Prediction of two novel overlapping ORFs in the genome of SARS-CoV-2.
Codon usage
Membrane protein
Multivariate statistics
Overlapping reading frame
Selection pressure
Spike protein
Virus evolution
Journal
Virology
ISSN: 1096-0341
Titre abrégé: Virology
Pays: United States
ID NLM: 0110674
Informations de publication
Date de publication:
10 2021
10 2021
Historique:
received:
15
03
2021
revised:
21
07
2021
accepted:
21
07
2021
pubmed:
3
8
2021
medline:
14
9
2021
entrez:
2
8
2021
Statut:
ppublish
Résumé
Six candidate overlapping genes have been detected in SARS-CoV-2, yet current methods struggle to detect overlapping genes that recently originated. However, such genes might encode proteins beneficial to the virus, and provide a model system to understand gene birth. To complement existing detection methods, I first demonstrated that selection pressure to avoid stop codons in alternative reading frames is a driving force in the origin and retention of overlapping genes. I then built a detection method, CodScr, based on this selection pressure. Finally, I combined CodScr with methods that detect other properties of overlapping genes, such as a biased nucleotide and amino acid composition. I detected two novel ORFs (ORF-Sh and ORF-Mh), overlapping the spike and membrane genes respectively, which are under selection pressure and may be beneficial to SARS-CoV-2. ORF-Sh and ORF-Mh are present, as ORF uninterrupted by stop codons, in 100% and 95% of the SARS-CoV-2 genomes, respectively.
Identifiants
pubmed: 34339929
pii: S0042-6822(21)00159-8
doi: 10.1016/j.virol.2021.07.011
pmc: PMC8317007
pii:
doi:
Substances chimiques
Spike Glycoprotein, Coronavirus
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
149-157Informations de copyright
Copyright © 2021 Elsevier Inc. All rights reserved.
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