COVID 19 THREE PRONGED SOLUTION CHALLENGE
THREE PRONGED STRATEGY TO A SOLUTION
We have been doing an extensive research on the current Coronavirus SARS-CoV-2 (2019-nCoV) and the interventions that need be taken. On the basis of our findings, we are pushing forward a three pronged solution.
B. Strengthening the innate and adaptive immune systems.
A. Vaccine — We shall divide this into 2 parts .
1. Actions on the virus side.
2. Actions on the human cells side.
1. Virus Side Actions
a. Coronavirus Family Code
i. Coronaviruses contain a genome composed of a long RNA strand (SARS-CoV-2 is about 30,000 nucleotides long) one of the largest of all RNA viruses. This genome acts just like a messenger RNA when it infects a cell, and directs the synthesis of two long polyproteins that include the machinery that the virus needs to replicate new viruses. These proteins include a replication/transcription complex that makes more RNA, several structural proteins called viroporine that construct new virions, and two proteases. The proteases play essential roles in cutting the polyproteins into all of these functional pieces.
ii. Thus coronavirus is limited to just 2 following subunits and both can be attacked to stop it.
1. The protease exterior
2. The lengthy stand of RNA which serves as the viruses’ genetic material
iii. Actions on Protease :
1. The protease’s activity is triggered by the binding of molecules to specific points on the protease called active sites. The binding of a substrate effectively switches the protease on, allowing it to cut the long viral protein strands into smaller chains. The protease’s activity can also be blocked by molecules called inhibitors. When an inhibitor attaches to an active site, it prevents the binding of substrates stopping the action of the protease altogether. Therefore, finding an inhibitor for COVID-19’s heart-shaped protease is the first step to beating the epidemic which is what the current research and trials being conducted is all about.
2. Current effort to save time are more towards repurposing existing antiviral drugs as protease inhibitors. WHO is focusing on what it says are the four most promising therapies:
a. An experimental antiviral compound called remdesivir;
b. The malaria medications chloroquine and hydroxychloroquine;
c. A combination of two HIV drugs, lopinavir and ritonavir;
d. And that same combination plus interferon-beta, an immune system messenger that can help cripple viruses.
3. Some data on their use in COVID-19 patients have already emerged — the HIV combo failed in a small study in China — but WHO believes a large trial with a greater variety of patients is warranted.
iv. Actions on RNA — Using CRISPER enzyme CAS13
1. The COVID-19 public health emergency is due to a coronavirus, which contains an RNA — not DNA — genome.
2. Researchers in the lab of Neville Sanjana, PhD, at the New York Genome Center and New York University have developed a new kind of CRISPR screen technology to target RNA.
3. Cas13 enzymes are Type VI CRISPR (clustered regularly interspaced short palindromic repeats) enzymes that have recently been identified as programmable RNA-guided, RNA-targeting proteins with nuclease activity that allows for target gene knockdown without altering the genome.
4. This property makes Cas13 a potentially significant therapeutic for influencing gene expression without permanently altering genome sequence.
5. Using the model derived from their massively-parallel screens, optimally guided RNAs can help detection and therapeutic applications.
a. Diversity of the Coronavirus :
i. Diversity of coronaviruses poses a great challenge with this as the proteases of these viruses can be very different. So drugs designed to fight one may not be effective against others.
b. Mutation :
i. SARS-CoV-2, is believed to have 2 “strains”: the “L” type and the “S” out of which “L” type, is deemed to be more aggressive type and found in 70% of the virus samples. But its prevalence decreased after early January. The more commonly found type today is the older, “S” type, because “human intervention” such as quarantines may have reduced the ability of the “L” type to spread. For one thing, the mutations are incredibly small on the order of a couple of nucleotides, the basic building blocks of genes. (SARS-CoV-2 is about 30,000 nucleotides long). These slight changes likely wouldn’t have a major impact, if any at all, on the functioning of the virus, so it would be “inaccurate” to say that these differences mean there are different strains. These viruses are still so genetically similar that these mutations shouldn’t alter a new vaccine. Once the vaccine is out, however, the virus could adapt to it and develop resistance, but considering that other RNA viruses such as those that cause measles, mumps and yellow fever didn’t develop resistance to vaccines, that scenario is unlikely.
2. Human Cells Side Actions :
a. Coronaviruses both the SARS coronavirus of 2003 and the novel coronavirus of 2019/20 uses the SARS-CoV receptor ACE2 for entry and the serine protease TMPRSS2 for S protein priming.
b. The spike glycoproteins have two subunits; one subunit, S1, binds to the receptors on the cell surface; the other subunit, S2, fuses with the cell membrane. A host transmembrane serine protease, TMPRSS2, promotes entry of SARS-Cov into cells by two separate mechanisms. After the S1 subunit of the spike binds to the ACE-2 enzyme on the cell membrane surface, TMPRSS2 activates the spike and cleaves ACE-2. TMPRSS2 also acts on the S2 subunit of the spike glycoprotein, causing an irreversible conformational change, activating it, and facilitating fusion of the virus to the cell membrane. The virus then enters the cell.
c. Actions on ACE2 side
i. The receptor for the SARS cough virus that causes COVID19 is the ACE2 receptor. The virus enters the body through the nose, mouth or eyes, then attaches to cells in the airway GI tract that produce a protein called ACE2 which is where the s protein docks. Then there’s another protein called a serine protease TMPRSS2 which is also here in the membrane which helps to internalize this virus into the cell and it allows the messenger RNA which is in here to come in and infect the cell. This protein on the human cell side is exactly the same protein that was the receptor for the SARS. Treatment with an anti ACE-2 antibody can block entry of SARS-CoV-2 expressing S protein.
ii. The ACE 1 and ARB inhibitors used for the treatment of blood pressure and cardiac diseases are being talked about of increasing the ACE2 receptors but there is no evidence so far.
iii. Janus-associated kinase (JAK) inhibitor Olumiant (baricitinib), approved for rheumatoid arthritis, was identified using machine learning algorithms on the basis of its inhibition of ACE2-mediated endocytosis.
iv Another JAK inhibitor, Jakafi (ruxolitinib), is in trials (combined with mesenchymal stem cell infusion) for ACE2.
d. Actions on TMPRSS2 side
i. SARS-CoV-2 requires the protease TMPRSS2, which is present in the human body, to enter cells. This protease is a potential target for therapeutic intervention if blocked by an inhibitor. Since it is known that the drug camostat mesilate inhibits the protease TMPRSS2, research is going on here to whether this inhibition can also prevent infection with SARS-CoV-2.
e. Actions On Other Methods : Sera from recovering SARS patients reduced SARS-CoV-2 S protein-driven entry into Vero-E6 cells. Different Covalescent Blood Produtcs (CBP) being tried to achieve artificially acquired passive immunity include all of the following
1. Convalescent whole blood (CWB), convalescent plasma (CP) or convalescent serum (CS);
2. Pooled human immunoglobulin (Ig) for intravenous or intramuscular administration;
3. High-titre human Ig;
4. Polyclonal or monoclonal antibodies.
5. A future vaccine could help the body produce antibodies that target the SARS-CoV-2 virus and prevent it from infecting human cells. The flu vaccine works in a similar way, but antibodies generated from a flu vaccine do not protect against coronavirus.
3. Strengthening the innate and adaptive immune systems.
a. Learning’s from SARS Proteases
i. The SARS-COV2 proteases while cutting the polyproteins also clips several proteins in the infected cell, including removing ubiquitin from ubiquitinated proteins. One of the consequences of this deubiquitination is that it interferes with production of interferons in the innate immune system, short-circuiting some of our defenses against the virus.
ii. Because the interferon system ( communication system between our innate and adaptive immune system ) is compromised, the adaptive system cannot be put to work.
b. Understanding Current Model Of Immune System Beyond The Old Two Box Model Immune System : We have four parts to the new model of immune system away from the old two box model.
i. Innate immune system which then integrates with the
ii. Adaptive immune system to create antibodies.
1. Innate Immune Stem
The innate immune system is that aspect of our body at the physical level, organ level all the way down to the cellular level that interacts with these pathogens that come from the outside — through our eyes, right through our mucosa in our nose, through our mouth, through our ears, through our skin and other orifices of our body. This is where these pathogens when they come, first interact with what is called as our innate immune system. This includes things like neutrophils and macrophages. The goal of innate immune system is to knock things out quickly and if things are working right it happens during the first few hours when we are experiencing some pathogens and thereafter what happens is the adaptive immune system kicks in.
2. Adaptive Immune System
a. The adaptive immune system include T cells and B cells which attempt to take out that particular pathogens by creating a particular antibody.
b. In a healthy individual the innate kicks in first and we don’t even notice it. This may be a little sniffle that we get and don’t feel that well and then adaptive kicks in and we create these antibodies and next time we are exposed to that particular pathogen we don’t even notice that nothing really happens.
3. The Interferon System
The innate immune system communicates to the adaptive immune system and this interaction is through what is called as the interferon system. The interferon system regulates all sorts of genes to interfere with viruses. This means our body is expecting pathogens and it trains its stuff to get stronger. But these three systems are not alone there’s a fourth system called the microbiome.
4. The Microbiome :
This system also includes what’s called the biome which has trillions of viruses in our body. The microbiome is bacteria. For our six trillion cells, we have about ten times ie sixty trillion bacteria and then around three hundred sixty trillion viruses with a small number of fungi.
c. Viruses Don’t Kill — The Compromised Immune System Does
1. Thus we already have hundreds of trillions of viruses in our body and tens of trillions of bacteria and all of these things are actually supporting life within us.
2. Viruses do not harm or kill us. It is the overreaction of a weakened and dysfunctional immune system to the virus that results in our own body attacking its own cells, tissues and organs.
3. Now these dysfunctional immune response is a result of underlying pre-existing conditions like Obesity, Diabetes, Heart disease which are because of Poor lifestyle, lack of sleep, poor dietary choices, lack of exercise, eating sugar, smoking people being immuno compromised.
4. Thyroid dis-functioning leading to our body not able to take carotenoids that we eat and convert them into vitamin A and we get less cytokeratins which create a wall around our cells to really protect us.
5. Lower HCL levels rising to lower our gut acidophilus due to which microbiome goes into dysfunction.
6. High sugar diet leading to candida and a whole other set of organisms that start growing leading to growth in glio toxins which destroy our macrophages and t-cells(innate and adaptive immune system).
d. Cytokine Storm :
1. Unable to help itself due to the broken immune system, the body while trying to heal itself against pathogens unleashes cytokine storm . All these other chemicals start raging to try to make up for the fact that the other subsystems have failed. When this cytokine storm happens, these chemicals go and start attacking our own tissues.
2. Now in corona it is our cytokine storm that attacks the epithelium which is a different set of cells in our lungs leading to ARDS ( Acquired Respiratory Distress Syndrome). The epithelial cells and mucosa and mucous tissue in integrity in our lungs, function as a front line of defense against pathogen and bae invasion. So when things are coming into us when someone with corona sneezes these pathogens come across the frontline defense which is our epithelial mucosa tissue.
3. Here Vitamin A plays a crucial role in the morphological formation of the epithelium epithelial keratinization stratification differentiation and functional maturation of the epithelial cells. Vitamin A is literally used to produce cytokeratins which are the building blocks protecting our cell walls and they’re the ones who provide the border and in the epithelial cells of our lungs they’re the ones who create the proper infrastructure so our body doesn’t get attacked by these pathogens. So that’s like the first defense system. Vitamin A is an integral part of the mucus layer of both the respiratory tract and our intestines. If we look at our grunt gut and our respiratory tract vitamin A is an integral part of that mucus layer and vitamin A promotes a mucus secretion it improves antigen nonspecific immunity of our innate and adaptive system so vitamin A is a hormone.
4. Vitamin A protects our cell walls but more importantly it also makes sure that our immune system is properly modulated and it down regulates those cytokines that will cause a cytokine storm that goes and attacks us.
5. A large percent of the people who test positive and die are on ventilators and they died with something called a ARDS.
6. ARDS is how corona virus kills it’s not just the corona virus but many other viruses including the influenza virus that we have every year.
7. As described above the virus attacks the cells of the 600 million alveoli that human lungs have. The entire lungs become inflamed creating a large barrier. A fluid goes into the interstitial space. Furthermore the blood capillaries start to become leaky and fluid starts to leak into the alveolar space as well and this starts to fill up with proteinaceous liquid that prevents oxygen from getting into the bloodstream.
8. So instead of having nice oxygenated blood this blood becomes hypoxic and we become hypoxic. If we have ARDS and we have a hard time breathing and that’s when we get placed on the ventilator.
9. We have to be supported on the ventilator so that we’re getting enough oxygen and that the machine can breathe for us .
10. Another amazing nutrient from the Sun called vitamin D which produces chemicals which are antiviral is also important
11. So vitamin A, vitamin D and Vitamin C are major for the immunity and we can add more.
Thus we have to understand the above immune system holistically and then aggressively build immunity enhancement theureupatics to curtail infection at its source .
3. Testing Side : Following are the efforts going on.
a. RT-PCR :
When testing for a new virus like SARS-Cov-2, the first wave of diagnostics almost always relies on two important (though not particularly modern) technologies.
i. The first, PCR, or polymerase chain reaction, is a DNA amplification technique that is routinely used in the lab to turn tiny amounts of DNA into large enough quantities that they can be analyzed.
ii. But if scientists want to detect a virus like SARS-CoV-2, they first have to turn its genome, which is made of single-stranded RNA, into DNA. They do that with a handy enzyme called reverse-transcriptase. Combine the two techniques and you’ve got RT-PCR. Currently, RT-PCR is the only way to determine if a person has Covid-19.
iii. Starting in January, shortly after Chinese researchers released the first whole genome sequence of SARS-CoV-2, groups around the world began designing, testing, and publicly posting protocols for detecting the new coronavirus with RT-PCR. As a resource for testing labs, the World Health Organization has been keeping a list of these protocols, as well as guidelines for best practices. All countries experiencing their own outbreaks moved to adopt other protocols publicized by the WHO.
iv. Roche and Thermo Fisher, which recently had their in-clinic tests approved by the FDA, have been forced to reckon with supply chain issues that have limited their distribution.
b. Crispr-based diagnostics:
i. These tests use Crispr’s programmable gene-seeking capabilities to deliver a diagnosis in under an hour without the need for fussy lab instruments.
ii. Startups like Sherlock Biosciences and Mammoth Biosciences are very active here. Mammoth published a preprint on March 10, describing a test the company developed for SARS-CoV-2 that works with paper test strips like those in a drugstore for pregnancy test. The company is currently in the process of further validating its initial results.
c. Serological Test
i. These tests look for antibodies to the virus in the blood of patients which would be useful, because in addition to identifying people with Covid-19, it could tell if someone was once infected but then recovered.
ii. Cheaper than PCR but not as accurate as molecular, this does detect SARS-COV-2.
d. Teleheatlth At Home tests
i. These are molecular point of care tests which companies are targeting to deliver a test in 30 minutes.
ii. A swab that’s done too shallowly could wrongly convince someone that they don’t have Covid-19.
iii. People getting a test result at home may react in unexpected ways compared with how they might handle the news where a clinician delivering it in-person.
iv. Nurx, Everlywell, LetsGetChecked, Carbon and few other startups had started home testing but FDA has declared that it has not prescribed any at home tests and hence those are stopped.
As we can see that the actions under the three pronged strategy will clearly lead to to reach the root cause and a solution to kill this virus forever.
We are in touch with various IITs in India and many institutes abroad are working on the above.
We intend to interact for solutions in vaccines , immunity and testing.
If you have one, reach out.