Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen.

Virus host shifts are generally associated with novel adaptations to exploit the cells of the new host species optimally. Surprisingly, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has apparently required little to no significant adaptation to humans since the start of the Coronaviru...

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Autores principales:	Oscar A MacLean, Spyros Lytras, Steven Weaver, Joshua B Singer, Maciej F Boni, Philippe Lemey, Sergei L Kosakovsky Pond, David L Robertson
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/69d3f0a61330400a8ff75a6037d7b399
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spelling	oai:doaj.org-article:69d3f0a61330400a8ff75a6037d7b3992021-12-02T19:54:18ZNatural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen.1544-91731545-788510.1371/journal.pbio.3001115https://doaj.org/article/69d3f0a61330400a8ff75a6037d7b3992021-03-01T00:00:00Zhttps://doi.org/10.1371/journal.pbio.3001115https://doaj.org/toc/1544-9173https://doaj.org/toc/1545-7885Virus host shifts are generally associated with novel adaptations to exploit the cells of the new host species optimally. Surprisingly, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has apparently required little to no significant adaptation to humans since the start of the Coronavirus Disease 2019 (COVID-19) pandemic and to October 2020. Here we assess the types of natural selection taking place in Sarbecoviruses in horseshoe bats versus the early SARS-CoV-2 evolution in humans. While there is moderate evidence of diversifying positive selection in SARS-CoV-2 in humans, it is limited to the early phase of the pandemic, and purifying selection is much weaker in SARS-CoV-2 than in related bat Sarbecoviruses. In contrast, our analysis detects evidence for significant positive episodic diversifying selection acting at the base of the bat virus lineage SARS-CoV-2 emerged from, accompanied by an adaptive depletion in CpG composition presumed to be linked to the action of antiviral mechanisms in these ancestral bat hosts. The closest bat virus to SARS-CoV-2, RmYN02 (sharing an ancestor about 1976), is a recombinant with a structure that includes differential CpG content in Spike; clear evidence of coinfection and evolution in bats without involvement of other species. While an undiscovered "facilitating" intermediate species cannot be discounted, collectively, our results support the progenitor of SARS-CoV-2 being capable of efficient human-human transmission as a consequence of its adaptive evolutionary history in bats, not humans, which created a relatively generalist virus.Oscar A MacLeanSpyros LytrasSteven WeaverJoshua B SingerMaciej F BoniPhilippe LemeySergei L Kosakovsky PondDavid L RobertsonPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Biology, Vol 19, Iss 3, p e3001115 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Oscar A MacLean Spyros Lytras Steven Weaver Joshua B Singer Maciej F Boni Philippe Lemey Sergei L Kosakovsky Pond David L Robertson Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen.
description	Virus host shifts are generally associated with novel adaptations to exploit the cells of the new host species optimally. Surprisingly, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has apparently required little to no significant adaptation to humans since the start of the Coronavirus Disease 2019 (COVID-19) pandemic and to October 2020. Here we assess the types of natural selection taking place in Sarbecoviruses in horseshoe bats versus the early SARS-CoV-2 evolution in humans. While there is moderate evidence of diversifying positive selection in SARS-CoV-2 in humans, it is limited to the early phase of the pandemic, and purifying selection is much weaker in SARS-CoV-2 than in related bat Sarbecoviruses. In contrast, our analysis detects evidence for significant positive episodic diversifying selection acting at the base of the bat virus lineage SARS-CoV-2 emerged from, accompanied by an adaptive depletion in CpG composition presumed to be linked to the action of antiviral mechanisms in these ancestral bat hosts. The closest bat virus to SARS-CoV-2, RmYN02 (sharing an ancestor about 1976), is a recombinant with a structure that includes differential CpG content in Spike; clear evidence of coinfection and evolution in bats without involvement of other species. While an undiscovered "facilitating" intermediate species cannot be discounted, collectively, our results support the progenitor of SARS-CoV-2 being capable of efficient human-human transmission as a consequence of its adaptive evolutionary history in bats, not humans, which created a relatively generalist virus.
format	article
author	Oscar A MacLean Spyros Lytras Steven Weaver Joshua B Singer Maciej F Boni Philippe Lemey Sergei L Kosakovsky Pond David L Robertson
author_facet	Oscar A MacLean Spyros Lytras Steven Weaver Joshua B Singer Maciej F Boni Philippe Lemey Sergei L Kosakovsky Pond David L Robertson
author_sort	Oscar A MacLean
title	Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen.
title_short	Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen.
title_full	Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen.
title_fullStr	Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen.
title_full_unstemmed	Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen.
title_sort	natural selection in the evolution of sars-cov-2 in bats created a generalist virus and highly capable human pathogen.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/69d3f0a61330400a8ff75a6037d7b399
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Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen.

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