staying alive

In the madness of the UK's Covid response, public health expert Devi Sridhar was a lone voice of reason. Remembering this, I was keen to read her book about the wider application of her thinking to population scale life and death from all causes and found it quite enlightening. Most importantly, she demonstrates how dramatically the political decisions affecting public health differ between countries and how that leads to very different results in avoidable deaths from causes ranging from guns to cars.

How Not to Die (too soon): The Lies We’ve Been Sold and the Policies That Can Save Us
Devi Sridhar
Penguin Viking 2025

My review of the book is now out in the April issue of Chemistry & Industry:

Health accountability

Chemistry & Industry Volume 90, Issue 4, April 2026, Page 34

access via:

Wiley Online Library (paywalled PDF of the whole review section)

SCI (premium content, ie members only)

In the same issue I also have a feature about plant microbiomes. I've covered the field a couple of times in Current Biology (most recently in 2022), but this one is slightly different in emphasis as C&I wanted more about the application side of it than I have previously covered.

Plant probiotics

Chemistry & Industry Volume 90, Issue 4, April 2026, Pages 22-25

access via:

Wiley Online Library (preview of the first page and link to paywalled PDF)

SCI (premium content, ie members only)

travelling pathogens

When humans travel, they tend to bring their infectious diseases along. With Covid and air travel we have seen that an outbreak can become a global pandemic within weeks. With historic, slower mode of travels, the situation is more complex. Consider a sailship going half way round the world - by the time it reaches the destination, the pathogen may have run out of hosts to infect and thus the disease may have died out without any intervention. I spotted a paper applying the tools of ecological theory to the intercontinental transfer of pathogens in the times of sail and steam and found that topic really fascinating, so I mixed in a bit of Covid and air travel and some pre-historic travellers to widen the scope and made it my latest feature which is out now.

Travelling pathogens

Current Biology Volume 34, Issue 16, 19 August 2024, Pages R747-R749

FREE access to full text and PDF download

See also my Mastodon thread where I highlighted all CB features of 2024.

The thread for 2023 is here .

This painting by Jacob Knijff (1639–1681) purportedly shows “Ships, Galleys and Other Vessels off an Italian Port”, although the location could not be identified and the scene is not thought to depict a specific event. (Image: Jacob Knijff/Wikimedia Commons.)

silver linings

It's three years since some political leaders learned about exponentials and we all started the journey of discovering the lockdowns, contact tracing, zoom meetings, PPE crises, and all the other side effects of the COVID-19 pandemic. There have also been some silver linings, and one of them is that it has given a massive boost to medical research. We will soon see other mRNA vaccines for instance, and even the fight against malaria, a disease that has nothing in common with Covid, stands to benefit from some silver linings of the covid cloud, after a setback at the beginning of the pandemic.

So I've written a feature on the post-pandemic fresh start in the malaria field, which is out now:

New beginnings for malaria research

Current Biology Volume 33, Issue 6, 27. March 2023, Pages R203-R205

FREE access to full text and PDF download

See also my Mastodon thread where I highlighted all CB features of 2023.

I'm not on Instagram myself, but I believe if you follow CurrentBiology there, you'll find my features highlighted there as well.

The photo shows Anopheles stephensi, a mosquito species that is native to Asia but has recently been linked to urban outbreaks of malaria in Africa. (Photo: Jim Gathany.)

from plague to covid

I noticed recently that the ancient DNA researchers are finding out lots of fascinating things about historic plague pandemics and other diseases, and it occurred to me that we are catching up with those pandemics of the past, while also still handling our present pandemic. And how lucky we are that at least we can very quickly figure out what our problem is and what to do to fix it, whereas people hit by the Black Death had no clue and could do nothing. Now we only have to find a cure for misinformation ...

So anyhow, out of these thoughts grew my latest feature which is out now:

Pandemics past and present

Current Biology Volume 32, Issue 16, 22 August 2022, Pages R855-R857

FREE access to full text and PDF download

NB: as the 2022 features move into the open archives, I will add them to this thread on Mastodon.

The National COVID-19 memorial in London commemorates the 200,000 who died with the disease in the UK. (Photo: Geoff Henso/Flickr (CC BY-ND 2.0).)

anosmia gets a boost

Anosmia - the loss of smell - was a neglected condition until Covid-19 came along. Then the loss of smell as a diagnostic criterion, and also as a lingering long-term consequence of the disease rose to prominence. While devastating for all concerned, this sudden increase in awareness of the condition and interest in research into it may have a happy ending in that it could lead to better understanding of the mechanisms and more effective treatments.

So I've taken this silver lining as an opportunity to revisit smell science and Covid, now combined under the banner of anosmia. The resulting feature is out now:

In search of lost smell

Current Biology Volume 32, Issue 14, 25 July 2022, Pages R757-R759

FREE access to full text and PDF download

NB: as the 2022 features move into the open archives, I will add them to this thread on Mastodon.

The COVID-19 pandemic has caused widespread loss of smell and thereby led to a renewed scientific interest in anosmia research. (Photo: Mark C. Olsen/New Jersey National Guard.)

revisiting wastewater

During this pandemic it has been fascinating to learn how much information about disease spread can be obtained from wastewater analytics, even several weeks before patients start turning up in hospitals. It has also been frustrating to learn that the political leadership at least in this country has no interest in this information, as they prefer to wait and see if it really gets that bad, and then take measures only two weeks after it gets really bad.

I wrote a feature on the importance of wastewater monitoring around this time last year, when I still had some hope the information might be used to wipe out Covid-19. Now I revisited the field in a more sober (read: frustrated) state of mind and also looked at the uses of wastewater monitoring in other diseases, present and future. Maybe we have more luck with our leadership the next time a zoonotic disease outbreak threatens to turn into a global pandemic.

This new feature is out now in C&I:

Wastewater monitoring

Chemistry & Industry Volume 86, Issue 2, February 2022, Pages 26-29

access via:

Wiley Online Library (paywalled)

SCI (members only)

Any access problems give me a shout and I can send a PDF file.

In the same issue, on page 36, you'll also find my review of the book Colliding Worlds by Simone Marchi, which is astrobiology-related in that it reports the evolution of the Solar system under the aspect of collisions between bodies.

Wiley Online Library (paywalled)

As the book is more photogenic than a wastewater treatment plant, I'll use the cover here too:

I'm now running a twitter thread with this year's C&I features here.

why the vaccine-only approach will backfire

After yesterday's announcement of betting everything on the booster programme to hold the omicron variant at bay I hear that the medical staff meant to deliver a million jabs per day from today were as surprised as the rest of us to find out about it from yesterday's speech.

Nothing wrong with protecting people with a third dose of vaccine, and I've had mine a week ago, but it's a bad idea to rely only on a vaccine in the face of a raging epidemic and do nothing else. Here's just one little number crunching to show why:

If the booster (or any other vaccine applied in an ongoing epidemic) is 90% effective in preventing undesirable outcome (eg hospitalisation, or deaths) and makes people feel safe so they engage in 20x more risky behaviour (eg take the tube to work and come into close contact with 60 people per day, rather 3 if they cycle to work; or they go out clubbing rather than staying safe at home), what happens?

The 90% efficient booster divides the likelyhood of the undesirable outcome by 10, but the behaviour change multiplies it by 20, so you get twice as many cases of the undesirable outcome. Which is why relying _only_ on a vaccination with less than 100% efficiency may produce the opposite of the desired effect. Behaviour/culture eats vaccination/policy for breakfast as the old saying goes.

I remember epidemiologists warning of this backlash effect since before we even had vaccines, and it's been the reason why we've had unsustainably high numbers since September inspite of good vaccine coverage, but the UK govt still does not understand this. So, starting from a high plateau we're going straight over the cliff with omicron again, and will need another screeching U-turn to sort this out. When will they ever learn?

Update 15.12.: Here's a good opinion piece from SAGE member Stephen Reicher on the mess we're in with omicron's arrival. As Reicher points out, the booster programme is a slow-acting measure, so the important bit is to have contact reduction to slow omicron down until the boosters take effect.

omicron blues

So here we go again, for the fourth time in a row, the UK govt (acting only for England as the devolved administrations have wisely gone their own ways) is doing too little too late and spouting nonsense while blatantly advertising the most important rule of all, namely that rules don't apply to them and their friends. (Impersonating police officers, anyone? Punishable offence for most of us, but not for the shifty character recently photographed at a dawn raid.) Their rules are only made for the rest of us, and we should be grateful, apparently. After today's news of how deatheaters are basically dancing on the graves of the people they killed with their stupidity (current hashtag on twitter: #ToriesPartiedWhilePeopleDied), I'm seriously running out of effs to give.

So, well, the science from wastewater monitoring (about which I've written a new article last week, due out early next year) through to vaccine development is still brilliant, but it doesn't save us from a never-ending chain of disasters if the guys at the top eff it all up. I could throw around some numbers etc, but probably won't bother. We don't have a shortage of scientific facts and figures, we just have a surplus of dangerous lunatics in high places. The immunisation against that is yet to be discovered.

What cheered me up immensely, however, was the recent front page of the taz (disclaimer: I own a share in the cooperative) linking the change of government in Germany to the change of coronavirus variant:

Source.

Rough translation: New Merkel variant prevails.

Oh, just now I also enjoyed the subtitles on today's Channel 5 News suggesting BJ was talking about Oma Crown. Sounds like a bilingual toddler trying to define the Queen.

how many more will die?

As the UK govt. (henceforth referred to as the Death Eaters) has now switched its Covid "strategy" to pouring fuel on the fire, I wondered how many more will die as a consequence of this reckless disregard for public health.

They say hospitalisations and deaths are now uncoupled from the case numbers thanks to the vaccination, but that's another lie. They are still coupled, just with a larger factor. If the risk of death was 2% before vaccinations, it may end up at 0.2 percent with everybody vaccinated and 90% protected by the vaccine. But let's look at where the factor stands now.

Dividing the cases in the seven days up to 23.6. (79,481) by the deaths in the seven days up to 7.7., i.e. two weeks later, that's 161 deaths, I get a factor of 494, so a 0.2 % risk of dying if you had a positive test. Not a risk I'd fancy taking, but 10 times better than before the vaccines.

This number has improved in the last five weeks:

9.6. 284
16.6. 382
23.6. 415
30.6. 489
7.7. 494

This looks like a move in the right direction, but note that the last weekly increase has shrunk significantly, so it looks as if we may have reached the limit of the improvement that we can get out of vaccines. Worth keeping an eye on that number.

So let's assume that of the people tested positive, on the order of 1/500 will die. So two million further infections by the end of this month (as admitted by the Death Eaters) may mean 4,000 additional deaths. Another 8 million in August (remember more than 20 million people will still be not fully protected), even if the curve will go down then, another 16,000. So I reckon 20,000 additional deaths before the third wave recedes are a realistic estimate.

Or if you prefer your horror in daily doses, 160,000 daily cases by August 7 would mean 320 daily deaths around August 21. The associated burden on the health system may well mean that we'll need another lockdown to avert collapse. And then there is the even bigger issue of long Covid, which the Death Eaters studiously avoid to mention.

And this is still under the optimistic / unlikely assumption that the virus doesn't evolve. In fact though, it does evolve, and it may very well find a way around the vaccine. As many people have pointed out, if you wanted to do a huge experiment to evolve a virus that is resistant to vaccines, letting it run wild in a partially vaccinated population is exactly the way you would do it (assuming you had no care for ethical concerns whatsoever).

This number looks a bit too high ... a recent anti-vaxxers demo I stumbled across at Carfax, Oxford (own photo).

Some fresh resources:

Mass infection is not an option: we must do more to protect our young (Deepti Gurdasani et al. in The Lancet)

delta taking off

With July and the rescheduled re-opening of everything in the UK approaching, let's do some back-of-the envelope calculations again to see what may happen in July and August, seeing that the UK govt. seems to think the vaccination programme is a magical solution to everything, including the exponential spread of the delta variant.

As per today's figures, there have been 32.2 million second doses, meaning that in two weeks time, when those second doses have all done their magic, there will still be 34.6 million people not completely protected. Some will be partially protected by a first dose, but, on the other hand, in some 10% of the doubly-vaccinated people the protection won't work, so let's assume these two imperfections cancel out and we will have 34.6 million unprotected people on Saturday July 10th (which happens to be the day before some football game planned to take place in Wembley Stadium).

Cases are currently increasing at more than 50% per week - earlier this month the figure had peaked at 66% and dipped to 31%, so 50% is a good midpoint between these extremes and easy to calculate. Going up by factor 1.5 each week means factor 2.25 in two weeks, so a doubling time of less than two weeks.

As per today's govt. figures, there were 98,460 new cases in the last 7 days, which gives us 14,065 for our 7-day rolling average of daily cases. Times 2.25 makes 31,650 new cases on the Saturday before the final.

Let's carry on in 2-week steps assuming (generously) 200,000 second doses are given every single day (2.8. million in two weeks):

24. 7. 71,208 daily cases, 31.8 million still unprotected.

7.8. 160,217 daily cases, 29 million still unprotected

21.8. 360,490 daily cases, 26,2 million still unprotected

4.9. 811.100 daily cases, 23.4 million still unprotected

18.9. ? 1.82 million daily cases, 20.6 million still unprotected

OK, so that last step in September is the one where I'm reasonably optimistic that it won't happen - with more than 2/3 of the population protected, the virus won't find another 1.8 million susceptible people it can infect. Especially because millions will already have had it. But before that, I wouldn't bet against the delta variant or expect any miracles from the vaccines.

Hundreds of thousands of cases in late August appear possible, and even with the mortality reduced to 1/1000 thanks to the vaccine protecting most of the previously vulnerable groups, this translates to hundreds of daily deaths. As we had in January, and last year in the first wave.

I made an assumption that may prove to be too optimistic, namely that the vaccine remains as effective as it is now. Letting the virus run free while conducting mass vaccinations against it is essentially an experiment in virus evolution. Given hundreds of thousands of opportunities to mutate, it may very well find a way around the vaccine. And then we will be back to square one. (It doesn't have to become completely resistant, even if it reduces vaccine protection from 90% to 45% we're facing a major disaster.)

To me the lesson is you shouldn't try to race an exponential function, unless you have exponentially growing power yourself, which would be unlikely. You need to catch and confine it while the case numbers are manageable, which the govt has failed to do for the third time in 18 months. As I was writing this post, the health secretary has handed in his resignation, but not for dismally failing to protect the health of the population.

first checkpoint 10.7.: I predicted 31,650 new cases for today. The 7-day rolling average falls a bit short with 30504, but the daily figure is above the prediction, with 32367. Second doses haven't come close to the 200k per day rate I assumed, so protection is generally less than anticipated.

delta rising

It is fairly obvious now that the delta variant (formerly known as B.1.617.2, first identified in India) is out of control in the UK, as the week-on-week increase in case numbers has been accelerating dramatically over the last 10 days.

Week-on-week rise in new cases, last 12 days, according to the govt. data site:
24.5. + 17.0 %
25.5. + 18.0 %
26.5. + 18.0 %
27.5. + 20.5 %
28.5. + 24.0 %
29.5. + 23.3 %
30.5. + 26.8 %
31.5. + 28.8 %
1.6. + 31.9 %
2.6. + 34.7 %
3.6. + 38.9 %

To unpack those data: any positive percentage means new cases in the last seven days are higher than they were in the previous seven days. A constant percentage means an exponential rise, but at around 20% per week, it would only double in four weeks or so, so if the figure stayed at 20% it would be nothing to panic about.

What really worries me is that the percentages are increasing, and even this increase seems to be getting faster. From Tue to Wed it was 4.2 percentage points more, a jump of a size we haven't seen recently. The likely explanation is that it started in a few clusters, but as these clusters haven't been containe, it's gaining more and more territory to spread in. If this trend holds up we will end up with a doubling time well under a week before the month is out, and then we're in trouble. Even if many of the most vulnerable people are vaccinated, the extra risks that they are likely to take because they feel safe after being vaccinated may well compensate part of the gain. The other part may be wiped out by the Delta variant being more agressive than the original version. Early data suggests it may well be, see today's report in the Guardian.

Hospital admissions are also on the way up, while deaths have just begun to rise again after Monday's minimum of 43 deaths in the last 7 days. Today this fitgure is 54. As cases have been rising for more than two weeks now, I am guessing that this was the turning point and deaths are also creeping up again.

I really don't think the lifting of all regulations can go ahead on June 21 as scheduled, and if it does we're bound to have a rather murderous summer which could rival the previous waves not just in cases but even in hospitalisations and deaths. There are always people unprotected, and an epidemic running out of control will eventually find them.

The other big covid news in the UK is that Portugal has been removed from the green list, which means people returning from there are not exempt from quarantine. This is of course a distraction. As we have a Variant of Concern spreading out of control in the UK, nobody should have been allowed to travel to Portugal in the first place, especially not those footballers who could have just sas well played their game in Wembley.

Update 6.6.: the last three days have continued the trend shown above. If anything, the percentages are rising faster ...
4.6. + 39.8 %
5.6. + 46.2 %
6.6. + 49.0 %

Meanwhile, clusters of Delta are also beginning to pop up in France ...

new wave

So here we go again, the UK govt is making the same mistakes with the new variant first identified in India (B.1.617.2) as it did with the original Covid and then with the Kent variant (B.1.1.7) - play down the problem, let it spread, and only act when people die in their hundreds.

As the Death Eaters are going to deny it later, here's what we know today, 3 weeks before the planned end of all restrictions. B.1.617.2 is spreading exponentially in England. So far, this rise has been masked in the overall stats by the decline of the Kent variant, but now that B.1.617.2 is the dominant version, it is beginning to dominate the stats, and those stats are pointing upwards, at up to 30% increase week on week. I reckon that figure will still get worse as the variant spreads to places as yet unaffected. Follow Christina Pagel on twitter for the latest warnings. Also this analysis by David Spiegelhalter and Anthony Masters which just came out in the Observer today.

I hear the AZ vaccine which is predominantly used here, protects to 60%, so we have still 40% of the original risk. So if with B.1.617.2 as compared to the original strain, and all other things being equal, we're 2.5 times more likely to get infected, this cancels out, and we're just as screwed as we were last year with no vaccine. [Update: numbers corrected 1.6. - in the original version I stated wrongly that it would only take a 1.6 fold increase in infection risk. Still quite realistic possibility that this will happen, eg it's 60% more contagious than the Kent variant, which was 60% more contagious than the original strain, 1.6 squared is 2.56.]

Meanwhile, two English football clubs played the champions league final at Porto, Portugal, yesterday, and English fans were allowed to travel there and spread the the new variant a bit more. Spain is also welcoming tourists from the UK in June. Both countries will come to regret this before the summer is out. As Champions League games played a significant part in spreading the original Covid around Europe (First Valencia fans travelling to Covid-infested Italy, then Madrid fans travelling to Liverpool as Spain was preparing for lockdown), I really don't understand why these things are still allowed to happen.

So even though we're fully vaxxed now, we're still stuck on Mutant Island for the foreseeable future ...

street scene from the first pandemic summer, own photo.

PS: Today's figures from the govt website just in:

22474 new cases in the last 7 days, that's 4755 more than the previous week, up 26.8% in a week. 60 deaths in seven days, up 18 or 42.9%. Hospital admissions up 23% week on week.

If you ask me, don't plan anything for June 21 onwards that you wouldn't be comfortable with right now, or better still live by the rules we had before May 17th. The third wave is happening.

watch your wastewater

During this pandemic I kept hearing about the great work researchers are doing detecting SARS-CoV-2 in wastewater as an early warning of coming waves and new variants up to two weeks before the relevant patients show up in hospitals. From the politicians, at least in this country, we have warnings only two weeks after the hospitals begin to fill up, and measures are generally taken several weeks too late, making the problem worse.

So I had a look around at what is being done in the wastewater epidemiology of Covid-19, and how in some countries it informs the political measures, while in some others it clearly doesn't, even though the methodology and the data are available. Still not clear why some people don't want to heed the warnings when they arrive well in time to allow them to adapt, but it is kind of reassuring that there are very clear lessons here to be learned for the next outbreak of a zoonotic disease. Reading the warnings from wastewater, we can stop the next pandemic from happening. Might require different political leadership, however, at least in some countries I can think of.

As part of the special treatment for Covid related information, my feature has been available as an open access preprint for the last two weeks, but today it is officially out in the proper format, and still on open access:

Wastewater warnings

Current Biology Volume 31, issue 06, pages R267-R269, March 22, 2021

FREE access to full text and PDF download

Samples taken from the raw sewage entering water treatment plants can be used to monitor the spread of infectious diseases, including COVID-19. The image shows aeration tanks at a water treatment plant in Upper Providence, Pennsylvania, USA. (Photo: Montgomery County Planning Commission/Flickr (CC BY-SA 2.0).)

some viral stories

Quite Covid-heavy this round-up of German pieces, with the variants covered in December (just before the issue exploded) and the vaccines in February (see the cover below), as well as a tongue-in-cheek appreciation of the dog-led diagnostics. Other topics available include soil biodiversity, ammonia emissions from human skin, and protein crystals found inside the glass needles of marine sponges.

The Covid stories are on open access, and some of the others appear to be too, not sure why.

Ausgeforscht: Wir Emittenten
Nachrichten aus der Chemie Volume 68, Issue 11, November 2020, Page 98
Access via Wiley Online Library

Der Stammbaum der Pandemie
Nachrichten aus der Chemie Volume 68, Issue 12, December 2020, Pages 64-65
FREE access via Wiley Online Library
related content in English: Pandemic genomics

Verflixt verschachtelt
Nachrichten aus der Chemie Volume 69, Issue 1, January 2021, Pages 87-88
FREE access via Wiley Online Library

Der Covid-Schnuppertest
Nachrichten aus der Chemie Volume 69, Issue 1, January 2021, Page 114
FREE access via Wiley Online Library

Biomineralisation: Im Innern der Glasnadeln
Chemie in unserer Zeit Volume 55, Issue 1, February 2021, Page 12
Access via Wiley Online Library
related content in English: Sponges feature

Impfen gegen Covid-19
Nachrichten aus der Chemie Volume 69, Issue 1, January 2021, Pages 50-53
Access via Wiley Online Library
related content in English: Vaccines feature

cool cover of the Feb issue of Nachrichten aus der Chemie, although not quite a representation of how the vaccines work ...

vaccines revolution

By mid January, a year after the novel coronavirus was formally identified and sequenced, eight new vaccines of three different types were approved in full or in emergency mode by at least one country. So I though this was a good time to have a look at how this miracle happened. Especially here in the UK we're still rubbing our eyes a bit as it is about the only aspect of the Covid response that has worked better than expected (so far).

As part of the special treatment for Covid related information, my feature has been available as an open access preprint for the last two weeks, but today it is officially out in the proper format, and still on open access:

How to develop 8 vaccines in 12 months

Current Biology Volume 31, issue 03, pages R101-R103, February 08, 2021

FREE access to full text and PDF download

Although the new vaccines have materialised at record speed, they have been tested as thoroughly as any previous vaccines. (Photo: Lisa Ferdinando/US Secretary of Defense (CC BY 2.0).)

Looking ahead, I do hope that the success story of vaccine developments also translates into successful elimination of the disease, but it's too early to start victory celebrations. One thing I worry about here in the UK is the large gap between first and second dose which produces two problems:

1) patients feeling somewhat protected by the first dose increasing their risk behaviour may very well overcompensate the extent of protection they have. So if their infection risk is reduced by a factor of 2 but they are having 3 times as many risky encounters, they may in the end be more likely to catch it. So the only relaxing (of rules and precautions) should be happening as a function of second doses given, not of first ones.

2) having a vast population partially protected and still exposed to the virus could be a breeding ground for mutants resistant to the vaccine.

So, in the UK in particular, given how Johnson's government has mishandled and amplified the first and the second wave, I wouldn't rule out the possibility that they are cutting corners again and thereby facilitating the third wave.

PS In nerdy note-taking news, this feature completes 10 years since I started writing a feature for every issue of CB. Since issue 4 of 2011, there have been 235 features in 240 issues, so it worked out quite nicely, even if I say so myself.

entering plague year 2

The novel coronavirus started spreading in the UK around this time last year, so we're now entering the second year. And we've passed 100,000 deaths even by the most conservative metrics used by the government. And with the new vaccines and the new variants, the second year will be a completely different game, although I'm not confident the UK government will handle it much better than the first one.

Oh and my new feature on the development of the vaccines that are now being used is out as a preprint, free access here, the regular publication date will be Monday Feb 8th. I'll do a proper blog post for it then.

Might be a good time to round up the Covid-related contributions from the first year:

Features

• Pandemic genomics (21.12.)
• Communicating science in a crisis (6.7.)
• Finding comfort in nature (20.4.)
• Virus outbreak crosses boundaries (9.3.)

Blog entries

• the first 40,000 (6.6.)
• numbers crunched (17.5.)
• maths for dummies (9.5.)
• stuck inside (26.4.)
• chronicle of a disaster foretold (19.4.)
• mind your exponentials (27.3.)
• stay home save lives (22.3.)

I'm a great fan of the Corona cover art of Der Spiegel, this is issue 03 of 2021.

Links

This Guardian editorial concludes: "the story of Britain’s pandemic will long serve as a monument to bad government."

See also the very depressing video summary from Led by donkeys.

viral variants

Four weeks ago I prepared the last Curr. Biol. feature for this year, about Covid-19 related sequencing work and the mutations and variants observed. (Even longer ago I planned this topic as a way of drawing a line under this plague year. Didn't quite work out that way.) It has been online as a preprint for a couple of weeks, but the proper version just came out today, as the whole world is debating this new UK variant of the virus. Oh well.

Pandemic genomics

Current Biology Volume 30, issue 24, pages R1455-R1457, December 21, 2020

FREE access to full text and PDF download

The coronavirus SARS-CoV-2 has spread globally and caused a pandemic on the scale of the 1918 flu pandemic. The rapid elucidation of its structural biology and genomics, however, offers opportunities to better understand its spread and to develop vaccines and treatments. (Photo: used with permission of Sai Li, Tsinghua University (Cell (2020) 183, 730–738).)

science news 10.7.2020

Just some covid-19 news today (from zoonotic sources to human behaviour issues), there doesn't seem to be much else:


A global system for monitoring wildlife pathogens to prevent zoonotic disease spillover
In a Perspective, Mrinalini Watsa argues that a rigorous decentralized system for global wildlife disease surveillance is needed to address the looming potential for outbreaks of novel zoonotic diseases.

Bats offer clues to treating COVID-19
Bats carry many viruses, including COVID-19, without becoming ill. Biologists at the University of Rochester are studying the immune system of bats to find potential ways to "mimic" that system in humans.



Bats--the only flying mammals--are highly mobile, constantly bringing new pathogens into their communities. According to University of Rochester biologists, that's one reason they have evolved to have immunity to so many viruses that plague humans, who have only recently (in evolutionary terms) come to be highly mobile and more likely to live in densely populated centers.
Credit: Getty Images photo


For background for these two, see my recent feature on the zoonotic sources of Covid-19 (Open Access).


New study supports remdesivir as COVID-19 treatment


Distorted passage of time during the COVID-19 lockdown
A survey conducted in the U.K. suggests that social and physical distancing measures put in place during the Covid-19 pandemic significantly impacted people's perception of how quickly time passed compared to their pre-lockdown perceptions. Ruth S. Ogden of Liverpool John Moores University, U.K., presented these findings in the open-access journal PLOS ONE on July 6, 2020.

Our itch to share helps spread COVID-19 misinformation
A study co-authored by MIT scholars contains bad news and good news about Covid-19 misinformation -- and a new insight that may help reduce the problem.
See also my feature on covid communications, which is out now and on open access.

covid communications

Covid-19 challenges the whole world in multiple ways, but possibly the most important crunch points are at the science communication / policy interface, because this is where failures lead to bad decisions, and bad decisions cost lives. Many thousands of lives.

I'm trying not to be parochial, ie not to give the UK perspective undue preference when writing about global issues, but in this case the UK happened to be one of the most outstanding examples, namely on how not to do communications in a public health crisis. So I'm afraid there is quite a lot about the UK's bungled Covid-19 response and science/policy/communications muddle in my feature, but other countries are also mentioned sometimes. And positive examples of good communications also get a shoutout.

As all the content of Cell Press journals relating to Covid-19, this is appearing on open access, but I have also been sent a magic link. So if open access doesn't work for you or stops working within the first seven weeks, try that.


Communicating science in a crisis


Current Biology Volume 30, Issue 13, 06 July 2020, Pages R737-R739

Free access to full text and PDF download




When to wear face protection has been one of the many issues on which conflicting and changeable information has been given to the general public. (Photo: Engin_Akyurt/Pixabay.)

the first 40,000

So the official deaths from Covid-19 in the UK passed 40,000 with those announced yesterday (the real death toll is more likely to be above 60,000, but let's stick with the official figures for now). As the mishandling of the crisis continues at full speed, I fear there will be many more to come.

According to yesterday's govt. briefing, there are now only 5,600 new infections per day - I don't believe a word of this. I follow the daily deaths announced and calculate the rolling 7-day average, which I think is the only halfway reliable figure. (Previous results and predictions here.) Unfortunately, this figure has remained roughly constant for the last ten days, probably as the result of the May 11 switch from "stay home" to "stay alert" messaging. It was 236 yesterday and 244 on May 26. (Update: Today, Saturday the figure stands at 235, the 13th day without significant decrease.) On June 2 and 3 it even appeared to be rising (by 10% and 5%, respectively) compared to the value a week earlier.

So when the govt. ministers and "scientists" are saying "it's not going down as fast as we would wish" this is misleading. In truth, it's not going down at all. And on the assumption that we are stuck on well above 200 daily deaths, that means that there must have been more than 20,000 new infections per day in recent weeks. Telling the public that we have 5,600 new infections per day without adding that this is only the tip of the iceberg and that we don't see the real figure due to insufficient testing, this is not only misleading but it gives people a false sense of security and thus contributes to producing a new wave of infections as people relax their protective measures and behaviours.

Oh and the fact that the health secretary, in the daily briefing of June 1, attempted to sweep 445 deaths under the rug and hoped that nobody would notice, that hasn't really helped to build trust. In case you missed it: the June 1 announcement had 39045 deaths including 111 new deaths. But the figure from the day before was 38489, so the difference was really 556. I tweeted about this while the briefing was still ongoing, but the govt. only "clarified" afterwards that the missing 445 deaths were "historic" ones that they had not included in the daily toll. As I haven't seen details of when these deaths happened, I'm not including them in my calculations. So I am now having to substract the 445 from the total each day for a week to get my rolling average right.

I have a nagging suspicion that the people in charge (i.e. DC, presumably) actually want the second wave to happen now. I reckon their calculation is that we got through peak one within three months, with 40k deaths, and without a total collapse of the health system. Give it four or five more rounds like this, they're thinking, and we have the infection numbers required for possible herd immunity. Fatal flaws in the argument are, of course,
1) we don't have confirmation that people are really immune after they have had the virus
2) running wild in such a huge host population, the virus could evolve into something else that may be more difficult to manage and that may not be covered by immunity produced by the initial version;
3) as I've calculated on March 13, when Vallance brought up herd immunity, this strategy would produce 400,000 avoidable deaths from Covid-19 plus additional ones from the impact it has on the health system.

But after the political fallout of the last 7 days it's clear that the govt doesn't care how many more people die. The important thing for them is to get back to their ideology-driven programme, including Brexit, privatisations etc.

In a way, it is understandable that they were caught out by the pandemic. The idea that a government might care for the wellbeing of the people was never ever on their radar, never mind their agenda.


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Some recent pieces from the media



How can any scientists stand by this government now? Richard Horton wondered in the Guardian, after the scandal around Cummings' breach of quarantine. I've been wondering that for a while, which is why I now avoid to refer to the govt muppets as scientists, and have put scientists in quote marks above.

Also, read anything by Devi Sridhar that you can get hold of (not only in the Guardian, there have been pieces in other papers as well).