Introduction
COVID-19 has remained a major health concern since the World Health
Organization (WHO) declared it a pandemic on 11 March 2020 (1). As of 16
May 2021, severe acute respiratory syndrome (SARS) coronavirus 2
(SARS-CoV-2) has infected more than 161 million people worldwide, with
over 3 million deaths (2). This has imposed a huge burden on health care
systems worldwide and provoked a serious economic crisis following
inevitable social lockdown (3). Thus, there is a desperate need for
developing sensitive and robust diagnostic tests and potentially
effective vaccines for SARS-CoV-2 to alleviate the growing socioeconomic
impacts. To this goal, obtaining illuminating insights into the immune
response, particularly the antibody response, to SARS-CoV2 is obviously
crucial. From the experience with SARS-CoV virus, it is postulated that
neutralizing antibodies elicited against SARS-CoV-2 in convalescent
individuals may be important correlates of protection (aroused either by
natural infection or vaccination) (4, 5), and detection of
virus-specific antibodies may provide a robust diagnostic tool for
epidemiological purposes. Moreover, early seroconversion and high
antibody titers could be used as a prognostic marker for disease
severity and ARDS development in patients with SARS-CoV-2 (5). However,
despite extensive investigations, precise definition of the immune
responses, especially targets of adaptive immune responses to SARS-CoV-2
infection is still elusive.
Like other coronaviruses infecting humans, SARS-CoV-2 is an enveloped
positive-sense RNA virus, composed of four structural proteins known as
spike (S), envelope (E), membrane (M), and nucleocapsid (NP) proteins
(6). Apart from NP which is associated to the viral RNA genome, the
other three, S, E, and M proteins organize the viral envelope and are
directly accessible to the host immune system (6). The S protein is a
large type I transmembrane glycoprotein that is responsible for receptor
binding and membrane fusion. With a total length of 1273 amino acids, S
protein has two functional domains, S1 and S2, located in the N- and
C-terminal, respectively (7, 8). S1 subunit itself consists of an
N-terminal domain (14–305 residues) and a receptor-binding domain (RBD,
319–541 residues) which binds to the host receptor angiotensin
converting enzyme 2 (ACE2), while the S2 subunit which plays an
important role in SARS-CoV-2 fusion with the target cells, harbors the
fusion peptide (FP) (788–806 residues), heptapeptide repeat sequence 1
(HR1) (912–984 residues), HR2 (1163–1213 residues), transmembrane (TM)
domain (1213–1237 residues), and cytoplasmic domain (1237–1273
residues) (8, 9). It has become evident that SARS-CoV-2 like other
human-infecting coronaviruses (e.g. SARS-CoV, MERS-CoV) can elicit IgM
and IgG antibodies directed against the S and NP protein, and the RBD of
S protein, after initial infection (10). This antibody response is
initially used in serological assays for diagnostic purposes (11).
However, due to the presence of several cross-reactive epitopes in NP
and S with SARS-CoV and MERS-CoV (12), the detected antibody response
may not represent only anti-SARS-CoV-2 antibodies and could be a
reflection of previous exposures to other human coronaviruses (13).
Moreover, these serology-based assays do not offer any clue about
antibody functionality, including neutralization potential which is a
prerequisite in vaccine development. On the other hand,
antibody-dependent enhancement (ADE) through low quality, low quantity,
and non-neutralizing antibodies is a concern with human coronaviruses
(14), further necessitates epitope dissection in order to resolve
virus-specific and favorable antibodies from unfavorable cross-reactive
antibodies.
Since SARS-CoV-2 virus largely depends on the spike glycoprotein for
binding to ACE2 receptor and cell entry (6), several studies have
focused on detecting antibodies against S protein and its RBD to assess
their neutralizing effect. However, antibodies against nucleoprotein
appear earlier in the course of seroconversion (15) and could be more
indicative for diagnostic applications. In the current study, we present
several immunodominant epitopes on the S and NP proteins by Pepscan
analysis on the sera from Iranian SARS-CoV-2 patients. This information
may be useful for designing COVID-19 diagnostics and vaccines.
Materials and Methods