Doesn’t it just drive you mad! Just as we are beginning to understand the dynamics and spread of the Delta variant, along comes another variant of concern which could change the whole picture.


Omicron has more mutations that anything we seen up till now, 50 in all, and 32 of those on the Spike protein, the viral key which opens the locks on the membranes of our cells and against which much immunity is targeted. Many have been seen before, though not all on the same virus, and some are completely novel. This map highlights the difference on the now all too familiar spike protein.

Delta vs Omicron – quite a difference.


A likely hypothesis is that in South Africa there are many people with poorly treated or untreated HIV/AIDS. They have compromised immune systems which can take longer to clear viruses. Thus COVID19 as longer incubation times and this increases the opportunities for successful mutations to occur. Ideally, of course, anyone with such vulnerabilities would be a priority for vaccination, but I’ll bet there is a direct association between poor HIV treatment and low rates of vaccination. Quietly, away from the glare of the worlds attention, 680,000 people died of HIV last year. Needlessly.

Among all the current uncertainties, it is certain that the mutation occurred in just one of these poor people who could have been infected for weeks before succumbing or recovering. So out of this grim global inequality emerges the latest, and significantly different variant. International air travel does the rest. Bad human behaviour all round.

Winter woes

The progress of the Delta variant is already causing problems in the northern hemisphere as we begin our winter experience, with Christmas – the biggest spreading event imaginable – not far away. With scant lockdowns and far less restrictions, it has spread widely and those with no prior immunity are suffering in particular. Those with prior immunity have to wait for their T and B cells to kick in, before which, infection does get a start and causes, generaly, a less severe illness. My hopes that Delta was the worst that Sars-Cov-2 are not quite dashed, but definitely wobbling.

Three questions

Transmissibility? It already looks as if the new variant will be more transmissible. Hopes that its spread will be contained are quixotic, even with reduced flights from South Africa.

It is not so much shutting the stable door after the horse has bolted, but more like realising the door was open all the time and the horse is long gone.

A ban on all flights and international travel would be needed to have any effect – and this is in effect, being trialled in Israel and Japan – but experience has shown that even that causes mere delay. Every time I tune in it has spread further and Im sure we will now see it battling it out for dominance against Delta. So the evidence from its lightning spread around the world suggests that is is more transmissible. The Delta – Omicron battle is on!

Who wins will become more clear in the next few weeks with our incredible new capabilities for genomic testing. We are pretty good at staying one step behind the virus, even if, right now, the virus has leapt a few steps ahead. Conveniently, the PCR test can also hint at the variant’s presence as it is “S-negative”. Like the Alpha variant, it gives a false negative for the S gene aspect of the PCR’s three targets and will this be able to show how it spreads.

Virulence? Optimism suggests that those folk in South Africa whose infections led to the R0 being calculated at 2 were out and about more because they felt less ill. This is the experience of the South African doctor who spotted the first clusters. Countering that is the likelihood that the first cases were younger and possibly spending more time outside in the less inclement South African weather. We shall soon find out as the real world data rolls in. As I said, we will not have to wait long.

Evasion of immunity? This is the big question. The effectiveness of vaccines or previous infection does wane, at least in terms of the neutralising antibodies they generate and also their protection against infection. Beyond that is T and B based cellular immunity which continues to be effective at preventing severe illness. Thankfully, they are not wholly dependent on the configuration of the spike protein, so there is real hope that the protection they offer will continue. The boss of Moderna, who should be in the know but also perhaps biased by the profits from having to re-vaccinate the world, thinks there will be a material difference in vaccine responsiveness. Markets have fallen in response.

It is reasonable to hope that most of us will have some defences against Omicron, and these are a whole lot better than none. Indeed, well over 90% of people in the UK have some antibodies to the previous variants.

Thankfully, anti-virals are not far away, though Molnupiravir is having some big doubts cast on its side effects and safety. By the new year there may be options there to back op the vaccines preventative power.

The almost utopian hope is that a far more transmissible variant could outpace and replace the Delta variant and be less virulent even if it does partially evade previous immunity. Then infections would rapidly spread but not cause increased severe illness or clog up the NHS and other struggling global health systems. Once again we are in the lap of the gods.

What to do:

Revisit my advice regarding prehabilitation, and get as fit as you can before coming across the virus, which is likely to happen some point or another.

Make sure your Vitamin D levels are high, at this time of the year by taking supplements as the sun, so low in the sky, will generate little as it hits our much covered skin. For me it is almost madness not to be supplementing with Vitamin D as its lack is one of the most easily corrected risk factors for infection and illness.

Getting vaccinated and boosted continues to make incredible sense. Back out with the masks, and some degree of social distancing. Surely plan B is worth dusting off, but the government are, as usual, waiting until it is too late to be of benefit.

A recent meta analysis of the evidence has shown that mask wearing makes a significant difference as does social distancing and hand washing. Suddenly these simple habits matter more. The authors conclude:

This systematic review and meta-analysis suggests that several personal protective and social measures, including handwashing, mask wearing, and physical distancing are associated with reductions in the incidence covid-19

Big issues.

International air travel has once again been demonstrated to be a big killer. Not only in terms of air pollution, unsustainable development and its hugely underestimated impact on the climate, but also its ability to spread pathogens. For these and more reasons, I would love to see the airlines go bust, one by one until they are almost all gone, leaving a rump industry to cater for those who need to travel to see loved ones and for essential business only.

With COP26 come and gone, our addiction to flying seems to be untouched. Flights from the UK to Spain can be bought for less than £20 and the myth of combating climate change while continuing with mass air transportation persists.

Humanities daily flight map

We need a sea change in the international order when it comes to health. In the West we have become complacent about HIV as it is treatable. Yet 680,000 people died from HIV or its complications last year. Our human neglect of the less well off in the world is now bouncing back to make our wealthier lives far more difficult and is a startling demonstration of how far behind the science are our politicians. This have been mirrored in our hoarding of vaccines, with some being shipped to distant shores within weeks of their expiry date, leaving them unusable

We were lucky with SARS 1 – it no longer exists. SARS2 will be here for ever. We might get lucky with this variant, we might not. Either way, we are living in a new world which demands new ways of doing things as a global community; as a species. We cannot have a future with unabated climate change, or continued massive mis-spending on weapons, we cannot have a future with wealth cascading into ever fewer pockets. All our resources need to be applied to the task of global gardening – caring, tending, working hard to improve the environment before the chance slips away.

If we don’t change, the forces of nature, of which COVID19 is a gentle example, will change us. Nature, we should remember, is utterly indifferent to our fate.

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