V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity

Abstract

The current 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 RBD mutations during the early transmission phase have altered the receptor binding affinity and infectivity, firstly we analyzed in silico the binding dynamics between SARS-CoV-2 RBD mutants and the human ACE2 receptor. Among 32,123 genomes of SARS-CoV-2 isolates (January through March, 2020), 302 non-synonymous RBD mutants were identified and clustered into 96 mutant types. The six dominant mutations were analyzed applying molecular dynamics simulations (MDS). The mutant type V367F continuously circulating worldwide displayed higher binding affinity to human ACE2 due to the enhanced structural stabilization of the RBD beta-sheet scaffold. The MDS also indicated that it would be difficult for bat SARS-like CoV to infect humans. However, the pangolin CoV is potentially infectious to humans. The increased infectivity of V367 mutants was further validated by performing receptor-ligand binding ELISA, surface plasmon resonance, and pseudotyped virus assays. Phylogenetic analysis of the genomes 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 may derivate from recombination. The analysis of critical RBD mutations provides further insights into the evolutionary trajectory of early SARS-CoV-2 variants of zoonotic origin under negative selection pressure and supports the continuing surveillance of spike mutations to aid in the development of new COVID-19 drugs and vaccines. Importance A novel coronavirus SARS-CoV-2 has caused the pandemic of COVID-19. The origin of SARS-CoV-2 was associated with zoonotic infections. The spike protein receptor-binding domain (RBD) is identified as the critical determinant of viral tropism and infectivity. Thus, whether the mutations in the RBD of the circulating SARS-CoV-2 isolates have altered the receptor binding affinity and made them more infectious, has been the research hotspot. Given that SARS-CoV-2 is a novel coronavirus, the significance of our research is in identifying and validating the RBD mutant types emerging during the early transmission phase and increasing human ACE2 receptor binding affinity and infectivity. Our study provides insights into the evolutionary trajectory of early SARS-CoV-2 variants of zoonotic origin. The continuing surveillance of RBD mutations with increased human ACE2 affinity in human or other animals is critical to the development of new COVID-19 drugs and vaccines against these variants during the sustained COVID-19 pandemic.

Sensitivity of SARS-CoV-2 Variants to Neutralization by Convalescent Sera and a VH3-30 Monoclonal Antibody

“…In addition to E484K, L452R, and K417N/T mutations, numerous RBD mutations (including F342L, N354D, V367F, A435S, W436R, K458R, G476S, and V483A) have also been detected in non-VOC variants ( 36 , 37 ). Though these RBD mutants show significantly increased affinity to hACE2 ( 36 , 37 ), we found largely unaffected neutralizing potencies of convalescent sera and mAb 32D4 against SARS-CoV-2 variants with relevant RBD mutation. These results might explain the rare cases of these non-VOC variants during the COVID-19 pandemic and further indicated a crosstalk between human host immune pressure and SARS-CoV-2 variant selection.…”

“…As with other RNA viruses such as influenza and HIV, SARS-CoV-2 is also characterized by antigenic drift (17). In addition to E484K, L452R, and K417N/T mutations, numerous RBD mutations (including F342L, N354D, V367F, A435S, W436R, K458R, G476S, and V483A) have also been detected in non-VOC variants (36,37). Though these RBD mutants show significantly increased affinity to hACE2 (36,37), we found largely unaffected neutralizing potencies of convalescent sera and mAb 32D4 against SARS-CoV-2 variants with relevant RBD mutation.…”

Potent prophylactic and therapeutic efficacy of recombinant human ACE2-Fc against SARS-CoV-2 infection in vivo

“…8,12,40,41 . Spike protein with the D614G mutation was considered as a key mutation to increase virus transmission and infectivity, and the V367F mutant exhibited significantly increased affinity to hACE2, while VOCs may increase virulence and reduce sensitivity to some neutralizing antibodies and convalescent sera at different extent 9,10,[40][41][42][43][44][45] . As shown in Fig.…”

The Rapid Assessment of Aggregated Wastewater Samples for Genomic Surveillance of SARS-CoV-2 on a City-Wide Scale

“…First, is the apparent significant sequence variation in the SD2 domain of the S1 fragment. This region of S1 is associated with the flexibility with which the Receptor Binding Domain (RBD) can transition between the "up" and "down" conformations, which has been previously associated with receptor binding and entry [35][36][37]. Curiously, none of the polymorphisms associated with the SD2 domain (which encompasses amino acids 589-677) achieve high prevalence, indicating that perhaps the cost-benefit of these variations is not significantly capable of driving selective pressure.…”