Abstract
The rapid adaptation of SARS-CoV-2 within the host species and the increased viral transmission triggered the evolution of different SARS-CoV-2 variants. Though numerous monoclonal antibodies (mAbs) have been identified as prophylactic therapy for SARS-CoV-2, the ongoing surge in the number of SARS-CoV-2 infections shows the importance of understanding the mutations in the spike and developing novel vaccine strategies to target all variants. Here, we report the map of experimentally validated 74 SARS-CoV-2 neutralizing mAb binding epitopes of all variants. The majority (87.84%) of the potent neutralizing epitopes are localized to the receptor-binding domain (RBD) and overlap with each other, whereas limited (12.16%) epitopes are found in the N-terminal domain (NTD). Notably, 69 out of 74 mAb targets have at least one mutation at the epitope sites. The potent epitopes found in the RBD show higher mutations (4-10aa) compared to lower or modest neutralizing antibodies, suggesting that these epitopes might co-evolve with the immune pressure. The current study shows the importance of determining the critical mutations at the antibody recognition epitopes, leading to the development of broadly reactive immunogens targeting multiple SARS-CoV-2 variants. Further, vaccines inducing both humoral and cell-mediated immune responses might prevent the escape of SARS-CoV-2 variants from neutralizing antibodies.
Keywords: SARS-CoV-2, Epitopes, Omicron variant, Delta variant, Monoclonal antibodies
Introduction
Severe acute respiratory syndrome coronavirus -2 (SARS-CoV-2) emerged in Wuhan, China in 2019 [1] and rapidly spread across the globe with more than 220 countries being affected [2]. SARS-CoV-2 is highly contagious and causes mild to severe respiratory illness in humans and more than 600 million confirmed cases with 6 million deaths have been reported worldwide [2]. Coronavirus infection begins by the attachment of its trimeric spike glycoprotein to the host cell membrane receptor to enter into the cells. The spike protein consists of S1 and S2 domains, S1 contains the receptor-binding domain (RBD) which interacts with the cellular receptor, whereas S2 is involved in cell fusion [3]. Intervening the interaction of spike and its receptor would aid in the early prevention of virus infections. Therefore, spike glycoprotein is a key target for developing vaccines or therapeutics. The spike protein of SARS-CoV-2 uses angiotensin-converting enzyme-2 (ACE2) [3] an ectopeptidase as an entry receptor to initiate the infection cycle. Several vaccine candidates have been developed soon after the SARS-CoV-2 outbreak using the spike glycoprotein, which induces robust humoral re-sponses against SARS-CoV-2 and has been approved and licensed by WHO for human administration [4,5]. However, during the pandemic, the sudden increase in the human-human transmission and severity of the disease mainly caused by the spike varants such as the Delta promoted the usage of convalescent serum/plasma therapy as an immediate treatment option for SARS-CoV-2[6,7]. The modest efficacy of the plasma therapy [8] due to the diverse non-specific neutralizing antibodies led several research groups to develop highly specific potent monoclonal antibodies (mAbs) targeting spike protein. The recent advancements in molecular biology led to the rapid identification, engineering and production of potent mAbs against infectious diseases in a short time frame [9,10]. This has been exemplified from the recent SARS-CoV-2 outbreak wherein several potent neutralizing mAbs have been developed either directly from the B-cells or by phage display library of lymphocytes from the patients recovered from SARS-CoV-2 infection [5,11]. Due to the rapid clearance of the virus from severely infected patients, several mAbs with high sensitivity or specificity have been approved by FDA for immediate human administration [5].
The increasing trend of human-human transmission and accumulation of diverse favorable mutations in the spike protein of SARS-CoV-2 leads to the generation of several naturally occurring variants including the Delta and Omicron [7]. Recent reports demonstrates that selective pressures mediated by mass vaccinations as well as adaptation of SARS-CoV-2 to mAb treatment might facilitate the emergence of novel variants which are resistant to antibodies and shows higher transmission [12,13]. Proper understanding of the conservation of amino acid mutations within the Alpha, Beta, Gamma, Delta, and Omicron variants and changes associated at critical epitope residues of neutralizing monoclonal antibodies delineates the importance of developing novel vaccine candidates or therapeutics targeting current or future SARS-CoV-2 variants. A combined comparison between the neutralizing antibody binding epitopes and their mutations in the spike protein of all major variants of SARS-CoV-2 remain unclear which is important to understand the chances of immune escape by SARS-CoV-2 variants. In this study, we report the map of experimentally evaluated 74 SARS-CoV-2 po-tent neutralizing monoclonal antibody epitopes and compared them with naturally occurring escape variants of SARS-CoV-2.
Materials and Methods
2.1. Global map of SARS-CoV-2 variants of concern (VOC) and its timeline of emergence Data reporting the emergence of different VOCs of SARS-CoV-2 was collected on February 17, 2022 from the World Health Organization (WHO) and was depicted manually in the world map generated in Adobe Illustrator. Independent color-coded circles were assigned for each variant (Beta- dark blue, Alpha-green, Delta- yellow, Gamma- red and Omicron- light blue) and were annotated based on the country of its first occurrence. To represent the global timeline of SARS-CoV-2 variants, the number of SARS-CoV-2 confirmed cases were retrieved from the Global Initiative on Sharing All Influenza Data (GISAID) database on February 17, 2022. The submission count per week for each variant was summed for all countries and plotted using Microsoft Excel as an area plot. The X-axis denotes the timeline and the Y-axis represents the weekly total number of cases worldwide in thousands. Each variant was depicted with different colors (Beta- dark blue, Alpha-green, Delta- yellow, Gamma- red and Omicron- light blue).