There a lot of scientists in reflective mood as we face up the prospect of an autumn second wave of SARS CoV2 and what it may or may not mean, and in particular whether we can or even should contemplate further lockdowns. So I’ll add my twopenneth’ 1/n
At the beginning we didn’t heed the warnings from China and Italy until it was too late and we ended up playing catch up with a rapidly spreading virus that we didn’t understand. 2/n
The ability to test samples and act on that knowledge was rapidly outstripped by resources and the govt were woefully slow to alleviate bottlenecks in testing, diagnostics and PPE, all of which had been highlighted when wargaming a pandemic 2 years earlier. 3/n
ICUs filled up, not just with the old and infirm, but with middle aged (and younger) with chronic, but not terminal, conditions, many of whom died horrible deaths. 4/n
Academic scientists up and down the country volunteered, cajoled, begged the DoH and PHE to be allowed to help. And while understandably there were concerns about quality and regulation, a very large talent pool went unused for a long time. 5/n
And then we locked down in late March – too late in retrospect. I was personally very wary of lockdown for exactly the reasons we all know. I was particularly worried that the of strategy about how we were going to get out of it wasn’t clear. 6/n
But at the point I think we had no choice. The Health Service would simply have fallen over and had to be protected. 7/n
But, and this is absolutely key, by then we knew that most people who get SARS CoV2 only have a self-limiting respiratory illness, and some (proportion still debated) have no discernible symptoms at all. 8/n
If, as we had to assume, everyone was susceptible to infection, the small percentage of people who get very sick was still going to be a very big number, and certainly bigger than can be coped with by an overstretched health service in the autumn and winter months. 9/n
Eventually Matt Hancock set out his tests for lifting lockdown. And they essentially boiled down to being able to test, trace and isolate infected people. Great fanfare was being made about the number of tests, but what really mattered was deploying them right. 10/n
The govt set up the Lighthouse labs, staffed by volunteers and run by people who really know what they’re doing. But the problem is the highly centralized nature of them and their reliance on private logistics firms, making them very big ships. 11/n
That’s ok if you have more agile little ships to manoeuvre, as Paul Nurse put it. We didn’t really for a very long time. 12/n
And of course the IT and tracing has been an absolute disaster, compounded by putting someone so unqualified in charge (Dido Harding) as to be beyond satire. 13/n
So by the time that the economic and social cost of lockdown began to bite, and growing clamour to exit, with Cummings being the final nail, bounced us out. 14/n
Summer was always going to be a phony war. Many respiratory viral infections don’t transmit that well. And SAGE told the Govt and Harding repeatedly that preparation for autumn and winter needed to be sorted by Sept. 15/n
Going back to work, schools and college were obviously going to lead to a re-emergence of the virus. It was also going to be (at least to start with) in a younger demographic so the pathogenesis will be lower. 16/n
So where are we: IMO we have to be able to manage the transmission of infection in the population without further blanket lockdowns, I just can’t see how one could do it again both economically and socially. Kids need to be at school, people need to be able to work. 17/n
But we need to understand where the virus is so that we can protect the vulnerable, and need to retain some necessary (if uncomfortable) restrictions on our day-to-day lives that together will take the edge off transmission. And this is where we are failing. 18/n
We didn’t use the time well enough to put in the TTI systems properly over the late Spring/Summer, or deploy more targeted community monitoring in a way that would steal a march on the virus. 19/n
Another thing we really need to understand much better, and build into the strategy, is the relative risk of transmission by asymptomatic individuals. And even more importantly, the level of positive signal in a test that correlates with infectious virus. 20/n
This latter point is crucial. It isn’t ‘false positives’ that are the issue really, it is people who have been infected and cleared the virus remaining RNA positive for some weeks afterwards. 21/n
We have known this for a while, and it is much harder to do. But if we don’t, we will be closing schools a lot based on positive PCRs. And the public will put up with a lot but messing around with their kids’ education will be the killer. 22/n
So, we are coming into autumn. Covid is coming back, it’s probably here to stay as a new seasonal coronavirus (I’m not convinced Covid Zero is realistic, sorry). We don’t know how it will behave when other respiratory viruses start coming out. 23/n
Testing, testing, testing is still key, but it is how we test, who we test and what we do with the information that is really important. Despite the hard work of so many on this, we have been so brutally let down by the government that it almost feels like square 1. 24/n
So we can’t lockdown again, but we don’t yet have the strategy and the tools to protect the vulnerable and keep life going on as normal(ish). That’s what scares me about winter. 25/n
Long thread, but one last plea to everyone: Wear your bloody masks, maintain the social distancing, support the NHS and the people trying to sort this out, and get a Flu vaccine 26/n
(oh, and if you care about this country, irrespective of your party allegiance, never vote for someone like Boris again)

Fin

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More from @stuartjdneil

Sep 28
1.Fantastic and mildly (😂) opinionated TWIV with Eddie Holmes on viral emergence and the origins (and the politicization of the origins) of SARS-CoV-2. Really worth your time.
2.It’s guaranteed to wind up the usual suspects but contains nice historical recollections and vignettes about some of the vexed issues that the LL make a big deal over.
3.Firstly, a nice recollection of the actual timeline of the now infamous ‘Fauci Phone call’ (in reality organized by Jeremy Farrar) spelling out exactly why Eddie ‘changed his mind’
Read 14 tweets
Aug 2
1: One canard you see from the professionally-invested lab leakers and their followers, which they use to sow doubt that COVID came from wildlife farms in Hubei, is the impression that no human-tropic bat sarbeco, and no S2-family members, have been found outside Yunnan in China.
2: Two pieces of evidence that should make you pause and realize that they are talking patent nonsense.
Firstly, his paper from 2007: journals.asm.org/doi/10.1128/JV…
3: In this paper, the authors identified, effectively, SARS1 in civets farmed in Hubei, hundreds of miles from Yunnan where the closest relative of SARS1 (WIV1) was discovered in wild horseshoe bat populations in 2012.
Read 13 tweets
Jul 1
1: Very interesting paper from Pasteur looking at the pathogenesis of BANAL-236. The results are important, valuable and the experiments are well done. However, it seems to me some commentators selling books, are significantly overinterpreting the results
researchsquare.com/article/rs-180…
2: BANAL-236 is one of the closest known relatives of SARS-CoV-2 found in bats, in Laos (yet still approx. 30yr distant). In particular it has a Spike whose RBD is as near as dammit the same as SARS-CoV-2, but no furin cleavage site.
3. Historical samples of pre-pandemic bloods from 100 individuals who would be likely to have had contact with the caves in Laos where BANAL-236 was found showed no evidence of serum antibodies consistent with past exposure.
Read 19 tweets
Jul 1
While the prurient Clintonesque interest in this story will probably have most BBQ attendees this weekend avoiding the hot dogs, this is simply another example of Johnson’s normalization of corruption with the aid of client journalism.
He tried to give a 100K job to an ‘aid’ which would have worked if Williamson (allegedly) hadn’t walked in on them while the the Foreign Secretary should have been at his desk working on (er) foreign relations. So on top of that it reveals someone who really wasn’t doing his job
How many other people in this country would have got away with just that?

But then of course, in order to spare (now) wife’s blushes. He calls up Murdoch’s number 2 to get the story pulled, and gives Williamson an underserved knighthood effectively to keep his mouth shut.
Read 4 tweets
Jun 17
“The exact FCS sequence present in SARS-CoV-2 has recently been introduced into the spike protein of SARS-CoV-1 in the laboratory, in an elegant series of experiments (12, 30), with predictable consequences in terms of enhanced viral transmissibility and pathogenicity”

Quote
Ref 12 analyzes a natural clutter deletion of the FCS in SARS CoV-2 as a Loss of Function mutation in pathogenesis and transmission experiments

No insertion in any virus and certainly not SARS1

nature.com/articles/s4156…
Shows the SARS2 FCS has an intermediate phenotype for entry route and IFITM2 sensitivity in SARS1 spike ONLY in a lentiviral pseudotype. No insertion in a real virus, no GOF, and no analysis of transmission or pathogenesis

journals.asm.org/doi/full/10.11…
Read 5 tweets
Jun 9
nothing new then because the Chinese haven't shared anything more, be it about markets, labs, or animal farms

cdn.who.int/media/docs/def…
probably should have put #SAGO in that
The report makes an entirely reasonable set of recommendations and proposals for further investigations, but without cooperation from Chinese authorities it is kind of stuck in the mud
Read 11 tweets

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