A reminder and perspective on this COVID, mid November.
(context: I am an expert in genetics/genomics and computational biology research; I know experts in a variety of other domains; I have a COI as I am a long established consultant to Oxford Nanopore, which makes a new COVID test, LamPORE).
As ever, it is good to start with the overall perspective - SARS_CoV_2 is an infectious human virus which causes a nasty disease for a subset of people, often leading to death.
Since its discovery in Jan 2020 we now know far far more about it; we understand better its transmission rates and some aspects of risky transmission environments; we understand the disease it causes and have repositioned drugs to ameliorate the disease.
If we let the virus transmit freely in a relatively old population a huge number of people would be severely ill, many people would die of the virus and even more would die from other health concerns because the health system would have to prioritise care so starkly.
Even if we did this rationally and with care it would be horrific; far more likely most citizens and systems would not be able to cope, and entire healthcare systems would cease to function.
We can dramatically reduce the amount of transmission of the virus. In the cruel world of infectious disease dynamics, where epidemics are either growing or shrinking these quite big reductions of transmission in targeted mode are not enough, in particular in the winter.
This is clear across Europe, where the vast majority of countries have had to institute blanket restrictions to control transmission, and even then it is still uncomfortably close to health care capacity levels.
The major bright spot on the horizon are vaccines. Two mRNA vaccines have posted very favourable results; no vaccine in a control trial has not passed efficacy tests yet - giving hope to there being a broad choice of vaccines for the world in 2021.
The plans for vaccine delivery have complex logistics, but reduction in risk for disease for at risk individuals will be a godsend and it is likely (but not yet shown) that vaccination will also reduce transmission.
As more people get vaccinated, adding to people who already have had the disease (5-15% ish of populations - up to 30% perhaps in some locations in Europe) will dampen transmission; this means targetted (TTI) approaches will work better
(Side note: we can - and should - always improve TTI. There is no level of efficiency in TTI we shouldn't strive for).
Even cheaper - and thus deeper - testing options are also available, in particular Lateral Flow Antigen tests (look like, and works like, pregnancy tests). These give countries options for deeper testing, though using the tests are both logistical and conceptual challenges
(it's important to note that testing alone - with no action, eg, isolation - is pointless, and furthermore testing broader populations is both logistically complex and one has to carefully consider how to handle/communicate false positives and false negatives)
I definitely feel the sun rising on the horizon for COVID, most of the warmth and comfort from vaccines. But in fact, right now, we are still in that false-dawn, depth of night, period - we have perhaps 2 months or so before vaccinations can be deep enough to change transmission
Even then it will not be back to 2019 - it will take into March for everyone who wants a vaccine to get one (interesting questions of vaccine uptake across regions and countries) and we will be living with the virus through 2021, if not 'forever' as we do other coronaviruses.
Back to the short term - 2 months is too far away just to "go for it" - this virus can double its infection levels every 3 days if unabated. But I do think this horizon should give us more confidence just to get through these months.
I certainly hope some modest family winter festivals (whatever your choice!) will be sensible and allowed, but I don't want much - just enough to reaffirm that family bond and love and I'd far prefer our population + healthcare systems to make it through to Feb/March.
There is a very complex aspect of the economic importance of the christmas period in many countries, shops and companies - these are livelihoods which are key parts of people's lives and we will want a nice, friendly 2021, 2022, 2023 Christmas ....
... not my area of expertise to guide us through Christmas 2020 retail economically compared to infection dynamics, something I am closer to (though even then, not an expert).
So - mid and long term I am optimistic, and this time I don't think optimism is curse. Short term we still have a complex landscape to navigate, and I don't envy the people giving advice nor the decision makers leading into midwinter.
My final thoughts as ever. First despite the tendency to frame many things inside national boundaries this is a global problem. Ultimately this is a human vs virus conflict, and us humans need to stick together on this.
Second is the need to be kind and generous, in particular through the depth of winter in the Northern hemisphere. To neighbours, family and colleagues - even random people on Twitter - strive for best intent and kindness.

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More from @ewanbirney

22 Nov
More musings on human genetics and race, but this time from a personal level to explain I think the different ways people "think about" racism and their role in it.
In this thread I am going to be critical about how many people think about broad structural racism/unconscious bias, but I will do this via critiquing my younger self, as it is super-hard to do this broadly without offending people; I can own offending myself :)
In my 20s I spent a fair bit of time in America and considered myself reasonably cool and trendy - worked hard at Cold Spring Harbor Laboratories, partied hard in NYC and Harvard, where I had friends.
Read 25 tweets
21 Nov
The ... level of self belief on Twitter is quite remarkable and apparently I don’t know much about the human genome or genetics. That’s me told ...
More seriously, conversations about ethnicity and race are loaded because it is both a big active part of many societies and discourse - most obviously US but many western countries (UK included of course) and >>
<< for many people this is a key part of their identity. There are shallow issues here -it is far too easy to use words that mean different things or for people to read strong motivational stances or inferences into statements
Read 9 tweets
21 Nov
Another evergreen reminder - ethnicity (or "race") is a process of self identification, often ticking a set of boxes, or gestalt assessment using visible characteristics of people (skin colour, hair type, clothes) by others. It is *not* a good representation of anyone's genetics.
The collapsing of ethnicity or race concepts as some sort of crude readout of genetics is plain wrong.
We can sometimes go the other way - genetic measurements in some places can predict the ethnicity box you will tick on a form - but we definitely can't predict your genetics from the box you tick.
Read 15 tweets
17 Nov
Vaccine safety thread - briefing to journalists as much as anyone else as ever, and an offer.
Vaccines are safe. They are safe principally because of the extensive and multiple testing that happens before they are licensed, and that ultimately is due to 100,000s of people who volunteer for trials to assess and quantify safety. I am a scientist and one of these volunteers
"Safe" here of course can never mean never - strange things happen in life, healthcare and biology and like many things we do in life - crossing roads, going biking, drinking wine - we have constantly do things which are safe but have some small risk of something going wrong.
Read 14 tweets
15 Nov
Good case numbers in France, Germany yesterday and the Welsh firebreak definitely worked. (What a surprise - reducing person contacts slow transmission). Northern Ireland controlled well but plateauing high -another push needed
Need to see the impact of the English Nov lockdown - next week sometime one should see lower infection numbers after the 7 day ish incubation period from last Friday plus the test and reporting cycles.
Scotland’s Tiering scheme and particular the central belt work also has done well - though I suspect they want to achieve now more decrease in infection
Read 6 tweets
14 Nov
Right. Deep Breath. RT-PCR "false positives" and Ct numbers (again). tl;dr it is complex, but the RT-PCR testing systems deployed across the world are sound and the people who run them report positives are positives and little can be improved obviously.
Context: I am a genomics/genetics + computational biology expert. I know a large number of infectious disease testing experts. I have a COI in that I am a long established consultant for a company (ONT) that makes a new test here; this gives me additional insight
There a number of classes of false positives which don't concern the current debate (eg, sample swaps, lab contamination). To repeat an early point all the people I know in this are paranoid about this, test and check in a rather detailed way and these are looooow.
Read 22 tweets

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