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.

Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus

“…Three porcine viruses, including porcine kobuvirus, porcine mamastrovirus and enterovirus G, were identified in sample 17V079. Astro-and enteroviruses have been detected earlier in both diarrheic and non-diarrheic feces of Belgian pigs and in feces from pigs around the globe 9,10,27 . In a recent study from Thailand, the difference in prevalence of astrovirus in diarrheic (8.4%) versus non-diarrheic (4.6%) piglets less than 4-weeks-old was not statistically significant.…”

“…Only the most likely cause(s) of the disease will be diagnostically investigated, often leading to negative, inconclusive or incomplete results. However, metagenomics studies have indicated the existence of viral enteric disease complexes, potentially involving multiple known and novel viruses 3,4,6,7,9,10 . Detection of nucleic acids from pathogens using NGS-based metagenomics approaches is a partial solution to diagnostic testing problems and can provide a complete readout of viruses and other pathogens present in a sample.…”

First detection of novel enterovirus G recombining a torovirus papain‐like protease gene associated with diarrhoea in swine in South Korea

“…Furthermore, a previous study using reverse genetics revealed that the US EV‐G17‐PLCP strain functionally produces the exogenous PLCP gene in virus‐infected cells, demonstrating its own ALFQ↓GPPV and AEFQ↓GPPT sequences as the putative cleavage sites (Shang et al., ). Considering the sequence similarity of the putative cleavage sites including GPPT−ALFQ, GPPA−ALFQ, and GPPE−ALPQ among global strains (Conceição‐Neto et al., ; Knutson et al., ; Tsuchiaka et al., ), therefore, the cleavage of the inserted PLCP gene appears to be guaranteed using each corresponding cleavage sequence. Consistently, the recombinant ToV‐PLCP of the EV‐G KNU‐1811 strain is bordered by two analogous predicted 3C pro cleavage sites, ALFQ↓GPPV and AVFQ↓GPPT, at its N and C termini, respectively, indicating its proteolytic processing by 3C pro into a functional product (Figure a).…”

A novel defective recombinant porcine enterovirus G virus carrying a porcine torovirus papain-like cysteine protease gene and a putative anti-apoptosis gene in place of viral structural protein genes

“…In addition to type 1 recombinant EV-G, second type of recombinant EV-G (we call type 2 recombinant EV-G in this study), which carried the PLCP gene in place of viral structural genes, has been identified in a Chinese pig farm (Wang et al, 2018). The PLCP gene is encoded in the ORF1 of the genome of torovirus, a member of family Coronaviridae, and the order Nidovirales (Conceição-Neto et al, 2017;Knutson et al, 2017;Shang et al, 2017;Tsuchiaka et al, 2017;Wang et al, 2018). The PLCP of nidoviruses serves as a protease to cleave viral gene 1 polyproteins to mature proteins (Mielech et al, 2014).…”

“…1016/j.meegid.2019.103975 Received 18 April 2019; Received in revised form 17 July 2019; Accepted 19 July 2019 prevalence of type 1 recombinant EV-G in the EV-G population (Tsuchiaka et al, 2018). Type 1 recombinant EV-Gs have been discovered from feces of neonatal pigs showing clinical symptoms, such as diarrhea, in the US, Belgium, Germany and South Korea (Bunke et al, 2018;Conceição-Lee and Lee, 2019;Neto et al, 2017;Knutson et al, 2017;Shang et al, 2017), while type 1 recombinant EV-Gs identified in Japan are detected from normal as well as diarrhea pig feces (Tsuchiaka Fig. 1.…”