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...

Descripción completa

Guardado en:
Detalles Bibliográficos
Autores principales: Sean B. King, Mona Singh
Formato: article
Lenguaje:EN
Publicado: Public Library of Science (PLoS) 2021
Materias:
Acceso en línea:https://doaj.org/article/c1e3c0419b344bf4aea3b864e1bfc1d6
Etiquetas: Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
id oai:doaj.org-article:c1e3c0419b344bf4aea3b864e1bfc1d6
record_format dspace
spelling oai:doaj.org-article:c1e3c0419b344bf4aea3b864e1bfc1d62021-11-25T05:42:06ZComparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections1553-734X1553-7358https://doaj.org/article/c1e3c0419b344bf4aea3b864e1bfc1d62021-11-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8601562/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Severe 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. Author summary SARS-like coronaviruses, such as SARS-CoV and SARS-CoV-2, are a class of pathogens that have been a significant threat to human health. Across the animal kingdom, we see considerable differences in the severity of symptoms caused by these types of viruses. Previous research has shown adaptations to SARS-like viruses in known viral vectors such as Chinese Horseshoe bats. Uncovering evidence of adaptations to SARS-like viral infections in proteins of other hosts would shed light on whether additional mammalian clades have been previously exposed to these viruses. In our study, we characterize the evolution of the mammalian host receptor of SARS-like viruses, ACE2, across a broad mammalian phylogeny. Our comparative genomic insights reveal a pattern of rapid evolution of the ACE2/virus binding interface within the rodent clade, while finding little adaptation within primates or among other mammals not already known to be SARS hosts. These results suggest that some rodent species may have acquired some form of tolerance or resistance to infections from SARS-like coronaviruses, while non-adapted mammals and primates may be more susceptible to symptomatic disease.Sean B. KingMona SinghPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 11 (2021)
institution DOAJ
collection DOAJ
language EN
topic Biology (General)
QH301-705.5
spellingShingle Biology (General)
QH301-705.5
Sean B. King
Mona Singh
Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections
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. Author summary SARS-like coronaviruses, such as SARS-CoV and SARS-CoV-2, are a class of pathogens that have been a significant threat to human health. Across the animal kingdom, we see considerable differences in the severity of symptoms caused by these types of viruses. Previous research has shown adaptations to SARS-like viruses in known viral vectors such as Chinese Horseshoe bats. Uncovering evidence of adaptations to SARS-like viral infections in proteins of other hosts would shed light on whether additional mammalian clades have been previously exposed to these viruses. In our study, we characterize the evolution of the mammalian host receptor of SARS-like viruses, ACE2, across a broad mammalian phylogeny. Our comparative genomic insights reveal a pattern of rapid evolution of the ACE2/virus binding interface within the rodent clade, while finding little adaptation within primates or among other mammals not already known to be SARS hosts. These results suggest that some rodent species may have acquired some form of tolerance or resistance to infections from SARS-like coronaviruses, while non-adapted mammals and primates may be more susceptible to symptomatic disease.
format article
author Sean B. King
Mona Singh
author_facet Sean B. King
Mona Singh
author_sort Sean B. King
title 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_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_sort comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections
publisher Public Library of Science (PLoS)
publishDate 2021
url https://doaj.org/article/c1e3c0419b344bf4aea3b864e1bfc1d6
work_keys_str_mv AT seanbking comparativegenomicanalysisrevealsvaryinglevelsofmammalianadaptationtocoronavirusinfections
AT monasingh comparativegenomicanalysisrevealsvaryinglevelsofmammalianadaptationtocoronavirusinfections
_version_ 1718414542353989632