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Sourdough – Creating The “Starter” December 18, 2020

Posted by mwidlake in Baking, off-topic, Private Life.
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2 comments

Making and Baking A Sourdough Loaf –>>

A couple of people have asked me to describe how I create the Sourdough bread that I often tweet about baking. It’s too much for a Facebook post, and waaaay too much for a twitter thread, so I’m putting it here on my blog. This is part one – you need something called a “Sourdough Starter” to make sourdough bread, this is how I create my starter. Part two will describe making an actual loaf of sourdough.

Nothing much beats a sandwich made with home made sourdough

I know this is seriously off-topic for a blog that is supposed to mostly considers Oracle tech & performance, working in Oracle/I.T, and thoughts on IT management & how people work, but let’s face it – the more semi-retired I get the more this blog is becoming somewhere I simply share “stuff”. However, there is a bit of a link. Over the last few years baking bread has been taken up by a surprising number of people in the Oracle Presenting sphere (and this pre-dates the craze for making your own bread that came with Covid-19). One presenter, Jože Senegačnik, even wins national awards for his bread in Slovenia.

What is Sourdough?

Sourdough is a rustic type of bread, usually white, with a dark, thick crust and usually more flavour than a standard loaf of white bread. I know I am biased, but the sourdough bread I make is about the nicest bread I have ever eaten (with perhaps the exception of the bread of some of my other baking friends). It is certainly nicer than your average loaf and better than “normal” bread I have made at home.

Sourdough bread has an open texture (lots of holes), so it is quite light and, at the centre, soft. Sometimes the bread has large voids in it. If you buy sourdough in a shop or it is part of a meal in a café/restaurant (it’s almost always the bread used in posh cafes with your smashed avocado and free range egg for breakfast) it seems to me that the posher the place, the larger the voids. Sometimes a slice of sourdough toast can be more void than bread. It does not need the large voids and, in my opinion, they are detrimental to the bread. You can’t make a sandwich or put anything on the bread without the contents falling through the big holes! It’s fine with soup & stews I suppose, where you are dipping chunks in liquid.

Sourdough is a type of wheat-based bread where instead of using dried yeast or fresh yeast that comes in blocks that look like soft cheese, you use an active, growing “porridge” of yeast. This is a fairly thick mixture of strong bread flour and water, with the yeast growing in it, slowly consuming the flour to produce more yeast.

big voids to lose your topping through…

This “porridge” is called the Starter, and you add it to a mixture of more bread flour, water, and a little salt, to make your bread dough for baking. The starter smells quite strongly, distinctly sour, and I suspect (but am not sure) that sourdough bread is named more for the smell of the starter than the final loaf, which only has a hint of the smell if any at all.

The bread itself also has a distinctive tang to it, not as marked as the smell of the starter mixture, but it is a key part of the flavour.

The crust is an important part of a sourdough loaf. It tends to be thicker, stronger, and (when fresh), well… crustier than normal bread.

The key to it all is the starter, so how do you create and keep your starter?

 

 

The Jar

You need a sealable jar to hold your starter. I use a Kilner jar, as pictured, but a very large jam jar will probably be fine. The jar needs to be able to hold well over a pint/half litre. My jar can hold a litre, which is large enough to generate enough sourdough starter for a good sized loaf but not so large it won’t fit in my fridge (which is important).

Once you have your jar, make sure you have:

  • a packet of white strong bread flour.
  • either some grapes or apples or, if you can manage it, some starter from a friend.
  • at least a week before you want an actual loaf of your own sourdough bread.

I would recommend you use white bread flour as brown or wholemeal (or even seeded) not only provides bits in your mixture where yeast cells would struggle to get to (so might make it more likely for your starter to get infected and “go off”) but as you add quite a bit of starter to the final dough, it’s always going to be partially wholemeal or brown if that is what your starter is based on, no matter what you want.

It has to be strong bread flour. Strong bread flour has a higher percentage of protein, gluten, in it. This is vital to support the texture of bread. Cake is lighter than bread and normal flour that you make cakes out of has less gluten in it.

Sterilise your jar before you use it. Either wash it in really hot water or, preferably, but it in an oven at about 120C for 20, 30 minutes. Let it cool to room temperature before you use it though. You want to sterilise it as the idea is to get a yeast colony growing in the jar that will out-compete bacteria and not-yeast fungi and keep the mixture clean and edible and not poisonous. To begin with there will not be a lot of yeast cells and any bacteria or fungus present could make the mixture bad before the yeast takes hold.

Making the starter

This just needs a little more mixing

Put about 300 grams of the strong white bread flour in the jar and add about 300ml of water, stirring it. you might want to add the water in two or three parts, mixing it well as you go but don’t stir it for minutes. You will hopefully end up with a smooth mixture that is a bit thicker than porridge/wallpaper paste/pesto. Now add a little more water until it *is* the consistency of porridge. Thin enough that it would pour, thickly, but thick enough so that a spoon stuck in it will probably stay in place. Don’t forget to take the spoon out…

Now the tricky bit. Getting the yeast in it. Don’t use baker’s yeast or brewer’s yeast or anything you would buy to make a normal loaf of bread, you want something slower growing and, if possible, local. In some places, at least in the UK, you might have enough yeast in the air to get it going, especially if you live in the countryside near orchards. Leave the jar with the lid open for a few hours and then shut it. A more reliable way to get the yeast is to take the skin off four or five grapes, preferably ones you have had in the house a few days, or some peel (just a couple of long stripes) from an apple, either a locally grown one or one that’s been hanging about in the fruit bowl a few days (but is not rotten!!!). The peel from fruits like this are covered in many yeasts. Use only the peel, not the pulp of the fruit. Chop the peel into little bits and throw it in the mixture and stir.

The yeasts on the skin will get it all going

If you are lucky enough to know someone who already makes sourdough who is local (in which case, why are you reading this?!? Go have a cup of tea with them or a glass of wine and get them to show you how to do all this – relevant covid-19 restrictions allowing of course) then get some off them, about 30ml will be more than enough. I got some from a local bakery a couple of years back who specialised in sourdough. You can even use dried out sourdough, as I did once. I’ll put the little story of that in another post.

The advantage of using some existing starter mix is that it gets going quicker and you an be pretty sure it will work. Getting your starter fully active from scratch using peel or the air can take weeks, a dollop of starter in it’s prime will get you a fully active new starter in days. I swap the jar I keep my starter in every few months, as they can get a bit gungy & crusty, I make the bread/water porridge and chuck in about 200ml of my existing mixture – usually what is left when I am making a loaf. I can use the “new” starter created in this way in a couple of days.

Shut the jar. If you were lucky enough to use existing starter, keep it out at cool room temperature if you are making a loaf in a day or two. Otherwise put it in the fridge.

If you really are starting from fresh, with peel, put the jar somewhere that is “cool room temperature”, that is about 16-18C, not near a radiator or source of heat, not somewhere cold. Hopefully, in a few days you will see little bubbles in the mixture. That means the yeast is growing and releasing carbon dioxide! After about 5 days, whether you see little bubbles or not, take out about a third of the mixture and discard, replace with the same volume of flour/water mix that you removed, give it all a good stir and seal the jar again. Do so again in another 5 days. If you do not see any bubbles by now, it has probably failed. Discard and start again.

A starter in it’s prime, a day after being fed

If the mixture develops any colour other than pale cream/oatmeal (so if it goes green or purple or pink or grey) you now have a jar of poison. Bacteria or fungus have won and out-competed the yeast. If there are spots of grey or other colour on the surface, or fluffy spots, again it is poison. Throw the contents away, sterilise the jar, try again.

Once you have a pale cream/maybe very slightly oatmeal coloured gloop that bubbles a bit you have your starter. Well done. You now have a new pet in your life.

Looking After The Starter

Once you have created the starter you have actually created a living colony – and you have to feed and care for it. If the yeast runs out of food it will go dormant and that opens the door to bacteria or moulds getting a foothold and growing. You have to keep the yeast active and reproducing. To do this you feed it.

Professional bakers who are making a lot of sourdough bread are constantly taking out part of the starter mixture and using it in the dough. An 800 gram loaf will use between 150 and 250 grams of starter depending on how they make the dough. This is replaced with the same volume of flour/water mixture they take out. You can do this yourself, if you are going to make a new loaf every few days you can keep the starter at room temperature and replace what you take out with flour/water mix. The yeast in the remaining starter quickly works through the added mix and new yeast cells grow.

If you are going to make a loaf once a week you can extend this process by putting the starter in the fridge. You take the starter out the fridge a day before you are going to use it. This is so it warms up and becomes more active. If you have space in the jar, you might want to add a bit of extra flour/water mix for the yeast’s breakfast (about 100 grams flour) when you take it out the fridge – I do. You take out about a third of the starter when you make the loaf the next day and replace it with flour/water mix. I leave my jar out for a few hours/overnight after this to let it get going and then you put it back in the fridge.

If you keep your starter for more than a week in the fridge, or 3 or 4 days at room temperature, without using it, you have to feed it. Take out a third of the mixture and discard, replace with water/flour mix that you stir into the starter. So long as you regularly feed the starter it will last pretty much forever, but of course you are simply throwing away flour all the time.

If you are a bad starter owner and you forget about it, it won’t be happy. A layer of fluid will separate out at the top of the mixture and it will go grey. Grey is bad. If this happens, if the fluid and only the very surface of the starter are a light grey, no fluff, you can pour off the fluid and the top third of the starter, feed it, and it might be OK. I’ve brought back starters from grey gloom a few times. However, the starter won’t make a good loaf again until you have fed it a couple of times. If the grey comes back straight away, you best put the poor thing down.

If your starter or anything in the jar goes pink, orange, purple, green, or fluffy, you have let the yeast get too weak and you have grown something new. It might be useful to a microbiologist, it could even contain a new antibiotic unknown to man, but it is far, far more likely to be poison. Throw it away, start again.

When you feed the starter, make sure there is space for it to expand. I keep my jar about half full. When I feed it, the contents expand with the CO2 and then subside. If the jar is too full, there is no space to expand. Also, I suspect my jar leaks every so slightly so no pressure builds up. If your jar is totally sealed you might have issues with it spraying out when you open it. Let me know if you do, photographs of the mess would be appreciated.

The more regularly you use the starter, the better will be the bread you make. When I’ve kept my starter out of the fridge for a week or two and either made a loaf or simply fed the starter every 3 or 4 days, it gets more active and the dough rises more readily when I make a loaf. If I leave the mixture in the fridge for a month, only occasionally feeding it, the first loaf I make from it struggles to rise.

Starters Vary

I’ve occasionally had two starters running at the same time. I once had my home-grown starter and also one seeded from some starter given to me by Jože. I’ve also had a starter that was initiated from a sample from a local baker’s, as I have said, and I’ve created a new starter from scratch when I already had one going. The bread made from different starters have slightly different tastes. And the one I got from Jože was more active than my home grown one. I have to say, I did not notice much difference between the two home grown starters I had. I am sure this is down to a difference in the actual yeasts in the mixture (or not, in the case of my two home-grown ones).

Hmmmmm…. Tasty

I discussed this with a fellow Oracle Presenter Baker and we decided it was highly likely that the actual yeasts in there not only vary with where the seed material came from but also how you keep it. If you keep it in the fridge, yeasts that are more tolerant of cold conditions will survive better, keep the starter at room temperature and those yeasts that reproduce faster in warmer conditions will take over.

Whatever, a loaf of sourdough bread you make from your own starter is a real treat. I’ll describe my baking process in the next post.

 

Friday Philosophy – My First Foray Into I.T November 13, 2020

Posted by mwidlake in ethics, Friday Philosophy, humour, Perceptions, Private Life.
Tags: , , , ,
1 comment so far

This is the first computer I ever used. The actual one. It is a Sinclair ZX Spectrum 48K. It was at the heart of a long, terrible family feud – the source of much angst, anger, and even fist fights. Blood was spilt over this machine. Literally!

Picture of a Spectrum home computer

The actual first computer I ever used

Anyone who lived in the UK in the early 1980’s and is currently about half a century old will recognise this box with the grey, rubber (sometimes called “dead flesh”) keyboard. It was the model that came out after the Sinclair ZX81, which is itself a classic of early home computers, and sometimes the ZX Spectrum was called the ZX82. The Spectrum could put colour on the screen (up to 8 different colours at a time!), had a resolution of 256*192 pixels, the Z80A CPU ran at 3.5MHz, and it could make a sound. A beep, basically (for a wide variation of too few hertz to hear to too many hertz to hear and all tones in between, and of any duration – but it was still just a beep).

The Spectrum was initially a rival in the UK for the Commodore VIC 20, BBC Micro, Atari 400 and, later, the Commodore 64 (C64). They all had their advantages, the Spectrum’s was it was cheap! Even the more expensive 48K version (as opposed to the basic 16K) was cheaper than most rivals. Sinclair Research even tried to make out it was superior to it’s rivals as it was simpler and had fewer chips inside it. That was pure marketing BS of course. But the Spectrum and the C64 were probably the most common home computers in the UK in the early 80’s and they remainder popular even when more capable machines came out. They might not have been the best machines technically, but they both ended up having a huge number of games you could play on them, and that’s what counted. In my local computer games shop most games were for the Spectrum, then the C64, and all other machines got lumped together in a corner at the back.

The Spectrum was the first computer in the Widlake household. My dad agreed to buy it for my older brother Simon, who made a strong argument that it was an educational tool – and the early advertising material for the machine made a lot of it’s suitability as a such, with lots of worthy software for doing graphs and learning computer languages. About the only game available for it on release was chess. Dad was of the opinion Simon was the genius in the family – Simon was going to go to University! (At the time no one in the family had ever gone into higher education, only about 5% of people in the U.K. did then. As it turned out, all three of us kids went into higher education). So Dad felt it was worth spending the money, as he felt computers were going to become something. He wasn’t wrong.

But before Dad agreed to get Simon the Spectrum, he made Simon agree it was something the whole family was to have access to. He was to share it with myself and Steve, the eldest. Simon agreed.

Spectrum with games and tape recorder

The spectrum needed a tape record and a TV to be used

So the Spectrum arrived. Back then, home computers almost never came with everything needed to use them. The Spectrum, like several rival computers, needed a cassette tape record to save and load programs from tapes, and a TV on which to show the image. Simon had his own tape recorder and he was of the firm belief that, except when Dad wanted to watch the news, he could use the family TV whenever he wanted. As he was a genius after all.

He quickly lost the TV argument, the last thing our parents wanted was to lose the power of distraction that the TV provided for the other two kids – especially me as I watched a lot of TV and was a right PIA when I wasn’t. Steve did not watch a lot of TV but as he wanted nothing to do with the computer, it would have been really unfair on him to not get to see the few things he wanted.

However, Simon had a back-up plan. I had a portable black & white TV (so much for those 8 colours) and Simon was older & bigger than me. So he took possession of my TV. I complained to the court of Mum & Dad but the Tyrant justified his acquisition of the resource on the grounds that he was going to have to share his Spectrum, a far more valuable resource, with me – so it was only fair?!? “Yes” I agreed, but only when I was not using MY TV for MY watching of what ever (probably crap) I was wanting to watch. The court came down on the side of the Tyrant, but with caveat of the plaintive upheld. Tyrant could use the TV when Plaintive was not watching it. It turned out that the reality of the situation was that Simon was still bigger than me and to my considerable surprise “I didn’t want to watch anything” whenever Simon wanted to use his – err, sorry, “our” – Spectrum.

The next blow to the plans of Tyrant bigger brother was that it turned out his tape deck (the one in the picture) was crap. Most games would fail to load from it. But my tape recorder worked just fine for this purpose, it was a really quite nice JVC model… So, yes, you guessed it, another possession of mine was now to be treated as his – sorry, “our” – possession, still on the basis of shared access to the Spectrum.

So Simon used my stuff as and when he wanted, but did he share? Well, sort of…

Sinclair User Magazine

Those of us of the correct vintage who got into early home computers would buy magazines like (in our case) “Your Spectrum” or “Sinclair User”. Inside there would be long code listings of programs. Simon “let me” read the text of the code out to him to help him type it in more easily. Or, if he was in a really good mood, he would let me type the code in on my own – whilst he was doing something else (like seeing his friends or watching the colour TV or picking on the cat). If I finished typing it in I was not allowed to play it until he got back. Yeah, like I paid any attention to THAT rule…

These games you laboriously typed in often had bugs in them, especially if they had a lot of code. Some were down to entering the wrong code in, more were down to the actual code really being wrong – quality control was non-existent. And, to give him his due, Simon was really very good at finding and fixing the bugs. Once there was a flight simulator in the magazine, spread over a couple of issues. I think it later got developed further and become “Psion Flight Simulator”. But the version in the magazine did not work properly. Simon found and fixed the bugs and even got them published in a later copy of the magazine. It taught us both that software could be wrong and that it could be fixed. I did fix some of the games myself, especially if I had been left typing it in and got it finished. And sometimes Under Orders from the Tyrant (who was out setting light to papers in people’s front doors or something…)

But I was not allowed to play with the computer myself without permission, and certainly not if he was out. Apparently I was old enough to enter code for him unattended but not to load up “Meteor Alert” or “Ant Attack” and have fun. You’d think from this I was maybe 8 or 10, but I was actually about 14 and more than old enough to recognise hypocrisy and injustice. I would say that’s what older siblings are primarily for, to teach you about these philosophies. Not by saying “this is something you should not do, oh younger brother of mine” but by amply demonstrating for real what it feels like to be on the receiving end of such bullying and unfair treatment. But my oldest brother felt no need to deliver such life lessons, so I could be wrong.

Simon would let me play “with him”. This usually took the form of him playing the game and, once he lost, letting me play until I lost – and then we would swap again. Sounds fair? Not really, as a lot of the time he would be playing on his own or with his friends and I was not invited. He would be using “our” TV and “our” tape recorder but it was still His computer and he was not letting me join in. So given my lack of practice and that I was younger and not so good at computer games as him, when he did let me join in his go would last 20 minutes and mine would last 2 minutes. Basically, he liked to be beating someone. I was better than him at a couple of games, one being “Attic Attack”, as I had learned the layout. We never played Attic Attack. Oh, he did play Attic Attack. He played it on his own, trying to get better, good enough to beat me…

I could beat the Tyrant at Attic Attack

After maybe a year, 18 months, things came to a head. Simon was never going to play fair, in his mind it really was his Spectrum and also now his TV and his tape recorder. After all, as he kept telling me, his computer was the more expensive item. Only, in reality, it was less expensive than my contribution combined. I started playing on the Spectrum when he was not in, as far as I was concerned I’d put more into this pot than he had and I was not going to accept this shit. I could not use it against his will when he was there but once he was out, I damned well was going to get some of my fair share. As you can guess, this did not go down well with him when he found out and the Tyrant did what all bullying, older brothers did and he physically asserted his authority. He’d hit me. I was not really pleased about that, so when he’d go out I would absolutely bloody well would play on it if I wanted to or not, out of spite & defiance (and also to keep my edge in Attic Attack) – and it would repeat. It came to a head when he made my nose bleed – and it dripped on the computer. That was, of course, my fault… “If you’ve damaged the Spectrum I’ll kill you!” Oh, I’m so sorry for bleeding on things after you hit me. Maybe that should teach you something…

It was now warfare.  Screw you, I said, you’ve never shared as agreed, keep your Spectrum, it’s useless without my bits. I banned him from using my equipment. A ban which he now ignored of course. I went to the court of Mum & Dad, but not only was Simon “the genius” but he was, back in reality, a lying & manipulative sod and he made out he was sharing and I was being a spoilt child and I was told I had to share as he was (!!!!). So I took things into my own hands – and I started hiding the cables to my tape recorder and taking the plug off my TV. Yes, I physically removed the plug from the cable and hid it. He tried to work around my sabotage, one day I came home from somewhere to find he had plugged the Spectrum into the family TV and he’d got hold of a spare power cable for my tape recorder and he was using it, despite me banning him from it, playing games with his mates.

I went utterly, lost-the-plot nuts. I demanded my stuff back and an apology or something or let me play too and he was having none of it. So I tried to take my tape recorded back and he tried to stop me, but I was so mad I got hold of it (I think I was finally getting strong enough to fight back a bit) and, shouting something like “and you used it to load that game, so I’m taking THAT as well!” I kicked the power plug out the Spectrum. Game gone, no tape player to load one up, games afternoon with his friends was over and there was nothing he could do about it. He went BERZERK, trying to wrench the tape drive back off me and hitting me but I was so furious I held my own and I think I even kicked his computer again. He was straight off to Mum saying I was trying to break his computer. And this time, the Court of Mum & Dad finally realised Simon was being a little shit. He could not deny he had used my things, even though I had told him he could not, and he could not claim I attacked him first (his usual stance), as his mates backed me up and said Simon had hit me first. Yeah, his mates dobbed him in it!  I think they found it all hilarious.

This led to a full judicial review and this time the voice of the Plaintive was heard. I might have been a little sod but I had never tried to break stuff before and I utterly refused to accept it when The Tyrant lied that he shared at all – why would I be this mad and and even taking the plug off my TV? Simon had not helped himself in other ways as he’d been caught bullying me by Mum recently and been in trouble at school. Timing was on my side. He was told to play fairly or else… have his precious Spectrum removed. Dad would monitor.

Amstrad CPC 464

This was my Amstrad, I bought it, Simon was not using it.

After that, it got a bit more equal. I did get some time on the Spectrum myself (though I did sometimes have to get enforcement from the judiciary) and I did not just play games. I had typed in a lot of programs for Simon and fixed a few of them, so I slowly learnt how to program. I wrote a couple of my own simple games and put in stuff from magazines I wanted to try but Simon had no interest in.

But it never did really completely end. He could no longer stop me using the Spectrum. But if I was using it and Simon decided he wanted it, he would just bully me, or tell dad I was stopping him “learning” (I am not so sure what you learn from playing “Jet Set Willy”). That Spectrum came, for me, to represent what a selfish, lying, bullying, devious shit my older brother was. I swore one day the Spectrum would be mine.

And then it all changed, I got my own computer, an Amstrad CPC464. I bought it with my own money I earnt from months of back-breaking fruit-picking work (Simon was “too good” to do manual labour, so he had no money). It had not been bought by Mum and Dad, it was in no way a shared resource, it was totally mine. And guess what I said to him when he asked (well, demanded) to use it?

Yes, he could Fuck Right Off. He had his Spectrum.

And if he tried his old tricks of hitting me, it would be a more equal fight (he was still taller and older than me but manual labour had made me a hell of a lot stronger), so he decided against that. He could keep his crappy Spectrum.

The irony was that, even though my Amstrad was a much more advanced and capable piece of kit, the Spectrum and it’s vast library of games was still the best option for fun.

Well, the Spectrum is now mine. I picked it up from Mum’s house this week. Simon passed away many years ago, so it’s been sitting in a drawer for almost 2 decades. Being a Friday Philosophy I guess I should now tell you what the Spectrum now means to me, the healing process, what we can learn from this? How family, in the end, is more important than mere possessions? Stuff like that?

Well, I can.

I learnt that Simon was always a bullying, nasty, selfish, self serving sod and he got no better as he got older. So there.

And the Spectrum is now mine I guess.

But I don’t have a TV with the right socket to plug it into, and I know already – that tape drive won’t load games…

Friday Philosophy – Is The Problem The Small Things? August 7, 2020

Posted by mwidlake in ethics, Friday Philosophy, off-topic, rant, User Groups.
Tags: , ,
6 comments

Something has been bothering me for a while. In fact, I’d go as far as to say it’s been depressing me. It’s you. Well, many of you.

Well, it’s not MY problem!

What do I mean? Well I’ll give you an example. A week or so ago I went out in the car to get some shopping. A few minutes into the journey, as I go around a gentle bend, I see there is a car coming towards me – on my side of the road. I had to brake to give it space to get back over and I see it has swerved to avoid a branch in the road. As you can see in the picture, it’s not a huge branch, it covers less than one lane. I’m past it now so I go on to the shops and get my stuff.

30 minutes later I’m coming back. And I’m thinking to myself “I bet that branch is still there.” And it is. I can see it from maybe 300 meters back. The two cars in front of me barely slow down and they swerve past it. An oncoming vehicle that *I* can see coming, let alone the two cars in front of me, has to slow down for the swervers like I did. That slight bend means you get a much better warning of the obstacle from the side of the road it is on and as it is on your side, it’s really your responsibility so slow or even briefly stop, but the people in front of me just went for it. They did not care.

I did not swerve. I slowed down. And I put on my hazard lights, and stopped about 20 meters back from the branch. I double checked that no car has appeared behind me and I got out the car. In 20 seconds (including taking the snap), I’ve moved the branch off the road with no danger at all and I’m back to my car.

I know, you would have done the same.

Only no. No, you would not have.

Some of you would like to think you would have stopped and moved the obstacle.

I suspect most of you would claim, if asked, that you would have stopped and moved the branch.

And of course all of you would have slowed to avoid inconveniencing others.

But reality shows that nearly all of you would not.

As I left the scene, I was wondering how many people would have passed that branch in that 30 minutes I knew for sure this small branch had been an obstacle on the road. I’m going to let people going the other way off, as they would have to do a u-turn to come back to it, so how many people would have had to swerve past it?I know that road well, it would have been hmm, 4 or 5 cars a minute going past in one direction – certainly more than 3 cars, less than 10. So well over a hundred drivers would have seen that branch from a distance, most would have been able to safely slow and stop – and yet not one of them had. I have no idea how long the branch had been there, it was not too beaten up so maybe not long, but it could have been a couple of hours. It was easy to avoid – especially if you swerved with little concern for any on-coming traffic…

It turns out I’m the one in a hundred.

Are you thinking “well, it’s not my job to move branches of a road!”

So who’s job is it? And if you could label it as someone’s job (let’s go for someone in the “highways agency”) how do they get to know it needs doing? I don’t know about you but I see dozens of highways agency maintenance people on every journey I do, just cruising around looking for things that need doing. {sarcasm}.

When was the last time you saw something that needed doing in a public place and took the time to think about who should be told, try to contact them, get told to contact someone else, find out it’s not their job but are asked to ring Dave, who you do ring and he says thanks (before making a note to think about it, whilst probably muttering “this is not my job, I’ve got major roadworks to look after”). Hell, it’s easier to stop and move the branch.

Generally in life, in so many situations, I am constantly wondering why someone has not done X (or has done Y). Why don’t you reach for the jar in the shop the old lady can’t quite reach? Why don’t you hold the door? Why did you drop that litter when the bin is JUST THERE! That person  in front of you buying a parking ticket can’t find 10p in their purse to make the correct change? You have loads of 10p pieces… some in your hand already.

This is what is depressing me. Even though nearly everyone likes to think they are the nice person who will do a little for the common good, the reality is that most people won’t when it comes to it – but most people think we all should, and you tell yourselves you do the little things. You are telling yourself now, aren’t you? You are trying to think of the little things you have done for the common good. If you can think of a half dozen in the last month then you really are one of the good guys/gals. If you can only come up with a few…and actually most of them were ages ago… well, sorry but you are the problem.

The strange thing is that, having just insulted you all, as a group you lot are much more likely to be in the 1% than normal. Even though out of the general public not even 1 in 100 people would put in a little effort to move that branch, out of the people reading this, I’d say 10% would. Because I spend a lot of time in the Oracle user community, packed with people who give up their time, knowledge, even their holidays, to speak at conferences, help organise meetings, answer on forums, write blogs, answer questions on twitter, and all that stuff. Many of you reading this are active members of the User Community doing not just small things but often large things for the community. That’s why the community works.

To the rest of you, instead of liking to think you would move the branch or claiming you would (as everyone wants to be thought of as the nice guy/gal) just occasionally move the branch. Or pick that piece of litter up. Or do something small that cost you so little but it just would be nice if someone did it.

No one will thank you.

But you will know you did it. And you are becoming no longer part of the problem but part of the solution. I’m not asking you to give 10% of your salary to charity or give up an important part of your life, just do a bit of the small stuff.

If more of us do it, we will have a better world. If someone had moved that branch soon after it fell, I would not have had to  avoid some swerving dickhead, and the person I saw later would have not had to avoid people who could not even be bothered to slow down or stop briefly. And, in the worst case, that needless accident need not have happened. It really is as simple as spending 1 minute moving a branch.

Don’t be part of the problem, be part of the solution. It’s really, really, really easy.

 

COVID-19: The Current Situation in the UK and June. May 30, 2020

Posted by mwidlake in COVID-19, Perceptions, Private Life, rant, science.
Tags: , , , ,
7 comments

I’ve not said anything about Covid-19 for much longer than I expected, but really it has been a case of watching the coming peak come and go, pretty much following the pattern of Italy, Spain, Belgium and France. I plan to do a post soon which pulls together the current scientific position, but for now I wanted to record where we are and where my gut feeling (based as ever on reliable scientific sources and not so much on what the daily government updates would like us to think) says we will be in a month or so.

The number of UK recorded deaths where C-19 was present, and detected cases

We’ve not done very well in the UK. If you are based in the UK you may not be aware of the fact that most of Europe think we have,as a nation, been idiots – failing to learn from other countries, late to lock-down, lock-down was not strict enough, too early to open up, our PPE fiasco… I can’t say I can disagree with them. We have one of the highest deaths-per-million-population rates in Europe, exceeded only by Spain and Belgium. But it could have been worse. A lot worse.

I’m truly relieved my predictions in my last post were (for once) too pessimistic. I misjudged when the peak in deaths would be by over a week – it was 9 days earlier than I thought, happening around the 11th April. As a result of coming sooner, the peak was lower than my little model predicted. Even allowing for that, the increase in number of deaths did not mirror the increase in cases (I used the cases pattern as my template for deaths). I think this is because the UK finally started ramping up it’s testing rate. The more testing you do, the more of the real cases you detect, so some of the increase in cases was simply better testing and not continuing spreading. That’s what happens when the source of your metrics changes, your model loses accuracy.

Deaths are directly related to real case numbers, it does not actually matter how many cases you detect. This is part of why case numbers are a much poorer metric for epidemics, whereas deaths are better. The best metric is a random, large sample for those who have had the disease – but we still do not have reliable, large-scale antibody or similar tests to tell us this.

If you look at the actual figures and compare to what I predicted for the peak of deaths, I seem to have been pretty accurate. I said 1,200 to 1,500 around the 20th April and the peak was 1,172 in the 21st April. But I was predicting hospital deaths only. Up until 29th April this was the number reported each day but since then the daily number of deaths reported included community (mostly care home) deaths. The previous figures were altered to reflect this and the graphs to the right are based on these updated figures. Hospital deaths seem to have peaked at 980 on the 11th April, so I was wrong.

I think it is crucial in science and technology (and actually, just in general) that you be honest when you are wrong – even if (like in this case) I could made a fallacious claim to have hit the nail on the head.

The bottom line is, we are well past the first peak and it did not overwhelm the NHS. It got really close and our issues with personal protective equipment was a scandal and must have resulted in more illness and some avoidable deaths to our front-line NHS staff. But, apparently, saying so is Political.

All in all we followed the pattern of European counties that were impacted by Covid-19 before us and implemented similar country-wide lock-downs.

One difference between us and other European countries that have been hit hard is our tail of cases is thicker and longer. We have not been as rigorous in our lock-down as those other countries (e.g we did not have to have written permission to leave or enter an area and children were not utterly forbidden from leaving home, which are just two examples how our lock-down was softer). I know it might not feel like it, but we were not.

What really concerns me is that we are easing lock-down measures so soon in the UK. Our daily new case rate and number of deaths are both still really quite high. The figures always drop over the weekend, especially Sunday and Monday (due to the numbers reported being for the day before). Over the last 3 days (Wed to Fri) we averaged 1998 new cases and 371 deaths per day. If you think Covid-19 has gone away, every single day there are 371 families who sadly know different.

I understand that the economy is important, that unless things are being manufactured, services provided, money earned and spent, that a large part of our society is not functioning. Maybe I don’t really appreciate how important it is as economics has always looked more like a dark art based on greed than anything logical, but some people feel getting back to normal business is critical and the long-term impact of not doing so is potentially as serious as Covid-19.

I also know that not being able to go to places, eat out, have a drink in the pub, meet up with friends in a building or in more than small numbers is frustrating. For many, not seeing your family and loved ones who are not in your home is very upsetting.

I’m sure that parents are desperate for kids to go back to school (partly for education and partly as it turns out kids are a lot of work), couples need a bit of time apart, people are missing their jobs. Nearly all of us have never had to spend so much time with a very small number of other people.

But I’m also sure that what we don’t want is in 4-8 weeks to have to go into the same level of lock-down as we spent most of this spring in. And the next lock-down may be even more draconian as there is a difference now to where we were at the second week of March when we should have locked down first.

SARS-Cov-2 is now endemic and prevalent across the UK. It is everywhere.

At the start of an epidemic the disease is growing in a small number of places, so usually (such as was the case with MERS and SARS) you can contain it by strong isolation and tracking efforts in those areas it occurs, as most of the population are not exposed. This is why you cannot contain seasonal ‘flu epidemics by isolating people, it does not work if it is wide-spread enough. ‘Flu simply flows through the population and it does in some years kill a lot of people.

With Covid-19 right now, If our R(e) – the effective reproduction number – goes above 1 anywhere across the UK, Covid-19 cases will rapidly increase in that area. And with restrictions being lifted across the whole UK and in England especially, I am privately convinced the disease will burst fourth again in many, many places and it is going to go very wrong again. I think the government is being utterly disingenuous about the impact of opening up schools and my friends who are teachers and medics have no doubt this is a significantly more dangerous step than it is being sold as. It might be the right move, but lying about it’s potential impact is not helpful long-term.

Not only are we relaxing social distancing steps too early, but I feel the government has utterly bolloxed up (technical term meaning “done a jolly poor job of”) the messaging. As examples:

  • The very clear “Stay at Home” became the vacuous “Stay Alert”, which no one seems to be able to clearly define and every one seems to have a different interpretation of.
  • We were given contradicting and non-nonsensical rules such as you could see one family member from outside your household in the park, but you could have people come and view your house. So if you want to see your mum & dad at the same time, put your house up for sale and have them view it.
  • Parts of the UK (Wales, Northern Ireland, Scotland) have said they were not consulted on changes, they do not agree with them, and they are doing their own thing. That’s not confusing to people is it?
  • The whole Cummings affair. Dominic Cummings did break the rules, he acted like a selfish idiot, he lied about what he did, he had pathetically stupid excuses (“I drove my child around in a car to test my eyesight” which shows he either does not care at all for other people’s safety or has too low an IQ to be allowed out on his own). The issue is not that one arrogant, self-important person decided the rules do not apply to him. It is that the government fail to understand that not sanctioning him is being interpreted by many to mean they can make up their own minds about which rules apply to them and which they can ignore. Continuing to say “look, get over it” is simply coming across as telling us all to bugger off.

To help steer us through this crisis, we really needed a government with both the mandate to introduce new rules and also the acceptance by most of the population of those rules, and at least acquiescence from the majority to put up with limitations placed upon us. What we have now is a not just the hard-core “we won’t be told what to do” people that would always be a negative factor in limiting the spread of a disease, but a large number of angry, confused, worried people across the country. Almost everyone I personally know in the UK feel angry, confused, worried, and mostly with a progressively declining respect for the government and their advice.

I know I’m not very good at understanding people, it does not come naturally to me. If someone does not think like I do, I can have a devil of a job working out why. But I’m pretty sure that here in the UK a lot of people are going to start saying “to hell with the lock-down rules, everyone else is ignoring them and I’ve not seen anyone die in front of me…”

I went to see my Mum this week. I had to drive 100+ miles to do it. Unlike in Dominic’s case, it’s allowed now and I have no Covid-19 symptoms. I took a mask, I took my own food, we sat in her garden (I got sunburn, so Covid-19 might not get me but skin cancer might). I assured myself she was OK and that her tech will keep working so we can stay in touch. And I felt a little naughty doing it.

But I made a conscious decision to do it now – as I think SARS-CoV-2 is about at it’s lowest prevalence in our population right now (end of May 2020) than it is going to be for months. Admissions and deaths are going down and I expect at least deaths to continue to do so for another week or two. Personally I am deeply worried that in 4 weeks time new cases, hospital admissions, and deaths will be going up again. I don’t want them to be but I’ll be (very happily) surprised if they don’t go up  – what we see in cases & deaths at any point in time is based on the level of spread one or two weeks ago respectively. I suspect that as I type our R(e) number is going up and will exceed 1 this week.

If you don’t agree with me, just keep an eye on what the scientists are saying. Some are already making noises of anxiety as an article on the BBC is already saying today. Scientists tend to make cautious statements such as “we do not think this is wise” or “we feel there is a danger in this choice of action”. It’s a normal person’s equivalent of screaming “Are you bloody idiots?!?”.  Once again, the experts are saying we should do one thing and the government are doing another. It’s not gone too well to ignore the scientists so far.

There is a T-shirt you can get at the moment, which I really must order a dozen of.

“All disaster movies start with someone ignoring a scientist”.

 

 

Friday Philosophy: The Intersecting Worlds Around Oracle April 24, 2020

Posted by mwidlake in conference, Friday Philosophy, humour, User Groups.
Tags: , , ,
5 comments

Some of you may have noticed something about the Oracle Community: How certain other aspects of human nature, factors, and outside activities are unusually common.  An abiding love of the works of Douglas Adams (If you have never read “The Hitch Hikers Guide To The Galaxy” you should question if you are right for this community – and if you have read it/seen the series/watched the film and disliked it, I’m afraid you have to leave now); Lego was probably an important part of your childhood (and quite possibly your adulthood, though some “project” this fixation on to their kids). A lot of the most talented people, especially presenters, are called “Martin” or similar :-}.

Three Different Worlds Meet

There are two other groups of people that are large within the Oracle community and that I fit into.

  1. Oracle people who have a thing about cats. A positive thing, not those weird people who don’t like cats. It seems to me a lot of people in the Oracle community are happy to serve our feline overlords. This can polarise the community though, so introduce the topic of cats carefully. If the other person mentions how evil or unfriendly cats are, put them on The List Of The Damned and move on to something else.
  2. Making bread, especially of the sourdough variety. This is a growing passion I’ve noticed (quite literally, given the careful tendering of starter mixtures and also expanding waistlines). It seems to be especially common with technical Oracle people. More often than not, when I get together with a flange of Oracle Professionals (or is it a whoop or a herd?) the topic of baking bread will come up. Unlike technical topics, such as what is the fastest way to get a count of all the rows in a table, baking topics are rarely contentious and lead to fights. If you want to put spelt wheat in you mix, that’s just fine.

Mrs Widlake and I were talking about this last night (one of the problems with all this social isolation business is that Mrs Widlake is being forced to spend a lot of time with me – after 27 years of marriage idle conversation was already a challenge for us and now with over a month together all the time, we are getting desperate for topics). She asked how many of my Oracle friends liked both cats AND baking bread?

It struck me that it seemed to be very, very few. Unusually few. I think this is something that needs to be investigated.  This pattern would suggest that bread makers are cat haters. But in my non-Oracle world, this is not the case. The best people are, of course,  Ailurophiles and many of my feline-fixated friends are also bakers of bread. Just not in the Oracle world.

What makes Oracle people so weird?

Does anyone have any ideas? And have you noticed any other common areas of interest (excluding computers of course, that’s just obvious)?

A few that spring to mind are:

  • Terry Pratchett and the Discworld
  • Running
  • Weird science
  • XKCD
  • The Far Side
  • Star bloody Wars.

Let me know. Or don’t.

And for all of you who don’t like cats…

Meow

COVID-19: The Coming Peak in the UK & Beyond. April 9, 2020

Posted by mwidlake in biology, COVID-19, off-topic, science.
Tags: , ,
9 comments

<<<<<<Introduction to Covid-19
<<<< Why we had to go into lock-down
<< What we could do to help ease social distancing

The UK government is now talking more in it’s daily briefings about what will come “next”, that is after we have seen the number of diagnosed cases & deaths continue to grow, plateau, and then fall. It will plateau & fall, so long as we all keep staying at home and limiting our social interactions. If we do not, we risk the virus spreading out of control again.

When Will the Peak Be?

My estimates so Do Not Trust At All

First of all, there will be two peaks. First the number of new cases a day will peak and then, about 8 days later, the number of deaths per day will peak. This is because of the average gap between being diagnosed in hospital and succumbing, for those unfortunate enough to do so.

The number of deaths a day looks to me like it will peak around April 20th, at somewhere between 1,200 and 1,500 a day (see below why I think tracking deaths is more reliable than case numbers and why case numbers are a poor metric). We will know that peak is coming as, if the lock-down measures have worked as intend, their effect will result in a plateauing and then drop in new cases during next week ( April 12th-18th). We might be seeing that plateauing already. Deaths will plateau (stay steady) for maybe a longer period than cases due to the fact that the gap between diagnosis and recovery or death is variable. That period will be something like April; 20-27th

If we follow the same “curve” as Italy and Spain,  the number of new cases will slowly start dropping but not as sharply as early models indicated. Deaths will also drop, about 8-10 days later. What happens then I have no idea really, it depends on how well the current social distancing measures work and if people continue to stick to them as spring progresses and people want to escape confinement.

A disproportionate number of deaths in this peak will be from our health services and critical works – people working in shops, bus drivers, refuse collectors, GP’s, teachers – because they are the most exposed. The care industry workers and lower paid people in our society will be hardest hit, which seems monumentally unfair.

The plan of pretty much all national governments so far is the same:

  • Isolation of all people who are non-key workers
  • Slow the spread
  • Expand the respiratory Intensive Care capabilities of the health services as much as possible
  • Look after as many of the wave of people already infected & becoming ill as possible

As I’ve covered in prior blogs, if the government’s measures work we are then we are left “sleeping with the tiger”. The virus is in our population, it will be slowly spreading still, and when social isolation measures relax there is a real risk of the illness and deaths exploding again because most of us are not immune. This is know by all epidemiologists studying this, it is a situation that China, Italy, Spain, and most other countries will face.

The big question is – what comes after the peak?

I’m going to cover three four things:

  1. Why we cannot go on “Cases” the number most often graphed and discussed. We have to go on deaths, and even then there are some confusing factors.
  2. Why the Infection Fatality Rate is key – and we do not know that yet
  3. A “test” or “vaccine” is not a black and white thing, it’s grey, and especially for a Vaccine, it is not coming soon.
  4. How we might manage the period between either a reliable vaccine or herd immunity. Both currently look like at least 18-24 months away.

Why Case Numbers Cannot Be Relied On.

Case Numbers do not tell you as much as you may think

Case numbers (the number of people who have been confirmed as having Covid-19) are the most commonly reported figures, many of us track if things are getting better or worse by them. But they are a very poor indicator really and they certainly cannot be used to compare between countries.

First of all, how are the diagnoses being made? Most countries are using the WHO-approved test or a very similar one, called a PCR test. I won’t go into the details here, I’ll put them in the section of the post on testing, but the test is accurate if done in a laboratory. Why in a lab? because any cross-contamination can give a false positive and if the sample or test chemicals are not kept/handled correctly, can give a false negative.

Not all countries are using just PCR tests. China made some diagnoses based only on symptoms. I’m not sure if other countries are making diagnoses from symptoms only and including them in official figures.

More significantly is who is being tested. In the UK the test was originally only being done on seriously ill patients in hospital. It is now being done on a few NHS staff and certain key people (like Boris Johnson!). In South Korea and Germany, many, many more people were tested, so there will be more cases identified. Add on to that the number of tests a country can do.

In the UK are testing rates have been very poor

In the UK we were limited to a pitifully small number of tests per day, less than 6,000 until March 17th and we only reached 10,000 test a day at the start of April. You cannot detect cases in people you have not tested.

Case numbers will also vary from country to country based on the country’s population! The UK is going to have a lot more cases than Denmark as we have over 10 times as many people.

The final confusion is that even in a single country, what counts as a day for reporting can vary and it can take time for information to be recorded. The UK sees a drop of cases against the prevailing trend on Sunday and Monday. As the cases are for the prior day and it seems like the data is not being as well processed at weekend.

Estimations of how many people really have Covid-19 at any time, as opposed to validated Case numbers, vary wildly. In the UK I doubt we are detecting even 1/3 of cases.

So, all in all, Case Rates are pretty poor as an indicator of how many people are really ill.

Infection Fatality Rate and Tracking Deaths Not Cases.

As I mentioned in my previous post last week, what we really need to know is the Infection Fatality Rate (IFR). This is the percentage of infected people who die. It is not the same as the Case Fatality Rate (CFR), which is the percentage of known cases that die. As the number of known cases is such an unreliable number (see above!) then of course the CFR is going to be rubbish. This is a large part of why the CFR varies so wildly from country to country. France has a CFR of 8.7%, almost as bad as the UK at 10.4%. The US has a CFR of 2.9% (but they will catch up).

As I also covered last week, we cannot calculate the IFR until we know the number of people who have been infected. For that we need a reliable antibody test and one does not exist yet. Yes, they are being sold, but the reliability is poor. Last I knew the UK NHS had reviewed several candidates and none were reliable enough to use.

Scientist have suggested many Infection Fatality rates. I feel 0.5% is a fair estimate. It is vital we know this number with some accuracy as if we have an Infection Fatality Rate we can flip the coin and calculate the number of people who have been infected from the number of people who have died.

IFR * deaths =  number immune

You can go from a graph like the example one I show (either from a model or, after the peak, from real figures) and as you have the number who died (say 20,000 to keep it simple) and the IFR of 0.5% you know that 4 million people (minus the 20,000 who died) had the disease and are now immune.

Of course, once we have a reliable antibody test we can verify the exact value for Infection Fatality Rate and the percentage of the population now immune.  But we only need that information from one country and it can be used, with minor modifications for population age and capacity of the health services, to estimate how many people are immune and thus how many are still at risk from Covid-19. In my example, about 62.5 million people in the UK would still be susceptible to Covid-19. Which is why this will be far from over after this initial peak.

There is one huge caveat in respect of the IFR. If in the UK the NHS is over-run, we will have extra deaths. People who would have survived with treatment die as too many people needed treatment at the same time. This is the whole “flattening the curve” argument, we have to protect the NHS from being over-run to limit this extra, avoidable deaths. In effect the IFR is elevated due to the limitations of the health system.

Countries which do have a poor health service or other aspects of their society that block them from the health service (cultural bias, fear of crippling debt) or more likely to have an elevated IFR, as are countries that allow Covid-19 to run unchecked through their population.

There is another aspect to the IFR and measuring progress of Covid-19 via the death rate. The number of deaths is a more reliable measure. I know that sounds callous, but as we have seen, the Case Number is totally reliant on how you do your testing and there needs to be a huge testing capacity to keep up. Deaths are simpler:

  • There are fewer deaths so fewer tests are needed (to confirm SARS-CoV-2 was present in the deceased, if not already tested).
  • Deaths have to be recorded in a timely manner.
  • Deaths are noticed. There are going to be people who are seriously ill and would be tested if they went to hospital but don’t, they get better and it is not recorded. They are “invisible”. Dead people invariably get noticed.
  • A country that wants to hide the active level of Covid-19 can do so by not testing, under-testing, or not reporting honestly on the tests. It’s not impossible, but it’s hard to cover up a significant increase in the number of deaths.

I stress that is is not a perfect indicator though. There is no clear distinction made as to whether the patient dies of some other illness but SARS-CoV-2 was present; whether the patient was likely to die “soon” anyway – again due to other illnesses; patients who die outside hospitals are not counted in the UK daily figures yet. (If you follow me on Twitter you will have possibly seen me querying the figures last Monday – and people pointing out the reason!)

Reported deaths will also suffer from spikes and dips due to how the reporting is done. The UK and some other countries I checked (France, Italy, Spain) show a dip in all figures, against trend, on Sunday or Monday (or both).

There is a really nice article on all of this this by New Scientist which is itself partly based on this paper by the lancet that gives an IFR of 0.66%

There is also a whole plethora of graphs and information on ourworldindata.org/coronavirus , as well as text explaining in more detail what I have said here. It is well worth a look and you can change which countries appear on the graphs.

 

Test are Not Black And White

There has been a lot of talk in the UK and elsewhere (including the USA), about not doing enough testing. On the other hand their is a constant stream of media reports about quick home tests, both for if you have Covid-19 or have antibodies to SARS-CoV-2 and so are immune. So what is the reality?

A test is only any good if it is reliable as used. For something like a deadly pandemic, it needs to be really reliable. Let me explain why.

Let’s say a company is selling an antibody test and someone uses it, it says they are immune,  and they stop self-isolating. But the test is 75% accurate. 75% sounds good, yes? No. it means 1 in 4 people who take that test and it says they are immune are not –  and they have now gone out, spread the disease to their aunt Mary and she dies. Plus infecting a large number of people and keeping the whole sorry mess going.

{Update – as a friend reminded me, when you are testing for an “unlikely” event, which being immune to C-19 is right now, even a 95% accurate test will give far more false positives than real positives across the whole population – I’ll try and do another blog to explain why}.

And that is if they take the test properly – companies are most likely to give you the best, under-ideal-conditions accuracy rate as they want to sell more kits than Sproggins Pharma selling a similar kit which they claim is 73% accurate.

If you are reading this, you are probably the sort of person who will read the instructions, follow them carefully, not put the swab down on a table,  not let the dog chew it.  And you note the bit on reliability. Most won’t. They will do the test quickly, it says they are immune and they will believe it, especially if the quoted reliability rate is high.

Any home test that can be used by the public has to be both very reliable (less then 5% false positives) and utterly idiot-proof. I’m really concerned that countries that put money first will allow companies to sell tests that do not meet these criteria and it will make the situation a lot, lot worse. It might even result in the pandemic running out of control.

Test For Being Infected – PCR test

PCR stands for Polymerase Chain Reaction. The WHO-approved test for Covid-19 is a PCR test and has been fully described since the end of January. You can even download the details of the test and methods from the WHO page I link to.

A PCR test is a genetic test. A primer is added to the sample to be tested and that primer latches on to a very specific DNA or RNA sequence. A biochemical reaction is then used, called a Polymerase Chain Reaction, to make copies of that DNA/RNA, doubling the number in the sample. These steps are repeated 30 to 40 times to make millions of copies of DNA/RNA. With an old-style PCR test you would then need to run the processed sample through a second process to detect it, like a Southern Blot – you get a square of gel with black lines on it. The PCR test for COVID-19 should be a real-time PCR test. With this the new copies made are attached to a florescent dye so that it can be easily detected as soon as there are enough copies in the sample, say after 30 iterations not the full 40, saving time.

If the original sample contains even just a few pieces of the DNA/RNA you are testing for, you will detect it. The process takes a few hours.

The RNA of the SARS-CoV-2 virus was sequenced (read) back in January and the WHO identified sequences that were unique to the virus, and these are used to make the primers. As I understand it most countries use the WHO identified primers but the USA had some “discussions” between commercial companies over which primers they thought should be used. I won’t suggest there was an element of these commercial companies looking to make a fortune from this, i’m sure it was all about identifying an even more unique RNA sequence to target.

The test has to be done in laboratory conditions. Because the test is so sensitive any cross contamination can give a false positive. e.g the sample taken from a patient was done by someone with COVID-19 themselves or there was SARS-Cov-2 virus in the air from another nearby patient. If a swab is used to get a sample from the back of the throat, it has to be put into a sealed tube as soon as it is used.

If the sample to be tested has not been looked after properly (kept cool, not kept for too long etc) or the chemicals for running the test are similarly not kept in a laboratory environment, you may fail to detect the RNA – a false negative.

Finally, the virus RNA has to be there to be detected. A patient early in their illness may not be shedding virus at a high enough level for the swab to pick up some of it. Once a patient’s own immune system has wiped out the virus (or almost wiped it out) again the swap may not have any or enough virus in it to be detected.

Done right a PCR test is a powerful, incredibly reliable (over 99%) diagnostic tool and is used for detecting many viral diseases, including HIV, Influenza, and MERS.

How a simple yes/no infected test might work

You can probably now understand why creating a PCR test for Covid-19 that can be used at home or in the ward and gives a result in minutes is a bit of a challenge.

Some companies are trying to create a different sort of test. These depend on creating a chemical that will bind to the virus itself, probably one of the viral surface proteins. That chemical or part of it will then react with something else, a marker chemical, to give a visible change, much like a pregnancy test. You put the sample in a well or spot where the detecting chemical is. Fluid is then dragged along the strip carrying the thing to be detected (the virus in this case) and the detecting chemical. Any detecting chemical that did not bind will be left behind. When the fluid goes past the marker chemical, if there is enough detecting chemical, it will change colour. Neat!

Best I know at time of writing, no one has come up with such a test that was reliable. I’m pretty sure someone will, in a few weeks or months. It should be accurate but no where near as sensitive as a PCR test. I must stress, to actually be of use in handling Covid-19 as a nation, the rate of false positive would need to be very low. False negative, though not good for the individual, is nothing like as big a problem in containing the pandemic).

Antibody Test

An Antibody test will show if you have had Covid-19. It will not show if you currently have it, or at least not until the very late stages. This is because it is testing for the natural ability for your immune system, via antibodies, to recognise and attack the SARS-Cov-2 virus.

We desperately need an antibody test as it will allow us to identify people who have had the disease and are now immune. This is vital for 2 reasons:

  1. Someone who is immune does not need to be restricted by social distancing. See my prior post on why this is vital and how we might identify such people.
  2. We can find out how many people have had the disease and compare it to the number of people who have died of the disease and get that very useful Infection Fatality Rate.

Unfortunately, making an antibody test is not easy. Some are in trials and I think the UK government have tried some –  and none have proven trustworthy.

An antibody test is simply not simple. What you need to do is design something that an antibody reacts against, so let me just describe something about antibodies. Before I go any further, I must make it very, very, very clear that of all the biological things I have touched on so far, antibody technology is something my academic background hardly touched on and most of what I know comes from popular science magazines and a few discussions with real experts last year when my work life touched that area.

Your body creates antibodies when it detects something to fight, an invader in our tissues. This is usually a viral or bacterial infection. It also includes cells that “are not our own”, which is why we reject organ transplants unless they are both “matched” to us and we take drugs to dial down our immune response. Our antibodies recognise bits of the invader, in the case of viruses that is (usually) proteins that are in the coat, the outer layer, of viruses. Usually it’s the key proteins, the ones that give them access to our cells. Our immune cells learn to recognise these proteins and attack anything with them on it.

Anyone infected with SARS-Cov-2 who survives (which is, thankfully, most of us) now have antibodies that recognise the virus. There is no guarantee that what Dave’s immune system recognises SATS-CoV-2 by is what Shanti’s immune system does. It will be a bit of the virus, but not necessarily the same bit!

So an antibody test has to include proteins or fragments of proteins that most human immune systems that recognise SARS-Cov-2 will recognise. And as that will potentially vary from person to person…. Oh dear. Thus a good antibody test probably needs to have several proteins or protein fragments in it to work. This is why it is complex.

Again, the tests will come but the first ones will almost certainly not be specific/reliable enough to really trust.

 

Vaccine

The bad news? Despite all the media hype and suggestions in government announcements of creating a vaccination in 18 months (maybe sooner), it is very unlikely. Sorry. It is very, very unlikely. Don’t get me wrong, I would love us to have one right now, or in a month, or even in 6 months. But unless there is a medical miracle, we won’t and by suggesting to everyone that we might, I think the powers that be are storing up a lot of anger, frustration and other issues

A vaccine needs to do something similar to the Antibody test. It needs to contain something that either is part of the virus or looks like part of it. This is usually:

  • An inactivated version of the virus
  • a fragment of the virus
  • One of the key proteins on the virus
  • Rarely, a related virus that is much less harmful (for example cowpox for smallpox vaccine).

The vaccine is administered and the person creates antibodies to it. Now, when the person is exposed to the real virus, the immune system is ready to attack it. Neat!

Influenza Vaccine is often less than 50% effective

Creating vaccines is a long process. You need to come up with something that is safe to administer, prompts our immune systems to create the antibodies, and the antibody reliably attack the virus the vaccine is for – and nothing else! (Occasionally a new vaccine is found to prompt some people’s immune system to attack other things – like the healthy, useful protein the virus actually attacks). And you have to produce a LOT of that thing if you are going to administer it to a large number of people, such as most of the UK population.

The vaccine has to work on most people as you need 60-70% of people to be immune to SAR-CoV-2 get herd immunity from Covid-19 – the higher the better. The influenza vaccine is often much less effective than 50%, especially in older people.

You are giving the vaccine to healthy people and to lots and lots of them. It has to be really, really, really safe. If it seriously harms 1 in a thousand people (which might sound reasonable at first glance, for treating something as bad as Covid-19) – well, that is almost as bad as Covid-19 itself. You would be harming hundreds of thousands of people.

With a drug you use to treat the ill, you can afford for it to be less safe – as you are only giving it to people who are ill (so a smaller number) and they have more to lose. The risk/reward balance is more likely to be positive for a drug. Even if a drug for a life-threatening illness harms 5% of people but cures 50%, it is worth (with informed consent) using it.

We have never, ever created a vaccine in 18 months before. I’m struggling to get a scientific reference as searches are swamped with talk pieces (like this one!) on why it will take a long time. However, this video by an American doctor  Zubin Damnia who does social media about medical matters explains better than I can and this history of vaccines makes it clear at the top it often takes 10 years.

The bottom line is, much though I want to be wrong, the often stated aim of having a suitable vaccine in 18 months or less will need a medical miracle and a huge amount of work.

After The Peak And With No Vaccine – How Do We Cope?

After the peak, most people are still at risk from Covid-19. As I said earlier, if the Infection Fatality Rate is 0.5% then for each person who died there will be 200 people who are now immune, so if there are 20,000 deaths that is 4 million people immune. 6

If there is no vaccine then we have, I think, four options:

  1. Continue social isolation measures as they are to keep the virus from spreading.
  2. Relax isolation a little and let cases creep up but held as steady rate, but within the capacity of the NHS.
  3. Relax isolation quite a bit, monitor number of admissions to ICU (or something similar) and re-impose strict social isolation at  the current level if things start getting worse.
  4. Relax isolation a lot and massively increase testing and case tracking – copying the South Korea/Singapore approach.

Option 1 to hold us all in isolation is, I think, untenable. People will stop doing it and the impact on our economy must be massive. The impact on our society will also be massive, especially if this continues into the next academic year.

I don’t think we can manage option 4 in the UK yet.

So I think we will see an attempt at option 2, relaxing some social isolation rules (such as allowing restaurants to open and small gatherings) but then option 3, tightening social isolation if numbers of new cases start to build.

Option 4 could become a reality in a few months, especially if we can get people to use mobile phone apps to track movements and aid identifying the contacts of people who become ill,  but not everyone has a mobile phone and I think a good percentage of people will not agree to be tracked.

At present, without a vaccine, we will be living with some sort of social until we reach herd immunity, with at the very least 60% of us immune. How long will that take? 60% of the UK population is 40.5 million people. That equates to 202,500 deaths from Covid-19 to get there (remember, see the bit on IFR above).

This current peak of Covid-19 will last about 3 months, from the start of March to the end of May. It remains to be seen if we exceed the NHS expanded capacity. If we allow 20,000 deaths a peak with 4 million people becoming immune each peak, that’s 10 peaks, so 2.5 years.

A better option could well be to aim for a steady rate of new cases and deaths from Covid-19, say 1000 a week. At that rate herd immunity will take just over 200 weeks, 4 years. If we allow 4000 deaths a week than we could be there in a year, but our NHS would have to be handling the many, many thousands of ill patients that would entail.

Of course, in reality, our treatment of Covid-19 patients will get better over time, so fewer people will die from it, but it will still be a horrible thing to go through. And, if we DO get a vaccine sooner rather than later, many of those people will have died needlessly.

So, as you can see, we are in this for a long while.

The expanded health services, better knowledge of what social movement restrictions work, improved testing (including home testing), even my idea of cards for those immune, would all make life easier, it is not all doom and gloom. But I just wish all of what I have put here was being discussed and shared with people (preferably in a shorter form than this blog!) in a clear and constant message. I think if more people understood where we are and what is likely to to happen (or not), we will save ourselves a lot of issues weeks/months/even years down the line.

I honestly don’t know what the answer is – I don’t think anyone does. Which is why all of this talk about an “exit strategy” results in lots of hand waving and no clear plan.

As ever, if you think I’ve got something wrong, you know of a good academic source covering this, or you simply have a comment – let me know.

Friday Philosophy – Concentrating and Keeping Calm. April 3, 2020

Posted by mwidlake in biology, COVID-19, Friday Philosophy, Perceptions, Private Life, science.
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I was talking with a friend this week (via a webcam of course) about how he had been looking & looking at some misbehaving code for days. His team mates had looked too. It was not working and logically it should work. None of them could work it out. The problem turned out to be a small but obvious mistake.

My guesses for UK cases & deaths. Do Not Trust

This of course happens to us all occasionally, but we both agreed that, at the moment, we have the attention spans of a goldfish and are as easily distracted as a dog in squirrel country. I asked around a few other friends and it seems pretty much universal. All of us are making cups of tea and then taking the milk into the lounge & putting the cup of tea in the fridge. Or walking into the kitchen and asking who got the bread out to make lunch. It was you. The cat is wondering why I open the pouch of cat food and then leave it on the worktop and go do my email for 20 minutes. She’s getting annoyed.

Why are we all failing to function? Because we are all worried. This is one of the things anxiety does to us.

The whole COVID-19 thing is stressful – the feeling of being trapped inside, concern for friends and family, the ever growing numbers of infected & dying. I actually think if you are not at all worried then you are either:

  • Not understanding the situation
  • In denial
  • A total sociopath
  • Someone who should not be allowed out alone
  • Have reached a level of Zen calm usually only attainable by old oriental masters/mistresses

I’m by my nature often in camp 3 above, but even I am worried about this and I know it is making me tetchy and less able to focus. I’m struggling to keep my mind on things. Except on COVID-19. I tend to handle things I find unnerving by studying them and I probably spend about 3 or 4 hours a day looking at the latest information and scientific output on COVID-19. However, I note more things to “look at later” than I actually look at, as I am trying to manage my stress.

After an hour I make myself get up, go trim some roses, play a computer game, read a book. Anything to distract me. I’ve even started talking to the other person in the house and my wife is finding that particularly annoying. Sue seems easily annoyed and quite distracted at the moment. I wonder why?

Another way I cope is I talk with people about topics that are causing me stress. If I can’t talk, I write. Thus I wrote this Friday Philosophy – think of yourself as my counsellor.

I’ve seen a lot of social media “memes” about how long ago the 1st of March feels like, when we first started worrying about this. It seems like months ago, yes? To me it seems like a year. I started worrying about this a good while before the 1st March. I think the worry started about early/mid-February. Why? Because I’m a genius of course. {Note, this is called British self-deprecating sarcasm – I’m not a genius!}. No, the reason I picked up on all of this early was that chance primed me to.

I have a background in biology and some of the job roles I have held over my career have been in healthcare and the biological sciences. One role last year was working with a small biotech company working on immunology. So I take an interest in this sort of thing, it’s “my bag”. I was also pretty ill in December with Influenza (and yes, it WAS influenza, type A – I am not “the first case of COVID-19 in the UK”). So I was convalescing at home and took a specific interest in a new illness spreading through China that was influenza-like… And was worrying the hell out of the Chinese authorities who were coming down on it in a way we have not seen before, even with SARS and MERS.

My play spreadsheet.  I should leave this to the experts really

I have to confess, I initially suspected (wrongly, I hasten to add) that this new disease had escaped from a lab. The way it spread, that it seemed to be ‘flu-like, the rapid response by the authorities. I don’t doubt research into modifying diseases goes on – by the UK, China, USA, the Vatican, by every country with a biotech industry. I know we have the tools to directly mess with genomes, I did it myself, crudely, 30 years ago and I know people now who do it now, with considerable accuracy, for medical and other altruistic reasons. However, genetically engineering an organism leaves traces and when COVID-19 was sequenced there was no sign of this and it could be tracked to similar, previously known samples. I might even know some of the people who sequenced it and checked. But, anyway, that suspicion also made me watch.

The rate of spread in Wuhan was as shocking as the authority’s response and then through February the scientific analyses started appearing. The R(0) number (infection rate) and the high case fatality rate were both high. I’m not an epidemiologist but I had been taught the basics of it and I knew what was coming. No, that’s not right, I suspected what was coming, and I was worried. It was when the number of countries with cases started to increase that I felt I knew what was coming. By the end of February I was sure that unless something huge happened to change it, 2-3% of people, everywhere, would be killed. This was going to be like Spanish ‘flu only quicker (as we all travel so much). I became “The Voice Of Doom”.

On 2nd March I recommended to our CEO that UKOUG cancelled our Ireland event (people & organisations were pulling out so it was making it financially untenable anyway, but my major concern was that this was going to explode in the population). Thankfully the rest of the board agreed. I created my tracking spreadsheet about the 5th March. So far it’s been depressingly good at predicting where we are about a week in advance, and not bad for 10 days. I leave it to the experts for anything beyond that. All so depressing so far.

But Something Huge has happened. Governments did take it seriously. Well, most of them. And those who took it seriously soonest and hardest have fared best. The social lock-downs and preparation work that is going on in the UK is going to reduce the impact down dramatically and, more importantly, give us time to try and find solutions. But it still worries me. And I think they could have done it sooner. But most of the world is taking this very seriously – as it is very serious.

Part of me wants to keep watching how COVID-19 develops, and maybe writing more articles on it. I’ve had some really nice feedback on the first two and I want to do a post on where we might go in the coming months and why. But part of me wants to stop as it is making me very anxious and I’m sick of losing my cups of tea, or being stared at hard by the cat, and the wife asking me what the hell am I doing with the spanner and tin of peas.

I can’t easily listen to the government announcements each day as it is obvious, if you look at the scientific data and what medical professionals are saying, that they are simply not being candid. It’s all “we can beat this in the next few weeks” and “we will get you testing kits this month that are utterly reliable” despite the fact that’s going to need a scientific miracle to do that, let alone develop a reliable vaccine. I understand we need to keep positive but I think bullshitting the population now is only going to make telling them anything they will believe in 2 months even harder. In 6 months time when there is still no reliable vaccine and so many people have been wrongly diagnosed and the first few countries have had this rip through them almost uncontrolled, the lack of candid honesty will come back to roost. I worry about that a lot.

So I’m worried and I’m worried I’m going to be worried for months and months and months.

But for now I’m going to go for my daily (local) walk along a path I know will be almost empty of people and relax.

 

* Note, the graph and the spreadsheet are just “decoration”. They are my wild guesses on what may happen and have no reliability at all. Just saying

 

 

 

COVID-19: What Can We Do to Reduce Social Distancing March 27, 2020

Posted by mwidlake in biology, COVID-19, off-topic, science.
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<<<< COVID-19 Basics: What it is & what it does to us
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The Coming UK Peak and Beyond >>

Summary

The impact of COVID-19 on our society and our economy is going to be long and hard. I hope I am not the first to come up with this idea, but just in case…

Having everyone on lock-down on and off for months will be hard to maintain. But not everyone will need to be in lock-down. You do not need to be locked down if you are immune.

I think we need to look at having a “COVID-19 Immunity Card” – you get the card to prove that you are probably immune to COVID-19 and that you are no longer a danger to others and are not in danger yourself.

Once you have a card you no longer have to abide by social distancing measures in the same way as those not immune. You are also a known “safe” person who can interact with those who are not. This would be particularly reassuring in the “caring” industries.

The number of people with cards will grow over time due to:

  • People being diagnosed with the disease and recovering – not many yet.
  • People being tested and found to have had the disease (possibly without knowing and have recovered) – coming soon?
  • People who have been vaccinated against it – future group.

There are potentially serous drawbacks to this idea. Such a card would be a source of division for as long as we have them and they would be a huge target for criminal activity, but it could help us “sleep with the tiger” of COVID-19.

It could/would allow our economy, health services, and society function more effectively whilst we are living with COVID-19.

Background – Once we “stop” COVID-19 this time, we have a problem…

The UK, like a growing number of countries, is now in a strong, country-wide, social shut-down. The aim is to suppress COVID-19 (see COVID-19: What’s Going To Happen Now ) i.e. drop the levels of person-to-person transmission (The “R” number) below 1. If each person with COVID_19 infects fewer than 1 other person on average, the spread stops. Quickly. It will take another 2-3 weeks for those already infected or sick (as of the date I am writing this, 27/3/20) to develop the symptoms and possibly need hospital treatment, so between now and mid-April we will see cases continuing to rise rapidly, followed by the number of deaths.

Then, something like Mid-April onwards, new cases will drop and, less slowly, the number of deaths.

COVID-19 will have been stopped. However, it will not have gone away, it will still be in the population. If we relax the social isolation we are currently living under, it will start spreading again and we will have another outbreak. Why? As only a small percentage of the population will be immune to the SARS-COV-2 virus. Governments are giving the impression that we will have “beaten COVID-19!” at this point, when the first peak of cases has come and gone, but the scientific consensus is clear that it will return if we all start living normally again. There are several studies going on at present to model what we can do and how. For example, China is relaxing restrictions and the world-wide epidemiological community is watching. For example, this Imperial College Paper on how China is coming out of strict social distancing is interesting.

I think of this as sleeping with a tiger that we don’t want to wake up.

The Imperial/WHO/MRC paper does cover all of this and suggests a way of relaxing social isolation steps and re-introducing them, over a 2 year period. The chances are, this is all going to go on far longer than most people realise and way longer than any of us want!

Reasoning on why COVID-19 will be with us “until something changes”.

The rest of this post is me being an “Armchair Epidemiologist” – proposing untested ideas with only a tenuous grasp of the true facts. But I thought I would put this out there. Note, there will be a lack of links to any solid references from this point. When you see this in articles discussing scientific ideas, it usually indicates it is a thought experiment.

There is general scientific consensus that, if we had better testing, the Case Fatality Rate would be about 1-2%. Case Fatality Rate (CFR) is the percentage of diagnosed cases that die. What we actually need is the Infection Fatality Rate (IFR) of COVID-19:- Taking into account all people who get the disease (whether they show symptoms or not or were tested or not) what is the percentage of people who die. See the Wikipedia entry on CFR for more details of CFR and IFR.

IFR is being argued about by the scientific community as you have to test a large, random set of people to see how common the disease is and testing by most countries is limited to suspected cases. Thus estimates are being made. The really good news is that the estimates of IFR are a lot lower than CFR. numbers seem to vary from 0.2% to 0.6%. See this pre-print of an article on CFR/IFR  and this paper by Nuffield Primary Care Health Sciences  at Oxford University. I’ll be pessimistic and take 0.5%

I am assuming the  Infection Fatality Rate is 0.5%

The reason we need the Infection Fatality Rate is that we can then calculate the number of infected people from the number of people who died – ONCE number of infection and deaths have reduced to low numbers again. You can’t do this (well, I can’t) when the number of new cases or deaths is increasing.

If 10,000 people die in the peak of cases we are currently enduring, if it is killing 0.5% of people and ICU limits are NOT exceeded, that means 2 million people will be immune once the peak has passed (as 99.5% of that 2 million have it and survive).

However, 64 Million will not be immune.

As has been described, we could now relax social distancing and let businesses and the economy start up to some degree again – but then tighten up social distancing again when cases or ICU admissions rise. We have a series of mini-outbreaks.

We have a population of 66 million. At 2 Million becoming immune in each “Outbreak”, we would need 20 outbreaks to get to a level of people who have had the disease where herd immunity is stopping the disease spreading – 60% or 44 or so million people (but we would still have 22 million susceptible to the disease).

With a peak every 2 months (so no single one exceeds the expanded capabilities of our NHS) getting to 60% immunity would take… several years. This is why all those discussions about getting herd immunity in weeks or months is, frankly, naive. We could only have that happen if we did not control the outbreak.

It might be that we can work out a level of social distancing that allows the economy to keep some semblance of normality and the COVID-19 cases at a level the NHS can keep up with, but that is a very, very fine tightrope to walk.

In any case, if we do not simply let COVID-19 rip through our society (killing more people than it would if controlled, as it vastly overwhelms the health services) we have to sleep with the tiger until we we have another option. But I think there is a way to make sleeping with the tiger more comfortable.

People will become immune to SARS-COV-2

A reliable, widely available test for seeing if someone has had COVID-19 and is now resistant to the  SARS-COV-2 is desperately needed and, I think, will become available soon – in a couple of months, long before a vaccine arrives.

We will then have 2 ways of knowing someone is immune:

  • Those who were tested positive for COVID and survived. They are immune.
  • Those that pass an antibody test. They are probably immune – depending on the reliability of the test. There could be several tests that have different levels of reliability.

These people can be given an “I am immune” card and they will not be limited (at least not so much) in lock downs.

Initially there will only be a hundred thousand people who can have the card, as they have been identified by testing to have had COVID_19,  have got better, and are now immune . But, crucially, a disproportionately high percentage of them will be NHS and first responder workers. This is because those groups are suffering very high exposure to COVID-19, by the very nature of what they do. The ranks of these groups are (and will continue to be) literally decimated by COVID-19. Lots and lots and lots of nurses, doctors, lab staff, cleaners, police, paramedics, GPs are going to be in the first wave getting ill.

Once we have the cheap, reliable antibody test , we can look for the rest of the 2 million.

As you can see, the more testing we do, both for having COVID-19 or for having antibodies against SARS-COV-2, the more people we can give an immunity card.

Over time, especially if we have further outbreaks, the number of people who are immune and are found via the above will increase.

Later, when vaccines are developed, there will be a third group of people we can count as immune:

  • Those who are vaccinated
  • Better still, those who are vaccinated and are latter tested for (and pass) an antibody test.

The first vaccines are likely to not be very effective – think the low end of the level of protection the annul ‘flu vaccines achieve, 20-40%. The antibody tests to confirm you have immune to SARS-COV-2 might also vary. But the details on the card will give which tests and vaccines you have had.

The card will hold details of why the person is immune, what test(s) were used to identify they had the disease, what vaccine(s) they had had, and when these events occurred. Minimal details would be held on the card itself.

A central database would hold the details of vaccination & test efficacy, corroborative information about the person etc.

If the reliability of historical tests or vaccinations change, then the immunity status of the individual may change.

The database of information would of course need to be well secured, kept in more than one place (so that a single IT disaster does not destroy all this key information) and protected. These are technical problems that can be solved.

Drawbacks off the COVID-19 Immunity Card

The cards will need to be very reliable, trusted, and protected from abuse.

Both the data they hold (or link to) and the information about the person the card is for needs to be highly dependable. The data needs to specify which sort of immunity this person has, when they were ill (if they have been) or tested, when any vaccine(s) were administered and when. It may turn out that immunity to SARS-COV-2 will reduce over time (that is, our immune systems “forget” about the disease) and the virus may mutate over time such that it avoids our immune response (whether natural or via vaccine).

The link to the person will need to be reliable, so no one can use a stolen or fake card. Obviously pictures, basic information, etc need to be on the card for a quick check, and information on the card links to a data source that can be used to further check identity and give more detailed information about immunity, such as may be needed if the person is in a medical situation.

It strikes me that this is a perfect use for blockchain. Each card, the data associated with it, when & how it is updates, can be accurately tracked in a way that is very, very hard to fake.

The data and the card should link to nothing else. There would be a temptation to be able cross reference the medical data with socioeconomic data, geographic information, even information about shopping habits to see if there are any correlations between between these factors and how people respond to COVID-19. This would be a nightmare as it introduces questions of consent, privacy, abuse of the data, fear of being spied upon.  Ensuring this card is for one purpose alone, with no link to anything else, would reduce the next drawback.

ID cards by the back door.

This will effectively be introducing ID cards, which some people object to strongly on moral or philosophical grounds. I’m not going to do more than note that this is an issue and observe that many societies have ID cards already. If these cards are kept to this one purpose, it would help make them more acceptable.

Criminality

Of course, as soon as such a valuable thing as a card that allows you to avoid social limitations is available, some people will want one, even though they know they are not immune. Criminals will want to create and sell them, so we need something, probably several things, (again, like a blockchain identifier on the card) to help guard against this. I would also suggest we would want to see strong punishment of individuals who try to use a fake card or get one by deceit. After all, these are probably the same selfish gits who bought all the toilet paper. As for criminals trying to make and sell fake cards, the punishments would be draconian – they would be putting a lot of people at risk.

Two-Tier Society

The cards would by their nature split society. Those who have a card would have more freedom. Those who do not would not.

Some people would never be able to get a card as they are immunocompromised  or similarly unable to be vaccinated.

Human nature says some people would discriminate or persecute people who are not immune if there was a way to identify this. I actually see this as the main reason to not have such a card.

Laws would be required to back up a repeated and strong message about why such discrimination is utterly wrong.

SARS-COV-2 Could Change

We do not yet know how the virus underlying COVID-19 will change over time. It is mutating – but ALL life mutates. We use the mutation to track how SARS-COV-2 has spread across the globe and the mutations, so far, are not known to alter it’s infection rate or how it impacts people (though I think I have seen some suggestions about this on social media that are more trustworthy than general scuttle).

However if it turns out that C-19 becomes C-23 and C-28 etc like Influenzela A, the card scheme still works but you are now stuck with identity cards and potential discrimination against those who are not immune etc.

End Life of the cards

I would want to see an agreed termination point for the cards stated when they are brought in. They or the data they link to will be deleted utterly in 3 years time. This can only be changed by a cross-political-party agreement.

 

That’s my idea. If you have any comments – for, against, highlight things I have wrong – I would love to hear.

COVID-19: What’s Going To Happen Now March 24, 2020

Posted by mwidlake in biology, COVID-19, off-topic, Perceptions, Private Life, science.
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<< COVID-19 Basics. What it is & what it does to us

  COVID-19: What can we do to Reduce Social Distancing >>

I thought I’d record what the scientific evidence and epidemiological modelling is saying about what is going to happen in respect of COVID-19 in the UK (and, to some extent, elsewhere) over the next weeks and months. As with my intro to COVID-19 this post is mostly “for me”. I’m sharing it but please, please, treat all of this post (not the science I link to!) with some scepticism.

The figures are shocking so I want to spell out right at the start that, if our governments does what it needs to do and does it right (and over the last 2 or 3 weeks the UK government has fallen a tad short on this, but it’s improving) in the end over 99% of us will be OK. If they get it wrong, it’s more like 97% of us will come through this.

And, I feel it is important to say:

90% of even high risk people will also be OK.

I strongly feel that the message is constantly that it is the at-risk people who are dying and not that most people at risk will be OK. Yes, COVID-19 is more of a danger to those over 70 and those with underlying medical conditions, but with the media and government constantly saying “the people who died are old” etc it makes it sound like COVID-19 is a death sentence to them – and it is not.

Yes, I’m quite angry about that that poor messaging.

Source of Epidemiological information

ICU beds needed per 100,000 people

My main source is This paper by Imperial College in collaboration with the World Health Organisation and British Medical Research Council. If you can, please read this paper. It spells out how COVID-19 will spread and what happens when the NHS intensive care unit (ICU) beds are all full. It’s a hard read in two ways.  It is technically dense; and it says things people are still refusing to believe:

  • If we had done nothing and had an infinite number of critical care beds, it would burn through the population of the UK (and all other countries) in 3 months, infecting 81% of people. At that point herd immunity stops it.
  • In the UK 510,000 people would die (COVID-19 kills about 1% of people even with ICU treatment). 2.2M would die in the USA.
  • At the time of publication of the report, the “mitigation” plans by the UK government would have failed to stop even more deaths (more than 1%) as the NHS would have been overwhelmed by the 2nd week of April.
  • At the peak we would have needed 30 times the number of ICU beds we have.
  • The paper does not fully spell this out, but if you need an ICU bed and there is not one, you will almost certainly die. Thus the death rate would be more like 2.3% {Note, that is my figure, I have not spotted it in the report. It is based on 4.4% of the population needing hospitalisation and 30% of them needing critical care, figures that are in the report}. I’ll let you work that out based on the UK population of 66.5 million. OK, it’s about 1.17 million.

These figures are truly scary. They won’t happen now as it shocked our government enough to ramp up the social isolation. If anyone questions why we need the social isolation, give them the figures. If they refuse to believe them,  tell them to read the paper and various articles based on it and point out where they are significantly wrong. If they won’t, thank them for their baseless “opinion”.

The calculation of 510,000 deaths in the UK did not factor in self-isolating naturally, as we all saw people fall ill and die. That would slow down the disease.

However, if the hospital is full to absolute bursting capacity with COVID-19 patients, any person who needs ICU care for other illnesses (cancer, cardiovascular disease, stroke) or accident. How do you fit them in? Deaths for other reasons will increase.

One thing I am not sure of is that in the paper critical care is stated as “invasive mechanical ventilation or ECMO”. If you need just a ventilator and one is not available, I’m pretty sure you would also be likely to die or suffer brain and other organ damage from oxygen deprivation.

As I understand it, this report is what made the UK and other governments take COVID-19 a lot more seriously and really understand the need to implement strict social isolation.

I’d like to say why I put so much trust in this source:

  1. The three organisations behind it are all highly respected (WHO, MRC, and Imperial College)
  2. They state clearly at the top their assumptions – the R number, incubation period, types of social isolation, the percentage of people who will comply with each one.
  3. They created a model that was then verified by running the numbers and seeing if it predicted what had happened in reality to that point.
  4. The subject matter experts I follow have all endorsed this piece of work.

Mitigation or Suppression

The Imperial College report spells out the distinction between Mitigation and Suppression:

Mitigation is where you reduce the R number (the number of people each infected person in turn infects) down from the natural number of around 2.4 but it is still above 1. At this rate the disease continues to spread and the number of cases per day continues to increase, but more slowly. The idea seems to be that it would lead to herd immunity. This was the UK governments aim until Monday 16th March.

Suppression is where you reduce the R number below 1. Within a few weeks the disease is no longer spreading. But it is still there in the population. This is what Wuhan did and Italy is making progress on.

To achieve mitigation the government isolated people infected, asked those who had had contact with them to self isolate, and asked us all to wash our hands and keep a distance and think about working from home. The impact on daily life, business, the economy is minimal. Further steps would be introduced later, like closing universities and schools.

The Imperial college report demonstrated that mitigation was a terrible idea as the number of cases would still explode, but just be delayed a little, and the NHS would be absolutely overwhelmed.

The graph at the top of this article shows the mitigation steps being considered and how it only shifted the curve and did not lower to anywhere like the NHS ICU capacity. It was simply not enough.

Isolation involves the sort of steps most of us would have previously thought only an authoritarian regime like China or North Korea could manage. Schools, universities and non-critical business shut, everyone not doing a critical job made to stay at home except to buy food etc. Basically, Wuhan. And now Italy is doing very similar. As of the 23rd March the UK is following suit.

Most western countries are now implementing many of the steps needed for isolation levels that will suppress COVID-19, but not all the steps needed.

The graph to the right shows the impact of two implementations of Isolation, both implementing several measures but the orange line does not include closing schools and universities. The green line does. The green line keeps the number of cases within the NHS ICU capactiy, the orange does not. That is why schools and universities were closed.

The graph also makes the point about the main problem with Isolation. It is only stopping the virus spreading, it is NOT getting rid of it. Remember, no one is immune unless they have had COVID-19. When the steps to enforce isolation are relaxed, COVID-19 will burst back.

This is potentially the position that China is in. They have locked down Wuhan province tightly and it worked. The number of cases there rocketed even after the lock-down but have since reduced, almost as fast as they increased. China as a whole now have very few new cases. The lock-down is being relaxed as I prepare this post. Epidemiologists expect the number of cases in China to increase again.

The degree to which either mitigation or suppression is enforced obviously impacts society and commerce. The Imperial College report makes the point that they are not addressing those concerns, they are simply saying what social isolation changes will have what effect on COVID_19 spread, deaths, and the ability of the NHS to cope.

Delayed impact.

UK daily cases to March 20th, Italy deaths to March 20.

This next point is being made widely, by both non-scientific observers and the scientific community, but I want to re-iterate it as it is so far being played down by government (which could be changing at the very moment I am typing).

There is no way to avoid the huge increase in COVID-19 cases and deaths that are going to happen in the UK over the next 2-3 weeks. Expect our levels to be the same levels as Italy. In fact, expect them to be 20, 30% higher. This is because the UK government were too slow to lock down and did it in stages when, based on the epidemiology, we should have shut down totally on Monday 16th when the paper I reference was published, or within 2 days to allow for planning.

Up until now COVID-19 has been spreading exponentially (1 person has it, passes it to 2-3 people. They pass it to 4 people who pass it to 8…16…. 32… 64… 128… 256… 512… 1024). This has been seen in the way the number of case had double every 3-4 days, deaths are now following the same pattern.

The two graphs to the right show the number of cases in the UK to the 20th March above, and the number of deaths in Italy to the 20th. They look like the same graph as they sort of are. This is how something grows exponentially when the growth rate is the same – the same as both cases and deaths are caused by the same thing.

(these graphs are from Worldometers – I use this site as I think the John Hopkins site has more incorrect information on it).

Covid-19 takes on average 5.1 days to show symptoms from when you catch it (this can be up to 2 weeks – with all these averages there will be some cases which are two or three times as long). It takes less time, 4.6 days on average, from when you catch it to when you spread it. So you can spread the disease before you get ill. And some people do not get ill (or only very mildly) and spread it. Like “Typhoid Mary”. If you are going to be ill enough to need hospitalisation it takes 5 days from first symptoms for you to deteriorate to that point.. At this point you will be admitted to hospital, tested, and will join the number of confirmed cases. If you are going to die (I know, this sounds really callous) that is another few days. The report does not spell it out but going on the figures they use for time spent in intensive care in the model, about a week.

Add it all together and someone who dies of COVID-19 today caught it 15-20 days ago on average, so the spike will be delayed that much.

Yesterday, 23rd March, almost total lock-down in the UK was announced. Cases and deaths will rise for 20 more days in the UK. Exponentially. To Italy levels, maybe 20-30% higher. Then they will plateau for a few days and drop quickly, depending on how well people respect the social distancing or are forced to. I am expecting over 9,000 will die in this first spike, with a peak number of deaths between 750 and 900 in one day. Sadly my predictions so far have all been correct or a little too optimistic.

That is the reality and that is why we are seeing the actions of our government that have never been seen outside World Wars before.

Three choices – or is it four?

To summarise the above, there were 3 choices available to the UK (and all other countries):

  1. Let COVID-19 burn through the population in 3 months. It would kill 2-3% of the population as the NHS collapsed and also anyone who needed medical treatment during that time would probably not get it. During the 3 months lots of people would have “bad ‘flu”. 80%  of survivors would be resistant to COVID-19 for now.
  2. Mitigate the impact by the measures implemented in stages during mid-March, reduce the impact a little and stretch the curve a little, and have 1.5-2.5% of the population die over 4 months. 70% of survivors {my guess!} would be resistant to COVID-19 for now.
  3. Suppress COVID-19, 10,000 dead and everyone in lock-down until “something changes”, which could be 18 months or more.  A tiny percent, maybe 5% {my guess} resistant to COVID-19.

The UK government chose option 3, after considering 2 for a while (and thus increasing the death count by, hmmm, 3,000 in that first spike).

The “something changes” in option 3 is that scientist create a vaccine for SARS-COV-2, the underlying organism to COVID-19, or we have a quick and reliable immunity test for it that allows those who have survived the disease to move about unrestricted. See further down in this post. Most of us stay in lock-down until “something changes”

But this Imperial College paper has a solution 4:

Turning social isolation up and down

  1. sorry, 4. I can’t get the layout to work. solution 4 is to
    1. suppress.
    2. Let the known bubble of cases come and deal with it.
    3. Once it has passed, relax (not remove!) the Suppression rules to let business and normal life start up again.
    4. Monitor the number of COVID-19 cases coming into ICU.
    5. When it hits a threshold, back to total lockdown and deal with the next bubble.
    6. Repeat.

It is a clever idea. No one wants to stay at home until a vaccine is created in 18 months. Economically, total lock-down until we have a vaccine would be a disaster. So varying the lock-down based on NHS demand indicators would allow some relief from the restrictions. But not back to normal.

Option 4 comes at a cost. More people will die reach time you relax the lock-down, depending on what is allowed. Much of the rest of the paper details this plan and, based on the figures they state at the top of the report in respect of how many people will abide by the rules, what different isolation strategies and key triggers (how many new COVID-19 ICU cases in a week) to increase isolation levels, gives death rates varying from 8,700 to 120,000. This also takes into account a range of R values (how easy it spreads naturally) as there is still some uncertainty about this.

The paper makes one thing clear – we would need to maintain the isolation levels for suppression for 2 years – their cautious estimate of how long it will be until we have a widely available vaccine.

The best case is deaths creep up (after the initial surge we can no longer avoid) with very strong lockdown only relaxed at very low levels of ICU cases and deaths. I personally doubt very strongly that enough people will abide by the rules for long and, as people start ignoring them, others will feel “why should I play by the rules when they don’t”.

I do not have anything like the understanding of human nature needed to predict how people are going to react so I won’t. But the figures being bandied around a few days of keeping UK deaths to 8,000 or less seem utter fantasy to me.

The “The hammer and the dance” paper…

Some of you may have come across “The hammer and the dance”, which is based on a paper by Tomas Pueyo on “Medium”, a home for science papers that have not been verified by anyone. I would not normally look at things here very much but several people have mentioned the paper or even linked to it. If you recognise the term, you will probably recognise the “dance” part as choice 4 above.

Context is paramount

Lots of numbers are being thrown about, but to understand the true impact of COVID-19 those numbers need to be interpreted in light of some general background.

Let’s start with the base rate of mortality. In the UK there were 541,589 deaths in 2018. That give 9.3 deaths per 1,000 residents. See the office for national statistics article for this figure. Over the year that is 1,483 deaths a day, from all causes. People keep on insisting on comparing COVID-19 to influenza. I’ve struggled to get a definitive number of deaths due to Influenza in the UK but it seems to be between 8,000 and 17,000 a year. Let’s take 17,000 as a top estimate, that is 46 a day.

(you may wonder why it is hard to say how many people die of influenza. Well, influenza kills people who are already seriously ill and likely to die anyway, and I believe not every death attributed to influenza is tested for sure to be influenza.

Our key figures are 1,482 deaths by any means a day and 46 a day from influenza, in the UK.

On the 21st March 56 people in the UK died of COVID-19. More than Influenza, about 4% of the daily mortality rate. Bad, but nothing that significant. In Italy, 793 people died of COVID-19 on 21st March (and it looks like that might be the peak). Our figures in the UK for known diagnoses and deaths are following the Italy pattern very closely (for very good scientific reasons) just 2 weeks behind – 15 days to be more precise. In 15 days the death rate for COVID_19 is likely to be very similar to Italy so, despite my hunch the UK peak will be higher, let’s use Italy’s peak number:

  • 50% of the total death rate for everything in the UK.
  • And 17 times the death rate by ‘flu.

So COVID-19 is incredibly serious,  but it could have been worse. It looks like for a period at least, for each country, it will increase the daily death rate by 50% and maybe more. But it is not killing a large percentages of the population.

I’ve seen some scare stories about this disease sending us back to the dark ages as it kills half the population of the world. Rubbish. It might stop the world population growing for a year.

Why will social distancing last 18 months?

No one is naturally immune to COVID-19 until they have had it. Let’s assume that once you have had it you are immune for several years, as you are with many other viral diseases (Influenza A is a special case as changes so fast and in a way that reduces the effectiveness of both vaccines and immunity via exposure).

We could let COVID-19 spread naturally or at least in a contained way – but it will overwhelm our health services as discussed, and 1-3% of us would die.

The other way is to create a vaccine, which gives immunity or partial immunity without having the disease (or maybe a very mild version of it). Vaccination works, it rid us of smallpox totally and, until the loony anti-vaxxer movement got going, it was vastly reducing measles, rubella and many other diseases.

But creating a vaccine that works is hard. Lots of biomedical scientists are working on it and we might get lucky and someone comes up with a very effective vaccine that can be created in bulk, but by lucky we are still talking months. (There is at least one early trial running – but that absolutely does not mean it will be available next month!)

Any vaccine has to be tested, proven effective, and shown not to itself harm.

All of this is why specialist in the field all say “18 months”. It’s a guess based on science and experience. It could take longer, it could be only 12 months, it might be that an initial vaccine is only as effective as the yearly flu vaccine (the flu vaccine generally protects 40-60% of people – see  this oxford university paper).

We can test for if people currently have COVID-19, the test is accurate and relatively cheap. It checks for the RNA of the virus, an established diagnostic practice. Production of the test is being massively increased and improved and we need that so we can better track the disease and accurately identify who has the disease and put them in isolation. In the short term, wider testing will help a lot and those countries that have gone in for huge testing efforts (South Korea and Singapore are examples) have done well in containing COVID-19.

The other tool we really need is a test for immunity, which is usually for the antibodies to a disease. Again, these tests take time to devise. If we could identify those who have had the disease (but were not tested) and are now immune. They would not need to be isolating themselves. A small and growing part of our population could return to normal. But we have no idea when such a tool will be ready, how accurate it is, how cheap it is to do etc.

Finally, scientists need to work out if immunity to COVID-19 is long-lasting, for how long, and if the immunity is strong or weak. We just do not know yet.

Until we have a vaccine (ideally), or the immunity test (it would really help) we have to suppress COVID-19 via social distancing etc.

Basically we are sleeping with a tiger. Best not wake her.

Disclaimer

All of what I put here is based on what is said by experts, scientists, epidemiologists. I’m just pulling some of it together. As I said in the previous blog, I am not an expert in any of this. I’ll make it clear when something is my opinion. I also want to highlight that I only look at sources that I feel are backed by good science. The only information I take from the government is official statistics on cases & deaths. I’m heartened that our government is now taking the spread and impact of COVID-19 more seriously but I remain angry that the experts told them what was coming weeks ago and they were slow to act, putting business concerns before lives.

Any mistakes in this blog post are mine. There are bound to be a couple.

I would love to hear about sources of information you feel are good. I had several excellent sources pointed out to me after my last post, including being corrected on a couple of counts – which I am very happy about.

However, I will probably ignore anything based on rumour or anecdote. Ginger & Garlic are not going to boost your immune system and protect you, quinine is almost certainly not a magic protector. If you have a peer reviewed article in a reputable journal or the support of a respected epidemiologist to back those opinions, then let me know.

 

COVID-19: Information And Outlook March 13, 2020

Posted by mwidlake in biology, COVID-19, off-topic, Private Life, science, Uncategorized.
Tags: , , , ,
11 comments

Outlook for the months ahead >>
Reducing the need for social distancing by knowing who is immune>>>>
The coming UK Peak and Beyond >>>>>>

I decided to put together some information on COVID-19 purely for my own interest – but then decided I might as well put it on a blog post. I’m only going to link to what I feel are reputable sources, nothing from tabloid papers or people promoting conspiracy theories.

If you know of a good site I should include or there is an area I have not touched on that you would like more information on, please feel free to let me know.

Update. At long last, as of the evening of Monday 16th March, the UK government listened to the WHO and other epidemiologists and accepted that draconian measures to suppress COVID-19 (reduce the R rate, the number of people each infected person in turn infects to below 1) rather than mitigate it (reduce the natural R value of 2.4 towards 1 but above 1) will save thousands of lives.

This paper by the Imperial College London in conjunction with the Medical Reaserch Council & WHO is being cited as the root of this change in opinion. It’s a hard read as it is a scientific paper, but it is excellent. It helps make clear many things such as the local spread rate, infection rate, how it transmits between countries. the likely number of real cases as opposed to tested and verified cases. And the simulations match what we have seen to date.

In summary, suppression, such has been managed in South Korea and China, virtually stops the disease for a while. It does not end it. When the measures to suppress it (very strong social control) it will burst out again. There is always a chance it will escaped to areas it is not suppressed and blow up again. But it buys time to work on a vaccine and develop better treatment regimes.

Mitigation slows the spread down. But it continues to spread. An argument was put forward that this will develop “herd immunity” by letting most people get the disease. It means it would be over sooner – but at the cost of hundreds of thousands of lives, just in the UK. The NHS would be utterly swamped during this time.

I’ll move this down into the body of this post later.

{Update 15/4 – I obviously did not move this down as I feel that change of direction was so key}.

 

Firstly, for anyone who does not know me or just stumbles over this page via “Google”, I am not an expert in any of this – I am not a medic, I am not a scientist, and I am certainly not an epidemiologist (someone who studies the transmission of disease). I’m a computer professional with a really old degree in genetics & zoology who has at times worked on systems for the UK National Health Service (NHS), the Human Genome project, and some other scientific organisations.

Secondly, although this is a very serious disease and it is going to continue to have a huge impact,  most people who get it will not be seriously ill. We are not all going to die!

Most people with underlying medical conditions or who are elderly are also going to be fine

The press, at least in the UK, keeps making a huge point that anyone who dies had “Underlying medical conditions” and it is affecting “the old” more. This is true, but the message that comes across is that if you are old or have an underlying medical condition you will die. This is not true.

Even if you are 79 with diabetes and are diagnosed with COVID-19, you have over an 85% chance of being OK, even if you develop the symptoms.

However, the fact that this disease is eventually going to kill tens, hundreds of thousands of people {Update 15/3: 127,000 worldwide so far and that will be an under-estimate , so hundreds of thousands. I’m sure it will hit the million by June. UK it is 13,000 including care homes} is why saying “I’m stronger than this” or “I’m not letting it impact ME!” is, in my opinion, a highly arrogant or stupid approach. Just as wrong is making it the focus of your life. Most of us, around 90-95%, will be mildly ill at most, or not noticeably ill at all. {Caveat – by mildly ill, you may well feel terrible and spend a few days in bed, but that’s like a normal dose of ‘flu.  Take it from someone who has spent a week on ventilators recently, a few days in bed is nothing 🙂 }

Thirdly, though COVID-19 is going to kill quite a few people, the main impact is probably going to be what it does to our health services. It is almost certainly going to over-whelm the health services of most countries, as it has in Italy. Preventative actions, 99% of what we can do, is aimed to spread the load on the health services so that as many people can be treated as best as possible. It is absolutely key that we slow down the rate of cases by not getting together as groups and taking the simple precautions of washing hands well with soap, catching coughs in tissues, things like that. {update 15/4 – THe NHS did an amazing job of preparation. The field hospitals built are not being used very much yet, but the NHS has been sorely tested. Any treatment for other conditions that can be delayed seems to have been deleyed}

This article by The Lancet explains in some detail (maybe too much for general consumption) why social distancing and hand washing are vital to “flattening the hump” and helping the health services cope.

As ever, the best approach is a balance. Personally, I am concerned and I am going to avoid mixing with large numbers of people I do not know. I am actually in an “at risk” category as I was ill with influenza & pneumonia in December, in intensive care getting the sort of treatment bad cases of COVID-19 are getting now. But I am not self-isolating. If I get symptoms, I will self-isolate.

Basics

Names and terms

COVID-19 is the name of the disease. It was first reported in Wuhan in China on the 17th November 2019 but came to general prominence in early 2020 as it spread and infected more people, who then started dying in numbers. The World Health Organisation was informed (WHO).

 

The disease is caused by a virus called SARS-CoV-2. SARS stands for “Severe Acute Respiratory Syndrome” which describes what it does to people. It can cause a serious and sudden problem with breathing, which is when it can be fatal. CoV stands for Coronavirus, which is the type of virus.

It is commonly referred to in the media as “Coronavirus”, which is not a very accurate name. It would be a bit like going to a restaurant and ordering “mammal” (beef, lamb, pork, cat). But the name has stuck and is understood to mean the disease COVID-19 that is worrying everyone at the moment.

This wikipedia article describes the COVID-19 epidemic and this wiipedia article describes the disease itself

What COVID-19 does to you

The virus infects your lungs. It attacks the lining of the alveoli, the little “bags” in the lungs which absorb oxygen and release carbon dioxide. That’s why in mild cases you cough and in serious cases you get short of breath while at rest. If you are sitting quietly but finding you are having to breath hard (as if you have just exercised but you have not), contact the health services immediately. And if you pass out due to not being able to breath, call an ambulance (when you wake up, obviously…).

When the alveoli are infected by the virus they fill with fluid and their linings are damaged. This stops them from absorbing oxygen. All the cells in your body need oxygen, delivered by your blood. In a serious case of COVID-19 you have to breath harder and harder to get that oxygen until you reach a point where you simply cannot breath in and out hard enough.

The treatment is simple. Normal air holds about 20% oxygen, so the medical staff give patients air with extra oxygen in it, or even 100% oxygen, via a mask. If this is not enough a ventilator is used, which is basically a pump or fan that blows the oxygen out under pressure and pushes it into the patient’s lungs. It reduces the effort of breathing also. Ventilators come in increasing powers.

If this is still not enough, the patient is anaesthetised to make them unconscious and a tube is put down the throat (this is called intubation) which is used to push oxygen directly into the lungs. Making patients unconscious also reduces their need for oxygen. If even this is not enough the only final step is to use an artificial lung such as is used in major heart surgery. Hospitals won’t have many (or any!) of those.

In these extreme cases where more and more powerful ventilation is needed then the patient is possibly suffering from something called a Cytokine storm. Basically, the immune system over-reacts and causes damage to other organs like the kidneys.

Normal influenza tends to attack higher in the lungs, so is less dangerous. This is part of the reason COVID-19 is worse than influenza.

This article on how it impacts your lungs is quite technical but very good. The article then goes on to explain how the impact on our health services is a massive concern.

 

What we need to do to slow the spread

COVID-19 can no longer be stopped. To be frank,  it could not be stopped 3 weeks ago. Once enough people were infected with the disease, it became impossible to track them all down by contacting all the people who someone diagnosed with the disease had interacted with. What we could have done is taken the advice of the WHO and the example/evidence of what was coming set by other European countries and locked down earlier. {Update 15/4 – I strongly feel that the government had clear evidence to take each step it took at least a week earlier and it would have saved thousands of lives}.

Two main factors control how quickly a disease spreads:

  • How easily it is passed from one person to another
  • How many people an infected person is in contact with

That second point is not just the people the infected person is physically in a room with. It is, for example, if they cough on a door handle or touch it after coughing into their hand, the live virus will be on the handle. The people who then touch the door handle can be infected.

Washing yours hands with soap and not touching your face is reducing how easily it is passed.

Banning large gatherings reduces how many people are in contact.

Self-isolating will greatly reduce how many people you can infect (or can infect you).

This video describes how exponential growth works  and why reducing gatherings and simply hygiene will slow down the spread of the disease, with COVID-19 as the example.

It also explains how you can tell if things are getting worse or could be getting better. It is to do with the “inflection point”, when the number of new cases starts to drop. Until that happens, it’s going to get worse. This is a significant part on what epidemiologists look at in respect of how a current illness is spreading. In the UK, Spain, US, pretty much all countries where you cannot control the population, the rate of spread is staying high and the numbers of new cases and deaths is growing exponentially. This is what makes COVID-19 such a problem and why scientists worried back in January. It spreads really well and sometimes before symptoms show, which is why we all need to wash our hands, keep away from large gatherings, cover our coughs. You might feel fine, you could be spreading this.

Why washing with soap is the best protection

A virus is piece of RNA (very similar to DNA) covered in a coat of fat – called a lipid layer. Soap dissolves fat. That is why soap is so good at destroying viruses like COVID-19. Alcohol can do the same but it needs to be strong alcohol (70% or more) and works best if it also contains a soap or detergent.

The antibacterial chemicals in antibacterial cleaner do nothing to viruses. Bacteria are totally different to viruses, Bacteria are much more complex.

This twitter thread explains in some detail how soap destroys viruses

 

Monitoring (probably what most people are staring at)

The below are links to pages with info that is updated regularly.

****

Update, 19/3. The data on number of cases coming out for the UK has become less unreliable. The official Public Health England page is not being update until later and later in the day – and it is for figures for the previous day. Worldometers figures do not match the Public Health England figures for most of the last 2 weeks now, except the last 3 days. I think the official figures get corrected but worldometers is not picking up those corrections.

I still check both but I use the official public health England figures for my own trending.

Some days, most annoyingly for me the 16th March, have a figure for new cases that is not at all in line with those before and after. In fact, I think unbelievably different.

****

I tend to go to this worldometers  site as it is updated quicker than the official UK one.  On Friday 13th in the evening it showed an increase in the day’s total and the 11th death before the official UK site did. However, it does not seem to be corrected in retrospect like the official UK one is (I am not sure if that is good or bad)

This is the UK government page that tracks UK COVID-19 cases . It is designed for PC. For mobile phones go to this entry point and pick the option Note that it is a day behind. Information is gathered as-of 9am in the morning and is usually published at around 2pm. {this is now more like 6pm in the evening)

{update 24/3 I removed the link to John Hopkins as their figures consistently fail to match the UK government figures in any way, or the worldometers numbers – which are more consistent between them. Also, a JH person was tweeting how it was THE BEST source and did not reply to two response pointing out it is flawed. It might look nice but it is a poor source of data.}

Lots of people have shared the John Hopkins institute site, but I find information drops off it or the list of countries on the left do not match what is highlighted on the map, so I don’t it.

This page is a global view.  I have to confess, I have not looked at it in a couple of days, but it has lots of interesting information

 

Why certain diseases make things worse

As has been widely shared, a lot of people dying “have underlying medical conditions” or are old. I want to stress that people who are old or have these conditions (and even both)  will most likely recover. But it is true that if you have cardiovascular disease, diabetes, high blood pressure and several other conditions, you are at higher risk. The advice is to maintain your treatment and to keep as fit and healthy as you can. If you can exercise, do so!

If you are generally in poor health or have a debilitating condition, all disease are going to impact you more. Especially anything that reduces your lung function or blood supply as the virus makes you ill by reducing how much oxygen is absorbed by your lungs and taken to e.g. your brain and liver by the blood. Maybe now is a good time to stop smoking if you do!

I could not understand the increased diabetes risk. A suggested answer is very technical, but it might be to do with the levels of ACE & ACE2 proteins you have. COVID-19 seems to enter cells by using our own ACE2 proteins, but it is unknown if this is a genuine link or not.

This “The Lancet” article describes  suggests why diabetes and hypertension make you more susceptible to COVID 19. It’s short but quite technical. To balance that, the European Society of Cardiology claim there is no link (thank you David Harper for that).

This does highlight that COVID-19 is a new disease, most focus is on understanding and treating it and details like this will become clearer over time.

I should stress, never stop taking medicine based on social media guff – including this page! Even *IF* there is a link between drug X and COVID-19 susceptibility, you are taking drug X for a good reason and that reason has not disappeared. If the potential impact is large, it will be obvious to medics who will highlight it as an issue.

What facilities do the UK have to treat COVID-19?

According to announcements by the government on how well prepared we are in the UK for the “peak” of cases (which we are no where near yet):

Apparently in the UK we have 4,000 intensive care beds and “more are being made available” but there seems to be no detail on that.

We have 5,000 ventilators. The government is asking other companies to make them.

Update 19/3 the UK government is talking to companies about the details of making more ventilators and I know of at least one company that is offering to make many more. The issues is that there are stringent tests for suppliers of medical equipment and of the equipment itself. Any equipment used for medical purposes has to be built in a clean environment.

5 hospitals are stated as having ECMO equipment (Extra-corporeal Membrane Oxygenation machines) available for treating COVID-19 patients. These can re-oxygenate blood in the the same way the lungs do. They are massive and complex and they won’t be able to build extra ones for months – and of course every country will want them.

These figures are oddly “round” which suggests they are estimates or guesses. As the only real treatment for COVID-19 is extra oxygen and ventilating patients, then treatment will again be limited by the equipment we have or can be made. I’m no expert on equipment manufacture, I’ve seen no information on how easy it would be to ramp up production but I do know that when our Prime Minister asked companies that don’t make them to swap production to them the answer was “give us a full specification and a set of patterns and we *might* be able to). Medical equipment has to work, no company is going to want to “give it a go” and, if the machines don’t work or break down or harm the patient, face being sued into bankruptcy once this is over.

 

There is no vaccine and there is no known drug treatment that has anything but sketchy “it seems it might help” evidence.

Vaccines take years to develop normally. This can be fast-tracked by reducing the level of testing and precautions, but that means risking creating an ineffective vaccine at best or even killing more people. On the plus side, scientists already have targets for creating a vaccine – the RNA of COVID-19 has been sequenced (read), we know some of the proteins involved, it looks like the main target to infect cells is known (ACE2). The trick is to develop something that looks like one of those elements and that prompts the human immune system to develop antibodies against it (without harming the human) that then attacks the COVID-19 virus (without attacking anything else in the human) and that can be created in huge amounts (there are a huge number of humans).

There is no existing drug that seems to work very well. Existing antiviral treatments are being tested. Anything with any hope at all are being tested. If they worked well, we’d probably know already and the international medical community would be making it known. ANYthing you see on the internet about a miracle cure or “In India they have discovered that vitamin C, Ibuprofen and Tamiflu taken in large quantities together cures 76% of cases” is utter bullshit. Spreading this bullshit on social media is extremely not-helpful as some people will believe it and start demanding a treatment that does not work.

Medics and scientists will continue to work and they will get something eventually, but almost certainly not in the next few months. Sorry.

There appears to be no natural immunity

Like most viruses that attack us, the only way to be immune to it is to either catch the disease and get better, or be given a vaccine (which, in effect, is the same to the body as getting the disease but without most of the illness).  This means that, given how well COVID-19 spreads, we will all get this eventually until herd immunity slows it right down. At that point, everyone who has not had it will still be at risk of getting COVID-19 if they meet someone with the disease.

Bottom line, until a vaccine is created and everyone takes it, COVID-19 will continue to spread until most people have had it. The key thing is to try to slow it down so that our medical services can cope with the number of people it makes seriously ill.

 

Predictions

Before reading any of this, remember – I am not an expert! I’m a computer programmer with a smattering of some relevant experience.

However, about 3 weeks ago I felt I knew what was coming and I’ve spent the last 2 weeks being “the voice of doom”. Sadly I think I have been mostly right. So I thought I’d put somewhere how I think some things are going to play out.

I’m not trying to scare people. Well, sort of I am. I want people to be aware that it is going to be bad for a while, that as nations and individuals we need to take the right, simple actions. And that governments will lie to you about some of this stuff. Look for scientific/medical information.

(predictions made on 13th March 2020)

  • In the UK we will have about 250-350 new cases on Monday 16th March.
  • By the weekend of the 21st/22nd we will see 1000 new cases a day in the UK.
  • Numbers of deaths will “take off” around the 18th March and will double about every 3 days for at least 2 weeks.
  • Deaths as a percentage of known cases in the UK will be between 0.8% and 1.8% by the end of the month and will escalate.
  • The rate of new cases will stop growing so fast, but the rate of deaths will continue to grow as a faster rate. This is due to 2 factors – (1) the delay from getting ill to dying is on average a week or so (2) the UK is no longer testing everyone, buggering up the figures.

****

Update 19/3 – how did I do prediction-wise. Well, on the 16th March there were officially 152 new cases. But on the 15th there were 330, and 407 on the 17th. So I was wrong in both directions! On the actual date, I overestimated. But for the 3 days around the 15th and going on the trend, I had underestimated. I was not pessimistic enough.

The deaths did take of in the middle of this week – 16,33, and 41 for the 17th, 18, &19th March.

And we are well on track to hit 1,000 new cases by the weekend, but given the ever changing information on who is being tested, I’m not sure that confirmed cases is very accurate. I think the percentage death rate will have to be increased to take into account the lack of testing.

So, sadly, I seem to be still predicting quite well what is happening. BTW I base my predictions by stealing the work of proper, real scientists and mostly ignoring the UK government. I’m not doing anything more “clever” than choosing my sources and a simple spreadsheet.

Update 21/3. We hit over 1,000 cases – 1,035 today. So “my” prediction (really I just use a simple calculation based on the work of the real epidemiologist) is sadly spot on.

Deaths reported, 56. It’s taken off but not doubling every 3 days. It will.

Update 15/4 – Death rates did indeed double every three days – actually 3.3.

23/3       54
26/3       115
29/3       209
1/4        563!
4/4        708

Thankfully, the various distancing measures started to slow the rate in the first week of April, as self isolating and then pub etc closures kicked in

As predicated,  the slowdown of new cases predicates the slow down of deaths, but the UK’s poor testing numbers make this connection weaker and weaker

*****

19/3/20

  • Daily deaths in the UK due to COVID-19 will exceed a thousand in the first week of April.

Update 15/4 – thankfully I was wrong, but we hit 980 on the 8/4. If we include the 10% of care home deaths missing from the figures, we did hit 1,000

  • I’m not so sure about this one – I think we will have a slowdown of new UK cases in about a month and than after a gap of about a month  it will take off again.

 

  • COVID-19 will reach every country by April

Update 15/4 – pretty much true

  • China will have a second wave of infections in a month or two.

I think this because although they managed to control the first outbreak (by taking measures most western countries would not entertain), the virus has not spread through the rest of the population and it will get re-introduced from another location.

Update 15/4 – I’m not sure on this. Their figures are really good at them moment. They have shut down and quarantined another area but there has not been a second large outbreak we know of.

  • This is going to hit the USA very hard indeed.

This is because:

They initially had little capacity for testing (it is still poor despite political promises – and they have been having a damned argument about which commercial company gets to set up a new, Invented In America test to make a few people very rich indeed)

Their health service is far more about making a profit than treating people, so ill people will not get treated (or tested!);

The percentage death rate is going to look terrible, maybe 3 or 4%, as the number of cases actually tested will be low (if they “guess” at the infected numbers this might not happen);

Ill people will not self isolate as most US employees have little or no sickness pay.

Update 15/4 – The US has been really badly hit and when it took off, it took off large. I think a large part of this is because President Trump was a bloody moron and spent weeks downplaying this. As he likes to say “it’s all on tape” – he claimed this would be finished by Easter, was not as bad as ‘flu etc. The only thing he can claim to have done (and has done so repeatedly) was to stop flights from China. But he was advised then it was not going to have any impact as it had spread. And was already in the US.

I think it will continue to hit the US really hard, not just for the reasons I cited before, but because the president seems determined to do exactly the wrong things to contain this, such  as “opening for business” very soon and sacking anyone who disagrees with him.

I was wrong on the % death rate as they have massively increased testing, which was an amazing achievement.