Multivariate mining of an alpaca immune repertoire identifies potent cross-neutralizing SARS-CoV-2 nanobodies
Open accessPublished version of a preprint
Abstract
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.
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- Authors
- Hanke, L., Sheward, D. J., Pankow, A., Vidakovics, L. P., Karl, V., Kim, C., Urgard, E., Smith, N. L., Astorga-Wells, J., Ekström, S., Coquet, J. M., McInerney, G. M., & Murrell, B.
- Affiliations
- Karolinska Institutet (SE)
- University of Cape Town (ZA)
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden.
- Lund University (SE)
- Corresponding author
- McInerney, Gerald M.
- Murrell, Ben
- ORCID
- Venue
- Science Advances
- Published
- 2022-03-25
- Volume
- 8
- Issue
- 12
- Pages
- eabm0220-eabm0220
- ISSN
- 2375-2548 (ISSN-L)
- PMC
- PMC8956255
- OpenAlex
- W4220841727
- Cited by
- 38
- References
- 12
- Citations by year
- 2026: 6 · 2025: 6 · 2024: 14 · 2023: 8 · 2022: 4
- FWCI
- 3.90
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Science Advances (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Lund University Publications (Lund University) (submittedVersion)
- Funders
- European Commission (101003653)
- Vetenskapsrådet (2018-03914, 2018-02381)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Monoclonal and Polyclonal Antibodies Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Keywords
- SARS-CoV-2, nanobodies, cross-neutralizing antibodies, receptor binding domain, phage display, neutralization potency, Beta variant, SARS-CoV-1, epitope mapping, hydrogen-deuterium exchange mass spectrometry
- MeSH terms
- COVID-19, SARS-CoV-2, Animals, Antibodies, Monoclonal, Antibodies, Viral, Camelids, New World, Humans, Membrane Glycoproteins, Neutralization Tests, Viral Envelope Proteins, Single-Domain Antibodies, Spike Glycoprotein, Coronavirus
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