Full-genome sequence analysis of an uncommon norovirus genotype, GII.21, from South Korea

Abstract

Noroviruses (NoVs) are major causal agents of acute gastroenteritis in humans. NoV GII.4 is the predominant genotype globally. However, uncommon and minor types of NoVs are consistently detected and some have been shown to dominate over GII.4. Therefore, the prevalence of dominant and uncommon NoVs makes the identification of these viruses important for the prediction and prevention of pandemics. In this study, the full-genome sequence of a NoV (strain JW) detected in Korea was extensively characterized. The full-length genome was 7510 nucleotides long, and phylogenetic analysis based on the whole-genome sequences, including open reading frame (ORF)1, ORF2, and ORF3, indicated that it belonged to the GII.21 genotype. Strain JW showed maximum identity with strain YO284; however, comparison of the amino acid sequence of ORF2, which functions as an antigen, showed substitutions in several amino acids. GII.21 is not a prevalent epidemiological agent of acute gastroenteritis in humans, but it is consistently found in gastroenteritis patients from several countries. The present study provides the first full-genome sequence analysis of NoV GII.21 isolated from a patient in Korea. Our findings provide not only valuable genome information but also data for epidemiology studies, epidemic prevention, and vaccine development strategies.

Keywords: GII.21; NoV; Norovirus; sequence analysis; uncommon NoV.

Fig. 1.

Phylogenetic analysis of NoV based on nucleotide and amino acid sequences. The neighbor-joining method in MEGA was used to construct phylogenetic trees. The numbers associated with each branch indicate the bootstrap values for the genotype. Phylogenetic trees based on (a) full-length nucleotide sequence, (b) amino acid sequence of ORF1, (c) amino acid sequence of ORF2, and (d) amino acid sequence of ORF3. Strain JW is highlighted with a solid red circle. The representative strains are named by ‘accession number/host/genogroup’ and ‘genotype/strain/collection date/country’. Country codes: CHN, China; HKG, Hong Kong; JPN, Japan; USA, United States of America; AUS, Australia; TWN, Taiwan; NLD, Netherlands; MYS, Malaysia; KOR, Korea.

Fig. 2.

Phylogenetic analysis and amino acid sequence comparison of partial ORF2 gene. (a) Neighbor-joining phylogenetic analysis of the partial nucleotide sequences of the VP1 genes for strain JW (solid red circle). Strain JW clustered in GII.21.b1. (b) The comparison of the partial amino acid sequence of VP1 genes is shown as amino acid substitution patterns. The consensus sequence was based on the corresponding amino acid sequence that was most highly conserved. The substituted amino acids are in red boxes. The representative strains are named by ‘isolation source/strain/collection date/country’. Country codes: CHN, China; JPN, Japan; USA, United States of America; TWN, Taiwan; BGD, Bangladesh; THA, Thailand; IND, India; IRQ, Iraq; SGP, Singapore; NZL, New Zealand; ESP, Spain; KOR, Korea.

Fig. 3.

Comparison of amino acid substitutions of five strains. Alignment of VP1 amino acid sequences of NoV strains YO284 (GenBank accession number KJ196284), Salisbury150 (GenBank accession number JN899245), CUHK-NS-293 (GenBank accession number KR921937), GL02BLPV2 (GenBank accession number AMO28394), and JW (GenBank accession number KX079488). A total of 19 amino acid alterations (red arrows) were noted in the previously (cluster A) and recently collected strains (cluster B). Most substitutions were present within the hypervariable P2 subdomain (residues 279–405).

Fig. 4.

Amino acid sequence alignment of the surface loops of the P domains forming HBGA-binding interfaces. Sequences of the three surface loops on the HBGA-binding interfaces (B, N, and T loops) representing the genotype of the GII.21 [34]. The conserved residues forming the binding interface are indicated with asterisks. Two substituted amino acids in the N and T loops are shown in red boxes. The representative strains were named by ‘accession number/host/genogroup’ and ‘genotype/strain/collection date/country’. Country codes: JPN, Japan; USA, United States of America; IRQ, Iraq; KOR, Korea.