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The emergence of high-fitness variants accelerates the decay of genome heterogeneity in the coronavirus

View ORCID ProfileJosé L. Oliver, Pedro Bernaola-Galván, Francisco Perfectti, Cristina Gómez-Martín, View ORCID ProfileSilvia Castiglione, View ORCID ProfilePasquale Raia, Miguel Verdú, Andrés Moya
doi: https://doi.org/10.1101/2021.11.06.467547
José L. Oliver
1Department of Genetics, Faculty of Sciences, University of Granada, 18071, Granada, Spain
2Laboratory of Bioinformatics, Institute of Biotechnology, Center of Biomedical Research, 18100, Granada, Spain
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  • For correspondence: oliver@ugr.es Miguel.Verdu@ext.uv.es Andres.Moya@uv.es
Pedro Bernaola-Galván
3Department of Applied Physics II and Institute Carlos I for Theoretical and Computational Physics, University of Málaga, 29071, Málaga, Spain
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Francisco Perfectti
1Department of Genetics, Faculty of Sciences, University of Granada, 18071, Granada, Spain
4Research Unit Modeling Nature, Universidad de Granada, 18071 Granada, Spain
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Cristina Gómez-Martín
1Department of Genetics, Faculty of Sciences, University of Granada, 18071, Granada, Spain
2Laboratory of Bioinformatics, Institute of Biotechnology, Center of Biomedical Research, 18100, Granada, Spain
5Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, Amsterdam, Netherlands
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Silvia Castiglione
6Dipartimento di Scienze della Terra, dell’Ambiente e delle Risorse, Università di Napoli Federico II, 80126, Napoli, Italy
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Pasquale Raia
6Dipartimento di Scienze della Terra, dell’Ambiente e delle Risorse, Università di Napoli Federico II, 80126, Napoli, Italy
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  • ORCID record for Pasquale Raia
Miguel Verdú
7Centro de Investigaciones sobre Desertificación, Consejo Superior de Investigaciones Científicas (CSIC), University of València and Generalitat Valenciana, 46113, Valencia, Spain
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  • For correspondence: oliver@ugr.es Miguel.Verdu@ext.uv.es Andres.Moya@uv.es
Andrés Moya
8Institute of Integrative Systems Biology (I2Sysbio), University of València and Consejo Superior de Investigaciones Científicas (CSIC), 46980, Valencia, Spain
9Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), 46020, Valencia, Spain
10CIBER in Epidemiology and Public Health, 28029, Madrid, Spain
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  • For correspondence: oliver@ugr.es Miguel.Verdu@ext.uv.es Andres.Moya@uv.es
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Abstract

Since the outbreak of the COVID-19 pandemic, the SARS-CoV-2 coronavirus accumulated an important amount of genome compositional heterogeneity through mutation and recombination, which can be summarized by means of a measure of Sequence Compositional Complexity (SCC). To test evolutionary trends that could inform us on the adaptive process of the virus to its human host, we compute SCC in high-quality coronavirus genomes from across the globe, covering the full span of the pandemic. By using phylogenetic ridge regression, we find trends for SCC in the short time-span of SARS-CoV-2 pandemic expansion. In early samples, we find no statistical support for any trend in SCC values over time, although the virus genome appears to evolve faster than Brownian Motion expectation. However, in samples taken after the emergence of Variants of Concern with higher transmissibility, and controlling for phylogenetic and sampling effects, we detect a declining trend for SCC and an increasing one for its absolute evolutionary rate. This means that the decay in SCC itself accelerated over time, and that increasing fitness of variant genomes lead to a reduction of their genome sequence heterogeneity. Therefore, our work shows that phylogenetic trends, typical of macroevolutionary time scales, can be also revealed on the shorter time spans typical of viral genomes.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • E-mails: José L. Oliver, oliver{at}ugr.es

    Pedro Bernaola-Galván, rick{at}uma.es

    Francisco Perfectti, fperfect{at}ugr.es

    Cristina Gómez Martín, c.a.gomezmartin{at}amsterdamumc.nl

    Silvia Castiglione, silviacastiglione2{at}gmail.com

    Pasquale Raia, pasquale.raia{at}unina.it

    Miguel Verdú, Miguel.Verdu{at}ext.uv.es

    Andrés Moya, Andres.Moya{at}uv.es

  • Updated authors list

  • https://zenodo.org/record/6844917

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted August 16, 2022.
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The emergence of high-fitness variants accelerates the decay of genome heterogeneity in the coronavirus
José L. Oliver, Pedro Bernaola-Galván, Francisco Perfectti, Cristina Gómez-Martín, Silvia Castiglione, Pasquale Raia, Miguel Verdú, Andrés Moya
bioRxiv 2021.11.06.467547; doi: https://doi.org/10.1101/2021.11.06.467547
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The emergence of high-fitness variants accelerates the decay of genome heterogeneity in the coronavirus
José L. Oliver, Pedro Bernaola-Galván, Francisco Perfectti, Cristina Gómez-Martín, Silvia Castiglione, Pasquale Raia, Miguel Verdú, Andrés Moya
bioRxiv 2021.11.06.467547; doi: https://doi.org/10.1101/2021.11.06.467547

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