About: Characterization of accessory genes in coronavirus genomes

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Characterization of accessory genes in coronavirus genomes
Creator	Mayer, Claudine Michel, Christian Poch, Olivier Thompson, Julie
source	BioRxiv
abstract	The Covid19 infection is caused by the SARS-CoV-2 virus, a novel member of the coronavirus (CoV) family. CoV genomes code for a ORF1a / ORF1ab polyprotein and four structural proteins widely studied as major drug targets. The genomes also contain a variable number of open reading frames (ORFs) coding for accessory proteins that are not essential for virus replication, but appear to have a role in pathogenesis. The accessory proteins have been less well characterized and are difficult to predict by classical bioinformatics methods. We propose a computational tool GOFIX to characterize potential ORFs in virus genomes. In particular, ORF coding potential is estimated by searching for enrichment in motifs of the X circular code, that is known to be over-represented in the reading frames of viral genes. We applied GOFIX to study the SARS-CoV-2 and related genomes including SARS-CoV and SARS-like viruses from bat, civet and pangolin hosts, focusing on the accessory proteins. Our analysis provides evidence supporting the presence of overlapping ORFs 7b, 9b and 9c in all the genomes and thus helps to resolve some differences in current genome annotations. In contrast, we predict that ORF3b is not functional in all genomes. Novel putative ORFs were also predicted, including a truncated form of the ORF10 previously identified in SARS-CoV-2 and a little known ORF overlapping the Spike protein in Civet-CoV and SARS-CoV. Our findings contribute to characterizing sequence properties of accessory genes of SARS coronaviruses, and especially the newly acquired genes making use of overlapping reading frames.
has issue date	2020-05-28(xsd:dateTime)
bibo:doi	10.1101/2020.05.26.118208
has license	biorxiv
sha1sum (hex)	87c21297fa66a066a4e6c591e533311b84bcea55
schema:url	https://doi.org/10.1101/2020.05.26.118208
resource representing a document's title	Characterization of accessory genes in coronavirus genomes
schema:publication	bioRxiv
resource representing a document's body	covid:87c21297fa66a066a4e6c591e533311b84bcea55#body_text
is schema:about of	named entity 'USE OF' named entity 'POLYPROTEIN' named entity 'EVIDENCE' named entity 'SARS-COV' named entity 'NUMBER OF' »more»

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