Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2

In the frames of a One Health strategy, i.e. a strategy should be able to predict susceptibility to infection in both humans and animals, developing a SARS-CoV-2 mutation tracking system is a goal. We observed that the phylogenetic proximity of vertebrate ACE2 receptors does not affect the binding e...

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Autores principales:	Matteo Calcagnile, Tiziano Verri, Maurizio Salvatore Tredici, Patricia Forgez, Marco Alifano, Pietro Alifano
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	ACE2 ACE2 phylogeny Animal host B.1.1.7 (alpha) SARS-CoV-2 variant B.1.351 (Beta) SARS-CoV-2 variant B.1.617.2 (delta) SARS-CoV-2 variant Codon usage Medicine (General) R5-920
Acceso en línea:	https://doaj.org/article/6f3ecbc29706432687c152b78247b41f
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id	oai:doaj.org-article:6f3ecbc29706432687c152b78247b41f
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spelling	oai:doaj.org-article:6f3ecbc29706432687c152b78247b41f2021-12-02T05:02:10ZCodon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-22352-771410.1016/j.onehlt.2021.100352https://doaj.org/article/6f3ecbc29706432687c152b78247b41f2021-12-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2352771421001427https://doaj.org/toc/2352-7714In the frames of a One Health strategy, i.e. a strategy should be able to predict susceptibility to infection in both humans and animals, developing a SARS-CoV-2 mutation tracking system is a goal. We observed that the phylogenetic proximity of vertebrate ACE2 receptors does not affect the binding energy for the viral spike protein. However, all viral variants seem to bind ACE2 better in many animals than in humans. Moreover, two observations highlight that the evolution of the virus started at the beginning of 2020 and culminated with the appearance of the variants. First, codon usage analysis shows that the B.1.1.7 (alpha), B.1.351 (beta) and B.1.617.2 (delta) variants, similar in the use of codons, are also similar to a virus sampled in January 2020. Second, the host-specific D614G mutation becomes prevalent starting from March 2020. Overall, we show that SARS-CoV-2 undergoes a process of molecular evolution that begins with the optimization of codons followed by the functional optimization of the spike protein.Matteo CalcagnileTiziano VerriMaurizio Salvatore TrediciPatricia ForgezMarco AlifanoPietro AlifanoElsevierarticleACE2ACE2 phylogenyAnimal hostB.1.1.7 (alpha) SARS-CoV-2 variant B.1.351 (Beta) SARS-CoV-2 variantB.1.617.2 (delta) SARS-CoV-2 variantCodon usageMedicine (General)R5-920ENOne Health, Vol 13, Iss , Pp 100352- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	ACE2 ACE2 phylogeny Animal host B.1.1.7 (alpha) SARS-CoV-2 variant B.1.351 (Beta) SARS-CoV-2 variant B.1.617.2 (delta) SARS-CoV-2 variant Codon usage Medicine (General) R5-920
spellingShingle	ACE2 ACE2 phylogeny Animal host B.1.1.7 (alpha) SARS-CoV-2 variant B.1.351 (Beta) SARS-CoV-2 variant B.1.617.2 (delta) SARS-CoV-2 variant Codon usage Medicine (General) R5-920 Matteo Calcagnile Tiziano Verri Maurizio Salvatore Tredici Patricia Forgez Marco Alifano Pietro Alifano Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2
description	In the frames of a One Health strategy, i.e. a strategy should be able to predict susceptibility to infection in both humans and animals, developing a SARS-CoV-2 mutation tracking system is a goal. We observed that the phylogenetic proximity of vertebrate ACE2 receptors does not affect the binding energy for the viral spike protein. However, all viral variants seem to bind ACE2 better in many animals than in humans. Moreover, two observations highlight that the evolution of the virus started at the beginning of 2020 and culminated with the appearance of the variants. First, codon usage analysis shows that the B.1.1.7 (alpha), B.1.351 (beta) and B.1.617.2 (delta) variants, similar in the use of codons, are also similar to a virus sampled in January 2020. Second, the host-specific D614G mutation becomes prevalent starting from March 2020. Overall, we show that SARS-CoV-2 undergoes a process of molecular evolution that begins with the optimization of codons followed by the functional optimization of the spike protein.
format	article
author	Matteo Calcagnile Tiziano Verri Maurizio Salvatore Tredici Patricia Forgez Marco Alifano Pietro Alifano
author_facet	Matteo Calcagnile Tiziano Verri Maurizio Salvatore Tredici Patricia Forgez Marco Alifano Pietro Alifano
author_sort	Matteo Calcagnile
title	Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2
title_short	Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2
title_full	Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2
title_fullStr	Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2
title_full_unstemmed	Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2
title_sort	codon usage, phylogeny and binding energy estimation predict the evolution of sars-cov-2
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/6f3ecbc29706432687c152b78247b41f
work_keys_str_mv	AT matteocalcagnile codonusagephylogenyandbindingenergyestimationpredicttheevolutionofsarscov2 AT tizianoverri codonusagephylogenyandbindingenergyestimationpredicttheevolutionofsarscov2 AT mauriziosalvatoretredici codonusagephylogenyandbindingenergyestimationpredicttheevolutionofsarscov2 AT patriciaforgez codonusagephylogenyandbindingenergyestimationpredicttheevolutionofsarscov2 AT marcoalifano codonusagephylogenyandbindingenergyestimationpredicttheevolutionofsarscov2 AT pietroalifano codonusagephylogenyandbindingenergyestimationpredicttheevolutionofsarscov2
_version_	1718400771212443648

Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2

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