RBD mutations from circulating SARS-CoV-2 strains enhance the structural stability and human ACE2 affinity of the spike protein

A novel coronavirus SARS-CoV-2 is associated with the current global pandemic of Coronavirus Disease 2019 (COVID-19). Bats and pangolins are suspected as the reservoir and the intermediate host. The receptor binding domain (RBD) of the SARS-CoV-2 S protein plays the key role in the tight binding to human receptor ACE2 for viral entry. Here, we analyzed the worldwide RBD mutants and found 18 mutant strains fell into 8 mutation types under high positive selection pressure during the spread. The equilibrium dissociation constant (KD) of three types of RBD mutants emerging in Wuhan, Shenzhen, Hong Kong and France were two orders of magnitude lower than the prototype Wuhan-Hu-1 strain due to the stabilization of the beta-sheet scaffold of the RBD. This indicated that the mutated viruses may have evolved to acquire remarkably increased infectivity. Five France isolates and one Hong Kong isolate shared the same RBD mutation enhancing the binding affinity, which suggested that they may have originated as a novel sub-lineage. The KD values for the bat and the pangolin SARS-like CoV RBDs indicated that it would be difficult for bat SARS-like CoV to infect humans; however, the pangolin CoV is potentially infectious to humans with respect to its RBD. These analyses of critical RBD mutations provide further insights into the evolutionary trend of SARS-CoV-2 under high selection pressure. The enhancement of the SARS-CoV-2 binding affinity to ACE2 reveals a possible higher risk of more severe virus transmissions during a sustained pandemic of COVID-19 if no effective precautions are implemented.