A recent article published on the website of the bioRxiv* preprint server demonstrated the structural basis for the neutralization of Omicron variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by 002-S21F2, an extended neutralizing antibody of SARS-CoV-2.
Study: Structural perspectives for the neutralization of BA.1 and BA.2 Omicron variants by a broadly neutralizing SARS-CoV-2 antibody. Image credit: Huen Structure Bio / Shutterstock
context
The current coronavirus disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 has resulted in more than 524 million cases and six million deaths worldwide. Intensive efforts continue worldwide to develop, analyze and adopt vaccines or other medical alternatives against COVID-19, such as monoclonal antibody (mAb) treatment. However, SARS-CoV-2 variants that evade neutralization conferred by therapeutic COVID-19 antibodies and immunity acquired through vaccination or infection have emerged due to widespread viral transmission and crucial mutations. .
In particular, most of the currently approved COVID-19 therapeutic antibodies have shown reduced neutralizing efficacy against the Omicron variant of SARS-CoV-2 and its sublines, such as BA.2 and BA.1, due to approximately 30 mutations in its spike (S) protein. This underscores the continuing need to discover mAbs that are effective against new mutants of SARS-CoV-2.
About the study
The authors of the present research previously assessed humoral immunity in 42 COVID-19 convalescents who experienced mild symptoms after transmission of the ancestral Wuhan (WA.1) strain of SARS-CoV-2 in 2020.
Identification of a broad and potent SARS-CoV-2 RBD-specific human monoclonal antibody 002-S21F2. (A) The overall strategy for the isolation of RBD-specific mAbs described in this study. (B) 002-S21F2 was tested for binding to SARS-CoV-2 variants of concern (VOC) WA.1, Alpha, Beta, Gamma, Delta and Omicron spike proteins. (C) Authentic live virus neutralization curves of 002-S21F2 for SARS-CoV-2 WA.1, Alpha, Beta, Gamma, Delta, and Omicron (BA.1 and BA.2) VOCs. Neutralization was determined on Vero-TMPRSS2 cells using a focus reduction assay. (D) IC50 values of the 50% inhibitory concentration of 002-S21F2-mediated neutralization were obtained from live SARS-CoV-2 COV neutralization assays. Affinity constant (KD) values calculated from binding curves for two mAbs, as measured by MSD binding assays, are plotted.
In the current study, researchers selected five subjects from previous research with measurable frequencies of SARS-CoV-2 receptor binding domain (RBD)-specific memory B cells, high concentrations of RBD binding and substantial levels of neutralization of live SARS-CoV-2 strain WA.1 for the production of mAbs targeting the RBD of SARS-CoV-2.
The team screened 804 class-switched B cells engaging with the SARS-CoV-2 fluorescent RBD probe and amplified 398 coupled light and heavy chain antibody gene sequences. In addition, they performed enzyme-linked immunosorbent assay (ELISA) profiling of the selected mAbs.
Scientists assessed the protein S-binding abilities of antibody 002-S21F2 of several SARS-CoV-2 variants of concern (VOCs) through a multiplex electrochemiluminescence experiment. They used cryogenic electron microscopy (cryo-EM) structures of full-length immunoglobulin G (IgG) 002-S21F2 complexed with the S proteins Omicron and WA.1 to delineate the molecular features and mechanisms of broad-spectrum neutralization from SARS-CoV-2 from 002-S21F2.
Results
The results of the study indicate that the authors successfully cloned and produced 208 mAbs targeting the RBD of SARS-CoV-2 from the 398 matched amplified light and heavy chain antibody sequences. In addition, ELISA screening yielded 92 mAbs binding to SARS-CoV-2 RBD. The majority of these mAbs exhibited low levels of somatic hypermutations (SHMs) in their light and heavy chains, indicating that they were recently generated from a naïve B cell population. Of these antibodies, 48 mAbs successfully prevented contact between host angiotensin-converting enzyme 2 (ACE2) and viral RBD, and 18 effectively neutralized live virus with half-maximal inhibitory concentrations. (IC50) ranging from 0.05 to 17 µg/ml.
The 002-S21F2 antibody has distinct genetic and epitope contact characteristics compared to therapeutic SARS-CoV-2 antibodies.(A) Comparison of the genetic characteristic of mAb 002-S21F2 with therapeutic mAbs in the clinic. The mAbs neutralizing the Omicron are highlighted in bold and in red. (B) Comparison of epitope site 002-S21F2 (green) with S309 (Sotrovimab) (red outline), Ly-CoV1404 (Bebtelovimab) (yellow outline) epitopes on the RBD of SARS-CoV-2.
The authors noted that of all mAbs that neutralized the live WA.1 sequence of SARS-CoV-2, the 002-S21F2 antibody was the most effective. They found that the 002-S21F2 antibody adhered to all SARS-CoV-2 variant S proteins analyzed with the same affinity. In addition, the 002-S21F2 antibody bound to the prefusion-stabilized S protein WA.1 showing picomolar affinity according to dual layer interferometry. In addition, the human antibody 002-S21F2, which targets the RBD of SARS-CoV-2, effectively neutralized live viral isolates of SARS-CoV-2 VOCs, including VOCs Beta, Alpha, Delta, Gamma and Omicron BA.2 and BA.1 with CI50 ranging from 0.02 to 0.05 µg/ml.
This quasi-germline antibody has genetic characteristics that distinguish it from other SARS-CoV-2 mAbs. 002-S21F2 identified an epitope on the outer surface of RBD, i.e. the class 3 surface, according to structural cryo-EM studies. Moreover, this epitope was outside the ACE2 commitment motif, and its distinct molecular properties allowed it to overcome the mutations seen in Omicron variants.
The antigenic residues addressed by the broadly neutralizing antibody (bnAb), 002-S21F2, were significantly conserved between previous and current SARS-CoV-2 COVs. Structural data revealed that antibody 002-S21F2 maintained effective neutralization against Omicron BA.2 and BA.1 variants possessing epitope mutations at N440K and G339D. Since the recently listed Omicron variants BA.2.12.1, BA.2.13, BA.5, BA.4 and BA.3 did not show additional changes in the area of the 002-S21F2 epitope, scientists assumed that the neutralizing ability of this monoclonal antibody would persist against them. Furthermore, sequence alignment of Sarbecovirus RBDs demonstrated that 10 of the 19 conserved SARS-CoV residues were addressed by 002-S21F2, indicating the possibility of cross-reactivity with other Sarbecoviruses.
The structural comparison of other class 3 mAbs, such as the two current therapeutic mAbs targeting Omicron, Bebtelovimab (Ly-CoV1404) and Sotrovimab (S309), and the 002-S21F2 epitope demonstrated certain similarities between the C135 and 002-S21F binding sites. However, C135 did not neutralize Omicron’s VOC.
Furthermore, structural analysis revealed that the small number of SHMs found in this near-germline bnAb 002-S21F2 were not involved in antigenic site recognition, suggesting that the fingerprints of these bnAbs could offer a model for the rational development of the COVID-19 vaccine.
Overall, the authors mentioned that the identification and detailed structural characterization of 002-S21F2 in this study provided important information regarding their broad and efficient neutralization of SARS-CoV-2 VOCs.
*bird is important
bioRxiv publishes preliminary scientific reports that are not peer-reviewed and therefore should not be considered conclusive, guide clinical practice/health behavior or be treated as established information.
Journal reference:
- Perspectives structurelles pour la neutralization des variants Omicron BA.1 and BA.2 for an anticorps SARS-CoV-2 à large neutralization. Sanjeev Kumar, Anamika Patel, Lilin Lai, Chennareddy Chakravarthy, Rajesh Valanparambil, Meredith E. Davis-Gardner, Venkata Viswanadh Edara, Susanne Linderman, Elluri Seetharami Reddy, Kamalvishnu Gottimukkala, Kaustuv Nayak, Prashant Bajpai, Vanshika Singh, Vanshika Singh, , Hans Verkerke, Andrew S. Neish, John D. Roback, Grace Mantus, Pawan Kumar Goel, Manju Rahi, Carl W. Davis, Jens Wrammert, Mehul S. Suthar, Rafi Ahmed, Eric Ortlund, Amit Sharma, Kaja Murali Krishna, Anmol Chandele. bioRxiv preprint 2022, DOI: https://doi.org/10.1101/2022.05.13.491770, https://www.biorxiv.org/content/10.1101/2022.05.13.491770v1