Mapping SARS-CoV-2 spike determinants of escape from antibodies

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19 disease and has resulted in a global pandemic that has subsequently led to the search for effective interventions. The spike protein plays a crucial role in viral entry into host cells and it has many epitopes that are recognized by neutralizing antibodies making it a target of vaccines. Monitoring and evaluation of the evolution of SARS-CoV-2 is essential as emerging variants may alter the effectiveness of natural and vaccine induced immune responses. The aim of this study was to probe the effect of emerging variants detected in South Africa on neutralization by SARS-CoV-2 directed antibodies in convalescent plasma. Four SARS-CoV-2 sublineages circulating in South Africa during December 2020 were identified in a parent study and characterized in this study. Protein analysis software tools were used to visualize changes in structural interactions between the spike and the angiotensin-converting enzyme 2 (ACE2) receptor and monoclonal antibodies after in silico mutation of relevant residues in the protein structure. Site-directed mutagenesis was used to introduce sublineage mutations into the wild type spike gene sequence. Wild type and mutated SARS-CoV-2 spike trimer proteins were generated and characterized by mammalian cell expression, chromatography-based protein purification and Sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The effect of mutations on the binding of SARS-CoV-2 directed antibodies was assessed by enzyme-linked immunoassay (ELISA). Wild type and mutated SARS-CoV-2 spike-pseudotyped viruses were also generated. The impact of viral mutations on the neutralization capacity of the antibodies present in convalescent plasma elicited by the ancestral strain was assessed. The results of this study revealed that convalescent plasma had reduced binding to two local sub-lineage viruses when compared to the wild type virus. The change in binding may have resulted from mutations that cause the loss of epitope recognition. No significant changes were observed in the neutralization sensitivity when the wild type was compared to sub-lineage pseudoviruses, however, significant differences in neutralization sensitivity were observed when sublineages were compared with other sub-lineages characterized in this study. This study supports current literature on the need for robust genomic surveillance and immune characterization of emerging variants and related sub-lineages.