Identification of an enterovirus recombinant with a torovirus-like gene insertion during a diarrhea outbreak in fattening pigs

Abstract

Diarrhea outbreaks in pig farms have raised major concerns in Europe and USA, as they can lead to dramatic pig losses. During a suspected outbreak in Belgium of porcine epidemic diarrhea virus (PEDV), we performed viral metagenomics to assess other potential viral pathogens. Although PEDV was detected, its low abundance indicated that other viruses were involved in the outbreak. Interestingly, a porcine bocavirus and several enteroviruses were most abundant in the sample. We also observed the presence of a porcine enterovirus genome with a gene insertion, resembling a C28 peptidase gene found in toroviruses, which was confirmed using re-sequencing, bioinformatics, and proteomics approaches. Moreover, the predicted cleavage sites for the insertion suggest that this gene was being expressed as a single protein, rather than a fused protein. Recombination in enteroviruses has been reported as a major mechanism to generate genetic diversity, but gene insertions across viral families are rather uncommon. Although such inter-family recombinations are rare, our finding suggests that these events may significantly contribute to viral evolution.

Keywords: bocavirus; enterovirus; recombinant virus; viral metagenomics; virome; virus evolution.

Figure 1.

(A) Maximum likelihood phylogenetic tree with 500 bootstraps of the C28 gene insertion. (B) Genome organization of the enterovirus–torovirus recombinant BEL/15V010 and cleavage site prediction. (C and D) Maximum likelihood phylogenetic trees with 500 bootstraps of enteroviruses before and after the gene insertion. Only bootstrap values even or > 70 are shown. The two complete enteroviruses found in this study are shown in bold and the strain with the torovirus insertion is depicted with a square. (E) Structure prediction of the insertion protein, FMDV L^pro, and porcine torovirus C28.

Figure 2.

Maximum likelihood phylogenetic tree of the NS1 protein of bocaviruses. Bootstrap values even or > 70 are shown. The sequence identified in this study is shown in bold with a black square.

Figure 3.

Maximum likelihood phylogenetic tree of the RdRp protein of astroviruses (A), the REP protein of gemycircularviruses (B), REP protein of circularviruses (C), the RdRp protein (D), and capsid (E) sequences of picobirnaviruses. Bootstrap values even or > 70 are shown. Sequences identified in this study are shown in bold with a black square.