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The SARS-CoV-2 Virus: Spike Proteins, Glycans, and Vaccines

Linda Crampton is an experienced teacher with a first-class honors degree in biology. She writes about the scientific basis of disease.

A colourized transmission electron microscope image of the SARS-CoV-2 virus obtained from a patient

A colourized transmission electron microscope image of the SARS-CoV-2 virus obtained from a patient

SARS-CoV-2 Virus and the COVID-19 Disease

The coronavirus pandemic caused by the SARS-CoV-2 virus has produced some very sad results, including deaths and long-term health problems. Biologically, however, the virus is an interesting entity. Studying it is important beyond scientific interest. The surface of the virus is proving to be significant with respect to fighting the disease that it causes.

The spike proteins on the surface of the virus are involved in its entry into our cells and in the creation of vaccines to fight the coronavirus. They are also responsible for the general name “coronavirus,” because they are reminiscent of the spikes on a crown. Glycans are carbohydrates that are found on the spike proteins and may help the virus to evade our immune system. In addition, they may enable the virus to maintain the correct shape for latching onto our cells.

Understanding the functions and behaviour of the spike proteins and glycans could help us fight the disease caused by SARS-CoV-2. This disease is known as COVID-19. It may also help us in the fight against problems caused by other coronaviruses.

Illustration of a typical coronavirus

Illustration of a typical coronavirus

Coronaviruses are a large family. Some members of the family infect humans. Some of the infections are not serious, but others, such as MERS (Middle East Respiratory Syndrome), SARS (Severe Acute Respiratory Syndrome), and COVID-19 (Coronavirus Disease 2019) are serious conditions in some people.

The Nature of a Virus

Let's take a deeper look at the nature of viruses in general, including their structure and their method of reproduction.


The simplest viruses contain genetic material (DNA or RNA) surrounded by a protein coat known as a capsid. The capsid is sometimes surrounded by a lipid envelope. The entities have diverse structures. I’ve used the term “entities” because there is some debate about whether viruses are alive. There is no debate that like living things they have genes that control their features, however. Some viruses have a more complex form than the basic body plan.

Viruses are typically much smaller than bacteria, which can make them hard to study. Researchers have discovered so-called “giant viruses”, however, which are bigger than some bacteria. The group seems to have hold many surprises for us. Since some viruses can cause disease, studying them is important.


An individual virus particle is often referred to as a virion. Unlike other forms of life, viruses don’t consist of cells with organelles. Though they contain genetic material, they can’t reproduce on their own. They require the aid of a living cell in order to make new virions. For this reason, some scientists don’t consider them to be living organisms. They are not simple entities with respect to their behaviour, however. They are sometimes considered to be living creatures because of their behaviour on and inside a host.

Some types of viruses enter a cell in order to direct their own reproduction by using cell structures and processes. Others send their genetic material into the cell to direct their reproduction. Once the new virions are made, they leave the cell by breaking it open and destroying it (lysis) or by a gentler process known as budding, which may or may not kill the cell. The exit process depends on the type of virus.

Structure of the SARS-CoV-2 Virus

Now let's take a closer look at the particularities of SARS-CoV-2 and what makes it so dangerous.

Genetic Material

SARS-CoV-2 is an RNA virus. Its genes are located in RNA (ribonucleic acid). Our cells contain RNA, but our genes are located in a related chemical called DNA (deoxyribonucleic acid) that is found in the nucleus of our cells. A gene is a section of nucleic acid that codes for a particular protein. The genes give an entity many of its characteristics.

Nucleic acids are made from chemicals known as nucleotides that are joined together to make a chain. The DNA in our nuclei consists of a double strand of nucleotides, though only one is “read” when a protein is being made. The DNA genes are transcribed into messenger RNA, which then directs the formation of proteins.

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Some viruses have double-stranded DNA like our nuclei, but others have single-stranded DNA, single-stranded RNA, or double-stranded RNA. The SARS-CoV-2 virus contains single-stranded RNA, or ssRNA.

Positive and Negative-Sense RNA

The illustration below indicates that the RNA of the coronavirus is “+ sense.” Positive-sense RNA is ready for use in the process of translation, or protein manufacture. Some viruses have negative-sense RNA. Before this can exert its effects, it must be transcribed into positive-sense RNA.

Proteins and Lipids

Proteins are joined to the RNA in the coronavirus, as shown in the video above. They are sometimes referred to as nucleoproteins. The virus is covered by an envelope made of lipids and containing envelope proteins. The lipid envelope of viruses is derived from the membrane of a cell. The envelope of the coronavirus also contains spike proteins, which protrude into the outer environment and attach to the cell membrane of a host during the infection process.

Spike Proteins

The spike proteins of SARS-COV-2 virions are important for the virus and for us. The proteins bind to the ACE2 (angiotensin-converting enzyme 2) receptor on the surface of our cell membranes. A spike protein changes its shape slightly so that the binding site (the receptor binding domain) is exposed. This enables it to bind to the receptor.

Like other proteins, a spike protein is made of amino acids joined together. A single spike protein molecule contains three folded amino acid chains joined in a specific arrangement and is said to be a trimer. The protein is studded with glycan molecules. Research indicates that the glycan coat is denser in some parts of the protein than in others.

A more detailed look at the structure of the virus

A more detailed look at the structure of the virus

Current Coronavirus mRNA Vaccines

In human cells, the DNA containing the genes is unable to leave the nucleus of a cell. The genetic code for making a protein is transferred to a messenger RNA molecule (mRNA). This molecule then leaves the nucleus and goes to a ribosome in the cell. Here the relevant amino acids are assembled to make the protein that was coded for in the DNA.

The leading SARS-COV-2 vaccines that have been created so far affect the spike proteins of virions. Researchers have been able to assemble a piece of mRNA that codes for part of the spike protein. When this is added to a vaccine, our body follows the instructions in the code and makes the protein, as it does for our own mRNA. Once the protein is constructed, the immune system recognizes that it doesn’t belong in the body and produces antibodies to attack it. The mRNA is destroyed once it has done its job.

After this process described above is complete, the immune system will have “learned“ how to protect the body as it does in other infections, and the antibodies will attack the real coronavirus spike protein if it enters the body.

The Nature of Glycans

Much of the research into how the virus infects us and how we might prevent this has been based on the spike proteins. As mentioned above, these proteins are partially coated with glycan molecules. Researchers have recently started exploring the role of these molecules.

Glycans are carbohydrates (a group that includes sugars, starch, and fibre). Sometimes the words glycan and carbohydrate are synonymous. Some researchers use the term “glycan” to mean any type of carbohydrate except monosaccharides, however. In this case, the words glycan and polysaccharide are synonymous.

Monosaccharides consist of a single sugar molecule (using the word “sugar” in its biological sense rather than its culinary one). Glucose and fructose are monosaccharides, for example. Polysaccharides consist of many sugar molecules joined together. Starch and glycogen are examples.

Because the virus hijacks the host cellular machinery for replication and subsequent glycosylation, the viral glycan shield may be composed of familiar host glycans; thereby suppressing an anti-carbohydrate immune response.

— Oliver C. Grant et al, via Nature Scientific Reports

A Glycan Shield for Spike Proteins

The glycan molecules coating the spike proteins are said to form a glycan shield for the virus. The addition of a glycan to another molecule (often a protein) is known as glycosylation.

During viral reproduction, the composition of the nucleic acid and the protein in the new virions is determined by the instructions in the invading virion’s RNA. The cell is forced to make the viral components. The virion also depends on the host cell’s ability to cover proteins with glycans during glycosylation, but it doesn't contain the code for making the glycans. The molecules are made by the host. As the quote above indicates, this may mean that the glycans will be recognized by the host cell and by other cells in the body and won’t be attacked. The glycan shield may be in effect acting as a disguise or a shield for the virus.

The glycans on the spike proteins may have another useful function for the virus. Perhaps very significantly, an article published by the American Chemical Society says that glycan molecules modulate the shape of the receptor binding domain on a virion, thereby determining whether it can bind to a cell.

Determining where the glycans bind to the proteins and ways to prevent this union from happening could be very useful in dealing with infections and might be useful in vaccine development.

An international team of researchers has identified two sugar-binding proteins that act as the “Achilles’ heel” of SARS-CoV-2 variants – point to in a promising direction towards treatment for COVID-19 in all its variations.

— University of British Columbia (UBC)

Preventing the Formation of the Glycan Shield

Researchers have paid a lot of attention to the spike proteins of the coronavirus, since these enable it to attach to cells. The glycans are believed to play a role in hiding the virus from the host's immune system. As the last reference below says, the virus could be viewed as a wolf in sheep's clothing.

An international team of researchers has recently discovered that the sites where the glycans join to the spike proteins are "highly conserved" in the different variants of the virus. This means that a substance that interferes with the binding could be very useful in the fight against the virus. Researchers have found two lectins that block the bond. The discovery may be important.

Hope for the Future

The fact that vaccines for the current coronavirus pandemic have been and are being created is great news. Hopefully, the long-term outcome of the vaccines will be very successful. Scientists are still learning about the virus and its behaviour, however. It’s possible that investigating the role of glycans in our body might be useful in many ways.

One benefit of studying glycans might be helping the fight against SARS-CoV-2, which would be a wonderful outcome. It’s important to be prepared for future possibilities, such as mutations (genetic changes) in the virus. The more that we know about the structure and behaviour of the virus, the more likely it will be that we will be able to respond appropriately if it changes.


  • The viral life cycle from Oregon State University
  • Parts of a coronavirus from Scripps Research
  • "Introduction to RNA Viruses" from the National Library of Medicine
  • Spike protein variants from Connor Bamford, Queen’s University Belfast, via The Conversation
  • Coronavirus vaccine information from the CDC (Centers for Disease Control and Prevention)
  • Analysis of the SARS-CoV-2 spike protein glycan shield from Nature Scientific Reports
  • The role of glycans in the SARS-CoV-2 spike protein from the ACS (American Chemical Society)
  • Neutralizing the sugar coat of the virus from the University of British Columbia

This content is accurate and true to the best of the author’s knowledge and does not substitute for diagnosis, prognosis, treatment, prescription, and/or dietary advice from a licensed health professional. Drugs, supplements, and natural remedies may have dangerous side effects. If pregnant or nursing, consult with a qualified provider on an individual basis. Seek immediate help if you are experiencing a medical emergency.

© 2021 Linda Crampton


Linda Crampton (author) from British Columbia, Canada on March 03, 2021:

Thank you very much, Fran. It may be some time before I get my first shot. Things seem to be moving quite slowly here.

fran rooks from Toledo, Ohio on March 03, 2021:

Alicia, I always find your articles informative and certainly useful. Thanks for your information. I received my first covid shot, soon the 2nd.

Linda Crampton (author) from British Columbia, Canada on March 02, 2021:

Hi, EK. Thank you very much for such a lovely comment. I appreciate your visit. I hope your exams went well.

EK Jadoon from Abbottabad Pakistan on March 02, 2021:

After a long time, I am able to get in touch with all of you. I missed you all, especially you, Alicia. I was busy with my exams. Your article is fabulous as always. Lots of love and respect for you.

Linda Crampton (author) from British Columbia, Canada on March 02, 2021:

Hi, Devika. Unfortunately, the coronavirus pandemic has become part of our lives. I hope the situation improves soon.

Devika Primić from Dubrovnik, Croatia on March 02, 2021:

Hi AliciaC an interesting and well-informed hub on this research. It has become part of our lives and more new information or the unnoticed information always helps us to know more.

Linda Crampton (author) from British Columbia, Canada on March 02, 2021:

I’m glad they survived, too. Many people do get mild cases of the disease, but unfortunately a significant number experience serious symptoms.

Linda Crampton (author) from British Columbia, Canada on March 02, 2021:

I appreciate your visit and the kind comment, Maren.

Linda Crampton (author) from British Columbia, Canada on March 02, 2021:

Thank you very much, Fran.

gyanendra mocktan from Kathmandu,Nepal on March 02, 2021:

You have exactly told me here. They had mild symptoms. Their positive report from the doctor terrified the neighbourhood. One of them said people were afraid to pass by their home. Thank God they survived.

Maren Elizabeth Morgan from Pennsylvania on March 02, 2021:

Fabulous research and explanation. Thank you!

fran rooks from Toledo, Ohio on March 02, 2021:

Alicia, Thanks so much for your informative article. Tou are always so precise with valuable info.

Linda Crampton (author) from British Columbia, Canada on March 01, 2021:

Hi, Heidi. Yes, I’m watching the news closely, especially as it applies to Canada and specifically to British Columbia. It’s an interesting time! Thanks for the visit.

Heidi Thorne from Chicago Area on March 01, 2021:

Always great info! I'm sure you're watching the news on the rollout of the current vaccines for the pandemic. It looks very promising. Thanks for offering the science behind the pandemic!

Linda Crampton (author) from British Columbia, Canada on March 01, 2021:

Hi, Mary. Yes, the ability of the virus to mutate is a concern. Hopefully, increased knowledge will help our fight against this virus and other ones, as you say.

Mary Norton from Ontario, Canada on March 01, 2021:

Thank you for making us understand this virus better. We continue to learn about this virus but it also continues to baffle us when it mutates. I am sure that more knowledge will be very helpful to stop another virus' impact.

Linda Crampton (author) from British Columbia, Canada on March 01, 2021:

Thank you, Laynie.

Laynie H from Bend, Oregon on March 01, 2021:

Great coverage here, Alicia.

Linda Crampton (author) from British Columbia, Canada on March 01, 2021:

I hope the disease soon becomes a bad memory. The virus is not pleasant, to put it mildly. Thanks for commenting, Adrienne.

Linda Crampton (author) from British Columbia, Canada on March 01, 2021:

I appreciate your comment very much, Chitrangada. I hope the coronavirus situation improves soon.

Adrienne Farricelli on March 01, 2021:

The more we learn about this virus, the better. Knowledge is power. Hopefully this disease will shortly become a bad memory.

Chitrangada Sharan from New Delhi, India on March 01, 2021:

A very important and well researched article. You have done a wonderful job by explaining it, in an easy to understand language.

The vaccines have brought the much needed relief, and I hope things improve further in the coming times.

Thank you for sharing this excellent and well writing article.

Linda Crampton (author) from British Columbia, Canada on March 01, 2021:

Thanks, Bill. I appreciate your comment. I hope you have a good week.

Linda Crampton (author) from British Columbia, Canada on March 01, 2021:

Thanks for the kind comment, Manatita. Llamas and their potential ability to help us are intriguing. We do seem to be making strides in the right direction, as you say. I hope the momentum continues.

Linda Crampton (author) from British Columbia, Canada on March 01, 2021:

Hi, Eman. It's interesting to think about the future and about how the virus may affect our lives over the long term. I hope things return to normal or at least as normal as possible.

Linda Crampton (author) from British Columbia, Canada on March 01, 2021:

Thanks for commenting and for sharing the information, Gyanendra. I'm glad the people that you know recovered. It seems like the infection often produces mild or no symptoms, but in some people it produces horrible effects.

Linda Crampton (author) from British Columbia, Canada on March 01, 2021:

Thank you for the comment, Misbah. Blessings to you as well.

Linda Crampton (author) from British Columbia, Canada on March 01, 2021:

Thank you very much, Flourish. I appreciate your kind comment.

Linda Crampton (author) from British Columbia, Canada on March 01, 2021:

I appreciate your visit and comment, Dora. I hope things are going well for you.

Linda Crampton (author) from British Columbia, Canada on March 01, 2021:

Thanks for the comment, Peggy. I'm going to get the first vaccination when it's available for my age group.

Bill Holland from Olympia, WA on March 01, 2021:

Some of this is simply over my head, but I understood a lot of it thanks to your excellent explanation. Thank you, Linda!

manatita44 from london on March 01, 2021:

Alicia, I don't know how you write these pieces! Brilliant and engaging, as usual and subject on point, too. The videos helped. Was it Llamas you said in another Hub, which has the potential for helping us in the future?

Anyway, we seem to be making strides in the right direction. Thanks for the further enlightenment about this topical subject

Eman Abdallah Kamel from Egypt on March 01, 2021:

Thank you, Linda, for this educational article on Coronavirus. I hope that the infection with this virus will decrease and conditions will return to some extent as we were before.

gyanendra mocktan from Kathmandu,Nepal on March 01, 2021:

Linda, Thank you for your indepth information about the corona virus and progess the scientists are making They are working hard in their lab, the doctors and nurses who serving the affected by the virus. Hope soon the scientists will come up with vaccine that can protect us

Personally, I happen to meet three persons who were corona virus positive. They said they isolated themselves and used herbs and spices instead of modern medicine. They got cured!! Strange!!

Misbah Sheikh from — This Existence Is Only an Illusion on February 28, 2021:

Linda as always, you provided us a wonderful and informative article

You did a good research work

I appreciate your efforts

Thanks for sharing


FlourishAnyway from USA on February 28, 2021:

Your detailed research and the way you presented this complex information in bite-sized pieces is helpful. You're a talented science writer, Linda.

Dora Weithers from The Caribbean on February 28, 2021:

Much of this is over my non-scientic head, however I do understand that they are working on the vaccines. Thanks for the in-depth research which we can always have for reference.

Peggy Woods from Houston, Texas on February 28, 2021:

Thanks for your in-depth look at how these viruses spread and replicate. The sooner most people in the world get the vaccines, the sooner we may help stop the spread of this pandemic. My husband and I both got our first injections this past week. He got the Moderna vaccine, and I was given the Pfizer. Johnson and Johnson was approved today in the U.S. for distribution.

Linda Crampton (author) from British Columbia, Canada on February 28, 2021:

Thanks, John. The coronavirus is interesting biologically, but some of its effects are horrible.

Linda Crampton (author) from British Columbia, Canada on February 28, 2021:

Thank you very much for the comment and for sharing the information, E. Randall. I hope we can defeat this virus as soon as possible. I also hope that you stay safe.

John Hansen from Gondwana Land on February 28, 2021:

Lynda, thank you for sharing this in-depth information on the SARS-CoV-2 coronavirus. Very informative and I appreciate your research.

E Randall from United States on February 28, 2021:

As always you have written a fantastic article. Thank you for writing this. Johnson & Johnson is supposed to be rolling out that new vaccine soon. They were saying it will be one dose and does not require refrigeration. We will see what happens. Take care.

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