RESULTS:

Since 2013 equine-like G3 rotavirus (eG3) strains have been detected throughout the world including in Japan and the strains were found to be dominant in some countries. In 2016 the first eG3 outbreak in Japan occurred in Tomakomai Hokkaido prefecture and the strains became dominant in other Hokkaido areas the following year. There were no significant differences in the clinical characteristics of eG3 and non-eG3 rotavirus infections. The eG3 strains detected in Hokkaido across 2 years from 2016 to 2017 had DS-1-like constellations (i.e. G3-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2) and the genes were highly conserved (97.5–100 %). One strain designated as To16-12 was selected as the representative strain for these strains and all 11 genes of this strain (To16-12) exhibited the closest identity to one foreign eG3 strain (STM050) seen in Indonesia in 2015 and two eG3 strains (IS1090 and MI1125) in another Japanese prefecture in 2016 suggesting that this strain might be introduced into Japan from Indonesia. Sequence analyses of VP7 genes from animal and human G3 strains found worldwide did not identify any with close identity (>92 %) to eG3 strains including equine RV Erv105. Analysis of another ten genes indicated that the eG3 strain had low similarity to G2P[4] strains which are considered traditional DS-1-like strains but high similarity to DS-1-like G1P[8] strains which first appeared in Asia in 2012. These data suggest that eG3 strains were recently generated in Asia as mono-reassortant strain between DS-1-like G1P[8] strains and unspecified animal G3 strains. Our results indicate that rotavirus surveillance in the postvaccine era requires whole-genome analyses.

The family Caliciviridae includes viruses with single-stranded positive-sense RNA genomes of 7.4–8.3 kb. The most clinically important representatives are human noroviruses which are a leading cause of acute gastroenteritis in humans. Virions are non-enveloped with icosahedral symmetry. Members of seven genera infect mammals (Lagovirus Norovirus Nebovirus Recovirus Sapovirus Valovirus and Vesivirus) members of two genera infect birds (Bavovirus and Nacovirus) and members of two genera infect fish (Minovirus and Salovirus). This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Caliciviridae which is available at ictv.global/report/caliciviridae.

Sapovirus (SaV) a member of the family Caliciviridae is a causative agent of acute gastroenteritis in humans and swine and is currently divided into five genogroups GI–GV. The proteolytic processing of the SaV open reading frame 1 (ORF1) polyprotein with a human GII SaV Mc10 strain has recently been determined and the products are arranged in the following order: NH2–p11–p28–p35 (NTPase)–p32–p14 (VPg)–p70 (Pro–Pol)–p60 (VP1)–COOH. The cleavage site between p14 (VPg) and p70 (Pro–Pol) was identified as E1055/A1056 by N-terminal amino acid sequencing. To identify other cleavage sites a series of GII SaV Mc10 full-length clones containing disrupted potential cleavage sites in the ORF1 polyprotein were constructed and used to generate linear DNA templates for in vitro coupled transcription–translation. The translation products were analysed by SDS-PAGE or by immunoprecipitation with region-specific antibodies. N-terminal amino acid sequencing with Escherichia coli-expressed recombinant proteins was also used to identify the cleavage site between p32 and p14. These approaches enabled identification of the six cleavage sites of the Mc10 ORF1 polyprotein as E69/G70 Q325/G326 Q666/G667 E940/A941 E1055/A1056 and E1722/G1723. The alignment of the SaV full-length ORF1 amino acid sequences indicated that the dipeptides used for the cleavage sites were either E or Q at the P1 position and A G or S at the P1′ position which were conserved in the GI GII GIII GIV and GV SaV ORF1 polyprotein.