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

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.

PLOS ONE

Public Library of Science

13

1

e0190819

10.1371/journal.pone.0190819