at Ghent University. PEDV RNA was detected using an in-house RT-qPCR, but high Cq values (Cq > 30) suggested a rather low viral load, whereas typical clinical infections in gnotobiotic piglets results in shedding of the virus at loads >10 10 copies per milliliter of feces (Jung et al. 2014 ). Still, a full genome characterization was performed and this indicated that the strain was genetically highly similar to the INDEL strains circulating in Germany and USA, as reported elsewhere (Theuns et al. 2015) . Given the low abundance of PEDV in the fecal sample, and the large number of other viruses which can also cause gastro-intestinal disease in pigs, it was questioned in the present study if other viruses might have been present in the pig's fecal virome and if they could have contributed to the emergence of diarrhea on this farm.