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.
vax-baby-vax

Vaccines really work; most importantly they reduce (~5-20 fold) your chance of going into hospital; they also reduce transmission of many variants (we need to see this on omicron).
So get vaccinated, gently persuade anyone around you who is not vaccinated to vax up
boost-baby-boost

The 3-dose vaccine schedule is clearly better than 2 doses. It not just "tops you up" - it super charges your immune system to go beyond the second dose, which wanes over time.
So - get boosted, and for anyone wavering, let them know this super-charges them.
test-baby-test

If you are going to meet people, lateral flow tests are rapid and pretty darn good, in particular for infectious scenarios. They aren't perfect, but they are very useful.

My what's app now has meet ups with LFTs posted. This is a good thing. Lead by example.
vent-baby-vent

SARS-CoV-2 is airborne which is bad (it does far) but it also can be cleared by air exchange. Even a small bit of open air into a room can make a big difference. If, post LFT, someone is infectious (can happen) the fresh air will disperse the virus.
mask-baby-mask

Masks work. They aren't a pancea but in particular where they don't impact your life (eg, when on public transport, in the coffee queue, etc) they help. You could be asymptomatic LFT-negative (it happens) and by wearing a mask you *really* help everyone else.

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More from @ewanbirney

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
24 Nov
In my voyages in maths with my daughter series - we've been discussing geometry (seed question - can you prove the (n-2)*180 for the interior angles of an n-sided polygon) and this threw up some interesting things.
First off, a discussion of 180 leading to radians + Pi. Thought experiment - if there was a planet of intelligent otters and they used a different number/angle system, they would no doubt not divide the circle into 360, but the concept of a circle, half circle, would be the same
(you might guess my daughter is a fan of otters. We decided they would likely work in base 7 I think due to their tails being the extra "unsymmetric" digit. Don't ask for more details).
Read 10 tweets
22 Nov
Thoughts on COVID in Europe from a crisp morning in London; we understand this virus, its likely endpoint, but it is hard road to follow. Central/Northern Europe start a 4th nasty wave; South West Europe has vaccinated well, (currently) less of a wave; the UK remains a conundrum
Context: I am an expert in human genetics and computational biology. I know experts in infection biology, viral genomics, clinical trials. I have COIs - I am longstanding consultant to Oxford Nanopore (makes sequencing machines) and was on the Ox/Az trial.
Reminder: Assumming there is no major new SARS-CoV-2 variant, we have the measure of this virus and its horrible disease - it transmits rapidly between humans, causing a nasty, often lethal disease (COVID) in some (older, more overweight) people who are immunlogically naive.
Read 25 tweets
6 Nov
Ethnicity, Ancestry Groups and Biology in humans; some thoughts triggered by @molly_przew threads and the recent Oxford paper on the likely mechanism of action for the COVID risk locus on chr3. TL;DR This is area is complex; racism +discrimination are real; biology is universal.
It's useful to remind yourself what some of these terms mean (or might mean). Ethnicity (also "Race" in US context) is usually defined via self identification - a person is given a number of options to tick, sometimes with hierarchy, and they tick one (or more) option.
These boxes are very culturally and nation-state defined. eg: The US has it's census terms (census.gov/topics/populat…); the UK has different terms (ethnicity-facts-figures.service.gov.uk/dashboards/eth…); Japan their own scheme; in France it is illegal to ask this question.
Read 36 tweets

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