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Posts Tagged ‘vaccines

Is/was the Covid 19 pandemic overblown?

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Jacinta: So clearly Covid-19 fatigue is becoming a worldwide phenomenon, and I’m not talking about long Covid. Mask-wearing here in Australia has reduced almost to pre-Pandemic levels, and I’m beginning to hear more claims that it was never really that much worse than the flu, and that the world has suffered more from lock-downs and other restrictions than from the virus itself. This is a bit shocking, so it’s time to evaluate these claims, for what they’re worth.

Canto: Well we haven’t been keeping tabs on this lately, but in the first year of the pandemic we regularly visited the Johns Hopkins and Worldometer sites to keep track of the global and nation-by-nation statistics on SARS CoV-2. Returning now, I find that Worldometer provides an overall death toll so far of a little over 6.7 million. The Johns Hopkins Coronavirus Resource Center has almost exactly the same figures…

Jacinta: And how does this compare to flu figures? Someone asked. 

Canto: Actually, this is not a simple question. For a start, people may die with a particular illness or infection but not necessarily of it. And death certificates can often be ambiguous on this matter. This also allows ‘Covid skeptics’ – and there have long been plenty of them – to distort the figures any way they can. Death certificates are used by the UK’s Office for National Statistics:

The ONS uses data from death certificates to count deaths from Covid-19 and all other causes. This is distinct from public health measures, which include deaths within 28 days of a positive Covid-19 test. We use the term ‘due to Covid-19’ when referring only to deaths with an underlying cause of death of Covid-19. When taking into account all of the deaths that had Covid-19 mentioned anywhere on the death certificate, whether as an underlying cause or not, we use the term ‘involving Covid-19’. This is also the same for flu and pneumonia. 

Jacinta: Yes, this is good policy, as it puts Covid-19 and flu etc on the same footing. But mightn’t it be the case that, due to the prevalence and greater public face of Covid-19 in these times, medical authorities would be more likely to attribute cause of death to Covid-19 than to anything else, just because the patient tested positive? I mean, why test for anything else when they’re sick and Covid-positive? 

Canto: Hmmm, well why indeed – if they’re sick and have the symptoms of Covid, trying to reduce those symptoms would be the medico’s first duty. After all, Covid-19 is a far more deadly disease than flu.

Jacinta: But not everyone agrees, apparently.

Canto: Yeah, and not everyone agrees that the Earth is an oblate spheroid – so what? You asked about deaths from Covid v flu. Looking at the data from the UK is a good idea, because both the flu and pneumonia are more prevalent there than in Australia. 

Jacinta: And yet interestingly the relaxed restrictions and reduced mask-wearing that occurred from mid-22 resulted in our worst – most deadly – flu season in five years. Influenza was considerably reduced in Australia in the winters of 2020 and 2021, obviously due to those restrictions. 

Canto: Well we’ve asked, by someone sceptical of the fuss and perhaps the over-reaction to this pandemic, to look into it more deeply, though this is probably a task way beyond our powers. We’ve been given a reference to start us off, an essay by John Ioannidis, a professor of medicine, epidemiology and population health at Stanford – at least he was at the time of writing the essay, back in March 2020, only 2 months into the pandemic. 

Jacinta: Yes I remember there was something of a furore around this essay, a lot of blowback as the Yanks say. I never read it, but we did do a lot of reading and listening vis-a-vis SARS-CoV2 in the first months of 2020. 

Canto: That’s right – the Medcram coronavirus updates, delivered by Dr Roger Seheult and designed, as the name suggests, for medical students, were always our first port of call. I watched over a hundred of them on YouTube, and educated myself pretty well on the structure of the virus, its method of action within the body, from the lungs into the epithelial tissue and the bloodstream, the ensuing cytokine storm, and of course the method of transmission from person to person. It was quite an education. 

Jacinta: When Ioannidis wrote his piece there were 68 recorded deaths from Covid-19 – according to his own figures. 

Canto: yes, here’s a quote from the essay: 

Some worry that the 68 deaths from Covid-19 in the U.S. as of March 16 will increase exponentially to 680, 6,800, 68,000, 680,000 … along with similar catastrophic patterns around the globe. Is that a realistic scenario, or bad science fiction? How can we tell at what point such a curve might stop?The most valuable piece of information for answering those questions would be to know the current prevalence of the infection in a random sample of a population and to repeat this exercise at regular time intervals to estimate the incidence of new infections. Sadly, that’s information we don’t have.

Jacinta: And Johns Hopkins puts the total number of US deaths from Covid-19 at 1,097, 660, as of January 10 2023 – far worse than Ioannidis’ most catastrophic scenario. And yet, Ioannidis has never backed down from the claim that the world is over-reacting. One has to wonder how many people would have to die before he changed his mind. 

Canto: Maybe he wants to argue that many of these people didn’t ‘really’ die of Covid-19 – that they would’ve died anyway. Now that’s a hard thing to prove. We all die, after all. 

Jacinta: And interestingly, the USA’s death toll is about 16% of the global toll, though the USA has only about 4% of the world’s population. Does this mean the USA’s response has been a big failure, or are they attributing more deaths to Covid-19? 

Canto: The USA has suffered way more deaths from Covid-19 than any other country, and it jumped to the lead very early on. In that period there was huge criticism about how the Trump administration had gutted the CDC and the FDA, and of course Trump’s response to the outbreak was to mock mask-wearing and to compare it to the flu – ‘it’ll be gone in weeks’. That’s when his approval rating – already much lower than his disapproval rating – really tanked, and he started talking – in April – about the November election being rigged, but only if he lost!

Jacinta: Well some thugocracies like Russia and China can’t be trusted on their figures, but getting back to Ioannidis, in his March 2020 essay, he seemed to be concerned more about the under-estimation of figures rather than the opposite:

Given the limited testing to date, some deaths and probably the vast majority of infections due to SARS-CoV-2 are being missed. We don’t know if we are failing to capture infections by a factor of three or 300. Three months after the outbreak emerged, most countries, including the U.S., lack the ability to test a large number of people and no countries have reliable data on the prevalence of the virus in a representative random sample of the general population.

Canto: Yes, and the ability to test clearly improved in most developed countries over time, but Ioannidis still wasn’t satisfied. And how do you measure a country’s ‘ability to test’? Clearly you can’t force everyone to be tested – not even the Chinese Testosterone Party can do that – because they’ve allowed too many people to exist. Even a ‘no child policy’ would take too long to improve the situation, they need another Mao-style ‘great leap forward’ to do the job. But that only killed 70 million at most, a mere drop in the bucket…

Jacinta: Yeah well, back to the topic. Ioannidis talks about an ‘evidence fiasco’, but surely he’s being unrealistic – we could never expect to test everyone, and so of course plenty of unsymptomatic carriers, especially the young, would pass through the net and unsuspectingly pass on the virus. That’s why physical distancing and mask-wearing became a high priority as we learned how the virus was being transmitted. 

Canto: Of course it must be remembered that Ioannidis wrote this essay (referenced below) at the very outset of the pandemic. Even so, his predictions were way off. He projected case fatality rates from the Diamond Princess outbreak onto the general (US) population:

Projecting the Diamond Princess mortality rate onto the age structure of the U.S. population, the death rate among people infected with Covid-19 would be 0.125%. But since this estimate is based on extremely thin data — there were just seven deaths among the 700 infected passengers and crew — the real death rate could stretch from five times lower (0.025%) to five times higher (0.625%).

Please note that Ioannidis’ projected worst-case scenario, adjusting for the higher age range of the Diamond Princess crew, was 0.625%. According to the latest figures from Johns Hopkins and the WHO, the USA’s current case fatality rate is about 1.1%, almost twice Ioannidis’ worst case projection. Of course, Ioannidis can’t be blamed for his under-estimation in the early stages of the pandemic, but it’s rather surprising that he hasn’t modified his views in line with ongoing evidence. So, unfortunately, he has become a beacon for contrarian views about the impact of and response to Covid-19. Even the highly-regarded Scientific American magazine defended Ioannidis in a brief November 2020 article that it later apologised for as an ‘opinion piece’ containing a series of factual errors. 

Ioannidis doubled down on his claims of an over-reaction to the pandemic, appearing on various news networks throughout 2020 to express caution and to question the measures taken to prevent spread, but he was arguing against a growing consensus. The Washington Post put it this way in December 2020, after a terrible year in the USA:

… as the pandemic enters its deadliest phase, Ioannidis is losing the argument over how to combat covid-19. Among epidemiologists, consensus now exists that it was inaction, not overreaction, that helped create the worst public health crisis in a century. The uncontrolled spread of the virus has led to overrun ICUs in South Dakota and makeshift morgues in Texas. States and countries are locking down in a bid to preserve lives as vaccines start to roll out. Even Sweden, which resisted tough restrictions through the spring, is now reversing course to avert catastrophe.

So, of course we can’t compare what happened with restrictions, lockdowns and mandatory mask-wearing with what might have happened had we continued with business as usual and relied on herd immunity (that’s to say, the development of natural immunity without vaccines), but it’s surely worth listening to those who work in the field of virology and immunology. And within those circles there appears to be broad agreement. Here’s what the Mayo Clinic has to say:

There are some major problems with relying on community infection to create herd immunity to the virus that causes COVID-19:

  • Reinfection. It’s estimated that getting COVID-19 results in a low risk of another infection with a similar variant for at least six months. However, even if you have antibodies, you could get COVID-19 again. Because reinfection can cause severe medical complications, it’s recommended that people who have already had COVID-19 get a COVID-19 vaccine.
  • Health impact. Infection with the COVID-19 virus could lead to serious complications and millions of deaths, especially among older people and those who have existing health conditions. The health care system could quickly become overwhelmed.

Vaccines

Herd immunity also can be reached when enough people have been vaccinated against a disease and have developed protective antibodies against future infection. Unlike the natural infection method, vaccines create immunity without causing illness or resulting complications. Using the concept of herd immunity, vaccines have successfully controlled contagious diseases such as smallpox, polio, diphtheria, rubella and many others.

I should also add that the pandemic, for all the suffering caused, has led to a marked improvement in the time-frame for effective vaccine production, and of course a breakthrough in the form of mRNA vaccines, which has been something of a revolution in immunology. 

I’ve not properly answered the question – are there more deaths from flu than from covid? A 2021 article from the British Medical Journal answers precisely that question, again quoting the ONS:

Data from the Office for National Statistics show that in England and Wales the number of deaths from influenza was 1598 in 2018 and 1223 in 2019. This is way below the annual deaths from covid-19, which at the current rate of around 800 deaths a week in England and Wales equates to more than 40 000 a year.

That’s a huge difference, despite all the caveats mentioned above and repeated in the BMJ article. But unfortunately people will believe what they want to believe. 

References

A fiasco in the making? As the coronavirus pandemic takes hold, we are making decisions without reliable data

https://www.scientificamerican.com/article/the-ioannidis-affair-a-tale-of-major-scientific-overreaction/

https://www.washingtonpost.com/dc-md-va/2020/12/16/john-ioannidis-coronavirus-lockdowns-fox-news/

https://www.bmj.com/content/375/bmj.n2514

Americans who turn to the White House for coronavirus news tend to think the media’s pandemic coverage is overblown

Written by stewart henderson

January 13, 2023 at 1:08 pm

A coronavirus update: new variants

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Everyone wearing a mask in this Tokyo airport, but still there are lots of problems, and lots of travellers

So there’s much concern about new variants of the SARS-CoV2 virus, one from the UK, now known as the Kent variant, and one from South Africa. My main source of info on this will be the SGU podcast 809, from January 6.
The Kent strain is more infectious than the original, by 50-60%, though not more deadly. However its infectiousness is fast making it the more dominant strain. The South African variant, though, is causing most concern, as virologists are uncertain about its response to the vaccines now available. It has some of the same mutations that are in the Kent variant, making it also more infectious, but it also has mutations that allow it to evade antibodies targeting previous variants. This won’t make the variant immune to the vaccine, but it will make the vaccine less effective, though exactly how much less effective is the big question currently.
Another major concern is that this new variant can infect people who’ve already contracted and recovered from the virus. As Dr Steven Novella and others on the podcast argue (and this quote is ‘tidied up’ from direct speech):

This is the result of allowing a pandemic to simmer along over time. Mutations are inevitable, though different viruses mutate at different rates. SARS-CoV2 has error-correction mechanisms when it replicates, so that’s why it mutates more slowly. But if an infection in an individual, or an epidemic, lingers long enough, you’ll still get mutations. Part of the problem is that, with so many people infected, for so long, there are a great number of opportunities for new variants to arise. There are thousands of roughly equivalent variants, which are neutral or inconsequential in effect, but now we have two variants that are more mutated, and more consequential. They have a suite of mutations that seem to have developed much faster than the background mutation rate of the virus. It’s thought that this is because in individual patients who’d had the infection for months and were being treated during that time, the increased selective pressure on the virus may have caused this suite of mutations to be formed. This kind of mutation rate has been shown in the lab with respect to antibiotic resistance in bacteria. 

The point here for the future is to get to a level of herd immunity through vaccination. Considering that new strains arise regularly, as with the flu (and we don’t yet know how regularly this will happen with SARS-CoV-2), it may be that the vaccine will have to be tweaked regularly to cover these new strains. Time will tell, and of course we don’t yet know how effective the new vaccines will be against these current major variants. In fact we don’t know for sure how long the vaccines, or the antibodies they create, will be effective, regardless of these variants. But mRNA vaccines can apparently be produced, and tweaked, quite quickly, once the variant’s RNA is sequenced.

All of this tells us that the science is generally on top of this. The major problem is political, and social. Trying to get people to do the right thing, to wear a mask, physically distance, avoid large indoor gatherings and to get vaccinated when the vaccine becomes available. This is easier in some regions of the world than in others, and the problems ranges from distrust or ignorance of modern science, to conspiratorial thinking, to rights over responsibilities, to cultures of compliance and non-compliance. Humans are delightfully diverse, or just a mess, and the WHO warns us that this may not be ‘the big one’ in pandemic terms. The year 2021 will not see the end of all this – far from it. 

Stop press – a new variant has just been found in Japan in four travellers from Brazil, the Sydney Morning Herald reports. Twelve mutations have been identified, one of which is shared by the UK and South African strains, suggesting a higher infection rate. The travellers are in quarantine in Tokyo airport. Due to a steep rise in cases, a state of emergency has been declared for Tokyo and surrounding prefectures. And so it goes.

Reference

https://www.theskepticsguide.org/podcasts

Written by stewart henderson

January 11, 2021 at 10:47 am

more on rapid antigen testing, and the vaccine race

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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.

Written by stewart henderson

December 9, 2020 at 5:44 pm