Full-genomic analysis of a human norovirus recombinant GII.12/13 novel strain isolated from South Korea. 2013

Yu-Jung Won, and Jeong-Woong Park, and Sang-ha Han, and Han-Gil Cho, and Lae-Hyung Kang, and Sung-Geun Lee, and Sang-Ryeol Ryu, and Soon-Young Paik
Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.

Norovirus (NoV) genogroups I and II are frequently recognized as the main causes of acute gastroenteritis and outbreaks of non-bacterial foodborne diseases. Furthermore, variants and recombinant strains of this virus are continuously emerging worldwide. The aim of this study was to identify NoV strains and to investigate and characterize rare genotypes. Stool samples (n = 500) were collected from patients with symptoms of acute gastroenteritis in Korea between December 2004 and November 2007. For analysis of the samples, rapid genotype screening was performed using reverse transcriptase-polymerase chain reaction. Full sequencing, using a newly designed set of 12 primers, revealed GII-12/13 strain. The partial sequence of GII-12/13 strain was compared with published NoV (GII-1 - 14) sequences targeting RdRp and capsid regions using phylogenetic analysis with the SimPlot program, which could evaluate recombination breakpoints. SimPlot analysis was also performed with the strain GII-12/Gifu-96/JPN (AB045603) for the RdRp region and with GII-13/G5175B-83/AUS(DQ379714) for the capsid region. NoV was detected in 19 of the 500 stool samples (3.8%). Genogroup GII-4 was found most frequently (n = 9, 1.8%), followed by GII-3 (n = 4, 0.8%), GII-6 (n = 3, 0.6%), GI-6 (n = 2, 0.4%), and GII-12/13 (n = 1, 0.2%). Importantly, we identified a novel NoV recombinant strain, C9-439 (KF289337), indicating potential risks, which suggested that, recombination occurred in the region between open reading frames 1 and 2 of the GII-12/13 strain and that breakpoints occurred in the polymerase region.

UI MeSH Term Description Entries
D008969 Molecular Sequence Data Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D010802 Phylogeny The relationships of groups of organisms as reflected by their genetic makeup. Community Phylogenetics,Molecular Phylogenetics,Phylogenetic Analyses,Phylogenetic Analysis,Phylogenetic Clustering,Phylogenetic Comparative Analysis,Phylogenetic Comparative Methods,Phylogenetic Distance,Phylogenetic Generalized Least Squares,Phylogenetic Groups,Phylogenetic Incongruence,Phylogenetic Inference,Phylogenetic Networks,Phylogenetic Reconstruction,Phylogenetic Relatedness,Phylogenetic Relationships,Phylogenetic Signal,Phylogenetic Structure,Phylogenetic Tree,Phylogenetic Trees,Phylogenomics,Analyse, Phylogenetic,Analysis, Phylogenetic,Analysis, Phylogenetic Comparative,Clustering, Phylogenetic,Community Phylogenetic,Comparative Analysis, Phylogenetic,Comparative Method, Phylogenetic,Distance, Phylogenetic,Group, Phylogenetic,Incongruence, Phylogenetic,Inference, Phylogenetic,Method, Phylogenetic Comparative,Molecular Phylogenetic,Network, Phylogenetic,Phylogenetic Analyse,Phylogenetic Clusterings,Phylogenetic Comparative Analyses,Phylogenetic Comparative Method,Phylogenetic Distances,Phylogenetic Group,Phylogenetic Incongruences,Phylogenetic Inferences,Phylogenetic Network,Phylogenetic Reconstructions,Phylogenetic Relatednesses,Phylogenetic Relationship,Phylogenetic Signals,Phylogenetic Structures,Phylogenetic, Community,Phylogenetic, Molecular,Phylogenies,Phylogenomic,Reconstruction, Phylogenetic,Relatedness, Phylogenetic,Relationship, Phylogenetic,Signal, Phylogenetic,Structure, Phylogenetic,Tree, Phylogenetic
D003001 Cloning, Molecular The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells. Molecular Cloning
D005243 Feces Excrement from the INTESTINES, containing unabsorbed solids, waste products, secretions, and BACTERIA of the DIGESTIVE SYSTEM.
D005759 Gastroenteritis INFLAMMATION of any segment of the GASTROINTESTINAL TRACT from ESOPHAGUS to RECTUM. Causes of gastroenteritis are many including genetic, infection, HYPERSENSITIVITY, drug effects, and CANCER. Gastroenteritides
D005838 Genotype The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS. Genogroup,Genogroups,Genotypes
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D001483 Base Sequence The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA
D012313 RNA A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed) RNA, Non-Polyadenylated,Ribonucleic Acid,Gene Products, RNA,Non-Polyadenylated RNA,Acid, Ribonucleic,Non Polyadenylated RNA,RNA Gene Products,RNA, Non Polyadenylated
D013045 Species Specificity The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species. Species Specificities,Specificities, Species,Specificity, Species

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