Thread by @ewanbirney

Omicron thoughts from dark, Christmas London. TL;DR - Europe+World is facing the Omicron storm and it looks increasingly bad; and, obviously, the virus doesn't care about Christmas. Despite some serious response in the UK, this virus is replicating fast; more action likely needed

Context: I am an expert in human genetics and computational biology. I know experts in infectious epidemiology, viral genomics, immunology and clinical trials. I have some COIs: I am consultant and shareholder of ONT and was on the Ox/Az trial.

Reminder: SARS-CoV-2 is a recently jumped coronavirus into humans which causes a very nasty disease, COVID, in a subset of people. It has rushed across the world over 2 years, combatted by lockdowns and more recently vaccines, but causing death and disease in many places.

The SARS-CoV-2 virus has evolved to create it's first "antigen drift" variant - Omircon - a common way coronaviruses continue to circulate in populations by having enough changes in their spike protein to look different.

Omicron was first characterised in South Africa, which remains furthest along the Omicron wave so far. It would have been awful if many people died or were in hospital in SA, but, thankfully it looks like the wave in SA is less damaging than the previous Delta wave.

But this experience need not match to Europe - Europe's population is older and there has been far far less prior infection (due to lockdowns and vaccines). This means one can't map one to one the experience in SA to Europe or other places (each with it's own mix).

The UK and Denmark, presumably along with the rest of Europe, was seeded with Omicron some 3 weeks ago (the time scale is *so short*) and probably due to both countries relying on vaccination, strong vs Delta, Omicron established quickly in both locations.

In both places Omicron's doubling rate has been in the order of 2 to 3 days. This means 4-8 fold a week - and *25-128* fold per 2 weeks. The graphs are bonkers and scary. All SARS-CoV-2 infection graphs will "hockey stick" pretty much everywhere I suspect over this month.

At this rate lags of days (or weeks in some countries for some data assets) between for swabbing, testing, testing/sequencing for omicron, data flow and analysis are meaningful. For example, it's simply not clear to me what the level of Omicron is in France.

Reassuringly and mainly due to prompt data flows from the UK we can be pretty certain that 3 doses (3x mRNA or 2x Adeno, 1x mRNA) greatly reduces symptoms and most likely really suppresses severe disease. ie, Boosters work. Boost-baby-Boost.

Infection is one thing, but what decision makers want to know about is hospitalisations; again, the time from sense to decide to respond to change infection patterns is probably too short to be sure; one has to make decisions on far lighter data than one would wish.

It's worth pointing out the obvious. The virus isn't sentient (duh!); it doesn't know about Christmas or any winter events, and it genuinely does not care. Throw out your human schedule, view the schedule from the viruses' perspective to understand the risks.

The most recent (today's publication) from the UK's well respected SPI-M group is pretty clear about the risks in the UK (assets.publishing.service.gov.uk/government/upl…)

"For the forthcoming wave to remain around or below 1,000 to 2,000 total hospital admissions per day without intervention, low immune escape and very high protection from boosters are required to be consistent with the estimated omicron growth rate >>

[reasonable modelling assumptions] for omicron growth advantage, generally have a minimum of 5,000 hospital admissions per day at the peak with many scenarios significantly worse during the first few months of 2022"

"To prevent a wave of hospitalisations similar to those seen in Spring 2020 and January 2021, without the need to slow growth with interventions, the severity of omicron would need to be between 10% and 30% that of delta."

This is a small parameter space for the UK to be "ok" (for some definition of ok) and importantly by the time we have good evidence of Omicron severity it is likely to be too late to react. Crunching the numbers from SA is useful but not the UK/European scenario.

Plus really large infection has incredible complications on healthcare (eg, rostas, dealing with healthcare staff infected) even if in theory ok and de facto lockdown like situations for hospitality (staff reasons, customer fear).

Other high elderly vaxed countries with a prompt booster campaign - Denmark, Portgual, Ireland for example - are likely to be a similar position to the UK. Lower vaxed, in particular in the old ages, such as likely in some parts of Germany (eg, Saxony) have still thinner margins

Eastern Europe, with higher previous infection but less vaccination is harder to call - one would need to do modelling of this and again many parameters one would just have to guess at now.

I can't see western Europe getting through this without some level of lockdowns, perhaps circuit breaker ones to ease off healthcare pressure, let booster campaigns complete, leaving some NPIs to see out Omicron wave.

For countries with significant numbers of vaccine hestitant people, it is going to be far more complex. A mixture of carrots and sticks likely needed (personally I think there's been too much focus on sticks - mandates, fines etc; Slovakia's vaccine voucher inverts this).

Looking beyond Omicron - hard to do at the moment - we are going to have to regularly deal with antigenic drift of this virus (as we do, unknowingly, for the other 4 endemic coronavirus). This level of disrupution is ... not sustainable, so we will need everything to work better

Rounds of infection will no doubt help; I still think we need to have some level of focus on the (inappropriate) host response for COVID, which is a CFS like viral-triggered auto-immune disease; ie, tackling the disease not the infection. A long road for new drugs though.

In the meantime we've got to get through the Omicron wave. Remember to be kind to yourself, your family, friends and strangers - nearby and worldwide. This is getting humans through this thing, and we're going to have to be resilent and caring to all.