Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections. Author Sean King, Mona Singh Publication Year 2021 Type Journal Article Abstract 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. Keywords Animals, Humans, Computational Biology, Selection, Genetic, Amino Acid Substitution, Genomics, Mammals, Adaptation, Physiological, Protein Interaction Domains and Motifs, Virus Internalization, Phylogeny, Evolution, Molecular, Host Specificity, Receptors, Virus, Host Microbial Interactions, Coronavirus Infections, COVID-19, SARS-CoV-2, Angiotensin-Converting Enzyme 2, CD13 Antigens, Common Cold, Coronavirus 229E, Human, Spike Glycoprotein, Coronavirus Journal PLoS Comput Biol Volume 17 Issue 11 Pages e1009560 Date Published 2021 Nov ISSN Number 1553-7358 DOI 10.1371/journal.pcbi.1009560 Alternate Journal PLoS Comput Biol PMCID PMC8601562 PMID 34793437 PubMedPubMed CentralGoogle ScholarBibTeXEndNote X3 XML