Thread by @BillHanage

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

https://twitter.com/theosanderson/status/1466808535338168324?s=20

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