omicron omicron omicron
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.
References
https://theconversation.com/whats-the-new-omicron-xe-variant-and-should-i-be-worried-180584
https://www.gavi.org/vaccineswork/five-things-weve-learned-about-ba4-and-ba5-omicron-variants
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