The Compensatory Effect of S375F on S371F Is Vital for Maintaining the Infectivity of SARS-CoV-2 Omicron Variants

Abstract

The emergence of Omicron variants dramatically changed the transmission rate and infection characteristics compared to previously prevalent strains, primarily due to spike protein mutations. However, the impact of individual mutations remained unclear. Here, we used virus-like particle (VLP) pseudotyped to investigate the functional contributions by 12 common mutations in the spike protein. We found that the S371F mutation in the receptor binding domain (RBD) of spike protein led to a 5- and 10-fold decrease of ACE2 utilization efficiency and viral infectivity, respectively, accompanied by a 5- to 11-fold reduction of neutralization sensitivity to monoclonal antibodies. However, the S375F mutation in the RBD had a compensatory effect, rescuing the infectivity of the S371F Omicron variant. Based on molecular dynamics simulations, we proposed a “tug of war” model to explain this compensation phenomenon. These results provide a comprehensive and dynamic perspective on the evolution of this important pandemic virus.