title: Full-genomic analysis of a human norovirus recombinant GII.12/13 novel strain isolated from South Korea.
abstract: 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.
authors.affiliation: Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
authors.forename: Yu-Jung
authors.initials: YJ
authors.lastname: Won
authors.affiliation: Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Agricultural Biomaterials, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
authors.forename: Jeong-Woong
authors.initials: JW
authors.lastname: Park
authors.affiliation: Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
authors.forename: Sang-ha
authors.initials: SH
authors.lastname: Han
authors.affiliation: Division of Virology, Gyeonggi Provincial Research Institute of Public Health and Environment, Suwon, Republic of Korea.
authors.forename: Han-Gil
authors.initials: HG
authors.lastname: Cho
authors.affiliation: Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
authors.forename: Lae-Hyung
authors.initials: LH
authors.lastname: Kang
authors.affiliation: Korea Zoonosis Research Institute, Chonbuk National University, Jeonju, Republic of Korea.
authors.forename: Sung-Geun
authors.initials: SG
authors.lastname: Lee
authors.affiliation: Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Agricultural Biomaterials, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
authors.forename: Sang-Ryeol
authors.initials: SR
authors.lastname: Ryu
authors.affiliation: Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
authors.forename: Soon-Young
authors.initials: SY
authors.lastname: Paik
mesh_terms: D001483:Base Sequence; D003001:Cloning, Molecular; D016000:Cluster Analysis; D019295:Computational Biology; D017931:DNA Primers / Q000235:genetics; D005243:Feces / Q000821:virology; D005759:Gastroenteritis / Q000821:virology*; D016679:Genome, Viral / Q000235:genetics*; D023281:Genomics; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D029322:Norovirus / Q000235:genetics*; D010802:Phylogeny; D012313:RNA / Q000235:genetics*; D056910:Republic of Korea; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D017931:DNA Primers; C039919:RNA, recombinant; D012313:RNA