TY - JOUR

T1 - Full-length genome sequences of porcine epidemic diarrhoea virus strain CV777; Use of NGS to analyse genomic and sub-genomic RNAs

AU - Rasmussen, Thomas Bruun

AU - Boniotti, Maria Beatrice

AU - Papetti, Alice

AU - Grasland, Béatrice

AU - Frossard, Jean-Pierre

AU - Dastjerdi, Akbar

AU - Hulst, Marcel

AU - Hanke, Dennis

AU - Pohlmann, Anne

AU - Blome, Sandra

AU - van der Poel, Wim H M

AU - Steinbach, Falko

AU - Blanchard, Yannick

AU - Lavazza, Antonio

AU - Bøtner, Anette

AU - Belsham, Graham J

PY - 2018

Y1 - 2018

N2 - 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.

AB - 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.

KW - Animals

KW - Base Sequence

KW - Coronavirus Infections/virology

KW - Evolution, Molecular

KW - Genome, Viral

KW - High-Throughput Nucleotide Sequencing/methods

KW - Open Reading Frames

KW - Phylogeny

KW - Point Mutation

KW - Porcine epidemic diarrhea virus/genetics

KW - RNA, Viral/chemistry

KW - Sequence Analysis, RNA/methods

KW - Sequence Deletion

KW - Swine

KW - Swine Diseases/virology

U2 - 10.1371/journal.pone.0193682

DO - 10.1371/journal.pone.0193682

M3 - Journal article

C2 - 29494671

VL - 13

SP - e0193682

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 3

ER -