Immunology, Microbiology, SARS-CoV-2

Targeting the Spike glycoprotein of SARS-CoV2: From the standpoint of Immunology

Student contributors: Subhrajyoti Misra & Dhrubajyoti  Chatterjee [Department. Of Microbiology(UG IV)]


With the significant increase in the number of positive cases of COVID-19 everywhere, overriding one hospital after another and pushing the global death toll past 2.2 lakhs, the sprint to identify the patho-mechanism of SARS-CoV-2 has hastened radically. SARS-CoV-2 is the seventh member of the family Coronaviridae that can cause human disease.While infection with HKU1, NL63, OC43, and 229E can show trivial symptoms, that of SARS-CoV, MERS-CoV, and SARS-CoV2 cause severe disease.The identification of virulence factors of SARS-CoV-2 will enable us to put an end to the atrocity of COVID19 through targeted drug therapy or vaccines.

How does the virus invade the host body?

SARS-CoV-2 entry into host cells is a complex process mediated by the homo-trimeric protrusion of trans-membrane spike (S) glycoprotein on the viral surface. The S protein is classified into 3 subparts: (a) large ectodomain(160Å long, 2.8 Å in diameter, classified into S1 & S2 subdomains) (b) a single-pass transmembrane domain & (c) an intracellular tail. The concerted action of the receptor-binding domain in the distal S1 subunit together with proteolytic processing of the S2 subunit containing the fusion machinery to stimulate virus-cell fusion through ACE2 receptor on lung and of the respiratory tract cells allows the entry of coronavirus in susceptible cells.Once internalized, the viral RNA gets incorporated in the host cell’s protein synthesis machinery, produces thousands of new viruses which when released causing cell death or damage and contribute to disease spread. So the disease can be stopped by preventing the virus from entering the cell. Vaccines, being a pure preparation of one/more viral components can train the human body to identify and attack the virus before it can infect healthy human cells by presenting a preview of the virus without causing disease.Therefore, spike protein is the primary antigenic target of neutralizing antibodies and vaccines.

SARS-CoV2 is different from the rest:

Although SARS-CoV2 shares significant structural and genetic similarity with SARS-CoV and MERS-CoV, epitope analysis has shown significant variability in the antigenicity of the spike protein of SARS-CoV2 from the other two coronaviruses. The variability is sequestered in the non-conserved domain.Some unique features of the receptor-binding domain of SARS-CoV2 are as follows:

  • The Receptor Binding Domain(RBD) of spike protein is the most variable part encoded by the COVID-19 genome, having binding domains like L455, F486, Q493, S494, N501, Y505.Five of these six residues are unique to SARS-CoV2 and these unique epitopes, are derived from either the non-conserved regions or the combinations of the conserved and non-conserved regions of the genome.
  • The sequence variability of these epitopes attributes to the stronger binding of SARS-CoV2in the interaction interface with ACE2.
  • Another feature exclusive of SARS-CoV2that determines viral infectivity is a polybasic cleavage site at the junction of S1 and S2, targeted by furin and other proteases. The presence of a proline residue that creates a turn in the cleavage site to enable the addition of O-linked glycans to S673, T678, and S686 also contributes to the novelty of this domain. (1)

Potential candidature for therapy:

Interestingly, a recent study revealed the lack of antibody cross-reactivity by monoclonal antibodies specific for SARS-CoV RBD against SARS-CoV2 RBD. SARS-CoV2 spike protein is reported to have ~ 24.5% amino acid sequence non-conserved to that of SARS-CoV. Moreover, despite five epitopes being shared between SARS-CoV and SARS-CoV2, apparent dominances of unique epitopes in SRAS-CoV (83.9%) and SRAS-CoV-2 (85.3%) have been demonstrated (2). So by exploiting the novelty of the interactive domains in SARS-CoV-2 RBD, the vaccine can be designed with monoclonal antibodies specific for these surface antigens of SARS-CoV2.

However, the production of protein vaccines demands large-scale production of purified viral proteins. Viral growth and protein purification at clinically acceptable pharmaceutical scales is a time-consuming process that may not be very ideal at the current period of a public health emergency.  As an alternative approach, synthetic mRNA vaccines carrying molecular instructions for protein synthesis can be an attractive candidate that can be used by the host body to produce the viral proteins on their own. The mRNA vaccines would also be safer than the attenuated viral or protein-based vaccines as they are devoid of the risk of reactivation of the injected virus, or protein contamination. Inspired by this strategy, an experimental COVID-19 mRNA vaccine called mRNA-1273 has been produced and is being used for clinical trials in humans.

COVID19 and Immunology

To understand the patho-physiology of viral pathogen and significance of immunization as a probable tool for disease management, the concept of microbiology and immunology is essential. An elaborate knowledge of the subject not only makes a student proficient in addressing disease prognosis but also helps them in tailoring disease management. Thus the students can progress in his/her career in the field of academics, research, drug designing, pharmaceutical industry, etc. At Adamas University, the School of Life Science and Biotechnology offers B.Sc and M.Sc courses in Microbiology where Immunology is a major component in both under-graduate and postgraduate levels. We hope the immunologists will come up with an anti-COVID19 vaccine soon as ammunition to fight back the crisis created by the COVID19 pandemic.


  1. Kristian G. Andersen, Andrew Rambaut, W. Ian Lipkin, Edward C. Holmes & Robert F. Garry. The proximal origin of SARS-CoV-2.Nature Medicine volume 26, pages450–452(2020).
  2. Ming Zheng&Lun Song. Novel antibody epitopes dominate the antigenicity of spike glycoprotein in SARS-CoV-2 compared to SARS-CoV. Cellular & Molecular Immunology volume 17, pages536–538(2020).

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