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Adaptive trends of sequence compositional complexity over pandemic time in the SARS-CoV-2 coronavirus

View ORCID ProfileJosé L. Oliver, View ORCID ProfilePedro Bernaola-Galván, View ORCID ProfileFrancisco Perfectti, View ORCID ProfileCristina Gómez-Martín, View ORCID ProfileSilvia Castiglione, View ORCID ProfilePasuale Raia, View ORCID ProfileMiguel Verdú, View ORCID ProfileAndrés 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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Pasuale Raia
6Dipartimento di Scienze della Terra, dell’Ambiente e delle Risorse, Università di Napoli Federico II, 80126, Napoli, Italy
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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

During the spread of the COVID-19 pandemic, the SARS-CoV-2 coronavirus underwent mutation and recombination events that altered its genome compositional structure, thus providing an unprecedented opportunity to check an evolutionary process in real time. The mutation rate is known to be lower than expected for neutral evolution, suggesting purifying selection and convergent evolution. We begin by summarizing the compositional heterogeneity of each viral genome by computing its Sequence Compositional Complexity (SCC). To analyze the full range of SCC diversity, we select random samples of high-quality coronavirus genomes covering the full span of the pandemic. We then search for evolutionary trends that could inform us on the adaptive process of the virus to its human host by computing the phylogenetic ridge regression of SCC against time (i.e., the collection date of each viral isolate). In early samples, we find no statistical support for any trend in SCC values, although the viral genome appears to evolve faster than Brownian Motion (BM) expectation. However, in samples taken after the emergence of high fitness variants, and despite the brief time span elapsed, a driven decreasing trend for SCC and an increasing one for its absolute evolutionary rate are detected, pointing to a role for purifying selection in the evolution of SCC in the coronavirus. The higher fitness of variant genomes leads to adaptive trends of SCC over pandemic time in the coronavirus.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • The title and the abstract have been reworded. References have been updated.

  • 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 October 25, 2022.
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Adaptive trends of sequence compositional complexity over pandemic time in the SARS-CoV-2 coronavirus
José L. Oliver, Pedro Bernaola-Galván, Francisco Perfectti, Cristina Gómez-Martín, Silvia Castiglione, Pasuale Raia, Miguel Verdú, Andrés Moya
bioRxiv 2021.11.06.467547; doi: https://doi.org/10.1101/2021.11.06.467547
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Adaptive trends of sequence compositional complexity over pandemic time in the SARS-CoV-2 coronavirus
José L. Oliver, Pedro Bernaola-Galván, Francisco Perfectti, Cristina Gómez-Martín, Silvia Castiglione, Pasuale Raia, Miguel Verdú, Andrés Moya
bioRxiv 2021.11.06.467547; doi: https://doi.org/10.1101/2021.11.06.467547

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