PLoS ONE (Jan 2017)

Distinct genetic clades of enterovirus D68 detected in 2010, 2013, and 2015 in Osaka City, Japan.

  • Atsushi Kaida,
  • Nobuhiro Iritani,
  • Seiji P Yamamoto,
  • Daiki Kanbayashi,
  • Yuki Hirai,
  • Masao Togawa,
  • Kiyoko Amo,
  • Urara Kohdera,
  • Toshinori Nishigaki,
  • Masashi Shiomi,
  • Sadasaburo Asai,
  • Tsutomu Kageyama,
  • Hideyuki Kubo

DOI
https://doi.org/10.1371/journal.pone.0184335
Journal volume & issue
Vol. 12, no. 9
p. e0184335

Abstract

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The first upsurge of enterovirus D68 (EV-D68), a causative agent of acute respiratory infections (ARIs), in Japan was reported in Osaka City in 2010. In this study, which began in 2010, we surveyed EV-D68 in children with ARIs and analyzed sequences of EV-D68 strains detected. Real-time PCR of 19 respiratory viruses or subtypes of viruses, including enterovirus, was performed on 2,215 specimens from ARI patients (<10 years of age) collected between November 2010 and December 2015 in Osaka City, Japan. EV-D68 was identified in 18 enterovirus-positive specimens (n = 4 in 2013, n = 1 in 2014, and n = 13 in 2015) by analysis of viral protein 1 (VP1) or VP4 sequences, followed by a BLAST search for similar sequences. All EV-D68 strains were detected between June and October (summer to autumn), except for one strain detected in 2014. A phylogenetic analysis of available VP1 sequences revealed that the Osaka strains detected in 2010, 2013, and 2015 belonged to distinct clusters (Clades C, A, and B [Subclade B3], respectively). Comparison of the 5' untranslated regions of these viruses showed that Osaka strains in Clades A, B (Subclade B3), and C commonly had deletions at nucleotide positions 681-703 corresponding to the prototype Fermon strain. Clades B and C had deletions from nucleotide positions 713-724. Since the EV-D68 epidemic in 2010, EV-D68 re-emerged in Osaka City, Japan, in 2013 and 2015. Results of this study indicate that distinct clades of EV-D68 contributed to re-emergences of this virus in 2010, 2013, and 2015 in this limited region.