Abstract
A comprehensive molecular epidemiological study using next-generation sequencing technology was conducted on 333 rotavirus A (RVA)-positive specimens collected from six sentinel hospitals across Japan over three consecutive seasons (2012–2014). The majority of the RVA isolates 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 RVAs spread.
Highlights
Rotavirus A (RVA) is a major cause of gastroenteritis in infants and young children worldwide
rotavirus A (RVA)-positive samples were identified by ELISA screening: the http://tree.bio.ed.ac.uk/software/tracer/
The other three subclusters belong to lineage 1; one consists of 149 DS-1-like G1P[8] strains, another is mainly composed of strains from Akita in 2012 (YR-2012), and the third is mainly composed of strains from Yamaguchi in 2013 (YM-2013)
Summary
Rotavirus A (RVA) is a major cause of gastroenteritis in infants and young children worldwide. In the first year of surveillance (2012), we reported the predominance of the unusual G1P[8] strain, which possesses a DS-1-like genotype constellation (DS-1-like G1P[8]: G1-P[8]-I2-R2-C2-M2-A2-N2T2-E2-H2), in Japan (Fujii et al, 2014). We performed comprehensive molecular epidemiological research, based on next-generation sequencing (NGS) of RVA strains in 2013–2014 and added published results from 2012, to generate a phylogenetic tree. Viral RNA was extracted from stool suspensions with the Directzol RNA MiniPrep kit (Zymo Research, Irvine, CA, United States) according to manufacturer’s instructions as previously described (Fujii et al, 2014). The NGS analysis yielded several sequences that lacked one or both ends of segments. This result usually depends on amount of virus in the stool specimen. GenBank and the lineage designations defined based on previous studies for G1 (Arista et al, 2006; Le et al, 2010), G2 (Doan et al, 2015), G3 (Wang et al, 2014), and G9 trees (Phan et al., 2007)
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