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

To further investigate the presence of this highly unusual recombinant virus, we designed synthetic peptides from the 5 0 -AGTCTTCTCTCATCTACTGGG-3 0 5016 Enterovirus recombinant virus, which we then used for selected reaction monitoring (SRM). These synthetic peptides were predicted to be generated after trypsin digestion. This frequently used approach in mass-spectrometry, allows to focus on the detection of a preselected group of peptides. The instrument was run on SRM mode on synthetic peptides of the insertion and on the peptide extracted fecal sample. Using SEQUEST, we were able to identify two peptides from the insertion region of the enterovirus-torovirus recombinant (Table 3 and Supplementary Tables). Table 3 shows the retention time and mass-over-charge ratio (m/z) of both the synthetic peptides and the homologues found in the original sample.