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Identification and characterization of porcine kobuvirus variant isolated from suckling piglet in Gansu province, China.

Fan S, Sun H, Ying Y, Gao X, Wang Z, Yu Y, Li Y, Wang T, Yu Z, Yang S, Zhao Y, Qin C, Gao Y, Xia X - Viruses (2013)

Bottom Line: A 90-nucleotide deletion in the 2B protein and a single nucleotide insertion in the 3'UTR were found in the variant strains.Ten common amino acid mutations were found specifically at certain positions within the VP1 region.These findings suggest that mutations and recombination events may have contributed to the high level of genetic diversity of porcine kobuviruses and serve as a driving force in its evolution.

View Article: PubMed Central - PubMed

Affiliation: Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China. gaoyuwei@gmail.com.

ABSTRACT
Kobuviruses comprise three species, the Aichivirus A, Aichivirus B, and Aichivirus C (porcine kobuvirus). Porcine kobuvirus is endemic to pig farms and is not restricted geographically but, rather, is distributed worldwide. The complete genomic sequences of four porcine kobuvirus strains isolated during a diarrhea outbreak in piglets in the Gansu province of China were determined. Two of these strains exhibited variations relative to the traditional strains. The potential 3C/3D cleavage sites of the variant strains were Q/C, which differed from the Q/S in the traditional porcine kobuvirus genome. A 90-nucleotide deletion in the 2B protein and a single nucleotide insertion in the 3'UTR were found in the variant strains. The VP1 regions of all four porcine kobuviruses in our study were highly variable (81%-86%). Ten common amino acid mutations were found specifically at certain positions within the VP1 region. Significant recombination sites were identified using SimPlot scans of whole genome sequences. Porcine kobuviruses were also detected in pig serum, indicating that the virus can escape the gastrointestinal tract and travel to the circulatory system. These findings suggest that mutations and recombination events may have contributed to the high level of genetic diversity of porcine kobuviruses and serve as a driving force in its evolution.

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Related in: MedlinePlus

Nucleotide similarities and recombination among the kobuvirus genomes. (A) Nucleotide similarities among theK-4/2012/CH, K-11/2012/CH, GS-1/2012/CH, and GS-2/2012/CH genomes, as determined using the SimPlot program. The x-axis indicates the nucleotide position along the alignment, and the y-axis shows the similarity; (B) Bootscan plot of the GS-1/2012/CH strain with GS-1/2012/CH, K-4/2012/CH, and K-4/2012/CH reference sequences as out groups. The analysis was performed using pairwise distance, modeled with a window size of 200, step size of 20, and 100 bootstrap replicates.
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viruses-05-02548-f001: Nucleotide similarities and recombination among the kobuvirus genomes. (A) Nucleotide similarities among theK-4/2012/CH, K-11/2012/CH, GS-1/2012/CH, and GS-2/2012/CH genomes, as determined using the SimPlot program. The x-axis indicates the nucleotide position along the alignment, and the y-axis shows the similarity; (B) Bootscan plot of the GS-1/2012/CH strain with GS-1/2012/CH, K-4/2012/CH, and K-4/2012/CH reference sequences as out groups. The analysis was performed using pairwise distance, modeled with a window size of 200, step size of 20, and 100 bootstrap replicates.

Mentions: The four complete kobuvirus genome sequences were analyzed using Simplot. The similarity plot displays the consecutive nucleotide identity (%) among the queried strain and parental strains. The Bootscan plots display the likelihood of recombination within the GS-1/2012/CH variant strain; the 481–1,414 and 3,482–4,100 nucleotide regions are similar to regions found in the K-4/2012/CH strain. The other genomic regions of the GS-1/2012/CH variant strain, including 4,100–4,369, 7,143–7,384, and 7,760–8,068, are closely related to the K-11/2012/CH strain (Figure 1A). Significant recombination signals were identified in the 481–774, 1,165–1,414, 3,842–4,369, 4,842–5,121, 7,143–7,384, and 7,760–8,068 nucleotide regions (Figure 1B).


Identification and characterization of porcine kobuvirus variant isolated from suckling piglet in Gansu province, China.

Fan S, Sun H, Ying Y, Gao X, Wang Z, Yu Y, Li Y, Wang T, Yu Z, Yang S, Zhao Y, Qin C, Gao Y, Xia X - Viruses (2013)

Nucleotide similarities and recombination among the kobuvirus genomes. (A) Nucleotide similarities among theK-4/2012/CH, K-11/2012/CH, GS-1/2012/CH, and GS-2/2012/CH genomes, as determined using the SimPlot program. The x-axis indicates the nucleotide position along the alignment, and the y-axis shows the similarity; (B) Bootscan plot of the GS-1/2012/CH strain with GS-1/2012/CH, K-4/2012/CH, and K-4/2012/CH reference sequences as out groups. The analysis was performed using pairwise distance, modeled with a window size of 200, step size of 20, and 100 bootstrap replicates.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814603&req=5

viruses-05-02548-f001: Nucleotide similarities and recombination among the kobuvirus genomes. (A) Nucleotide similarities among theK-4/2012/CH, K-11/2012/CH, GS-1/2012/CH, and GS-2/2012/CH genomes, as determined using the SimPlot program. The x-axis indicates the nucleotide position along the alignment, and the y-axis shows the similarity; (B) Bootscan plot of the GS-1/2012/CH strain with GS-1/2012/CH, K-4/2012/CH, and K-4/2012/CH reference sequences as out groups. The analysis was performed using pairwise distance, modeled with a window size of 200, step size of 20, and 100 bootstrap replicates.
Mentions: The four complete kobuvirus genome sequences were analyzed using Simplot. The similarity plot displays the consecutive nucleotide identity (%) among the queried strain and parental strains. The Bootscan plots display the likelihood of recombination within the GS-1/2012/CH variant strain; the 481–1,414 and 3,482–4,100 nucleotide regions are similar to regions found in the K-4/2012/CH strain. The other genomic regions of the GS-1/2012/CH variant strain, including 4,100–4,369, 7,143–7,384, and 7,760–8,068, are closely related to the K-11/2012/CH strain (Figure 1A). Significant recombination signals were identified in the 481–774, 1,165–1,414, 3,842–4,369, 4,842–5,121, 7,143–7,384, and 7,760–8,068 nucleotide regions (Figure 1B).

Bottom Line: A 90-nucleotide deletion in the 2B protein and a single nucleotide insertion in the 3'UTR were found in the variant strains.Ten common amino acid mutations were found specifically at certain positions within the VP1 region.These findings suggest that mutations and recombination events may have contributed to the high level of genetic diversity of porcine kobuviruses and serve as a driving force in its evolution.

View Article: PubMed Central - PubMed

Affiliation: Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China. gaoyuwei@gmail.com.

ABSTRACT
Kobuviruses comprise three species, the Aichivirus A, Aichivirus B, and Aichivirus C (porcine kobuvirus). Porcine kobuvirus is endemic to pig farms and is not restricted geographically but, rather, is distributed worldwide. The complete genomic sequences of four porcine kobuvirus strains isolated during a diarrhea outbreak in piglets in the Gansu province of China were determined. Two of these strains exhibited variations relative to the traditional strains. The potential 3C/3D cleavage sites of the variant strains were Q/C, which differed from the Q/S in the traditional porcine kobuvirus genome. A 90-nucleotide deletion in the 2B protein and a single nucleotide insertion in the 3'UTR were found in the variant strains. The VP1 regions of all four porcine kobuviruses in our study were highly variable (81%-86%). Ten common amino acid mutations were found specifically at certain positions within the VP1 region. Significant recombination sites were identified using SimPlot scans of whole genome sequences. Porcine kobuviruses were also detected in pig serum, indicating that the virus can escape the gastrointestinal tract and travel to the circulatory system. These findings suggest that mutations and recombination events may have contributed to the high level of genetic diversity of porcine kobuviruses and serve as a driving force in its evolution.

Show MeSH
Related in: MedlinePlus