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Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes
BACKGROUND: SARS-CoV-2 is a novel coronavirus that causes COVID-19 infection, with a closest known relative found in bats. For this virus, hundreds of genomes have been sequenced. This data provides insights into SARS-CoV-2 adaptations, determinants of pathogenicity and mutation patterns. A comparis...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7394058/ https://www.ncbi.nlm.nih.gov/pubmed/33194341 http://dx.doi.org/10.7717/peerj.9648 |
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author | Panchin, Alexander Y. Panchin, Yuri V. |
author_facet | Panchin, Alexander Y. Panchin, Yuri V. |
author_sort | Panchin, Alexander Y. |
collection | PubMed |
description | BACKGROUND: SARS-CoV-2 is a novel coronavirus that causes COVID-19 infection, with a closest known relative found in bats. For this virus, hundreds of genomes have been sequenced. This data provides insights into SARS-CoV-2 adaptations, determinants of pathogenicity and mutation patterns. A comparison between patterns of mutations that occurred before and after SARS-CoV-2 jumped to human hosts may reveal important evolutionary consequences of zoonotic transmission. METHODS: We used publically available complete genomes of SARS-CoV-2 to calculate relative frequencies of single nucleotide variations. These frequencies were compared with relative substitutions frequencies between SARS-CoV-2 and related animal coronaviruses. A similar analysis was performed for human coronaviruses SARS-CoV and HKU1. RESULTS: We found a 9-fold excess of G–U transversions among SARS-CoV-2 mutations over relative substitution frequencies between SARS-CoV-2 and a close relative coronavirus from bats (RaTG13). This suggests that mutation patterns of SARS-CoV-2 have changed after transmission to humans. The excess of G–U transversions was much smaller in a similar analysis for SARS-CoV and non-existent for HKU1. Remarkably, we did not find a similar excess of complementary C–A mutations in SARS-CoV-2. We discuss possible explanations for these observations. |
format | Online Article Text |
id | pubmed-7394058 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-73940582020-11-12 Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes Panchin, Alexander Y. Panchin, Yuri V. PeerJ Bioinformatics BACKGROUND: SARS-CoV-2 is a novel coronavirus that causes COVID-19 infection, with a closest known relative found in bats. For this virus, hundreds of genomes have been sequenced. This data provides insights into SARS-CoV-2 adaptations, determinants of pathogenicity and mutation patterns. A comparison between patterns of mutations that occurred before and after SARS-CoV-2 jumped to human hosts may reveal important evolutionary consequences of zoonotic transmission. METHODS: We used publically available complete genomes of SARS-CoV-2 to calculate relative frequencies of single nucleotide variations. These frequencies were compared with relative substitutions frequencies between SARS-CoV-2 and related animal coronaviruses. A similar analysis was performed for human coronaviruses SARS-CoV and HKU1. RESULTS: We found a 9-fold excess of G–U transversions among SARS-CoV-2 mutations over relative substitution frequencies between SARS-CoV-2 and a close relative coronavirus from bats (RaTG13). This suggests that mutation patterns of SARS-CoV-2 have changed after transmission to humans. The excess of G–U transversions was much smaller in a similar analysis for SARS-CoV and non-existent for HKU1. Remarkably, we did not find a similar excess of complementary C–A mutations in SARS-CoV-2. We discuss possible explanations for these observations. PeerJ Inc. 2020-07-28 /pmc/articles/PMC7394058/ /pubmed/33194341 http://dx.doi.org/10.7717/peerj.9648 Text en © 2020 Panchin and Panchin https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Bioinformatics Panchin, Alexander Y. Panchin, Yuri V. Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes |
title | Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes |
title_full | Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes |
title_fullStr | Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes |
title_full_unstemmed | Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes |
title_short | Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes |
title_sort | excessive g–u transversions in novel allele variants in sars-cov-2 genomes |
topic | Bioinformatics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7394058/ https://www.ncbi.nlm.nih.gov/pubmed/33194341 http://dx.doi.org/10.7717/peerj.9648 |
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