Characterization of accessory genes in coronavirus genomes.
Virol J
; 17(1): 131, 2020 08 27.
Article
in English
| MEDLINE | ID: covidwho-733041
ABSTRACT
BACKGROUND:
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.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.RESULTS:
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.CONCLUSIONS:
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.Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Open Reading Frames
/
Genome, Viral
/
Severe acute respiratory syndrome-related coronavirus
/
Viral Regulatory and Accessory Proteins
/
Betacoronavirus
Type of study:
Prognostic study
Limits:
Animals
/
Humans
Language:
English
Journal:
Virol J
Journal subject:
Virology
Year:
2020
Document Type:
Article
Affiliation country:
S12985-020-01402-1
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