Prediction of two novel overlapping ORFs in the genome of SARS-CoV-2
Copyright © 2021 Elsevier Inc. All rights reserved..
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.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2021 |
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| Erschienen: |
2021 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:562 |
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| Enthalten in: |
Virology - 562(2021) vom: 01. Okt., Seite 149-157 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Pavesi, Angelo [VerfasserIn] |
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| Links: |
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| Anmerkungen: |
Date Completed 13.09.2021 Date Revised 17.12.2022 published: Print-Electronic Citation Status MEDLINE |
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| doi: |
10.1016/j.virol.2021.07.011 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| 500 | |a Date Revised 17.12.2022 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2021 Elsevier Inc. All rights reserved. | ||
| 520 | |a 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 | ||
| 650 | 4 | |a Journal Article | |
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| 650 | 4 | |a Codon usage | |
| 650 | 4 | |a Membrane protein | |
| 650 | 4 | |a Multivariate statistics | |
| 650 | 4 | |a Overlapping reading frame | |
| 650 | 4 | |a Selection pressure | |
| 650 | 4 | |a Spike protein | |
| 650 | 4 | |a Virus evolution | |
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