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

Melcher, Ulrich, Rasmussen, Thomas Bruun, Boniotti, Maria Beatrice, Papetti, Alice, Grasland, Béatrice, Frossard, Jean-Pierre, Dastjerdi, Akbar, Hulst, Marcel, Hanke, Dennis, Pohlmann, Anne et al, Blome, Sandra, van der Poel, Wim H. M., Steinbach, Falko, Blanchard, Yannick, Lavazza, Antonio, Bøtner, Anette and Belsham, Graham J. (2018) Full-length genome sequences of porcine epidemic diarrhoea virus strain CV777; Use of NGS to analyse genomic and sub-genomic RNAs PLOS ONE, 13 (3), e0193682. e0193682-1.

Preview	Text Full-length genome sequences of porcine epidemic diarrhoea virus strain CV777.pdf - Version of Record Available under License Creative Commons Attribution. Download (2MB) | Preview
	Text (S1 Table. Missing sequences (i.e. zero coverage) in WBR sequence compared to the reference CV777 sequence (AF353511.1).) journal.pone.0193682.s001.docx - Supplemental Material Available under License Creative Commons Attribution. Download (13kB)
	Text (S2 Table. Homogenous nt differences in WBR CV777 sequence compared to reference CV777 sequence (in 100% of the NGS reads)) journal.pone.0193682.s002.docx - Supplemental Material Available under License Creative Commons Attribution. Download (13kB)
	Text (S3 Table. Heterogeneous sequence differences in WBR CV777 sequence compared to reference CV777 sequence (heterogeneity present in >33% and ≤50% of the NGS reads)) journal.pone.0193682.s003.docx - Supplemental Material Available under License Creative Commons Attribution. Download (13kB)
	Text (S4 Table. Number of read variants (with 100% identity) present in two independent Br1/87 RNA preparations from virus-infected cells made at 24h and 48h post infection (hpi)) journal.pone.0193682.s004.docx - Supplemental Material Available under License Creative Commons Attribution. Download (13kB)
	Text (S5 Table. Oligonucleotide primers used for the production of overlapping amplicons at IZSLER) journal.pone.0193682.s005.docx - Supplemental Material Available under License Creative Commons Attribution. Download (13kB)

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 from infected cells. It is clearly important to know the features of the specific sample of CV777 being used for experimental studies.

Item Type:	Article
Divisions :	Faculty of Health and Medical Sciences > School of Veterinary Medicine
Authors :	Name Email ORCID Melcher, Ulrich Rasmussen, Thomas Bruun Boniotti, Maria Beatrice Papetti, Alice Grasland, Béatrice Frossard, Jean-Pierre Dastjerdi, Akbar Hulst, Marcel Hanke, Dennis Pohlmann, Anne Blome, Sandra van der Poel, Wim H. M. Steinbach, Falko f.steinbach@surrey.ac.uk Blanchard, Yannick Lavazza, Antonio Bøtner, Anette Belsham, Graham J.
Date :	1 March 2018
DOI :	10.1371/journal.pone.0193682
Copyright Disclaimer :	© 2018 Rasmussen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Related URLs :	Dataset https://doi.org/10.1371/journal.pone.019... https://doi.org/10.1371/journal.pone.019... https://doi.org/10.1371/journal.pone.019... https://doi.org/10.1371/journal.pone.019...
Additional Information :	Note to S4 table: For each preparation the total collection of reads were mapped separately to the Br1/87 leader/TRS-L and the CV777 leader/TRS-L
Depositing User :	Clive Harris
Date Deposited :	12 Apr 2018 13:34
Last Modified :	16 Jan 2019 19:09
URI:	http://epubs.surrey.ac.uk/id/eprint/846205

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