Full-length genome sequences of porcine epidemic diarrhoea virus strain CV777; Use of NGS to analyse genomic and sub-genomic RNAs

Research output: Contribution to journalJournal articleResearchpeer-review

  • Thomas Bruun Rasmussen
  • Maria Beatrice Boniotti
  • Alice Papetti
  • Béatrice Grasland
  • Jean-Pierre Frossard
  • Akbar Dastjerdi
  • Marcel Hulst
  • Dennis Hanke
  • Anne Pohlmann
  • Sandra Blome
  • Wim H M van der Poel
  • Falko Steinbach
  • Yannick Blanchard
  • Antonio Lavazza
  • Anette Bøtner
  • Belsham, Graham John

Porcine epidemic diarrhoea virus, strain CV777, was initially characterized in 1978 as the causative agent of a disease first identified in the UK in 1971. This coronavirus has been widely distributed among laboratories and has been passaged both within pigs and in cell culture. To determine the variability between different stocks of the PEDV strain CV777, sequencing of the full-length genome (ca. 28kb) has been performed in 6 different laboratories, using different protocols. Not surprisingly, each of the different full genome sequences were distinct from each other and from the reference sequence (Accession number AF353511) but they are >99% identical. Unique and shared differences between sequences were identified. The coding region for the surface-exposed spike protein showed the highest proportion of variability including both point mutations and small deletions. The predicted expression of the ORF3 gene product was more dramatically affected in three different variants of this virus through either loss of the initiation codon or gain of a premature termination codon. The genome of one isolate had a substantially rearranged 5´-terminal sequence. This rearrangement was validated through the analysis of sub-genomic mRNAs from infected cells. It is clearly important to know the features of the specific sample of CV777 being used for experimental studies.

Original languageEnglish
JournalPLoS ONE
Issue number3
Pages (from-to)e0193682
Publication statusPublished - 2018
Externally publishedYes

    Research areas

  • Animals, Base Sequence, Coronavirus Infections/virology, Evolution, Molecular, Genome, Viral, High-Throughput Nucleotide Sequencing/methods, Open Reading Frames, Phylogeny, Point Mutation, Porcine epidemic diarrhea virus/genetics, RNA, Viral/chemistry, Sequence Analysis, RNA/methods, Sequence Deletion, Swine, Swine Diseases/virology

ID: 257914647