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Front. Microbiol. | doi: 10.3389/fmicb.2019.00038

Study of Complete Genome Sequences of Rotavirus A Epidemics and Evolution in Japan in 2012–2014

  • 1Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Kitasato University, Japan
  • 2National Institute of Infectious Diseases (NIID), Japan
  • 3Graduate School of Natural Sciences Nagoya City University, Japan
  • 4Graduate School of Biomedical Sciences, Nagasaki University, Japan

A comprehensive molecular epidemiological study using next generation sequencing technology was conducted on 333 rotavirus-positive specimens collected from six sentinel hospitals across Japan over three consecutive seasons (2012–2014). Most of rotaviruses were grouped into five genotype constellations: Wa-like G1P[8], DS-1-like G1P[8], G2P[4], G3P[8] and G9P[8]. Phylogenetic analysis showed that the distribution of strains varied by geographical locations and epidemic seasons. The VP7 genes of different G types were estimated to evolve at 7.26×10^-4 – 1.04×10^-3 nucleotide substitutions per site per year. The Bayesian time-scaled tree of VP7 showed that the time to the most recent common ancestor of epidemic strains within a region was 1–3 years, whereas that of the epidemic strains across the country was 2–6 years. This study provided, for the first time, the timeframe during which an epidemic strain spread locally and within the country and baseline information needed to predict how rapidly rotaviruses spread.

Keywords: Rotavirus, Japan, full-genome, next-generation sequencing (NGS), Reassortment, Bayesian Analysis

Received: 12 Oct 2018; Accepted: 10 Jan 2019.

Edited by:

Souvik Ghosh, Ross University School of Veterinary Medicine, Saint Kitts and Nevis

Reviewed by:

Helen O'Shea, Cork Institute of Technology, Ireland
Nobumichi Kobayashi, Sapporo Medical University, Japan  

Copyright: © 2019 Katayama, Fujii, DOAN, Suzuki, Nakagomi and Nakagomi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Kazuhiko Katayama, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan, katayama@nih.go.jp