Ongoing global and regional adaptive evolution of SARS-CoV-2
Name
e2104241118.full.pdf
Description
Published version
Size
2.39 MB
Format
Adobe PDF
Checksum (MD5)
7982b2cbf5642c0a3dcd70f4e37ea61d
Author(s)
Rochman, Nash D.
Wolf, Yuri I.
Faure, Guilhem
Mutz, Pascal
Zhang, Feng
Koonin, Eugene V.
Date Issued
July 2021
Journal
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Citation
Rochman, Nash D. et al. "Ongoing global and regional adaptive evolution of SARS-CoV-2." Proceedings of the National Academy of Sciences 118, 29 (July 2021): e2104241118. © 2021 the Author(s)
Version
Final published version
Abstract
Understanding the trends in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution is paramount to control the COVID-19 pandemic. We analyzed more than 300,000 high-quality genome sequences of SARS-CoV-2 variants available as of January 2021. The results show that the ongoing evolution of SARS-CoV-2 during the pandemic is characterized primarily by purifying selection, but a small set of sites appear to evolve under positive selection. The receptor-binding domain of the spike protein and the region of the nucleocapsid protein associated with nuclear localization signals (NLS) are enriched with positively selected amino acid replacements. These replacements form a strongly connected network of apparent epistatic interactions and are signatures of major partitions in the SARS-CoV-2 phylogeny. Virus diversity within each geographic region has been steadily growing for the entirety of the pandemic, but analysis of the phylogenetic distances between pairs of regions reveals four distinct periods based on global partitioning of the tree and the emergence of key mutations. The initial period of rapid diversification into region-specific phylogenies that ended in February 2020 was followed by a major extinction event and global homogenization concomitant with the spread of D614G in the spike protein, ending in March 2020. The NLS-associated variants across multiple partitions rose to global prominence in March to July, during a period of stasis in terms of interregional diversity. Finally, beginning in July 2020, multiple mutations, some of which have since been demonstrated to enable antibody evasion, began to emerge associated with ongoing regional diversification, which might be indicative of speciation.
MIT Department
McGovern Institute for Brain Research at MIT
Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology. Department of Biological Engineering
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Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
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DOI of Published Version
https://doi.org/10.1073/pnas.2104241118
