an autodidact meets a dilettante…

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

Archive for the ‘virology’ Category

stuff on covid19 and immunology

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Canto: Well it’s a great time to be living in quiet South Australia, with a global pandemic raging in many places elsewhere..

Jacinta: Particularly the US, which we’ve long been focussing on, maybe in a schadenfreude kind of way.

Canto: Yes or maybe in a lazy way, because we’re so inundated by American media, social media, cable news, the NYT, the WaPo, the Atlantic, Politico, the Medcram lecture series, it just seems easier to plug into US info these days. Which makes me wonder…

Jacinta: And all hell’s breaking loose with Trump having come down with covid19 and the misinformation machine starting to overheat. Currently – October 5 – according to the Worldometer figures, which we’ve been using since the start of the pandemic – the USA has suffered 214,611 deaths, more than a fifth of the world’s deaths by that database’s figures. 

Canto: Yes, we’ve noticed that the US media always has figures a little below ours – I presume because they’re using the Johns Hopkins figures, which seem to have a time lag. We can’t say which is more reliable of course. Complete reliability for all sources is unlikely. 

Jacinta: In any case the USA has spectacularly failed to get on top of this virus, and is still experiencing high case-rates and death-rates, though the variations between states are constantly changing, and tell their own complex story. Overall, though, unless something drastic happens, the US is on track to have suffered 250,000 to 300,000 deaths by the end of the year – and I haven’t accounted for the winter season. 

Canto: Yes and that’s no outlier prediction, that’s just a very simple forward projection. 

Jacinta: I’m half-wondering when the Trump administration will try to throw cold water – or bleach perhaps – at the covid figures, as they’ve tried to misinform with everything else to do with the virus, including Trump’s condition and the timeline of his infection. But I want to look at what we’re hearing from the Walter Reed medicos about his treatment, and more generally about immunology and the virus’ progress. From the figures, it doesn’t seem as if anything is working very effectively, but Trump will be getting treatment that isn’t widely available to anyone else in that country, and we’re getting no clear answers as to how he’s faring. 

Canto: The treatment everyone’s reporting on currently is the ‘antibody cocktail’ produced by the drug company Regeneron. This was made available through an emergency use authorisation, and unsurprisingly there’s now demand pressure on the product. He’s also on the antiviral remdesivir, and the steroid dexamethasone, and it seems he’s been given oxygen, though medical and other experts have had to read between the lines of public announcements to work out what exactly is going on. 

Jacinta: Yes, many experts suspect he’s been sicker than he’s been prepared to admit, and of course the Democrats and health officials are all wishing him well and ‘praying for him’ in their American way. Frankly, I hope he dies, for the simple reason that his death will likely save thousands of lives, as it will stem the flow of misinformation, and scare even his dumbest followers into wearing masks, physically distancing and generally starting to act sensibly and humanely. It will have been the best thing he’s ever done with his life. But enough controversy, let’s look at immunology and treatment. According to the NYT, Trump has also been taking Vitamin D, zinc, the hormone melatonin, and famotidine, an anti-heartburn medication. 

Canto: So he’s fit as a fiddle, then? 

Jacinta: Hmm. As we know, Dr Seheult on Medcram has spoken of the benefits of zinc and vitamin D, as well as remdesivir and dexamethasone, but none of these treatments have been subjected to rigorous clinical trials in relation to SARS-CoV2 as yet. It’s my guess that Trump himself is pushing the envelope to be treated with these drugs, though it could also be that he’s actually quite sick, as I’ve said. And unless he actually dies, it could be that we’ll never know. 

Canto: He won’t die. Anyway, what about Regeneron, and these monoclonal antibodies? 

Jacinta: Well we’ve talked about them before, but they’ve been mostly used in the past against cancer cells. In fact they’re finding uses in many medical fields but they’re tricky to manufacture, and would be expensive to roll out…

Canto: Actually I’ve heard some reports that it’s polyclonal antibodies they’re giving him. Is there a difference? I thought maybe because they were giving him a ‘cocktail’ of monoclonal antibodies, this amounted to polyclonal…?

Jacinta: Well, who knows what they’re actually giving him, but according to my reading, researchers have engineered (cloned) immune cells that produce specific antibodies – antibodies to a specific antigen, or more accurately, to the epitope, or binding site, of that antigen. That’s monoclonal antibodies. Polyclonal antibodies can bind to multiple epitopes, which sounds better but maybe they’re harder to manufacture in an effective form. 

Canto: So these monoclonal or polyclonal antibodies are proteins, synthesised versions of proteins produced by the immune system. Is it that, due to the virus, the body is prevented from producing these antibody proteins naturally, or can’t produce enough of them, or what? 

Jacinta: What I gather is that the response to the virus varies – some are producing antibodies, some aren’t. A report came out last week about Regeneron’s treatment, this ‘cocktail of two monoclonal antibodies’:

The company showed slides with detailed data from 275 infected people in a placebo-controlled trial that ultimately plans to enrol 2100 individuals who are asymptomatic or, at worst, moderately ill. The analysis divides patients into two groups: those who had detectable antibodies against SARS-CoV-2 at the trial’s start and those who did not, a so-called seronegative group. The monoclonal cocktail showed little effect on people who already had antibodies against the virus. But it appeared to help the seronegative patients, powerfully reducing the amount of virus found in nasopharyngeal swabs and alleviating symptoms more quickly. 

So it appears to boost the immune system of those who haven’t, or haven’t yet produced antibodies to the virus. So, useful for those in the earliest phase of having contracted covid19. But all of this has to be more thoroughly tested – for example, would the treatment work as a general preventive? 

Canto: There’s another company, Eli Lilly, which has been trialling a single monoclonal antibody treatment, with slightly different results – both companies have given low-dose and high-dose treatments, and Regeneron found no statistically significant difference, whereas Lilly found the high dose ineffective – which is good news as the lower dose will presumably be cheaper to manufacture, with fewer adverse effects, if any. The two companies have a slightly different approach to using their medications – though this might change in such a fluid situation. Regeneron is thinking of developing diagnostic tools to identify those most in need of the treatment, e.g those with the highest viral load, and those with low antibody levels (serology). Lily, on the other hand, are thinking that any covid19-positive people at higher risk – diabetics, overweight, or simply elderly – should be given the treatment, if possible. 

Jacinta: In the meantime, the dangers of this virus are constantly being underplayed by this administration under pressure, clearly, from the Boy-King, while a large cluster of people who’ve had contact with him, either at the White House or on any of his jaunts around the country. Exactly who set off the cluster will probably never be known, because it sounds like they’re refusing, again under the orders of a clearly incompetent wee boy, to engage in contact tracing!

Canto: It’s a SNAFU to be sure. Apparently one of this number – 34 at last count –  is gravely ill in hospital. It’s like we’re watching an episode of ‘Horrible Histories’ in real time. It’s good to see that the polls are predicting a landslide. That means if the actual numbers come in and it’s close, it may be to do with the dirty business Trump and the Republican ‘leadership’ appear to be trying on vis-à-vis voter suppression. And then all hell will break loose.

Jacinta: Hell will break loose no matter what happens. This next month or two will be a cracker for us non-Americans. We’re certainly living in interesting times. But seriously, my condolences to the American people. 


Coronavirus Pandemic Update 97: Vitamin D & COVID-19 Immunity, The Endothelium, & Deficiencies

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

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

covid19: monoclonal antibodies, symptomatic v asymptomatic, corticosteroids, comorbidities

Written by stewart henderson

October 8, 2020 at 11:55 pm

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

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

the science of Covid-19: vaccines and trials in the pipeline

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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.


Vaccine Clinical Trials 101: How do we develop and test new vaccines? (video)

Written by stewart henderson

April 15, 2020 at 8:55 pm

the science of Covid-19: global collaboration and broad-spectrum antivirals

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not claiming I understand this diagram …. yet

An interesting article in the New Yorker has introduced me to David Ho, whose work on AIDS in the eighties and nineties led Time magazine to name him its person of the year in 1996. Almost forty years on from reporting the first AIDS cases in 1981, Ho continues to fight the disease, which still kills a million people a year. That might shock some people, but out of sight, out of mind, it’s not happening here. Covid-19 has killed about 100,000 in a few months, all over the world, and the global curve is no cause for complacency, to put it mildly. And you can catch it just by breathing. And many researchers have said this is just a rehearsal for the big one. Well, let’s just deal with this one first, and learn from it. People like David Ho are on the front line, desperately seeking new, comprehensive antiviral solutions.

Drug companies, however, have tended to invest in chronic viral infections, such as AIDS and hepatitis B, rather than acute ones which do deadly damage then disappear, as did SARS and MERS. Both these infections were gone before a vaccine was fully developed, so there would have been no return on investment. Many researchers are pointing out that it’s therefore not a task suited to private enterprise, which tends to be competitive rather than collaborative, as well as having other priorities. This article linked to the Johns Hopkins website focuses on some of the problems related to lack of co-ordination regarding messaging and possible treatments. The pandemic is global, it obviously disregards boundaries, so we need to be less nationalistic and proprietorial and more humanistic in response. To quote the article,

As a first step, the biomedical community needs to insist on consistent use of central registries of clinical studies and on early sharing of complete details of both successful and failed studies, and not withhold important scientific evidence as proprietary information.

If adequate testing shows promising results, that information needs to be shared immediately, in a way that can be analysed and the testing replicated. This of course includes methods of analysing and tracking the virus and its proteins. Developing treatments at the moment is tricky due to the apparently huge variation in the responses to infection – from being completely asymptomatic to the other extreme. Drugs may have to vary in toxicity to treat these varying symptoms. With effective collaboration, rigorous testing of treatments doesn’t have to be a slow process – at least it can can be much quicker than it has been before.

Meanwhile, not all health authorities are on the same page regarding physical distancing measures. The USA’s Centers for Disease Control and Prevention (CDC), a federal government agency, has sparked controversy by allowing asymptomatic ‘critical infrastructure’ workers who’ve been exposed to SARS-CoV-2 to return to work under strict guidelines. It’s noteworthy that the US federal government has been pushing a rapid return-to-work scenario for some weeks, though it has often been inconsistent in its messaging. Asymptomatic carriers of the virus are officially estimated at about 25%, though some experts argue that the figure could be as high as 50%. Individuals can also be presymptomatic rather than asymptomatic, and this is difficult to identify due to the variability of the onset of symptoms. In any case there is still the possibility of spread from either group. The lack of precise evidence about asymptomatic transmission tends to make most experts err on the side of reducing the risk. Also, according to this paper, distancing measures have likely reduced the spread of seasonal influenza (particularly virulent this season), especially in countries such as Japan, where there was an early awareness of Covid-19 prevention measures.

Not surprisingly, the advent of this virus, which has brought with it a return of all the unheeded warnings of the past decade or more, has inspired and spurred a lot of interesting new research and approaches to dealing with viruses – long regarded as the most potentially dangerous pathogens out there. The New Yorker article relates some of the history, from the first antiviral drug to be marketed in the early sixties, ‘a repurposed anti-cancer drug put to use as a topical treatment for a herpes infection that attacked the cornea’, to drugs such as ribavirin and acyclovir in the seventies, and then on to breakthroughs in the eighties in the battle against HIV/AIDS. There will be more breakthroughs with this new pandemic, but the point is that the threat of new viral outbreaks has been touted for years, but antiviral research gets limited funding and all but shuts down when there’s no clear and present danger. The current pandemic may or may not convince us that work on broad-spectrum antivirals needs to be ongoing and cannot be subject to private market fluctuations or whims.

Lest I lead people into thinking I have much of a clue as to what broad-spectrum antivirals are, let me assure you… but there’s something of a clue in the name. It should be about finding some common factor in the invasive behaviour of viruses, and what they do to replicate once inside, and using that knowledge to develop or activate agents that will shut down or act against such behaviour. A website called Creative Biolabs has a bit more to say on its front page:

By inhibiting virus replication/reproduction in infected cells or improving cellular defense system, these broad-spectrum antiviral drugs are effective in the clinical treatment of viral infection, as well as for SARS-CoV-2 infection. Mechanisms drugs with broad-spectrum SARS-CoV-2 antiviral activities mainly involve:

– Inhibiting or killing the virus directly

– Interference with virus attachment/membrane fusion

– Preventing the virus from penetrating into cells

– Inhibiting the biosynthesis of the virus

– Inhibiting the assembly and release of the virus

– Enhancing the antiviral ability of the host

From what I can gather, Creative Biolabs is a bonafide life-science company servicing various private pharmaceutical companies as well as government agencies. So hopefully I can learn, from their website and many others, more about broad-spectrum antivirals and any other possible treatments and ventures that might reduce the threat of viral epidemics.


Written by stewart henderson

April 12, 2020 at 4:03 pm

Posted in antivirals, covid19, virology

Tagged with , ,

the science of Covid19: testing

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filched from the excellent JAMA website

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!


Written by stewart henderson

April 7, 2020 at 12:34 pm

2019-nCoV: where does it come from?

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whether or not they led to 2019-nCoV in humans, leave pangolins alone

As mentioned previously, there are lots of coronaviruses. The four most commonly found in humans have these memorable names: 229E, NL63, OC43 and HKU1. These are humanly-borne viruses that seem to be more interested in increasing spread than increasing pathogenicity. We seem to have developed enough of an immunity from these common coronaviruses for them not to be a major problem. It’s perhaps the new strains that jump from bats to humans via an intermediate species – civets in the case of SARS, dromedary camels (probably) in the case of MERS – that are most likely to be pathogenic. Researchers are on the hunt for the intermediate carrier in the case of 2019-nCoV. Snakes were first suggested, but this has now been dismissed. The most recent candidate has been the pangolin, after research from the South China Agricultural University on the genome sequences of pangolin viruses found them to be 99 percent identical to those in coronavirus patients, but this is unpublished, unverified data at present.

Civets, pangolins? These are just some of the more or less exotic wild animals that some Chinese people like to consume or use for ‘medicinal’ purposes. Traditional Chinese medicine, aka medicine that doesn’t work, has a lot to answer for. Health experts are now recommending that the Chinese government clamp down on this practice. The presence of these creatures in open Chinese markets is disturbing. A prohibition was apparently put in place by the Chinese government just last month, a matter of shutting the stable door, but how well this will be enforced is a question.

Civet – harmless purveyor of SARS, and forget the coffee hype

Over the past 24 hours I’ve been coughing up a storm, and I’m due to work tomorrow. Medications are reducing the inflammation, and I note that wearing a common or garden surgical mask, which we see everywhere now, will not help. To quote from Live Science:

Coronaviruses can be transmitted between humans through respiratory droplets that infected people expel when they breathe, cough or sneeze. A typical surgical mask cannot block out the viral particles contained in these droplets, but simple measures — such as washing your hands, disinfecting frequently touched surfaces and objects, and avoiding touching your face, eyes and mouth — can greatly lower your risk of infection.

Of course I don’t have such a virus, and there are no known cases of it in Australia, though at least five Australians on a cruise ship off Japan have been confirmed as having contracted it. But as to surgical masks, the point is that viruses are much smaller than bacteria (on average about 1000 times smaller). They’re not cells, with their full complement of DNA, but strands of nucleic acid (DNA or RNA) encased within protein. They’re parasitic on hosts, unlike bacteria, and they’re generally pathogenic – we don’t have ‘good’ viruses as we have good bacteria. They can live outside of hosts for a limited period of time – hence the need for hand-washing and general cleanliness. Viruses in general may take a variety of shapes and sizes, ranging from the recently-identified DNA-based pandoraviruses at 1000 or so nanometres (1 micrometer) down to 20 nanometres or less. As to coronaviruses in particular (the largest of the RNA viruses) their structure and their ‘spike proteins’ will be glanced at in the next post.


Written by stewart henderson

February 9, 2020 at 12:27 pm

some more stuff we’ve learned about vaccines

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Vaccinology, I would say that it’s not rocket science. It’s a lot harder than rocket science.

Alan Schmaljohn, virologist, 2014


Canto: So, reading The Vaccine Race, by Meredith Wadman – maybe we should just do book reviews? – I find myself getting excited, or confused, by a passage, and wanting to do more research, and then forgetting about it…

Jacinta: It’s probably pretty normal to forget 95% of what you read within a week or so of having read it. You just hope the things you retain are the principal things.

Canto: Yeah well, I was probably hoping the book would help me get my head around how vaccines work, as well as providing juicy and inspiring tales of heroism and malpractice in the history of vaccine development, and it has helped, but I think I’d need to read half a dozen such books and watch a dozen videos before it penetrated my thick skull…

Jacinta: Yes, for example, when I found myself reading, well into the book, about Leonard Hayflick’s human diploid cells, taken from the lungs of an aborted foetus, which were used to provide a sort of base for creating vaccines against all sorts of diseases, most notably rubella, I thought ‘obviously the author has explained human diploid cells, probably in great detail, before, but I can’t recall a whit’…

Canto: That’s what comes of reading too many books at once, and spreading your focus. You know it’s a myth that women can multi-task better than men, but the major finding of research is that multi-tasking is bad for everyone. Let’s resolve to read books one at a time, from start to finish.

Jacinta: Resolved. Anyway, diploid cells are just standard human cells, with 23 pairs of chromosomes. The only other human cells are haploid sperm and eggs, with 23 unpaired chromosomes. Hayflick’s cell line, gathered in the fifties, was ‘cleaner’ than the cells previously used from other animals, such as monkey kidney cells, which contained many viruses. I used the index.

Canto: So these cells were taken from the lungs of a foetus, and Hayflick was able to produce a cell line from them, that’s to say a line of almost endlessly reproducing cells, I’m not sure how that worked, but these cells, which had to be free of every virus or pathogen, would then be somehow injected with, say, the rubella virus, in some sort of reduced form, so as to produce antibodies in those who are vaccinated. The trick with vaccinology, it seems, is to produce a safe vaccine with no side effects, or minimal side effects, but with enough potency to produce a reaction, thus producing antibodies to the antigens in the vaccine. The vaccine must contain antigens, must have some potency, otherwise it’s useless. And every immune system is subtly different, so producing a one-size-fits-all vaccine is in many respects a monumental undertaking. I may have this completely wrong by the way.

Jacinta: Probably only partially wrong, let’s not be absolutists. What about this difference between killed vaccines and live vaccines. Can we talk about that?

Canto: Well first I want to understand how a ‘cell line’ is produced. How were Hayflick’s famous WI-38 (human diploid) cells produced in a constant stream from the lungs of a single legally aborted foetus in 1962?

Jacinta: Let me try to summarise Wadman’s description of the process from this online article. The tiny lungs were minced up and then placed in a container with a mix of enzymes that separated them into individual cells. These cells were separated again into small glass bottles, and a ‘nutrient broth’ was added, causing the cells to divide. thus began the most thoroughly described, studied and utilised human cell line to date, from which was created vaccines for rubella, rabies, adenovirus, measles, polio, chicken pox and shingles.

Canto: A nutrient both? You mean ‘at this point a miracle happens’?

Jacinta: Well, this was a well-established miracle, only previously it was done with non-human cells, and still is. Monkey and canine kidney cells, chicken embryo fibroblasts, hamster ovary cells… Of course using human cells was bound to be controversial.

Canto: So – obviously the cells in these tiny lungs would’ve gone on dividing had the foetus survived, so microbiologists had worked out a way, of making this happen – mitosis, isn’t it? – outside the host. How long have they been able to do this?

Jacinta: Well the first vaccine was created by Edward Jenner in the late eighteenth century, but they weren’t actually culturing cells then. Cell culture is a broad term meaning a process of growing cells – obviously by cell division – outside of their natural environment, usually in a lab. A cell line (e.g. Hayflick’s WI-38 cells) is ‘a population of cells descended from a single cell and containing the same genetic makeup’, to quote Wikipedia. Cell culture started with the maintenance of cell tissue independent of the host animal in the late nineteenth century, but techniques advanced rapidly in the 1940s and 50s to support virology and the manufacture of vaccines. A key event was the growing of poliovirus in monkey kidney cells in 1949, for which John Enders, Tom Weller and Fred Robbins won the Nobel Prize. Their methods were used by Jonas Salk and others to produce the first polio vaccine.

Canto: But the problem with using monkey kidney cells was that they potentially carried their own viruses, right? Which may or may not be harmful to humans, and how would they know? Without using human guinea pigs?

Jacinta: Human subjects, yes. And there’s also the question of the potency of the virus being used, presumably to stimulate the production of antibodies. Is it just a question of stimulating enough antibodies? And isn’t there an obvious danger of infecting subjects with the virus itself? Presumably a killed virus solves that problem, but is it really effective?

Canto: Yes, Wadman’s book has been fascinating on the politics of the vaccine race, but I’m still left much confused – probably due to stupidity or inattentiveness – as to how some vaccines work better than others, and how a cell line – I know it’s essentially about exponential growth – can produce enough material for millions of vaccine doses.

Jacinta: Yes it’s about exponential growth, and it was once thought that, given the right conditions, these cells could go on multiplying ad infinitum, to immortality so to speak, but it was Hayflick who showed this not to be true in a much-cited paper. Even so, the number of replications of individual cells assured a sufficient supply of cells for generations. And since then, much more has been discovered about cell ageing and its causes, what with telomeres and telomerase, but that’s another story. As to why vaccines developed from the WI-38 cells have been so much less problematic than others, it clearly has much to do with their being ‘clean’ human foetal cells, with no other lurgies lurking.

Canto: So let me get this clear. The WI-38 cells are provided to different labs that are wanting to create a vaccine for, say, measles. Or that have already created a vaccine, or at least have isolated the virus – but then of course viruses can’t be isolated, they need cells to survive in. So they get the WI-38 cells, and then they inject them with the virus – killed or attenuated – and then they start trialling it on rats or mice or something, trying out different strengths of the virus, without really having much idea whether the dose will translate to humans, so they must find some willing volunteers (or, in the early days, orphaned or intellectually disabled kids) to experiment on, making sure they err on the conservative side initially, then upping the dosage? I’m no doubt simplifying and speculating wildly here.

Jacinta: yes and I’m no wiser  than you, but it’s a good thing we have people taking these risks, and working so hard in this field –  with clearer ethical guidelines than before – because millions of lives have been saved by vaccines, and so much has been learned about our immune system in the process of developing them.


Wadman, Meredith. The Vaccine Race. Doubleday 2017.

Written by stewart henderson

June 11, 2017 at 7:39 pm