Complete sequence analysis of human norovirus GII.17 detected in South Korea

Abstract

Norovirus, a major cause of gastroenteritis in people of all ages worldwide, was first reported in South Korea in 1999. The most common causal agents of pediatric acute gastroenteritis are norovirus and rotavirus. While vaccination has reduced the pediatric rotavirus infection rate, norovirus vaccines have not been developed. Therefore, prediction and prevention of norovirus are very important. Norovirus is divided into genogroups GI-GVII, with GII.4 being the most prevalent. However, in 2012-2013, GII.17 showed a higher incidence than GII.4 and a novel variant, GII.P17-GII.17, appeared. In this study, 204 stool samples collected in 2013-2014 were screened by reverse transcriptase-polymerase chain reaction; 11 GI (5.39%) and 45 GII (22.06%) noroviruses were identified. GI.4, GI.5, GII.4, GII.6 and GII.17 were detected. The whole genomes of the three norovirus GII.17 were sequenced. The whole genome of GII.17 consists of three open reading frames of 5109, 1623 and 780 bp. Compared with 20 GII.17 strains isolated in other countries, we observed numerous changes in the protruding P2 domain of VP1 in the Korean GII.17 viruses. Our study provided genome information that might aid in epidemic prevention, epidemiology studies and vaccine development.

Keywords: GII.17.; Gastroenteritis; norovirus; phylogenetic tree; sequence analysis.

Fig. 1.

Phylogenetic analysis of the full-length sequences of the GII type detected determined by genotyping and reference strains isolated worldwide.

Fig. 2.

Phylogenetic analysis of norovirus based on nucleotide sequences. The trees were constructed with the neighbour-joining method. Phylogenetic trees based on (a) amino acid sequence of ORF1, (b) amino acid sequence of ORF2 and (c) amino acid sequence of ORF3. CMC-01, CMC-02 and CMC-03 are indicated by red circles.

Fig. 3.

Amino acid substitutions in the viruses in this study (GII.17; black colour, GII.P17-GII.17; red colour). Alignment of VP1 amino acid sequences of CMC-01, CMC-02 and CMC-03 strains. Dots indicate sequence identity among sequences presented. Dashes indicate deletions/insertions of amino acid residues. LVCA24606 (KY392867), CGMH69 (KR154230), GaithersburgD14 (KY424350), 41621 (KR020503), Nagano8-1 (LC043305), Kawasaki323 (AB983218), CAU-55(KU561250), Saitama5309 (LC043168), 13010141 (KU757046), 2238 (KU557788), Katrina-17 (DQ438972), 27-3 (AB684681).

Fig. 4.

Comparison of major amino acid substitutions in viral specimens of 2013–2016 (GII.17; black colour, GII.P17-GII.17; red colour). Dots indicate sequence identity among sequences presented. Dashes indicate deletions/insertions of the amino acid residues. Amino acid numbering is based on the sequence of the Saitama5309 strain. Ljubljana535(KX134671), Osaka15-377(LC148852), X27-16NV149 (KX371112), 1613179(KU953395), 1613305(KU953397), X15_15NV796 (KX371109), 23438 (KX216804), LVCA_24606 (KY392867), 23233 (KX216793), E12972 (KU587628), 15-EN-10 (KT732275), CGMH69 (KR154230), GD-GZ (KU557801), CUHK-NS-502 (KT780399), 14200 (KT380915), 41621 (KR020503), GaithersburgD14 (KY424350), GZ2014-L313 (KT970370), 14-BQ-2 (KT906670), Nagano8-1 (LC043305), Kawasaki323 (AB983218), Saitama5309 (LC043168), CAU-55 (KU561250), 13-BH-1 (KJ156329), 2238-GD-JM(KU557788), 13010141 (KU757046).