Broadly neutralizing and protective nanobodies against SARS-CoV-2 Omicron subvariants BA.1, BA.2, and BA.4/5 and diverse sarbecoviruses

Abstract

As SARS-CoV-2 Omicron and other variants of concern (VOCs) continue spreading worldwide, development of antibodies and vaccines to confer broad and protective activity is a global priority. Here, we report on the identification of a special group of nanobodies from immunized alpaca with potency against diverse VOCs including Omicron subvariants BA.1, BA.2 and BA.4/5, SARS-CoV-1, and major sarbecoviruses. Crystal structure analysis of one representative nanobody, 3-2A2-4, discovers a highly conserved epitope located between the cryptic and the outer face of the receptor binding domain (RBD), distinctive from the receptor ACE2 binding site. Cryo-EM and biochemical evaluation reveal that 3-2A2-4 interferes structural alteration of RBD required for ACE2 binding. Passive delivery of 3-2A2-4 protects K18-hACE2 mice from infection of authentic SARS-CoV-2 Delta and Omicron. Identification of these unique nanobodies will inform the development of next generation antibody therapies and design of pan-sarbecovirus vaccines.

Nanobodies against SARS-CoV-2 reduced virus load in the brain of challenged mice and neutralized Wuhan, Delta and Omicron Variants

“…We obtained different groups of Nbs that exhibited high sequence variability and were originated from a diverse set of V, D, and J genes (Fig 1). Our results are consistent with those obtained by other groups screening camelid-derived libraries, where an impressive diversity in the Nb nucleotide sequence, specificity and neutralizing capacity was found, especially after successive immunizations to promote the development of superimmunity [48,49]. This is particularly relevant considering the emergence of new VOCs, since the screening of a large library, like the one we described in this work, constructed from hyperimmunized animals, can broaden the type of Nbs obtained and increase the probability of finding binders that recognize new variants.…”

Proteomics Platform Reveals Broad-Spectrum Nanobodies for SARS-CoV-2 Variant Neutralization

“…Importantly, both C-282 and C-39 showed superior affinities when binding to multiple SARS-CoV-2 variants compared to previously reported nanobodies (Figure ). , Furthermore, a comparison with results from pseudovirus experiments revealed that these nanobodies exhibit high neutralizing activity against multiple mutant variants, with IC 50 values comparable to those of previously reported nanobodies (Supporting Information Table S2).…”

“…In 2022, researchers identified and prepared 124 purified nanobodies exhibiting neutralizing activity against the prototype SARS-CoV-2 pseudovirus. However, only three nanobodies demonstrated broad neutralizing activity against WT, Alpha, Delta, and Omicron variants . These findings underscore the limitations of relying exclusively on traditional ELISA, or pseudovirus, and live virus-based assays, as they can identify only one variant at a time.…”

“…The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID- 19), has sparked a global pandemic, with the number of COVID-19-related deaths surpassing 7 million as of May 2023. The virus gains entry into the host through its spike protein, which binds to the host cell's angiotensin-converting enzyme 2 (ACE2) receptor.…”

Biomimetic Nanotechnology for SARS-CoV-2 Treatment

“…Recently, researchers reported the isolation and characterization of a novel group of nanobodies from immunized alpacas [ 57 ]. These nanobodies, exemplified by the protein 3-2A2-4, have potency against Omicron subvariants BA.1, BA.2, BA.2.12.1, and BA.4/5, SARS-CoV-1, and key representative coronaviruses from bats and pangolins.…”