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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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Phylogenetic tree of porcine kobuviruses based on the sequences from the 3D region (588 nt). The phylogenetic tree was constructed using the neighbor-joining clustering method; distance was calculated using the maximum composite likelihood correction for evolutionary rate in MEGA version 5.0. Bootstrap values (based on 1,000 replicates) for each node are provided when >50%.
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viruses-05-02548-f004: Phylogenetic tree of porcine kobuviruses based on the sequences from the 3D region (588 nt). The phylogenetic tree was constructed using the neighbor-joining clustering method; distance was calculated using the maximum composite likelihood correction for evolutionary rate in MEGA version 5.0. Bootstrap values (based on 1,000 replicates) for each node are provided when >50%.

Mentions: The sequences of the 3D region have been particularly useful for placing viruses within species or genera and for comparing viruses of different genera or families [17]. A phylogenetic analysis shows two genetic lineages of porcine kobuviruses, however, these viruses are phylogenetically distinct from both bovine kobuviruses and Aichi viruses based on partial sequences of the 3D region (Figure 4). The four porcine kobuviruses isolated in our study and the Hungarian strains were in the same lineage, and the South Korean strains were placed in another lineage.


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)

Phylogenetic tree of porcine kobuviruses based on the sequences from the 3D region (588 nt). The phylogenetic tree was constructed using the neighbor-joining clustering method; distance was calculated using the maximum composite likelihood correction for evolutionary rate in MEGA version 5.0. Bootstrap values (based on 1,000 replicates) for each node are provided when >50%.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

viruses-05-02548-f004: Phylogenetic tree of porcine kobuviruses based on the sequences from the 3D region (588 nt). The phylogenetic tree was constructed using the neighbor-joining clustering method; distance was calculated using the maximum composite likelihood correction for evolutionary rate in MEGA version 5.0. Bootstrap values (based on 1,000 replicates) for each node are provided when >50%.
Mentions: The sequences of the 3D region have been particularly useful for placing viruses within species or genera and for comparing viruses of different genera or families [17]. A phylogenetic analysis shows two genetic lineages of porcine kobuviruses, however, these viruses are phylogenetically distinct from both bovine kobuviruses and Aichi viruses based on partial sequences of the 3D region (Figure 4). The four porcine kobuviruses isolated in our study and the Hungarian strains were in the same lineage, and the South Korean strains were placed in another lineage.

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