High-throughput screening of spike variants uncovers the key residues that alter the affinity and antigenicity of SARS-CoV-2

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has elicited a worldwide pandemic since late 2019. There has been ~675 million confirmed coronavirus disease 2019 (COVID-19) cases, leading to more than 6.8 million deaths as of March 1, 2023. Five SARS-CoV-2 variants of concern (VOCs) were tracked as they emerged and were subsequently characterized. However, it is still difficult to predict the next dominant variant due to the rapid evolution of its spike (S) glycoprotein, which affects the binding activity between cellular receptor angiotensin-converting enzyme 2 (ACE2) and blocks the presenting epitope from humoral monoclonal antibody (mAb) recognition. Here, we established a robust mammalian cell-surface-display platform to study the interactions of S-ACE2 and S-mAb on a large scale. A lentivirus library of S variants was generated via in silico chip synthesis followed by site-directed saturation mutagenesis, after which the enriched candidates were acquired through single-cell fluorescence sorting and analyzed by third-generation DNA sequencing technologies. The mutational landscape provides a blueprint for understanding the key residues of the S protein binding affinity to ACE2 and mAb evasion. It was found that S205F, Y453F, Q493A, Q493M, Q498H, Q498Y, N501F, and N501T showed a 3–12-fold increase in infectivity, of which Y453F, Q493A, and Q498Y exhibited at least a 10-fold resistance to mAbs REGN10933, LY-CoV555, and REGN10987, respectively. These methods for mammalian cells may assist in the precise control of SARS-CoV-2 in the future.

Optimization and validation of a virus‐like particle pseudotyped virus neutralization assay for SARS‐CoV‐2

“…SARS‐CoV‐2 is characterized by a large, positive‐sense, single‐stranded genomic RNA that approximately 30 kb in length. This RNA encodes 16 nonstructural proteins and four structural proteins: the membrane (M), envelope (E), spike (S), and nucleocapsid (N) proteins 7 . Spike of the virus directly interacts with the ACE2 protein and is the main target of vaccines and therapeutic drugs 8,9 .…”

Sera from breakthrough infections with SARS-CoV-2 BA.5 or BF.7 showed lower neutralization activity against XBB.1.5 and CH.1.1

“…The virus evolution from Wuhan-Hu-1, B.1, Alpha, Beta, Gamma, Delta virus has led to the diverse immune escape patterns. Since the emergence of the Omicron variant, which has shown marked immune escape capabilities, an increasing number of breakthrough infection cases have been reported [ 5 ].…”