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 -