Multimeric nanobodies from camelid engineered mice and llamas potently neutralize SARS-CoV-2 variants
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Abstract
Since the start of the coronavirus disease-2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused more than 2 million deaths worldwide. Multiple vaccines have been deployed to date, but the continual evolution of the viral receptor-binding domain (RBD) has recently challenged their efficacy. In particular, SARS-CoV-2 variants originating in the U.K. (B.1.1.7), South Africa (B.1.351) and New York (B.1.526) have reduced neutralization activity from convalescent sera and compromised the efficacy of antibody cocktails that received emergency use authorization. Whereas vaccines can be updated periodically to account for emerging variants, complementary strategies are urgently needed to avert viral escape. One potential alternative is the use of camelid VHHs (also known as nanobodies), which due to their small size can recognize protein crevices that are inaccessible to conventional antibodies. Here, we isolate anti-RBD nanobodies from llamas and “nanomice” we engineered to produce VHHs cloned from alpacas, dromedaries and camels. Through binding assays and cryo-electron microscopy, we identified two sets of highly neutralizing nanobodies. The first group expresses VHHs that circumvent RBD antigenic drift by recognizing a region outside the ACE2-binding site that is conserved in coronaviruses but is not typically targeted by monoclonal antibodies. The second group is almost exclusively focused to the RBD-ACE2 interface and fails to neutralize pseudoviruses carrying the E484K or N501Y substitutions. Notably however, they do neutralize the RBD variants when expressed as homotrimers, rivaling the most potent antibodies produced to date against SARS-CoV-2. These findings demonstrate that multivalent nanobodies overcome SARS-CoV-2 variant mutations through two separate mechanisms: enhanced avidity for the ACE2 binding domain, and recognition of conserved epitopes largely inaccessible to human antibodies. Therefore, while new SARS-CoV-2 mutants will continue to emerge, nanobodies represent promising tools to prevent COVID-19 mortality when vaccines are compromised.
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SciScore for 10.1101/2021.03.04.433768: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:To overcome the limitations of conventional antibodies we produced anti-RBD Nbs. As previous studies have shown, Nbs are well poised to accomplish this because of their versatility and capacity for multivalency (Esparza et al., …
SciScore for 10.1101/2021.03.04.433768: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:To overcome the limitations of conventional antibodies we produced anti-RBD Nbs. As previous studies have shown, Nbs are well poised to accomplish this because of their versatility and capacity for multivalency (Esparza et al., 2020; Hanke et al., 2020; Huo et al., 2020; Koenig et al., 2021; Schoof et al., 2020; Tortorici et al., 2020; Wrapp et al., 2020). From immunized llamas and nanomice we have isolated and characterized two sets of Nbs that effectively neutralize pseudotyped viruses carrying RBD mutations from U.K. and South African-New York variants. Similar to human antibodies, Nbs from the first group (Nb15, Nb56) hinder ACE2 binding to the spike of the original virus, but they are ineffective against viruses that carry E484K or N501Y substitutions in the RBD. However, in multimeric form, these Nbs overcome the block and display remarkable neutralization potency. This reversal is likely the result of increased avidity for the trimeric spike, or possibly the simultaneous cross-linking of multiple spikes on the viral membrane. The second group of Nbs (Nb12, Nb30) associates with a region that is highly conserved among coronaviridae (Wrapp et al., 2020) but remains inaccessible to most human antibodies. As this region lies outside the ACE2 binding motif, Nb-RBD contacts are unaffected by E484K or N501Y. Importantly, even though the conserved domain does not overlap with the ACE2 binding motif, our structural studies show that Nbs of this class sterically interfere with A...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
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