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Posts Tagged ‘SARS-CoV-2

more covid 19: vitamin D, helper T cells, testing

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I’m continuing with my gleanings from the Medcram Covid-19 updates presented by Dr Roger Seheult, though I’m not up to date with them, because they’re quite comprehensive and nuanced, and I want that detail more than anything. I’m also reading the book Outbreaks and epidemics: battling infection from measles to coronavirus, by Meera Senthilingam, which among other things, highlights the importance of preparedness, co-ordination and resourcing to deal with new and unexpected pathogens but also upsurges and cross-border spread of diseases we haven’t sufficiently dealt with in the past. As we hurtle at an unprecedented rate towards a number of vaccines against SARS-CoV2, for example, we may have to deal firmly, on a governmental level, with the anti-vaccination movement and its disinformation campaigns, but we also have to deal with grossly uneven levels of healthcare within and across nations. This current pandemic has been revelatory, for all but those on the front lines, of the variable impact such outbreaks have on the different levels of empowerment within societies. To take a stark example, Boris Johnson, the British Prime Minister, very likely owes his life to the fact that he is the British Prime Minister. Had he been a fifty-something person of colour living in Dagenham (or most anywhere outside of a UK city), his Covid-19 case would surely have turned out quite differently.

Update 74 is quite brief and mainly touches on vitamin D, the ‘sunlight’ vitamin, also obtained from foods such as fish, especially salmon and tuna, and egg yolks, and mushrooms raised using UV light – but mostly from the sun’s UV. Vitamin D enhances bone and muscle strength and function. A Lancet article is discussed, which correlates ‘vitamin D status’, presumably meaning bodily levels, with Covid-19 mortality. Some surprises in the data – vitamin D deficiency was common in ‘sunny’ Italy and Spain, but less of a problem in Nordic countries, perhaps due to a high vitamin D diet. Deficiencies were greater in poorer regions and in black communities, as of course were higher Covid-19 mortalities. in fact, ‘black people in England and Wales are 4 times more likely to die from Covid-19 than white people’ according to the UK’s Office for National Statistics.

The Lancet article referred to points out two aspects of vitamin D’s possible protection against Covid-19. First, it ‘supports production of antimicrobial peptides in the respiratory epithelium’, which sounds positive, and second it may help to reduce the inflammatory response to the virus because it’s known to interact with and promote the ACE-2 protein, which the virus suppresses. Other articles emphasise the benefits, with no attendant harm, of vitamin D supplements, particularly for the elderly. There have been no systemised, detailed trials as yet relating vitamin D levels to Covid-19 outcomes, but it seems like a no-brainer.

Update 75 continues the argument about SARS-Cov2 attacking the lining of the blood vessels, i.e. the endothelium, with the resultant effect on von Willibrand factor. This happens in the lungs as well as the vascular system, creating clots as well as the growth of new blood vessels as a type of immune response. This essentially marks it out from any kind of influenza. The New England Journal of Medicine has an article, published late May, looking exactly at these differences in the autopsies of Covid-19 victims – endothelialitis (inflammation of the endothelium) and angiogenesis (the formation of new blood vessels). They compared Covid-19 lungs with the lungs of ARDS (acute respiratory distress syndrome) victims, associated with influenza A (H1N1), and with uninfected lungs. They found ‘alveolar capillary microthrombi’ – often difficult to detect with scans – in the Covid-19 lungs at nine times the level of the influenza lungs, and new vessel growth at almost three times that of the influenza lungs. Clearly the new vessel growth is caused by the blockages, and the need to circulate around them. Microscopic analysis shows lymphocytes infiltrating the lungs, adding to inflammation, stiffness and tissue damage. The clotting prevents oxygen being picked up from the alveolar space, leading to low oxygen saturation of the blood. Scanning electron micrographs of the lung endothelium revealed viral particles in the extracellular space, suggesting strongly that the virus itself, and not simply the immune response to it (perivascular inflammation) is causing damage. Dr Seheult brings up NAC again here, as a possible disruptor of the cascade of events, especially in the suppression of superoxide and in the cleaving of disulphide bonds in VWF.

An article in Science, which refers to the adaptive immune system, is next discussed. The adaptive immune system, as opposed to the innate immune system, is a system that creates a memory of a pathogen in order to develop an enhanced response, a system exploited by vaccines. This system includes T cells, of which there are three types, memory, cytotoxic and helper. These cells are apparently involved in lifelong immunity. Vaccine researchers are concerned to create antibodies as protection against the virus, but T cells are also important in this regard, and researchers have found that many infected patients, and non-infected people, do have T cells that attack the virus, probably because they have been infected with other coronaviruses that share proteins, such as the spike protein, with SARS-CoV2. Researchers in fact found that Covid-19 patients all harboured helper T cells that recognised the SARS-CoV2 spike protein, and other SARS-CoV2 proteins, again suggesting the possibility/probability of lifelong immunity. Many others harboured the same helper T cells, which may be protecting them against the worst Covid-19 symptoms, before the fact. This is possibly a very important, and highly explanatory finding. Or maybe not. T cells are long-lasting, so these findings are certainly positive.

Update 76 starts with antibodies, and it’s a bit difficult to follow. It looks at the CDC’s ‘interim guidelines for Covid-19 antibody testing’, and a CNN health article summerizes it thus:

The CDC explains why testing can be wrong so often. A lot has to do with how common the virus is in the population being tested. For example, in a population where the prevalence is 5%, a test with 90% sensitivity and 95% specificity will yield a positive predictive value of 49%. In other words, less than half of those testing positive will truly have antibodies’, the CDC said.

This is hard to follow, but 5% prevalence is fairly standard for this virus, at least at the outset. And so false positives are a problem. To be clear about testing – a person either has the disease or not. If you have it and you test positive, fine, that’s a true positive. If you have it and test negative, that’s a false-negative. If you don’t have it and you test positive, that’s a false-positive. If you don’t have it and test negative, that’s a true negative.

So we can look at percentages and maths, and I’m following Seheult strictly here. So imagine we’ve tested 2100 people in a particular region – that’s everyone in the region. At this stage the disease has a prevalence of 5%, so about 100 out of 2100 have the disease (strictly speaking that’s 4.76%). The test has a sensitivity of 90% and specificity of 95% as above. 90% sensitivity means that the number of true positives from the test will be 90% of the number of those who actually have been infected by the virus. That means 90 people. 95% specificity is about those not infected. So you divide the true negatives by those uninfected to arrive at the 95%. The true negatives will amount to 1900. So 10 people will be false positive and 100 false negatives. When specificity rises, false positives decrease. When sensitivity increases, false negatives decrease. So with high sensitivity a negative result is more conclusive, and with high specificity, a positive result is more conclusive.

Imagine then that the prevalence of the infection has risen to 52% in the same population of 2100. That gives us 1094 with the disease, 1006 without. With the same values for sensitivity and specificity of testing, you’ll have 985 true positives and 50 false positives, and 956 true negatives and 109 false negatives. What you need to know with these results is how things stand for patient x, the person you’re dealing with. This means you need to know the predictive values, positive (PPV) or negative (NPV). This requires some simple maths. Given a positive test result, what chance is there of x having the disease? Or vice versa for a negative result. This means that for the PPV you divide the true positives by the total number of positives, and the same process applies for NPV. Going back to the situation where the prevalence was 5% we get a PPV of 47% and a NPV of 99%. What this means is that when the prevalence is low, the negative predictive value is much higher than the positive predictive value. The implication is important. It’s just not clear at this stage whether you have antibodies against the virus. So you need to raise the specificity of the test, especially if the virus or pathogen has a low prevalence. But looking at the 52% prevalence case, and using the same simple maths we find that the PPV is up at 95% and the NPV goes down to 90%. Prevalence, then, is the main determinant of predictive values.

For testing, this means, just as the disease is becoming prevalent, that’s to say, as it’s just being detected, you need a test with a very high specificity (admittedly a big ask) and/or you need to test those with a high probability, based on current knowledge, of being infected, and those in contact with them.

References

Coronavirus Pandemic Update 74: Vitamin D & COVID 19; Academic Censorship

Coronavirus Pandemic Update 75: COVID-19 Lung Autopsies – New Data

Coronavirus Pandemic Update 76: Antibody Testing False Positives in COVID-19

https://en.wikipedia.org/wiki/T_helper_cell

Written by stewart henderson

August 9, 2020 at 12:34 pm

more Covid-19 gleanings from MedCram updates 67-69

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polymorphonuclear leukocytes (white blood cells)

I’m continuing my self-education re everything Covid-19 thanks to Dr Seheult’s updates and other useful sites. Update 67 carries on from where we left off, summarising again how SARS-CoV2 induces endothelial dysfunction, before focusing on thrombosis. So we repeat again that a key molecule in normal endothelial function and in the working of AT-1,7 is nitric oxide (NO). Endothelial function (and, to be clear, the endothelium lines the vasculature, which means the body’s blood vessels) is also dependent on the various other enzymes mentioned in the last post, e.g. superoxide dismutase (SOD), and glutathione peroxidase (GPx).

So how does Covid-19 bring about oxidative stress and how does this effect thrombosis? Seheult discusses an article from April this year which addresses this. It describes a previously healthy elderly male admitted to hospital with fever and respiratory symptoms. After rapid deterioration he was sent to ICU, having developed ARDS, acute renal insufficiency and other health problems. Among various measures noted was a ‘massive elevation of von Willebrand factor (VWF), as well as ‘factor VIII of the coagulation cascade’. To quote from the article:

The increased VWF points toward massive endothelial stimulation and damage with release of VWF from Weibel-Palade bodies. Interestingly, endothelial cells express ACE-2, the receptor for SARS-CoV2, thus possibly mediating endothelial activation.

To explain some of these terms: Weibel-Palade bodies are found only in epithelial cells, and they contain VWF, which are released when required for haemostasis and coagulation. VWF is a stringy material of amino acid proteins which combine with platelets (aka thrombocytes) to coagulate the blood. When endothelial cells suffer serious damage, Weibel-Palade bodies inject large amounts of VWF into the bloodstream. Dr Seheult presents the abstract from a 2017 article on the topic:

The main function of VWF is to initiate platelet adhesion upon vascular injury. The hallmark of acute and chronic inflammation is the widespread activation of endothelial cells which provokes excessive VWF secretion from the endothelial cell storage pool. The level of VWF in blood not only reflects the state of endothelial activation early on in the pathogenesis, but also predicts disease outcome. Elevation in the blood level of VWF occurs either by pathologic increase in the rate of basal VWF secretion or by increased evoked VWF release from dysfunctional/activated endothelial cells. The increase in plasma VWF is predictive of prothrombotic complications and multi-organ system failure associated with reduced survival in the context of severe inflammatory response syndrome, type 2 diabetes mellitus, stroke and other inflammatory cardiovascular disease states.

The article points out that an over-production of VWF in highly elongated form is an indication of pathology. This is apparently being seen in serious Covid-19 patients. On the molecular level, the VWF is able to remodel itself from its usual globular conformation when it senses shear forces – note this definition from Science Direct: Shear stress is defined as the frictional force generated by blood flow in the endothelium, that is, the force that the blood flow exerts on the vessel wall, expressed in force-area unit (typically dynes/cm2). The VWF, under this stress, ‘turns into an extended chain format that forms ultra-large strings to which platelets bind to initiate clot formation at sites of vascular damage’. When the shear stress reaches a certain level, factor VIII is released. All of this can be essential for haemostasis, but too much of the multimeric, elongated form of VWF will lead to thrombosis, as appeared to be occurring in the patient described above.

So, as Seheult summarises, SARS-CoV2 binds to ACE-2 receptors and reduces ACE-2 production. This reduction has the effect of increasing AT-2 production and reducing AT-1,7. This results in an increase in superoxide production, oxidative stress and endothelial dysfunction. This in turns leads to an increase in VWF activity in the bloodstream, and local thrombosis. There is evidence from autopsies that thrombosis is a feature of Covid-19 mortality.

In his update 68 Dr Seheult looks at the predisposition of some ethnic groups (in the USA) to the more severe symptoms associated with Covid-19. He discussed a May CDC MMWR (morbidity and mortality weekly report) on 580 hospitalised Covid-19 patients which found that 45% were white, as far as they could ascertain, compared to 55% in that region’s community. 33% were black, compared to 18% in the community, and 8% were Hispanic compared to 14% in the community. A smallish sample, but suggestive. The CDC also reported on New York figures showing that Covid-19 death rates among black/African Americans and Hispanic/Latino persons were substantially higher than in the white population. Many possible reasons – work and living conditions, lower access to care – all generally related to relative poverty. There may also be other, purely physiological grounds for the disparity. A 16-year-old research article published in Circulation describes the results of placing nanosensors in isolated human umbilical vein endothelial cells (HUVECS) from blacks and whites (pardon the over-simplification, I’m only the messenger), as an attempt to measure endothelial oxidative stress. I can’t follow the details of the research, but what they found was that blacks expressed much more NADPH oxidase than whites (that’s bad). Nitric oxide, a reducer of oxidative stress, was produced in greater quantities in whites than in blacks, and the bad superoxides were produced in greater quantities in blacks. I won’t go further into the complex biochemistry, but I must say I find these apparent racial differences very surprising.

Update 68 also looks at increasing hospitalisations (at least in May) of young children due to Kawasaki disease, or something similar. The disease is characterised by inflammation of blood vessels. Symptoms include fever, high heart rate and possibly sepsis. There are a number of similarities to Covid-19, including ‘systemic vascular lesions’. Kawasaki disease is normally rare, and believed to be viral, or a response to a virus. A ten-year-old research paper on the disease hypothesises that the infection enters through the respiratory or gastro-intestinal systems, and so unsurprisingly there are similarities to the reaction to SARS-CoV2. Whether there’s a connection between Covid-19 and an uptick in Kawasaki disease has yet to be confirmed (but I’m behind the times on the research on this).

I’m moving now to update 69, and I’m going to follow Dr Seheult through the whole oxidative stress process again. It’s about reduction of oxygen – the adding of electrons. Adding an electron to oxygen, mediated by NADPH oxidase, produces superoxide. Add another electron and you get hydrogen peroxide. Another electron produces hydroxyl, and yet another produces water, moving from most oxidised to most reduced, and adding electrons also brings on protons. So at both ends of this chain you have neutral or positive molecules, but in between you have, I think ROS, reactive oxygen species, which are a problem. The body’s defence against these include the enzyme superoxide dismutase (SOD), which converts superoxide into hydrogen peroxide and also back into oxygen, and catalase which converts hydrogen peroxide into water and oxygen. Another important enzyme which protects against oxidative damage is glutathione peroxidase (GPx). It takes reduced glutathione (2GS-H, called a sulph-hydryl group) and uses it to reduce hydrogen peroxide into water, in the process oxidising the glutathione into a form of disulphide G-S-S-G. This oxidised form is in turn ‘regenerated back’ by taking the reduced form of NADP+ (NADPH) and converting it via glutathione reductase to NADP+.

So the point is that the accumulation of superoxide in people with diabetes, hypertension, coronory disease etc will be exacerbated by Covid-19. And going through that once more, Covid-19 blocks the ACE-2 receptor, causing an accumulation of AT-2 which stimulates superoxide production, and also a deficiency of AT-1,7, which, mediated by nitric oxide, inhibits superoxide production. The SARS-CoV2 virus also attracts PMNs (polymorphonuclear leukocytes – immune cells including neutrophils), which boost superoxide production, with attendant endothelial damage.

I’ll be continuing this series, and no doubt getting further behind, over the next few weeks.

References

Coronavirus pandemic update 67, presented by Dr Roger Seheult, as with all other updates

Coronavirus pandemic update 68

Coronavirus pandemic update 69 (first 5 minutes or so)

https://www.verywellhealth.com/polymorphonuclear-leukocyte-2252099

Written by stewart henderson

July 29, 2020 at 11:11 am

more on oxidative stress and covid-19

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So, much of this piece will rely on Dr Seheult’s coronavirus update 65. We have this constant set of reactions in the body that reduce oxygen – adding electrons – until we get to water molecules, producing reactive oxygen species (ROS) along the way. This is often described as the oxygen metabolism process. Reactive oxygen species come essentially in three types, superoxides, hydroxy radicals and hydrogen peroxide. The three forms of the enzyme SOD, superoxide dismutase, convert superoxide into oxygen and hydrogen peroxide (H2O2), and then the H2O2 is reduced to H2O by means of glutathione peroxidase (GPx). The GPx, which is broken down in the process is recharged by the enzyme glutathione reductase (GR), which is in turn recharged by other antioxidant products. Also the enzyme catalase, which requires iron, can break H2O2 down into O2 and H2O.

People with diabetes, hypertension and overweight issues, among other things, may have compromised antioxidant systems (too many ROS), linked to angiotensin-converting enzyme 2 (ACE-2) and angiotensin-2. In creating ROS, oxygen is reduced to superoxide by means of the enzyme NADPH oxidase. So, as part of the renin-angiotensin system, angiotensin-2 (AT-2) is converted to angiotensin 1,7 (AT-1,7) by means of angiotensin-converting enzyme 2 (ACE-2). This is important because AT-1,7 effectively blocks superoxide production, while AT-2 promotes it. The virus SARS-CoV2 binds with, and so inactivates, ACE-2, preventing the production of AT-1,7. This action also means that there will be more AT-2 available, and so more superoxides. SARS-CoV2 also, according to Seheult, causes inflammation by recruiting polymorphonuclear neutrophils (PMNs), which stimulate production of superoxides by means of NADPH oxidase. So this, in essence, is why Covid-19 is bringing about oxidative stress.

Seheult next goes on to look at the research evidence for the preceding. A review article from 2005 points out that evidence from animal studies and cell culture studies shows that NADPH oxidase-derived oxidative stress is increased in vascular cells by AT-2, among other ‘agonists’ (chemicals that bind to receptors, thereby producing a response). Another article from 2012 describes several enzyme systems that act to form ROS, including ‘mitochondrial electron leakage from the electron transport chain’ as described in my previous post on the subject, and in Seheult’s update 63. It points out that ROS levels can rise dramatically in older people suffering from oxidative stress due to heart issues such as ischemia-reperfusion (referring to problems with oxygenated blood supply to the heart or other organs). It also points out that it has been shown experimentally that AT-2 stimulates an increase in ROS. A more recent article pertaining to SARS-CoV2 looked at patients in Wuhan and found a substantial increase in neutrophils in the most severe cases. Neutrophils cause ROS to be generated by NADPH oxidase. So Dr Seheult is carefully building up evidence for the case. The last point to deal with is AT-1,7 effects. Seheult has found a 2008 article entitled ‘Angiotensin converting enzyme 2 confers endothelial protection and attenuates atherosclerosis’. Seheult quotes the last line from the abstract:

These data indicate that ACE-2, in an AT-1,7-dependent fashion, functions to improve endothelial homeostasis via a mechanism that may involve attenuation of NADPHox-induced reactive oxygen species production. ACE-2-based treatment approaches may be a novel approach to limit aberrant vascular responses and atherothrombosis.

Atherothrombosis involves disruption of atherosclerotic plaques, which can be an immediate cause of heart attacks. Another article from 2015 essentially confirms the findings, as indicated by its title, ‘ACE-2 and AT-1,7 protect endothelial cell function and prevent early atherosclerosis by inhibiting inflammatory response’. A more recent article, from January 2020, describes how AT-1,7 administration improves endothelial function in women who have suffered from preeclampsia (vasoconstriction, high blood pressure and organ damage due to pregnancy). To give more detail, women in the last stages of pregnancy often suffer vasoconstriction and high protein levels, which is believed to be related to AT-2 levels. Researchers administered local AT-1,7, which is ‘an endogenous inhibitor of... AT-2′, to see if this reduced vasodilation and other symptoms of preeclampsia. What they found was that ‘AT-1,7 increased endothelium-dependent vasodilation via nitric oxide synthase-mediated pathways and attenuated AT-2-mediated constriction in women who have had preeclampsia, suggesting that AT-1,7 may be a viable therapeutic target for improve d microvascular function in women who have had a preeclamptic pregnancy’.

All of this is interesting in itself, of course, and is a little crash course in how research is helping us to tweak our immune systems, but in relation to Covid-19 these finding are of importance due to the comorbidities and general characteristics of patients being hospitalised with Covid-19. Dr Seheult, in his update 65 video, shows that, contrary to what was initially thought, i.e that Covid-19 is primarily a virus affecting the lungs and respiratory system, it may be much more of a problem for those with hypertension, cardiovascular issues and obesity – all of which are related to oxidative stress, as are diabetes and many forms of cancer. They contribute to endothelial dysfunction, which inevitably leads to oxidative stress, and may lead to thrombosis. Seheult here refers to a lengthy 2018 review article, ‘nutrients and oxidative stress: friend or foe?’, which among other things makes useful dietary suggestions for the combatting of oxidative stress – whole grains, nuts, fruit and vegetables, fish and legumes.

It’s been known for some time that endothelial cell dysfunction (ECD) can lead to thrombosis, as it is a major function of these cells to prevent thrombosis. The abstract from a 2002 study finds that ECD ‘is associated with decreased synthesis and oxidative inactivation of nitric oxide (NO)’ and it lists four types of antioxidant enzymes ‘essential for eliminating ROS that can inactivate NO’. It seems that the promotion of these enzymes can be associated with diet as above and with the reduction of risk factors such as hypertension, hypercholesterolaemia (high blood cholesterol), hyperhomocysteinaemia (homocysteine is an amino acid which can contribute to arterial damage and blood clots, and the condition is often associated with lack of vitamin B-12 or folate), cigarette smoking and diabetes mellitus. NO is the key molecule in maintaining endothelial function through these enzymes.

Now I’m having a look at Dr Seheult’s update 66 on blood pressure medications known as ACE inhibitors or ARBs. He cites an editorial article for the New England Journal of Medicine, on ‘inhibitors of the renin-angiotensin-aldosterone system and Covid-19’. This is a triple hormone system responsible for blood pressure regulation and fluid balance. Now, to return to what was outlined before, angiotensin-2 (AT-2) is converted to AT-1,7 by an angiotensin-converting enzyme (ACE-2). The SARS-CoV2 virus binds to the ACE-2 receptor and inhibits the enzyme’s production. This is problematic because AT-2 stimulates superoxide production (that’s bad), while the antioxidant AT-1,7 blocks it, so reducing oxidative stress. SARS-CoV2 also stimulates the production of PMNs, as above, which activates oxidative stress. Another part of this picture is that AT-1 is converted to AT-2 by ACE. There are blood pressure lowering medications, such as benazepril and lisinopril, aka ACE inhibitors, which reduce the production of AT-2. There are also angiotensin receptor blockers (ARBs), which may up-regulate ACE-2 (it isn’t clear, apparently). ACE inhibitors may do the same. The question being asked is, assuming these medications produce more ACE-2, will this lead to more infections because SARS-CoV2 has more ACE-2 to work with? Clearly it would be important to know whether to maintain these medications or not, that’s to say, whether these medications are a risk factor for contracting the virus or recovering from it. The above-mentioned article discusses three studies from different parts of the world, each involving thousands of participants. They all found no risks associating ACE inhibitors and ARBs with a higher risk of infection, severity of illness or death from Covid-19. One of the studies found that ACE inhibitors and statins were associated with a decreased risk of mortality, but these are observational studies and further research would need to be done.

So the above is a rather technical piece, highly reliant on the experts. I write to inform myself, and I’ve certainly been informed by writing this one. Apologies for its laboriousness, but I’ll be continuing… Please consult the references yourself if there’s anything you don’t understand.

References

Coronavirus Pandemic Update 65: COVID-19 and Oxidative Stress (Prevention & Risk Factors)

Coronavirus Pandemic Update 66: ACE-Inhibitors and ARBs – Hypertension Medications with COVID-1

https://www.mayoclinic.org/diseases-conditions/high-blood-pressure/in-depth/ace-inhibitors/art-20047480

https://www.healthline.com/health/homocysteine-levels

https://www.mayoclinic.org/diseases-conditions/high-blood-pressure/in-depth/ace-inhibitors/art-20047480

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5831951/

Written by stewart henderson

July 16, 2020 at 4:21 pm

SARS-Cov2 and oxidative stress

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Dr Roger Seheult, just doing his job, workaholically

So I feel it’s time for me to get back to the epidemiology and immunology stuff that I know so little about, especially as it pertains to SARS-Cov2. Watching Dr Seheult’s Medcram updates again after a long hiatus, and catching up with them from the end of April, I note that he’s arguing – and I presume this is a mainstream view, as he clearly keeps an eye on the latest research – that the virus mostly does its damage in attacking the body’s endothelium, and that this in turn causes oxidative stress. The endothelium is a thin layer of cells, or a layer of thin cells, that form the inner lining of the blood and lymph vessels (one day I’ll find out what lymph actually is and does).

Oxidative stress is associated with an imbalance in the level of oxidants such as super-oxide anion and hydrogen peroxide, reduced forms of oxygen (with extra electrons). I don’t really understand this, so I’ll start from scratch. But just preliminary to that, the effects of oxidative stress are manifold. Here’s a summary from news-medical.net:

Oxidative stress leads to many pathophysiological conditions in the body. Some of these include neurodegenerative diseases such as Parkinson’s disease and Alzheimer’s disease, gene mutations and cancers, chronic fatigue syndrome, fragile X syndrome, heart and blood vessel disorders, atherosclerosis, heart failure, heart attack and inflammatory diseases.

It’s known that SARS-Cov2 enters via the lungs, and does damage there, but it’s now thought that most of the damage is done in the endothelium. To understand this, Dr Seheult is going to teach me some ‘basic’ stuff about metabolism, oxidation, energy production and such. So, we start with mitochondria, the energy-producing organelles inside our cells, which have their own DNA passed down the female line. Looking into a mitochondrion, we have the matrix inside, and around it, between the inner and outer membranes, is the inter-membrane space (IMS). Our food, broken down into its essential components, carbs, fats and proteins, is absorbed into the matrix, and somehow turned into ‘two-carbon units’ called acetyl coenzyme A. This is metabolism, apparently. These molecules go through a famous process called the Krebs cycle, of which I know nothing except that it’s about more metabolism… Although now I know that it produces electrons, tied up in two important molecules, NADH and FADH2. These electrons ‘love to be given up’, a way of saying they ‘want’ to be reduced. The molecule that gives up electrons is said to be oxidised, the receiving molecule is reduced. So think of a molecule being reduced as the opposite of losing, rather counter-intuitively. The oxidised molecule is the one that loses electrons. All this is about energy production within the matrix, and the aim is to end up with a molecule I’ve heard and forgotten much about, adenosine triphosphate (ATP). This molecule is the energy molecule, apparently, and the energy is produced by ‘knocking off’ one of the phosphates, according to Dr Seheult, leaving, apparently, adenosine diphosphate (ADP) plus ‘energy’ (clearly, this part needs a little more detail). So going from the diphosphate form to the triphosphate requires energy, going the other way releases energy – none of which really explains why ATP is the body’s energy source. Anyway…

Returning to the carbs, fats and proteins, they go through these mitochondrial processes to produce electrons which want to reduce stuff. So NADH goes to the membrane which separates the IMS from the matrix of the mitochondrion, where proteins can be found that are willing to accept electrons, i.e. to be reduced. The electrons are brought in ‘at the very top of the scale’ (?) and lose some of their reducing ability, so they go down to a lower state of reduction, and protons are pumped into the IMS. (I’m sure this is all true but making sense of it is another matter. It certainly makes me think of proton pump inhibitors, drugs that reduce gastric reflux, but that would be the subject of another set of posts). Then ‘it goes to another species’ by which I think Seheult means another protein, judging from the video, but what he means by ‘it’ I’ve no idea. The NADH? The wave/body of electrons? Anyway, things keep going down to a lower level, becoming more oxidised, and more and more protons are pumped out. So there comes to be a very high concentration of protons (H+) in the IMS, creating a very low PH (high acidity). Meanwhile, the electron transport chain has gone down so many levels that it can only reduce oxygen itself, which by accepting electrons turns finally into water. It’s apparently essential to have sufficient oxygen to keep this cycle going, and to keep the protons pumping, because the protons in the IMS want to move to a place of lower concentration, in the matrix. In doing this, they pass through a channel, which involves, somehow, a coupling of ADP to ATP. Without enough oxygen, this process is stymied, ATP can’t be supplied, leading to insufficient energy and cell death.

So, I think I understand this, as far as it goes. Now, if you over-eat, with lots of high-calorie fats and carbs entering the cells, you’ll likely end up with a surplus of electrons, tied up in NADH and FADH2, which can cause problems. This is where super-oxides come in.

Oxygen is the final electron acceptor in the electron transport chain, and when you add an electron to this final acceptor you get a super-oxide, an oxygen molecule with an additional electron, aka a radical. These are very reactive and dangerous. They can cause DNA damage and serious inflammation, and the body uses them to kill bacteria. If you add another electron, you get H2O2, hydrogen peroxide, and another one again produces a hydroxy radical, OH. Another electron gives water, so it’s these intermediate molecules that are called ‘dangerous species’. Cells such as neutrophils (a type of white blood cell) make these, via an enzyme called NADPH oxidase, as part of their defence against antigens, but an accumulation of these radicals is problematic and needs to be dealt with.

from Dr Seheult’s presentation, showing the production of reactive oxygen species (ROS) – super-oxide, hydrogen peroxide and hydroxy radicals

One enzyme the body uses to bring down these accumulating radicals is super-oxide dismutase (SOD), which takes two super-oxides and converts them into O2 and H2O2. SOD comes in three types, related to where they reside – in the mitochondria, the cytosol and the extracellular matrix. These enzymes are powered by zinc, copper and, in the mitochondria, manganese. So what happens to the extra hydrogen peroxide created? An enzyme called glutathione peroxidase (GPx) reduces H2O2 to water by giving it two electrons. Where do these electrons come from? According to Seheult, and this is presumably ‘basic’ microbiology, the antioxidant glutathione has two forms, oxidised and reduced. The reduced form is 2GS-H, with a hydrogen bonded to the sulphur group. The oxidised form is G-S-S-G, a disulphide bond replacing the hydrogen. With the reduced form, GPx donates its extra two electrons to H2O2, reducing it to water. The glutathione system is recharged by reducing it back with NADPH, which has two electrons which are converted to NADP+ (?) Glutathione reductase is the key enzyme in that process. It might take me a few lifetimes to get my head around just this much.

Meanwhile there’s another system… Catalase, an iron-boosted enzyme, can convert two molecules of H2O2 into O2 and H2O. This occurs in organelles called peroxisomes. The major point to remember in all this is that super-oxides are harmful species that can cause oxidative stress, and the major solutions come in the form of SOD and GPx. In fact the general name for these harmful molecules – super-oxides, hydrogen peroxide, and hydroxy radicals – is reactive oxygen species (ROS).

So we have to relate all this to the effects of SARS-Cov2, which enters the body through the ACE-2 (angiotensin-converting enzyme-2) receptor. According to a 2008 research paper, ACE-2, the receptor for which is blocked by SARS-Cov2, ‘confers endothelial protection and attenuates atherosclerosis’. Quoting from the paper, we find a section called ‘ACE-2 modulates ANG II(angiotensin 2)-induced ROS production in endothelial cells’. The researchers’ essential finding was that ‘ACE-2 functions to improve endothelial homeostasis’, and it seems this function is being disrupted by SARS-Cov2. As Dr Seheult puts it, SARS-Cov2 inhibits the inhibitor, that is it inhibits ACE-2, which normally acts to regulate angiotensin 1,7 (not explained in this particular video), thus allowing NADPH oxidase to keep producing super-oxides, with the resultant oxidative stress. As Seheult concludes here, subjects with compromised systems caused by diabetes, cardiovascular disease or obesity, affecting the production or effectiveness of SOD and GPx, might be relying on ACE-2 and angiotensin 1,7 to maintain some semblance of health. Are these the subjects that are succumbing most to the virus? That’s to be explored in future videos, and future posts here.

Reference

Coronavirus Pandemic Update 63: Is COVID-19 a Disease of the Endothelium (Blood Vessels and Clots)? (video by Dr Roger Seheult – clearly a hero in this time)


Written by stewart henderson

July 5, 2020 at 11:46 pm

Covid 19: How the SARS-CoV-2 virion does its thing

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filched from The Economist, a US website

Canto: We’ve been lapping up the excellent Medcram series of videos on the pandemic, and we’re now at episode 32 I think, from March 6, and a week’s a long time in Covid-19-world.

Jacinta: Yes and back then the largest number of confirmed cases outside of China was in South Korea, and that, I now understand, was largely because of the massive testing they’d engaged in – so elsewhere the infection was being under-reported, or barely known about.

Canto: And today, April 23, South Korea has dropped down to 27th on the list of reported cases. Interesting to note that by March 6 South Korea had tested some 140,000 people, almost 100 times more than the USA had done. As we know, the CDC had stuffed up by producing a flawed testing kit, which resulted in crucial delays.

Jacinta: And weren’t the South Korean tests more effective? They used a different type of test didn’t they?

Canto: According to a Bloomberg article referred to in the video, South Korea’s tests had a 95% sensitivity rate, much higher than those of the USA at the time. But neither the article nor the video went into detail about the type of test.

Jacinta: So I think the standard type of test used is called PCR, or RT-PCR, which means reverse transcriptase polymerase chain reaction, but I don’t really know what that means or how the tests work.

Canto: We’ll look at how the tests work later. Let’s use this video 32 to help us understand how this virus gets into a host cell and replicates.

Jacinta: Ok, so we have a cell with its nucleus, and its DNA in there, and outside the nucleus is the cell’s cytoplasm containing organelles such as ribosomes, mitochondria, lysosomes, microtubules and the like. The DNA is transcribed into single-stranded precursor messenger RNA. The RNA is then transported into the cytoplasm, where it’s modified, giving it a ‘five prime cap and a poly-A tail’. So one end has its nucleotide altered by the enzyme guanyl transferase. It has to be a guanine nucleotide connected to the mRNA with a particular triphosphate linkage. The poly-A tail is a string of adenine bases. These modifications form what’s called post-transcriptional RNA processing. Then the ribosome, about which we’ve learned so much from Venki Ramakrishnan, reads the mRNA from the five-prime end to the three-prime end. That’s in the ‘positive’ direction. It reads the nucleotides three at a time and comes up with a code (here it gets a bit vague), so that when three particular nucleotides line up, ‘a specific amino acid has to be placed on there’. And transfer RNA is involved here. So a by-product of this process is a protein (consisting of amino acids), made by the ribosome. That’s translation, not so clearly explained. Anyway, proteins are the central building blocks of our bodies, without which not.

Canto: Okay, sufficient unto the day. And remember, this transcription/translation process is known as ‘the central dogma of molecular biology’, in case you’re tested. Now we’ll turn to the virion. So the cell membrane that the virus needs to penetrate is a lipid bilayer. That bilayer is hydrophilic on the outside (that’s facing out from the cell and into the cell) and lipophilic on the inside. The coronovirus has the same lipid bilayer, with embedded proteins, notably the s-proteins or spike proteins which we know are used to attach to host cells. There are other structural proteins such as m-proteins (membrane proteins) and e-proteins (envelope proteins). Inside is the large RNA genome, protected by n-proteins (nucleocapsid proteins). Presumably there are other proteins too. Now, note that this is one virion, which is the built structure housing the virus (what enables it to survive for however long outside of a host), but also including the virus itself, which is essentially the genome. For the virus to replicate and spread, all those structural proteins have to be reproduced too.

Jacinta: The s-protein just happens to fit, like a key in a lock, a receptor protein in the human host cell membrane called the ACE-2 receptor. These ACE-2 receptors, full name angiotensin-converting enzymes, are found in our lungs, and elsewhere, such as the heart, the kidneys and the intestines. Once this connection is made, the viral RNA is released into the cytosol. And as it happens, this viral RNA also has a 5 prime cap and a poly-A tail just like the host’s mRNA. It isn’t clear from the video whether this is because it gets modified within the cytoplasm or it’s already ‘primed’ so to speak. Anyway, the cell’s ribosomes start to act on this rogue RNA as it would on its own mRNA. Meanwhile the structural proteins from the viral membrane are incorporated into the host membrane, possibly earmarking it for destruction.

Canto: The ribosome makes a protein from the viral RNA, called RNA-dependent RNA polymerase (RdRP), or an RNA replicase. The protein somehow makes another complementary strand of RNA, running in the opposite direction, from which the ribosome makes more protein, which makes more RNA and so forth. This RNA also codes for the structural proteins of the virion (because the RdRP somehow forms shorter strands of RNA, called sub-genomic RNAs, specific to the making of those proteins by the hijacked ribosomes), so enabling the spread of the virus.

Jacinta: The key, the video tells me, is in the name polymerase. That’s an enzyme that puts nucleotides together in long chains. Also, many ribosomes – there are thousands in our cells – are connected to the cell membrane and can help create new virions that can leave the cell in much the opposite way they entered, being packaged and then budded off. Through this hijacking process, one virion can come in, and any number of them can go out, and generally from the lung region. They’re naturally attacked by the immune system causing inflammation, possibly pneumonia and respiratory failure.

Canto: Yes and thanks to Dr Roger Seheult for all this, we hope we’re not misreading his work. He goes on to talk about the possibility of inhibiting this nasty polymerase, RdRP. We might talk about this, or not, in the next post.

References

Coronavirus update 32, with Dr Seheult – series of videos

https://www.economist.com/briefing/2020/03/12/understanding-sars-cov-2-and-the-drugs-that-might-lessen-its-power

The gene machine, by Venki Ramakrishnan

Written by stewart henderson

April 25, 2020 at 2:04 pm