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.
The extremely large number of people on trials means the scientists who run the trials (I am not one of these scientists - here I am just a volunteer) can estimate even quite rare events. So they know. They do these trials with squeaky clean "no cheating" ways to be sure.
For some of the vaccines to COVID-19 we know they are briefly unpleasant- really quite unpleasant fever+aches for some people. This is those people's immune system reacting appropriately to this disabled virus and learning about it. It's a sign of a healthy immune system.
(In my case, as I am on a clinical trial for the vaccine, I don't know if I got the COVID19 Vaccine or the other "mock" treatment which was in fact a different vaccine to a different disease. My arm ached for a day, like I hit a wall hard with my shoulder. No fever for me).
At this point one could dive more into the science, clinical trial protocols, statistics of rare events and the reasons people who do this alot really think these things are safe. For some people this will be reassuring.
But I think a lot of fears of the vaccine are simpler than this; it is a dislike of hospitals, medicine and needles - a desire to live life independent of this all for as long as possible - and a mistrust sometimes of these very systems that say "safe" with freaky confidence
Just to say straightforwardly I get the dislike of hospitals and needles - I am not a fan of either (I have to look away when I get injected or people take blood - I am really not good there!) and I also would like to live a healthy life on my own terms.
But, I know that taking a vaccine is far far safer than most of the other things a regularly do, and furthermore I know that by volunteering for this trial I can give other people the confidence of this particular vaccine being safe.
The freaky confidence you will hear more and more about is due to the 100,000s volunteers, like me, who had to take a marginally higher risk (because we didn't know the safety aspects) so people *can* be confident about the safety.
This argument about whether vaccines are safe is starting now; the precise details of how they work is still hot news (and it is very exciting), but it is really important to get this confidence about safety to people in an appropriate, empathetic way
(editorial note: I am not a fan here of a shock-and-awe on statistics or science - this is not where the challenge lies - it is the emotional distrust and disconnect people feel in my view).
Finally - an offer to journalists - I and probably other trial participants I am sure are happy to be interviewed and provide that human view of this (other trial participants on twitter happy to be interviewed - perhaps respond here so journalists have smorgasbord of options)

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More from @ewanbirney

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
13 Nov
Small moan about models and parameters in COVID. R - the number of infections each person makes on average is a parameter but it is also something that one can measure. Each infected person has their own "R" - it is a count - and one could in theory measure all these little Rs
This R is both something one can measure and the average R, or the distribution of R is often components of model. It is a "real measurable thing" and it is "part of our COVID models".
You might want to model other things; one is the distribution of how R varies between people/events. A sensible choice is a negative binomial. Often people use k as a parameter (in fact, in other uses, they often use the letter r as a parameter, but this would be confusing!)
Read 5 tweets
13 Nov
Again, a briefing for journalists, this time on vaccine trials, types of vaccine, efficacy and safety.
(Context: I am a two-steps expert away from vaccine development; I am a one-step away from clinical trials; I am an expert on genetics + computational data science. I am, finally, on one of these clinical trials as a participant)
Standard context: SARS_CoV_2 is an infectious virus that causes a nasty disease, often leading to death, in a subset of humans. It will continue to be a massive issue to manage until we either have good enough vaccines or good enough treatments for the disease.
Read 37 tweets
12 Nov
It's great to see this paper on scaled up Cactus graphs (Progressive Cactus) - on 600 vertebrate genomes - from the great team lead by @BenedictPaten nature.com/articles/s4158…
This paper is a very much a methods paper, but I hope Benedict and colleagues will also dive into the data - I don't think we have use the realised ancestor reconstructions (reminds me of the older Enredo days - also with Benedict!). There is a treasure trove in there
Just repeat evolution I think is fascinating here, but also niche-loss pseudogenes for example.
Read 6 tweets
10 Nov
A riff on data, models and intervention in a COVID world.
When you don't have data, you absolutely need models - it helps you understand what could happen, good and bad scenarios and what you need to measure to understand more thing. With no - or little - data, models are king.
When you have data, the role of models change. In fast moving epidemic even working out what is happening *right now* is complex; your data is coming in different streams, it has biases (which change over time), technical issues (also time dependent) >>
Read 18 tweets

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