The end game?

I’ve been distracted by the storm blowing over a formerly glorious oak, taking down with it the overhead cables supplying electricity to my and 52 others homes. That has blown over now, unlike the crisis in the Ukraine. There, festering European conflicts continue to signal our ability to act for the global good has not moved on much after all the lessons of the pandemic. Speaking of which…

With restrictions melting away after the Omicron wave’s decline, hope that we might be finally heading towards the end of the pandemic has to be balanced against the global reality of how viruses and our immune systems behave. I have to wonder what living with this new coronavirus with all its future variants might entail.

In some ways we have already been ‘living with COVID’ for some time with restrictions in the UK being light touch since last year and now mass testing set to end. Meanwhile, the virus has been busy…..

The Omicron extended family

Evolution doesn’t stand still and is at its most rapid in the world of viruses. There is an ‘Omicron Plus’ already out there which is called BA.2, with all of BA1’s mutations plus 6 more plus 3 deletions, with three of these on the critical Receptor Binding Domain. There are now 1000 BA.2 cases in the UK and counting. So what does this mean?

This variant is more transmissible than the original BA1, though its too early to say if it is more harmful. Early experience suggests anyone infected with BA.1 or boosted with vaccines will almost certainly be protected against harm from BA.2, but there is uncertainty. The latest mutation has nipped off the remaining effectiveness of antibody cocktails given to prevent illness in the vulnerable. Before the ink is dry on this page, along comes BA.3 whose impact remains to be seen: the image below sums up the situation:

A look at Hong Kong shows that SARS2 can still pack a punch for the non immune and make the provision of heath care tricky. There, vaccination rates are relatively low particularly (40%) in the elderly, and the resulting hospital chaos show that Omicron can still cause much misery. Hong Kong’s zero covid approach has saved lives over the last two years, but the resulting complacency regarding vaccination and increased infectivity of the new variant is sufficient for patients in hospital beds to be overflowing into car parks. Without some degree of immunity, Omicron is still a nasty illness for many.

More widely, cases have rocketed peaked and are now falling over most of the world, and thankfully without overloading health care systems with all the knock on effects on anyone needing help with health issues.

Infection after infection….

As well as vaccine escape, reinfections are far more common now with Omicron. Most will be mild, many unnoticed. Reports suggest that reinfections with alpha gave people symptoms only 20% of the time, whereas delta reinfections caused symptoms in 44% of cases and now omicron in 46%. Early scare stories about subsequent infections being worse than the first, due to the Antibody Dependant Enhancement seen in Dengue fever, have thankfully not been seen with COVID either after vaccines or infection.

So is this really the end?

However badly managed in England, (Plan B for “Belated”) the decline in case numbers is good news. The WHO’s Europe director, Hans Kluge said “It’s plausible that the region is moving towards a kind of pandemic endgame.” Soon, he added, soon 60% of Europeans will have been infected with Omicron and so we will move towards a quieter year with high levels of immunity and the summer season. Others in WHO used the more sensible, term “truce”.

As shown by BA.2, the virus continues to evolve so who knows what is around the corner. I think the pandemic might be called ‘over’ one day, but endemic diseases are hardly fun. We will have to deal with variants which will emerge and spread rapidly as air travel resumes and will continue to pose a threat to the vulnerable. Early treatments and targeted vaccination campaigns are likely to be a key in helping there. Effective anti virals may make the need for lockdowns a thing of the past. We shall see.

Evolution again

Here, I have to correct myself. Earlier in the pandemic I learned that viruses tend to evolve into milder strains – that seems to have been the case with Omicron, though not with Alpha or Delta. It seems viruses only evolve to be more transmissible. That is what makes them ‘win’ their evolutionary race; how dangerous they are is a matter of chance as with a long incubation period almost all of their spread takes place before they kill their host.

So, we have been lucky with Omicron. As I have posted before, I do wonder if mice are helping. The virus might well have hopped over to them, evolved into something quite different and hopped back. If this is the case, then it almost certainly will happen again. House mice live in relatively isolated communities and so serious illness might well wipe out colonies and end there. Milder variants could spread more widely and be more likely to reinfect a human being somehow somewhere. Thats my optimistic evolutionary theory.

Pharma and infections disease.

There is another problem in the pipeline. Antibody cocktails manufactured antibodies, used so far for the vulnerable are now pretty much useless against BA.2. Governments who have signed contracts for these will take some of the financial hit, but leaves the problem of who will invest in the development of antibiotics and antivirals in the face of rapidly mutating foes which leave expensive products on the shelf?

The answer, rather like vaccines, lies in the public sector. Unless there are ways of sharing the risks then this critical area will not be seen as lucrative and yet more people will die of resistant bacterial as well as viral infections. This will have to be managed in terms of some kind of public indemnity and might, hope against hope, mean that while profits are made, not the obscene financial killings which sadly with COVID seems to have happened.

Avoiding infection and Long COVID

In the background are the needs of those with ongoing symptoms from the infection. Viruses can cause a host of long term effects. My own MS for instance, is increasingly believed to be a long term consequence of Glandular fever caused by the Epstein-Barr Virus. Spanish flu had long term effects on the brain and lungs. Covid is not alone in causing long term effects, but they do seem more common.

Another problem is the big increased risk of an array of mental health problems, opiate use and cognitive decline in the year after infection with COVID, including those not admitted to hospital. The authors conclude:

“People with covid-19 show increased risks of incident mental health disorders (eg, anxiety disorders, depressive disorders, stress and adjustment disorders, opioid use disorders, other (non-opioid) substance use disorders, neurocognitive decline, and sleep disorders) compared with contemporary controls without SARS-CoV-2 or historical controls before the pandemic”

This another reason why I am keen to avoid the infection altogether if possible. If I can’t, and it increasingly seems inevitable that we will all come across it, then it looks as if the vaccination will be helpful in steering me away from long covid. Those vaccinated with two doses reduced their risk of long COVID when infected by half and this adds to the benefit of the reduced risk of getting infected at all.

Testing – throat not nose for Omicron

The LFT’s on which much of the data now depends, while accurate if positive, give high false negative rates. In other words, they miss many cases. To boot, they are performing worse with the new variant. It seems now that unlike Delta, Omicron is better swabbed from saliva . So it you really want to know, take a throat swab instead.

So how well are vaccines doing?

The graph below shows from the regular vaccine surveillance how Omicron has outsmarted our vaccines, with the AZ effectiveness at preventing infection dropping pretty much to zero against Omicron and just about 50% for Delta. The booster bumps this back to 40% with the Pfizer and 60% for the more potent Moderna. This is disappointing, but a whole lot better than nothing. Importantly, if you don’t get the infection, you cant pass it on, so vaccination will still reduce transmission – critically important for the vulnerable.

Effectiveness is likely to drop further with time, but that does take us beyond the Omicron wave, so it might be seen as having done its job.

And what about serious illness,

Here, the vaccines are doing very much better, as this table shows:

The bottom line is that vaccine effectiveness, though waning against any infection, is 83% effective at keeping us out of hospital and is expected to reduce the risk of death by more – though for Omicron, the data is still in the pipeline.

Natural versus unnatural?

With the non-immune occupying disproportional numbers of COVID beds in hospitals right now, can those with immunity can somewhat relax? I dislike the dichotomy between natural or vaccine based immunity.

The difference is between ‘natural’ immunity provoked by the infection or the vaccine. Both seem to lead to at least some degree of long term cell based immunity which prevents severe illness in those with decent immune systems, but don’t provide the neutralising antibodies needed to prevent infection in the long term. If they, and all the infections we face did this, our blood would be as thick as treacle. Rather like a house containing every newspaper you have ever read.

Vaccination might be less effective than we would like right now, but reinfections, that is, infection of those who have already had COVID19 are running at 15% of the total, meaning that immunity against infection declines with time after a dose of COVID19. The REACT study highlights that two thirds of people with Omicron say they have been infected before, so immunity from ‘natural’ infection, like vaccination, wanes with time. There have been 500,000 or more of these since counting began.

What next?

As I have said before, this mixture of viral evolution and immune development harks back to a coronavirus called OC4, derived from the deadly Russian “Flu” in the 19th century., and now one cause of the common cold. Like that pandemic, SARS2 is likely to come back with further variants and further waves which will infect us every few years. Hopefully they will be milder, but clearly there will be problems is they are not.

The duration of our long term immunity lasts will be the key. The two opposing forces of waning immunity to severe disease due to time, and increasing population immunity from a steady rate of background infections, plus topping up of up to date vaccines for those who need it will determine how things play out.

We now live in pandemic prone world, with lightening spread of any new variant or virus

Meanwhile, the protests in Ottawa seem to be heading for their next phase, whatever that might be. The protesters and the lorries are being removed to leave the city centre once again to shopper, residents and the vast bulk of the 1.2 million Ottawan residents who voted with their feet and had nothing to do with it. Lessons there too. Human unity is a myth testified to by deadly inequalities as well as the face off in Canada as well as in the Ukraine.

Relief at this truce with SARS2 is palpable, but its descent into complacency could be the worst enemy of learning vital lessons from the pandemic. We have got used to so many things which are unsustainable. One generations glorious Freedoms will seem to another like grim irresponsibility.

Disaffection with the powers that be have manifested themselves in a way that was bound not to be tolerated. I can’t help but think we need to be more adept in communication about what is needed and why and that in this modern world, even taking 90% of the people with you can still lead to big problems which need to be addressed by governments which have often been elected by a much smaller chunk of the population.

If you have got to the end of this post them well done and thank you.

As ever, any comments or questions will be answered as soon as I can, just leave them in the comments box at the end and for now, I wish you the best of health!