Novel recombinant porcine enterovirus G viruses lacking structural proteins are maintained in pig farms in Japan

Abstract

Type 1 recombinant enterovirus G (EV-G), which carries the papain-like cysteine protease (PLCP) gene of torovirus between its 2C/3A regions, and type 2 recombinant EV-G, which carries the torovirus PLCP gene with its flanking regions having non-EV-G sequences in place of the viral structural genes, have been detected in pig farms in several countries. In a previous study, we collected 222 fecal samples from 77 pig farms from 2104 to 2016 and detected one type 2 recombinant EV-G genome by metagenomics sequencing. In this study, we reanalyzed the metagenomic data and detected 11 type 2 recombinant EV-G genomes. In addition, we discovered new type 2 recombinant EV-G genomes of the two strains from two pig farms samples in 2018 and 2019. Thus, we identified the genomes of 13 novel type 2 recombinant EV-Gs isolated from several pig farms in Japan. Type 2 recombinant EV-G has previously been detected only in neonatal piglets. The present findings suggest that type 2 recombinant EV-G replicates in weaning piglets and sows. The detection of type 1 recombinant EV-Gs and type 2 recombinant EV-Gs at 3-year and 2-year intervals, respectively, from the same pig farm suggests that the viruses were persistently infecting or circulating in these farms.

First Detection of Recombinant Enterovirus G Carrying a Torovirus Papain-like cysteine protease Gene from India

“…The type 1 recombinant have insertion sequence at 2C-3A junction and detected from fecal samples of porcine diarrhea cases in USA, Belgium, Germany, South Korea (Bunke et al, 2018; Knutson et al, 2017; Shang et al, 2017; Conceição-Neto et al, 2017; Lee & Lee, 2019), while from asymptomatic and diarrheic pigs in Japan (Tsuchiaka et al, 2018). The recombinant type 2 viruses containing torovirus PLCP gene flanked by long unique genes 1 and unique region gene 2 in the place of viral structural genes has been detected in Chinese and Japanese pigs (Wang et al, 2018; Imai et al, 2023). Another novel type 2 recombinant replacing viral structural protein genes by PLCP gene with upstream (without homology with GenBank deposited protein) and downstream (homology with a baculoviral inhibitor of apoptosis repeat superfamily) sequences was detected in Japanese pig faeces (Imai et al, 2019).…”