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

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

https://twitter.com/BillHanage/status/1638161575356903425

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

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

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

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

New paper in @JIDJournal from a great collaboration with @kar_jacobson among others (HT @SundermannAJ for putting it on my radar!)

Will attempt to summarize key points...

academic.oup.com/jid/advance-ar… 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 was posted while I was away, but very interesting and important work on the date the current monkeypox outbreak virus start circulating among humans - it's been a while
virological.org/t/an-apobec3-m… 1/n The outbreak virus is accumulating change that looks a bit weird - in terms of the precise 'mutations' and the rate (more than you'd expect). This is consistent with editing of the genome during infection of human cells 2/n

Having to head to the airport early after a meeting that was marked by so many parallel sessions I wanted to go to that I had to keep hopping between them. Sorry to miss the great @NathanGrubaugh speaking ☹️ #ICEID 1/n Many standouts including a great session on misinformation featuring @PeterHotez @KatherineJWu and @cward1e and Neil Johnson 2/n

There are several things about @mattwridley’s article that are misleading (and self contradictory) but this, for me, is the most flagrant (read on - more than 280 characters required) 1/n

https://twitter.com/billhanage/status/1554661872619687936

The left screen grab is from his article. The right is from the paper he’s criticizing - it specifically is limited to early cases *without* known links to the market. Ridley’s article ignores this

Spent the last few days at an awesome, thoughtful meeting on pandemic data streams and modeling alongside the likes of @AnisabelBento @johnbrownstein @svscarpino @DrJayVarma and @JustinLessler. Special shout out to long time friend and colleague @SRileyIDD Lots of serious discussion and nuance - in other words the opposite of social media (as one speaker put it, "Twitter is about winning") but hopefully as I what I learned it will be reflected on here

This article about possible long term replication of virus in some Long Covid patients is pretty good and measured, but this comment about antivirals is off base 1/n theguardian.com/society/2022/j… Firstly, in the absence of trials that demonstrate benefit, this is hypothetical – it is not a reason to not do the trials. Especially when so many are suffering from long covid (and the numbers are growing) 2/n

So much of this is also relevant to the way people have approached the pandemic on twitter, and continue to do so as opinions become ever more polarized (and not always tethered to evidence - which makes them harder to discuss or debunk)
nytimes.com/2022/06/15/opi… 1/n I mean, just delete 'politically' from this, or replace it with 'scientifically'
2/n

Despite the fact that the linked article specifically says “don’t QT” I’m quoting and RTing this because more people should read it

https://twitter.com/apsmunro/status/1528268190110859264

I’ve had a number of quite sharp points of disagreement with @apsmunro but I hope we’ve each emerged from them with a better understanding of the science involved. In large part that’s down to discourse of the sort described in his post

I am no kind of specific expert in monkeypox (or orthopoxviruses). That being said, given what I know about disease transmission the clusters of monkeypox infections that are turning up should be treated with the utmost seriousness 1/n We have unconnected infections in the UK, Portugal, Spain and Canada. This means community transmission, unobserved 2/n

1 million US deaths into the pandemic, things seem to be perceived as quieter - but that reflects how much our frame of reference has shifted. The current weekly deaths remain historically remarkable 1/n let's have a look. This is from the @nytimes. This would translate to over 2000 deaths each week. And way more than 100k each year - how does that compare with something like flu? 2/n

Some of the replies to this are pretty wild. Some things I thought were obvious plainly aren't so...

https://twitter.com/BillHanage/status/1520033496948953091

This is not because people go on vacation. I am suggesting that the change in contact patterns as a result of kids not gathering and transmitting in schools would be expected to make a difference. Fewer contacts (to non immune people) = less transmission

Boston wastewater watch. There was a sustained decline over the last week or so in the North System. Before getting ahead of ourselves we should remember this coincides with spring recess in the schools I don't want to over interpret that blip up in the most recent sample, but if the trend reverses transmission in K-12 education is a potential contributor. This has been the case elsewhere (eg the UK) and mitigations are less complete than previously

There seems to be a sense building that there’s a lot of missed BA.2 infections, because lots of people are getting symptoms but never testing positive for covid. I am hence here to remind you that other respiratory viruses exist and will cause more infections as people relax 1/n I’ve been sick the last week with sore throat, cough, congestion, headache myalgia etc (not anosmia unless you count my nose being too blocked to breathe through it). Do I think it’s covid? No 2/n

BA.2 has ended the plateau of daily cases in the North East US. We can't be sure what the next month or so will hold, but I expect a bump in infections that may not be as large as many fear - although it could be at least locally serious. Here's why 1/n nytimes.com/live/2022/04/0… First thing is - BA.2 is once again *even more contagious* than what went before. This should not be unexpected, if it were less so we wouldn't be seeing it. While it's not clear how much is down to intrinsic factors vs sidestepping immunity, it's probably a bit of both 2/n

Following attempts to 'move past' the pandemic, healthcare in the UK is compromised - again (even if with lower vaccination rates it could easily be so much worse)
theguardian.com/world/2022/apr… you don't need to be a zerocovid hawk to think that stopping funding for the genuinely world beating #REACT study at the point when the highest prevalence has been recorded is shortsighted

https://twitter.com/john_actuary/status/1511647049590231040?s=20&t=QRCKZsN0LAgAnpYgxdD2Iw

Before and after photos of the TB hospital in Chernihiv, Ukraine, shared by a colleague of @jenkinshelen recently evacuated from Kyiv. The war will impact the treatment of many infectious diseases, but TB is especially important 1/n Ukraine and other parts of the former Soviet Union have very high rates of multi drug resistant TB. Failure to treat this adequately will lead to more infections, and if you don't want covid you *really* don't want MDRTB 2/n