an autodidact meets a dilettante…

‘Rise above yourself and grasp the world’ Archimedes – attribution

covid19: corticosteroids, male susceptibility, evaluating health, remdesivir, coagulation factors

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from The Lancet, ‘the four horsemen of a viral apocalpse’


Canto: So short-course use of some steroids was being advocated in the medcram update 88, though without thorough RCT evidence. 

Jacinta: Well, data was presented from the Oxford RCT on those on oxygen or on ventilators showing a statistically significant reduction of mortality from short-course (up to 10 days) low dosage of dexamethasone, a freely-available steroid medication. The study involved some 2000 patients, but only those severely afflicted were helped by the medication. 

Canto: An interesting aside to the data is that in the study males outnumbered females by almost 2 to 1, and that accords with the overall ratio of male to female covid19 patients Dr Seheult is finding, which rather shocked me. Why would more males be coming down with the disease? Presumably that’s not the infection rate, but the rate at which they need to be hospitalised. 

Jacinta: Yes, you’re right, according to this Australian site (unfortunately undated):

Reports continue to emerge that men are significantly more vulnerable to COVID-19 than women. The commonly held perception that more men smoke and this makes them more susceptible along with other lifestyle factors does not tell the whole picture. White House COVID-19 Task Force director Dr Deborah Birx highlighted a “concerning trend” that men in all age brackets were becoming seriously ill from the virus at a higher rate than women, including younger males.

They’re suggesting more research needs to be done on this gender difference, for health issues in general. Some are claiming that estrogen makes a difference. In any case I think cardiovascular problems are more common in males – but maybe not so much in younger males. 

Canto: So update 89 is fairly short, and deals with US data about cases and deaths, most of it out of date now, and more on corticosteroids and the dangers of unsupervised use. Update 90 introduces us to a tool I’ve never heard of called ‘Discern’. Very useful for we autodidacts in helping us, for example, to enlighten our doctors as to our condition. Discern is a tool for evaluating internet health info, such as medcram’s updates on youtube, or anything else on youtube. The instrument asks you to evaluate the material according to 16 different criteria. Interestingly, this tool has been tested on covid19 material by a study out of Poland done in March. The results weren’t so good, especially for news channels. 

Jacinta: Yes, physicians’ information did best – but of course we don’t go to news channels for health information, and we’d advise against anyone else doing so. The study evaluated the Discern tool itself and found it excellent, then used the tool to evaluate health information, specifically on youtube. Of course know that there’s ‘viral misinformation’ from various news outlets that gets posted on youtube. And good to see that the medcram updates were some of the most highly rated using the Discern tool. 

Canto: So we’re now into reporting from early July with update 91. It starts by looking at a ‘covid risk calculator’ in which you can type in your age, gender, BMI, underlying conditions, waist circumference, and other data which you might need a full medical checkup to find out about (and that’s overdue for me), including, for example, %FMD, a measure I’ve never heard of, but which has to do with endothelial function. 

Jacinta: FMD stands for fibromuscular dysplasia. The Johns Hopkins medicine site describes it as a rare blood vessel disease in which the cells of some arteries become more stiff and fibrous and less flexible. This leads to weakness and damage. Not sure how it relates to covid19 but surely any pre-existing blood vessel damage is a danger for those contracting the virus. 

Canto: Right, so it’s unlikely anyone will know offhand their percentage of FMD. I don’t even know my HDL and LDL levels, never mind my HbA1c or lipids. I’d love to be able to take measures of all these myself, without visiting a doctor.

Jacinta: Typical male control freak. So all of this is to measure your risk of covid19 hospitalisation, ICU admission or mortality. Fun times. So next the update looks at Gilead, the makers of the antiviral remdesivir, who donated all their supplies of the drug to the USA in early May. But of course they kept manufacturing the drug and have to recoup the money they spent researching, developing and trialling it etc. The Wall Street Journal reports that a typical course of the drug will cost over $3000 per patient. Interestingly the Trump administration is wanting the drug to stay in the USA as much as possible, rather than be available overseas, and is spending money to that effect. 

Canto: Hmm. Is that protectionism? 

Jacinta: Yes I suppose. It’s not surprising that a country wants to look after its own first, especially via a product produced within its own borders. But I suspect this government would’t be interested in helping any other country – unless there was a quid pro quo. And there’s another antiviral, favipiravir, currently being trialled in Japan and the USA (I mean as of early July), and a vaccine, developed in China, is being used on the Chinese military in what seems a rather rushed and somewhat secretive fashion – we don’t know if they got the soldiers’ permission on this seemingly untried vaccine. At least at the phase 3 level.

Canto: Very CCP. 

Jacinta: So onto update 92, and we revisit the electron transport chain, with four successive electron transfers converting molecular oxygen into water. Problems within this chain can produce reactive oxygen species (ROS) such as superoxide, hydrogen peroxide and hydroxy radicals, which are destructive in excess. We also look, yet again, at covid19’s impact on angiotensin and particularly the production of superoxide, which in turn causes endothelial dysfunction, increased von Willebrand factor activity, which leads to thrombosis. People were presenting as ‘happy hypoxics’, looking and feeling fine but with very low oxygen levels, and autopsies revealed ‘microthrombi in the interalveolar septa’ of victims’ lungs. All this leading to a paper published in The Lancet which looked at factors in this process of coagulation and thrombosis:

We assessed markers of endothelial cell and platelet activation, including VWF antigen, soluble thrombomodulin [a marker of endothelial cell activation], soluble P-selectin [a marker of endothelial cell and platelet activation], and soluble CD40 ligand [a marker of platelet and T-cell activation], as well as coagulation factors, endogenous anticoagulants, and fibrinolytic enzymes.

So this was about getting to the bottom of the increased clotting. And the results were hardly surprising, but the final discussion section is worth quoting at length, as it seems to capture much that we know about covid19’s effects (at least short-term effects) at the moment: 

We therefore propose that COVID-19-associated coagulopathy is an endotheliopathy that results in augmented VWF release, platelet activation, and hypercoagulability, leading to the clinical prothrombotic manifestations of COVID-19-associated coagulopathy, which can include venous, arterial, and microvascular thrombosis. The factors responsible for this endotheliopathy and platelet activation are uncertain but could include direct viral infection of endothelial cells, collateral damage to the tissue as a result of immune infiltration and activation, complement activation, or any number of inflammatory cytokines believed to play a role in COVID-19 disease.

They suggest anti-platelet therapy and endothelial cell modification treatments as well as anticoagulation treatments, and they suggest some agents ‘which might have therapeutic potential’.

Canto: Potential? You’d think they’d be onto all this by now. 

Jacinta: Well there’s also potential for untried medications – at least untried in this context – to go terribly wrong. And it’s also likely that some hospitals are already onto using the safer forms of treatment. Dr Seheult speaks of the antioxidant N-acetylcysteine (NAC) in this context, as it has been shown to be a thrombolytic when used intravenously. There are studies pending on the effects of NAC in treating covid19 patients. 

Canto: Now, I’ve just been watching something on monoclonal antibodies as perhaps the most promising treatment yet, short of a vaccine. Can you explain….

Jacinta: Yes I’ll try, maybe next time.


Coronavirus Pandemic Update 88: Dexamethasone History & Mortality Benefit Data Released From UK

Coronavirus Pandemic Update 89: COVID 19 Infections Rising in Many States; Dexamethasone Cautions

Coronavirus Pandemic Update 90: Assess The Quality of COVID-19 Info With A Validated Research Tool

Coronavirus Pandemic Update 91: Remdesivir Pricing & Disparities in Drug Availability

Coronavirus Pandemic Update 92: Blood Clots & COVID-19 – New Research & Potential Role of NAC


Covid 19: corticosteroids, inflammatory markers, comorbidities

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Canto’s bronchiectasis – a relatively mild case, thank dog


Canto: So update 87, in late June, reflects a period when daily cases were just starting to rise, but deaths were apparently reducing – and various reasons were being given for this.

Jacinta: And interesting to note all the skepticism around Oxford University’s dexamethasone trial, which has led (the trial, not the skepticism) to a huge demand for the steroid. Dr Paul Sax of Harvard Medical School has expressed some dismay at the negativity, as this was a randomised controlled trial (RTC) of a widely available drug by a highly reputable, government-funded institution. 

Canto: Yet it seems that the website on this trial has since been taken down, so maybe there are some issues…

Jacinta: Okay, so let’s move on. Dr Seheult talks about raised ‘inflammatory markers’ in patients he observes coming in with covid-19. He names them, and I want to do a shallow dive into what they are and what they mean: Ferritin, C-reactive protein (CRP), CPK (to do with muscle breakdown), erithrocyte sedimentation rate (ESR), and d-dimer levels. So, ferritin is an iron-containing protein. It stores the iron and releases it when needed. Ferritin is mostly concentrated in the liver cells (hepatocytes) and in the reticuloendothelial cells of the immune system. That endothelial word again. As for CRP, this abstract from a 2018 paper Frontiers in Immunology tells me that ‘C-reactive protein (CRP) is an acute inflammatory protein that increases up to 1,000-fold at sites of infection or inflammation….CRP is synthesized primarily in liver hepatocytes but also by smooth muscle cells, macrophages, endothelial cells, lymphocytes, and adipocytes’. Need I say/quote more? And on CPK, this from the Johns Hopkins Lupus Center: 

Creatine phosphokinase (a.k.a., creatine kinase, CPK, or CK) is an enzyme (a protein that helps to elicit chemical changes in your body) found in your heart, brain, and skeletal muscles. When muscle tissue is damaged, CPK leaks into your blood. Therefore, high levels of CPK usually indicate some sort of stress or injury to your heart or other muscles.

And the US website has this to say on ESR:

An erythrocyte sedimentation rate (ESR) is a type of blood test that measures how quickly erythrocytes (red blood cells) settle at the bottom of a test tube that contains a blood sample. Normally, red blood cells settle relatively slowly. A faster-than-normal rate may indicate inflammation in the body. 

So, a fast ESR is an inflammation marker. High levels of CPK in the blood are too, presumably, as are high levels of CRP, wherever. And ferritin. Lastly, d-dimer levels, which are also related to clotting. This Australian site, healthdirect, tells me that ‘D-dimer is a type of protein your body produces to break down the blood clot’. So, a d-dimer test is ‘a blood test usually used to help check for or monitor blood clotting problems. A positive test means the D-dimer level in your body is higher than normal and suggests you might have blood clots’.

Canto: With all that let’s continue with the update. In Seheult’s hospital they started using dexamethasone as soon as the Oxford results came out and they’ve seen a reduction in all these rising inflammation markers. He recognises issues here though. Is this just anecdotal? Is this just a drop in the markers without real-life effects? Could it be recall bias? We know how conveniently inaccurate memory can be. 

Jacinta: My impression is that’s not going so well, though there’s no doubt still a varied use of dexamethasone and other corticosteroids throughout the USA. We’re at the point with the updates where they’re still thinking deaths in particular are reducing. We now know better. So the update next looks at a Chinese study from mid-June entitled ‘clinical and immunological assessment of asymptomatic SARS-CoV2 infections’. This small study looked at 37 asymptomatic patients and found that viral shedding (the release of virus from an infected person into the environment – the period of contagiousness) was 19 days, presumably on average. This compared with 14 days for symptomatics. A pretty significant finding. Immunoglobulin G (IgG) levels – essentially antibodies – were about six times higher in the symptomatic cases. That seems unsurprising I think, because it’s the antibodies that largely create the symptoms – the inflammation and clotting, the cytokine storm. Another finding was that, eight weeks after being discharged from hospital, the asymptomatic cases were 40% seronegative (having no antibodies) against SARS-CoV2, compared to 12.9% for the symptomatic cases. This suggests that neutralising antibodies may be ‘disappearing’ over time, though other immune cells, such as T cells may have a mitigating effect. Overall, though, the study advises extreme caution:

Together, these data might indicate the risks of using covid19 ‘immunity passports’ and support the prolongation of public health interventions, including social distancing, hygiene, isolation of high-risk groups and widespread testing.

Canto: Not suggestions the current Trump administration would be likely to pay attention to. 

Jacinta: Well the question here is one of re-infection, and I don’t know if there are any clear answers to that. Anyway update 87 goes on to look again briefly at vitamin D, and research in the UK, where vitamin D deficiency is more of a problem, and is associated with viral chest infections and with covid19 outcomes, with people of colour being disproportionately affected. They’re looking to people to sign up with a study called ‘covidence UK’. Dr Seheult also looks at a ‘Research Letter’ from the JAMA network entitled ‘prone positioning in awake, non-intubated patients with covid19 hypoxemic respiratory failure’. Prone positioning – lying on your tummy – was highlighted in one of the earliest of these covid19 updates as improving the symptoms of patients with ARDS. The findings from this JAMA are instructive:

In this small, single-centre cohort study, we found that the use of the prone position for awake, spontaneously breathing patients with covid19 severe hypoxemic respiratory failure was associated with improved oxygenation. In addition, patients with an SPo2 [pulse oximetry, a measure of blood oxygen level] of 95% or greater after one hour of the prone position was associated with a greater rate of intubation.

So, though there’s a need for RCTs etc etc, Dr Seheult has found dramatic improvements in oxygenation in his own patients through prone positioning.

Canto: Who are we to argue? And this update 87 ends on a positive note due to these combined findings about treatment. Prone positioning, remdesivir, dexamethasone, vitamins D and C, zinc, and maybe convalescent plasma, which needs to be explored further..

Jacinta: That’s blood plasma from recovered covid19 patients, with of course the antibodies to go with it, and I’ve looked at the National Covid19 Convalescent Plasma Project website to see if there are recent studies on this, but there’s nothing since March – small studies from China, which seem promising.

Canto: Update 88 starts again with dexamethasone, the cheap and widely available steroid, which – and this is back in late June – the British government got behind after the Oxford study was published, authorising its use ‘for patients hospitalised with covid19 who required oxygen, including those on ventilators’. It’s interesting that clinical views have changed on corticosteroids for covid19 over time, and there are still concerns about dosage and time periods on the drugs. 

Jacinta: Yes, short courses of corticosteroid treatment seem to be recommended, and not just dexamethasone. And many studies showed this before the release of the Oxford data. 

Canto: So the Oxford data itself is fascinating, especially for comorbidities or previous conditions. Especially interesting to me as I have such a condition, one that fits under their heading ‘chronic lung disease’, in my case bronchiectasis. They’re finding that people with such conditions are ending up on ventilators far less than those with diabetes or heart disease. So that’s good news for me. The disease, as they’ve been finding, is that covid19 is essentially an inflammatory disease of the vascular system. However, it seems that Dr Seheult’s hopes, at the end of update 88, that the greater introduction of short-term corticosteroids, and the use of other medications that might be efficacious, would reduce the mortality rate, have been dashed. We’ll be interested to find out why in upcoming posts.   


Coronavirus Pandemic Update 87: More on Dexamethasone; Do COVID-19 antibodies last?

Coronavirus Pandemic Update 88: Dexamethasone History & Mortality Benefit Data Released From UK,indicate%20inflammation%20in%20the%20body.

Written by stewart henderson

August 22, 2020 at 10:57 pm

covid-19, more on fructose, vitamin D, treatments and the vagaries of testing

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Canto: Ok, so note that in the graphic from the previous post, Australia is third highest in the group of 31 countries studied for caloric intake from sweeteners, but we don’t use HFCS much at all.

Jacinta: It might be a misleading graphic too. You might be forgiven for thinking that it somehow shows the USA as the most unhealthy, sweet-toothy country on the list, and Australia in third position, but since we’re more concerned here with links between fructose and covid-19 co-morbidities such as obesity, diabetes, cardiovascular problems and oxidative stress, the graphic doesn’t tell us much.

Canto: Yes so I found on this indexmundi site a list of 195 countries – and that’s all of them – showing prevalence of diabetes 1 and 2. That’s to say, the percentage of the adult population (from 20 to 79) that is diabetic. The USA ranks 43rd on that list, and Australia is down at 137th, level with Finland and Japan. But the site doesn’t name sources, and provides an end-note on the unreliability of much evidence: ‘National health authorities differ widely in capacity and willingness to collect or report information’. I should also add that though the USA is 43rd, the only other major nations above them are just about every Middle Eastern country, Pakistan, South Africa, Egypt, Sudan and Mexico. Make of that what you will.

Jacinta: Let’s avoid that rabbit hole, and return to medcram update 83, which briefly describes vitamin D3 (cholecalciferol) metabolism. This may involve a bit of repetition but that’s rarely a bad thing for us. So the D3 that we absorb or ingest goes to the liver and is hydroxylased at the 25th position (25-OH), but it doesn’t become activated until it’s again hydroxylased at the first position by the kidney (1,25-diOH, aka 1,25 dihydroxy vitamin D). And there’s another enzyme that can convert the vitamin to inactive forms. 

Canto: With that, Dr Seheult looks at another article from 2013 which describes a rat study that indicates that if fed on a high fructose diet, lactating rats suffered reduced rates of active intestinal calcium transport and active vitamin D. Or, more, accurately I think, they didn’t get the increased rates and levels that would be expected during lactation. So, because calcium is essential for skeletal growth, the study says ‘our discovery may explain findings that excessive consumption of sweeteners compromises bone integrity in children’.

Jacinta: Interesting, and I presume that means consumption by the mother during pregnancy. Anyway, in more detail, what they found was that increased fructose intake inhibited the enzyme that converted vitamin D into the active form in the kidney, and promoted the enzyme responsible for the inactive forms. Disturbing, as Seheult says, for the excessive fructose in American diets, which may consequently affect calcium and vitamin D levels, though that would surely require more research. 

Canto: Well, the same group released more research in 2014 which found that chronic high fructose intake in calcium-sufficient rodents (rats and mice) reduced their active vitamin D levels. And a 2015 study from Iran looked at something different but again having to do with effects on enzymes and metabolism. They looked at S-methyl cysteine (SMC), and this recalls the investigation of N-acetyl cysteine (NAC) a few updates ago. Found naturally in garlic and onions, SMC is described as a hydrophilic cysteine-containing compound, which they investigated for its putative effects against oxidative stress and inflammation. So they induced oxidative stress in rats via a high-fructose diet over 8 weeks and then dosed them with SMC. Results from the high fructose diet were – here goes – increased blood levels of glucose, insulin, malondialdehyde, and tumour necrosis factor-alpha.

Jacinta: Okay so the increased insulin is presumably a reaction to the increased glucose. Its role is to absorb excess blood glucose, and too much of it can result in hypoglycaemia, low serum glucose levels. Malondialdehyde (MDA) is described as a marker for oxidative stress, so it’s not good. Tumour necrosis factor (TNF or TNFα) is a ‘multifunctional cytokine’, and although cytokines (types of proteins) perform many vital functions, the cytokine storm that appears to be associated with oxidative stress and covid-19 is a bad thing. 

Canto: But there were also decreased levels of glutathione (GSH), glutathione peroxidase (GPx) and catalase as a result of this fructose diet, and Seheult talked about these enzymes and such as important in reducing oxidative stress. However, the SMC dosing improved antioxidant enzyme activities and reduced levels of glucose, insulin and TNFα. 

Jacinta: So this SNC seems another promising antioxidant treatment. Meanwhile, watch your sugar intake, especially with fructose. More studies required of course, but I suppose there are ethical issues involved in fattening up and inducing oxidative stress on human subjects with a high fructose diet. Okay updates 84 and 85 deal with questions that hospitalised covid-19 patients might want answered, so we’re going to skip those or we’ll never catch up on these updates. With update 86 they’re into the second half of June and noticing a resurgence of the virus. So at the Johns Hopkins site they’ve ‘working to fill the void of publicly accessible covid-19 testing data’, because without testing you obviously can’t work out the numbers.

Canto: But more than testing itself, the turnaround of results is a problem. A young woman was just on the tube saying it took three weeks to get her test results, which renders the test useless. And another person on the tube reported that she’d tested positive, felt generally okay or asymptomatic, then tested negative, after which she came down with a heavy case replete with many of the covid-19 symptoms, and then tested positive again. How can this happen?

Jacinta: It’s still a mysterious virus, but to return to the update and Johns Hopkins, they’re generally looking at US data, but I’m interested in understanding the testing process and how well it maps the prevalence of this virus. The website has a graphic which shows the fairly rapid rise in daily testing from March through to June (with a drop-off from mid-June, when perhaps they thought it was more under control), and the number of positive daily tests, which hasn’t of course risen so much, so that the percentage of positive test results has gradually fallen. The WHO recommends that the percentage of positive tests, the positive percentage rate (PPR), in nations or states where there’s widespread testing, should be under 5% for at least fourteen days before those states can start ‘relaxing’, but I’ve read different, more flexible recommendations elsewhere from health authorities, so it seems still a matter of educated guesswork with an unpredictable pandemic. 

Canto: For the different US states, looking at the figures now in mid-August, the figures are weird. Washington has a PPR of 100% (?!) and are testing 1 in every 10,000, so it seems they’re only testing those they know are positive? That’s top of the list and bottom is North Carolina with a PPR of -13.1, and yes that’s a minus, and they’re testing -.09 in every thousand, and I’ve no idea what that means.

Jacinta: But most states’ figures are clear enough. New York is at 0.8% PPR with over 4 tests per 1000, which is good, but Nevada, Idaho and Florida are at over 16% PPR, each with around 1.5 tests per 1000, and that’s obviously a problem. An indication of the lack of centralised control of the situation – it’s hard to compare data from state to state. Anyway, the key, some say, is to scale the testing to the size of the epidemic in that nation/state, not to the state’s population – but how can you do that when you’re using the testing to determine the size of the epidemic?

Canto: Well presumably if nobody is reporting unusual, covid-like symptoms, as is the case here in South Australia, you don’t need to spend so much time, money and energy on testing. Not the case in the USA. Anyway, in this update, Dr Seheult noted, as we have been, that the case numbers for covid-19 are increasing, but the death rate is decreasing slightly, or at least levelling off. Possibly a result of more testing combined with better treatment. They may also be catching weaker levels of the virus due to measures put in place. But there’s no evidence as yet that the virus itself has become less potent, and this seems unlikely. 

Jacinta: And speaking of treatments, the steroid dexamethasone is apparently reducing mortality by as much as 35% for covid-19 patients on ventilation, according to a WHO preliminary report of work done at Oxford. It’s only good for those with severe hypoxia and associated problems though, but its a cheap, off-patent medication which can be added to the box of tricks for ICUs, once the data is confirmed. 

Canto: Okay, next time….


Coronavirus Pandemic Update 83: High Fructose, Vitamin D, & Oxidative Stress in COVID-19

Coronavirus Pandemic Update 86: COVID-19 Testing & Cases Increasing but Daily Deaths Decreasing


Written by stewart henderson

August 19, 2020 at 1:50 pm

reading matters 9

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New Scientist – the collection: mysteries of the human brain. 2019

  • content hints – history of neurology, Galen, Hippocrates, Descartes, Galvani, Thomas Willis, Emil Du Bois-Reymond, Santiago Ramon y Cajal, connectionism, plasticity, mind-maps, forebrain, midbrain, hindbrain, frontal, parietal and occipital lobes, basal ganglia, thalamus, hypothalamus, amygdala, hippocampus, cerebral cortex, substantia nigra, pons, cerebellum, medulla oblongata, connectome, action potentials, axons and dendritic spines, neurotransmitters, axon terminals, signalling, ion channels and receptors, deep brain stimulation, transcranial direct current stimulation, hyper-connected hubs, 170,000 kilometres of nerve fibres, trains of thought, unbidden thoughts, memory and imagination, the sleeping brain, unconscious activity, the role of dreams, brainwaves during sleep, sleep cycles, traumatic stress disorder, Parkinsons, ADHD, dementia, depression, epilepsy, anaesthesia, attention, working memory, first memories, rationality, consciousness, von Economo neurons, the sense of self…


Written by stewart henderson

August 16, 2020 at 3:57 pm

covid-19: vitamin D, fructose and oxidative stress

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So looking at the Medcram coronavirus update 82, approaching mid-June, we find that many of the monitoring websites give the impression that case rates are falling in the USA and elsewhere….

The update also looks at diabetes as a risk factor for covid-19. It discusses data from China linking mortality to blood sugar levels. Glycated haemoglobin (HbA1c) was brought up in a previous post, though there are different ways of measuring it – I’ll keep to the percentages. The normal HbA1c should be below 6%, though presumably not too far below, as can happen for diabetics that over-medicate. Your HbA1c measure tells you what your blood sugar level has been over the last two-month period, approximately. So, to quote from the study:

the researchers found an increased mortality risk associated with any form of previously undiagnosed elevated blood glucose at the time of admission among 453 patients hospitalised with laboratory-confirmed SARS-CoV2 infection

One would imagine that, with the oxidative stress that SARS-CoV2 brings on, diabetics or pre-diabetics not on medication might be more at risk than those on regular medication with a consequently relatively low HbA1c. This is the kind of association found here.

The update goes on to discuss an article on race and covid-19 mortality in England, which has a supposedly open-access National Health Service (NHS), which in fact has been subject to savage cuts from successive conservative governments. The article concludes, unsurprisingly, that BAME (i.e Black, Asian and Minority Ethnic) persons are ‘at increased risk of death from covid-19 even after adjusting for geographic region’. Suggestions for reducing these apparent inequities include ensuring adequate income protection, reducing occupational risks, reducing barriers in accessing healthcare and providing culturally and linguistically appropriate services. Of course, these problems exist within all countries with substantial immigrant populations, many of whom are more exposed to the virus than others.

Vitamin D is next revisited, with an article entitled ‘Vitamin D deficiency in Europe: pandemic?’, which was actually published back in 2016. Now I note from some of the comments on this update that there’s a lot of hype and apparent misinformation on vitamin D out there, so I want to dwell on this, for my own education.

The article refers to a Vitamin D Standardisation Program (VDSP) which has developed protocols to look at serum vitamin D data from differently-aged European populations, ‘to better quantify the prevalence of vitamin D deficiency in Europe’. So they applied these protocols to 14 different population studies, looking at serum 25-hydroxyvitamin D [25(OH)D]. Vitamin D has five different types, but the pertinent one for human health is D3, aka cholecalciferol, which is made by the skin when exposed to sunlight, and is also found in foods and supplements. D3 is hydroxylated by the liver at the ’25 position’, according to Seheult. Presumably this is a position on the D3 molecule where a hydroxyl group is added. 25(OH)D refers to the molecule after this hydroxylation, but before it becomes activated by further hydroxylation at position 1 by the kidney. So they looked at this molecule in a number of studies using ‘certified liquid chromatography – tandem mass spectrometry on biobanked sera’. Combined with other standardised serum data, data was collected from almost 56,000 patients, and the findings were that 13% of them, regardless of category, had serum levels seriously below normal, especially during the winter months. 40% were below the generally accepted norm. The problem was considerably exacerbated in dark-skinned ethnic sub-groups. 

Back to 2020, and an article looking at the role of vitamin D in the prevention of covid-19 infection and mortality. It noted that ‘Vitamin D levels are severely low in the aging population especially in Spain, Italy and Switzerland’, so this is obviously a covid-19 co-morbidity factor. The article goes on to describe the mechanism of vitamin D’s action in the body, the details of which I’ll pass over, but it does involve ACE-2 and angiotensin 1,7, and also many other factors including macrophage development. With all this they raise the question of widespread vitamin D supplementation, which is apparently a hot topic beyond strictly scientific media, as mega-doses of vitamin D are being argued for on certain social media platforms, and even in the comments to this update. There are messy arguments going around about safe upper limits. Dr Seheult simply reports the article’s concern about ‘popular information channels’ spruiking the use of vitamin D3 above the generally accepted safe upper limit of 4000 international units per day. There is of course a battle here, not only in relation to vitamin D3, between those who demand proper trialling and vetting of medications and supplements and those looking for quick fixes. In any case, modest, regular dosing of the vitamin seems to be most effective.  

Update 83 goes intensively into a very important and interesting health topic, which has been quite controversial and also revelatory of late; the role of fructose in our diet, and how it works in our bodies. So to refresh – which is always good for me, at least – about the issue of oxidative stress and how it is exacerbated by SARS-CoV2. So we have oxidative stress in the form of an excess of superoxide and reactive oxygen species (ROS). The SARS-CoV2 virus enters the cell via the ACE2 receptor, blocking angiotensin-converting enzyme 2 (ACE2) from converting angiotensin-2 (AT-2) to angiotensin 1,7 (AT-1,7). AT-2 promotes superoxide production, while AT-1,7 inhibits it. This problem is in addition to the effect of SARS-CoV2 itself in bringing about an increase in polymorphonuclear leukocytes (PMNs), which are white blood cells such as neutrophils, basophils and eosinophils. These also lead to increased superoxide production, and more oxidative stress. An essential feature of oxidative stress is that it can result in endothelial cell dysfunction. These cells line the vascular system that feeds the body’s major organs. This dysfunction brings about an increase in von Willibrand factor which leads to clotting and thrombosis. Recent analysis of autopsies found that covid-19 patients had nine times more lung clotting than control groups including influenza patients. 

So the point of all this is that not having oxidative stress in the first place will be an important prophylactic against the virus. As Dr Seheult relates from the coalface, it’s those with a high BMI, with kidney and cardiovascular issues, and with diabetes, that seem to be at most risk of succumbing to the virus. Also, those with apparently normal HbA1c but with increased glucose were about 10 times more likely to have serious complications associated with the virus. This raises the question of diet, specifically bad diet. 

We then go back to 2017 and an article, or compendium of articles, published in Nutrients. Its title is ‘fructose consumption in the development of obesity and the effects of different protocols of physical exercise on the hepatic metabolism’. So fructose is a simple sugar or monosaccharide which combines with glucose to form the disaccharide sucrose. There are two forms of fructose (and of glucose), which are enantiomers, which is to say they have opposite chirality, which gives them different reactive properties. They’e called D-fructose and L-fructose. They’re six-carbon sugars, and D-fructose is the prominent form in the body. Sucrose links together a molecule of glucose with one of fructose, so that sucrose (table sugar) is essentially 50% fructose. Fructose is added to many foods as a sweetener, particularly in the form of high fructose corn syrup (HFCS) and this has become controversial, in case you didn’t know. It’s not such as issue in Australia, where we mostly use cane sugar as a sweetener, but it features in imported processed foods, and in many sweetened drinks. So how does fructose impact on obesity and oxidative stress? To quote from the abstract of the above-named article, ‘studies indicate that fructose may be a carbohydrate with greater obesogenic potential than other sugars’. The article provides a compendium of such studies and how fructose affects glucose metabolism in the liver, adversely affects hepatocyte function and engenders inflammatory responses. It also advocates physical exercise for reduction of symptoms and as harm-minimisation practice. An experiment on rodents in which half were fed on fructose, the other half on sucrose (50% fructose, 50% glucose), the fructose-fed rodents gained more weight, and over time that extra weight involved an increase in abdominal adipose tissue and increased serum triglyceride levels:

Moreover, several studies corroborated the evidence that high fructose consumption might lead to accumulation of adipose tissue, systematic inflammation, obesity, oxidative stress and consequently insulin resistance in different tissues.

 And there’s much more on the same lines, with relevant references. Dr Seheult describes other articles and studies over the last ten years identifying fructose and HFCS and their relationship to type 2 diabetes prevalence. One interesting article, which looked at HFCS alone, and surveyed diabetes on a global level, found that ‘diabetes prevalence was 20% higher in countries with higher availability of HFCS compared to countries with low availability’ and these results were adjusted for BMI, population, GDP and other factors. Greatest use of HFCS was in the USA, which of course has the highest rate of diabetes, and is leading the world in covid-19 cases.  


Coronavirus Pandemic Update 82: Racial Disparities with COVID-19 & Vitamin D

Coronavirus Pandemic Update 83: High Fructose, Vitamin D, & Oxidative Stress in COVID-19




Written by stewart henderson

August 16, 2020 at 12:42 pm

Covid-19: remdesivir, masks, vaccine trials, arrhythmias

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So to Dr Seheult’s coronavirus update 77, where he looks again at the antiviral drug remdesivir. A preliminary report from the New England Journal of Medicine describes results from trials comparing remdesivir with placebo in covid-19 patients at various levels of treatment, i.e, those receiving oxygen, those not receiving oxygen, those receiving high-flow oxygen or ‘noninvasive mechanical ventilation’, and those receiving full mechanical ventilation or ECMO (extracorporeal membrane oxygenation), and the finding was that remdesivir only made a statistically significant difference in the oxygen-receiving patients, which is more or less an intermediate phase. This may be due to the larger sample size that fell into this category. There were apparently small benefits in the non-oxygen category, but nothing in the more serious patient categories. The report’s conclusion:

These preliminary findings support the use of remdesivir for patients who are hospitalised with Covid-19 and require supplemental oxygen therapy. However, given high mortality despite the use of remdesivir, it is clear that treatment with an antiviral drug alone is not likely to be sufficient.

So remdesivir appears to be just one of many agents and therapeutics in the armamentarium of health authorities dealing with this pandemic, which over the past few months appear to have been utilised to reduce mortality and improve recovery times since the early phase of the outbreak in the USA, to judge from figures comparing, say, New York with Texas and Florida.

The update also discusses heat-treating the interior of police vehicles as a disinfectant, using a computer program. Basically a system has been devised to heat-treat unoccupied vehicles for 15 minutes to 133 degrees fahrenheit, long enough and hot enough to kill 99% of known pathogens, including SARS-CoV2, and it’s already being rolled out for police SUVs. Interesting, and obviously adaptive to other circumstances. The rest of the update discusses promising approaches as of the end of May, including convalescent plasma therapy, which I hope to look at later.

Update 78 starts with face masks. We here in South Australia have only suffered 459 cases in total, with 457 recovered and only 4 deaths. The majority of cases by far occurred in the early stages (March-April), and much has opened up since then, and the wearing of masks has always been optional here. However, the virus has had a resurgence in Australia’s more populated eastern states, so we’re on alert, and there’s been a partial closing down again. Still, most people I notice aren’t wearing masks. In the USA there seems to have been some prevarication from authorities like the CDC on mask-wearing, but with a further understanding, especially of asymptomatic and pre-symptomatic cases, they came out more strongly in favour of cloth masks ‘in public settings where other physical distancing measures are difficult to maintain (e.g. grocery stores and pharmacies), especially in areas of significant community-based transmission’. The WHO’s guidelines aren’t so strict possibly because they’re dealing with a broader base in which effective face masks are less readily available and need to be prioritised.

Also related to masking is a New England Journal of Medicine article on aerosols and droplets generated by speech, which have been implicated in Covid-19 transmission. A simple experiment was conducted using laser light scattering to illuminate droplets from a speaker without a mask, and then with one, and the difference was quite dramatic. Update 78 shows the video, and it’s worth a thousand words.

This update also highlights a website which I intend to explore further, especially as I seem to be spending a lot of time in the world of disease, pathogens and the fight against them. It’s called Regulatory Focus, and there’s a further link to its covid-19 therapeutics tracker, which tracks all the research and studies, of antivirals, monoclonal antibodies and any other medications that might relate in any way to the pandemic, and another link takes us to the covid-19 vaccine tracker. It provides information on phase trials, the vaccine type, the institutions and sponsors involved, etc.

In update 79, Dr Seheult picks out a few of the vaccine trials that seem to show most promise and are most likely to be available by 2021. First is the Moderna mRNA-1273 candidate, which will inject mRNA to produce proteins that generate an immune response. Now the standard clinical trial process for testing a vaccine involves three phases. Phase 1 tests primarily for safety, phase 2 largely looks at appropriate dosage, and phase 3 is the final, large human population trial. These phases have been fast-tracked more than ever before, as is well known, sometimes without the usual animal testing, which would generally raise ethical issues, but that doesn’t seem to be happening for covid-19 trials. The University of Oxford candidate is ‘a chimpanzee adenovirus vaccine vector called AZD1222’. It injects an epitope for an antigen into the patient. An epitope is a region of an antigen that antibodies detect and bind to. Other candidates come from the Merck company, Johnson & Johnson and Pfizer.

Update 80 deals with a very controversial issue, which is possible research industry malpractice, in the form of massaged results relating to a relatively small company, Surgisphere. Interestingly, it involves an overstatement of deaths here in Australia, among other inconsistencies, which have led to retractions of papers on hydroxychloroquine and chloroquine in prestigious journals such as the Lancet and NEJM. It seems that the papers may have exaggerated negative effects from the use of these anti-malaria medications, with or without the addition of a macrolide (a class of antibiotics), which has just added to the controversy surrounding them. There’s also a question about the use of the anti-parasite drug ivermectin, and some common heart medications, due to these now-retracted results.

Interestingly, update 81, posted back on June 9, highlights Australia as still succeeding in keeping numbers down as we head into winter. That’s not the case today (August 11). It goes on to introduce another website,, comprising data on ‘over 1400 trials’ (now over 1900) worldwide relating to covid-19, including ‘alternative therapy’ and ‘traditional Chinese medicine’. Hmmm. And of course all the more promising treatments. This and the previously mentioned vaccine and therapeutics trackers provide a wealth of ongoing detail about the who, the how, the what, the how much, etc.

The update also describes a trial of hydroxychloroquine ‘as post-exposure prophylaxis’ published in NEJM. 821 people known to be exposed to the virus were treated with either hydroxychloroquine or a placebo, and then tested for the virus. The result was a non-statistically significant prophylactic effect. There were minor gastrointestinal side-effects in the hydroxychloroquine group, but no cardiac arrhythmias, often associated with the drug. Dr Seheult explains something about these arrhythmias, which is interesting enough for me to dwell on.

When we look at an electrocardiogram (ECG) we find something like the drawing here, with a P-wave, and a T-wave at the end. Some medications can cause a prolonged QTc (the c stands for ‘corrected’), and in combination with others, this can result in cardiac arrhythmias, which generally have two types, as shown in the illustration at the top of this post – an over-fast beat (tachycardia) or a too-slow one (bradycardia).

So, although the positive effects of hydroxychloroquine in this study were minor, there may have been a greater benefit from adding zinc to the treatment, as Seheult suggests, because the drug acts as a zinc ionophore. An ionophore is a fat-soluble transporter material which can carry non-fat-soluble minerals like zinc through the fatty cellular membrane. Zinc inhibits the RNA-dependent RNA polymerase of the coronavirus, but it seems that as of mid-June no full-blown studies had been done to show a benefit, or otherwise, from the combination.


Coronavirus Pandemic Update 77: Remdesivir Update; COVID-19 in Mexico

Coronavirus Pandemic Update 78: Mask Controversy; Vaccine Update for COVID-19

Coronavirus Pandemic Update 79: COVID-19 Vaccines to Keep an Eye On – mRNA, Antigen, Others

Coronavirus Pandemic Update 80: COVID-19 Retractions & Data (Hydroxychloroquine, ACE Inhibitors)

Coronavirus Pandemic Update 81: New Data on Hydroxychloroquine Side Effects & Prevention of COVID-19

Written by stewart henderson

August 12, 2020 at 1:10 pm

Reading matters 8

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Outbreaks and epidemics, by Meera Senthilingam, journalist, editor and public health researcher, specialising in global health and infectious disease.

  • content hints – Dr Liu Jianlun, index case, ancient viruses, smallpox, ancient Egypt, eradication v elimination, hookworm, yaws, polio types 1,2 and 3, malaria, measles, Guinea worm, Edward Jenner, cowpox, eradication programme 1967, WHO, Donald Henderson, SARS, Zika and microcephaly, Ebola, mosquitoes, MERS-CoV, Crimean-Congo Haemorrhagic fever, Rift Valley fever, Yellow fever, more mosquitoes, breeding grounds, Aedes aegypti, Lassa fever, tuberculosis, syphilis, gonorrhoea, chlamydia, MSF, International Red Cross, dengue fever, staphylococcus aureus, bacterial meningitis, rabies, zoonoses, vectors, vaccine hesitancy, seasonal influenza, types A (H1N1), B, C and D, asymptomatic spread, antibiotic resistance, failed infrastructure, effects on poverty, affected by poverty, Dr Jan Semenza, effects of globalisation, investment, learning, co-operation…

Written by stewart henderson

August 9, 2020 at 11:45 pm

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.


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

Written by stewart henderson

August 9, 2020 at 12:34 pm

covid-19 stuff: NAC, glutathione, RT-PCR testing, re-positives

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So, more struggles with biochemistry. Update 70 talks again about N-acetylcysteine (NAC), but goes on to talk about glutathione, and whether glutathione itself might be a type of medication. So let’s get clear, or try to.

Glutathione is a naturally occurring and abundant thiol polypeptide in animal cells. A thiol has an SH (sulfanyl) group attached to a hydrocarbon chain, essentially. As we know, it’s an antioxidant which can be reduced by NAC, and they have structural relations. As Dr Seheult describes glutathione, it’s a combination of three amino acids, with cysteine at the centre. The other two are glycine and glutamate, and the cysteine and the glycine together effectively make up N-acetylcysteine – so NAC is described as a by-product or precursor of glutathione. A case report (regarded as the weakest level of scientific evidence) describes efficacious treatment of two patients with Covid-19-type symptoms using IV and oral glutathione. This and other studies and analyses seem to be begging for full-scale clinical trials to be carried out, but nothing as of mid-May. The treatments could be effective for hypoxemia in particular, due to the action on the disulphide bonds in VWF which are leading to platelet-rich thrombosis.

In his update 71 Seheult broaches the controversial topic of hydroxychloroquine, along with azithromycin and zinc. He suggests there’s evidence that hydroxychloroquine can act as a ‘zinc ionophore’, inducing zinc uptake into cells. Zinc inhibits the RNA-dependent RNA polymerase which SARS-CoV-2 utilises to reproduce. There has been a retrospective study suggesting that treatment with this combination may ‘result in a statistically significant reduction of mortality’, though maybe this hasn’t borne more careful analysis considering the cold water being poured on chloroquine as a treatment in recent months. It may be because it just doesn’t raise zinc levels sufficiently. The findings of the study do suggest the treatment has a statistically significant effect on reducing symptoms in hospitalised patients who are not in ICU – that is, they have relatively mild symptoms. No significant effect for ICU patients.

I should add here that now in August health authorities are warning against any unprescribed use of hydroxychloroquine as a prophylactic due to ineffectiveness and side-effects.

Update 72 began by looking at the sensitivity and specificity of antibody tests available, presumably in the USA. A study examined ‘four new commercially available serological assays [i.e blood serum tests]’, from three German and one US company, and it was found that they all ‘have a sufficient sensitivity and specificity for identifying individuals with past SARS-CoV2 infection’. Of course, the principal issue with the testing is the time it takes to receive results, but maybe that’ll be addressed anon.

Apparently (news to me in very safe – so far – South Australia where hardly anyone I know has had to be tested) there’s a difference between sensitivity and specificity, illustrated by the ‘spin’ and ‘snout’ mnemonic. For a highly specific test if you test positive you’re very sure to be in trouble, and for a highly sensitive test if you test negative you’re sure to be out of danger.

Dr Seheult next describes a retrospective study which looks at glycosylated haemoglobin (HbA1c) as a Covid-19 risk factor. A person’s HbA1c levels (how much glucose is attached to their haemoglobin) are a measure of diabetes. A1c (blood sugar level) is measured in percentages, with 5-6% being normal. The study found that ‘high HbA1c levels is associated with inflammation, hypercoagulability and low SaO2 [oxygen saturation] in Covid-19 patients, and the mortality rate (27.7%) is higher in patients with diabetes’. So HbA1c levels need to be looked at as a priority.

The update next looks at dentistry during the pandemic, for which there’s been little guidance, at least from the CDC. Apparently, during the AIDS crisis, dentists were viewed as modes of transmission, partly due to a NYT article on the subject. In any case, fewer people are now seeing their dentists for obvious reasons, which could lead to an oral health crisis. A number of diseases, including coronary disease, are linked to periodontal problems, so this can exacerbate the pandemic – and dental health, in Australia as in the USA, is not treated with the same gravitas as other forms of health.

Update 73 starts with a look at testing, particularly the reverse transcriptase polymerase chain reaction (RT-PCR) test. So the coronavirus has these spike proteins protruding from a bilipid membrane, with the RNA wrapped inside bound together by disulphide bonds and the like, I think. The protein shell around the virus is called the nucleocapsid. Of course the RNA’s code is specific to SARS-CoV2, so a test needs to look at a segment of the viral RNA and identify it with sufficient – essentially total – specificity. RNA is made up of the four base pairs adenine (A), uracil (U), guanine (G) and cytosine (C), with A pairing always with U and G with C. With that I’m going to switch to Scientific American for more detail.

A test starts with a sterile swab from the back of the nasal passage, aka a sample. Sample collection needs to be done properly, or it could lead to a false-negative result. If there’s viral RNA present, it’s extracted and used to produce a complementary strand of DNA – that’s where the reverse transcriptase enzyme comes in, reversing the usual transcription process from DNA to RNA. This material is then amplified – thousands of copies are made – to ensure a measurable result. The different available test kits generally vary in the segment of genetic material chosen.

I’m hearing that there are serious delays, in the USA at least, in delivering test results. This is extraordinary as, according to the Scientific American article, which is dated late March,

the FDA recently began granting emergency use authorization (EUA) to rapid diagnostic PCR tests that manufacturers say can deliver results in less than an hour. The authorization allows medical devices that have not yet been approved by the agency to be used during public health emergencies. 

What’s happening? According to very recent article from Quartz magazine, the problem is that there are too many kinds of tests. The EUA system was utilised, partly because of the urgency, partly because of the disastrous problem caused by the use of faulty reagents by the CDC back in February. Now there are about 150 tests that have been given EUA approval. Testing delays at first resulted mainly from lack of general lab equipment and PPR for the testers, but increasingly there are problems due to different types of tests, the variability of the tests, knowing which test to use, having the right equipment for each test, the prioritising of certain groups, such as front-line health workers, over others, confirmation of test results by other labs, and of course the overload in demand. We’re talking about the USA here, of course, and it just seems another case of lack of centralised control and uniformity in a state with a failed federal government.

Returning to update 73, Seheult describes a situation in which a SARS-Cov2-infected individual’s immune system has broken down the virus into ineffectual strands of RNA, proteins and other particles. It’s possible that a RT-PCR test could pick up on an RNA fragment, and produce a positive test result in these apparently recovered patients, and in fact this has often occurred. This is called a re-positive. The update describes a study by the South Korean CDC which provides valuable evidence on these re-positive cases. Some 280 re-positive subjects were studied, and about half of them displayed Covid-19 symptoms (on average 14 days after ‘recovery’). Presumably this re-positive finding was after they’d tested negative, i.e they’d first tested positive, then negative, then later positive again, though this isn’t clear. In any case, they checked a percentage of the subjects for antibodies and the result was almost entirely positive. They checked a larger sample for viral particles and found ‘not a single whole viral particle’, according to Dr Seheult, by which I presume he means anything that was replicable or active. They also looked at close contacts of the subjects, in large numbers, and all of them tested negative. So the finding was that these re-positives were, it seemed, the results of ultra-sensitive testing that was picking up viral RNA fragments that were in effect innocuous. This would seem to be a lesson for developing the right types of test. Hopefully a lesson learned.


Coronavirus Pandemic Update 70: Glutathione Deficiency, Oxidative Stress, and COVID 19

Coronavirus Pandemic Update 71: New Data on Adding Zinc to Hydroxychloroquine + Azithromycin

Coronavirus Pandemic Update 72: Dentists; Diabetes; Sensitivity of COVID-19 Antibody Tests

Coronavirus Pandemic Update 73: Relapse, Reinfections, & Re-Positives – The Likely Explanation

Written by stewart henderson

August 5, 2020 at 2:34 pm

update 69: NAC, glutathione, oxidative stress, thrombosis

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glutathione – far more than just an antioxidant

So we start with a closer look at glutathione, and its backbone amino acid chain, including the amino acid cysteine. Cysteine has the formula HO2CCH(NH2)CH2SH. The thiol sub-chain (SH) is important because it can bind to another form of the molecule, with S binding to S (oxidised form) rather than binding to H (reduced form) as here. So, as Dr Seheult explains, if you have two glutathiones, in this reduced form (2GSH), oxidised via hydrogen peroxide (H2O2), you will create a bond (GS-SG) between the two oxidised glutathiones, together with water. This happens in the oxidisation processes in our cells.

Seheult next mentions ADAMTS13, which is also known as von Willibrand factor-cleaving protease, so it’s a zinc-containing enzyme. VWF polymerises via disulphide bonds, and ADAMTS13 can help in disrupting that process, I think. Seheult diverts us by mentioning the disulphide bonds that connect the spiral strands of keratin in hair. A ‘perm’ reduces the molecular structure, breaking the disulphide bonds, so that the individual strands can be straightened, or made more curly, after which ‘you neutralise the perm agent’?? via H2O2, allowing disulphide bonds to re-form keeping the new hair structure in place. That was almost interesting.

So what can we do to assist these glutathione-based processes in relieving oxidative stress? This is apparently where N-Acetylcysteine (NAC) comes in. This molecule, which is ‘the N-acetyl derivative of the natural amino acid L-cysteine’, is ‘an antioxidant and disulphide breaking agent’, according to a 2018 review article in the Journal of Free Radical Research (not a political journal). So NAC is a reducing agent, which, like cysteine, has an SH bond. It breaks disulphide bonds and adds hydrogen, reducing viscosity. NAC has been used as a mucolytic inhalant, and as an agent against tylenol (paracetamol) overdose. How this last effect works is complex and I’ll try to comprehend it.

As Seheult explains it, NAC would act on the metabolite of paracetamol in situations of overdose. In such cases the liver metabolises paracetamol via an alternative pathway, by means of the toxic metabolite NAPQI, which depletes the liver’s glutathione. NAC replenishes the glutathione, but I won’t try to analyse the mechanism here. The main point is that NAC’s glutathione-boosting effects may have potential in dealing with Covid-19 symptoms. According to the above-mentioned review article, glutathione depletion is related to oxidative stress associated with a wide range of illnesses and pathologies, as well as in general ageing. So, a 1997 study in Italy looked at H1N1 flu and NAC treatment in a randomised, double-blind trial of 262 individuals of both sexes, most of them suffering from non-respiratory chronic degenerative diseases. They were divided into a placebo group and a NAC tablet group for a period of six months. No difference was found in both groups contracting the virus, but the majority of the placebo group (79%) came down with symptomatic forms, compared to only 25% of the treatment group, a significant difference. The study concluded that NAC treatment ‘appears to provide a significant attenuation of influenza and influenza-like episodes, especially in elderly high-risk individuals.’

So, recognising that this update is 2-3 months old now, I went online to see if NAC treatment is being used, or more comprehensive trials are being undertaken, as I note that, though case-rates are still disturbingly high, especially in the USA, death-rates are somewhat reduced.

An article from NCBI (the National Center for Biotechnology Information), which post-dates update 69 by a couple of weeks, presents only a hypothesis:

that NAC could act as a potential therapeutic agent in the treatment of COVID-19 through a variety of potential mechanisms, including increasing glutathione, improving T cell response, and modulating inflammation.

However, it didn’t seem as if any effective clinical trials focusing specifically on Covid-19 had been completed at the time of the article. A much more recent article (July 14) in Future Medicine (not such a promising name, given the urgency), presents more biochemical detail of NAC’s action, along with the anticoagulant heparin, and mentions ongoing clinical trials, but not specific results. It also mentions NAC treatment as a preventive for frontline ICU workers and general healthcare workers. It may be that such treatment is already being applied.

So, returning to update 69, Seheult cites another article from 2010 in Biochemical Pharmacology which showed that NAC inhibited viral replication (here the virus was H5N1) and reduced inflammatory cytokines, and again they suggested it as a potential treatment in the case of future influenza pandemics. Another small trial suggested some limited efficacy for NAC in the treatment of acute respiratory distress syndrome (ARDS).

So on it goes. A 2018 article found that ‘[NAC] improves oxidative stress and inflammatory response in patients with community acquired pneumonia [CAP]’. This oxidative stress reduction may be more important for Covid-19 cases because of the possibility of thrombosis due to the effect on VWF. A 2013 study found a significant decrease in a number of coagulation factors with NAC treatment. Of course, with this blood-thinning facility, NAC should not be used for patients with increased bleeding risk during or resulting from surgery. In any case I note that NAC is on the WHO list of most safe drugs or treatments.

And there are more studies. Another 2018 study found that NAC could reverse cerebral injury from strokes exacerbated by diabetes. The study concludes that ‘the diabetic blood and brain become more susceptible to platelet activation and thrombosis’, and that NAC appears to offer protection against the risk of stroke. The study’s explanation of the process here gives me an opportunity for further revision:

[NAC protects against stroke] by altering both systemic and vascular prothrombotic responses via enhancing platelet GSH, and GSH-dependent MG elimination, as well as correcting levels of antioxidants such as SOD1 and GPx-1.

So that’s platelet glutathione, and glutathione-dependent methylglyoxal, and the antioxidants mentioned are superoxide dismutase 1 and glutathione peroxidase 1. The ScienceDirect website does an amazing job of informing us about every known aspect of molecular biochemistry, just saying. Its material on glutathione and its catalysis is exhaustive and exhausting. And it looks as though the silver lining to the tragedy of Covid-19 may be a spike in further research into this and other essential elements of the molecular basis of immune systems.

Dr Seheult goes on to cite one more study, which found that ‘NAC administration promotes lysis of arterial thrombi that are resistant to conventional approaches…’, principally by acting on VWF, and that it is even more effective in combination with ‘a nonpeptidic GpIIa/IIIb (glycoprotein) inhibitor’, with no observed worsening of symptoms or outcome vis-a-vis normal haemostasis.

So I’ll end this piece wondering how things are going with NAC and other applications to reduce both respiratory and thrombotic symptoms in regions where the virus continues to be spread through a mixture of government, business and personal irresponsibility and stupidity. The battle to keep people alive and relatively healthy will, I think, ultimately win over the stupidity of some, but at a terrible and tragic cost. Vaccines are in the offing, but fear, indifference and ignorance will probably have the most adverse influence on their effectiveness.


Coronavirus Pandemic Update 69: “NAC” Supplementation and COVID-19 (N-Acetylcysteine)

Written by stewart henderson

August 2, 2020 at 12:46 pm