Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2
The inflation of SARS-CoV-2 lineages with a high number of accumulated mutations (such as the recent case of Omicron) has risen concerns about the evolutionary capacity of this virus. Here, we propose a computational study to examine non-synonymous mutations gathered within genomes of SARS-CoV-2 fro...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037022003312 |
| _version_ | 1797978173895344128 |
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| author | Ruba Al Khalaf Anna Bernasconi Pietro Pinoli Stefano Ceri |
| author_facet | Ruba Al Khalaf Anna Bernasconi Pietro Pinoli Stefano Ceri |
| author_sort | Ruba Al Khalaf |
| collection | DOAJ |
| description | The inflation of SARS-CoV-2 lineages with a high number of accumulated mutations (such as the recent case of Omicron) has risen concerns about the evolutionary capacity of this virus. Here, we propose a computational study to examine non-synonymous mutations gathered within genomes of SARS-CoV-2 from the beginning of the pandemic until February 2022. We provide both qualitative and quantitative descriptions of such corpus, focusing on statistically significant co-occurring and mutually exclusive mutations within single genomes. Then, we examine in depth the distributions of mutations over defined lineages and compare those of frequently co-occurring mutation pairs. Based on this comparison, we study mutations’ convergence/divergence on the phylogenetic tree. As a result, we identify 1,818 co-occurring pairs of non-synonymous mutations showing at least one event of convergent evolution and 6,625 co-occurring pairs with at least one event of divergent evolution. Notable examples of both types are shown by means of a tree-based representation of lineages, visually capturing mutations’ behaviors. Our method confirms several well-known cases; moreover, the provided evidence suggests that our workflow can explain aspects of the future mutational evolution of SARS-CoV-2. |
| first_indexed | 2024-04-11T05:19:51Z |
| format | Article |
| id | doaj.art-bcba2c8f88474215acdf32b07d2cb246 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:19:51Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-bcba2c8f88474215acdf32b07d2cb2462022-12-24T04:53:43ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-012042384250Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2Ruba Al Khalaf0Anna Bernasconi1Pietro Pinoli2Stefano Ceri3Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, ItalyDipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy; Corresponding author.Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, ItalyDipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, ItalyThe inflation of SARS-CoV-2 lineages with a high number of accumulated mutations (such as the recent case of Omicron) has risen concerns about the evolutionary capacity of this virus. Here, we propose a computational study to examine non-synonymous mutations gathered within genomes of SARS-CoV-2 from the beginning of the pandemic until February 2022. We provide both qualitative and quantitative descriptions of such corpus, focusing on statistically significant co-occurring and mutually exclusive mutations within single genomes. Then, we examine in depth the distributions of mutations over defined lineages and compare those of frequently co-occurring mutation pairs. Based on this comparison, we study mutations’ convergence/divergence on the phylogenetic tree. As a result, we identify 1,818 co-occurring pairs of non-synonymous mutations showing at least one event of convergent evolution and 6,625 co-occurring pairs with at least one event of divergent evolution. Notable examples of both types are shown by means of a tree-based representation of lineages, visually capturing mutations’ behaviors. Our method confirms several well-known cases; moreover, the provided evidence suggests that our workflow can explain aspects of the future mutational evolution of SARS-CoV-2.http://www.sciencedirect.com/science/article/pii/S2001037022003312SARS-CoV-2Co-occurring mutationsMutually exclusive mutationsConvergent evolutionDivergent evolutionStatistical testing |
| spellingShingle | Ruba Al Khalaf Anna Bernasconi Pietro Pinoli Stefano Ceri Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2 Computational and Structural Biotechnology Journal SARS-CoV-2 Co-occurring mutations Mutually exclusive mutations Convergent evolution Divergent evolution Statistical testing |
| title | Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2 |
| title_full | Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2 |
| title_fullStr | Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2 |
| title_full_unstemmed | Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2 |
| title_short | Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2 |
| title_sort | analysis of co occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in sars cov 2 |
| topic | SARS-CoV-2 Co-occurring mutations Mutually exclusive mutations Convergent evolution Divergent evolution Statistical testing |
| url | http://www.sciencedirect.com/science/article/pii/S2001037022003312 |
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