Some comments on the last few days. I will start by saying I wish the President and First Lady a speedy recovery. This is about what the events as currently understood illustrate about transmission risks and handling the pandemic 🧵1/n
As I write more and more apparently connected infections are being reported. It is hard to interpret them without more information about contacts, but many appear linked to an event in the Rose Garden last weekend washingtonpost.com/politics/trump… 2/n
It should be noted that risks of transmission outdoors are usually considered low. So it would be valuable to know whether and which guests were indoors together, both in term of understanding risk of infection and tracking new chains of infection along contact networks 3/n
DC is notorious for its contact networks. And some tend to include powerful and relatively old people. Older people are at higher risk, even if that risk divides further on whether you are old and poor, or old and rich 4/n
The virus moves readily from rich to poor. Somewhat less readily back, but it can make it.
5/n
We know a large number can become infected in a single event. We should take steps to avoid a surge of infections over a short period in general, but that is even more important if people with important roles in the government could be infected in rapid succession 6/n
This is not based on exaggerated concern about risk of infection – most will recover – it is about ensuring infection is controlled. Which sensible people have always prioritized. “Uncontrolled transmission is bad” is something almost everyone agrees about 7/n
I would urge the @JoeBiden campaign to be cautious. The virus spreads rapidly and readily, and exposure at the debate Tuesday is a risk. It is reasonable to believe multiple members of the presidential entourage were potentially infectious 8/n
The test results today are good but not conclusive. We will need to wait awhile to be sure as could be early in the course of infection. And during that time the candidate should distance and avoid close contact indoors. Continue wearing masks. Only keep essential engagements 9/n
However there was little distancing to be seen at the Rose Garden. Nor has there been similar events at the WH. Infections around the periphery have been reported for months, to the extent I am not surprised this has happened 10/n
Give the virus a way in, it will take it. Even if the nature of transmission is that most introductions to a community go extinct of their own accord that's only comforting so far. You allow enough introductions you know what will happen?
One of them won't go extinct
11/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