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

Analysis for departure from neutral evolutionary rate in ACE2 with PHAST . Neutral models were trained on the specified species sets (Dataset S4) using the REV nucleotide substitution model implemented in phyloFit using an expectation maximization algorithm for parameter optimization. The neutral model fit was based on third codon positions to approximate the neutral evolution rate specific to the ACE2 gene, using a 410-species phylogenetic tree generated by IQTREE as described above and rooted on fishes. The program phyloP was then used to identify codons undergoing accelerated or conserved evolution relative to the neutral model using --features to specify codons, --method LRT --mode CONACC, and --subtree for lineage-specific tests, with p-values thus assigned per codon based on a likelihood ratio test. P-values were corrected for multiple testing using the Benjamini-Hochberg method (36) and sites with a corrected p-value less than 0.05 were considered significant. PhyloFit and phyloP are both part of the PHAST package v1.4 (85, 86) .