One consistent thing in this pandemic is for a given virus biology (parameters of infection, immune escape, disease severity) the growth or reduction fits models / understanding well
(A short diversion here between forecast/now cast models - accurately predicting the next handful of days - and scenario models - helping decision makers plan given uncertain parameters and choices for intervention-
Forecast models absolutely should be benchmarked to outturn. Scenario models for the discovered parameters and interventions benchmarked by shape and size but less so timing)
For omicron scientists rapidly worked out it escaped immunity and had high transmission; that 2 dose vaccines offer little protection to symptomatic infection (likely some protection vs severe) but 3 doses (boosted) works well bs mild and presumed severe
After the first week the scenario models all pointed to rapid growth in Europe - this has come to pass in London and Copenhagen; probably omicron is growing fast in other places in Europe, masked in aggregate due delta
For commentators, journalists and politicians therefore - the infection growth we are seeing was virtually inevitable. And there will be considerable hospitalisations ahead of us.
Can healthcare systems cope? I don’t know (I hope so) but a reminder that exponential growth is very hard to match with fixed or linearly increasing at best healthcare capacity
My heart goes out to London NHS colleagues who have another exhausting Christmas ahead. Stay safe all.

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More from @ewanbirney

18 Dec
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.
Read 25 tweets
11 Dec
COVID thoughts from cold, Christmas London. TL;DR The Omicron storm clouds are glowering above Europe, but its unclear whether this will just be rain and hail of COVID or rain, hail, tornados and hurricanes of infection and subsequent hospitalisation of COVID.
Context: I am an expert in human genetics and computational biology. I know experts in infectious epidemiology, viral genomics, immunology, public health and clinical trials. I have COIs - I am consultant and shareholder to Oxford Nanopore and was on the Ox/Az vaccine trial.
Reminder: COVID is horrible disease triggered by the infection of SARS-CoV-2 in a subset of people. A combination of reducing contacts (early), reducing travel (some countries) and vaccination brought SARS-CoV-2 towards a somewhat endemic trajectory over 2020 and 2021. However >>
Read 25 tweets
5 Dec
Some of my friends or friends of friends ask how to best "do something" for omicron. I have a little mantra in my head:
vax-baby-vax
boost-baby-boost
test-baby-test
vent-baby-vent
mask-baby-mask.
This is in my crude list of effectiveness; one is missing which is the "don't meet people" (its simple. not long term.) and this has to be kept on the table as a possibility. To step through them.
Read 8 tweets
28 Nov
My view of COVID from crisp, cold Helsinki (back to London - with PCR test - on Tue). TL;DR Omicron has thrown us back to a place of uncertainity; we have far more potent tools+understanding now but the trajectory will be mainly determined by the biological properties of Omicron
Context: I am expert in human genetics and computational biology. I know experts in viral genomics, infectious epidemiology, clinical trials and immunology. I have some conflicts of interest; I am paid consultant and shareholder of Oxford Nanopore and was on the Ox/Az trial.
Key background: COVID is a virus-triggered disease, with hallmarks of auto-immune disease, triggered by a novel, highly infectious Coronavirus, SARS-CoV-2. In naive populations many people would get this disease, many of those dieing, and healthcare would be overwhelmed
Read 24 tweets
26 Nov
A great collaboration on direct RNA sequencing of SARS-CoV-2 transcripts using nanopore sequencing from Camilla Ugolini (Italian Institute of Technology) and colleagues, lead by Tomasso Leonardi (IIT) and Dave Matthews (Bristol) - I am a co-author. biorxiv.org/content/10.110…
(note; I and some other authors, eg, @AkesonUCSC have conflict of interests to declare as I am long standing consultant to Oxford Nanopore and shareholder).
Camilla looked at SARS-CoV-2 transcripts using a neat new protocol that both captures capped (full length) RNAs and can sequence through them, NRCseq, developed by @ettwiller (also a co-author). This means Camilla can distinguish full length from degraded transcripts.
Read 9 tweets
25 Nov
A brief explainer thread on B.1.1.529, the latest SARS-CoV-2 variant which is throwing up concern after an excellent live streamed press conference from South Africa. TL;DR this variant both has many mutations but most importantly looks like it outcompeting delta in South Africa
Context: I am a expert in human genetics and computational biology; I know experts in viral genomics, infectious epidemiology, clinical trials and immunology. I have some conflicts of interest: I am longstanding consultant to Oxford Nanopore and was on the Ox/Az clincal trail
Background. The SARS-CoV-2 virus is made from RNA (its instruction set) wrapped in proteins. The RNA+proteins of the virus hijack our cells to make more of its RNA and proteins into a virus. This hijacking (infection) causes a response from our immune system.
Read 20 tweets

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