Advanced search
1 file | 2.14 MB

Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus

Author
Organization
Abstract
Enteric diseases in swine are often caused by different pathogens and thus metagenomics are a useful tool for diagnostics. The capacities of nanopore sequencing for viral diagnostics were investigated here. First, cell culture-grown porcine epidemic diarrhea virus and rotavirus A were pooled and sequenced on a MinION. Reads were already detected at 7 seconds after start of sequencing, resulting in high sequencing depths (19.2 to 103.5X) after 3 h. Next, diarrheic feces of a one-week-old piglet was analyzed. Almost all reads (99%) belonged to bacteriophages, which may have reshaped the piglet's microbiome. Contigs matched Bacteroides, Escherichia and Enterococcus phages. Moreover, porcine kobuvirus was discovered in the feces for the first time in Belgium. Suckling piglets shed kobuvirus from one week of age, but an association between peak of viral shedding (10(6.42)-10(7.01) copies/swab) and diarrheic signs was not observed during a follow-up study. Retrospective analysis showed the widespread (n = 25, 56.8% positive) of genetically moderately related kobuviruses among Belgian diarrheic piglets. MinION enables rapid detection of enteric viruses. Such new methodologies will change diagnostics, but more extensive validations should be conducted. The true enteric pathogenicity of porcine kobuvirus should be questioned, while its subclinical importance cannot be excluded.
Keywords
GROUP-A ROTAVIRUSES, PIG GROUP-A, FECAL VIROME, MOLECULAR CHARACTERIZATION, ASYMPTOMATIC PIGS, GENETIC DIVERSITY, CLINICAL-SAMPLES, EAST-AFRICA, REAL-TIME, DIARRHEA

Downloads

  • s41598-018-28180-9.pdf
    • full text
    • |
    • open access
    • |
    • PDF
    • |
    • 2.14 MB

Citation

Please use this url to cite or link to this publication:

Chicago
Theuns, Sebastiaan, Bert Vanmechelen, Quinten Bernaert, Ward Deboutte, Marilou Vandenhole, Leen Beller, Jelle Matthijnssens, Piet Maes, and Hans Nauwynck. 2018. “Nanopore Sequencing as a Revolutionary Diagnostic Tool for Porcine Viral Enteric Disease Complexes Identifies Porcine Kobuvirus as an Important Enteric Virus.” Scientific Reports 8.
APA
Theuns, S., Vanmechelen, B., Bernaert, Q., Deboutte, W., Vandenhole, M., Beller, L., Matthijnssens, J., et al. (2018). Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus. SCIENTIFIC REPORTS, 8.
Vancouver
1.
Theuns S, Vanmechelen B, Bernaert Q, Deboutte W, Vandenhole M, Beller L, et al. Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus. SCIENTIFIC REPORTS. 2018;8.
MLA
Theuns, Sebastiaan, Bert Vanmechelen, Quinten Bernaert, et al. “Nanopore Sequencing as a Revolutionary Diagnostic Tool for Porcine Viral Enteric Disease Complexes Identifies Porcine Kobuvirus as an Important Enteric Virus.” SCIENTIFIC REPORTS 8 (2018): n. pag. Print.
@article{8571274,
  abstract     = {Enteric diseases in swine are often caused by different pathogens and thus metagenomics are a useful tool for diagnostics. The capacities of nanopore sequencing for viral diagnostics were investigated here. First, cell culture-grown porcine epidemic diarrhea virus and rotavirus A were pooled and sequenced on a MinION. Reads were already detected at 7 seconds after start of sequencing, resulting in high sequencing depths (19.2 to 103.5X) after 3 h. Next, diarrheic feces of a one-week-old piglet was analyzed. Almost all reads (99\%) belonged to bacteriophages, which may have reshaped the piglet's microbiome. Contigs matched Bacteroides, Escherichia and Enterococcus phages. Moreover, porcine kobuvirus was discovered in the feces for the first time in Belgium. Suckling piglets shed kobuvirus from one week of age, but an association between peak of viral shedding (10(6.42)-10(7.01) copies/swab) and diarrheic signs was not observed during a follow-up study. Retrospective analysis showed the widespread (n = 25, 56.8\% positive) of genetically moderately related kobuviruses among Belgian diarrheic piglets. MinION enables rapid detection of enteric viruses. Such new methodologies will change diagnostics, but more extensive validations should be conducted. The true enteric pathogenicity of porcine kobuvirus should be questioned, while its subclinical importance cannot be excluded.},
  articleno    = {9830},
  author       = {Theuns, Sebastiaan and Vanmechelen, Bert and Bernaert, Quinten and Deboutte, Ward and Vandenhole, Marilou and Beller, Leen and Matthijnssens, Jelle and Maes, Piet and Nauwynck, Hans},
  issn         = {2045-2322},
  journal      = {SCIENTIFIC REPORTS},
  keyword      = {GROUP-A ROTAVIRUSES,PIG GROUP-A,FECAL VIROME,MOLECULAR CHARACTERIZATION,ASYMPTOMATIC PIGS,GENETIC DIVERSITY,CLINICAL-SAMPLES,EAST-AFRICA,REAL-TIME,DIARRHEA},
  language     = {eng},
  pages        = {13},
  title        = {Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus},
  url          = {http://dx.doi.org/10.1038/s41598-018-28180-9},
  volume       = {8},
  year         = {2018},
}

Altmetric
View in Altmetric
Web of Science
Times cited: