Main menu

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


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 diarrhoea 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 faeces of a one-week-old piglet was analysed. Almost all reads (99%) belonged to bacteriophages, which may have reshaped the piglet’s microbiome. Contigs matched Bacteroides, Eascherichia and Enterococcus phages. Moreover, porcine kobuvirus was discovered in the faeces for the first time in Belgium. Suckling piglets shed kobuvirus from one week of age, but an association between peak of viral shedding (106.42–107.01 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.

‘…the first reads matching porcine epidemic diarrhea virus (PEDV) and rotavirus a (RVA) were generated respectively after 7 and 24 seconds of sequencing’

Theuns, S. et al

Authors: Sebastiaan Theuns, Bert Vanmechelen, Quinten Bernaert, Ward Deboutte, Marilou Vandenhole, Leen Beller, Jelle Matthijnssens, Piet Maes, Hans J. Nauwynck

入门指南

购买 MinION 启动包 Nanopore 商城 测序服务提供商 全球代理商

联系我们

Intellectual property Cookie policy Corporate reporting Privacy policy Terms & conditions Accessibility

关于 Oxford Nanopore

Contact us 领导团队 媒体资源和联系方式 投资者 在 Oxford Nanopore 工作 BSI 27001 accreditationBSI 90001 accreditationBSI mark of trust
Chinese flag