It has been a long tiring and, in many ways, terrifying week in the US. The events in DC have nevertheless obscured the growing public health crisis, which even with vaccines available can be expected to get WORSE over the short term - a thread
Where are we right now? Daily deaths cleared 4000 this week. That will get worse. How do I know? Because the deaths are the results of infections in the past, and infections got worse in the last few weeks. I'm so sorry, but it is coming
The amounts of infection now are so high, and the comparative vaccination rates so low, that we have to be prepared for a coming surge into healthcare across the nation. It is already going to be bad enough. It might well be worse given the threat of more transmissible variants
The variant B.1.1.7 which was first detected in the UK, is certainly IMO more transmissible. That has a bunch of consequences that we should prepare for even if it is not in your town yet and it *is* in the US, in at least some places, if rare for now. But that will change
B.1.1.7 has run rampant through the UK, at a time that country had *relatively* firm restrictions in place. I know the UK’s restrictions have not been all they might be, but that’s for another thread – still they were stronger than those in much of the US.
The higher transmissibility of B.1.1.7 means more people need to be vaccinated to control the disease. Very roughly speaking (and with a lot of assumptions) it takes the critical vaccination threshold to control transmission from ~60% to ~75%.
That’s not nothing especially when you are struggling to vaccinate people At All
B.1.1.7 is now outside the UK. Look at Ireland (HT @VanGennepD ) There are likely multiple introductions, but seriously, look at it. It is reasonable to suggest B.1.1.7 is a major driver in that, given available genomic data (figure from @Worldometers)
And Israel – a world leader in vaccination, with a history of switching between lockdown/not lockdown. Now closing up again in the face of B.1.1.7 even as population immunity builds to impressive levels nytimes.com/2021/01/07/wor…
We are very very far from out of the woods. We've got more in our corner now in the form of vaccines, but so has the virus. Most places have a year of the experience of underestimating it
When are you gonna change? /end
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There is a super interesting quote from John Edmunds in this article on the brewing row over the UK’s Covid inquiry and it’s relevant way beyond that country. It concerns the use of scientific advice by politicians 1/n theguardian.com/business/2023/…
To start with I have to say “follow the science” has always been a slogan rather than a policy. Follow it where? That depends on what we want to achieve. Provided the goal is clear, then scientists can say whether a policy will likely help or hinder. And there’s more to it… 2/n
Even if the goal is unclear, you can still ask scientists what they think the likely consequences of a policy would be. And so this quote is key 3/n
Finally returning to this, long after it has been digested by the twitterati. As someone who has worked on molecular epi, transmission, (meta)genomes etc it seems to me that the great majority of the commentary has spectacularly missed the point 1/n
This is not direct evidence of animals (raccoon dogs prominent among them, although far from the only possibility) being infected, but it is *exactly* what we would expect to find if they were 2/n
Had virus *only* been found in samples with human genetic material, it would be different. Even that would not allow us to rule out animals being infected too, just not among the samples collected. But we would not have evidence they *had* been exposed/infected 3/n
This is a very interesting article, featuring a quote from yours truly about how many lives *could* have been lost in the US due to the pandemic before vaccines. This is my reasoning 1/n washingtonpost.com/health/2023/03…
This figure from Jones et al JAMA 2021 shows estimates of how many Americans were infected by the time vaccines were available (the dotted line). As you can see, it is a little more than 10%. Maybe 13%. These are estimates from 1443519 blood donations collected over this time 2/n
In the spring of 2020, some people who really ought to know better had compared the threat of covid to the threat of flu. By dec 14th 2020, more than 300 thousand Americans had already lost their lives to this virus that only got a name in February 3/n
When the local wastewater numbers go up, people often pay attention and get anxious - so worth noting that they just dropped *a lot*. What does that mean, and what's with this plateau since the summer? 1/n
first a little caution - as you can see these numbers can fluctuate quite a lot, and so the next sample might be up again. But that doesn't explain the plateau, and the fact we see similar in the south system makes me take it more seriously 2/n
In fact, this sort of pattern should not be considered very surprising at the moment. After all, the point when the virus was equally able to infect all of us is far in the past. Now there is a patchwork of immunity in the population, which makes it harder 3/n
If you think mask use has insignificant benefits and is unjustified under all circumstances, you are wrong.
If you think that changing levels of immunity and available therapies don’t change the benefits of masks, you’re also wrong
If you choose to not wear a mask when asked to, I disagree strongly. It’s polite and kind to do so
Likewise masks can and should be used to mitigate transmission in high risk environments like healthcare
All masks are not alike. A fact which delights those who seek to weaponise them for political gain because they can always default to whichever most helps their point and riles up their base (compare - all masks are good, some masks are good, no masks are good)
Genomic epidemiology is a wonderful new tool in our kit for detecting cases of transmission - but we always need to consider whether two independent cases might have very similar or even identical genomes by chance
this problem is especially acute early in outbreaks, when there has been insufficient time for the pathogen population to accumulate diversity, such that independent transmission chains are readily distinguished