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Full sequence analysis and characterization of the South Korean Norovirus GII-4 variant CUK-3.

Park JW, Lee SG, Lee YM, Jheong WH, Ryu S, Paik SY - Virol. J. (2011)

Bottom Line: Each genetic relationship of CUK-3 variant analysis located the ORF1 (5,100 bp) in Cluster I, ORF2 (1623 bp) in Cluster I (2006b), ORF3 (807 bp) in Cluster I, and the whole genome sequence (about 5.1 kb) in Cluster I in the phylogenetic tree.And the phylogenetic analyses showed the same location of CUK-3 strain with the GII-4/2006b cluster in the phylogenetic tree.In This study, a first concerning the full-length sequence of a NoV variant in South Korea is meaningful in that it can be used not only as a full-length NoV variant sequence standard for future comparison studies, but also as useful material for the public health field by enabling the diagnosis, vaccine development, and prediction of new emerging variants.

View Article: PubMed Central - HTML - PubMed

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 151-921, Republic of Korea. sangryu@snu.ac.kr.

ABSTRACT

Background: Many of researchers have focused on the emerging pathogen, Norovirus, since its first identification as the causing agent of nonbacterial acute gastroenteritis in humans. One of the virulence factors of norovirus, the great genetic diversity attributed to point mutations and recombinations, has brought forth the result of significant changes in the circulating norovirus genotype patterns.

Findings: In recognition of the necessity for tracking and monitoring of genetic diversity, a norovirus variant among the most prevalent genotype GII-4, Norovirus Hu/GII-4/CUK-3/2008/KR (CUK-3), was isolated from stool samples and analyzed on the level of whole genome sequence. Whole genome sequence analysis revealed three ORF composites of the whole genome, ORF1 (5100 bp), ORF2 (1623 bp), and ORF3 (807 bp). Each genetic relationship of CUK-3 variant analysis located the ORF1 (5,100 bp) in Cluster I, ORF2 (1623 bp) in Cluster I (2006b), ORF3 (807 bp) in Cluster I, and the whole genome sequence (about 5.1 kb) in Cluster I in the phylogenetic tree. And the phylogenetic analyses showed the same location of CUK-3 strain with the GII-4/2006b cluster in the phylogenetic tree.

Conclusions: In This study, a first concerning the full-length sequence of a NoV variant in South Korea is meaningful in that it can be used not only as a full-length NoV variant sequence standard for future comparison studies, but also as useful material for the public health field by enabling the diagnosis, vaccine development, and prediction of new emerging variants.

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Related in: MedlinePlus

Phylogenetic trees of the nucleotide sequences of the complete regions of NoV GII/4. Phylogenetic tree generated based on the complete sequence of the ORF1 (about 5.1 kb) (A), ORF2 (about 1.6 kb) (B), ORF3 (about 0.8 kb) (C), and near-full-length genome (7.5 kb) (D)
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Figure 1: Phylogenetic trees of the nucleotide sequences of the complete regions of NoV GII/4. Phylogenetic tree generated based on the complete sequence of the ORF1 (about 5.1 kb) (A), ORF2 (about 1.6 kb) (B), ORF3 (about 0.8 kb) (C), and near-full-length genome (7.5 kb) (D)

Mentions: To analyze the genetic relationship between the CUK-3 variant and the other variants reported worldwide, the sequences of ORF sequences and the whole genome were processed with multiple sequence alignment. Each analysis of CUK-3 located the ORF1 (5,100 bp) in Cluster I, ORF2 (1623 bp) in Cluster I (2006b), and ORF3 (807 bp) in Cluster I as well as the whole genome sequence (about 5.1 kb) in Cluster I (Figure 1).


Full sequence analysis and characterization of the South Korean Norovirus GII-4 variant CUK-3.

Park JW, Lee SG, Lee YM, Jheong WH, Ryu S, Paik SY - Virol. J. (2011)

Phylogenetic trees of the nucleotide sequences of the complete regions of NoV GII/4. Phylogenetic tree generated based on the complete sequence of the ORF1 (about 5.1 kb) (A), ORF2 (about 1.6 kb) (B), ORF3 (about 0.8 kb) (C), and near-full-length genome (7.5 kb) (D)
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3094297&req=5

Figure 1: Phylogenetic trees of the nucleotide sequences of the complete regions of NoV GII/4. Phylogenetic tree generated based on the complete sequence of the ORF1 (about 5.1 kb) (A), ORF2 (about 1.6 kb) (B), ORF3 (about 0.8 kb) (C), and near-full-length genome (7.5 kb) (D)
Mentions: To analyze the genetic relationship between the CUK-3 variant and the other variants reported worldwide, the sequences of ORF sequences and the whole genome were processed with multiple sequence alignment. Each analysis of CUK-3 located the ORF1 (5,100 bp) in Cluster I, ORF2 (1623 bp) in Cluster I (2006b), and ORF3 (807 bp) in Cluster I as well as the whole genome sequence (about 5.1 kb) in Cluster I (Figure 1).

Bottom Line: Each genetic relationship of CUK-3 variant analysis located the ORF1 (5,100 bp) in Cluster I, ORF2 (1623 bp) in Cluster I (2006b), ORF3 (807 bp) in Cluster I, and the whole genome sequence (about 5.1 kb) in Cluster I in the phylogenetic tree.And the phylogenetic analyses showed the same location of CUK-3 strain with the GII-4/2006b cluster in the phylogenetic tree.In This study, a first concerning the full-length sequence of a NoV variant in South Korea is meaningful in that it can be used not only as a full-length NoV variant sequence standard for future comparison studies, but also as useful material for the public health field by enabling the diagnosis, vaccine development, and prediction of new emerging variants.

View Article: PubMed Central - HTML - PubMed

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 151-921, Republic of Korea. sangryu@snu.ac.kr.

ABSTRACT

Background: Many of researchers have focused on the emerging pathogen, Norovirus, since its first identification as the causing agent of nonbacterial acute gastroenteritis in humans. One of the virulence factors of norovirus, the great genetic diversity attributed to point mutations and recombinations, has brought forth the result of significant changes in the circulating norovirus genotype patterns.

Findings: In recognition of the necessity for tracking and monitoring of genetic diversity, a norovirus variant among the most prevalent genotype GII-4, Norovirus Hu/GII-4/CUK-3/2008/KR (CUK-3), was isolated from stool samples and analyzed on the level of whole genome sequence. Whole genome sequence analysis revealed three ORF composites of the whole genome, ORF1 (5100 bp), ORF2 (1623 bp), and ORF3 (807 bp). Each genetic relationship of CUK-3 variant analysis located the ORF1 (5,100 bp) in Cluster I, ORF2 (1623 bp) in Cluster I (2006b), ORF3 (807 bp) in Cluster I, and the whole genome sequence (about 5.1 kb) in Cluster I in the phylogenetic tree. And the phylogenetic analyses showed the same location of CUK-3 strain with the GII-4/2006b cluster in the phylogenetic tree.

Conclusions: In This study, a first concerning the full-length sequence of a NoV variant in South Korea is meaningful in that it can be used not only as a full-length NoV variant sequence standard for future comparison studies, but also as useful material for the public health field by enabling the diagnosis, vaccine development, and prediction of new emerging variants.

Show MeSH
Related in: MedlinePlus