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Communicating on Covid-19 Again December 27, 2020

Posted by mwidlake in COVID-19.
Tags: ,

New Variant & impact on NHS->>

<<- Start of Original Post beginning in March 

After quite a break, I’ve decided to return to converting my notes & thoughts on Covid-19 and SARS-CoV-2 into blog posts again, but I’m going to do so in a slightly different format. Why am I returning to blogging on the topic? Well, people do still keep asking me what is going on and I’ve mostly been answering on Twitter or Facebook (or in person on the rare occasions I meet people!), but I don’t feel Twitter and Facebook are particularly good forums for explaining things. And writing it down in a way I feel someone with a little bit of scientific understanding can understand helps me understand and, more importantly, makes me check the scientific output to try and make sure I am right.

As for the different format, I’m going to do shorter, less comprehensive posts. This is because when I did this last spring/early summer I would spend a week doing a post that I thought would take a day and, by the end of the week, some things were changing and the post was just too loooooong.  If you feel something is missing from my future posts or you have any question a post prompts, please ask. If I can I will try and answer, or at least point you in the direction of a scientist or similar expert saying something about it.

On the subject of expertise, as anyone who has followed my blog knows I am a computer person (I specialise in the performance of Oracle databases). As ever I am going to stress that I am not an epidemiologist, not a virologist, and I have no medical qualifications. I have never been a working scientist (closest I got was I did a summer as a volunteer in a genetics lab before my final year at university, I mutated moss). What I do do is look at the output of scientists who communicate on Covid-19. I only listen to scientific and medical output. I do look at what the UK government says but I don’t see their briefings as a reliable source. This is not due to conspiracy theory, it’s more that (a) the UK government does not have a good back history of actually ‘Following The Science’ as they keep claiming (b) their job is not to explain stuff, it’s to get the population to do what they want them to do and yet remain as popular as they can (c) when a minister or one of the experts on the public briefings do explain something, they have to keep it simple and short.   

Given I am not an expert, why do I think I can explain to you what is going on? Well, I have an ancient degree in genetics & zoology and I’ve maintained an interest in science all my adult life. I’ve worked (developing computer systems) in or alongside the UK NHS for 7 years, in biological academia (mostly ‘the human genome project’) for 7 years, so I have a lot of experience in communicating with medics and scientists. For the last 15 years I have presented at conferences (and I get good speaker scores), written articles, done the odd webinar, and produced this blog. So I have experience of communicating what I do know to an audience.

If you want a refresher on Covid-19 (what it is, what it does to you) there are endless resources out there, but This summary I wrote back in March is still mostly relevant and it is interesting to see the predictions I made and which were right and wrong. Spoiler, I’m pretty good at saying how things will go for a few weeks (as are millions of others), I’m not so good beyond that, so I’m leaving that to the epidemiologists!

I’m hoping to put out my first real posts on the current situation on Covid-19 in the UK over the next couple of days, but I wanted to mention what is really concerning me and what helped prompt me to dig back into the scientific details again.

Long term – I’m really hopeful.

One thing I was wrong about was how long it would take to create a vaccine that was safe and gave good protection. I’ve never been happier to be wrong!

It’s a testament to the long hours and days of work of thousands of scientists, the worldwide sharing of information between scientific groups, the funding made available to them by governments & charitable bodies, and the efforts of the regulators & pharmacovigilance experts working to ensure Due Diligence in compressed timescales – i.e. that the vaccines are proven safe.

We have three vaccines in the West that are approved or close to being approved over a growing number of countries – 

  • BioNTech/Pfizer and Moderna/NIAID that use the new mRNA-based methodology. They need to be kept very cold (minus 70C and minus 20C respectively) but are approximately 95% effective,
  • The Oxford University/AstraZeneca vaccine which is a more traditional vaccine that uses a modified, harmless adenovirus and is less effective (work still being done on how effective: 60-90%?) but does not need to be frozen and so is much, much easier to transport.

Many more vaccines are still in development. Having a set of vaccines will be a real boon as, for example, the Oxford/AZ one will be a lot easier to administer in warm countries lacking in ultracold-chain facilities, but where such infrastructure is present, we can use the more effective vaccines.

Gary Myers corrected  my information on how cold the two mRNA vaccines need to be kept and pointed me to this article by NPR

Nine months ago I would have been overjoyed for a single vaccine that was 75% effective by the summer of 2021, so to have three by the end of the year and more on the way is fantastic.

But it is a massive logistical effort to roll these vaccines out and the impact on the spread of Covid-19 and our lives will evolve over the next 12 months. For the whole globe we are looking at 2 years probably and I am sure there will be bumps along the way, such as one of the vaccines proving to be not very long lasting so re-vaccination is needed for some.

One thing I want to point out is that there have been over 1/2 a million 5 million people inoculated (wow, that’s shot up so quickly) to date with very, very few contraindications (things going wrong) reported. I am not aware of any life-threatening reactions to the vaccines to date but they protect the vast majority of people from a life-threatening disease.

You can track world numbers for vaccinations at this “ourworldindata” site. I have not looked at it much myself yet but it certainly seems to give you the key information.  

Short term – I am very worried

I was already concerned that world figures for cases & deaths continue to rise, the figures in the UK are constantly going up, and yet more and more people seem to be wanting to believe there is no problem. And now we have new variants of Covid-19 that spread more easily, both in the  UK and across the globe.

In summary, as some of you will be aware, we have a new, more contagious, variant of SARS-CoV-2 in the UK, which is most prevalent in the South of England. It appears to spread a lot more efficiently than other versions and it has worried the scientific community. For once, the UK government actually responded very quickly to this change and they “cancelled Christmas”, put the South East and London effectively into lockdown and soon after announced many other areas would go into the new Tier 4 the day after Christmas. (To be clear, many scientists had already called for the proposed relaxation of social distancing for 5 days over Christmas to be abandoned and replaced with tighter controls, based only on the growing case figures – which Boris Johnson and his cabinet seemed set to ignore).

With the new information about the new, more virulent variant of SARS-CoV-2, many countries have stopped flights to/from the UK or brought in stricter checks and/or rules on isolating people arriving from the UK. France closed their border with the UK preventing (amongst other things) any lorry freight (as people drive the lorries). This island became pretty much isolated (and people started worrying about getting fresh salad, which tells you a lot about some people’s priorities).

Cases of C-19 in UK Regions since August

It seems some people think these national and international restrictions were brought in simply because the number of cases of Covid-19 in the UK were escalating quickly, but it was this new variant that has mostly worried other countries.

The graph is from an excellent twitter thread by Christina Pagel, based on official UK government figures. It shows how the last UK lockdown had the intended effect of suppressing Covid-19 in most areas, reducing the number of people affected by the disease (unlike the regional tier approach which had struggled to really reduce transmission). However, look at the black East of England, orange London and green South East lines. The lockdown had less effect there and by the end of lockdown cases were rising in these areas. Why? It could have been more testing being done (so you see more cases) or people ignoring the rules, or something else. It turns out it was something else, this new variant. Correlation is not causation, but the percentage of people with the new variant of SARS-CoV-2 is much, much higher in these areas. Lap tests have shown the new variant latches onto ACE2 proteins, it’s door into our cells, more efficiently.

At the moment there is no evidence that this new variant is any more deadly or makes people sicker, or that it means the vaccines that are currently being rolled out will not work against it, but time and more study will tell.

C-19 patients in English hospital 14/12. It will increase.

So why is this new variant a worry? Because if this new variant is spreading more easily (and the figure quoted by the media is “70% faster” but I’ll dig into that in a later post) it means the number of people who are ill will double much more quickly – and we are in real danger of flooding the NHS with ill people. All along, since this new disease reared its head, the overwhelming of healthcare systems has been the main worry, much more than the actual raw number of people it will kill and harm. That is what all that talk about flattening the curve was about in March & April, spread the people getting sick over a longer period so at no point do you run out of hospital capacity. The more infectious version of Covid-19 is pushing up the curve, and threatens to do so very significantly.

The graph to the left is for hospital beds occupied by Covid-19 patients as of Christmas Eve – the latest day we have figures for as I type. They are only just below the April high. In Wales, for which we only have figures up to the 22nd December, bed occupancy greatly exceeds the spring high. I am sure that if we have not already exceeded the previous national high for hospital bed occupancy UK-wide then we will in a very few days and it will get worse, as people catching the disease over the last week or two get admitted. Cases precede hospital admissions precede number of deaths.

The new variant is most common in the South East, East and London areas of the UK, but it is present across the whole of the UK. (In Wales there appears to be slightly different more-contagious version of SARS-CoV-2 but again for a later post.)

Here in the UK we are in for a rough ride and the government is going to have to bring in more restrictions to try and keep this new variant under control. 

New Variant across the world

What about across the world? Well this new variant is already present in many countries. It might have originated in the UK, it might not, this is still being investigated. The reason we do not know for sure is that the UK sequences a lot more SARS-CoV-2 samples than other countries, so they might not have spotted what we did. Again, I plan to expand on this in a later post.

The new varient, B.1.1.7, has been seen now in France, Netherlands, Singapore, Italy, Israel, Denmark, Australia. The list will grow daily.

I’m afraid the genie is out the bottle and, much as we saw with the original spread of Covid-19, with international travel and it having got out before we could close borders on it, it is probably inevitable that this new variant will take over in all countries where SAR-CoV-2 is spreading.

In South Africa there is yet another more virulent strain, with some of the same mutations the new UK strain has, which seems to have arisen independently. I have no idea why more than one highly virulent strain has occurred in relatively close temporal proximity (same time) in different locations, it is probably just bad luck. Genetic mutation is random and directionless (well, with a few odd exceptions that as far as I know do not apply here). This other new strain is known as B.1.351

Both variants can be tracked at this site, which is where the image to the left is from. Updates are a little slow at the moment due to the time of year but, even with it being Chistmas, the people behind the site have added more information. Scientists, nothing stops them for long.

I think we are at a crucial point:

  • Vaccines are on their way and that is brilliant.
  • World wide we were already struggling to keep the Covid-19 situation from getting worse.
  • The new variant(s) are increasing the spread rate, possibly significantly.

Despite my reputation for it this year, I don’t like being all doom & gloom, but I feel right now like I did at the end of February/start of March. Very anxious about how this is going to play out for so many people, especially those who (for whatever reason) have decided Covid-19 is being blown out of all proportion or is not going to impact them.

I cancelled Christmas before the government did, it was not wise to go see my mother and brother, even though we all keep ourselves fairly isolated and take all the proper precautions. I think no matter what, for the next 6 months until the vaccines are making more of a difference (and by this I mean reducing the stress on the NHS by protecting those most likely to get critically ill, as opposed to herd immunity), I’m going to be a hermit, read books, sort out the garden, and keep watching what the scientists say.

I think Christina Pagel summed it up perfectly:



1. oraclebase - December 27, 2020

RE: “Genetic mutation is random and directionless”
True, but it’s too simplistic a statement, especially for people not versed in population genetics, who don’t understand selection pressure. When dealing with such short generation times, directionless mutations with suitable selection pressure can give the outward appearance of very directed mutation. Like everything in life, there is a lot of nuance. I know you know this, but I’m not sure people outside of this do. Sorry for being a bit of a dick about it. 🙂



mwidlake - December 27, 2020

True Tim, plus (as you know) are the impacts of Founder Effect, selection mountains, Genetic Drift, epigenetic factors giving space to true genomic changes, Hopeful Monsters (so hated by Dawkins) and many others – but all of them only make sense if you have a grounding in genomics which even the generally scientifically informed may well lack, as those factors are so Genetics specific (and I would say my personal current knowledge of those areas is equally too weak to rely on – this stuff changes so fast).

2. Gary Myers - December 28, 2020

The Moderna vaccine only requires regular freezer temperature, not the minus 70 needed for the Pfizer one.


mwidlake - December 28, 2020

Ahh, my mistake Gary and thanks for the correction (and link). I’ll update the post. When both vaccines were initially announced they both said -70 but Moderna then found -20 was enough for their vaccine.

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