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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

Comparison of the deduced protein amino acid sequences of the study strains and the reference strains. (A) Comparison of the deduced 2B protein amino acid sequences. An asterisk (*) indicates an amino acid substitution in the VP1 region; a dash (-) indicates an amino acid deletion in the variant strain; (B) Comparison of the deduced VP1 amino acid sequences. An asterisk (*) indicates no fewer than three amino acid substitutions within the VP1 region.
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viruses-05-02548-f002: Comparison of the deduced protein amino acid sequences of the study strains and the reference strains. (A) Comparison of the deduced 2B protein amino acid sequences. An asterisk (*) indicates an amino acid substitution in the VP1 region; a dash (-) indicates an amino acid deletion in the variant strain; (B) Comparison of the deduced VP1 amino acid sequences. An asterisk (*) indicates no fewer than three amino acid substitutions within the VP1 region.

Mentions: The structural and non-structural protein regions of the both K-4/2012/CH and K-11/2012/CH strains contain 2329aa and 4353aa, respectively. The amino acid identity identities among the of structural regions (VP0–VP3) are 90%–97%, and the non-structural regions (2A–3D) share 93%–100% amino acid identity with that of the S-1-HUN strain (Table 2). Compared with the K-4/2012/CH and K-11/2012/CH strains, the variant strain has a 30-animo acid deletion within the 2B protein. The amino acid identities among the structural regions (VP0–VP3) are 89%–97%, and the non-structural regions (2A–3D) share 90%–100% amino acid identity with that of the S-1-HUN strain (Table 2). The 2B amino acid sequence alignment for the 12 strains analyzed in this study and the eight strains from the GenBank database (K-30-HUN/2008 and S-1-HUN are Hungarian strains; others are Chinese strains) is shown in Figure 2A. Ten amino acid mutations were observed at positions 7, 11, 15, 28, 29, 30, 33, 37, 41, and 44. Though the function of the porcine kobuvirus 2B protein is not known, protein 2B has been shown to assume different functions in different kobuviruses [15].


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)

Comparison of the deduced protein amino acid sequences of the study strains and the reference strains. (A) Comparison of the deduced 2B protein amino acid sequences. An asterisk (*) indicates an amino acid substitution in the VP1 region; a dash (-) indicates an amino acid deletion in the variant strain; (B) Comparison of the deduced VP1 amino acid sequences. An asterisk (*) indicates no fewer than three amino acid substitutions within the VP1 region.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

viruses-05-02548-f002: Comparison of the deduced protein amino acid sequences of the study strains and the reference strains. (A) Comparison of the deduced 2B protein amino acid sequences. An asterisk (*) indicates an amino acid substitution in the VP1 region; a dash (-) indicates an amino acid deletion in the variant strain; (B) Comparison of the deduced VP1 amino acid sequences. An asterisk (*) indicates no fewer than three amino acid substitutions within the VP1 region.
Mentions: The structural and non-structural protein regions of the both K-4/2012/CH and K-11/2012/CH strains contain 2329aa and 4353aa, respectively. The amino acid identity identities among the of structural regions (VP0–VP3) are 90%–97%, and the non-structural regions (2A–3D) share 93%–100% amino acid identity with that of the S-1-HUN strain (Table 2). Compared with the K-4/2012/CH and K-11/2012/CH strains, the variant strain has a 30-animo acid deletion within the 2B protein. The amino acid identities among the structural regions (VP0–VP3) are 89%–97%, and the non-structural regions (2A–3D) share 90%–100% amino acid identity with that of the S-1-HUN strain (Table 2). The 2B amino acid sequence alignment for the 12 strains analyzed in this study and the eight strains from the GenBank database (K-30-HUN/2008 and S-1-HUN are Hungarian strains; others are Chinese strains) is shown in Figure 2A. Ten amino acid mutations were observed at positions 7, 11, 15, 28, 29, 30, 33, 37, 41, and 44. Though the function of the porcine kobuvirus 2B protein is not known, protein 2B has been shown to assume different functions in different kobuviruses [15].

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