The SARS-CoV-2 S glycoprotein


Abstract

The outbreak of Coronavirus disease (COVID-19) has posed a great threat to public health, and we are amid a pandemic. The disease is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Like other coronaviruses, the SARS-CoV-2 genome encodes spike (S) glycoproteins, which protrude from the surface of mature virions. The S glycoprotein plays essential roles in virus attachment, fusion, and entry into the host cell. The surface location of the S glycoprotein renders it a direct target for host immune responses, making it the main target of neutralizing antibodies. In the light of its crucial roles in viral infection and adaptive immunity, the S protein is the focus of most vaccine strategies as well as therapeutic interventions. In this review, we highlight and describe the recent progress that has been made in the biosynthesis, structure, function, and antigenicity of the SARS-CoV-2 S glycoprotein, aiming to provide valuable insights into the design and development of S protein-based vaccines as well as therapeutics.

Introduction

The ongoing global pandemic poses a social, economic, and public health-related challenge of unprecedented sorts. The etiological agent of COVID-19 is a new member of the Coronaviridae family that is closely related to severe acute respiratory syndrome coronavirus (SARS-CoV) and was recently referred to as SARS-CoV-2 by the Coronavirus Study Group of the International Committee on Taxonomy of Viruses. The virus has spread rapidly and sustainably around the globe, resulting in over twenty-one million cases and more than 750,000 deaths as of August 15, 2020.

Coronaviruses (CoVs) are enveloped positive-sense RNA viruses. Enveloped CoVs enter host cells and initiate infection through the fusion of viral and cellular membrane. Membrane fusion is mediated by the large type I transmembrane S glycoprotein on the viral envelope and the cognate receptor on the surface of host cells. The surface-exposed location of the S glycoprotein allows it to carry out membrane fusion and renders it a direct target for host immune responses, making it the major target of neutralizing antibodies. Because of its central roles in viral infection and eliciting protective humoral and cell-mediated immune responses in hosts during infection, the S protein is the primary target for vaccine design as well as antiviral therapeutics.

The SARS-CoV-2 spike (S) glycoprotein is a major component of the virus envelope, essential for receptor binding, fusion, virus entry, and a target of host immune defense. The SARS-CoV-2 S glycoprotein is a class I fusion protein produced as a prominent 1273 amino acid inactive precursor (S0). Unique to SARS-CoV-2 is the insertion of a polybasic RRAR furin-like cleavage motif in the S1/S2 cleavage site. Proteolytic cleavage of the S protein generates the S2 stalk that is conserved across human coronaviruses and the less conserved S1 cap. The N-terminal domain (NTD) and the receptor-binding domain (RBD) are located in the S1 subunit. The fusion peptide (FP), two heptad repeats (HR1 and HR2), central helix (CH), transmembrane (TM) domain, and cytoplasmic tail (CT) are located in the S2 subunit. Three S1/S2 protomers non-covalently associate to form the functional S-trimer. Like other fusion proteins, the SARS-CoV-2 S-trimer is metastable and undergoes significant structural rearrangement from a prefusion conformation to a thermostable postfusion conformation upon S-protein receptor binding and proteolytic cleavage, either at the plasma membrane or following endocytosis Rearrangement exposes the hydrophobic FP allowing insertion into the host cell membrane, facilitating virus/host cell membrane alignment, fusion, and virus entry.

Synthesis, Processing, and Trafficking of the SARS-CoV-2 S Glycoprotein

The SARS-CoV-2 S glycoprotein is synthesized as a 1273-amino acid polyprotein precursor on the rough endoplasmic reticulum (RER). The unprocessed precursor harbors an endoplasmic reticulum (ER) signal sequence located at the N terminus, which targets the S glycoprotein to the RER membrane and is removed by cellular signal peptidases in the lumen of the ER. A single stop-transfer, membrane-spanning sequence located at the C terminus of the S protein prevents it from being fully released into the lumen of the ER and subsequent secretion from the infected cell. Co-translationally, N-linked, high-mannose oligosaccharide side chains are added during synthesis. Shortly after synthesis, the S glycoprotein monomers trimerize, which might be thought to facilitate the transport from the ER to the Golgi complex. Once in the Golgi complex, most of the high-mannose oligosaccharide side chains are modified to more complex forms, and O-linked oligosaccharide side chains are also added.

SARS-CoV-2 S Protein Structure and Function

As mentioned above, the SARS-CoV-2 S glycoprotein plays pivotal role in viral infection and pathogenesis. Mature S glycoprotein on the viral surface is a heavily glycosylated trimer, each protomer of which is composed of 1260 amino acids (residues 14-1273). The surface subunit S1 is composed of 672 amino acids (residues 14–685) and organized into four domains: an N-terminal domain (NTD), a C-terminal domain (CTD, also known as the receptor-binding domain(RBD), and two subdomains (SD1 and SD2). The transmembrane S2 subunit is composed of 588 amino acids (residues 686-1273) and contains an N-terminal hydrophobic fusion peptide (FP), two heptad repeats (HR1 and HR2), a transmembrane domain (TM), and a cytoplasmic tail (CT), arranged as FP-HR1-HR2-TM-CT

SARS-CoV-2 S Glycoprotein-Mediated Membrane Fusion

Membrane fusion and viral entry of SARS-CoV-2 is initiated by binding of RBD in the viral S glycoprotein transiently sampling the functional conformation to ACE2 on the surface of target cells. After receptor engagement at the plasma membrane or ensuing virus endocytosis by the host cell, a second cleavage (S2′ cleavage site) is generated, which is mediated by a cellular serine protease TMPRSS2 or endosomal cysteine proteases cathepsins B and L. Protease cleavage at S2′ site frees the fusion peptide from the new S2 N-terminal region, further destabilizes the SARS-CoV-2 S glycoprotein and may initiate S2-mediated membrane fusion cascade. Following the second cleavage, the fusion peptide at the N terminus of the S2 trimer is inserted into the host membrane, forming the pre-hairpin intermediate state. Since the pre-hairpin intermediate state is extremely unstable, the S2 fusion protein is refolded quickly and irreversibly into the stable postfusion state. These large conformational rearrangements pull the viral and host cell membrane into close proximity, leading ultimately to membrane fusion.

Concluding Remarks and Prospects

SARS-CoV-2 is a highly contagious pathogen that continues to spread quickly around the globe, making COVID-19 one of the worst pandemics recorded in history. A safe and efficacious vaccine will be one of the best solutions to reduce or eliminate the COVID-19 pandemic. Unfortunately, no vaccines for any of the known human CoVs have been licensed. However, several potential SARS-CoV and MERS-CoV vaccines have advanced into human clinical trials for years, suggesting the development of effective vaccines against human CoVs has always been challenging. However, it has been shown that both SARS-CoV and SARS-CoV-2 could readily induce neutralizing antibodies following natural infection or immunization.

Moreover, a growing number of neutralizing monoclonal antibodies targeting the SARS-CoV-2 S glycoprotein with high potency have been isolated from plenty of convalescent donors and humanized mice, some of which have been shown to afford protection against SARS-CoV-2 challenge in animal models. It thus seems that vaccine candidates designed to elicit such neutralizing antibodies are feasible. It is widely accepted that the S protein of SARS-CoV-2 is the most promising immunogen for producing protective immunity. However, the S protein has likely evolved to perform its functions while evading host neutralizing antibody responses and thus should be engineered to ensure optimal immune response. The immunogen design strategies described in this review based on the wealth of the SARS-CoV-2 S glycoprotein research related to its biosynthesis, structure, function, antigenicity, and immunogenicity will likely contribute to the ultimate success of safe and efficacious vaccines against SARS-CoV-2/COVID-19.

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Mental Health & Covid-19


The toll on mental health as a by- product of COVID-19

On March 11, 2020, The World Health Organization declared a global pandemic, the outbreak of COVID-19. Traveling across borders, the virus had spread worldwide, and the situation was already out of control. The virus became the talking point everywhere and we have been living with constant fear for our lives ever since. The list of casualties has continued to grow; some have fallen prey to the virus, while others have been unfortunate with the mental and emotional toll it brings. Nobody is spared the horrors of this destitute condition.

Ever since the first case of COVID was reported in China in November 2019, life has not been the same. The disease is caused by SARS-COV-2 virus, which belongs to the large family of SARS virus that mainly causes respiratory illness. It has been over a year, and the world’s scientists are yet to find its origin. However, studies have been conducted worldwide, and they reveal that it is predominantly a bat virus that somehow reached humans.

Structurally, it is an enveloped virus, and its primary genetic material is RNA. A long, single RNA polymer is tightly packed at the center surrounded by the capsid made up of nucleocapsid protein. It is further surrounded by an envelope made up of lipid and inserted protein. A vital set of the protein in the outer membrane is known as Spike protein (S). This spike protein is recognized by the receptor on the host cell.

As the virus transmits through the air, it infects a large number of people very rapidly. The infected individual shows symptoms like fever, chills, cough, headache, body pain, sore throat, loss of smell and taste, vomiting, and diarrhea. In addition, it is found that the severity of the disease varies across different age groups, and the mortality rate is higher for people who have diabetes, are obese, or have coronary disease.

As the virus is of RNA nature, it mutates very rapidly, and many variants have been found across the globe.

  1. Variants of Concern: For these variants clear evidence is available indicating a significant impact on transmissibility and severity.
Variants First detected
B.1.1.7 United Kingdom
B.1.351 South Africa
B.1.427 United States-(California)
B.1.429 United States-(California)
P.1 Japan/Brazil
B.1.617.2 India

 

  1. Variants of Interest: For these variants genetic evidence is available but these are preliminary.
Variants First detected
B.1.525 United Kingdom/Nigeria – December 2020
B.1.526 United States (New York) – November 2020
B.1.526.1 United States (New York) – October 2020
B.1.617 India – February 2021
B.1.617.1 India – December 2020
B.1.617.2 India – December 2020
B.1.617.3 India – October 2020
P.2 Brazil – April 2020

Currently, there are four different kinds of Vaccines for COVID-19, available worldwide.

  1. Vaccine made from virus vector: COVISHIELD, OXFORD ASTRAZENCA vaccine, and Sputnik-V.
  2. Vaccine made from Nucleic acid (RNA) – Pfizer-BioNTech vaccine and Moderna vaccine.
  3. Whole virus Vaccine (weekend virus used as immunogens) – COVAXINE from Bharat Biotech and SINOVAX from China.
  4. Vaccine made of protein Subunit of virus – NOVAX (Under development).

Treatment strategy keeps changing as new variants are causing even more severe effects on patients; and also because no medicine has been developed to fight against the virus in the human body. During the first phase, HCQ and plasma therapy were used to treat serious patients but now both have been dismissed. In the second phase, serious patients were treated with drugs which contain steroid, to control cytotoxin storm in. Some of the drugs used were: Dexamethasone; anticoagulant (as most corona patients suffer from blood clotting and cardiac arrest is the leading cause of death among positive patients); paracetamol, multivitamins, and zinc.

We cannot kill the virus altogether, but we can prevent it from spreading by taking the necessary precautions such as sanitizing, washing our hands frequently, practicing social distancing, and most importantly, getting vaccinated.

Read more

COVID-19: ONE ENEMY, DIFFERENT NAMES


Ever since the first case of COVID was reported in China in November 2019, life has not been the same. The disease is caused by SARS-COV-2 virus, which belongs to the large family of SARS virus that mainly causes respiratory illness. It has been over a year, and the world’s scientists are yet to find its origin. However, studies have been conducted worldwide, and they reveal that it is predominantly a bat virus that somehow reached humans.

Structurally, it is an enveloped virus, and its primary genetic material is RNA. A long, single RNA polymer is tightly packed at the center surrounded by the capsid made up of nucleocapsid protein. It is further surrounded by an envelope made up of lipid and inserted protein. A vital set of the protein in the outer membrane is known as Spike protein (S). This spike protein is recognized by the receptor on the host cell.

As the virus transmits through the air, it infects a large number of people very rapidly. The infected individual shows symptoms like fever, chills, cough, headache, body pain, sore throat, loss of smell and taste, vomiting, and diarrhea. In addition, it is found that the severity of the disease varies across different age groups, and the mortality rate is higher for people who have diabetes, are obese, or have coronary disease.

As the virus is of RNA nature, it mutates very rapidly, and many variants have been found across the globe.

  1. Variants of Concern: For these variants clear evidence is available indicating a significant impact on transmissibility and severity.
Variants First detected
B.1.1.7 United Kingdom
B.1.351 South Africa
B.1.427 United States-(California)
B.1.429 United States-(California)
P.1 Japan/Brazil
B.1.617.2 India

 

  1. Variants of Interest: For these variants genetic evidence is available but these are preliminary.
Variants First detected
B.1.525 United Kingdom/Nigeria – December 2020
B.1.526 United States (New York) – November 2020
B.1.526.1 United States (New York) – October 2020
B.1.617 India – February 2021
B.1.617.1 India – December 2020
B.1.617.2 India – December 2020
B.1.617.3 India – October 2020
P.2 Brazil – April 2020

Currently, there are four different kinds of Vaccines for COVID-19, available worldwide.

  1. Vaccine made from virus vector: COVISHIELD, OXFORD ASTRAZENCA vaccine, and Sputnik-V.
  2. Vaccine made from Nucleic acid (RNA) – Pfizer-BioNTech vaccine and Moderna vaccine.
  3. Whole virus Vaccine (weekend virus used as immunogens) – COVAXINE from Bharat Biotech and SINOVAX from China.
  4. Vaccine made of protein Subunit of virus – NOVAX (Under development).

Treatment strategy keeps changing as new variants are causing even more severe effects on patients; and also because no medicine has been developed to fight against the virus in the human body. During the first phase, HCQ and plasma therapy were used to treat serious patients but now both have been dismissed. In the second phase, serious patients were treated with drugs which contain steroid, to control cytotoxin storm in. Some of the drugs used were: Dexamethasone; anticoagulant (as most corona patients suffer from blood clotting and cardiac arrest is the leading cause of death among positive patients); paracetamol, multivitamins, and zinc.

We cannot kill the virus altogether, but we can prevent it from spreading by taking the necessary precautions such as sanitizing, washing our hands frequently, practicing social distancing, and most importantly, getting vaccinated.

Read more

Mental Health and Covid-19: Finding peace locked inside a Burning House


It was only a few days back when India recorded its first COVID-19 patient. Since then, we have crossed over 500K nationwide cases which continue to rise at an increasing rate of 20K cases per day. It is no secret how the virus has not only disrupted the whole economy but has also posed a challenge for our existing medical infrastructure. The healthcare sector has been on its heels. While the research institutes and laboratories continue their search for the antidote that we all have been waiting for, doctors and medical staff all over the nation have emerged as the frontline warriors in this fight against coronavirus. Despite the limited infrastructure and shortage of resources, it is truly admirable to see medical professionals coming out of their comfort zones and devoting long hours for serving the infected patients.

Patient Management System for PGI Chandigarh

As a show of gratitude from our end, we decided to put in our little efforts too. We worked with the (PGI Chandigarh) Postgraduate Institute of Medical Education and Research, Chandigarh for developing a Patient Management System to help them in optimizing the internal processes and effectively managing the increasing footfall. We developed an application that allows the patients to generate tokens for PGI Chandigarh. Upon registering, the user/patient can book an appointment online with the requested doctor by filling an online form disclosing the concern and the doctor they wish to consult. The dataset of doctors, departments, patients and booked appointments is managed by admin from the backend.

The system is further configured to prioritize senior citizens and female patients as tokens are generated considering age and gender criteria. This would help the hospital to increase operational efficiency by effectively managing the increasing footfall of patients while maintaining social distancing norms. For patients, this translates into a streamlined platform where they can access information about the availability of doctors and generate appointments accordingly while staying at home and avoiding unnecessary physical contact by standing in long queues.
Through this article, we would like to express our gratitude as we stay indebted to all the frontline workers, who have led this relief operation and proven themselves to be the backbone of our country in this moment of crisis. We would also like to thank PGI Chandigarh along with other medical institutes across the country for their continued devotion, efforts, and dedication towards saving lives and keeping the needs of the nation above their own during these difficult times.

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