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Prediction of two novel overlapping ORFs in the genome of SARS-CoV-2
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 detectio...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier Inc.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317007/ https://www.ncbi.nlm.nih.gov/pubmed/34339929 http://dx.doi.org/10.1016/j.virol.2021.07.011 |
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author | Pavesi, Angelo |
author_facet | Pavesi, Angelo |
author_sort | Pavesi, Angelo |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8317007 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Elsevier Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-83170072021-07-28 Prediction of two novel overlapping ORFs in the genome of SARS-CoV-2 Pavesi, Angelo Virology Article 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. Elsevier Inc. 2021-10 2021-07-28 /pmc/articles/PMC8317007/ /pubmed/34339929 http://dx.doi.org/10.1016/j.virol.2021.07.011 Text en © 2021 Elsevier Inc. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. |
spellingShingle | Article Pavesi, Angelo Prediction of two novel overlapping ORFs in the genome of SARS-CoV-2 |
title | Prediction of two novel overlapping ORFs in the genome of SARS-CoV-2 |
title_full | Prediction of two novel overlapping ORFs in the genome of SARS-CoV-2 |
title_fullStr | Prediction of two novel overlapping ORFs in the genome of SARS-CoV-2 |
title_full_unstemmed | Prediction of two novel overlapping ORFs in the genome of SARS-CoV-2 |
title_short | Prediction of two novel overlapping ORFs in the genome of SARS-CoV-2 |
title_sort | prediction of two novel overlapping orfs in the genome of sars-cov-2 |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317007/ https://www.ncbi.nlm.nih.gov/pubmed/34339929 http://dx.doi.org/10.1016/j.virol.2021.07.011 |
work_keys_str_mv | AT pavesiangelo predictionoftwonoveloverlappingorfsinthegenomeofsarscov2 |