A little over a week since it was announced it is already clear that Omicron is really serious. Some important pieces of evidence have begun to coalesce. While the worst outcomes still seem unlikely, what we have is quite bad enough to be going on with, a thread, with nuance 1/n
First the spatial spread. Recall previous variants and the pace with which they were reported in different locations. Omicron is already on all continents other than Antarctica in slightly over a week since it got named. I mean... wow 2/n
Meanwhile we get some relatively positive news in that hospitalized cases seem milder than in previous waves. The concern is that those infected and hospitalized so far are mostly young. And we would expect younger folks to have milder infections statnews.com/2021/12/04/omi… 3/n
There are 2 places I am watching closely: Israel and the UK. Both are well vaccinated and studied by excellent scientists. One of them (the UK) also has a pretty huge amount of ongoing delta infection offering us a head to head comparison with Omicron. Delta was rare in ZA 4/n
Omicron gives a peculiar result to some diagnostic tests which we describe as “spike gene target failure” or SGTF. Essentially the test detects some of the genes in the virus and the spike gene is mutated so much the test can’t recognize it but it does pick up the other genes 5/n
This is the recent fluctuations in SGTF results in the UK. I want to emphasize that SGTF can be caused rarely by things other than omicron, and the numbers of SGTF results right now are small. But they have changed recently. There are more of them 6/n
Yes, that is consistent with Omicron cutting into Delta’s turf, in a place Delta had made its own and where it was causing a lot of infections and also plenty of mostly mild breakthrough cases. It has an advantage 7/n
(where that advantage comes from I honestly don't know because the amounts of immunity present offer a special advantage to escape - but delta is pretty good at infecting people with immunity too, or it wouldn't be causing tens of thousands of infection every day in the UK) 8/n
The UK has a pretty large amount of immunity from the combination of a good vaccination program and an incompetent initial pandemic response. If that doesn’t get in the way of omicron transmission, it’s not good 9/n
In Israel we have a fully boosted person transmitting to another. This is not data. It is anecdote. It’s not that it *can* happen, it's how *often* it happens that matters. That said, the fact that this has already been observed should be a contrast with previous variants 10/n
Taken together Omicron will be the story of the next few months. This is true regardless of how things like the severity shake out. Something so transmissible has consequences and they're not all rational. Look at the travel bans blog.ucsusa.org/derrick-jackso… 11/n
Consider the potential outcomes for rare but severe illness with common but mild illness, for something that is genuinely very transmissible, as Omicron appears to be in the best case 12/n
Transmissible means it all happens rapidly. So the severe cases clog healthcare (flatten the curve anyone?) while the milder ones are off work and supply chains stutter 13/n
None of this by the way is rocket science. And I don't enjoy any of it. But it is what we are looking at. Even in the very most positive future (very mild illness), we have gun-shy people jumping away from positive omicron case numbers for months. Transmission matters 14/n
There's still things we can do. Everything I know leads me to think vaxxed and boosted folks are in the best place to ride this out. And other stuff like masks will help control spikes. But I would be lying if I didn't say I was seriously worried. I am seriously worried 15/end

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More from @BillHanage

7 Dec
This is a little astonishing to see. Rapid tests are a part of the pandemic toolkit and should be readily available to everyone (*not* after any baroque claim on insurance). Things are, as ever, a little more complicated 1/n
For a start, Rapid Tests alone do not keep case counts low (even if they might be lower than they would be in their absence). Look at the UK where rapid tests have been handed out free for months. Those are not smoothly controlled epidemic curves 2/n Image
There are situations like this, where rapid tests shine 3/n
Read 9 tweets
6 Dec
Given how serious Omicron could easily be, some people might be breathing a sigh of relief if the worst possibilities are ruled out (I think they will be). But that still leaves a lot of possibilities most of which are Really Not Good. However this is not a thread about that 1/n
Pandemic twitter often tries to divide people into ‘pessimist’ or ‘optimist’ camps. This is not helpful. Especially when it comes to the folks who know most about infectious disease. I am neither an optimist nor a pessimist. I am a scientist and I try to call it like I see it 2/n
I’m not always right, but I am sincere and I try to correct when I am wrong. And I admire people who do the same. I don't always agree with them all, all the time. But that comes with the territory 3/n
Read 9 tweets
1 Dec
With #Omicron very real, I thought it worth going back to this, which I wrote with @mlipsitch at the start of the pandemic. It helps to think clearly about 3 types of information we have at the start of an outbreak amid uncertainty 1/n blogs.scientificamerican.com/observations/h…
First there are the facts, then there is the interpretation of those and what they might mean about things that we’ve not been able to yet nail down into facts. This means expert opinion, based on previous experience, unpublished data, and conversations with colleagues 2/n
Then there's speculation. Sure it can be useful. But without a way to test whether we should take it seriously, we shouldn’t. Note that this can include really important things like why a particular policy choice was favored, but that’s not science 3/n
Read 12 tweets
28 Nov
There are a few things to note here. First I want to remind people how many flights from ZA do *not* have cases on board - we won’t hear about those. It seems too that these 13/61 on this flight with omicron are those to have been identified *so far*… 1/n
It will be important to know if there are any common exposures (eg did they share a hotel?) and what on earth happened to any preflight screening protocols? This will be especially true if it turns out there are also any delta cases on the flight 2/n
Anyone who has traveled in the pandemic will know that some procedures are honored in the breach as well as the observance (going to the U.K. earlier this year, my forms were barely glanced at, by an official without a mask at a time they were supposedly required) 3/n
Read 4 tweets
21 Nov
I’ve no objection to working with economists and indeed I have done so during the pandemic! That’s just one of the reasons this article seems to be addressing a straw man. It also misses something really important that shouldn’t be forgotten 1/n nytimes.com/2021/11/19/opi…
Few serious people argue that there are not trade offs between costs and benefits of different elements of pandemic response, but there is only so much a combined model of the sort proposed in the article can do. And at the start of a pandemic it could be actually damaging 2/n
The more complicated a model, the more information you need to make it work. At the start of a pandemic this is typically in very short supply. Remember the arguments about the infection fatality rate that lasted nearly a year? 3/n
Read 10 tweets
14 Nov
Some outlets are trumpeting the currently small number of cases in Florida as vindicating the state’s covid-curious approach to the pandemic. The reality is different, and uncomfortable for undervaccinated communities here and around the world as the nights draw in 1/n
FL was always high risk for high mortality, if only because of the age profile of the population. However once effective vaccines were widely available in early 2021, there were reasons to think that bullet had been dodged. That’s not how things turned out 2/n
A combination of lax mitigation and poor vaccination in older age groups led to a large surge of infections with the Delta variant, which is both more transmissible and likely to lead to hospitalization 3/n
Read 14 tweets

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