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Whole-Genome Sequencing Analysis of Sapovirus Detected in South Korea.

Choi HL, Suh CI, Park SW, Jin JY, Cho HG, Paik SY - PLoS ONE (2015)

Bottom Line: The ROK62 genome of 7429 nucleotides contains 3 open-reading frames (ORF).Recently, SaV infection has been on the rise throughout the world, particularly in countries neighboring South Korea; however, very few academic studies have been done nationally.As the first whole-genome sequence analysis of SaV in South Korea, this research will help provide reference for the detection of recombination, tracking of epidemic spread, and development of diagnosis methods for SaV.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 137-701, Republic of Korea.

ABSTRACT
Sapovirus (SaV), a virus residing in the intestines, is one of the important causes of gastroenteritis in human beings. Human SaV genomes are classified into various genogroups and genotypes. Whole-genome analysis and phylogenetic analysis of ROK62, the SaV isolated in South Korea, were carried out. The ROK62 genome of 7429 nucleotides contains 3 open-reading frames (ORF). The genotype of ROK62 is SaV GI-1, and 94% of its nucleotide sequence is identical with other SaVs, namely Manchester and Mc114. Recently, SaV infection has been on the rise throughout the world, particularly in countries neighboring South Korea; however, very few academic studies have been done nationally. As the first whole-genome sequence analysis of SaV in South Korea, this research will help provide reference for the detection of recombination, tracking of epidemic spread, and development of diagnosis methods for SaV.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic trees of sapoviruses based on the sequences of (A) ORF1, (B) ORF2, (C) ORF3, and (D) VP1.The trees were constructed with the neighbor-joining method as in Fig 1. The analysis was carried out for 7 isolates of GI genogroup. Red circles in the trees indicate ROK62. The genogroup and genotype of each strain was indicated with strain name, inside (). The GenBank accession numbers for the reference strains are as follows: Mc114, AY237422; N21, AY237423; Manchester, X86560; Sapporo, HM002617; Chanthabri-74, AY646854; Nongkhai50, AY646853; Dresden, AY694184.
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pone.0132328.g002: Phylogenetic trees of sapoviruses based on the sequences of (A) ORF1, (B) ORF2, (C) ORF3, and (D) VP1.The trees were constructed with the neighbor-joining method as in Fig 1. The analysis was carried out for 7 isolates of GI genogroup. Red circles in the trees indicate ROK62. The genogroup and genotype of each strain was indicated with strain name, inside (). The GenBank accession numbers for the reference strains are as follows: Mc114, AY237422; N21, AY237423; Manchester, X86560; Sapporo, HM002617; Chanthabri-74, AY646854; Nongkhai50, AY646853; Dresden, AY694184.

Mentions: Even though phylogenetic analysis of ORF3 showed that ROK62 is close to the Sapporo strain, sequence identities with ORF1 (99.93%), ORF2 (99.93%), ORF3 (99.99%) and VP1 (99.95%) showed the closest relationships with the Manchester strain (Fig 2).


Whole-Genome Sequencing Analysis of Sapovirus Detected in South Korea.

Choi HL, Suh CI, Park SW, Jin JY, Cho HG, Paik SY - PLoS ONE (2015)

Phylogenetic trees of sapoviruses based on the sequences of (A) ORF1, (B) ORF2, (C) ORF3, and (D) VP1.The trees were constructed with the neighbor-joining method as in Fig 1. The analysis was carried out for 7 isolates of GI genogroup. Red circles in the trees indicate ROK62. The genogroup and genotype of each strain was indicated with strain name, inside (). The GenBank accession numbers for the reference strains are as follows: Mc114, AY237422; N21, AY237423; Manchester, X86560; Sapporo, HM002617; Chanthabri-74, AY646854; Nongkhai50, AY646853; Dresden, AY694184.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4498750&req=5

pone.0132328.g002: Phylogenetic trees of sapoviruses based on the sequences of (A) ORF1, (B) ORF2, (C) ORF3, and (D) VP1.The trees were constructed with the neighbor-joining method as in Fig 1. The analysis was carried out for 7 isolates of GI genogroup. Red circles in the trees indicate ROK62. The genogroup and genotype of each strain was indicated with strain name, inside (). The GenBank accession numbers for the reference strains are as follows: Mc114, AY237422; N21, AY237423; Manchester, X86560; Sapporo, HM002617; Chanthabri-74, AY646854; Nongkhai50, AY646853; Dresden, AY694184.
Mentions: Even though phylogenetic analysis of ORF3 showed that ROK62 is close to the Sapporo strain, sequence identities with ORF1 (99.93%), ORF2 (99.93%), ORF3 (99.99%) and VP1 (99.95%) showed the closest relationships with the Manchester strain (Fig 2).

Bottom Line: The ROK62 genome of 7429 nucleotides contains 3 open-reading frames (ORF).Recently, SaV infection has been on the rise throughout the world, particularly in countries neighboring South Korea; however, very few academic studies have been done nationally.As the first whole-genome sequence analysis of SaV in South Korea, this research will help provide reference for the detection of recombination, tracking of epidemic spread, and development of diagnosis methods for SaV.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 137-701, Republic of Korea.

ABSTRACT
Sapovirus (SaV), a virus residing in the intestines, is one of the important causes of gastroenteritis in human beings. Human SaV genomes are classified into various genogroups and genotypes. Whole-genome analysis and phylogenetic analysis of ROK62, the SaV isolated in South Korea, were carried out. The ROK62 genome of 7429 nucleotides contains 3 open-reading frames (ORF). The genotype of ROK62 is SaV GI-1, and 94% of its nucleotide sequence is identical with other SaVs, namely Manchester and Mc114. Recently, SaV infection has been on the rise throughout the world, particularly in countries neighboring South Korea; however, very few academic studies have been done nationally. As the first whole-genome sequence analysis of SaV in South Korea, this research will help provide reference for the detection of recombination, tracking of epidemic spread, and development of diagnosis methods for SaV.

No MeSH data available.


Related in: MedlinePlus