• Infection rate in the UK is falling after our third wave, but globally Sars-Cov2 continues to spread with little slowing of the worlds death rate.
  • Significant new mutations have occurred in the UK, South Africa and Brazil. It is likely there will be more. Is COVID19 still one step ahead?
  • Two new vaccines have shown effectiveness against new strains and are awaiting approval. 
  • Herd immunity look increasingly unlikely without vaccination.
  • Vaccines need to be shared so that all countries can vaccinate at risk groups and key workers at about the same time. Otherwise travellers need to be quarantined.
  • The aim of low infection rates and high levels of finding testing tracing, isolation and support to control outbreaks is the holy grail and could be achieved this summer. 
  • Society will not be the same after the pandemic has settled. Nor should it be.


It’s already a very odd year and its only just begun! We have good news with the third wave on the decline, yet there is a lack of optimism that we will soon be back to anything like normal. Perhaps passing the sad milestone that 100,000 people in the UK have lost their lives means that it is rather too late for optimism; damage limitation is now the name of the game.  

This is a pandemic like no other – never before have we all been able to observe the course of a global infection unfold and intervene with treatments and prevention (vaccines). One thing is sadly unchanged – like all the pandemics before it seems that misinformation and disinformation is just as common as ever – just with the rocket boosters of technology.

With with vaccines and viruses competing for the attention of our immune systems, let’s have a January round up….

Winter wave

Will lockdown sceptics please now eat their hats? (They won’t) Our winter wave, part one and two, both seem to have been responsive to restrictions of human and thus viral spread, as well at least in part fuelled by their premature festive relaxing. Thankfully we are now on the downslope with daily reductions in cases and peaking of admissions and deaths.

The second wave has been blamed on our new variant yet is certainly at least in part due to our usual slow political decision making and typical Boris befuddlement over those belated Xmas restrictions. The experts warned us that here would be a price to pay after Xmas, and so it turned out. Experts are generally expert! They can take a horse to water……

Locally. Here in Devon, Derriford hospital has caught up with the rest of the country in terms of having wards full of COVID patients and busy ICU’s. They are looking after over a hundred COVID19 patients; that is three wards full of patients with an illness that didn’t exist just over a year ago. Thankfully, flu is at very low levels right now – a side effect of less human to human contact and a better vaccination campaign.

Derriford Hospital C19 Admissions

As workload increases and resources are diverted to caring for patients with COVID it inevitably means reductions in resources available for non infectious patients, and potential delays with diagnosis of cancer in particular. 

Health care staff are struggling with the relentless nature of admissions and for them spring must seem a long way off. The thought that one all this is over, there will be a huge backlog of work to catch up must be morale sapping. This is not helped by the fact that delays will often mean late, more complex and sad to say, less effective treatment for some. 

Pandemic pain is many faceted. It’s not going to be an easy year for anyone working in the already stretched health sector, nor anyone with complex requirements for healthcare.

Our first three waves.

Nationally, we are the first country to pass the 100,000 milestone yet there is optimism that the fall in infections since the lockdown and consequent reductions in hospital admissions will soon lead to less need for intensive care beds and then less deaths. 

Given the average length of stay in hospital is about 17 days, there is a long way to go before we get back to 1:1 care on intensive care and so the Government are not promisng anything with respect to releasing lockdown measures anytime soon.  

Just as well! Their history of over promising and under-delivering was getting a tad repetitive. I now expect to see admissions slowly falling though it is too early to feel that is due to vaccination whose effect will hopefully build with time from, well, about now. The average age of admission is just about 60, and so the ‘average’ patient will not have been vaccinated as yet. 

Cumulative global deaths

Globally, the pandemic continues unabated. There have been 100 million cases, over 2 million deaths and the situation in many nations remains one of widespread infections.  The global situation remains as gloomy as the graph (left) shows. 

In the Americas in particular, deaths seems to be continuing at high levels and it seems that any hint on our own natural immunity ending the pandemic seems a long way off. 

This raises the issue of how pandemics end. I shall write more on this shortly, but summarise it to say that it seems we are striving to stay one step behind viral behaviour and evolution. It is horribly interesting and a very rapidly changing situation. 

Is Sars-Cov2 still one step ahead?

Early on after the emergence of the pandemic, I read that Sars-Cov2 was a relatively stable virus with a low rate of mutation. This is because it has genes for correcting errors in the mistake prone process of viral replication – its own genetic spellchecker. 

Yet the astonishing spread and sheer numbers of virus particles replicating globally means mutations are inevitable. This might be due to long illnesses in vulnerable people, giving the virus lots of time to mutate, and medical treatments such as convalescent sera which can give resistant viruses a free hand. Hopes that the pandemic would melt away under the heat of our own immunity and vaccination seem to be fading away like the recent Dartmoor snow.

Mutations are usually only significant in that they help track the evolution and spread of a virus, but are now changing its behaviour, leading to higher viral loads and possibly more deaths. Significant variants have evolved in South Africa (B1351), Brazil (P1), California (CAL20C) and of course, we led the way with our own temporarily world beating B117. If you want a look at 3D images of the mutations then look at the amazing GISAID mutation dashboard

Just as I finish writing this post, sad but unsurprising news is emerging that there is now community spread of the South African variant in the UK. It seems that 1,000 cases have been identified and 10% of them have no know South African contacts. This represents a failure to protect our borders with adequate quarantine. It really is one cock up after another. While Susan Hopkins from PHE hopes it can be contained, Im sure she must realise that it is too late. This genie is out of the bottle. I await similar news regarding the Brazil P1 variant. 

Pfizer and Moderna have done the lab work, testing sera from vaccinated people and testing them against the new strains. This showing their vaccines are active against the UK

Covid’s Spike protein

variant, but Moderna have found a 6 fold reduction in neutralising capacity against the South African B1351 – still enough to do the job they say, but hardly good news. 

The latest vaccine to arrive from Novovax also reports a reduction in efficacy against the South African and by implication, the Brazilian variants. 

They state this is still enough to provide an effective vaccine response judging by antibody levels and hope for a significant T cell response to the new mutations induced by vaccination will help also. We shall see. 

Behind all this lies our failure to control the spread of the virus by isolation and quarantine. UK surveys suggest that only 1 in 5 people  are able to isolate properly, and this is 3 times worse in those earning under £20,000 a year. Failure to manage infections in crowded households also plays a part in our hideous winter experience. Once infections are at high levels then lockdowns are needed, but avoiding them demands doing the basics better. 

Leading the way in the simpler task of vaccination should not camouflage the basic failure of pandemic management. Finding, testing tracing isolation and support can be done well, and we have done it terribly.  Does this mean that we arriving at herd immunity by the back door? 

What of herd immunity?

The reality of herd immunity through infection is emerging through the mist. Of 11,000 UK health care workers with evidence of infection in the first wave, none have had infection in the second wave, though better PPE might play a part in that. In another study, previous infection gave a protection rate of 90%. 

31 cases of re-infection with COVID19 have been recorded worldwide and all but two of them milder. So it seems that immunity to COVID has lasted this long, so far so good – but in the Americas, the emergence of variants might change all that. 

The Brazilian situation is a horror story based on politicians ignoring health experts. After little by way of attempts of reduce viral spread by restrictions, they had a significant first wave of infections in May which overloaded their health sector. 

Subsequent high levels of antibodies (60%) in the Manaus population were thought to be sufficient to induce herd immunity. This was seized upon by the scientifically illiterate President Bolsonaro and appeals from public health experts to introduce restrictions in the Autumn as cases reappeared were again ignored. 

Vaccines needed for herd immunity

The result? In a population of 2.2 million in Manaus, they have had 250,000 cases and 7,000 deaths in their new year summer wave. Even that is likely to be an underestimate due to poor public health infrastructure. It is the sad cost of unfettered end of year celebrations.  

As a consequence they are having a torrid time and demonstrating to the world what an overwhelmed health system looks like. Hospitals are unable to provide oxygen for patients and relatives scramble to secure supplies in what must be terrible situation with barely effective medical care and high mortality rates from infection. 

It seems the overwhelming wave of cases is due to a variant which has clearly escaped any immunity generated by the first wave. There has already been a cases of the Brazilian variant in eight countries including the US and its global spread seems likely. That might be the end of hoping for herd immunity and a return to the labs for the vaccine builders.

This hints that we might have to get used to the idea of being one step behind the virus, like flu, though with a more dangerous infection and regular updates of vaccines on a never ending production line one step behind viral evolution. 

This is not the normal evolutionary path of viruses. Left to their own devices, they tend to become more transmissible and less deadly. Now treatment and medical care for individuals who may be infected for some time encourages mutations and unprecedented travel accelerates spread. 

If we are lucky and get a more transmissible virus which is milder, then we can add it to the lengthening list of viruses which give us mild illnesses, like cold. If we are unlucky, then the more pathogenic Brazil strain will become dominant and we will have more waves to deal with.

Vaccines to the rescue!

On the positive side, there are two new vaccines in the pipeline with Novovax hitting the headlines and now with the regulators. They uses genetically engineered moth cells to make spike protein which is then combined with an adjuvant in a vaccine which is stable in common fridges. The efficacy numbers are interesting:
  • 95% against the previous UK strain
  • 86% against the new UK strain
  • 60% against the South African strain.
Johnson and Johnson have used a technology similar to Astra to make a single shot candidate with a 72% reduction in US cases in the treated group, though again, with less effectiveness against the South African variant (57%). So its hardly surprising that they are testing to see is a second dose will improve effectiveness and if this, as is likely, happens, then it will lost its “single shot” selling point. 

Thankfully, like the other vaccines they seem to reduce the risk of significant illness needing hospital care even more than the reduced level of infections which have to be the end point of trials. Yet with viral evolution is talking place before our eyes viral ‘immune escape’, the viral version of antibody resistance, will remain a threat. Booster jabs may well be needed.

Meanwhile, our vaccination programme is racing ahead, only behind Israel in terms of the race to the front. Corners are being cut once again, and the decision to concentrate on giving as many people the first jab by delaying the second is a moot point – some scientists agree, others point out that we are now in a foggy zone when we dont quite know where we are heading. Both have a point of course. Astra Zeneca and their Oxford colleagues seem bullish on this point – delay might even be an advantage – but right now it can’t be proven.

Vaccination in the real world

We are still in the honeymoon period of vaccination against COVID19. Right now it is understandably popular. It should be. 

Yet, like any medical intervention, there will be side effects and anti-vaxx websites like Mercola and many others will hunt for these and magnify their significance to further their own agendas. Some of their anti-vaxx claims are becoming nonsensical and even George Monbiot is beginning to think that anti-science should be controlled. He is right – vaccine lies cost lives. 

Anti-vaxxers at work!

Success of any vaccines means as the illness recedes from view the side effects hog more of the headlines and this can only be countered by careful science and education – reason is not a strong feature of social media. In preventing illness for some by vaccinating the very many, vaccines can be victims of their own success. Nothing new there.

Much vaccine hesitancy of course has its origin in distrust of government, currently and understandably running at high levels. This particularly affects the BAME community who would paradoxically benefit most from the vaccines protection. 

The social inequality driving this distrust is getting worse, so this problem is not going to go away unless trust can be established! The fact indeed, that the over 80’s are being targeted for the vaccine means that more well off sections of society are getting vaccinated first as there are less 80 year olds in poorer areas where people generally die far younger. Social inequality is hard wired in our society. 

Doctors will be critical to counter vaccine hesitancy, as this post from the front line shows, but we all need to do our bit to combat on line nonsense. I will post on this in more detail next month. 

Again, vaccination is not a matter of purely individual risk, it benefits everyone with whom we have contact. There will be issues of course as to how unvaccinated individuals will be treated when it comes to work and for instance, attending a football match along with tens of thousands of others or traveling on public transport. For now it makes sense to vaccinate our at risk and key workers, including teachers and other key groups. 

The WHO have asked us that once we have vaccinated our at risk groups and key workers, we hold it there for a while to ensure vaccine supply to poorer countries who desperately need to catch up. Will this biologically sensible request overcome the political reality of our leaders basking in the early success of vaccination programme? 

Hogging vaccines is wrong!

That we in the UK have ordered 375 million doses rather begs the question of just what we plan to do with them all? The resultant spat with the EU has not done the bloc proud! Border closures were never going to work for anyone, but it does reflect a frustration that vaccine nationalism if alive and strong in the UK, pre-ordering many more vaccines than we need is simply a mistake.

Given also that mutations are occurring all over the world, once key sectors have their jab one nation leaping ahead of the rest simply makes no practical sense for anyone. It seems me that we either agree to help vaccinate the world, or we make everyone coming into the country quarantine for two weeks. That is the only other way of keeping new variants developing in other nations out. And to keep ours in. 

What next?

All crystal balls are by their nature foggy. Yet is seems that we are on a roller coaster of infections rising as lockdown is eased and vice versa. Will this continue? Seasonality undoubtedly plays a part, we did after all, have quite a low infection rate last summer, but the Brazilian and South African experience of a summer wave gives cause for concern that COVID19 will not behaving like ‘normal’ seasonal flu.

Undoubtedly there are aspect of our society which will be forever changed. International travel will never be the same, mass gatherings like festivals likewise seem a long way off – Glastonbury have decided to throw in the towel early – rightly so. The balance between risk and benefits of what we do has changed and I cannot see it returning to pre-COVID levels. 

This virus has the capacity to mutate and jump one step ahead of our best efforts to catch up. We will always be seeing what happens and then trying to deal with it. Thanks to science, we do have the capacity to make that step smaller and smaller.


So until the spring, Im sure restrictions will continue in one form or another, masks in public places become the norm, social distancing will continue to be a part of our day to day way of living for some time.

Yet there remains an achievable holy grail – that we will arrive at a level of infection low enough to mean that new cases can be dealt with by finding, testing, tracing, isolation and support – then outbreaks can be snuffed out without excessive restrictions. We had that chance in the summer and failed to understand or rise to the challenge. 

The Holy grail = low levels of infection

COVID has made it self evident that need more funding of public health and health care. Vaccination programmes are expensive and essential. So too are public health teams and the support needed to contain new waves, new mutations and indeed new pandemics in our crowded world with all levels and forms of life competing for space. 

To achieve this will need new thinking on the part of politicians, particularly conservatives. Economists will have to scratch their heads while mulling the new certainty that we cannot afford not to increase public spending. Austerity simply did not work and will not work in the post COVID future.

We must begin to think about how different a post COVID world will look. To me, it is looking very different from that from what we leave behind. We will either “build back better”, or have to contemplate, as we have glimpsed with health, what failure of society looks like. That is beyond words.

11 thoughts on “January Update – vaccination, immunity and the world.

  1. Thank you for writing this piece, which I read thanks to a share from Mr SteveB; it seems insightful and balanced. I’ve enjoyed your overview of the current situation and look forward to reading more of your posts in the future.

  2. Thanks for this Colin, a great read and some very important messaging, especially on vaccines. Hope all is well with you,

  3. Thank you for writing this piece, which I read thanks to a share from Mr SteveB; it seems insightful and balanced. I’ve enjoyed your overview of the current situation and look forward to reading more of your posts in the future.

  4. Thanks Steve, Ive haven't put much energy into 'marketing' the blog so thanks for sharing it. Interesting times. Ii do think the pandemic will change history, rather like the Spanish Flu did in 1919. There are so many bigger problems looming! Hope you are both well x

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