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Archive for the ‘immunology’ Category

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

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

some thoughts on regression to the mean and what causes what

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Regression effects are ubiquitous, and so are misguided causal stories to explain them. Daniel Kahneman

Canto: So here’s an interesting thought, which in some ways is linked to the placebo effect and our attributing recovery from an illness to something we ate, drank or did, rather than to the silent and diligent work of our immune system. You know about the regression to the mean concept?

Jacinta: Of course. It’s a statistical phenomenon that we tend not to account for, because we’re always looking for or imagining causal effects when they don’t exist.

Canto: Well, they do exist but we attribute the wrong causal effects – we don’t account for ‘bad luck’, for example, which of course is caused, usually by factors we can’t easily uncover, so for convenience we give it that name. For example, a golfer might be said to have had an unlucky day with the putter because we observe that she she went incredibly close to dropping a number of difficult long putts, but none of them went in, so she made five over par instead of even. Of course every one of those failed putts was caused – one because her aim wasn’t quite true, another due to a tuft of grass, another because of a last moment gust of wind and so on… 

Jacinta: And some of those causes might be deemed unlucky, because on a less windy day, or with a better maintained green, those putts might’ve gone in.

Canto: Okay okay, there is such a thing as luck. But luck, I mean real luck, like the effect of a sudden gust of wind that nobody could’ve factored in, tends to even itself out, which is part of regression to the mean. But let me get back to illness. Take an everyday illness, like a cold, a mouth ulcer (which I suffered from recently)…

Jacinta: Or a bout of food poisoning, which I suffered from recently…

Canto: Yes, something from which we tend to recover after a few days. So the pattern of the illness goes something like this – Day 1, we’re fine. Day 2, we feel a bit off-colour. Day 3 we definitely feel much worse. Day 4, much the same. Day 5, starting to feel better. Day 6, definitely a lot better. Day 7, we’re fine. So it follows a nice little bit of a sine wave – two peaks and a trough – as shown above. 

Jacinta: So you’re saying that getting back up to the peak again is regression to the mean?

Canto: Well, sort of, but you’re getting ahead of me. Maybe it isn’t precisely, because a mean is the midpoint in a fluctuation between two extremes. Sort of. Anyway, let me explain. When you’re ill, you can choose to ride it out, or you can go to a doctor, or take some sort of medication, or some concoction recommended by a friend, or a reflexologist, whatever. But here’s the thing. You’re not likely to go to the doctor/acupuncturist/magus on day 2, when you’re just starting to feel queasy, you’re much more likely to go when you’re at the bottom of the trough, and then you’ll attribute your recovery to whatever treatment you’ve received, when it’s really more about regression to the mean. Sort of.

Jacinta: Hmmm. I agree that we’re unlikely to rush to the doctor or even the medicine cabinet when we’re just feeling a bit queasy, but that’s probably because experience tells us we’ll feel better soon – that maybe we’re already at the bottom of a little trough. But when we start going into a deeper trough, naturally we start getting worried – maybe it’s pneumonia, or tuberculosis…

Canto: Or diphtheria, malaria, typhoid, cholera, bubonic plague, acute myeloid leukaemia….

Jacinta: Don’t mock, I’ve had all of those. But it’s interesting to think of illness and wellness in this wave form. I’m not sure if it works as regression to the mean. Because wellness is just, well, feeling well. Feeling ‘normal’ or okay. We don’t tend to feel super-well – do we?

Canto: You mean you don’t believe in biorhythms? So you think the line pattern would be like, a straight horizontal one with a few little and big troughs here and there, and then finally off the cliff and straight down to death?

Jacinta: Well, no, isn’t it a slow decline into second childhood and mere oblivion – sans teeth, sans eyes, sans taste, sans everything?

Canto: Haha well not so much with modern medicine – though my hearing’s starting to go. But one of them-there invisible implants should fix that, at a price. But you’re probably right – what we call wellness at sixty is a lot different from the wellness we felt at twenty, but we’re probably lucky we can’t feel our way back to that twenty-something feeling. But getting back to the case of the person who applies a treatment and then gets better, there are, I suppose, three scenarios. The treatment caused the improvement, the treatment had no effect (the person improved for other reasons – such as our super-amazing immune system), or the treatment actually had a detrimental effect, but the person got better anyway, probably due to our wondrous immune system.

Jacinta: So that’s where the placebo idea comes in. And our tendency to over-determine for causality. You mention something like a cold, which is generally a viral infection, and mostly rhinoviral. The symptoms, like a runny nose and a sore throat, are actually caused by a mixture of the virus itself and the immune system fighting it, but mostly the latter….

Canto: Yeah, is that about antigens, or antibodies, I always get confused…

Jacinta: Well, it’s very very complicated, with T cells, immunoglobulin and whatnot, but essentially antigens are the baddies which trigger an antibody response, so antibodies are the goodies. So, if someone has a cold then unless they know their immune system is compromised in some way, the best thing is to let their immune system do its job, which might cause a few days’ discomfort, like extra phlegm production as the system, the antibodies or whatever, attempts to expel the invaders.

Canto: Yes, but the immune system is invisible to us, and is vastly under-estimated by many people, who tend to like to see something, like a big bright red pill, or a reflexology foot massage, or a bunch of needles needling their chi energy points, or unblocking their chakras…

Jacinta: Can they see their chakras?

Canto: No, but the magus can, with his various chakra-probing methods, and aural and oratorical senses developed over a lifetime – that’s why he’s a magus, dummy.

Jacinta: Yeah, and I’m sure we can all feel when our chakras are unblocked. It’s sort of like body plumbing.

Canto: So, getting back to reality, there is definitely something like this regression to the mean, to our own individual ‘normal’, but maybe ever-declining physical and mental state, that our wonderful immune system helps us to maintain, a system we rely on more than we realise….

Jacinta: Yes, but you know, it’s good that we don’t realise it so much, because think of all the acupuncturists, Alexander technicians, anthroposophicalists, antipharmaceuticalists, aromatherapists, auriculotherapists and ayurvedicists whose jobs might be on the line – and that’s just the A’s! Then we have the baineotherapist, the bead therapists and the bowen therapists, not to mention the chakra scalpel weaponmasters… can you imagine all those folk not being able to make a living?

Canto: Okay, that’s enough. It truly is a sad thing to think upon, but never fear, your horror scenario will never eventuate, my faith in human nature tells me….