Reading this, which looks like a pretty definitive take on the origins of the pandemic. Important conclusion: most zoonoses of this kind would go extinct of their own accord. science.sciencemag.org/content/early/…
That actually makes a lot of sense if you consider everything we know about the clustered nature of transmission. Like they say, we should do better at detecting zoonoses early on
Nice illustration of how a transmission chain could sputter along a bit before making it big. Note that what this means is that while the pandemic descends from the market in Wuhan, that's not necessarily where the index case occurred
Indeed, given the epidemiology of the disease, it would be surprising for the very first infection to initiate a superspreading event that was immediately noticed. And then there are the many mild infections that would *not* have attracted attention
I've commented several times that the virus must have come into humans some time before we noticed it, but this is setting out to quantify how long it might have been. Answer - not that long. Mid Oct to mid Nov 2019
That's done with simulations, which also allow estimates of how many people were actually infected before the pandemic was recognized, There is a lot of uncertainty as you can see. And note how in the simulations shown in C how many attempted outbreaks die out of their own accord
But when it comes to simulations, need to think carefully about the assumptions. So now I am going to read it more properly.

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More from @BillHanage

16 Mar
Absolutely right. The various aspects of the failure need more thorough unpacking in a medium that is probably not twitter, but it is actually striking to me how *much* we (meaning epidemiologists) knew a year ago about what this virus is capable of, and how little it has changed
Just as a for instance, the varying severity by age has been known pretty much since Jan 2020. And so has the potential for presymptomatic transmission, which is absolutely essential to the effort needed for control, and the importance of rapid testing
I was very aware of the potential for minimally symptomatic transmission because of my involvement in this (true story - I wrote my draft on an overnight flight at the end of feb. Then we all got slammed and it wasn't submitted for months) ncbi.nlm.nih.gov/pmc/articles/P…
Read 9 tweets
13 Mar
There are a lot of think pieces going around about the pandemic one year on. This is one of the best, from @jameshamblin, because it is upfront about the difficulties we face handling uncertainty. That's relevant to then, and now. A short 🧵commenting on the issues raised
The first thing to remember is that uncertainty about precise numbers is not an excuse to avoid action. This is a common misunderstanding about how mathematical modeling results should be interpreted. Depending on your inputs, you can get all sorts of results...
The goal is not to forecast exact outcomes, because you hope you never experience the world in which nobody intervenes *at all*, but to understand how seriously to take the threat. Qualitatively right is not the same as exactly quantitatively right.
Read 16 tweets
1 Mar
A long sobering look at the pandemic in the UK. The success of the vaccine rollout should not obscure the way that leaders failed to heed the lessons of spring 2020 to an extent that beggars belief nytimes.com/interactive/20…
Look at the cumulative deaths. Around 40k in spring of last year. In other words ~2/3rds of the total are from the last few months (data from worldometers.info/coronavirus/co…)
While some of this is down to the emergence of B.1.1.7, it is mostly down to an attitude that resisted taking appropriate action, and ignored scientific advice. As many will know, I think 'led by the science' isn't the right way round - we should be led by those we elect. But...
Read 5 tweets
21 Feb
The thing is that much of this article could have been written at multiple points over the last year. Viruses are not influenced by bluster. Fortunately they are impacted by vaccine induced immunity. A few thoughts... 1/n
theguardian.com/commentisfree/…
Cases are falling quickly in the UK and elsewhere, which is great. The reasons are not clear, but it is reasonable to think that some of it is down to the comparatively rapid and effective vaccine roll out *together with* current numbers of contacts 2/n
If those numbers of contacts and opportunities for transmission increase, then we can expect cases to increase too. That is why caution is merited. The more people are protected by vaccination, the more contacts can happen, and there is something else... 3/n
Read 11 tweets
2 Feb
I think it is fair to say now that B.1.1.7 is definitely more transmissible, and possibly more virulent. This also reports cases that have acquired E484K, a mutation found in the other variants. This is concerning, but not reason to go crazy. A thread 1/n assets.publishing.service.gov.uk/government/upl…
First let's put to bed any suggestion that overdispersion in transmission explains B.1.1.7's rise. Consider data from Denmark, Ireland and now LA to mention only a few. It's behaving as we expect 2/n
This is the weekly increase in England documented in the linked report since early October. It's quite interesting that it's not taken over completely but don't want to speculate why 3/n
Read 15 tweets
1 Feb
I am all for large amounts of testing, but I doubt this will be sufficient to do more than slow things down (good in its own right of course). There's also not much in here on what will be done in the event of a positive test. theguardian.com/world/2021/feb…
That's what people forget. If a positive test does not lead to action that stops transmission, meaning support to allow isolation and quarantine of contacts, you're really only keeping score for the virus
Read 4 tweets

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