Open AccessMultivariate mining of an alpaca immune repertoire identifies potent cross-neutralizing SARS-CoV-2 nanobodies
Author(s) -
Leo Hanke,
Daniel J. Sheward,
Alec Pankow,
Laura Perez Vidakovics,
Vivien Karl,
Chang-Il Kim,
Egon Urgard,
Natalie Smith,
Juan AstorgaWells,
Simon Ekström,
Jonathan M. Coquet,
Gerald M. McInerney,
Ben Murrell
Publication year - 2022
Publication title -
science advances
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.928
H-Index - 146
ISSN - 2375-2548
DOI - 10.1126/sciadv.abm0220
Subject(s) - phage display , computational biology , coronavirus , epitope , covid-19 , epitope mapping , neutralization , biology , antibody , virology , binding site , receptor , chemistry , virus , microbiology and biotechnology , biochemistry , medicine , genetics , disease , pathology , infectious disease (medical specialty)
Conventional approaches to isolate and characterize nanobodies are laborious. We combine phage display, multivariate enrichment, next-generation sequencing, and a streamlined screening strategy to identify numerous anti–severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nanobodies. We characterize their potency and specificity using neutralization assays and hydrogen/deuterium exchange mass spectrometry (HDX-MS). The most potent nanobodies bind to the receptor binding motif of the receptor binding domain (RBD), and we identify two exceptionally potent members of this category (with monomeric half-maximal inhibitory concentrations around 13 and 16 ng/ml). Other nanobodies bind to a more conserved epitope on the side of the RBD and are able to potently neutralize the SARS-CoV-2 founder virus (42 ng/ml), the Beta variant (B.1.351/501Y.V2) (35 ng/ml), and also cross-neutralize the more distantly related SARS-CoV-1 (0.46 μg/ml). The approach presented here is well suited for the screening of phage libraries to identify functional nanobodies for various biomedical and biochemical applications.