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Covid-19: The New Variant and the NHS December 29, 2020

Posted by mwidlake in COVID-19, ethics, rant, science.
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<<- Long term hopeful, short term worried

As I said in my blog post a couple of days ago, I’m very concerned about the new variant of SARS-CoV-2 that has been spreading through the UK and is now being found in countries all over the world. My main concern is that this could be what pushes our health services beyond the limit of what they can stretch to and, as a result deaths will jump up – and not just from Covid-19.

New Variant Impact

In my last post I highlighted the new variant of SARS-CoV-2 that is more infections (spreads more easily), but said that there was little evidence that it was any more fatal. Understanding what was going on was hampered at that point as we had hit the festive period and, with the best will in the world, everyone needs a break at some point. New data on hospital admissions, virus sequencing, case numbers were all missing or affected. Scientists studying aspects of Covid-19 were reminding themselves what their partners, kids, and pets looked like after what must have been a heavy year. Now the new information is coming out, as is the analysis by relevant experts.

There is a paper detailing this new variant by Public Health England which was published on 28/12/20. Much of the below is derived from that, but is backed up from many tweets and bits of evidence from the scientific community.

This new variant is know by a few names:

  • VOC 202012/01 – Variant of Concern identified in 2020 month 12, number 1
  • B.1.1.7 – the phylogenetic name of the variant (I think!)
  • 20B/501Y.V1 or simply 501Y.V1 – the identifier given by Nextstrain

B.1.1.7 has many mutations from the original SAR-CoV-2 virus (this STAT article states 17 mutations, the tracking page I mention below lists 17 SNP mutations, this overview by the CDC on VOC 201212/01 lists 20 SNPs and 3 deletions and seems to be the best source of information on this. I’ll explain all the mutations better in a later post) . Mutation is not unusual, viruses change all the time. Each time a virus is copied (and that is how viruses like coronaviruses reproduce, there is no sex, they are identical clones of their only parent) the RNA is copied and occasional mistakes are made and thus changes, mutations, happen. The most common change is a Single Nucleotide Polymorphism, or SNP. One letter of the 30,000 in the viral genome changes.

A single SNP change to the SARS-CoV-2 RNA does not seem to be enough to change the virus into a significantly more infective version (or more lethal, or more likely to infect children, or change it’s behaviour in a way to make it more dangerous). If it did, we would have seen this already – the virus has been so successful in spreading in humans and thus reproducing and so those SNPS occurring, that most individual SNP mutations that are possible will have happened by now (there is evidence for minor change by them though, but that’s for another time). It is going to be a combination of two or more changes I think that has altered the transmissibility.

B.1.1.7 has several changes to the gene that creates the spike protein.

The paper from Public Health England I reference reviews the data that was initially presented to the UK government (on around the 19th December I presume) and resulted in their initial analysis of the 21st, which this paper links to.  This review considers the degree to which the new strain transmits more easily and possible reasons why. It can  be summed up as saying:

  • This new variant is indeed spreading faster.
  • it is becoming the most dominant strain in all the areas it is in.
  • It’s ability to spread to others (secondary attack rate) is increased by about 55%.
  • It is not spreading faster as it is more successful in re-infecting people who have already had Covid-19.
  • There is no evidence it results in more hospital stays or is more fatal.

I’m not sure the evidence is yet firm that this new variant does not also increase the severity of the illness a little as there are too few cases to go on, but it does not like there can be a huge increase. Usual caveat, I’m no epidemiologist.

I’ve also looked at a paper by Nick Davies’ team at the London School of Hygiene and Tropical Medicine.

They considered 4 possible methods by which the new variant (they use the VOC202012/01 name) could be causing the rapid spread of the new variant

  • A) Increased Transmissibility
  • B) avoids current immunity
  • C) Children being more susceptible
  • D) shorter viral generation time

As you can see from the graphs, the model based on (A) Increased Transmissibility fitted the date better than anything else.

You may be aware of the new variant in South Africa that is also more transmissible. This is not the same as B.1.1.7, for example, it does not have the 69/70 deletion mentioned in Public Health England paper that is used as a proxy to identify B.1.1.7 in the UK population (again, more information later on the details of the new mutation). So this deletion either is not key to the increased transmission or else there are two methods by which the transmissibility can be increased (now, that’s a worrying thought).

There has been a lot of other analysis and commentary from the scientific community to back up the hypothesis that B.1.1.7 spreads 50%-55% faster.

Why Is 50% Faster Spread So Significant?

Why is this significant? Wouldn’t 50% more lethal be more of a worry?

No. The reason an epidemic is so scary and has such an impact is down to exponential growth. To use an extreme example such as exists before a new disease is recognised and steps taken to control it, If 1 person infects 2 people who infect 4, 8,16,32… Ten duplications later and you are at 1,024 infected people. If each person infects 3 then it goes 1 person, 3, 9,27, 81…ten tripling’s is 59,049. If you know how many people each infected person will infect (the R number) and how long it takes for an exposed person to themselves become infectious, then you can calculate how quickly the disease will spread and grow. So the transmissibility is key.

Adam Kucharski put it better than I can (if you are on twitter and you are interested in Covid-19 science, if you are not already following Adam then I highly recommend you do, and then follow some of the people he follows). This is how he explained it:

Here in the UK the number of cases and, more importantly, hospital admissions have been shooting up. You cannot compare case from the spring to now as testing now is orders of magnitude improved compared to the shambles back in April. But hospital beds occupied is a very powerful metric and can be compared. Up to a point.

I showed a graph in my last post about how many people are ill in hospital with Covid-19, going up to 24th December. The below is the graph up until the 28th December. We still don’t have data for Wales, Northern Ireland, and Scotland beyond the 22nd December – but England on it’s own ( 20,426) is not far off matching the UK peak of 21,683 back on 12th April. If we optimistically only add on 1,727 for Wales, 1,045 for Scotland, and 451 for Northern Ireland (their figures for the 22nd) we are at 23,649. I’m seeing a lot of stuff on social media and the BBC news about hospitals running out of capacity, cancelling routine work, calling staff in from holiday (and remember, this is staff who have nearly all been pulling extra and double shifts for 9 months already). We suspect are approaching 100% hospital capacity for the NHS.

Patients in hospital with Covid-19 across the UK, 28/12/20

Update, 30/12/20 – we now have the Welsh & Northern Irish data to 28/12, Scotland & England to the 29th . The UK total for the 28/12 is 23,771 (slightly above my optimistic lower threshold of 23,649, as is to be expected. Northern Ireland shows a modest increase that could just be random variation, all three other nations show an increase.

Patients in hospital with Covid-19 across the UK, 29/12/20

 

 

 

100% Hospital Capacity is a Really, Really Bad Thing

I said that hospital beds occupied is a powerful metric up to a point. Why up to a point? At some point that metric stops increasing so fast or even at all – but not because of a lack of patients to treat, but because you are running out of capacity in your hospitals.

I’m sorry, I’m going to go on a bit of a rant here. The below is why I get so vexed at people saying “I need to go on holiday” or “I must have my nails painted” or decide it’s OK if they have a party or that we don’t need a lockdown.

If you get Covid-19 and are badly affected, you may well need supplemental oxygen. You may also need treating for various blood clotting conditions, or to stop your immune system over-reacting, and several other things. That can only be done in hospital. If it is done, most people treated survive (though some of course still sadly die). If you are not treated, you will die. As some of you know, I had personal experience of this late last year when influenza type A and pneumonia landed me in intensive care for a week, on very powerful CPAP ventilators. If I had not had that treatment, I would not be typing this (or anything). So we can (and do) treat and save many people with compromised breathing and the other things that come with Covid-19. Until we run out of trained hospital staff. It’s not beds per se that are the issue, or ventilators, or really any equipment. It is people who have the skills to run that equipment, monitor you, keep you ticking over and otherwise not-dead whilst supporting the broken parts of your body until they heal. Once the capacity of the health service is exceeded, they have to pick who dies. And of course, we do not just have Covid-19, hospitals are dealing with all the other sick patients we always have – car accidents, cancer, influenza, septicaemia, heart attacks…

I’ve seen the stuff by some people about how “only” 377 or so healthy, young people have died of Covid-19. Part of me can’t be bothered explaining to them why they are selfish, clueless idiots right now but what I can say is if we run out of hospital staff capacity, you can be as young and fit and bloody callous as you like but you will die if you need oxygen treatment and do not get it.

I’ve seen some tweets by people who say things like “well, just get more nurses and doctors”. I checked, they are not made in a factory. Training to be a nurse is not like going on a week-long course to learn to use a chainsaw. Doctors and nurses and radiologists and lab staff (and all the others people forget about who are vital to the NHS) are trained for many years. Being an ICU doctor or nurse is particularly technical and needs months or years of training ON TOP of being a standard doctor or nurse.

The UK was desperately short of all NHS clinical staff before Covid-19. One of my closest friends organises the lab rotas for a very large hospital and she never has enough people to fill the rotas. She has to beg and hassle people to do more than their fair share of weekend and night shifts. They constantly have not just one or two but a dozen or more open positions for staff. I’m not getting political here but there was a crisis in care long before the pandemic.

If you see figures saying ICU capacity is at 90% you would probably naturally think “well, they still have 10% spare, it’s fine”. It’s not. One of my first jobs was writing bed management software for hospital systems and teaching hospital staff how to use the software. The software was a god-send for them. A hospital bed is not just a bed. It’s a type of bed, and there are several types in hospitals. Some are for children, most are for adults, some are powered to help move the patient about, some are specialist for ICU (such as being able to pass air around incapacitated patients to reduce bed sores)… And beds move. For my spell in ICU I was initially admitted to A&E and held in a storage room as there was no spare capacity. They brought a suitable bed to me and squeezed it into the storage room. About 12 hours later, 6 or 7 nurses took the bed with me and a shit load of equipment through the hospital to the ward.

You have to know who is in which bed, the consultant & specialty treating them. For very, very good reasons, the specialist or someone in their group needs to approve a lot of what is done to you in a hospital. To administer a drug to a patient you have to find the bed they are in and you have no time to go wandering around the ward as you have 101 other things to do. The same is true of feeding the patient. You have to track when a patient moves (either with their bed or moving from one bed to another) and you need to know where you can move them to, so you need to know what beds are spare or, more likely, probably going to come spare. I worked on another part of the hospital system, “notify patient as dead”. It was horribly complex, lots of stuff has to happen when a patient dies, for example some lab tests get cancelled, others get created. The bed is noted as empty pending a deep clean. Sometimes, heartless though it sounds, the staff need to know when a bed is likely to become available via that route.

The people in charge of beds need to know ASAP when a bed is free so they can try and do all the juggling above that I mentioned. The fewer spare beds they have the harder it gets to make use of the few spare ones you still have and move people around efficiently. Or even inefficiently.

When I moved out of ICU it was a rush job. Someone needed one of the very most critical ICU beds (yes, there are tiers to what we non-medics think of as ICU), they felt able to move another person into my intermediate dependency bed as they were improving – IF they could get me out of it and into the Respiratory Medicine ward. Which they did, at about midnight. The sticking point was I needed to be isolated to I could not give someone with COPD influenza and finish them off. Another complication. It being night there were fewer staff so only 2 people could be spared to move me. Admittedly, less equipment came with me but half of it (including a heavy oxygen cylinder) was on the bed with me, I had hold of something on wheels, the 2 nurses somehow corralled the bed and other equipment.

The point I am making is that the closer a hospital gets to 100% capacity, the harder all that juggling becomes, and you actually end up having to move patients to other hospitals – and moving a sick patient to a different hospital is generally not in the best interest of the moved patient – or discharge patients who could really benefit from being there longer (but don’t need it as much as the person who is dying that they can’t find a bed for).

I’ve only ranted about beds. I have no idea how they keep track of other equipment, plan who is allocated to do what, how to cover for say a member of staff going ill, a major road traffic accident when all ICU is full…

If we do not see some sort of miraculous downturn in hospital admissions (and all indicators are against this happening) I’m expecting the UK to be in full national lockdown in a week, kids returning to schools cancelled. If we hit 100% hospital capacity and are not in a strict lockdown, then our government will have failed us in this crisis once more.

Even more distressingly, we may see avoidable deaths.

 

 

Communicating on Covid-19 Again December 27, 2020

Posted by mwidlake in COVID-19.
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New Variant & impact on NHS->>

<<- Start of Original Post beginning in March 

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

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

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

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

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

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

Long term – I’m really hopeful.

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

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

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

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

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

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

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

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

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

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

Short term – I am very worried

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

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

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

Cases of C-19 in UK Regions since August

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

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

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

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

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

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

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

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

New Variant across the world

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

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

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

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

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

I think we are at a crucial point:

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

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

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

I think Christina Pagel summed it up perfectly:

Sourdough – Creating The “Starter” December 18, 2020

Posted by mwidlake in Baking, off-topic, Private Life.
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1 comment so far

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 cafe/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 a couple of grapes, preferably ones you have had in the house a few days, or some peel (just a couple of 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.