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Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2

Nash D. Rochman, Yuri I. Wolf, Guilhem Faure, Feng Zhang, View ORCID ProfileEugene V. Koonin
doi: https://doi.org/10.1101/2020.10.12.336644
Nash D. Rochman
1National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
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  • For correspondence: nash.rochman@nih.gov koonin@ncbi.nlm.nih.gov
Yuri I. Wolf
1National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
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Guilhem Faure
2Broad Institute of MIT and Harvard, Cambridge, MA 02142
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Feng Zhang
2Broad Institute of MIT and Harvard, Cambridge, MA 02142
3Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
4McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
5Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
6Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
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Eugene V. Koonin
1National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
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  • ORCID record for Eugene V. Koonin
  • For correspondence: nash.rochman@nih.gov koonin@ncbi.nlm.nih.gov
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Abstract

Unprecedented sequencing efforts have, as of October 2020, produced nearly 200,000 genomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19. Understanding the trends in SARS-CoV-2 evolution is paramount to control the pandemic, but analysis of this enormous dataset is a major challenge. We show that the ongoing evolution of SARS-CoV-2 over the course of the pandemic is characterized primarily by purifying selection but a small set of sites, including spike 614 and nucleocapsid 203-204 appear to evolve under positive selection. In addition to the substitutions in the spike protein, multiple substitutions in the nucleocapsid protein appear to be important for SARS-CoV-2 adaptation to the human host. The positively selected mutations form a strongly connected network of apparent epistatic interactions and are signatures of major partitions in the SARS-CoV-2 phylogeny. These partitions show distinct spatial and temporal dynamics, with both globalization and diversification trends being apparent.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • This version of the manuscript has been revised to update the collection of the SARS-CoV-2 genomes that were analyzed to identify the evolutionary regime of the virus along with the global and regional evolutionary trends.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 13, 2020.
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Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2
Nash D. Rochman, Yuri I. Wolf, Guilhem Faure, Feng Zhang, Eugene V. Koonin
bioRxiv 2020.10.12.336644; doi: https://doi.org/10.1101/2020.10.12.336644
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Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2
Nash D. Rochman, Yuri I. Wolf, Guilhem Faure, Feng Zhang, Eugene V. Koonin
bioRxiv 2020.10.12.336644; doi: https://doi.org/10.1101/2020.10.12.336644

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