Comparison of Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein Binding to ACE2 Receptors from Human, Pets, Farm Animals, and Putative Intermediate Hosts

Abstract

17The emergence of a novel coronavirus, SARS-CoV-2, resulted in a pandemic. Here, we used X-ray 18 structures of human ACE2 bound to the receptor-binding domain (RBD) of the spike protein (S) from 19 SARS-CoV-2 to predict its binding to ACE2 proteins from different animals, including pets, farm animals, 20 and putative intermediate hosts of SARS-CoV-2. Comparing the interaction sites of ACE2 proteins 21 known to serve or not serve as receptor allows to define residues important for binding. From the 20 22 amino acids in ACE2 that contact S up to seven can be replaced and ACE2 can still function as the SARS-23CoV-2 receptor. These variable amino acids are clustered at certain positions, mostly at the periphery 24 of the binding site, while changes of the invariable residues prevent S-binding or infection of the 25 respective animal. Some ACE2 proteins even tolerate the loss or the acquisition of N-glycosylation sites 26 located near the S-interface. Of note, Pigs and dogs, which are not or not effectively infected and have 27 only a few changes in the binding site, exhibit relatively low levels of ACE2 in the respiratory tract. 28Comparison of the RBD of S of SARS-CoV-2 with viruses from Bat-CoV-RaTG13 and Pangolin-CoV 29 revealed that the latter contains only one substitution, whereas the Bat-CoV-RaTG13 exhibits five. 30However, ACE2 of pangolin exhibit seven changes relative to human ACE2, a similar number of 31 substitutions is present in ACE2 of bats, raccoon, and civet suggesting that SARS-CoV-2 may not 32 especially adapted to ACE2 of any of its putative intermediate hosts. These analyses provide new 33 insight into the receptor usage and animal source/origin of SARS-CoV-2. 34 IMPORTANCE 35 SARS-CoV-2 is threatening people worldwide and there are no drugs or vaccines available to mitigate 36 its spread. The origin of the virus is still unclear and whether pets and livestock can be infected and 37 transmit SARS-CoV-2 are important and unknown scientific questions. Effective binding to the host 38 receptor ACE2 is the first prerequisite for infection of cells and determines the host range. Our analysis 39 provides a framework for the prediction of potential hosts of SARS-CoV-2. We found that ACE2 from 40 species known to support SARS-CoV-2 infection tolerate many amino acid changes indicating that the 41 species barrier might be low. An exception are dogs and especially pigs, which, however, revealed 42

Identifying zoonotic origin of SARS-CoV-2 by modeling the binding affinity between Spike receptor-binding domain and host ACE2

“…These results suggest that mammals rather than other species are likely to be the main source of SARS-CoV-2 and hence they should be the major focus. This finding is also consistent with previous studies [7,20,35,[37][38][39][40][41], but a more quantitative measurement was given here. Our findings also refute isolated reports claiming that non-mammal vertebrates such as reptiles could be the intermediate host [42,43].…”

Which animals are at risk? Predicting species susceptibility to Covid-19

“…Prior studies have similarly performed ACE2 sequence alignments across species and modeled structural effects of the amino acid changes on the SARS-CoV-2 and ACE2 interface. 7,[30][31][32][33][34][35] However, our study integrates experimentally validated susceptibility to SARS-CoV-2 with in-depth structural analyses to determine critical ACE2 residues for infection. In addition, we performed multiple structural analyses, including residue-residue interactions, RECON multistate design, and glycosylation analysis, to rigorously determine the structural basis for species differences in ACE2 interaction with SARS-CoV-2 RBD.…”

“…You can run the application by clicking # the 'Run App' button above or Ctrl-Enter on each line. # install.packages(c("protr", "devtools", "ggplot2", "dplyr", "shiny"), dependencies = TRUE) if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") if (!requireNamespace("Biostrings", quietly = TRUE)) species <-c("Felis catus", "Panthera tigris altaica", "Panthera leo", "Mesocriceteus auratus", "Macaca mulatta", "Mus musculus", "Aythya fuligula", "Gallus gallus", "Mustela putoriusfuro", "Sus scrofa", "Canis lupus familiaris", "Rhinolophus sinicus", "Equus caballus", "Bos taurus", "Manis javanica", "Capra hircus", "Ovis aries", "Camelus dromedarius", "Camelus bactrianus") species.scores <-c (27,27,27,23,31,11,8,8,14,21,22,31,27,19,13,19,19,27,27) df.species.score <-data.frame("Species" = species, "Score" = species.scores) df.species.score <-df.species.score[order(df.species.score$Species),] # We also add shading to represent cutoffs for susceptible and non-susceptible species output$plot <-renderPlot(ggplot(df.species.score, aes(y=Score,x='')) + geom_jitter(aes(color=Species, shape=Species), size = 2.5, width=0.5) + scale_shape_manual(values=c (15,16,17,18,15,16,17,18,15,16,17,18,15,16,17,18,15,16,17), RosettaScripts protocol for RosettaCM <ROSETTASCRIPTS> <TASKOPERATIONS> </TAS...…”

Cell entry of SARS-CoV-2 conferred by angiotensin-converting enzyme 2 (ACE2) of different species

“…We speculate that there exist other factors determining the host tropism besides receptor interaction. A recent study demonstrated that pigs and dogs exhibit relatively low levels of ACE2 in the respiratory tract, this may be the reason that SARS-CoV-2 replicated poorly in dogs and pigs (22). Although dogs and pigs may not sensitive for SARS-CoV-2 infection, we do not know whether these animals are appeared as asymptomatic carriers of SARS-CoV-2 in certain environments.…”