Dear journalists / editors covering COVID / this delta wave. Some of you are ... great (genuinely) - its not easy out there crafting a path thru information, speculation+ crankiness. But others... time to up your game. Here are some rookie mistakes in describing what is going on:
1. Please please stop with the % vaccinated in hospital. This is genuinely a meaningless statistic. It is just bonkers wrong to quote it. Trivially if a population is 100% vaccinated then 100% of the people in that population's hospital will be vaccinated.
What you want is something surprisingly tricky to calculate; the counterfactual of how many people should be in hospital if no vaccine. Thankfully there is an easy way of doing this which is referring back to the Alpha wave (wave 2/3 depending on counting system in each country)
So for example, you want the *number* of people in hospital when cases levels were at a similar level in the Alpha wave (note, not percentages). Many countries have calculated the counterfactual above (which is trickier than it looks due to age issues) - use that as well.
[for modellers/pros ; I know one should say with the appropriate infection->hospitalisation offset and worry about case detection levels, age stratification, but for an easy to understand number, I think the above 1-to-1 mapping of alpha to delta is ... not awful]
2. You don't need to make COVID any more scary. I know it is tempting, and indeed, there are more variants - the virus evolves all the time (as do... all viruses). It is an open question of whether there is going to be something "beyond Delta" but >>
<< you really don't need anything scarier than Delta. Delta transmits very fast if we do our normal human things (hang out, meet family, have wedding parties, have dinner parties, go to bars and clubs etc) and for unvaccinated/uninfected people, if >50, is very dangerous.
3. Vaccination changes the game, but it is not full time/slam dunk/walk away with the win. It is more like two red cards against the coronavirus (football analogy - english style), but we still need to field our team, play well, ie we've still got to navigate this period.
One v. frustrating (but unsurprising) thing is that some people who are double vaccinated can still catch and pass on Coronavirus. We don't really understand why this happens, but it does, and the vaccines are performing at the high end of expectations.
This is why most virologists / infectious epidemiologists I know, and myself (for what it is worth) think the stable end point of the pandemic is some level of endemic (circulating virus) in which SARS-CoV-2 will be nastiest of the coronaviruses that we live with.
(this is how coronaviruses roll; in humans we have 4 endemic - circulating - coronaviruses, one of which looks like it caused the "Russian 'flu" in Europe of 1888/9. They are one of the types of viruses which gives "the common cold" and responsible for viral pneumonia in the old)
4. What we need to do is now simple to state but still a long road - vaccinate everyone *in the world* at risk (crudely, >50, but a bit more nuanced) + vaccinate or tolerate infection for the rest of the world. Vaccination is far better than infection until you get to the young
as we get there, every bit of transmission we reduce is broadly a good thing. The easiest way to reduce transmission is to be in fresh air - good ventilation - this can be low tech (outdoor lunch, open windows) to high tech (fancy ventilation system) - air exchange is the key.
Other things that help include wearing masks, and not hanging out closely with other people (in particular inside).
5. I have genuine sympathy that this is still all front page news but it seems to move so slowly - one wants to find new things to talk about. My advice here I think is to at least balance scary stories with good stories - the good stories are often healthcare >>
<< healthcare has to cope with whatever the pandemic throws at them - they are the last line of defence, the final backstop and they continue to work through in many places just the flow of people who have this nasty disease. In that there are great stories of - frankly - heroism
A plea to stay away from the extremes. We're clearly in a better place (at least in the developed world) due to vaccines. We've clearly got a worse enemy, but one we understand pretty well. We've got to play this game out well with vaccines, and get vaccines across the planet.

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More from @ewanbirney

5 Aug
Had another moment of "well, yes, but people *are* different" and "you geneticists use continental groups in your analysis" as we skirted around discussions of ethnicity / race in health impacts. TL;DR Partially correct but the underlying mindset that ethnicity=genetics is wrong
Let's deal with the correct things first. Yes, people are different partly (sometimes mainly) due to genetics. Visibly, eg height, weight, hair colour, skin colour, smoking habits + invisibly, eg cholesterol levels, heart trabeculation levels, likelihood of getting breast cancer
Some of these visible differences we integrate into the gestalt assessment of ourselves and others for ethnicity, as represented by self identified ethnicity boxes which people tick, eg "Black British, White English, British Indian, British xxx", gloriously variable by society
Read 26 tweets
4 Aug
Ah. I love the smell of freshly baked data/analysis, well controlled false discovery rate (QQ plot) and just ... so many results. Which of the thousands of beautiful stars in the sky does one pull out to discuss? Biology is so endless and wonderful in its detail...
... to alter (butcher?) a passage from a far far wiser and more thoughtful man than me....
It is interesting to contemplate a tangled set of genetic results, associated to both well known genes and entirely anonymous regions of the genome, stories from physiology of old and hints of new insights, and to reflect ...
Read 5 tweets
4 Aug
Great history of the electric car / mobility - 1890s onwards. I really like switching sometimes to a historical perspective on science and technology; it reminds one of the unchanging nature of human foibles and drivers with "you know how the technology story turns out"
There is, for me, a similar history of technology / medicine about the complex introduction of Xrays into medicine (I blogged about this 6 years - (! 6 years!) ago - ewanbirney.com/2015/10/genomi…
The journey of Xrays from spanking new whizzy technology to routine part of medicine is surprisingly complex - it involves twists and turns, inappropriate use of technology "just for fun" (echos of 23andme), and non obvious advocates for the uptake of the technology.
Read 4 tweets
3 Aug
A COVID perspective: TL;DR - the pandemic in the developed world has shifted due to successful vaccines, though plenty of complex and tricky scenarios to navigate; the developed world is in the midst of even harsher transmission rate from Delta.
Context: I am an expert in human genetics and bioinformatics. I know experts in viral genomics, infectious epidemiology, public health, clinical trials and immunology. I have some COIs: I am longstanding consultant to Oxford Nanopore (sequencing company) and am on the Ox/AZ trial
With the perspective of a glorious holiday in Northumberland, the last week disconnected from work and twitter, I have some bigger picture musings on the pandemic from my perspective.
Read 29 tweets
22 Jul
A personal view point on the #AlphaFold announcement today from the @DeepMind and @emblebi team, part of @embl. TL;DR - I am *still* pinching myself about this.
When @demishassabis and the AlphaFold team first presented the results from CASP to me last November I genuinely almost fell off my chair. I think I swore quite a bit (in a British way) in amazement.
One of the reasons was I knew how rigorous CASP was - 20 years ago people published all sorts of "solving the folding problem" which then... didn't work beyond the training set. CASP cleverly used the fact that there are genuinely unknown structures each year solved by experiment
Read 15 tweets
28 Jun
*trumpets* A new preprint by colleagues in @PHE_uk from @isaperena's group and myself (my first infectious epidemiology paper!) on single source transmission of COVID19 using viral genotyping to understand relative risk of transmission settings. papers.ssrn.com/sol3/papers.cf…
Background; we have known for a long time that there is overdispersion of SARS-CoV-2 transmission; some estimates are that 20% of settings/events account for 80% of transmission. Understanding where these transmission events occur is important for non-pharmaceutical interventions
Furthermore, if we can be confident of spotting these individual small-scale super-spreading events and inform other individuals who are at risk of infection at the same time we can highlight people who are at the higher risk for infection, eg, asking them to get a test.
Read 23 tweets

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