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

ight explain why only a few of the predicted peptides could be identified. In recent years, the field of proteomics has evolved greatly, in fact, SRM has proven to be a powerful technique to detect and quantify proteins (Picotti and Aebersold 2012) . This is especially suitable for detecting low abundant peptides, since the mass spectrometer focuses on detecting a preselected group of peptides. Taking the metagenomics data, the Sanger sequence confirmation and the proteomics results all together we can conclude that this recombinant virus is present in the sample and that the inserted protein is being expressed. Interestingly, two recent studies described porcine enteroviruses with a similar insertion (Fig. 1A) (Knutson et al. 2017; Shang et al. 2017 ). One of these viruses was isolated and a knockout mutant virus without the insertion yielded impaired growth and higher expression levels of innate immune genes in infected cells (Shang et al. 2017 ). Our analyses suggests that these viruses have a common ancestor (Knutson et al. 2017) even though a significant diversity was noted among them (>90% aa identity) (Fig. 1A) . Moreover, the fact that our strain before the insertion clusters with the virus isolated in Texas and after the insertion with the virus isolated from both Texas and North Carolina, can hint that an additional recombination occurred after the insertion event. Even though our recombinant strain is the first reported in Europe, it is very likely that such viruses might be more widely spread in the pig population, as the in vitro experiments of Shang et al. (2017) indicate that the virus might induce higher pathogenesis.