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Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections

Severe acute respiratory coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is of zoonotic origin. Evolutionary analyses assessing whether coronaviruses similar to SARS-CoV-2 infected ancestral species of modern-day animal hosts could be useful in identifying additional reservoirs of poten...

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Autores principales: King, Sean B., Singh, Mona
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8601562/
https://www.ncbi.nlm.nih.gov/pubmed/34793437
http://dx.doi.org/10.1371/journal.pcbi.1009560
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author King, Sean B.
Singh, Mona
author_facet King, Sean B.
Singh, Mona
author_sort King, Sean B.
collection PubMed
description Severe acute respiratory coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is of zoonotic origin. Evolutionary analyses assessing whether coronaviruses similar to SARS-CoV-2 infected ancestral species of modern-day animal hosts could be useful in identifying additional reservoirs of potentially dangerous coronaviruses. We reasoned that if a clade of species has been repeatedly exposed to a virus, then their proteins relevant for viral entry may exhibit adaptations that affect host susceptibility or response. We perform comparative analyses across the mammalian phylogeny of angiotensin-converting enzyme 2 (ACE2), the cellular receptor for SARS-CoV-2, in order to uncover evidence for selection acting at its binding interface with the SARS-CoV-2 spike protein. We uncover that in rodents there is evidence for adaptive amino acid substitutions at positions comprising the ACE2-spike interaction interface, whereas the variation within ACE2 proteins in primates and some other mammalian clades is not consistent with evolutionary adaptations. We also analyze aminopeptidase N (APN), the receptor for the human coronavirus 229E, a virus that causes the common cold, and find evidence for adaptation in primates. Altogether, our results suggest that the rodent and primate lineages may have had ancient exposures to viruses similar to SARS-CoV-2 and HCoV-229E, respectively.
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spelling pubmed-86015622021-11-19 Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections King, Sean B. Singh, Mona PLoS Comput Biol Research Article Severe acute respiratory coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is of zoonotic origin. Evolutionary analyses assessing whether coronaviruses similar to SARS-CoV-2 infected ancestral species of modern-day animal hosts could be useful in identifying additional reservoirs of potentially dangerous coronaviruses. We reasoned that if a clade of species has been repeatedly exposed to a virus, then their proteins relevant for viral entry may exhibit adaptations that affect host susceptibility or response. We perform comparative analyses across the mammalian phylogeny of angiotensin-converting enzyme 2 (ACE2), the cellular receptor for SARS-CoV-2, in order to uncover evidence for selection acting at its binding interface with the SARS-CoV-2 spike protein. We uncover that in rodents there is evidence for adaptive amino acid substitutions at positions comprising the ACE2-spike interaction interface, whereas the variation within ACE2 proteins in primates and some other mammalian clades is not consistent with evolutionary adaptations. We also analyze aminopeptidase N (APN), the receptor for the human coronavirus 229E, a virus that causes the common cold, and find evidence for adaptation in primates. Altogether, our results suggest that the rodent and primate lineages may have had ancient exposures to viruses similar to SARS-CoV-2 and HCoV-229E, respectively. Public Library of Science 2021-11-18 /pmc/articles/PMC8601562/ /pubmed/34793437 http://dx.doi.org/10.1371/journal.pcbi.1009560 Text en © 2021 King, Singh https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
King, Sean B.
Singh, Mona
Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections
title Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections
title_full Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections
title_fullStr Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections
title_full_unstemmed Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections
title_short Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections
title_sort comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8601562/
https://www.ncbi.nlm.nih.gov/pubmed/34793437
http://dx.doi.org/10.1371/journal.pcbi.1009560
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