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

Apart from the recombinant enterovirus found in the sample, another 12,246 viral reads could be attributed to other enteroviruses. From these, 4,475 reads could be used to assemble a complete porcine enterovirus genome (Porcine enterovirus a 15V010/BEL/2015). The complete viral polyprotein showed its highest similarity on the amino-acid level (94.8%) with the porcine enterovirus 9 isolate Ch-ah-f1 (Zhang et al. 2012 ), which was found in 8.3% of screened pigs in China from 2007 to 2009. Using recombination detection approaches (program Rdp v4) (Martin et al. 2015) , no recombination event was detected for this strain, when comparing to all complete sequences of porcine enteroviruses (data not shown). However, the previously described Belgian strain 12R021 (Theuns et al. 2016 ) seems to have gone through a recombination event, which could explain the distinct clustering in Fig. 1C .