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).