Emergence of SARS-CoV-2 spike RBD mutants that enhance viral infectivity through increased human ACE2 receptor binding affinity

The current global pandemic of COVID-19 is caused by a novel coronavirus SARS-CoV-2. The SARS-CoV-2 spike protein receptor-binding domain (RBD) is the critical determinant of viral tropism and infectivity. To investigate whether naturally occurring mutations in the RBD have altered the receptor binding affinity and infectivity, firstly we analyzed in silico the binding dynamics between mutated SARS-CoV-2 RBDs and the human ACE2 receptor. Among 1609 genomes of SARS-CoV-2 strains isolated during the early transmission phase, 32 non-synonymous RBD mutants were identified and found clustered into nine mutant types under high positive selection pressure. Applying molecular dynamics simulations, three mutant types (V367F, W436R, N354D/D364Y) displayed higher binding affinity to human ACE2, likely due to the enhanced structural stabilization of the RBD beta-sheet scaffold. The increased infectivity of one mutant (V367F) circulating worldwide was further validated by performing receptor-ligand binding ELISA, surface plasmon resonance, and pseudotyped virus assays. Genome phylogenetic analysis of V367F mutants showed that during the early transmission phase, most V367F mutants clustered more closely with the SARS-CoV-2 prototype strain than the dual-mutation variants (V367F + D614G), which emerged later and formed a distinct sub-cluster. The analysis of critical RBD mutations provides further insights into the evolutionary trajectory of SARS-CoV-2 under high selection pressure and supports the continuing surveillance of spike mutations to aid in the development of COVID-19 drugs and vaccines.