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

Abstract

Enterovirus species G (EV‐G) comprises a highly diversity of 20 genotypes that is prevalent in pig populations, with or without diarrhoea. In the present study, a novel EV‐G strain (KOR/KNU‐1811/2018) that resulted from cross‐order recombination was discovered in diagnostic faecal samples from neonatal pigs with diarrhoea that were negative for swine enteric coronaviruses and rotavirus. The recombinant EV‐G genome possessed an exogenous 594‐nucleotide (198‐amino acid) sequence, flanked by two viral 3Cpro cleavage sites at the 5′ and 3′ ends in its 2C/3A junction region. This insertion encoded a predicted protease similar to the porcine torovirus papain‐like cysteine protease (PLCP), which was recently found in the EV‐G1, ‐G2, and ‐G17 genomes. The complete KNU‐1811 genome shared 73.7% nucleotide identity with a prototype EV‐G1 strain, but had 83.9%–86.7% sequence homology with the global EV‐G1‐PLCP strains. Genetic and phylogenetic analyses demonstrated that the Korean recombinant EV‐G's own VP1 and inserted foreign PLCP genes are most closely related independently to contemporary chimeric G1‐PLCP and G17‐PLCP strains respectively. These results implied that the torovirus‐derived PLCP gene might have undergone continuous nucleotide mutations in the respective EV‐G genome following its independent acquisition through naturally occurring recombination. Our results advance the understanding of the genetic evolution of EV‐G driven by infrequent viral recombination events, by which EV‐G populations laterally gain an exotic gene encoding a virulence factor from heterogeneous virus families, thereby causing clinical disease in swine.

Genetic diversity of enterovirus G detected in faecal samples of wild boars in Japan: identification of novel genotypes carrying a papain-like cysteine protease sequence

“…Interestingly, 2019-To-4 contained an extra 657 nt sequence within the 2C–3A junction region. This sequence showed homology to the PL-CP sequence variant that was recently found in EV-G1, G2 and G17 strains isolated in the USA, Belgium, Japan, China and Korea [15–21]. Standard similarity plot analysis in SimPlot software v.3.5.1 with the 2019-To-4 sequence as a separate query revealed that 2019-To-4 had a higher sequence similarity to EV-Gs carrying a PL-CP sequence (PL-CP EV-Gs) than to EV-G strains without a PL-CP in the non-structural protein regions ().…”

“…The role of EV-Gs as diarrhoea-causing enteric pathogens is still unclear [14]. However, recently, recombinant EV-Gs carrying a papain-like cysteine protease (PL-CP) sequence of torovirus, a member of the order Nidovirales , in the 2C/3A junction site of their genome were identified in the faecal samples of pigs with diarrhoea in the USA, Belgium, China, South Korea, Germany and Japan [8, 15–21]. The PL-CP sequence encodes a deubiquitinase/delSGylase that potentially improves the ability of a virus to evade host immunity, resulting in diarrhoea in neonatal pigs [16].…”

Development of a TaqMan-probe-based multiplex real-time PCR for the simultaneous detection of emerging and reemerging swine coronaviruses

“…PToV is regarded as a swine diarrhea virus that has not caused huge economic losses [ 25 ]. However, given the high recombination rate and evolutionary characteristics of coronavirus and torovirus, we cannot underestimate their potential threat [ 28 – 30 ]. It is very likely that a virulent strain could emerge and cause unpredictable damage to the pig industry [ 13 ].…”

“…However, it remains to be a potential pathogen in pigs [25][26][27]. It should be noted that frequent recombination events involving PToV have been discovered, some of which, especially those on the Hemagglutinin-esterases (HE) or Spike (S) genes, which encode proteins relating to attachment and invasion, could lead to changes in pathogenicity or host-specificity [28][29][30][31][32].…”

Recent Progress in Torovirus Molecular Biology

“…Their HE, which is related to haemagglutinin-esterase-fusion (HEF) protein of influenza C, and PDE are thought to have been independently obtained from these ancestors by heterologous recombination events ( Figure 2 ) [ 92 ]. Remarkably, heterologous recombination between ToV and picornavirus has been discovered recently in many countries; a ToV-like PL pro gene is inserted into the porcine enterovirus G (EV-G) genome at the 2C/3A junction [ 93 , 94 , 95 , 96 , 97 ] or completely replaces a viral structural gene up to the VP1/2A junction [ 98 , 99 ] ( Figure 3 c), suggesting that ToV-like PL pro benefits the growth of EV-G.…”