SARS COV2 ANTIGEN PRESENTATION PROCESS

BY IMMUNE CELLS
Immunology assignment -2

SUBMITTED BY

AZIMA FATIMA, 008

Msc Biotechnology, 2nd Sem

Submitted to

Dr. Rizwanul Haque

Associate Professor

Session-2019-21

Central University Of South Bihar

Gaya
GRAPHICAL ABSTRACT

Ref-https://www.sciencedirect.com/science/article/pii/S2095177920302045
 INTRODUCTION
Novel coronavirus-induced pneumonia, which was named as coronavirus disease 2019 (COVID-19) by
the WHO on the February 11, 2020, has rapidly increased in epidemic scale [. On the same day, the
international virus classification commission announced that the novel coronavirus was named as severe
acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is not the first severe respiratory
disease outbreak caused by the coronavirus. Just in the past two decades, coronaviruses have caused three
epidemic diseases, namely, COVID-19, severe acute respiratory syndrome (SARS) and Middle East
respiratory syndrome (MERS) . At present, the cases of COVID-19 have been found in many countries
around the world . According to the latest data, up to the March 1, 2020, the number of confirmed cases
in China reached 79,968, of which 2,873 were dead, and 41,681 were cured. In addition to China, the
number of confirmed cases in other countries also reached 7,041, of which 105 were dead, and 459 were
cured. On the 31st of January 2020, the World Health Organization (WHO) announced that COVID-19
was listed as the Public Health Emergency of International Concern (PHEIC), meaning that it may pose
risks to multiple countries and requires a coordinated international response.

SAR-CoV2 is an enveloped, non-segmented, positive sense RNA virus that is included in

thesarbecovirus, orthocoronavirinae subfamily which is broadly distributed in humans and other
mammals . Its diameter is about 65-125 nm, containing single strands of RNA and provided with crown-
like spikes on the outer surface. SARS-CoV2 is a novel β-coronavirus after the previously identified
SARS-CoV andMERS-CoV which led to pulmonary failure and potentially fatal respiratory tract
infection and causedoutbreaks mainly in Guandong, China and Saudi Arabia. In COVID-19 research,
many studies havedemonstrated that bats are suspected as the key reservoir of the viruses by finding as
much as 96.2%identical genome sequencing of SARS-CoV-2 with bat CoV RaTG13

Origin and Structure of SARS-CoV2

A sample isolation from pneumonia patients who were some of the workers in the Wuhan seafood
marketfound that strains of SARS-CoV-2 had a length of 29.9 kb . Structurally, SARS-CoV-2 has four
main structural proteins including spike (S) glycoprotein, small envelope (E) glycoprotein, membrane
(M)glycoprotein, and nucleocapsid (N) protein, and also several accessory proteins . The spike or
Sglycoprotein is a trans membrane protein with a molecular weight of about 150 kDa found in the
outerportion of the virus. S protein forms homotrimers protruding in the viral surface and facilitates
binding ofenvelope viruses to host cells by attraction with angiotensin-converting enzyme 2 (ACE2)
expressed inlower respiratory tract cells. This glycoprotein is cleaved by the host cell furin-like protease
into 2 subunits namely S1 and S2. Part S1 is responsible for the determination of the host virus range and
cellulartropism with the receptor binding domain make-up while S2 functions to mediate virus fusion
intransmitting host cells .The nucleocapsid known as N protein is the structural component of CoV
localizing in the endoplasmicreticulum-Golgi region that structurally is bound to the nucleic acid material
of the virus. Because theprotein is bound to RNA, the protein is involved in processes related to the viral
genome, the viralreplication cycle, and the cellular response of host cells to viral infections . N protein is
alsoheavily phosphorylated and suggested to lead to structural changes enhancing the affinity for viral
RNA

Figure 1. Structure of Severe Acute Respiratory Syndrome Coronavirus 2

Another important part of this virus is the membrane or M protein, which is the most structural structured
protein and plays a role in determining the shape of the virus envelope. This protein can bind to all
otherstructural proteins. Binding with M protein helps to stabilize nucleocapsids or N proteins and
promotes completion of viral assembly by stabilizing N protein-RNA complex, inside the internal virion.
The last component is the envelope or E protein which is the smallest protein in the SARS-CoV structure
that plays a role in the production and maturation of this virus . In supporting the process of entry of the
virus into the host cell, SARS-CoV2 binds to the ACE2 receiver that is highly expressed in the lower
respiratory tract such as type II alveolar cells (AT2) of the lungs, upper esophagus and stratified epithelial
cells, and other cells such as absorptive enterocytes from the ileum and colon, cholangiocytes, myocardial
cells, kidney proximal tubule cells, and bladder urothelial cells . Therefore, patients who are infected with
this virus not only experience respiratory problems such as pneumonia leading to Acute Respiratory
Distress Syndrome (ARDS), but also experience disorders of heart, kidneys, and digestive tract.

Entry and life cycle of SARS COV 2

This virus can enter the human body through its receptors, ACE2 which are found in various organs such
as heart, lungs, kidneys, and gastrointestinal tract, thus facilitating viral entry into target cells. The
process of CoV entering into the host cell begins through the attachment of the S glycoprotein to the
receptor, the ACE2 in the host cells (such as in type II pneumocytes in the lungs). This attachment occurs
in the binding domain of S protein of SARS-CoV-2 receptors which are present at 331 to 524 residues,
and can bind strongly to human ACE2 and bat ACE2 . The entry and binding processes are then followed
by fusion of the viral membrane and host cell .

After fusion occurs, the type II transmembrane serine protease (TMPRSS2) that is present on the
surface of the host cell will clear the ACE2 and activate the receptor-attached spike-like, S proteins .
Activation of the S proteins leads to conformational changes and allows the virus to enter the cells. Both
of these proteins (TMPRSS2 and ACE2) are the main determinants of the entry of this virus. Based on the
research of Sungnak et al., nasal epithelial cells, specifically goblet/secretory cells and ciliated cells,
display the highest ACE2 expression throughout the respiratory tract . Furthermore, entered-SARS-CoV-
2 will subsequently release its genomic material in the cytoplasm and become translated in The genomic
material released by this virus is mRNA that is ready to be translated into protein.

Next, the sub genomic proteins become translated into structural and accessories proteins
such as M, S, and E proteins that subsequently are insulated in the endoplasmic reticulum and then moved
to the endoplasmic reticulum-Golgi intermediate compartment (ERGIC). Meanwhile, the previously
replicated genome program can directly join the N protein to the nucleocapsid form and move into the
ERGIC. In this compartment, nucleocapsids will meet with several other structural proteins and form
small wallet vesicles to be exported out of the cell through exocytosis .
 Fig – entry and life cycle of SARS COV 2 into host cells

Antigen Presentation During Human SARS-CoV-2 Infection

 As an antiviral mechanism, antigen Presenting Cells (APC) are involve in the presentation of
viral antigenic peptides in complexed with MHC (major histocompatibility complex) class I
and class II molecules to CD8 and CD4 T cells. The selection of peptides and presentation
technique of the host leads to a better understanding of cellular immunity and vaccine
advancement. During any viral infection, DCs (dendritic cells) play a very important role as
an APC. DCs are a linkage between innate and adaptive immunity. Studies deciphering the
mechanism of antigen presentation during SARS-CoV-2 infection is not studied well
therefore, the mechanism of antigen presentation can be understood based on the available
data of predecessor strain infection (SARS-CoV & MERS-CoV) due to its analogy (Chen Et
al. 2010). Because DCs are found in the respiratory tract and react back whenever there is an
inflammation response, DCs are found to be a potential candidate in antigen presentation
during SARS infection and also in understanding the immunopathology of SARS (Lau et
al. 2012).
 During SARS infection, the up regulation of few chemokines such as IP-10 and MP1 is seen
very significantly, also few of the antiviral cytokines are found to be low in expression such
as IFN-alpha, IFN-beta, and IFN-gamma, and TNF-alpha and IL-6 are found to be at
moderate upregulation (Kuri and Weber 2010). Modulation of Toll-like receptors from TLR-
 1 to TLR-10 was seen to be at the same level; hence no modulation but chemokine receptors
such as CCR5, CCR3, and CCR1 are found to be at significant level of upregulation (Law et
al. 2009). When similar type of study is conducted in patients infected with Middle East
Respiratory Syndrome Coronavirus (MERS-CoV), it has been observed that this virus infects
DCs very prolifically by inducing higher expression of IFN-gamma and even cytokines and
chemokine related with IFN-gamma are found to be at a higher level. Altogether, antigen
presentation in case of MERS-CoV-infected dendritic cells is seen to be significantly higher
than in SARS-CoV-infected dendritic cells.
 In case of SARS-CoV, the antigen presentation is done most importantly by MHC-I followed
by MHC-II (Wieczorek et al. 2017). Studies were done in human macrophages during SARS-
CoV infection indicating an interesting observation that severe acute respiratory syndrome
coronavirus infects human macrophages due to antibody enhancement (ADE) mediated by
IgG. However, macrophages infected with SARS-CoV did not show productive viral
replication (Yip et al. 2014). MHC class II and I are further analyzed for epitope mapping
which is one of the key steps towards vaccine development and which is studied intensively
in case of SARS-CoV-2 infection (Sarkar et al. 2020). Post MHC-I analysis, it was observed
that the protein sequence of CoVID-19 is introduced by alleles of HLA-C rather than HLA-A
and HLA-B (Prompetchara et al. 2020). Alleles of HLA are studied in case of SARS-CoV
infection and have been categorized into protection alleles (HLA-Cw1502, HLA-DR0301,
and HLA-A∗0201) and susceptible alleles (HLA-B∗0703, HLA-Cw∗0801, HLA-DR
B1∗1202, and HLA-B∗4601) (Wang et al. 2011). In case of MERS-CoV infection, molecules
of MHC class II, HLA-DQB1∗02:0, and HLA-DRB1∗11:01 are related with the
susceptibility to infection (Fast and Chen 2020; Hajeer et al. 2016). While analyzing the viral
genome of COVID-19 for epitope prediction, around 405 T cell epitopes have been
determined which exhibits effective affinity towards MHC class I and II in addition two
potent neutralizing epitopes (B cell epitope) based on Spike (S) protein were found (Fast and
Chen 2020).

ANTIGEN PRESENTATION AND PROCCESSING BY

MHC-1 and MHC-2
 MHC -1 presented intracellular viral protein or nucleic acid of viruses . In case of SARS COV
Reported the viral antigen are processed by MHC -1 , but MHC II also contributes to its presentation.
Previous research shows numerous HLA polymorphisms correlate to the susceptibility of SARS-CoV,
such as HLA-B∗4601, HLA-B∗0703, HLA-DR B1∗1202 and HLA-Cw∗0801 , whereas the HLA-
DR0301, HLA-Cw1502 and HLA-A∗0201 alleles are related to the protection from SARS infection .

 
 In MERS-CoV infection, MHC II molecules, such as HLA-DRB1∗11:01 and HLA-DQB1 ∗02:0, are
associated with the susceptibility to MERS-CoV infection . Besides, gene polymorphisms of MBL
(mannose-binding lectin) associated with antigen presentation are related to the risk of SARS-CoV
infection . These researches will provide valuable clues for the prevention, treatment, and mechanism of
COVID-19.

Humoral and cellular immunity

Antigen presentation subsequently stimulates the body’s humoral and cellular immunity, which are
mediated by virus-specific B and T cells. Similar to common acute viral infections, the antibody profile
against SARS-CoV virus has a typical pattern of IgM and IgG production. The SARS-specific IgM antibodies
disappear at the end of week 12, while the IgG antibody can last for a long time, which indicates IgG
antibody may mainly play a protective role , and the SARS-specific IgG antibodies primarily are S-specific
and N-specific antibodies . Comparing to humoral responses, there are more researches on the cellular
immunity of coronavirus. The latest report shows the number of CD4 + and CD8+ T cells in the peripheral
blood of SARS-CoV-2-infected patients significantly is reduced, whereas its status is excessive activation,
as evidenced by high proportions of HLA-DR (CD4 3.47%) and CD38 (CD8 39.4%) double-positive
fractions . Similarly, the acute phase response in patients with SARS-CoV is associated with severe
decrease of CD4+ T and CD8+ T cells. Even if there is no antigen, CD4+ and CD8+ memory T cells can
persist for four years in a part of SARS-CoV recovered individuals and can perform T cell proliferation,
DTH response and production of IFN-γ . Six years after SARS-CoV infection, specific T-cell memory
responses to the SARS-CoV S peptide library could still be identified in 14 of 23 recovered SARS patients .
The specific CD8+ T cells also show a similar effect on MERS-CoV clearance in mice . These findings may
provide valuable information for the rational design of vaccines against SARS-CoV-2.
 Cytokine storm in COVID-19
The report in Lancet shows ARDS is the main death cause of COVID-19. Of the 41 SARS-CoV-
2-infected patients admitted in the early stages of the outbreak, six died from ARDS . ARDS is
the common immunopathological event for SARS-CoV-2, SARS-CoV and MERS-CoV
infections . One of the main mechanisms for ARDS is the cytokine storm, the deadly uncontrolled
systemic inflammatory response resulting from the release of large amounts of pro-inflammatory
cytokines (IFN-α, IFN-γ, IL-1β, IL-6, IL-12, IL-18, IL-33, TNF-α, TGFβ, etc.) and chemokines
(CCL2, CCL3, CCL5, CXCL8, CXCL9, CXCL10, etc.) by immune effector cells in SARS-CoV
infection. Similar to those with SARS-CoV, individuals with severe MERS-CoV infection show
elevated levels of IL-6, IFN-α, and CCL5, CXCL8, CXCL-10 in serum compared to those with
the mild-moderate disease . The cytokine storm will trigger a violent attack by the immune
system to the body, cause ARDS and multiple organ failure, and finally lead to death in severe
cases of SARS-CoV-2 infection, just like what occurs in SARS-CoV and MERS-CoV infection .
 Coronavirus immune evasion
To better survive in host cells, SARS-CoV and MERS-CoV use multiple strategies to avoid
immune responses. The evolutionarily conserved microbial structures called pathogen-associated
molecular patterns (PAMPs) can be recognized by pattern recognition receptors (PRRs).
However, SARS-CoV and MERS-CoV can induce the production of double-membrane vesicles
that lack PRRs and then replicate in these vesicles, thereby avoiding the host detection of their
dsRNA . IFN-I(IFN-α and IFN-β) has a protective effect on SARS-CoV and MERS-CoV
infection, but the IFN-I pathway is inhibited in infected mice . Accessory protein 4a of MERS-
CoV may block the induction of IFN at the level of MDA5 activation through direct interaction
with double-stranded RNA . Besides, ORF4a, ORF4b, ORF5, and membrane proteins of MERS-
CoV inhibit nuclear transport of IFN regulatory factor 3 (IRF3) and activation of IFN β
promoter . The antigen presentation can also be affected by the coronavirus. For example, gene
expression related to antigen presentation is down-regulated after MERS-CoV infection .
Therefore, destroying the immune evasion of SARS-CoV-2 is imperative in its treatment and
specific drug development.

Current treatment strategies for COVID-19

Just like SARS-CoV and MERS-CoV , there is currently no clinically proven specific antiviral
agent available for SARS-CoV-2 infection. The supportive treatment, including oxygen therapy,
conservation fluid management, and the use of broad-spectrum antibiotics to cover secondary
bacterial infection, remains to be the most important management strategy . According to the
research on molecular mechanisms of coronavirus infection and the genomic organization of
SARS-CoV-2 , there are several potential therapeutic targets to repurpose the existing antiviral
agents or develop effective interventions against this novel coronavirus.
 Virally targeted inhibitors
Remdesivir, an adenosine analogue that can target the RNA-dependent RNA polymerase and
block viral RNA synthesis, has been a promising antiviral drug against a wide array of RNA
viruses (including SARS/MERS-CoV) infections in cultured cells , mice and nonhuman primate
models . The Washington Department of Health administrated remdesivir intravenously first and
found that remdesivir might have potential protection from SARS-CoV-2 infection [. Then
remdesivir and chloroquine have been demonstrated to inhibit SARS-CoV-2 effectively in vitro .
Hence, other nucleoside analogues, such as favipiravir, ribavirin and galidesivir , may be
potentially clinically applicable against SARS-CoV-2. Chymotrypsin-like (3C-like protease,
3CLpro) and papain-like protease (PLP) are non-structural proteins, which have an essential
function for coronaviral replication and can inhibit the host innate immune responses . So 3CLpro
inhibitors, such as cinanserin and flavonoids , and PLP inhibitors, such as diarylheptanoids , are
other attractive choices to fight against SARS-CoV-2. ACE2 mediates SARS-CoV-2 entry into
the cell as a functional receptor of coronaviruses. So blocking the binding of S protein with ACE2
is also a meaningful strategy against SARS-CoV-2 infection .

Antibody and plasma therapy

It has also been reported that there are many convalescent patients donating plasma against
SARS-CoV-2, just as SARS-CoV and MERS-CoV trials. It has preliminary acquired favorable
results in acute, severe SARS-CoV-2 patients. Moreover, the generation of recombinant human
monoclonal antibody (mAb) is a fairly straightforward path to neutralize SARS-CoV. CR3022, a
SARS coronavirus-specific human monoclonal antibody, can bind potently with the receptor-
binding domain(RBD) of SARS-CoV-2 and has the potential to be developed as candidate
therapeutics of SARS-CoV-2 infections . Other monoclonal antibodies neutralizing SARS-CoV,
such as m396, CR3014, could be an alternative for the treatment of SARS-CoV-2 .

Vaccines
Effective SARS-CoV-2 vaccines are essential for reducing disease severity, viral shedding and
transmission, thus helping to control the coronavirus outbreaks. There are several vaccination
strategies against SARS-CoV, MERS-CoV tested in animals, including a live-attenuated virus,
viral vectors, inactivated virus, subunit vaccines, recombinant DNA, and proteins vaccines .
These studies are in progress, but it requires months to years to develop the vaccines for SARS-
CoV-2.
Currently, More than 90 vaccines are being developed against SARS-CoV-2 by research teams in
companies and universities across the world. Researchers are trialling different technologies,
some of which haven’t been used in a licensed vaccine before. At least six groups have already
begun injecting formulations into volunteers in safety trials; others have started testing in
animals. Nature’s graphical guide explains each vaccine design.
SARS-CoV-2 vaccines: a variety of approaches
All vaccines aim to expose the body to an antigen that won’t cause disease, but will provoke an
immune response that can block or kill the virus if a person becomes infected. There are at least
eight types being tried against the coronavirus, and they rely on different viruses or viral parts.
 Conclusions
The emergence and outbreak caused by SARS-CoV-2 is determined by the disruption of the host
immune system by the virus. The virus strain has been observed to disturb the immune system by
evasion of the immune response when a person is infected. It is on the safer side to predict that
coronaviruses, having the biggest RNA genome so far, do not depend upon sole harmfulness
factors; however they utilize a few layers of hostile to IFN procedures such as factors which
include the type of virus, the titer of virus, and the load of virus. Else they would not have the
strategy to exist, and even expand or mutate to a newer territory with strong antiviral IFN
reactions (host). With just their genetic blueprint made available so far, it has become difficult for
all research groups to identify the potential molecular targets of the virus. Immunopathology
studies of disease caused by SARS-CoV-2 are still being investigated globally. However, with
reference to the studies done so far on its predecessor infection, it can be concluded that few of
the mechanisms which explain the severity of the disease caused by SARS-CoV-2 is the enzyme
Furin, which is found at its activation site, and the mechanism of cytokine storm and immune
evasion.

Future Perspectives
There are many hurdles in designing a vaccine against CoVID-19 due to the fact that different age
group and individuals with pre-existing conditions react differently to this disease because of
their differences in immune responses, which is why one-size vaccine will not be enough but still
research groups are indulged in screening vaccine and the current vaccine candidate used is an
antigen of the spike protein of coronavirus. Due to the lack of many failed antiviral strategies in
order to efficiently treat infections by coronavirus, scientists are trying to come up with
preventive measure such as vaccination. Taking into account the previous cases of coronavirus
infection such as the infection of SARS-CoV and MERS-CoV, research groups have managed to
come up till the stage of clinical trials of few vaccines and which is an advancement when it
comes to the fight against such outbreaks. Hence, it will pave the way for some advancement in
designing drugs and vaccine against CoVID-19 too. This is possibly a positive outcome for the
vaccine candidate for SARS-CoV-2 disease in the future.

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