DOI: 10.7272/q68s4n53
title: Converting non-neutralizing SARS-CoV-2 antibodies targeting conserved epitopes into broad-spectrum inhibitors through receptor blockade

description: All but one of the authorized monoclonal antibody-based treatments for
 SARS-CoV-2 are ineffective against Omicron, highlighting the critical need
 for biologics capable of overcoming SARS-CoV-2 evolution. These
 ineffective therapeutic antibodies target epitopes that are not highly
 conserved. Here we describe broad-spectrum SARS-CoV-2 inhibitors developed
 by tethering the receptor-binding, angiotensin-converting enzyme 2 (ACE2)
 domain to antibodies that were originally defined as non-neutralizing, but
 that also target highly conserved epitopes in the viral spike protein.
 These inhibitors, called Receptor engaged conserved non-neutralizing
 Antibodies (ReconnAbs), potently neutralize all SARS-CoV-2 variants of
 concern (VOC), including Omicron. Neutralization potency is lost when the
 linker joining the two ReconnAb components is severed. A bispecific
 ReconnAb, made by linking ACE2 to two non-neutralizing antibodies with
 non-overlapping conserved epitopes, defined here, shows sub-nanomolar
 neutralizing activity against all VOCs, including Omicron. Given their
 conserved targets and modular nature, ReconnAbs have potential to act as
 broad-spectrum therapeutics against SARS-CoV-2 and other emerging pandemic
 diseases.
description: A library of antibodies directed against SARS-CoV-2 Spike (S) protein was developed using paired antibody sequences, meaning antibody sequences for which the heavy and light chain are both known, from the Coronavirus Antibody Database, CoV-AbDab. All antibody sequences from convalescent COVID-19 donors which had been deposited before July 9th, 2021 (http://opig.stats.ox.ac.uk/webapps/covabdab/static/downloads/CoV-AbDab_090721.csv), were inserted into a table, categorized by their binding to the SARS-CoV-2 RBD portion of the spike protein or to a non-RBD portion of SARS-CoV-2 spike. Following this analysis, antibodies that were cataloged for non-RBD binding were preferentially identified, resulting in a total of 385 paired antibody sequences. For these non-RBD binding antibodies, the amino acid sequences of the corresponding heavy chain and light chain V-genes and CDR3 regions, already compiled from the Coronavirus Antibody Database, were imported into Geneious Prime v2021.1.1 (a bioinformatics software; geneious.com). Using Geneious Prime, the heavy chain sequences and light chain sequences were separately analyzed to produce phylogenetic trees. For these phylogenetic trees, RBD binding antibodies were also included to ensure selection of antibody sequences that were both non-RBD binding and clearly distinct from RBD-binding sequences. 371 RBD binding antibody, 59 germline antibody, and 325 non-RBD binding antibody nucleic acid sequences of the corresponding heavy chain and light chain genes were imported, for a total of 755 heavy chain and light chain sequences (696 excluding germline antibodies). The sequences were first aligned using the MUSCLE algorithm, and then two phylogenetic trees were made, both using PhyML 3.3.20180621.
description: Alignments and phylognetic trees were made using Genious Prime
 v2021.1.1, but alignments and trees are saved as .fasta and .newick files
 and so compatible with open-source alternatives.