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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 , 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.

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[img] Text (S1 Table. Missing sequences (i.e. zero coverage) in WBR sequence compared to the reference CV777 sequence (AF353511.1).)
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[img] Text (S2 Table. Homogenous nt differences in WBR CV777 sequence compared to reference CV777 sequence (in 100% of the NGS reads))
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[img] 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))
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[img] 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))
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[img] Text (S5 Table. Oligonucleotide primers used for the production of overlapping amplicons at IZSLER)
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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 :
NameEmailORCID
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, Falkof.steinbach@surrey.ac.uk
Blanchard, Yannick
Lavazza, Antonio
Bøtner, Anette
Belsham, Graham J.
Date : 1 March 2018
Identification Number : 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 :
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 : 12 Apr 2018 13:35
URI: http://epubs.surrey.ac.uk/id/eprint/846205

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