Coronavirus SARS-CoV-2: Dissecting the virus
By: Jillian Ada Burrows
Tags: Covid-19, Sars Cov2

Coronavirus SARS-CoV-2: Dissecting the virus

An updated scientific and clinical overview

If you take any medication or alter you diet, you could still get infected and be a carrier, even if you have no symptoms. There is no approved treatment for COVID-19. Remember 19% percent of us will have severe to critical symptoms, so stay home if you are sick. If you haven’t read my last article, please do.

Most of what follows is aimed at health care practitioners and some of it requires a background in cellular biology, immunology, and biochemistry. None of the treatment options are proven to work with COVID-19. Many of the listed drugs have been used off-label or as a compassionate use. Do not use this as the final say in treating COVID-19, please seek out a health care professional if you believe you are ill with COVID-19 and do not attempt to treat yourself using any of the information herein unless you know what you’re doing.

SARS-CoV-2 & COVID-19

On 12 December, 2019 an outbreak of a new acute respiratory syndrome started. Since then the disease has been identified as COVID-19 and the virus has been identified as SARS-CoV-2. It is 79.6% percent related to SARS-CoV, but is more closely related to the bat coronavirus RaTG13 with a 96.2% match of genome sequence identity. The initial virus reservoirs were likely bats or palm civets. Additional research indicates that certain portion of the genome are more similar in pangolins. This seems to indicate that SARS-CoV-2 is a virus which formed from natural recombination of RaTG13 and a pangolin CoV. Additionally, the virus spreads effectively via droplets between cats and ferrets. It can also infect swine. [Zhou et al. 2020; Lai, Shih, Ko, Tang, & Hsueh 2020; Andersen, Rambaut, Lipkin, et al. 2020; Wan, Shan, Graham, Baric, Li 2020; Liu, Chen, & Chen 2019; Zhang, Wu, & Zhang 2020; Zhang, Zheng, Huang, Bell, Zhou, & Zhang 2020; Graham & Baric 2010; Shi, Wen, Zhong, Yang, Wang, Huang 2020]

A study has shown that the virus has a 1000 times the viral load compared to SARS-CoV. It has an incubation period that is a median of 5–6 days. It is skewed towards the 2–4 day side, and extends to 14 days. Genetic testing by swab seems to only be reliable during days 3 to 27 from infection. Outside of that period, the probability of detecting it drops to 50% and lower. There must be enough shed virus to be able to swab it and reliably sequence the RNA. [Lauer et al 2020; Lai, Shih, Ko, Tang, & Hsueh 2020; Woelfel, Corman, Guggemos, et al. 2020]

One transmission happened between people in a one hour long business meeting. The person who transmitted the disease had very mild symptoms masked by over the counter medication (Rothe et al. 2020). Tempurature screening can overlook people who are asymptomatic or low-symptom. This would allow SARS-CoV-2 to spread via those overlooked people (Hoehl et al. 2020). There are other reports of transmission from asymptomatic to low-symptom people (Tong et al. 2020; Wu et al. 2020; Lai et al. 2020).

Woelfel, Corman, Guggemos, et al. 2020 examined how the infection seems to infect the upper respiratory tract separately from the lower respiratory tract. They found evidence of digestive system infection. When serogenesis begins, the amount of shed viruses diminish, but this requires more study. In one patient, the viral load increased to detectable levels after decreasing to undetectable levels on day 22. This rebound effect has been studied by Chen et al. 2020.

Upper Respiratory Tract

When the virus infects the upper respiratory tract, there might be signs of lesions or swelling in the infected tissues (Hoehl et al. 2020). In many instances of COVID-19, there are occurrences of anosmia (Hopkins & Kumar 2020). This likely indicates inflammation near the olfactory bulb or inflammation of the olfactory bulb. It is possible for the virus to infect the nervous system (Baig, Khaleeq, Ali, & Syeda 2020).

Lower Respiratory Tract

When the virus infects the lungs, the first symptom appears to be a fever followed by coughing and sputum. As the disease progresses, the patient may experience shortness of breath, respiratory failure, or even death. The disease is characterized by ground-glass opacity, multiple lesions, fibrotic streaks and other CT scan features laid out in Zhou, Wang, Zhu & Xia 2020.

A hypothesis has been put forward that the ground-glass effect is from to recently discovered attributes about the virus. Once the virus infects the lungs, it starts producing proteins which can remove the iron from hemoglobin. The result is that CO2-O2 exchange is inhibited and the patient is nolonger able to respirate. [Wenzhong & Hualan 2020]

Digestive System

Out of 204 patients, 103 patients exhibited digestive symptoms. Symptoms include lack of appetite (81 cases), diarrhea (35 cases), vomiting (4 cases), and abdominal pain (2 cases). Of the 103 patients with digestive issues, only 6 presented no respiratory symptoms. [Pan, Mu, Yang, et al. 2020]

Patients from 10 months to 78 years of age had stools containing SARS-CoV-2 RNA. The virus RNA continued to be in the stool of 20% of patients after the respiratory tract RNA testing was negative for several days. Importantly, infectious SARS-CoV-2 viruses were recovered from the stools of patients. [Xiao et al. 2020; Yeo, Kaushal, Yeo 2020; Openshaw 2009]

Sepsis

In critical cases of COVID-19 there can be multiple organ failure either caused by the virus infecting those organs or from a cytokine storm syndrome (a form of sepsis). Cytokine storm syndrome is discussed below in more detail. [Mehta et al. 2020; Qin et al. 2020; Ruan, Yang, Wang et al. 2020]

Factors Effecting Transmission

SARS-CoV-2 transmissibility is modulated by the location of the infection. If the respiratory tract is infected, coughing can aerosolize the virus unless it is encased in sputum. If the digestive system is infected, improper handwashing after defecation may lead to spreading the virus. It is unkown if the virus is transmitted in urine. The only study testing urine consisted of 10 patients and found no virus in any urine samples over the 12 day study (Young et al. 2020). These kinds of factors would be further modulated by the following findings:

During a three hour long aerosol experiment the SARS-CoV-2 remained viable throughout the experiment. The predicted decay rate indicates aerosolized virus may remain viable for up to 8 hours, but a longer expiriment is needed to validate that prediction.

On plastic surfaces, the virus was detected up to 72 hours after application.

On steel surfaces, the virus was dected up to 48 hours after application.

On cardboard sufaces, no viable virus was detected after 24 hours.

On copper surfaces, no viable virus was detected after 4 hours.

[van Doremalen et al. 2020].

Supporting the Immune System through Nutrition

Food can be medicine. There is a recent article in Progress in Cardiovascular Diseases which suggests a daily regimen to reduce the severity of any RNA virus, including SARS-CoV-2 (McCarty & DiNicolantonio 2020). The research is summarized and enriched below:

Ferulic acid : 500–1,000 mg — This is found in all plants especially the skins and bark. It is also a metabolite of anthocyanins found in berries, coffee, whole grains, and typically anything that is red, blue, or black. Ferulic acid blocks the myeloid differentiation primary response gene 88 (MyD88) mediated inflammatory response. In the case of COVID-19, this could be important in preventing the cytokine storm syndrome associated with the most severe cases.

: 500–1,000 mg — This is found in all plants especially the skins and bark. It is also a metabolite of anthocyanins found in berries, coffee, whole grains, and typically anything that is red, blue, or black. Ferulic acid blocks the myeloid differentiation primary response gene 88 (MyD88) mediated inflammatory response. In the case of COVID-19, this could be important in preventing the cytokine storm syndrome associated with the most severe cases. Zinc : 30–50 mg — This is found in shellfish, dark chocolate, sesame seeds, pumpkin seeds, squash seeds, lentils, beans, and meats, and many other foods. Zinc was found to decrease mortality by 27% compared to control in the AREDS1 multicenter trial. Zinc can reduce the time a person is sick by 33% in the general case (Hemilä 2017). Zinc is very useful in regulating immune response. Zinc finger binding domains are very important for cells to help manage proteins, gene expression, and many other functions (Laity, Lee, & Wright 2001; Matthews & Sunde 2002; Brown 2005; Gamsjaeger et al. 2007).

: 30–50 mg — This is found in shellfish, dark chocolate, sesame seeds, pumpkin seeds, squash seeds, lentils, beans, and meats, and many other foods. Zinc was found to decrease mortality by 27% compared to control in the AREDS1 multicenter trial. Zinc can reduce the time a person is sick by 33% in the general case (Hemilä 2017). Zinc is very useful in regulating immune response. Zinc finger binding domains are very important for cells to help manage proteins, gene expression, and many other functions (Laity, Lee, & Wright 2001; Matthews & Sunde 2002; Brown 2005; Gamsjaeger et al. 2007). Brewers Yeast Beta-Glucan (1,3 & 1,6): 250–500 mg — A slightly larger amount of nutritional yeast could probably be used. The beta-glucans are in the cell wall. Can be obtained from the cell walls of sea weeds, certain mushrooms, and fermented foods.

(1,3 & 1,6): 250–500 mg — A slightly larger amount of nutritional yeast could probably be used. The beta-glucans are in the cell wall. Can be obtained from the cell walls of sea weeds, certain mushrooms, and fermented foods. Spirulina : 15 g — This is just a touch over two tablespoons (one tablespoon disolves well in one cup). Guards against inflammation. It also may help stimulate an interferon type I response.

: 15 g — This is just a touch over two tablespoons (one tablespoon disolves well in one cup). Guards against inflammation. It also may help stimulate an interferon type I response. Selenium : 50–100 mcg — The National Institute of Health has a great page on what foods have selenium. Selenium is a cofactor for certain peroxidases. According to McCarty & DiNicolantonio’s reading of another study “…influenza is more pathogenic in selenium-deficient mice, and selenium deficiency also increases the rate at which viruses can mutate, promoting the evolution of strains that are more pathogenic and capable of evading immune surveillance.”

: 50–100 mcg — The National Institute of Health has a great page on what foods have selenium. Selenium is a cofactor for certain peroxidases. According to McCarty & DiNicolantonio’s reading of another study “…influenza is more pathogenic in selenium-deficient mice, and selenium deficiency also increases the rate at which viruses can mutate, promoting the evolution of strains that are more pathogenic and capable of evading immune surveillance.” N-Acetylcysteine (NAC): 1,200–1,800 mg — This is a precursor to glutathione, an important peroxidase. The precursors to NAC are typically found in protein rich and sulfur rich foods. NAC itself is found in low quantities in food. To reach 1200mg of NAC, one would have to eat 27 kg of onions (Šalamon et al. 2019).

(NAC): 1,200–1,800 mg — This is a precursor to glutathione, an important peroxidase. The precursors to NAC are typically found in protein rich and sulfur rich foods. NAC itself is found in low quantities in food. To reach 1200mg of NAC, one would have to eat 27 kg of onions (Šalamon et al. 2019). Glucosamine : 3,000 mg or more — This may upregulate mitochondrial antiviral-signaling (MAVS) protein, which in turn allows the body to produce more interferon alpha. Interferon alpha has been used successfully against CORVID-19 in Cuba according to a news report in teleSUR. Glucosamine is typically extracted from shellfish. There seem to be other ways of getting it from fungii. It is in cartilage. In any case, it is most practically procured through a supplement unless you’re a hunter.

: 3,000 mg or more — This may upregulate mitochondrial antiviral-signaling (MAVS) protein, which in turn allows the body to produce more interferon alpha. Interferon alpha has been used successfully against CORVID-19 in Cuba according to a news report in teleSUR. Glucosamine is typically extracted from shellfish. There seem to be other ways of getting it from fungii. It is in cartilage. In any case, it is most practically procured through a supplement unless you’re a hunter. Elderberry : 600–1,500 mg — Research shows elderberry tincture as useful for fighting off similar viruses. According to Toraban et al., it might cause issues with stimulating cytokines (part of the inflammation response), however there is no evidence around which cytokines it stimulates. Many traditional preparations may have other medicines which can prevent the cytokine storm. Long term continuous consumption may have consequences, as one mechanism of operation interferes with how cells reproduce and build proteins. [Krawits et al. 2011; Kinoshita et al. 2012; Lin, Hsu, & Lin 2014; Chen et al. 2014; Tejero et al. 2015; Weng et al 2019; Torabian et al. 2019; McCarty & DiNicolantonio 2020]

: 600–1,500 mg — Research shows elderberry tincture as useful for fighting off similar viruses. According to Toraban et al., it might cause issues with stimulating cytokines (part of the inflammation response), however there is no evidence around which cytokines it stimulates. Many traditional preparations may have other medicines which can prevent the cytokine storm. Long term continuous consumption may have consequences, as one mechanism of operation interferes with how cells reproduce and build proteins. [Krawits et al. 2011; Kinoshita et al. 2012; Lin, Hsu, & Lin 2014; Chen et al. 2014; Tejero et al. 2015; Weng et al 2019; Torabian et al. 2019; McCarty & DiNicolantonio 2020] Vitamin C can reduce the time a person is sick by 8% in the general case (Hemilä & Chalker 2013).

Artemisia

Plants from the Artemisia family, since the also have some antiviral properties (mugwort, wormwood, etc.):

Romero et al. 2006 found a reduction in Bovine Viral Diarrhoea Virus load (through an RNA proxy) comparable to ribavirin at the same dose, indicating artemisinin is an effective inhibitor of Flaviviridae virus replication at both 50μM and 100 μM. The treatment of hepatitis C virus described in the paper is IFN-α coupled with ribavirin. It has noxious side effects and is only effective for 50% of patients. They determined that adding artemisinin would likely help hepatitis C patients.

Artemisia arborescens was prepared into an essential oil and the IC₅₀ determined to be 2.4 and 4.1 μg/mL for HSV-1 and HSV-2, respectively, and the cytotoxic dose (CC₅₀) was determined to be 132 μg/ml, all in Vero cells (Saddi et al. 2007).

Artemisia annua & Artemisia persica were better at inhibiting HSV-1 than acyclovir at 25 μg/mL, but at 50 μg/mL acyclovir was more effective (Karamoddini et al. 2011).

A derrivative of artemesinin, artesunate, has been found to be effective against Human Cytomegalovirus (HCMV), Epstein-Barr, Herpes Simplex Virus 1 (HSV1), Human Herpes Virus 6A (HHV6A), Hepatitis B Virus (HBV), Flaviviridae (like Hepatitis C Virus), and partially inhibits replication of HIV-1 (Efferth et al. 2008). However, artesunate was found to have no inhibition against several strands of Influenza virus A (Efferth 2018).

For a list of Artemisia plants and their various constituents and traditional uses, see: Abad, Bedoya, Apaza, & Bermejo 2012; Fontaine et al. 2013; Nigam et al. 2019.

1,8-Cineole (eucalyptol)

Plants which are high in 1,8-cineole (eucalyptol) have demonstrated antiviral properties. These plants include clove buds, cinnamon bark and leaves, tulsi leaves, turmeric, pepper, ginger, oregano, thyme, basil, marjoram, mace, nutmeg, bay leaf, eucalyptus, Artemisia plants, various Curcuma plants, and many other plants. [Abad, Bedoya, Apaza, & Bermejo 2012; Fontaine et al. 2013; Nigam et al. 2019; Loizzo et al. 2008; Sasikumar 2005; Khalil, ur Rahman, Khan, Sahar, Mehmood & Khan 2017]

Using the Laurel berry as a source of essential oil, a team was able to demonstrate efficacy against SARS-CoV which is not SARS-CoV-2 (it is still quite similar and should be investigated). A dose of 120mg/ml was able to inhibit 50% of virus growth. However, care must be taken because 500mg/ml was found to be the TC50 dose on Vero cells (the dose where the growth of human cells was cut in half). They also noted anti-SARS-CoV activity in two plants lacking 1,8-cineole, Trachystemon orientalis of the Borage family and Juniperus oxycedrus of the Cypress family. [Loizzo et al. 2008]

Laurel was quite good reducing virus replication in worm cell cultures and honeybees. Some plants may increase rather than inhibit viral reproduction. [Ertürk, Demirbgğ, & Beldüz 2000; Aurori et al. 2016]

Cinnamomum zeylanicum and Eucalyptus globulus essential oils had anti viral properties against H1N1 and HSV1, but it seems the source of the essential oil matters. 1,8-cineole and β‐caryophyllene from eucalyptus can deactivate HSV1 by an undetermined interaction with the virus. The full blend was made of eucalyptus leaf, cinnamon bark, rosemary leaf, wild carrot seed essential oils diluted in an oil substrate. [Brochot et al. 2017] In mice, 1,8-cineol (eucalyptol) protected against influenza in mice. [Li et al. 2016]

Others

See: Lin, L. T., Hsu, W. C., & Lin, C. C. (2014). Antiviral natural products and herbal medicines. Journal of traditional and complementary medicine, 4(1), 24 — 35. https://doi.org/10.4103/2225-4110.124335

Warning About Silver

In regards to colloidal silver: One might only be helping guard against bacterial infections with true colloidal silver. Additionally, most silver solutions made through electrolysis actually consist of ionic silver. Ionic silver is much more reactive and will likely end up discoloring one’s skin (here’s a wonderful account of this).

Too much true colloidal silver will also cause discoloration. There are ways silver can help, but it requires careful preparation so the metal ion binds to specific other compounds (Gallidero et al. 2011; Orlowski et al. 2014; Khandelwal et al. 2014; Singh et al. 2017; Akbarzadeh et al. 2018; Papp 2010). People should stick to just using silver on silverware, and not consuming it.

Cytokine Storm Syndrome

In some of critical cases of COVID-19, there is a cytokine storm which results in uncontrolled inflammation. The state is a particular variety of sepsis. It is estimated that about 10% to 15% of the population have one defective copy of the genes responsible for coding for perforin. When the immune system tries to use a defective perforin to pucture a cell it is trying to kill, it is faulty and they spend up to 5 times longer trying to kill the cells and released more cytokines in the process. This process pans out with proinflamatory stimuli, increased cytokines, macrophage activation, hemophagocytosis, multi-organ dysfunction or failure, and then possibly ends in death.

There are a class of syndromes which are all related and go by various names. The overall underlying syndrome is called reactive hemophagocytic lymphohistiocytosis (rHLH) or secondary hemophagocytic lymphohistiocytosis (sHLH). A related syndrome is macrophage activation syndrome (MAS). Canna, et al. 2017 notes, “HLH is classically associated with genetic defects in cytotoxicity, whereas MAS is observed as a complication of rheumatic diseases.” It is implicated in many different situations including in certain fatalities of H1N1, systemic juvenile idiopathic arthritis (sJIA), adult-onset Still disease (AOSD), and, most recently, COVID-19 fatalities.

The cheapest and most widely available test is the serum ferritin test. If it’s high, then there is a great probability there will be complications as COVID-19 progresses. In the case of HLH or MAS being present the serum ferritin level will be around 10,000 ng/mL. There also seems to be a correlation with elevated triglycerides (Canna & Beherens 2012). If the patient likely has MAS or HLH, the patient should cease taking anything which could increase inflammation and immediately increase flavenoid intake. Examples of medicines which could cause inflammation in certain cases are elderberry (Toraban et al. 2019) and echinacea (McGann et al. 2007), however it is likely that other medicines mixed with these could completely inhibit the pathway for the inflammation thus increasing the usefulness of those medicines.

Typically, interferon gamma is the most offensive cytokine. In some cases, there is involvement of the MyD88 pathway. Repeated TLR9 stimulation causes a MAS like effect in mice. Bacterial infections can stimulate TLR (Toll-like receptor). Certain viruses also have a tendency to trigger TLR9. Long term exposure to allergens which triggered cytokine IL-4 resulted in rHLH-like conditions.

In light of the hypothesis put forward by Wenzhong & Hualan 2020, the following may only help marginally. Without the heme restored to the hemoglobin normal respiration cannot be restored. Normal respiration is required in order to prevent tissue necrosis and multiorgan failure.

Preventing a Cytokine Storm

Hydroxychloroquine is useful in treating systematic lupus erythematosus, where TLR9 is implicated. An Ayuraveda formulation of Tinospora cordifolia and Zingiber officinale was comparable to hydroxycholoquine in treating rheumatoid arthritis, but not quite as effective (Chopra, Saluja, Tillu, et al 2012).

is useful in treating systematic lupus erythematosus, where TLR9 is implicated. An Ayuraveda formulation of was comparable to hydroxycholoquine in treating rheumatoid arthritis, but not quite as effective (Chopra, Saluja, Tillu, et al 2012). Ferulic acid has been shown to downregulate the MyD88 pathway. This is found in many plants.

has been shown to downregulate the MyD88 pathway. This is found in many plants. IL-1 (interleukin one) receptor agonists could also be effective in helping prevent a cytokine storm. Canna & Behrens mention the drug Anakinra by name. Leyva-López et al. 2016 review how the flavenoids apigenin, fisetin, luteolin, and quercetin all inhibit or reduce IL-1β. Also, apigenin, fisetin, luteolin, naringenin, and quercetin inhibit or diminish IL-6 along with other effects. They suggest flavenoids can replace usage of Anakinra and Tocilizumab.

could also be effective in helping prevent a cytokine storm. Canna & Behrens mention the drug by name. Leyva-López et al. 2016 review how the flavenoids all inhibit or reduce IL-1β. Also, inhibit or diminish IL-6 along with other effects. They suggest flavenoids can replace usage of Anakinra and Tocilizumab. Luteolin reduces IFN-γ. Quercetin inhibits IFN-γ. [Leyva-López et al. 2016] The effect of luteolin was previously confirmed by Dirscherl, Karlstetter, Ebert, et al. 2010. Sources of luteolin can be found in López-Lázaro 2009; Abad, Bedoya, Apaza, & Bermejo 2012; Fontaine et al. 2013; Nigam et al. 2019.

reduces IFN-γ. inhibits IFN-γ. [Leyva-López et al. 2016] The effect of luteolin was previously confirmed by Dirscherl, Karlstetter, Ebert, et al. 2010. Sources of luteolin can be found in López-Lázaro 2009; Abad, Bedoya, Apaza, & Bermejo 2012; Fontaine et al. 2013; Nigam et al. 2019. Luteolin diminishes NF-κB and AP-1 activation. Quercetin inhibits NF-κB and AP-1 activation. [Leyva-López et al. 2016.]

diminishes NF-κB and AP-1 activation. inhibits NF-κB and AP-1 activation. [Leyva-López et al. 2016.] 1,8-cineole decreased IL-4, IL-5, IL-10, and MCP-1 in nasal lavage fluids and IL-1β, IL-6, TNF-α, and IFN-γ in lung tissues. It reduced the expression of NF-kB p65, intercellular adhesion molecule (ICAM)-1, and vascular cell adhesion molecule (VCAM)-1. [Li et al. 2016] For sources of 1,8-cineole, see Sasikumar 2005; Abad, Bedoya, Apaza, & Bermejo 2012; Fontaine et al. 2013; Nigam et al. 2019; Loizzo et al. 2008; Ertürk, Demirbgğ, & Beldüz 2000; Aurori et al. 2016; Brochot et al. 2017; Li et al. 2016.

decreased IL-4, IL-5, IL-10, and MCP-1 in nasal lavage fluids and IL-1β, IL-6, TNF-α, and IFN-γ in lung tissues. It reduced the expression of NF-kB p65, intercellular adhesion molecule (ICAM)-1, and vascular cell adhesion molecule (VCAM)-1. [Li et al. 2016] For sources of 1,8-cineole, see Sasikumar 2005; Abad, Bedoya, Apaza, & Bermejo 2012; Fontaine et al. 2013; Nigam et al. 2019; Loizzo et al. 2008; Ertürk, Demirbgğ, & Beldüz 2000; Aurori et al. 2016; Brochot et al. 2017; Li et al. 2016. Recombinant human IL-18 binding protein (rhIL-18BP) was able to decrease all increased cytokines implicated in a NLRC4-MAS case (Canna et al. 2017).

was able to decrease all increased cytokines implicated in a NLRC4-MAS case (Canna et al. 2017). Intravenous emapalumab was able to regulate MAS within four treatments in a two week period (Benedetti et al. 2019).

For sources of quercetin, see Anand David, Arulmoli, & Parasuraman, 2016.

[Windsor 2020; Schulert 2016; Mehta et al. 2020; Qin et al. 2020; Ruan, Yang, Wang et al. 2020; Canna & Behrens 2012; Crayne, Albeituni, Nichols, & Cron 2019; Henderson & Cron 2019; Eloseily et al. 2019]

Halting the Virus

When a virus enters a cell it typically binds to a receptor. Depending on the conditions outside of the cell, the virus can attack through two different pathways which yield the same final result. One way is through endocytosis: the receptor trigers the cell to form an endosome around the virus with lipid rafts from it’s cell wall. This traverses the trans-golgi network, bringing the virus closer to the cellular mechanisms it uses to reproduce. While the virus is attached to the same receptor in the endosome, there are other proteases present which help the virus attach to the endosome, fuse with it, and then cleave the endosome — releasing the virion into the cell. The second method, shortcuts the endosome and the virus fuses withthe cell wall and the proteases cleave the fused cell wall and capsid releasing the virion into the cell. At this point the the virion starts comandeering the cellular mechanisms around the golgi body and the ribosomes to start producing proteins and assembling more viruses which are released out of the cell, possibly through exocytosis and also during cell apoptosis. [Cohen 2016; Braun & Sauter 2019]

In many RNA viruses there are mechnisms to evade the innate immune responses. The various tactics include creating reproductive organelles which shield the various internal pattern recognition receptors which play a role in the early response of both innate and adaptive immune systems. There are also various deubiquination proteases which interfere with immune responses, further postponing the immune system’s adaptation to the virus. This combined with frequent mutations is what prevents our immune systems from developing a permanent immunity to most influenzas and other RNA viruses. [Ning, Pagano, Barber 2011; Iwasaki & Pillai 2014; Liu et al. 2015; Chattopadhyay, Kuzmanovic, Zhang, Wetzel, & Sen 2016; Kikkert 2020]

SARS-CoV-2 is a coronavirus. It has a small capsid containing RNA. Interspersed around the capsid are glycoproteins called spike proteins. At the very end of the spike protein there is a receptor-binding domain (RBD). The RBD may have multiple affinities (the ability to attach to mutiple receptors). SARS-CoV-2 has a spike glycoprotein which is very similar to the SARS-CoV spike protein. After the virus binds to ACE2, the virus can be absorbed into the cell or it can fuse with the cell wall. In either case the virus is cleaved by several cell proteases to release of the virus RNA into the cell. [Wan et al. 2020; Zhou et al. 2020; Letko & Munster 2020; Liu et al. 2020; Yan et al. 2020; Wrapp et al. 2020; Zhang et al. 2020]

The SARS-CoV-2 spike protein has a RDB (receptor-binding domain) which binds to ACE2. ACE2 is expressed in intestines, kidney, stomach, heart, gall bladder, bile duct, liver, pancreas, oral cavity, tongue, lung, thyroid, esophagus, bladder, breast, overy, uterus, epididymus and prostate tissues (Gene ID: 59272; Fagerberg et al. 2014; Xu, Zhong, Deng, et al. 2020). This pattern of expression could be responsible for the some of the multi-organ failures in addition to cytokine storm conditions, but to be sure we need to examine the coexpression of ACE2 and several proteases and other possible binding domains.

Like SARS-CoV, the spike glycoprotein has an S1/S2 cleavage site which primes the spike when the serine protease TMPRSS2 (human epitheliasin). cleaves it (Hoffman et al. 2020). This is not unique to these related coronaviruses, it is also found in various influenza viruses (Böttcher et al. 2006). In the lungs, ACE2 and TMPRSS2 are both expressed in a secretory cell in bronchial branches (Lukassen et al. 2020). TMPRSS2 is also expressed in various tissues, such as the prostate, stomach, colon, small intestine, duodenum, kidney, lung, salivary gland, pancreas, gall bladder, liver, & appendix. [Hooper 2001; Jacquinet et al. 2001; Tanabe & List 2017; Gene ID: 7113; Fagerberg et al. 2014]

The SARS-CoV-2 spike protein has an additional furin cleavage site; while SARS-CoV bound to furin to increase adhesion to the cell when furin was present, but it did not use it for cleavage. In contrast, the furin cleavage site of SARS-CoV-2 may alter the transmissibility and cell types infected by the virus. Izaguirre 2019 mentions “it has been observed that when PCs [proprotein converteases, a class of proteases to which furin belongs] process viral proteins, some viruses become comparatively more infective and pathogenic.” This may be a result of most tissues expressing furin. [Coutard et a. 2020; Follis, York, & Nunberg 2006; Walls, Park, Totorici, Wall & Veesler 2020; Wang, Qiu, Li, et al. 2020; Izaguirre 2019; Gene ID: 5045; Fagerberg et al. 2014] Other viruses which use a furin cleavage site are: HPV, Herpes, Cytomegalovirus, Epstein-Barr, Varilcella-zoster, Dengue, Zika, Yellow fever, West Nile, Chikungunya, Semliki forest, MERS, avian influenza virus, ebola Zaire and Ivory Coast, HIV-1, measles virus, respiratory syncytial virus (human orthopneumovirus), and there are likely others. [Izaguire 2019; Stieneke‐Gröber et al. 1992; Thomas 2002; Richards et al. 2006; Peng et al. 2017; Braun & Sauter 2019]

Wenzhong & Hualan 2020 show that the virus codes for mutiple proteins which serve as additional binding domains and additional mechanisms for creating damage. In partiular, ORF8 and parts of the surface glcyoprotein facilitate binding to porphyrin (a base molecule of hemoglobin). Additionally, ORF1ab, ORF10, and ORF3a proteins can remove the heme from hemoglobin resulting in porphyrin. This freed porphyrin can be bound to new viruses and may increase the virion’s ability to penetrate cell walls while simultaineously causing severe carbon dioxide poisoning.

One paper found cell stress can cause GRP78 to translocate to the cell memebrane from the ER and that it can serve as an additional binding domain to mediate viral entry (Ibrahim et al. 2020). Another preprint has suggested that CD147 (basigin) serves as a binding domain, which coincidentally is also used by Plasmodium falciparum. Much is still unkown about this virus.

Blocking ACE2 receptor or flooding with soluble ACE2

One hypothetical solution is to provide some sort of molecule that binds to the ACE2 receptor or the receptor binding domain on the virus.

Another experimental option is to use a large amount of recombinant human ACE2. In this case the flood of soluble ACE2 would bind to the virus and prevent the virus from attaching to a real cell receptor. This option is currently being investigated (Clinicaltrials.gov #NCT04287686). [Zhang et al. 2020]

Inhibiting TMPRSS2

Hoffman et al. 2020 showed that the serine protease inhibitor camostat mesylate can block the spread of SARS in lung cells. They also showed that CatB/L protease inhibitors are required to fully inhibit the virus in colorectal cells. They hypothesized that furin protease may play a role in helping prime the cell for cleavage by TMPRSS2.

Bromhexine hydrochloride is mentioned by Tanabe & List 2017 as an inhibitor of TMPRSS2, but it is unknown to work in cases of SARS-CoV-2. However, one of its main uses is as a mucolytic, which may be advanageous for treating COVID-19.

Inhibiting cysteine proteases cathepsin B and L (CatB/L)

Hoffman et al. 2020 showed that E-64d combined with camostat mesylate effectively inhibited the virus in colorectal cells. E-64d is a permanent inhibitor.

Inhibiting Furin protease

Furin protease has been show to play a role in the reproduction of SARS-CoV-2. This means furin protease inhibitors could be used in combination with other inhibitors to stop the reproduction of the virus.

Common plant based furin inhibitors are: oroxylin a, baicalein, chrysin, oroxylin a glucoside, luteolin, rutin, naringin, and methyl hesperidin.

Interestingly, luteolin has been mentioned above as an anti-inflammatory agent. López-Lázaro has a list of 300 plants and associated studies which demonstrate the luteolin content. Peanut husk extract seems to have a really good effect and keep serum levels higher for longer.

[López-Lázaro 2009; Majumdar et al. 2010; Becker et al. 2012; Lalou et al. 2013; Osadchuk et al. 2016; Peng et al. 2017;]

1,8-Cineole

1,8-cinole increased IRF-3 activity beyond what the cell normally would accomplish using pattern recognition receptors alone. It also reduced TNF-α & IL-1β. It seems that the innate immune response must already be triggered. [Müller et al. 2016]

Chloroquine/hydroxychloroquine

Chloroquine and hydroxychloroquine are interesting, but likely not enough on their own. There is also the issue that many people are allergic/sensitive to this drug. Additionally, it increases the chance of a myocardial infarction. Much research needs to be done to determine a safe dosage for treatment.

They may be useful during a cytokine storm condition, since they reduce TLR9 triggered cytokines, reduce TNF-α & IL-6 and work as an autophagyinhibitor.

They may interfere with the glycolysation of cellular receptors at both entry and postentry stages, supposedly inhibiting SARS-CoV-2 in vitro.

They may inhibit pH level depedent replication steps (this would be cleavage by cathepsin B/L).

There are recorded uses of chloroquine phosphate as a treatment for porphyria and the it binds to the capsid glycoprotein and serveral of the proteins which remove the heme from the porphyrin (Wenzhong & Hualan 2020).

One study highlighted Lopinavir/Ritonavir and Shufeng Jiedu (a traditional Chinese medicine which is rich in flavenoids) as a possible alternative. However, it would have to studied more.

[Gou et al. 2020; Wang, Cao, Zhang et al. 2020]

Hydroxychloroquine and azithromycin

A study evaluated the effectiveness of adding azithromycin to a hyrdoxycholoquine treatment. It showed a great improvement in reduction of the viral load. Unfortunately, the study itself has flaws and will need to be repeated in order to confirm the efficacy of this treatement on SARS-CoV-2. [Gautret et al. 2020]

While the study was unsound the results were unsurprising given the mechanism of azithromycin and the research surrounding it. It increases a cells sensitivity to viral RNA and proteins through an increase in interferons (IFNs), IFN-stimulated genes (ISGs), pattern recognition receptors (PRRs). The PRRs include TLR2/3, RIG-I and melanoma differentiation-associated gene 5 (MDA5). Azithromycin does not reduce the expression of IL-8 and IL-6 induced cytokines, however, as noted above, chloroquine has the ability to reduce IL-6 and TNF-α.

[Gautret et al. 2020; Gielen, Johnston, Edwards 2010; Schögler et al. 2015; Li et al. 2019]

Remdesivir

A study evaluated ribavirin, penciclovir, nitazoxanide, nafamostat, chloroquine, remdesivir, favipiravir. Chloroquine first and remdesivir second had the greatest effect with the least cytotoxicity in vitro. [Wang, Cao, Zhang et al. 2020]

Favipiravir

Favipiravir prevented the virus from binding with porphyrin, thus reducing porphyrin assisted cell entry (Wenzhong & Hualan 2020).

Citations