a bonobo humanity?

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

Posts Tagged ‘omicron

omicron omicron omicron

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So I haven’t written about Covid for some time, and it hasn’t gone away, though I’ve managed to avoid it myself. I’m recovering from a bacterial infection which played havoc with my bronchiectasis, and had me coughing and sneezing so much that I felt for a few days that my usually life-saving course of antibiotics, together with steroids, wouldn’t be enough. I asked for a referral to a pulmonologist/respiratory specialist, but discovered that, due to Covid, they’re almost impossible to access. Anyway, I’m on a puffer and on the mend.

So according to worldometer’s coronavirus website, which I’ve regularly used, there have been about 6 and a quarter million deaths from Covid19, but the latest New Scientist podcast (118) informs me that there have been nearly 15 million deaths. That’s a huge discrepancy, and I suspect these rubbery figures will be a feature for years. What’s certainly true is that the various forms of this virus are going to be with us for some time. The latest Omicron sub-variants emanating from South Africa, BA.4 and BA.5 are still being monitored for their infectivity. Omicron in general (first discovered in Botswana) is a variant of concern, which has led to a new spike in cases, but it generally appears to be less lethal, though whether this is because most people, here in Australia at least, have been immunised, I’m not sure. Anyway, winter is on its way here, and I’m a bit worried. New covid cases are up by 127% in the USA in the last month, with hospitalisations up by 28% according to their ABC news. Omicron is mostly the culprit. Numbers are probably under-reported because effective testing has gone out the window. They’re testing waste water to measure the prevalence. In New Zealand, the Director-General of Health is warning of a new winter peak. Case numbers have bottomed there at a higher level than expected, and are now slightly on the rise. And of course not all cases are being reported, which would be expected with mild cases. In fact the DGH suggests that might amount to about half the cases. Influenza A is also on the rise there.

Omicron reproduces in the airways much much more rapidly than previous variants so it will pass quickly between people before they even know it, plus the mutation upon mutation will probably have rendered previous vaccines, and the antibodies they produce, less effective. Its precise infectiousness is hard to calculate because so many who are infected either aren’t aware of it or don’t report it. Animal studies of Omicron are showing that it goes into the lung less readily than previous variants, which is a relief to me at least, and probably a relief to most. But we shouldn’t describe it as a mild variant. There’s also the long Covid issue, which, being long, will take a long time to get a handle on. And there’s also the unvaccinated, who are more likely to be hospitalised. Of course, if you survive infection this will boost your immunity in future, at least for that particular variant. But it may well be the case that the virus will become endemic, that it’s on its way to being so.

It’s worth knowing some of the terminology regarding viruses and their mutations. They mutant constantly of course, though not always viably. Viable mutations will mutate further, and once they’ve gone further from the original they’re classed as a different lineage. That’s steps away from being classed as a variant, which is a lineage that has enhanced capability of infecting and causing damage to hosts. Omicron, because of its increased infectivity, is producing more lineages, and subsequently more variants. So we’re seeing reinfections, almost regardless of vaccination – depending no doubt on number and timing of vaccinations. The situation in South Africa is being watched, because they seem to be ahead in new infection rates. But there are concerns everywhere – at the end of April a new Omicron sub-variant, BA 2.12.1, was found in wastewater here in Australia (in Victoria). It’s deemed more transmissible, but no more severe, than previous variants. It should be noted, though, that influenza viruses still mutate more than four times faster than these Omicron variants, on average. However, some variants seem to have a brief ‘sprint’ period of high tranmissibility. Also, variants can arise through recombination. This appears to have occurred with the Omicron XE variant, the result of ‘two omicron strains merging together in a single host and then going on to infect others’. The genes of one variant can combine successfully with another infecting the host at the same time, and then spread to other hosts. There’s also been a ‘Deltacron’ recombinant variant.

Some 60 mutations have been identified since the original SARS-Cov2 virus was detected in Wuhan. 32 changes in the spike protein have been identified. This is the protein that attaches to human cells, and has been the principal target of vaccines.

The latest worry is the Omicron BA.4 and BA.5 sub-variants, which ‘threaten to trigger a new wave of COVID-19 infections in South Africa’, according to the VaccinesWork website, but the good news is that antibodies produced by those who had been vaccinated against COVID-19 were more effective than those from people who had recovered from natural infection. Vaccines work indeed. Still, the number of cases are rising. It may be due to waning immunity or increased infectivity or both. We can only continue to monitor the situation – it’s certainly not over yet. What an incredible journey this has been, and the fallout from reduced food production and other economic constraints is another problem for the future.






Written by stewart henderson

May 15, 2022 at 4:36 pm

stuff about Omicron

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testing queue in New York, early December

Canto: So we seem to be getting good news about Omicron from the researchers, even if it’s been rather muted by the media, the intermediaries between the research and the public. Of course, since there’s still something out there that’s highly transmissible and generally treated as SARS-CoV2, the deadly virus that’s killed almost 5.5 million people (according to data that’s only as reliable as its sources, which would be highly variable…

Jacinta: We’re using the worldometer covid-19 statistics, which has a very slightly higher death toll than the WHO. The Johns Hopkins death toll stats are also very similar, slotting between WHO and worldometer.

Canto: … and since we’ve been living with this deadly virus for almost two years now, everybody’s pretty spooked about new variants, as well as exhausted by all the lifestyle disruption – which for some is the least of their worries.

Jacinta: Yes, they might be mourning the death of loved ones or living with the after-effects of infection. But here in Australia we’re very low in the number of cases – 82nd in the world – and even lower in per capita death rate, at 168th. Currently we have just over 115,000 active cases, but just over 0.1% are described as serious or critical.

Canto: Well that massive gap between case numbers and serious, hospitalised covid-19 sufferers seems to be a story of Omicron.

Jacinta: Yes, looking at yet another data source, Our World in Data (all these sites can be easily googled), we can see graphic proof of Omicron’s rapid spread.

Canto: Yes, this scenario has been more or less duplicated in South Africa, the UK, just about everywhere that Omicron has taken hold. But it’s a very different beast from previous variants, and this post is an attempt to comprehend that more fully.

Jacinta: You jokingly referred to it at first hearing as the Omygod variant, but we’re thinking about it very differently now. But before we get into amateur microbiology, there are other stats to mention. As of 4 days ago, December 27, over 77% of Australia’s covid19 cases were Omicron, compared to 13% two weeks before, on December 13. It will surely be over 80% now. It is displacing the Delta variant, and the importance of this development can hardly be understated.

Canto: So we need to understand Omicron fully, or as fully as we can given our General Ignorance and the fact that research is obviously ongoing.

Jacinta: So this variant, which appears to have first sprung to viral life in Botswana, has mutated much further away from the original or most thoroughly spread early strain of SARS-CoV2, and this appears to be to our advantage. We’ve been following Dr John Campbell’s own analysis of data coming from South African research…

Canto: As well as watching the Medcram series of videos, designed, as the title suggests, for medical students of epidemiology, virology and such, but in terms even we General Ignoramuses can understand. Dr Roger Seheult has made over 130 of these videos, and we’ve watched over 100 of them, so hopefully it’s all in our heads somewhere.

Jacinta: Omicron appears to be so different from previous variants that it’s like a different disease, or perhaps we might say, a different condition. Obviously it’s spreading very fast, with an r number of between 3 and 5, but that number may already be out of date. And the rapid spread appears to be due to the way it affects the upper bronchi. Here’s the low-down from the University of Hong Kong’s faculty of medicine.

The researchers found that Omicron SARS-CoV-2 infects and multiplies 70 times faster than the Delta variant and original SARS-CoV-2 in human bronchus, which may explain why Omicron may transmit faster between humans than previous variants. Their study also showed that the Omicron infection in the lung is significantly lower than the original SARS-CoV-2, which may be an indicator of lower disease severity.

Canto: Yes, that indicates that this variant is very different. Geneticists have long been analysing differences in the variants, especially changes to the spike protein, but apparently the Omicron variant has about 20 mutations outside the spike gene, which may have a variety of impacts on our immunity. Researchers are scrambling to study all the mutations to see how they reinforce or counteract other mutations.

Jacinta: There’s been a focus for some time now on a viral protein called ORF9b, which is a mitochondria-targeting immunosuppressant. Clearly we’ll be in over our heads if we’re not careful here, but having read the abstracts of various research articles, what I’ve found is that ORF9b ‘immediately accumulates and antagonizes the antiviral type I IFN [interferon] response during SARS-CoV-2 infection on primary human pulmonary alveolar epithelial cells’, to quote from one article.

Canto: But Omicron, I’ve read, isn’t so much getting to those alveolar epithelial cells. Faster in airways, slower in lungs is the populist version. Or to be more ‘precise’, 70 times faster in upper airways, 10 times slower in lungs.

Jacinta: Well, slower doesn’t mean never. And this variant may well vary… none of this is predictable, which is why I tend to be more sympathetic than many to public health spokespeople and politicians as they try to give the best advice and develop the best policies for public safety.

Canto: The way it works in the airways helps to explain Omicron’s extreme transmissibility – we’re breathing and coughing it out all the time when we’re infected. They say we’re all going to get it, so the choice might be permissibility – let it spread and get it over with – or caution – flatten the curve with a tightening of mask-wearing, with better masks, and physical distancing, and boosters.

Jacinta: I don’t think too many governments will go the permissive way – everybody’s too spooked by this pandemic. And I notice that most media outlets are almost delightedly reporting on the huge spike in covid cases, without too much nuance. And of course there are people with comorbidities and weakened immune systems that would be put at risk.

Canto: But the spruiking of vaccines and boosters, and the lack of advice on prevention and general health, is striking. Pharmaceutical companies are making huge amounts of money in this period. The Biden administration is paying Pfizer $5 billion for their new covid pill, for example. I haven’t forgotten my reading of Ben Goldacre’s Bad Pharma. I wonder what he’s thinking of all this. 

Jacinta: To be fair, the pharmaceutical companies and the research virologists have been amazing in what they’ve come up with to meet the crisis. Surely it’s the so-called ‘vaccine hesitant’ sector, the numbers of which have grown so alarmingly, that’s the biggest headache at the moment. Who’d of thunk that a virus that’s killed five and a half million and counting, and which has produced record-breaking responses in life-saving immunological technology, would lead to an outbreak of anti-science fanaticism?

Canto: Mmmm. Having met people in the teaching profession who’re convinced that the moon landings were a hoax, and that the September 11 attacks were an inside job, I have to wonder. It doesn’t seem to be a lack of basic education. There’s a strange willingness to think in contrarian terms, for some. It doesn’t seem to be group-think either, and yet… they couldn’t have come up with these notions themselves, they must have been somehow captured, ideas-wise.

Jacinta: Anyway, I think we’re in an interesting phase of the pandemic. Optimists are calling it the beginning of the end, while others are cautiously watching the relationship between cases and hospitalisations and deaths over the next few weeks. Currently, the figures are totally confusing. Australia has seen a massive spike in cases, and a small increase in deaths over the past few days. In Russia – and I don’t much trust figures out of Russia, obviously – there have been about half as many cases over the same period, but more than a hundred times as many deaths! Presumably they’re still dealing with the Delta variant, but who knows – it’s hard to find figures connected to variants.

Canto: We’re having problems with outbreaks in remote indigenous communities, with low immunisation rates and probably low rates of previous covid infections. It makes me think, probably too dramatically, of how smallpox hit the indigenous community here when it was brought over by Europeans a couple of centuries ago. The Europeans had some immunity, but it was new to the Aborigines, otherwise noted for their health and fitness. About 70% of the indigenous population that was exposed died, in horrific circumstances.

Jacinta: Yes, that’s a bit dramatic, but an important lesson about the dangers of exotic pathogens. Our immune system can’t be prepared for everything that’s out there.

Canto: Omicron also seems to be infecting young children much more than any previous variant, partly because they haven’t been vaccinated as much, but there might be more to the story. In any case, it seems that, though there is ‘immunity escape’ with Omicron, vaccines appear to offer greater protection than previous infection, so again it’s the unvaccinated that will be hardest hit. And I’m at last getting my booster tomorrow. Yay!

Written by stewart henderson

January 3, 2022 at 4:15 pm

Posted in covid19, omicron

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