learn about COVID-19, its impact, and what you can do about it.
Viral Life Cycle
There are 8 main stages that a standard virus goes through. Depending on what type of virus it is (DNA, RNA, retro, etc.), some steps may take place differently. The steps discussed are representative of the novel SARS-CoV-2 virus.
Once in proximity of host cells, the virus can commence the first phase: attachment. Surface proteins on the virus (spike proteins) bind to other surface proteins on the membrane of the host cell (See Section 2.). Understanding this initial phase of the life cycle is crucial when developing vaccines as it is the easiest phase to interfere.
Once bound to the host cell, the virus undergoes penetration. During this phase, the viral contents are released from the virus into the host cell. This can happen in one of two ways: Receptor Mediated Endocytosis or Direct Membrane Fusion. The former occurs when a sub-vesicle is created from membrane material surrounding the contents as it flows to its destination. The latter occurs when the membrane of the virus and that of the host cell fuse into one and the contents are transported through coated vesicles.
When the virion particle is in the infected cell, uncoating and targeting occur. The contents (mRNA, DNA, etc) are released from the sort of vesicle that it traveled in and are delivered to their end location; mRNA gets released in the cytoplasm to be translated to proteins and DNA gets delivered to the nucleus.
Subsequently, gene expression along with genome replication occurs. In the case of RNA viruses, like SARS-CoV-2, gene expression occurs in the cytoplasm through the natural ribosomes. Later, the replication of the genome is performed ready to be reformed into new viruses.
Finally, viral assembly and release is the last step. The replicated viral contents are reassembled into new virion particles, transported outbond of the cell in vesicles, and released from the host to infect other cells.
The angiotensin converting enzyme’s (ACE) principle function is to convert a molecule called angiotensin, a molecule essential to regulating blood pressure, from its angiotensin II form to its angiotensin 1-7 form. Angiotensin II promotes high blood pressure while angiotensin 1-7 lowers it. For this reason, it’s existence and functionality in organs like the heart, kidney, lungs, and other arteries is essential to cardiovascular homeostasis. The gene that codes this protein (ACE2) is located on chromosome X, read on the negative strange, and has a genomic location of ~ 15,576,221 - 15,602,966. The protein is known to interact with nine other proteins, one of which is the Spike protein on SARS-CoV/SARS-CoV-2. In terms of these viruses, there are three positions (peptides 30-41, 82-84, and 353-357) in which they physically interact. See red sections in image.
The Spike protein has a receptor binding domain on the tip of it which is able to bind to the three positions listed above. When this occurs, the virus is granted access into the cell. Because of its vital role in maintaining proper cardiovascular function, ACE2 itself should not be blocked to inhibit coronavirus infection, rather the spike protein. Since research about the novel virus is very time sensitive, it is important that research is done on the ACE2 protein to understand how the Spike protein infects cells to learn how to stop it.
There are two other forms of the ACE2 protein: testis-specific (tACE) and Drosophila homolog (AnCE) which have 43% and 35% identities and 61% and 55% similarities to ACE2. For background, a certain percent of identity quantifies how much of two sequences (DNA or peptide) are exactly the same and percent of similarity quantifies how much of two sequences are the same or share very similar characteristics with one another; these numbers are calculated through a computational method called dynamic programming. Researchers were able to study the similarities between the three proteins to create a more accurate representation of ACE2 itself.
A main difference between SARS-CoV and SARS-CoV-2 are small differences in the Spike protein. The two spike proteins are very similar to one another but one main difference is in the RBD where a Valine amino acid turned into a Lysine amino acid which significantly strengthens the binding between the two proteins.
TMPRSS2 is the shorthand for transmembrane serine protease 2. It is also called serine protease 10. It is a protein on the surface of the cell membrane with 492 amino acids. Most of these amino acids are used in the extracellular part of the protein. The TMPRSS2 gene encodes a protein in the serine protease family. The main parts of the TMPRSS2 protein are its protease domain, a type II transmembrane domain, a receptor class A domain, and a scavenger receptor cysteine-rich domain. The protease domain is the spot on the protein that allows it to cleave other proteins, the type II transmembrane domain is the anchor on the cell membrane, the receptor class A domain has a promoting effect on zymogen activation (inactive precursors to enzymes) while also having a role in immunosuppression, and the scavenger receptor cysteine-rich domain subserves innate immune defense functions (among other homeostatic functions). Its principle function is assisting in the normal function of the prostate, yet there is still much to learn about the protein’s distinct functions. When induced by androgens, it can lead to the activation of several substrates that can lead to the spread of prostate cancer cells to other parts of the body. The protein’s involvement in the virus life cycle revolves around cleaving the spike proteins (S proteins) of several coronaviruses, most notably the SARS-CoV-1 and the SARS-CoV-2 outbreaks which started in 2003 and 2019, respectively.
By inhibiting TMPRSS2 proteins using the clinically proven compound camostat mesylate, researchers have been able to prevent SARS-CoV-1 and SARS-CoV-2 from entering the tested cells. However, this treatment was not 100% effective, and was in fact more effective on SARS-CoV-1 than SARS-CoV-2. However, since there are not many known functions of TMPRSS2 (other than the ones mentioned in this report) inhibiting it is a possible avenue for preventing the spread of SARS-CoV-2.
SARS-CoV-2 (Covid-19) is the newest coronavirus to impact humans. It first appeared in the Wuhan District of China in December, 2019, and has since spread globally, causing a global pandemic. While it is not the first coronavirus outbreak of the 21st century, it is the most deadly and widespread, having caused over 100,000 deaths in the United States alone as of the time of writing.
SARS-CoV-1 and SARS-CoV-2 have very similar methods of infection. SARS-CoV-1 has been shown to utilise several proteins to enter the cell. These include, but are not limited to, ACE2, TMPRSS2, and CAT L/B proteins. The SARS-CoV-1 spike protein (S protein) binds to the ACE2 protein, while the TMPRSS2 and CAT L/B proteins cleave the S protein into two parts, the S1/S2 part and the S2’ part. Since the TMPRSS2 and the CAT L/B proteins perform similar functions in the case of viral transmission, studies were conducted to determine which protein was more necessary for the cleavage of the S protein. These studies showed that while inhibiting the CAT L/B proteins would sometimes stop the viral transmission of the SARS-CoV-1 virus, the virus would still usually enter the cell. It was only after they inhibited TMPRSS2 that SARS-CoV-1 stopped entering the cells. This yielded almost foolproof results.
SARS-CoV-2 shares very similar traits to SARS-CoV-1 in this case, as its virality has been shown to be caused by its S protein. Similarly to SARS-CoV-1’s S protein, it interacts with the ACE2 and TMPRSS2 proteins in order to enter the cell. TMPRSS2 cleaves the S protein into two parts, the S1/S2 part and the S2’. ACE2 binds to the S protein, granting the virus entry into the cell. Alongside this, scientists have noted the apparent interaction between CAT L/B proteins and the SARS-CoV-2 S protein, yet there is still not enough research surrounding it to make many distinct conclusions.
To initially determine whether or not SARS-CoV-2 would bind to the ACE2 protein, the receptor bonding domains of SARS-CoV-1 and SARS-CoV-2 were compared, alongside other coronaviruses that were found in bats. Some of these viruses were known to attach to ACE2, like SARS-CoV-1, while others were known to use other proteins to enter into the cell. After comparing the RBD of SARS-CoV-2 to the others, it was determined through use of an identity matrix and set gap penalties that the SARS-CoV-2 RBD was highly similar to the RBD of SARS-CoV-1 and other coronaviruses that made use of ACE2, while it was dissimilar from those that did not use ACE2.
Another similarity between the two coronaviruses is the placement of the disulfide bonds in each of the S proteins. Not only do both coronavirus S proteins have six disulfide bonds, but they are in very similar locations.
Finally, antibodies from SARS-CoV-1 have been shown to be effective against SARS-CoV-2. However, these antibodies are not necessarily applicable to many situations, as they only last in the body for around two months, and considering how long ago the SARS-CoV-1 outbreak was, very few people are likely to have them naturally. However, they could be gathered through lab work. The bigger issue is that while they do assist with blocking the SARS-CoV-2 virus, the antibodies are not foolproof, and they will not completely stop the spread of SARS-CoV-2.
In conclusion, SARS-CoV-1 and SARS-CoV-2 are very similar, with very similar cellular entry functions and methods and a similar spike protein. However, the differences between them do mean that treatments and therapies that worked before will often not work nearly as well on SARS-CoV-2 as they did on SARS-CoV-1.
Written by Jonathan F & Oliver T
Authors and Editors