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...
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Autor*in:	Ruba Al Khalaf [verfasserIn] Anna Bernasconi [verfasserIn] Pietro Pinoli [verfasserIn] Stefano Ceri [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2022

Schlagwörter:	SARS-CoV-2 Co-occurring mutations Mutually exclusive mutations Convergent evolution Divergent evolution Statistical testing

Übergeordnetes Werk:	In: Computational and Structural Biotechnology Journal - Elsevier, 2013, 20(2022), Seite 4238-4250
Übergeordnetes Werk:	volume:20 ; year:2022 ; pages:4238-4250

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1016/j.csbj.2022.07.051

Katalog-ID:	DOAJ020831803

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520			\|a 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.
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callnumber-first	T - Technology
author	Ruba Al Khalaf
spellingShingle	Ruba Al Khalaf misc TP248.13-248.65 misc SARS-CoV-2 misc Co-occurring mutations misc Mutually exclusive mutations misc Convergent evolution misc Divergent evolution misc Statistical testing misc Biotechnology Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2
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topic_title	TP248.13-248.65 Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2 SARS-CoV-2 Co-occurring mutations Mutually exclusive mutations Convergent evolution Divergent evolution Statistical testing
topic	misc TP248.13-248.65 misc SARS-CoV-2 misc Co-occurring mutations misc Mutually exclusive mutations misc Convergent evolution misc Divergent evolution misc Statistical testing misc Biotechnology
topic_unstemmed	misc TP248.13-248.65 misc SARS-CoV-2 misc Co-occurring mutations misc Mutually exclusive mutations misc Convergent evolution misc Divergent evolution misc Statistical testing misc Biotechnology
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title	Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2
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title_full	Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2
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title_sort	analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in sars-cov-2
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title_auth	Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2
abstract	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.
abstractGer	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.
abstract_unstemmed	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.
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title_short	Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2
url	https://doi.org/10.1016/j.csbj.2022.07.051 https://doaj.org/article/bcba2c8f88474215acdf32b07d2cb246 http://www.sciencedirect.com/science/article/pii/S2001037022003312 https://doaj.org/toc/2001-0370
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Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2

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