Code and data from "Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections"

King, Sean
Issue date: 28 September 2021
Cite as:
King, Sean. (2021). Code and data from "Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections" [Data set]. Princeton University. https://doi.org/10.34770/8qb6-d143
@electronic{king_sean_2021,
  author      = {King, Sean},
  title       = {{Code and data from "Comparative genomic
                analysis reveals varying levels of mamma
                lian adaptation to coronavirus infection
                s"}},
  publisher   = {{Princeton University}},
  year        = 2021,
  url         = {https://doi.org/10.34770/8qb6-d143}
}
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. Included in this repository are the instructions and corresponding code required to build the dataset and run the analysis in the manuscript.

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# Filename Description Filesize
1 README.txt 12.1 KB
2 Alignments.zip 98.9 KB
3 High Resolution Manuscript Figures.zip 918 KB
4 PDB Structures.zip 820 KB
5 Sequences.zip 37.2 KB
6 Supplementary Information.zip 164 KB
7 data.zip 137 KB
8 master_script.sh 6.65 KB
9 scripts.zip 12.6 KB