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

PLoS One. 2018 Jan 11;13(1):e0190819. doi: 10.1371/journal.pone.0190819. eCollection 2018.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Capsid Proteins / genetics
  • Cysteine Proteases / genetics
  • Enterovirus Infections / epidemiology
  • Enterovirus Infections / virology*
  • Enteroviruses, Porcine / enzymology
  • Enteroviruses, Porcine / genetics*
  • Feces / virology
  • Genetic Variation*
  • Japan
  • Metagenome
  • Phylogeny
  • Prevalence
  • Recombination, Genetic*
  • Sus scrofa

Substances

  • Capsid Proteins
  • Cysteine Proteases

Grant support

This work was supported by The Ministry of Agriculture, Forestry and Fisheries of Japan, Award Number: the Research Project for Improving Food Safety and Animal Health of the Ministry of Agriculture, Forestry and Fisheries of Japan (716057223), Grant Recipient: Tetsuya Mizutani. We received three funding including JSPS KAKENHI 15K07718 to Makoto Nagai, Global Innovation Research of Tokyo University of Agriculture and Technology to Tetsuya Mizutani, and the Research Project for Improving Food Safety and Animal Health of the Ministry of Agriculture, Forestry and Fisheries of Japan.