Evolutionary Arms Race between Virus and Host Drives Genetic Diversity in Bat Severe Acute Respiratory Syndrome-Related Coronavirus Spike Genes

Abstract

The Chinese horseshoe bat (Rhinolophus sinicus), reservoir host of severe acute respiratory syndrome coronavirus (SARS-CoV), carries many bat SARS-related CoVs (SARSr-CoVs) with high genetic diversity, particularly in the spike gene. Despite these variations, some bat SARSr-CoVs can utilize the orthologs of human SARS-CoV receptor, angiotensin-converting enzyme 2 (ACE2), for entry. It is speculated that the interaction between bat ACE2 and SARSr-CoV spike proteins drives diversity. Here, we have identified a series of R. sinicus ACE2 variants with some polymorphic sites involved in the interaction with the SARS-CoV spike protein. Pseudoviruses or SARSr-CoVs carrying different spike proteins showed different infection efficiency in cells transiently expressing bat ACE2 variants. Consistent results were observed by binding affinity assays between SARS- and SARSr-CoV spike proteins and receptor molecules from bats and humans. All tested bat SARSr-CoV spike proteins had a higher binding affinity to human ACE2 than to bat ACE2, although they showed a 10-fold lower binding affinity to human ACE2 compared with their SARS-CoV counterpart. Structure modeling revealed that the difference in binding affinity between spike and ACE2 might be caused by the alteration of some key residues in the interface of these two molecules. Molecular evolution analysis indicates that some key residues were under positive selection. These results suggest that the SARSr-CoV spike protein and R. sinicus ACE2 may have coevolved over time and experienced selection pressure from each other, triggering the evolutionary arms race dynamics. Importance Evolutionary arms race dynamics shape the diversity of viruses and their receptors. Identification of key residues which are involved in interspecies transmission is important to predict potential pathogen spillover from wildlife to humans. Previously, we have identified genetically diverse SARSr-CoV in Chinese horseshoe bats. Here, we show the highly polymorphic ACE2 in Chinese horseshoe bat populations. These ACE2 variants support SARS- and SARSr-CoV infection but with different binding affinity to different spike proteins. The higher binding affinity of SARSr-CoV spike to human ACE2 suggests that these viruses have the capacity of spillover to humans. The positive selection of residues at the interface between ACE2 and SARSr-CoV spike protein suggests a long-term and ongoing coevolutionary dynamics between them. Continued surveillance of this group of viruses in bats is necessary for the prevention of the next SARS-like disease.

Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016

“…3, interactive visualizations at https://jbloomlab.github.io/SARS-CoV-2-RBD_MAP_LY-CoV555/). LY-CoV016 and LY-CoV555 bind opposite sides of the “receptor-binding ridge”, a structurally [23] and evolutionarily [24,25] dynamic region of the RBD that forms part of the ACE2 receptor contact surface. The hotspots of escape for each antibody map closely to the core of each antibody-RBD complex.…”

Broad host range of SARS-CoV-2 and the molecular basis for SARS-CoV-2 binding to cat ACE2

“…Unlike the bat CD26s from multiple species that binds to the MERS-CoV RBD with varied binding affinities 34 , the SARS-CoV-2 RBD interacts with the ACE2s from little brown bat and fulvous fruit bat, but not the ones from the three horseshoe bats tested in this study. Recently, a paper submitted in bioRxiv reported the polymorphism of Chinese horseshoe bats, especially at the N-terminal region is responsible for the binding to SARS-CoV-2 and SARS-CoV 35 . Eight different ACE2s were detected in Chinese horseshoe bats.…”

Cross-species recognition of SARS-CoV-2 to bat ACE2

“…The capacity of virus infection was further confirmed with SARS-CoV-2 wild virus to infect HeLa cells stably expressing bACE2-Rm. Guo et al ( 30 ) recently investigated the binding and infection of a series of SARS-related CoVs isolated from R. sinicus with ACE2 variants carrying polymorphic sites involved in the interaction with S protein, suggesting a long-term and ongoing coevolutionary dynamics between the S protein and ACE2 receptor. Additionally, two groups isolated SARS-CoV-2–related CoVs from Malayan pangolins, with one CoV showing a 90.7% identity of S genes and a virtually identical RBD with SARS-CoV-2 ( 16 , 31 ).…”

“…A growing body of research has identified that the binding capacity of ACE2 orthologs from different bat species to RBD of SARS-CoV or SARS-CoV-2 varied substantially, indicating the extensively diversified susceptibility of SARS-CoV and SARS-CoV-2 in different bat species ( 18 , 25 , 32 , 33 ). Guo et al ( 30 ) reported that ACE2 genes showed high polymorphism among the R. sinicus populations, and R. sinicus ACE2 variants possessed different susceptibility to SARS-related-CoV infection. In the present study, together with the results from our previous work, our data showed that R. sinicus ACE2 could not bind to SARS-CoV-2 RBD ( 34 ).…”