Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates

Joana Damas; Graham M. Hughes; Kathleen C. Keough; Corrie A. Painter; Nicole S. Persky; Marco Corbo; Michael Hiller; Klaus-Peter Koepfli; Andreas R. Pfenning; Huabin Zhao; Diane P. Genereux; Ross Swofford; Katherine S. Pollard; Oliver A. Ryder; Martin T. Nweeia; Kerstin Lindblad-Toh; Emma C. Teeling; Elinor K. Karlsson; Harris A. Lewin

Identifying sites undergoing positive selection . Signatures of site-specific positive selection in the ACE2 receptor were explored using CODEML, part of the Phylogenetic Analysis using Maximum Likelihood (PAML, (83) ) suite of software. Given CODEML's computational complexity, a smaller subset of mammalian taxa (N=64, Dataset S1), which included species from all prediction categories mentioned above, was used for selection analyses. To calculate likelihood-derived dN/dS rates (⍵), CODEML utilises both a species tree and a codon alignment. The species tree for all 64 taxa was calculated using IQTREE (80) and the inferred best-fit model of sequence evolution (JTT+F+R4). This gene topology was generally in agreement with the 410 taxa tree, however bats were now sister taxa to Perissodactyla. Therefore all selection analyses were run using both the inferred gene tree, and a modified tree with the position of bats manually modified to reflect the 410 taxa topology. All species trees used were unrooted. A codon alignment of the 64 mammals was generated using pal2nal (84) with protein alignments generated with Clustal Omega (73) and their respective CDS sequences.