Rapid evolution of SARS-CoV-2 challenges human defenses

Carlos M. Duarte; David I. Ketcheson; Víctor M. Eguíluz; Susana Agustí; Juan Fernández-Gracia; Tahira Jamil; Elisa Laiolo; Takashi Gojobori; Intikhab Alam

doi:10.1038/s41598-022-10097-z

Rapid evolution of SARS-CoV-2 challenges human defenses

Carlos M. Duarte^*, David I. Ketcheson, Víctor M. Eguíluz, Susana Agustí, Juan Fernández-Gracia, Tahira Jamil, Elisa Laiolo, Takashi Gojobori, Intikhab Alam

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

22 Scopus citations

Abstract

The race between pathogens and their hosts is a major evolutionary driver, where both reshuffle their genomes to overcome and reorganize the defenses for infection, respectively. Evolutionary theory helps formulate predictions on the future evolutionary dynamics of SARS-CoV-2, which can be monitored through unprecedented real-time tracking of SARS-CoV-2 population genomics at the global scale. Here we quantify the accelerating evolution of SARS-CoV-2 by tracking the SARS-CoV-2 mutation globally, with a focus on the Receptor Binding Domain (RBD) of the spike protein determining infection success. We estimate that the > 820 million people that had been infected by October 5, 2021, produced up to 10²¹ copies of the virus, with 12 new effective RBD variants appearing, on average, daily. Doubling of the number of RBD variants every 89 days, followed by selection of the most infective variants challenges our defenses and calls for a shift to anticipatory, rather than reactive tactics involving collaborative global sequencing and vaccination.

Original language	English (US)
Article number	6457
Journal	Scientific Reports
Volume	12
Issue number	1
DOIs	https://doi.org/10.1038/s41598-022-10097-z
State	Published - Dec 2022

ASJC Scopus subject areas

General

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/s41598-022-10097-z

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title = "Rapid evolution of SARS-CoV-2 challenges human defenses",

abstract = "The race between pathogens and their hosts is a major evolutionary driver, where both reshuffle their genomes to overcome and reorganize the defenses for infection, respectively. Evolutionary theory helps formulate predictions on the future evolutionary dynamics of SARS-CoV-2, which can be monitored through unprecedented real-time tracking of SARS-CoV-2 population genomics at the global scale. Here we quantify the accelerating evolution of SARS-CoV-2 by tracking the SARS-CoV-2 mutation globally, with a focus on the Receptor Binding Domain (RBD) of the spike protein determining infection success. We estimate that the > 820 million people that had been infected by October 5, 2021, produced up to 1021 copies of the virus, with 12 new effective RBD variants appearing, on average, daily. Doubling of the number of RBD variants every 89 days, followed by selection of the most infective variants challenges our defenses and calls for a shift to anticipatory, rather than reactive tactics involving collaborative global sequencing and vaccination.",

author = "Duarte, {Carlos M.} and Ketcheson, {David I.} and Egu{\'i}luz, {V{\'i}ctor M.} and Susana Agust{\'i} and Juan Fern{\'a}ndez-Gracia and Tahira Jamil and Elisa Laiolo and Takashi Gojobori and Intikhab Alam",

note = "Funding Information: This research was funded by King Abdullah University of Science and technology through research made available to the Computational BioScience Research Center, CMD and TG. TG. VME and JFG acknowledge funding from “la Caixa” Foundation under the project code SR20-00386 (COVID-SHINE). JFG was supported by Direcci{\'o} General de Pol{\'i}tica Universit{\`a}ria i Recerca from the government of the Balearic Islands through the postdoctoral program Vicen{\c c} Mut. Publisher Copyright: {\textcopyright} 2022, The Author(s).",

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doi = "10.1038/s41598-022-10097-z",

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AU - Duarte, Carlos M.

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AU - Fernández-Gracia, Juan

AU - Jamil, Tahira

AU - Laiolo, Elisa

AU - Gojobori, Takashi

AU - Alam, Intikhab

N1 - Funding Information: This research was funded by King Abdullah University of Science and technology through research made available to the Computational BioScience Research Center, CMD and TG. TG. VME and JFG acknowledge funding from “la Caixa” Foundation under the project code SR20-00386 (COVID-SHINE). JFG was supported by Direcció General de Política Universitària i Recerca from the government of the Balearic Islands through the postdoctoral program Vicenç Mut. Publisher Copyright: © 2022, The Author(s).

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N2 - The race between pathogens and their hosts is a major evolutionary driver, where both reshuffle their genomes to overcome and reorganize the defenses for infection, respectively. Evolutionary theory helps formulate predictions on the future evolutionary dynamics of SARS-CoV-2, which can be monitored through unprecedented real-time tracking of SARS-CoV-2 population genomics at the global scale. Here we quantify the accelerating evolution of SARS-CoV-2 by tracking the SARS-CoV-2 mutation globally, with a focus on the Receptor Binding Domain (RBD) of the spike protein determining infection success. We estimate that the > 820 million people that had been infected by October 5, 2021, produced up to 1021 copies of the virus, with 12 new effective RBD variants appearing, on average, daily. Doubling of the number of RBD variants every 89 days, followed by selection of the most infective variants challenges our defenses and calls for a shift to anticipatory, rather than reactive tactics involving collaborative global sequencing and vaccination.

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Rapid evolution of SARS-CoV-2 challenges human defenses

Abstract

ASJC Scopus subject areas

UN SDGs

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