Archive for the ‘antigens’ Category
Natural selection – how far does it go?
you don’t control this variability
So let me try to understand something completely different, to do with genetics, neurology and selection theory. I’m reading a rather complex, demanding and ambitious book, published back in 1992, by Michael Gazzaniga, called Nature’s Mind, and sub-titled ‘The biological roots of thinking, emotions, sexuality, language and intelligence’. Selection theory gets a regular mention, and I’m assuming what is meant is the Darwinian theory of natural selection. That’s to say, the idea or finding that phenotypic traits that enable individuals in a species to more effectively survive, thrive and reproduce in their particular environment will be ‘naturally selected’ as against other less favourable traits. And so the species will ‘evolve’, that’s to say change, because individuals with the better-adapted traits for a particular environment will out-compete those without those traits and, crucially, pass on those traits to their offspring. Darwin, of course, could only speculate about how those traits were passed down to the next generation, as the whole story of genetic inheritance and DNA wasn’t fully established until well into the 20th century.
Anyway, Gazzaniga seems to be writing about selection theory as some kind of controversial issue, which surprises me and makes me wonder whether I’m reading him right. So let me focus on Chapter 2, ‘The plastic brain and selection theory’, to help my understanding. Here’s the opening sentence:
Although there is little argument that the selection process is at work at both the molecular and the evolutionary levels in whole organisms, there are major questions about whether the brain develops and functions in accordance with the concept of selection.
I don’t understand what Gazzaniga means by these separate ‘molecular’ and ‘evolutionary’ levels. After all, evolution just means change of a certain type – that’s to say, changes in organisms. And organisms are, of course, made up of molecules, coded for by genes. So the organisational structure of the brain, down to the molecular level (or upwards from the molecular level), has everything to do with our genetic inheritance. So what, then, are these major questions? Gazzaniga puts it this way:
…if, as I argue… the majority of our psychological capacities are the result of natural selection, the developing and static adult brain, which houses the neural circuits that enable the human’s high-powered psychological mechanisms to exist, must develop in a surefire, genetically determined way. At the level of behaviour, for example, we want to see whether or not a baby learns to identify a face, or whether there exist in the brain specific circuits enabling facial recognition, circuits laid down by prior genetic forces arrived at through selection pressure.
So, as I conceive it, Gazzaniga is exploring facial recognition (presumably that of other humans, but ‘face’ isn’t of course restricted to humans) in terms of learning and distinguishing, but also in terms of genes and circuitry that have evolved to render such recognition as vitally important. He cites the Nobel Prize-winning immunologist Niels Jerne’s view that selection operates at the cellular level, even though ‘it might look like instruction occurred at a higher level of organisation’. A ‘signal’ of recognition will prompt a response, once described as ‘unconscious’ (but it seems most scientists today dismiss this as a ‘woo’ word), that has been selected for on the most basic, molecular level.
So this takes us into a bit of immunology. Jerne used three analogies, as described by Gazzaniga: first, ‘the immune system is forever changed by the appearance of each new antigen, just as the brain is somehow changed by each new experience’, second, ‘each system – brain and immune system, appears to have a memory: when the same antigen presents itself a second time to an organism, the latter produces more and better antibodies’, and third ‘the experience one organism has developed for its immune system is not transferable to its progeny, just as my skiing ability is not necessarily transferred to my offspring’.
So, to antibodies, and the kappa light chain, which is present in the antibodies of humans and other animals. In all creatures who have these molecules, there is a variable and a constant part of the chain. They’re made up of amino acids, and the constant section is constant for all humans (and presumably for other species), while the variable part varies individually, or ontogenetically.
It seems that Jerne, and Gazzaniga, have taken this as some kind of analogy for the brain, the plasticity of which has both an ontogenetic (individual) and phylogenetic (species-specific) element. That’s to say, there’s a great deal of ontogenetic plasticity within the brain’s overall phylogenetic structure. I’m not sure if I’m getting this right, though. Here’s more from Jerne, comparing the immune system and the central nervous system:
In the immune system, the constant part of the light chain is obviously laid down in the DNA of the zygote, and it is equally clear that there is DNA in the zygote that represents the variable part of the light chain, although, ontogenetically, this DNA may exhibit an immense plasticity.
In the central nervous system, instincts are also obviously encoded in the zygote, most probably in the DNA. But if DNA acts only through transcription into RNA and translation into protein, and if the phenotypic expression of instincts is based on particular arrangements of neuronal synapses, the DNA through RNA and protein must govern the synaptic network in the central nervous system.
Niels Jerne, ‘Antibodies and learning: selection versus instruction’, 1967
So what to make of this ‘magnificent analysis’ (according to Gazzaniga)? You could say that it’s another brick in the deterministic wall, that ontogenetic plasticity, that which makes me different from you, starts with ‘particular arrangement of neuronal synapses’, or the particular sets of proteins that bring about those arrangements, or, before that…
I’m no doubt being influenced right now by some very recent discussions/arguments I’ve had on the subject of determinism, so I’m probably going further than Gazzaniga intended with his thinking. Or not. I shall continue reading the book to see if he comes to any definite determinist conclusions, or if he even touches on such a touchy subject.
References
M Gazzaniga, Nature’s Mind, 1992
on the lymphatic system and its clever cells, mostly
Activation of macrophage or B cell by T helper cell
Jacinta: So we’re focussing now on the lymphatic system, ‘clear water’ remember. A most misleading definition. So there’s this network of vessels, nodes and ducts….
Canto: What’s a node?
Jacinta: It’s a point of connection, or connections. In plants, a node is a point of branching, like with leaves.
Canto: Yeah I knew that. What’s a duct?
Jacinta: Don’t kid kid. It’s like a vessel, only, somehow different. Maybe bigger? Anyway, nodes go with lymph. There are over 500 of these lymph nodes throughout our bodies. The system does a lot of clean-up work, preserving fluid balance. It’s also much implicated in the immune system of course, and it’s involved in other stuff that’s quite hard to summarise, as you know.
Canto: Something from a reliable enough website:
The lymphatic system plays a key role in intestinal function. It assists in transporting fat, fighting infections, and removing excess fluid. Part of the gut membrane in the small intestine contains tiny finger-like protrusions called villi. Each villus contains tiny lymph capillaries, known as lacteals. These absorb fats and fat-soluble vitamins to form a milky white fluid called chyle. This fluid contains lymph and emulsified fats, or free fatty acids. It delivers nutrients indirectly when it reaches the venous blood circulation. Blood capillaries take up other nutrients directly.
Jacinta: Never heard of lacteals. Have heard of chyle, but don’t know much about it. So chyle contains lymph. But what’s lymph?
Canto: It’s a not-so-clear beige-coloured milky fluid containing lots of WBCs, especially lymphocytes, of course, and fatty stuff. Well, actually, that’s not lymph, that’s chyle. Or both… So there’s this lacteal system of the small intestine, capillaries for absorbing fats – well, actually transporting them… but we need to know what bile is, and emulsification, and lipase, and glycerides and esters, and no doubt much much more.
Jacinta: Well we’ve committed ourselves to learning about the immune system and associated processes for some ineffable effing reason, so let’s soldier on.
Canto: Okay, so bile has nothing to do with Trump, at least not in this context. Bile ducts are this network of tubes inside the liver – well actually there are intrahepatic and extrahepatic bile ducts. Bile itself is a fluid made and released by the liver, for breaking fat down into fatty acids. For ‘digesting’ fat, sort of. Not particularly relevant to the immune system, but it’s all interesting en it? And it can cause problems, such as chronic bile reflux. I suspect I’ve experienced bile reflux, though not chronically. I think it’s also called acid reflux, suggesting bile is a kind of acid.
Jacinta: Or maybe not. Here’s another one of those websites that know more than us:
Bile is composed of ingredients designed to digest fat. While it isn’t an acidic formula, it’s harsh on the sensitive linings of your stomach and esophagus. Chronic bile reflux can erode these protective linings, causing painful inflammation and, eventually, tissue damage (esophagitis).
Anyway, I’m not sure how we got from chyle to bile.
Canto: Right, back to chyle and lymph. Have you heard of lymphoedema? That’s a blockage of the lymphatic system, which causes tissue swelling, mostly in the arms and legs but possibly just about everywhere.
Jacinta: Yes, and things fall apart, the centre doesn’t hold. So let’s get back to lymph nodes and the cells they contain. Within lymph nodes there are germinal centres containing a lot of B cells, or B lymphocytes. These have receptors (B cell receptors) on their membranes which are IgD antibodies, all of which have different binding domains, due to genetic recombination, which allows them to deal with differently structured antigens. Once binding occurs, signals are sent to the lymphocyte’s nucleus, resulting in what’s called receptor-mediated endocytosis. The signalling response creates pseudopods and/or clathrins which pull the membrane inside.
Canto: Ok, sorry to be boringly predicable, what are clathrins?
Jacinta: They’re proteins, very ‘clever’ proteins, as so many of them are. They mediate endocytosis, which is essentially the surrounding and cutting off of extracellular material within the cell, creating a vesicle, called an endosome I think, which might be transported to further action sites. So this is happening within the B lymphocyte. We have this B cell receptor bound to a foreign antigen, and chromosome 6 of this cell then can produce a molecule (MHC2) to ‘fit’ the antigen and fuse it to the cell membrane. This has the effect of activating the B cell, carrying an MHC2 antigen-carrying molecule on its surface, and IgD antibodies. Of course I haven’t explained how the clathrins actually carry out this transformation, because I can’t but I believe it’s all been worked out.
Canto: Yes of course, and now our lymphocyte is an antigen-presenting cell. There are three types of such cells – B lymphocytes, macrophages and dendritic cells. However, the lymphocytes still need to proliferate to be effective, and this requires a stimulus. And so enter the macrophages. These have MHC2 molecules on their surface, bound to a specific foreign antigen, and they also have MHC1 surface molecules bound to a self antigen (as do all nucleated cells). The macrophage presents this MHC2 molecule with its antigen to a type of T cell, described as a’naive’ (i.e. non-specific) T helper cell. These helper cells will have, somewhere on their surface, specific protein molecules, called CD4, that ‘fit’ with the MHC2 molecules, and other specific molecules (T cell receptors) that fit with the foreign antigen. Specific TCRs fit with specific antigens. It’s all a matter of geometry, sort of.
Jacinta: These different types of TCRs are a product of genetic recombination, which involves RAG1 and RAG2 genes, and I can only guess that the R stands for recombination… Now these helper cells have CD3 signalling molecules inside (they send signals to the nucleus), and a molecule called CD28 on their surface. The macrophage has a protein, B7, which interacts with the CD28, and this protein interaction, called a co-stimulation reaction, sends a secondary signal to the nucleus – as opposed to the first, primary signal. This is known as co-stimulation.
Canto: So next, the macrophage starts secreting a molecule called interleukin-1, which binds to a specific receptor on the T helper cell, which results in a third signal to the nucleus, and activation of the T cell. The cell’s genes now produce interleukin-2, which can be secreted and will then bind to a receptor, as an ‘autocrine’, resulting in genes secreting another cytocrine, interleukin-4, and then interleukin-5. With all this, the T helper cell moves to another stage, becoming either a T helper 1 cell (stimulated by interleukin 12) or a T helper 2 cell (stimulated by interleukin 4). So, focussing on the T helper 2, it has activated interleukins 2,4 and 5, the latter two of which are especially important, after these cells have started dividing. That’s when those cytokines are produced.
Jacinta: We might be learning something. Now to the proliferation of the B lymphocyte. Interleukin 4 activates the B lymphocyte to start turning on genes for its proliferation – called clonal expansion. And they will have receptors (BCRs) specific to the foreign antigen. They’ll also have MHC2 surface molecules with exposed foreign antigens. They’re now ‘immuno-competent’ cells, and then, through the medium of interleukin 5, they will start differentiating. Some of these new types of cells are called plasma cells, which have a very prominent rough endoplasmic reticulum (RER), others are called memory B cells. Interleukin 5 and 6 stimulate plasma cells to produce and secrete antibodies specific to particular foreign antigens – or, rather, having variable regions that can adapt to and bind to those antigens.
Canto: And these antigens might be on the surface of bacteria, or not as the case may be. If they can bind to all the antigens on the bacterial (or viral) surface they can render it ineffective (neutralisation). Binding to freely circulating antigens can, however, cause problems. Such binding creates a precipitation reaction and this can be deposited in tissue resulting in a type 3 hypersensitivity. Don’t ask.
Jacinta: This is what United Staters call getting into the weeds, maybe. So that’s surely enough for now.
stuff on the immune system and that recent pandemic: 1 – how to get lost in a single cell
got that?
Canto: So, looking way back to the Covid-19 year or two, which we survived (and I’m wondering if the virus has too), have we retained what we’ve learned from all those Medcram videos we watched, and from the various ‘vaccine hesitant’ characters we encountered…
Jacinta: One of whom was a nurse as I recall, but I must say, mind like a sieve, I don’t feel I’ve retained much, so we’re reading Nobel Prize-winning immunologist Peter Doherty’s An insider’s plague year, to help us set down some info and promote our lifelong learning.
Canto: So what’s the difference between a drug and a vaccine, Doherty asks, noting that even experienced journalists confuse the two. Drug of course is a broad term, for anything chemical used to treat people, by pill, injection, bottle, patch or suppository. At the beginning of his ‘plague journal’ Doherty mentions two drugs I recall from our Medcram viewings, hydroxychloraquine, an anti-malarial, and remdesivir, ‘an experimental anti-Ebola drug’.
Jacinta: Yes, hydroxychloraquine was touted early on in the year (2020) as being of some use. A USA site, Drugbank online, said this:
Chloroquine and hydroxychloroquine are both being investigated for the treatment of SARS-CoV-2
followed by this:
The FDA emergency use authorization for hydroxychloroquine and chloroquine in the treatment of COVID-19 was revoked on 15 June 2020.
Remdesivir seems to have been somewhat more effective in reducing symptoms, as was seen earlier in treating MERS-CoV sufferers. It received the FDA’s authorisation just a few weeks before the other drug’s authorisation was revoked.
Canto: The word drug features in the USA’s FDA (Food and Drug Administration), while in Australia we have the TGA (Therapeutic Goods Administration), and therapeutic is simply medicalese for drug. The first of these tended to be natural remedies such as quinine, a useful anti-malarial extracted from Cinchona tree bark. Tonic water has quinine in it, hence the name. Another natural anti-malarial is artemisinin, from sweet wormwood. These ingredients, extracted and purified, have been extremely important in combatting the biggest killer disease in the global south.
Jacinta: In treating SARS-CoV2, remdesivir was the only effective antiviral in the first 12 months, apart from – monoclonal antibodies. I’ve heard of them, now I’m going to try and explain them. I’ll start with this quote from the Mayo Clinic:
Monoclonal antibodies are laboratory-produced molecules engineered to serve as substitute antibodies that can restore, enhance, modify or mimic the immune system’s attack on cells that aren’t wanted, such as cancer cells.
Antibodies (aka immunoglobulin, of which there are 5 types) are Y-shaped proteins that can bind to specific antigens (the foreign nasties) via a lock-and-key mechanism. Monoclonal antibodies, as mentioned above, have been particularly effective in some cancer treatments.
Canto: Well, only this month our TGA has posted an update on the decreased effectiveness of monoclonal antibodies against emerging SARS-CoV2 variants:
emerging data show that anti-spike protein monoclonal antibodies demonstrate a significant decrease in their in-vitro neutralising activities against many newer circulating SARS-CoV-2 variants, particularly Omicron and its subvariants.
Jacinta: Mmm. So let’s go on with our very basic training in immunology. So it’s the organs of the lymphatic system – the lymph nodes, the thymus, the spleen and the bone marrow – that produce or harbour and further develop our immune cells. Now, these immune cells come in different types with different names, such as phagocytes, which are a type of white blood cell (WBC)…
Canto: Yes, this immune system stuff might require dozens or hundreds of posts. Phagocytes can be ‘professional’ or non-professional’ depending on effectiveness. The professionals include neutrophils, macrophages, mast cells, dendritic cells and monocytes – all WBCs. They’re all more or less good at detecting antigens. And I believe these WBCs form what’s called the innate, rather than adaptive, immune system.
Jacinta: So getting back to the SARS-CoV2 Betacoronavirus – we’ll be jumping around a lot in these posts, methinks – it has this thing called a spike protein on its outer coat, and this protein has a receptor-binding domain (RBD) with binds to the angiotensin-converting enzyme (ACE) receptor, or ACE2 receptor. ACE2 receptors exist throughout the body but the principal pathway for this virus involves the epithelial cells at the base of the lungs and in the blood vessels. So I’m reading a Nature article, referenced below, entitled ‘Mechanisms of SARS-CoV-2 entry into cells’, and I want to frame this stuff in my own words to understand it. Apparently ACE2 is the receptor for other Betacoronaviruses and Alphacoronaviruses, so immunologists and virologists are pretty familiar with it.
Canto: Yes, and there’s all this terminology – for example a virion is the whole viral particle – not just the DNA or RNA core and its proteins but the external envelope – everything that allows it to exist extra-cellularly. So a coronavirus virion is made up of nucleocapsid and other proteins, including the spike proteins that facilitate entry into potential host cells via the ACE2 receptors.
Jacinta: So let’s focus for now on the nucleocapsid (N) protein. Another Nature article, with multiple authors, has this title: ‘The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA’, which sounds ominous. And the article starts with a problem:
The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood.
Yes, especially by me. I get that these N proteins bind and ‘package’ the RNA, but I don’t get ‘phase separation’…
Canto: Phase separation is a key biological concept, it seems, but complex, and probably something that requires lab work to fully comprehend. Here’s a quote from ScienceDirect that might help:
Many biological macromolecules, such as proteins and nucleic acids, exert their biological functions by forming phase-separated condensates, and phase separation is closely related to various human diseases. Gene transcriptional regulation is an indispensable part of gene expression and normal function in cells. Its abnormal regulation often causes the occurrence of different diseases. In recent years, the occurrence of phase separation during transcriptional regulation has become an area of intense research.
It sounds like problems with phase separation may lead to irregular transcription, or vice versa, resulting in variants, mutations and such, but I’m guessing.
Jacinta: So reading further into the ScienceDirect article, you’re right, it’s near impossible to understand this stuff just through reading – you surely need to see it happening in cells. And cells, such as our own, are effing complex. Here’s another (long) quote to prove it:
In cells, which are the basic unit of the structure and function of organisms, the need for various components to perform their corresponding functions at the correct time and space is a problem that cells continuously need to solve. To this end, cells have evolved a set of organelles, including membrane-encapsulated organelles (such as mitochondria, nuclei, lysosomes, the Golgi apparatus, and endoplasmic reticulum) and membrane-less organelles (such as nucleoli, Cajal bodies, stress granules, P bodies, U bodies, and signaling bodies) …. Membrane-encapsulated organelles enclose specific proteins, nucleic acids and other substances to perform their functions within a particular space. Still, how other types of membrane-less organelles form and exert their biological functions has eluded investigators for many years. In recent years, it has been discovered that different intracellular biological macromolecules assemble and separate from each other to form liquid-like structures called “biomolecular condensates”….
and it goes on. It’s dauntingly complex, but I must say I wish I was 40 years younger and working in this fascinating field. To work out more precisely the processes involved and then to be able to manipulate them…
Canto: Homo deus indeed.
Jacinta: Femo deus if you don’t mind, and that’s not even a recognised term. I just can’t wait for the 31st century.
Canto: Well let’s just stay in the shallows and say a few words about these membraned and unmembraned intracellular organelles. Mitochondria we know a bit about, the ATP-yielding (making?) organelles that existed separately eons ago as prokaryotes…
Jacinta: Thank the indefatigable iconoclast Lynn Margulis for presenting this argument, and endosymbiosis in general, against vociferous mostly male opposition…
Canto: Lysosomes are the ‘digestive system’ of the cell, containing enzymes that break down the polymeric structures of proteins, lipids, nucleic acids and carbohydrates. They vary greatly in size depending on the digestive tasks they work on. The Golgi apparatus or complex is, unsurprisingly, a complex organelle that packages proteins to be sent out into the intracellular or intercellular world – nuff said. The endoplasmic reticulum has two sub-units, rough and smooth. They’re kind of attached to the nuclear membrane of the cell, the smooth further out than the rough. It’s involved in transportation and protein folding, let’s say no more.
Jacinta: So now to the membrane-less organelles – but it looks like phase transition as a subject for analysis is about how these organelles transition from dormant to active states or how they transition from one task to another. Anyway, just a few words to introduce these organelles. Nucleoli are defined briefly as ‘small dense spherical structures in the nucleus of a cell during interphase’. They also appear to segregate in unexpected ways as cells divide – again something about phase transition. Cajal bodies are often associated with nucleoli and are involved in the processing of some RNA molecules. They appear to have other roles that aren’t yet fully understood. Stress granules are these changeable, dynamic, liquid-solid entities made from RNP (ribonucleoprotein). P bodies are somewhat similar, as are U bodies, named for being ‘uridine-rich’, whatever that may mean. In any case P and U bodies appear to act co-operatively. Signalling bodies, according to Khan Academy:
A signaling molecule is released by one cell, then travels through the bloodstream to bind to receptors on a distant target cell elsewhere in the body.
Canto: Okay, that’s enough terminology, and we won’t do all the references as nobody reads this stuff anyway.
Jacinta: Fine, we’re having fun, though it may take till doomsday to get our heads around this stuff. Wish I could afford a lab, and all its equipment….
References
Peter Doherty, An insider’s plague year, 2021
https://go.drugbank.com/drugs/DB01611
https://www.nejm.org/doi/full/10.1056/nejmoa2007764
https://www.tga.gov.au/news/news/update-effectiveness-monoclonal-antibodies-against-covid-variants
more on rapid antigen testing, and the vaccine race
So to continue with this issue of rapid at-home testing, there are/were many tests of a more simple and potentially cheaper type being manufactured, but they were all diagnostic tests (i.e tests that require expert interpretation as part of a diagnosis), and even if they’d been scaled up fairly rapidly they wouldn’t meet the kind of demand Dr Mina was envisaging. That’s to say, not doubling the tests available but multiplying those tests by a hundred or more, for nationwide availability in the US.
I want to get clear here, for myself, about the difference between an antigen test and a PCR test. An antigen test detects viral proteins. The paper strip test Dr Mina refers to contains antibodies that will bind to the antigens, or proteins, if those antigens are present in sufficient numbers. The presence of those antigens, or viral proteins, indicates that the virus is active – it is producing the antigens via the ribosomes of host cells. The PCR test detects viral RNA, whether or not the RNA is active. And so the antigen test reveals infectivity. The PCR test more often than not finds inactive viral fragments, since this RNA remains in the cell for some time after the period of infectivity, the upswing, which is relatively short.
Dr Mina has this to say about the sensitivity of the two test types. The PCR test will pick up virus from a few days to six weeks (or more) after infection, but the subject may be infective, that is, able to spread the virus, for the first two weeks (or less) after acquiring it. So its sensitivity to detecting an infective subject is not so great as its sensitivity to the virus itself (living and reproducing, or dead, or disabled). An antigen will be testing negative, both in the very early phase of infection, when the virus isn’t yet producing enough viral protein to show up on the test, and in the long phase when the virus, or parts of it, are still present but no longer replicating and infecting. So it is actually more sensitive to infectivity, which is exactly what’s required. And this essentially has to do with the frequency with which the antigen test can be used, because the PCR test has this lag time built into it.
It’s hard to believe that it’s this simple and straightforward, and that supposedly smart regulators aren’t jumping on this and getting these tests out there. Could I be missing something? I note that Dr Mina uses transmissible rather than infective, by the way.
So why aren’t such tests available? In the USA, it’s because it sounds a lot like a diagnostic, which requires approval or licensing from an organisation called CLIA – but that’s for them to work out. As to the situation here in Australia, which hasn’t had to deal with anything like the mess they’ve made for themselves in the USA, such a testing system would still help to detect spreaders, providing there was blanket use, and this would mean fewer lock-downs and less economic impact. As would be the case globally. An ABC article from late October features an interview with Prof. Deborah Williamson, director of clinical microbiology at Melbourne’s Doherty Institute, who recognises the value of rapid antigen testing, but feels that we need ‘to better understand their effectiveness as a screening tool in different epidemiological contexts’. This is understandably cautious, but then there isn’t the urgency in Australia that there so obviously is in the USA. But the USA has another major problem, which is almost incomprehensible considering the disaster that has unfolded there – and that is lack of compliance. Even if rapid antigen testing – cheap and in such supply that it could be utilised on a daily basis by the whole population – even if this was made available, there’s surely a major question as to whether most people would use the test any time they looked a bit peely-wally [under the weather], let alone when they were completely asymptomatic. So you could say that Americans are paying the price for their ‘rights without responsibility’ ideology – not shared by all Americans of course, but apparently shared by too many for them to escape from this, or any other pandemic, lightly.
Anyway, if we imagine a world, or a country, of largely compliant, responsible individuals, and widely available, cheap or free antigen testing, there would be no need for the quite onerous contact tracing mechanisms that we now have – signing in by phone or by hand at restaurants, pubs and the like – because those testing positive at home wouldn’t be attending those places until they tested negative again. Businesses could run, schools, airlines, etc. Economies could function almost as normal.
Of course now we have the vaccine, or almost. So far though it’s the Pfizer/BioNTech two-shot vaccine, which needs to be kept at way below zero (celsius) temperature, so, difficult to scale up and make available to those without proper facilities. No sign of that one coming to Australia for a while. I read an article yesterday, ‘The Amazing Vaccine Race’, in Cosmos mag. It outlines some of the contenders – the companies and the vaccine types. It points out that some companies are trying to play the long game, to try not for the first vaccine, or one of the first, but the best. The problem though, says, Nicolai Petrovsky, whose company Vaxine is based here in Adelaide, is that ‘the first runners end up getting all the resources’. And it may take quite a while to work out the best, and if the early runners turn out to be good enough, we may never find out which would’ve been the best. Vaxine is currently trialling a covid19 vaccine which combines the virus’s spike protein with an adjuvant (a treatment which enhances the immune response of the vaccine) based on a plant polysaccharide. And there are some 160 other contenders, according to the article. One in Sydney is combining the spike protein with bacillus Calmette-Guerin (BCG) which has been shown to reduce mortality from a range of viral respiratory infections. And there are others, just sticking with Australia, some with a degree of complexity that defeats me, for now. However, there are scant resources for local production here.
Although phase 3 trials of the current front-runners tested for safety among many thousands, it’s unlikely that scaling up to the millions will be without casualties, however minimal. And there’s the question of long-term immunity, which can’t really be tested for in this rushed situation. So it will be very interesting to see which of the current contenders wins out in the ultra-long run, or if something we’ve barely heard of yet finally proves the best option.
References
Rapid Coronavirus Testing – At HOME (COVID-19 Antigen Tests) with Dr. Michael Mina (video)
https://www.abc.net.au/news/health/2020-10-24/rapid-antigen-tests-for-coronavirus-screening/12808176
Dyani Lewis, ‘The Amazing Vaccine Race’, in Cosmos: the science of everything, issue 88, September-December 2020.
the rapid testing system that went begging
this is a screen shot taken from the video – the Ct values are inversely proportional to the viral load, and are plotted on a logarithmic scale (not drawn to scale though!). the x-axis is the infection time scale. viral particles can remain in the host for some time
For something completely different, I want to return to the matter of this pandemic, which in the past 24 hours has claimed more reported deaths in the USA since it began – a disaster of mismanagement, neglect, and of course the selfish civil disregard so typical of that country.
But of course that’s a generalisation, there are plenty of productive, socially concerned, often frustrated individuals trying to buck the trend, and Dr Michael Mina is one of them. He’s been advocating for a type of cheap, home-based, fast turnaround test for this virus (actually for the proteins that the virus produces via the host’s own ribosomes) which would vastly reduce spread, eliminate the need for contact tracing, and help the economy. Had this type of monoclonal antibody testing been scaled up at the outset, and made available worldwide, it’s likely that countless lives would have been saved. And it may well be generalised for other outbreaks.
So I’m writing this based on a video I watched, called ‘Rapid Coronavirus Testing – At HOME (COVID-19 Antigen Tests) with Dr. Michael Mina’. The video was produced in late July, and of course no progress has been made, and in the US the case numbers and the death numbers have jumped to the highest so far recorded, and rising.
So Dr Mina is a well-qualified immunologist whose impressive bio is detailed in the video. His ideas on this topic are published in a paper entitled ‘Test sensitivity is secondary to frequency and turnaround time for Covid-19 surveillance’, which has eight co-authors. The title captures the whole argument really, but I want to clarify to myself and others these issues of sensitivity and frequency. The video begins with a point-by-point comparison of the ‘paper antigen testing’ Dr Mina advocates, and RT-PCR (reverse transcriptase – polymerised chain reaction) tests, which are currently considered the gold standard. Firstly, the antigen tests are potentially much cheaper, once scaled up, and can be made for $1 to $2 per test. The PCR tests currently cost between $35 and $100 each. Secondly, the result of the antigen test can be known in 15 minutes, while the PCR test takes a minimum of 3 days, sometimes 7 days or longer. Third, the antigen test can be self-administered at home, while the PCR cannot. Fourth, the antigen test can be used daily, or three times a week, or with as much regularity as can be wished for or afforded, whereas this isn’t really viable for the expensive PCR test. Fifth, the simple antigen test can easily be mass-produced, but the lab processing involved in the PCR test would make this difficult. The sixth comparison favours PCR, which has a high sensitivity at over 90%, meaning that if there’s any virus present, it is over 90% likely to detect it, whereas the antigen test has a likelihood of around 55%. However, the antigen test will be able to pick up the majority of infectious cases, which is the key requirement. This will be explained later.
As Dr Mina points out, the rapid antigen test is a public health measure, unlike vaccines and therapeutics, which are medical interventions. The vital point he is making is that much investment is being put into the medical interventions, which, if successful, will bring solid returns on those investments. And so that is why so many private firms are competing for producing these ‘quick’ and hopefully effective, fixes, whereas there’s no return on investment for a public health measure such as a rapid, effective testing regime, even though this would be the best thing for keeping an economy running during a pandemic. It would require effective, good faith governance – something in short supply, particularly in the US.
So there’s a lack of financial incentive to scale up this rapid testing system, and according to Dr Mina, there’s also a regulatory problem. There’s no technical problem to scaling up, but as Mina says, there is a grey zone for this kind of testing which means it doesn’t quite fall under FDA’s guidelines, and there seems to be no governmental will (given that the USA currently has no federal government, and hasn’t really had one for four years) to provide a regulatory pathway for this kind of unique public health tool. FDA or other authorised approval is essential for mass-manufacture, and this isn’t forthcoming. As Mina says, this isn’t a diagnostic test, and isn’t meant to compete as a diagnostic test, it’s meant as a public health measure to prevent spread. So it’s a human and political problem, and this period in the USA is obviously bad for that sort of thing.
So the regulators appear obsessed with high-sensitivity testing, which tends to be expensive. If PCR testing could be done cheaply, at home, with rapid turnaround, that would be ideal, bit it isn’t going to happen, for a variety of reasons. This sensitivity issue needs to be looked at more closely, in the context of a rapidly multiplying virus, within a particular host. The rapid antigen tests may be a thousand times less sensitive than PCR, which sounds useless but not if you understand the virus and its action. It starts with a tiny number of parts per millilitre, and when it gets to a larger number, the PCR test will pick it up, and then when it gets much larger still, the androgen test will pick it up. But even then, the viral load will not be enough to effect transmission (and this will vary between individuals). And the whole aim is to prevent transmission, rather than the virus itself. The antigen test will tell you that you are transmitting (more later), and is effective in stopping or breaking that transmission chain. Testing frequency becomes more important than sensitivity. PCR tests conducted weeks apart could miss a whole infection cycle.
The FDA at the time had a news release entitled ‘FDA posts new template for at-home and over-the-counter diagnostic tests for use in non-lab settings, such as homes, offices and schools’, which sounds like just what the doctor ordered, but Mina points out that, though the regulators are showing willingness to relinquish testing power to members of the public to some degree, they’re clearly not willing to swap what is in essence a lab-based, PCR-type test, with all its super-sensitivity, for a rapid antigen test. So, no real possibility of rapid turnaround, and they require reporting of all positive and negative tests to the relevant lab or the Department of Health, rather than at-home monitoring. Among other things that means more work and more expenses for the monitoring company. Most results would obviously be negative, so a great deal of logistics to cover every negative result, which people probably wouldn’t comply in reporting anyway. So, not very viable. Dr Mina compared it to cheap instant coffee compared to those super-expensive Nespresso coffee machines that presumably the elites buy. The instant coffee version does the job without the bells and whistles, and he believes it’s the best intervention possible, short of a vaccine.
And that was in July, and the current death rate and case rate are breaking all records, but of course a vaccine is round the corner – maybe. So the moment has probably gone, but the lessons still need to be learned, by a more responsible administration. I will keep on this topic for the next couple of posts.
Reference
Rapid Coronavirus Testing – At HOME (COVID-19 Antigen Tests) with Dr. Michael Mina (video)
the science of Covid-19: vaccines and trials in the pipeline
Experts are still claiming 18 months at best for an effective vaccine, and with reports of re-infection, or resurgent virus activity in supposedly recovered subjects, it has become clear (or seems to have?) that we don’t know quite what we’re dealing with. Which of course poses problems for immunologists.
Still, the race is on. The WHO recently reported ‘more than 5 dozen vaccine candidates being pursued around the world’. The essential reason for the ‘delay’, however, is the three-phase human testing program that has become de rigueur for vaccine development. This video from YourekaScience, made five years ago, goes through the process, and note that it talks about a 6 to 10 year process, sometimes longer. The first phase focuses on safety (e.g. are there notable side-effects?), tolerability (does the vaccine cause pain, if so, what type, how long etc) and immune reaction (does the immune response look like being effective?). Phase 2 will involve larger numbers of volunteers to further test safety, and to determine proper dosage and timing of vaccines for strongest immune response. If all goes well, testing will move to phase 3, the largest trials, in which the drug will be compared with placebo and its ability to prevent infection can be more accurately measured – for example, whether it’s more effective in some sub-groups than others. Efficacy will determine approval, with possible recommendations, positive or negative, for different sub-groups. (I should add, after further reading, that stage 2 trials are often further divided into a and b phases).
So first-step safety tests on individuals have begun, in China, the USA and no doubt elsewhere. China’s vaccine is a version of a genetically engineered product developed against Ebola, while the USA’s different candidates are made from copies of a part of the SARS-CoV-2 genetic code.
Meanwhile, in Western Australia, volunteers are being recruited from the staff of a group of hospitals for an interesting experiment. They will be given the Bacillus Calmette–Guerin (BCG) injection, developed against tuberculosis. The jab is also known to boost immunity to other respiratory infections, and has a long history of safe clinical use. The trial has already been endorsed by the WHO. A similar trial, using healthcare workers, is planned for South Australia.
Australia also has a potential Covid-19 vaccine ready to go into first-phase testing in mid-May. It’s called NVX-CoV2373 (remember that name – or maybe not). Its developer, the biopharma company Novovax Inc, has partnered with Australia’s Nuclear Network, a clinical trials specialist, for the trials. The online mag Biowold reports:
The candidate, NVX-CoV2373, is going to have “a very similar safety profile” to Novavax’s phase III Nanoflu nanoparticle vaccine and, given preclinical findings, appears to be stable and productive, [Gregory Glenn, Novovax president of R&D said]. “The conformation is exactly what you need. And now we’re seeing that manifest after immunizing animals [in which we’re seeing] very, very high neutralizing antibody, which I think everyone would agree is highly likely to be protective,” he added.
Although we may be able, with the sort of effective collaboration this pandemic requires, to reduce the time-frame for a vaccine, reducing the current fatality rate is also a priority, hence the importance of the Australian (and other) trials. We are benefitting from the experience of a host of immunologists and biochemists whose experience has helped us to to look at solutions in this area. An article in The Lancet from a week ago is a good example. The authors suggest that anti-tumour necrosis factor (TNF) therapy is a therapy well worth trying:
Anti-tumour necrosis factor (TNF) antibodies have been used for more than 20 years in severe cases of autoimmune inflammatory disease such as rheumatoid arthritis, inflammatory bowel disease, or ankylosing spondylitis. There are ten (as reported on Sept 29, 2019) US Food and Drug Administration approved and four off-label indications for anti-TNF therapy,4 indicating that TNF is a valid target in many inflammatory diseases. TNF is present in blood and disease tissues of patients with COVID-195 and TNF is important in nearly all acute inflammatory reactions, acting as an amplifier of inflammation. We propose that anti-TNF therapy should be evaluated in patients with COVID-19 on hospital admission to prevent progression to needing intensive care support.
Whether the WHO or national government bodies or private companies take up this proposal is a question, but this is a time when investments of this sort should be made, and the results shared worldwide. This and other pandemics should provide the best opportunity for the kind of collaboration that transcends boundaries and individual reputations. We’ve done inspiring work on so many diseases that once thrived in our own ancestral communities – smallpox, leprosy, cholera, typhoid, scurvy, polio, tuberculosis, measles, whooping cough and many more. Our detailed knowledge of our immune system and how it can be primed and harnessed is distributed in researchers and their writings worldwide. All we need is the collective will and the appropriate collaborative approach to take advantage, for humanity’s sake, of all we’ve learned.
References
https://abcnews.go.com/Health/wireStory/search-covid-19-vaccine-heats-china-us-70147204
Vaccine Clinical Trials 101: How do we develop and test new vaccines? (video)
the science of Covid19: testing
So here in South Australia we have fairly drastic social distancing rules with pubs and restaurants and many businesses closed and so on, though in terms of case numbers we’re doing better than other states, and Australia in general is doing a lot better than other countries with comparable populations. Our crude case fatality rates (deaths per million) are smaller than any country ahead of us in number of cases in general – we’re currently ranked twentieth in case numbers. All of this is based on worldometer figures, which we can only hope are as reliable as they can be.
Our relative success has been attributed by some to our testing system. Worldometer has recently added a couple of new lines to their country-by-country statistics, ‘total tests’ and ‘tests per million’, which gives some idea of the testing rate, though little idea of the testing criteria, or the spread of testing throughout the country. According to these figures, the testing rate here is impressive compared to any other country of similar or larger population. Of course, there are just too many variables to make a direct connection between testing and fatality rates, but all experts agree that high rates of testing are beneficial. Worldometer also allows us to make some telling comparisons. For example, neighbours Sweden and Norway are recording a similar number of Covid-19 cases, 6400 and 5500 respectively, though Sweden has almost twice the population. That looks bad for Norway. But Sweden has had 373 fatalities compared to only 62 for Norway. That looks very bad for Sweden. And when we compare the testing, we find that, for half the population, Norway has carried out almost three times the number of tests that Sweden has. That’s almost 6 times the rate of testing. In fact Norway has the highest testing rate in Europe (apart from those with much smaller populations such as Iceland and Luxembourg). Other countries that appear to have greatly reduced fatality rates through comprehensive testing include Germany and South Korea. Clearly, large scale testing is working to keep fatalities down. It’s not unreasonable to attribute the escalating rate of infections in the US to the lack of a co-ordinated and comprehensive testing system, though the fatality rate there is relatively low. It’s clear that, with testing as well as with other responses, the states have failed to unite, largely due to a complete absence of federal governance.
The essential test for Covid-19 is polymerase chain reaction (PCR), and the detection process is well explained in the illustration above, and a little more fully on the JAMA (Journal of the American Medical Association) website. Or, at least, I assume so, as a non-scientific person. But in order to fully understand the process I need to capture it in my own words.
So SARS CoV-2 infects humans by binding to their ACE2 receptors by means of their spike proteins, one of four types of structural proteins pertaining to the virus. Studies have found that SARS CoV-2 has ‘a higher affinity to human ACE2 than the original SARS virus strain’, which presumably goes some way to explain its greater infectiousness. A PCR test is able to detect specific genetic material within the virus. A swab sample is taken from the throat or the nose or the lower respiratory tract or the stool, depending on test type. The JAMA website puts it this way:
After a sample is collected, RNA, which is part of the virus particle, is extracted and converted to complementary DNA for testing. The PCR test involves binding sequences on the DNA that only are found in the virus and repeatedly copying everything in between. This process is repeated many times, with doubling of the target region with each cycle. A fluorescent signal is created when amplification occurs, and once the signal reaches a threshold, the test result is considered positive. If no viral sequence is present, amplification will not occur, resulting in a negative result.
Australia’s Department of Health describes two types of test for the presence of SARS-CoV-2, nucleic acid/PCR tests (as above) and serology antibody tests, but the department sounds a warning:
The reliability of COVID-19 tests is uncertain due to the limited evidence base. Available evidence mainly comes from symptomatic patients, and their clinical role in detecting asymptomatic carriers is unclear.
This statement is dated March 27, and with the fast-moving situation, may no longer be relevant. And speaking of fast-moving situations, here in South Australia we’ve had our first recorded death from the virus, while I’ve been writing this. There’s also news overnight that a tiger from the Bronx zoo has tested positive. This has been confirmed by further testing. Other cats there are showing milder versions of the same symptoms but haven’t been tested. The tiger is described as being in a stable condition, and authorities are claiming that there’s no evidence of transmission from zoo or domestic animals to humans, but this kind of news may well lead to a public panic. And after all, absence of evidence doesn’t necessarily mean evidence of absence. There’s no doubt that the tiger’s infection raises a host of worrisome questions. Was the tiger infected by humans, as seems likely? If not, where did it get the virus from? And if the other cats are positive (they haven’t been tested due to problems with anaesthetics), then where will it end?
Antibody tests look not at infection but immunity. An effective test will show whether a person’s immune system has detected and neutralised the virus. Demand for these types of tests is extremely high, as immunity would mean that these people would be able to return to normal activity., with all the attendant economic benefits. Antibody detection would be of particular importance for current health workers. Such tests would show that the workers have already been infected by SARS-CoV-2 (perhaps without symptoms), and have developed immunity. Widespread use of the tests would also reveal the number of asymptomatic cases. Currently the number of people infected can only be an estimate based on current testing (the worldometer figures tell of confirmed cases, which can only be confirmed by testing). Children, for example, may be infected (and infectious) but asymptomatic, but the extent of this is pure guesswork. Getting real data would be useful in determining schools’ operations.
However, there are difficulties with antibody tests. According to The Lancet,
the technology behind antibody tests is fundamentally distinct and generally harder to get right. “If you have a sequence today, you have a PCR tomorrow”, says Linfa Wang, director of Duke-NUS Medical School’s programme in emerging infectious diseases, in Singapore. “Whether the sensitivity [of PCR] will be enough is another thing, but usually in the first round, it will give you data that you can use. Serology is different.”
One of the issues is knowing which protein, or antigen, on the virus to target. The spike protein is seen as the obvious target, as it’s the means of entering the host cell. Virologists in China have been using the spike protein (due to its specificity) and the nucleocapsid protein (due to its abundance). At least ten antibody test types have already been used throughout China. Specificity is important because, according to The Lancet, ‘the more unique [the protein] is, the lower the odds of cross-reactivity with other coronaviruses—false positives resulting from immunity to other coronaviruses’. These include those that cause the common cold, as well as SARS-CoV.
So that’s enough for now, I’ll continue to try and inform myself, having nothing better to do, and post some more results from that process next time. Keep well!
References
https://jamanetwork.com/journals/jama/fullarticle/2764238
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30788-1/fulltext
https://www.livescience.com/how-coronavirus-tests-work.html