Genetic diversity and recombination of enterovirus G strains in Japanese pigs: High prevalence of strains carrying a papain-like cysteine protease sequence in the enterovirus G population.

Shinobu Tsuchiaka,Masataka Akagami,Yoshinao Ouchi,Shinji Makino,Hiroshi Aoki,Yuji Taniguchi,Ryo Imai,Tetsuya Mizutani,Masaki Takasu,Hiroo Madarame,Yukie Katayama,Fujiko Sunaga,Yasuhiro Takashima,Shoichi Sakaguchi,Makoto Nagai,Tsuneyuki Masuda,Kazuo Ishii,Tsutomu Omatsu,Yuki Satani,Mika Ito,Yuki Naoi,Mami Oba,Junsuke Shirai

doi:10.1371/journal.pone.0190819

Abstract

To study the genetic diversity of enterovirus G (EV-G) among Japanese pigs, metagenomics sequencing was performed on fecal samples from pigs with or without diarrhea, collected between 2014 and 2016. Fifty-nine EV-G sequences, which were >5,000 nucleotides long, were obtained. By complete VP1 sequence analysis, Japanese EV-G isolates were classified into G1 (17 strains), G2 (four strains), G3 (22 strains), G4 (two strains), G6 (two strains), G9 (six strains), G10 (five strains), and a new genotype (one strain). Remarkably, 16 G1 and one G2 strain identified in diarrheic (23.5%; four strains) or normal (76.5%; 13 strains) fecal samples possessed a papain-like cysteine protease (PL-CP) sequence, which was recently found in the USA and Belgium in the EV-G genome, at the 2C–3A junction site. This paper presents the first report of the high prevalence of viruses carrying PL-CP in the EV-G population. Furthermore, possible inter- and intragenotype recombination events were found among EV-G strains, including G1-PL-CP strains. Our findings may advance the understanding of the molecular epidemiology and genetic evolution of EV-Gs.

Highlights

Porcine enteroviruses (PEVs), members of the family Picornaviridae, are positive-sense, single-stranded nonenveloped RNA viruses, whose genomes consist of a single, large open reading frame encoding a single polyprotein flanked by 50 and 30 untranslated regions (50UTR and 30UTR) and a poly(A) tail at its 30 end [1]
16 enterovirus G (EV-G) genotypes are known to exist in Hungary, South Korea, the USA, China, Vietnam, and Belgium [8,9,10,11,12,13,14,15]
We investigated the genetic diversity of EV-G isolates from fecal samples from pigs in Japan via the metagenomics approach

Summary

Introduction

Porcine enteroviruses (PEVs), members of the family Picornaviridae, are positive-sense, single-stranded nonenveloped RNA viruses, whose genomes consist of a single, large open reading frame encoding a single polyprotein flanked by 50 and 30 untranslated regions (50UTR and 30UTR) and a poly(A) tail at its 30 end [1]. PEV-1 to -7 and PEV-11 to -13 have been reclassified and assigned to the genus Teschovirus and PEV-8, formally belonging to PEV-A, has been renamed porcine sapelovirus 1 and reclassified into the genus Sapelovirus [1, 4,5,6]. PEV-9 and -10, the prototypical EV-Gs isolated in 1973 and 1975 in UK, were renamed as EV-G1 and EV-G2, respectively [1, 7]. 16 EV-G genotypes are known to exist in Hungary, South Korea, the USA, China, Vietnam, and Belgium [8,9,10,11,12,13,14,15]

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Conclusion