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, 9 (12), e113966
eCollection

Evolutionary Phylodynamics of Korean Noroviruses Reveals a Novel GII.2/GII.10 Recombination Event

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Evolutionary Phylodynamics of Korean Noroviruses Reveals a Novel GII.2/GII.10 Recombination Event

Thoi Cong Truong et al. PLoS One.

Abstract

Viral gastroenteritis is the most common causal agent of public health problems worldwide. Noroviruses cause nonbacterial acute gastroenteritis in humans of all ages. In this study, we investigated the occurrence of norovirus infection in children with acute gastroenteritis admitted to university hospitals in South Korea. We also analyzed the genetic diversity of the viruses and identified novel recombination events among the identified viral strains. Of 502 children with acute gastroenteritis admitted to our three hospitals between January 2011 and March 2012, genotyping of human noroviruses was performed in 171 (34%) norovirus-positive samples. Of these samples, 170 (99.5%) were in genogroup II (GII), while only one (0.5%) was in genogroup I (GI). The most common GII strain was the GII.4-2006b variant (n = 96, 56.5%), followed by GII.6 (n = 23, 13.5%), GII.12 (n = 22, 12.9%), GII.3 (n = 20, 11.8%), GII.2 (n = 6, 3.5%), GII.b (n = 2, 1.2%), and GII.10 (n = 1, 0.6%). Potential recombination events (polymerase/capsid) were detected in 39 GII strains (22.9%), and the most frequent genotypes were GII.4/GII.12 (n = 12, 30.8%), GII.4/GII.6 (n = 12, 30.8%), GII.4/GII.3 (n = 8, 20.5%), GII.b/GII.3 (n = 3, 7.7%), GII.16/GII.2 (n = 2, 5.1%), GII.4/GII.2 (n = 1, 2.6%), and GII.2/GII.10 (n = 1, 2.6%). For the first time, a novel GII.2/GII.10 recombination was detected; we also identified the GII.16/GII.2 strain for the first time in South Korea. Our data provided important insights into new recombination events, which may prove valuable for predicting the emergence of circulating norovirus strains with global epidemic potential.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Phylogenetic tree analyse.
These analyses involved the partial nucleotide sequences of the norovirus GI strain capsid region detected in this study and the reference strains available in the Genbank database. The scale indicates nucleotide substitutions per position.
Figure 2
Figure 2. Phylogenetic analyses.
These analyses involved the norovirus GII strains detected in this study and the reference strains available in the Genbank database. (A) RdRp gene sequence (328 bp), (B) capsid gene sequence (287 bp). Reference strains are marked in bold type.
Figure 3
Figure 3. (A) SimPlot analysis of the partial RdRp and capsid gene sequences of the GII.b/GII.3 recombination strain, Gil-67.
SimPlot was constructed using Simplot version 3.5 with a slide window width of 200 bp and a step size of 20 bp. The vertical axis indicates nucleotide identities (%) between the query sequence (Gil-67) and the NoVs reference strains. The horizontal axis indicates the nucleotide positions of the analyzed genome regions. (B) Bootscan analysis of the genomic region involved in the recombination event at position 5,078 of the Gil-67 strain with the NoVs reference strains.
Figure 4
Figure 4. Phylogenetic dendrogram constructed using the neighbor-joining method.
The dendrogram was based on (A) the RdRp gene sequences and (B) the capsid gene sequences of the three study strains, Gil-70, 4CAU-38, and 4CAU-14, and of the reference strains available in the Genbank database. Recombinant strains are highlighted in italics.
Figure 5
Figure 5. Simplot and Bootscan analysis of the NoVs recombinant GII.16/GII.2, (A) Gil-70 and (B) 4CAU-38 strains.
SimPlot was constructed using Simplot version 3.5 with a slide window width of 200 bp and a step size of 20 bp. The vertical axis indicates nucleotide identities (%) between the query sequences (Gil-70 and 4CAU-38) and the reference strains. The horizontal axis indicates the nucleotide positions of the analyzed genomic regions. The vertical line indicates the beginning of ORF2 (5,028 bp) and 20 bp for the ORF1/ORF2 overlap region. Bootscan analysis of the genomic region involved in the recombination event at position 5,028 of the GIL-70 and 4CAU-38 strains with the NoVs reference strains.
Figure 6
Figure 6. (A) SimPlot analysis of the partial RdRp and capsid gene sequences of recombinant GII.2/GII.10, 4CAU-14 strain.
SimPlot was constructed using Simplot version 3.5 with a slide window width of 200 bp and a step size of 20 bp. The vertical axis indicates nucleotide identities (%) between the query sequence (4CAU-14) and the NoVs reference strains. The horizontal axis indicates the nucleotide positions of the analyzed genome regions. (B) Bootscan analysis of the genomic region involved in the recombination event at position 5,078 of the 4CAU-14 strain with the NoVs reference strains.

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Grant support

This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) (2013-R1A1A2A10012148) funded by the Ministry of Education. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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