Archives of Virology

, Volume 163, Issue 6, pp 1439–1447 | Cite as

Detection and genetic characterization of bovine kobuvirus from calves in Egypt

  • Fakry F. Mohamed
  • Shimaa M. G. Mansour
  • Ahmed Orabi
  • Iman E. El-Araby
  • Terry Fei Fan Ng
  • Sunil K. Mor
  • Sagar M. Goyal
Original Article
  • 377 Downloads

Abstract

Kobuviruses are small non-enveloped RNA viruses that probably cause diarrhea in cattle and swine. Since its discovery in 2003, few studies have addressed bovine kobuvirus (BKoV; a species of Aichivirus B) infections. BKoV has been reported in Europe, Asia, and South America, suggesting a worldwide distribution. To investigate the presence of BKoV in Egypt, 36 fecal specimens from diarrheic calves in two different Egyptian provinces (Cairo and Sharkia) were screened by RT-PCR and 24 (66.7%) were found positive for BKoV. RNA from one of the positive samples (BKoV/Egy-1/KY407744) was subjected to next-generation sequencing to determine the complete BKoV genome sequence. When compared to the only recorded BKoV genome sequence (BKoV/U-1/AB084788), the studied strain showed 94 amino acid (aa) substitutions through its entire polyprotein (2463 aa), one nucleotide (nt) insertion and one nt deletion in the 2B gene and 4-nt deletions in the UTRs (2 each). Additionally, five VP1 and seven 3D sequences were obtained from other samples by using RT-PCR and Sanger sequencing. A discrepancy in the phylogenetic topography of VP1 and 3D was observed, where the Egyptian VP1 sequences were classified as a distinct cluster within the proposed lineage 1 (genotype A), which also contained strains from the UK, Brazil, and Japan. While, the 3D sequences from Cairo were related to those of Chinese strains unlike Sharkia ones that were more closer to Korean  strains. To the best of our knowledge, this is the first detection and genomic characterization of BKoV in Egypt or indeed Africa.

Notes

Acknowledgements

We thank Dr. Hany Abdalla (Department of Theriogenology, Faculty of Veterinary Medicine, Zagazig University) for help in collection of samples and for providing historical data.

Compliance with ethical standards

Conflict of interest

Authors confirm that this article content has no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

705_2018_3758_MOESM1_ESM.jpg (65 kb)
Supplementary material 1 Fig. S1 A neighbor-joining phylogenetic tree of the complete coding region of BKoV/Egy-1/KY407744 as compared to other picornaviruses. Bootstrap values (> 50%) are shown above the branches. The sequence of our strain is indicated by a solid circle. BKoV, bovine kobuvirus; PKoV, porcine kobuvirus (JPEG 65 kb)
705_2018_3758_MOESM2_ESM.jpg (389 kb)
Supplementary material 2 Fig. S2 A neighbor-joining phylogenetic tree of BKoV VP1 sequences (801 bp) showing the new lineage 5 (genotype E); marked in red. Bootstrap values of >50% are shown above the branches. BKoV- bovine kobuvirus; PKoV- porcine kobuvirus (JPEG 389 kb)
705_2018_3758_MOESM3_ESM.doc (40 kb)
Supplementary material 3 (DOC 40 kb)

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Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2018

Authors and Affiliations

  • Fakry F. Mohamed
    • 1
    • 2
  • Shimaa M. G. Mansour
    • 1
  • Ahmed Orabi
    • 1
  • Iman E. El-Araby
    • 3
  • Terry Fei Fan Ng
    • 4
  • Sunil K. Mor
    • 2
  • Sagar M. Goyal
    • 2
  1. 1.Department of Virology, Faculty of Veterinary MedicineZagazig UniversityZagazigEgypt
  2. 2.Department of Veterinary Population Medicine and Veterinary Diagnostic LaboratoryUniversity of MinnesotaSt. PaulUSA
  3. 3.Department of Animal Wealth Development, Faculty of Veterinary MedicineZagazig UniversityZagazigEgypt
  4. 4.College of Veterinary MedicineUniversity of Georgia AthensAthensUSA

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