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

PloS One
Thomas Bruun RasmussenGraham J Belsham

Abstract

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 fr...Continue Reading

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Citations

Sep 29, 2020·Journal of Veterinary Research·Katarzyna Domańska-BlicharzBeata Cuvelier-Mizak
Jan 15, 2020·Journal of Veterinary Research·Marta Antas, Grzegorz Woźniakowski

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Datasets Mentioned

BETA
AF353511

Methods Mentioned

BETA
PCR
RNA-Seq
Chip

Software Mentioned

Velvet
DNASTAR
SeqMan Pro
kmergenie
Mauve
Genome Sequencer
Mira
fold
SeqMan
Trimmomatic

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