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Nanobody Repertoires for Exposing Vulnerabilities of SARS-CoV-2.

ABSTRACT: Despite the great promise of vaccines, the COVID-19 pandemic is ongoing and future serious outbreaks are highly likely, so that multi-pronged containment strategies will be required for many years. Nanobodies are the smallest naturally occurring single domain antigen binding proteins identified to date, possessing numerous properties advantageous to their production and use. We present a large repertoire of high affinity nanobodies against SARS-CoV-2 Spike protein with excellent kinetic and viral neutralization properties, which can be strongly enhanced with oligomerization. This repertoire samples the epitope landscape of the Spike ectodomain inside and outside the receptor binding domain, recognizing a multitude of distinct epitopes and revealing multiple neutralization targets of pseudoviruses and authentic SARS-CoV-2, including in primary human airway epithelial cells. Combinatorial nanobody mixtures show highly synergistic activities, and are resistant to mutational escape and emerging viral variants of concern. These nanobodies establish an exceptional resource for superior COVID-19 prophylactics and therapeutics.

SUBMITTER: Mast FD

PROVIDER: S-EPMC8043454 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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Nanobody Repertoires for Exposing Vulnerabilities of SARS-CoV-2.

Mast Fred D FD Fridy Peter C PC Ketaren Natalia E NE Wang Junjie J Jacobs Erica Y EY Olivier Jean Paul JP Sanyal Tanmoy T Molloy Kelly R KR Schmidt Fabian F Rutkowska Magda M Weisblum Yiska Y Rich Lucille M LM Vanderwall Elizabeth R ER Dambrauskas Nicolas N Vigdorovich Vladimir V Keegan Sarah S Jiler Jacob B JB Stein Milana E ME Olinares Paul Dominic B PDB Hatziioannou Theodora T Sather D Noah DN Debley Jason S JS Fenyö David D Sali Andrej A Bieniasz Paul D PD Aitchison John D JD Chait Brian T BT Rout Michael P MP

bioRxiv : the preprint server for biology 20210410

Despite the great promise of vaccines, the COVID-19 pandemic is ongoing and future serious outbreaks are highly likely, so that multi-pronged containment strategies will be required for many years. Nanobodies are the smallest naturally occurring single domain antigen binding proteins identified to date, possessing numerous properties advantageous to their production and use. We present a large repertoire of high affinity nanobodies against SARS-CoV-2 Spike protein with excellent kinetic and vira ...[more]

PMID: 33851164

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Project description:The highly transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected more than 253 million people, claiming ∼5.1 million lives to date. Although mandatory quarantines, lockdowns, and vaccinations help curb viral transmission, there is a pressing need for cost-effective systems to mitigate the viral spread. Here, we present a generic strategy for capturing SARS-CoV-2 through functionalized cellulose materials. Specifically, we developed a bifunctional fusion protein consisting of a cellulose-binding domain and a nanobody (Nb) targeting the receptor-binding domain of SARS-CoV-2. The immobilization of the fusion proteins on cellulose substrates enhanced the capture efficiency of Nbs against SARS-CoV-2 pseudoviruses of the wild type and the D614G variant, the latter of which has been shown to confer higher infectivity. Furthermore, the fusion protein was integrated into a customizable chromatography with highly porous cellulose to capture viruses from complex fluids in a continuous fashion. By capturing and containing viruses through the Nb-functionalized cellulose, our work may find utilities in virus sampling and filtration through the development of paper-based diagnostics, environmental tracking of viral spread, and reducing the viral load from infected individuals. IMPORTANCE The ongoing efforts to address the COVID-19 pandemic center around the development of diagnostics, preventative measures, and therapeutic strategies. In comparison to existing work, we have provided a complementary strategy to capture SARS-CoV-2 by functionalized cellulose materials through paper-based diagnostics as well as virus filtration in perishable samples. Specifically, we developed a bifunctional fusion protein consisting of both a cellulose-binding domain and a nanobody specific for the receptor-binding domain of SARS-CoV-2. As a proof of concept, the fusion protein-coated cellulose substrates exhibited enhanced capture efficiency against SARS-CoV-2 pseudovirus of both the wild type and the D614G variant, the latter of which has been shown to confer higher infectivity. Furthermore, the fusion protein was integrated into a customizable chromatography for binding viruses from complex biological fluids in a highly continuous and cost-effective manner. Such antigen-specific capture can potentially immobilize viruses of interest for viral detection and removal, which contrasts with the common size- or affinity-based filtration devices that bind a broad range of bacteria, viruses, fungi, and cytokines present in blood (https://clinicaltrials.gov/ct2/show/NCT04413955). Additionally, since our work focuses on capturing and concentrating viruses from surfaces and fluids as a means to improve detection, it can serve as an "add-on" technology to complement existing viral detection methods, many of which have been largely focusing on improving intrinsic sensitivities.

Dataset Information

Nanobody Repertoires for Exposing Vulnerabilities of SARS-CoV-2.

Publications

Nanobody Repertoires for Exposing Vulnerabilities of SARS-CoV-2.

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