Anti-SARS-CoV-2 Omicron Antibodies Isolated from a SARS-CoV-2 Delta Semi-Immune Phage Display Library

Abstract

This report describes the discovery and characterization of antibodies with potential broad SARS-CoV-2 neutralization profiles. The antibodies were obtained from a phage display library built with the VH repertoire of a convalescent COVID-19 patient who was infected with SARS-CoV-2 B.1.617.2 (Delta). The patient received a single dose of Ad5-nCoV vaccine (Convidecia™, CanSino Biologics Inc.) one month before developing COVID-19 symptoms. Four synthetic VL libraries were used as counterparts of the immune VH repertoire. After three rounds of panning with SARS-CoV-2 receptor-binding domain wildtype (RBD-WT) 34 unique scFvs, were identified, with 27 cross-reactive for the RBD-WT and RBD Delta (RBD-DT), and seven specifics for the RBD-WT. The cross-reactive scFvs were more diverse than the RBD-WT specific ones, being encoded by several IGHV genes from the IGHV1 and IGHV3 families combined with short HCDR3s. Six cross-reactive scFvs and one RBD-WT specific scFv were converted to human IgG1 (hIgG1). Out of the seven antibodies, six blocked the RBD-WT binding to angiotensin converting enzyme 2 (ACE2), suggesting these antibodies may neutralize the SARS-CoV-2 infection. Importantly, one of the antibodies also recognized the RBD from the B.1.1.529 (Omicron) isolate, implying that the VH repertoire of the convalescent patient would protect against SARS-CoV-2 Wildtype, Delta, and Omicron. From a practical viewpoint, the triple cross-reactive antibody provides the substrate for developing therapeutic antibodies with a broad SARS-CoV-2 neutralization profile.

In Vitro and In Vivo Characterization of a Broadly Neutralizing Anti-SARS-CoV-2 Antibody Isolated from a Semi-Immune Phage Display Library

“…Consistent with this suggestion, bebtelovimab belongs to class III of SARS-CoV-2 neutralizing antibodies, which are encoded by the IGHV1 and IGHV2 gene families. As reported previously [ 12 ] IgG-A7 is encoded by the IGHV1-24 germline gene, allowing to include IgG-A7 in this class of SARS-CoV-2 neutralizing antibodies.…”

“…Sotrovimab is the only therapeutic antibody binding residues away from the RBD:hACE2 interface ( Figure 6 , bottom panel) and hence, it does not block RBD:hACE2 interaction. IgG-A7 blocks the RBD:hACE2 interaction [ 12 ] and thus seems to recognize residues in the RBD interface with hACE2, suggesting a mechanism of neutralization which is different from sotrovimab.…”

“…IgG-A7 was cloned and expressed as reported in Mendoza-Salazar et al [ 12 ]. To set up and validate the assays, as well as a reference in the characterization of IgG-A7, CB6 was used as a positive control [ 14 ].…”

“…In a previous report [ 12 ], we described the isolation of antibodies from a semi-immune scFv phage display library built with four synthetic V L libraries combined with the immune V H repertoire of a convalescent COVID-19 patient. The patient received a single dose of Convidecia™ (CanSino Biologics Inc., Tianjin, China) and a few months later was infected with SARS-CoV-2 Delta, exhibiting typical symptoms of COVID-19.…”

Isolation of SARS-CoV-2-blocking recombinant antibody fragments and characterisation of their binding to variant spike proteins

“…A variety of recombinant antibody fragments have been isolated against SARS-CoV-2 to date, using cloning approaches from antibodies from COVID-19 patients (Ebihara et al, 2021), antibody gene libraries derived from convalescent COVID-19 patients (Bertoglio et al, 2021;Mendoza-Salazar et al, 2022;Minenkova et al, 2022), or by immunising animals such as alpacas (Güttler et al, 2021). Phage display has also been utilised to isolate nanobodies (single-domain antibodies derived from camelids; Muyldermans et al, 2013) with SARS-CoV-2 neutralising ability (Zhao et al, 2022), as well as scFv-Fc fusion proteins against nucleocapsid protein for use in diagnostics (Kim et al, 2021).…”