Data and Analysis Thread, started Oct 29

[PatriciaHolm]

With a link to the previous header for all the great links to data -

www.mumsnet.com/Talk/coronavirus/4057030-Pure-data-thread-1-Daily-numbers-graphs-focused-analyses?

And with a polite plea to keep the focus on data and analysis if you please.

thanks all

Oh thank God anyfucker is here. All's right with world with the world.

Welcome home @AnyFucker .

If we can all pretend my embarrassing lookup-while-watching-film didn't happen please.
Slovakia population 5,450,421; 9472 cases in week 42 (0.174%); positivity 13.58%.
Half the population 25,850 cases or 1%, so say 2% actually currently infected. 20% false negative rate usually, higher with this type of test, so say 2.5% positive and 71k cases.
The % of known cases multiplied by the positivity number is roughly the actual % of cases at a little over 2.3%. I doubt that holds true at crazily high positivity. It's probably a mathematical coincidence anyway.

We haven’t had an update on the sewage testing have we? I also thought it would work well in conjunction with the mass testing to identify people who need to self isolate.

No @bigchocfrenzy ? Bah.

Only a disappointingly brief comment that they're expanding it, and it's in 90 sewage works, here: www.gov.uk/government/news/sewage-signals-early-warning-of-coronavirus-outbreaks. Unclear what proportion of the country this covers as there are more central preliminary processing plants, but some are tiny and presumably they've gone for the main urban ones. I don't recall the maps to guess at optimistic / pessimistic coverage levels, we'd probably have to check each sewerage company independently to judge; depending on how the network works it could be covering almost any conceivable percentage of the country.

Oh, and the report said that sewage found the Plymouth cluster. Plus a lot of gubbins about how they've been learning how to interpret results. So it may or may not be fully ready to be useful, but it will be useful when it comes.

@AnyFucker - no, sorry.

I've been looking at RP131's chart of cases by specimen date and it does look to me as though things are levelling off a bit. I'd even say it seems more like a trend than a blip but happy to be Corte ted! There is a part of me that wishes they'd held their nerve with the Tier approach for another week...

I understand why they've pulled the lockdown trigger, no one wants to be responsible for the collapse of the health service after all but given that they only finished arguing with Andy Burnham about financial support for going up a Tier a few days ago it does seem a bit like they panicked.

I don't know how it works for covid sewage testing, but have some experience of a not entirely dissimilar area, so what follows is a mix of some expert knowledge, but vast extrapolation to a different situation (hope that's a clear enough back story for a data thread!).

Sewage is never going to be consistent, the sewers carry rain water and all sorts of other things, as well as what is flushed down the toilet. I don't know what units are used for covid testing, but if you get a result of 5 from one sample and 10 from another, they have to be put into context.

You need information about how much rainfall there's been and whether there's been any outfall pipe overflows, which will change all the ratios again and (I believe) the extent of these aren't fully quantified by water companies. Other tests might also help identify how sewagey your sewage sample is, but it's never going to be an exact science.

As a very simple example, if there has been heavy rainfall on the 5 day and none on the 10 day, it implies the level of sewage in the sample has halved, instead of the amount of covid positive people doubling.

With the right analysis, this kind of data can provide interesting info about rising/falling trends, but I doubt it could ever be accurate enough to extrapolate to a number per 100,000 in the population. There could easily be a way of doing this that I know nothing about, so this is speculation, but I suspect the reason the information is not being widely released is because it is so complicated to interpret.

That's really interesting, thanks, but apparently is has provided very accurate results both on the continent (can't remember where now?) and for Plymouth, so they must have developed the methods somehow....

@GetAMoveOnTroodon
agree (also in the NW).
The NW and NE charts seem to be actually going down now slightly if anything (if you look at the 7 day rolling average). My worry is that numbers will shoot back up again next week after half term. Even if actual numbers with the virus are unchanged more people will seek tests - parents of children during half term might not have bothered if they were not planning on taking the kids out anyway (and let's face it, the weather has been rubbish) . Parents of kids who think they might have the virus are far more likely to seek tests if they actually have to go out and about, eg to school. I reckon.

Anyway positive results are always highest for specimens on monday. Will be watching this monday's like a hawk (last monday 26th was slightly below monday 19th which is the highest positive specimen tests ever in the NW. Nationally 26th was higher)

Hello from New Zealand. Sorry things are so shit for you there right now. I have a lot of friends and family left in the UK, and it's awful seeing them so fed up while we continue with a relatively normal life.

Anyway, I thought I'd update you on that weird anomaly we had here a few weeks ago, when a returnee from India tested positive for Covid 18 days after arriving back in the country. This means he had had 2 negative tests on day 3 and day 12 in managed isolation and was released with managed isolation on day 14 as normal. He then developed symptoms on day 18 and tested positive. There was speculation that it was a very long incubation period. It has now been identified that he most probably caught it whilst in managed isolation, in the hotel, due to a shared rubbish bin with another returnee who did test positive. So, good news on the incubation front, but bad news on the ease of catching it from fomites front.

www.rnz.co.nz/news/national/427446/rubbish-bin-the-likely-source-of-covid-infection#:~:text=The%20Ministry%20of%20Health%20has,infected%20by%20a%20lift%20button.&text=The%20case%20centres%20on%20two,an%20isolation%20facility%20in%20Christchurch.

That's worrying biffle, though I imagine a heavy load of virus from a shared bin?

Those rapid tests - not what Boris thought they were.

Also linked within near the end is the article that detailed that councils were offered to test 10% of their population each week, but most have declined for outlined reasons.

https://www.theguardian.com/world/2020/nov/02/doubts-over-rapid-turnaround-covid-tests-pledged-by-johnson?CMP=ShareiOSAppp_Other

Sharing a bin, I assume inside and therefore in a communal area seems to be a very bad idea if you are meant to be self isolating. Especially if there are symptoms and therefore rubbish such as used tissues.

That's not good @Bifflepants, I've merrily quoted the research that most fomite risk is basically theoretical and will have to rethink. I have a question; if they were sharing a bin, then they were also in the same physical space at different times. Yes, perhaps it was from touching the bin lid (pretty gross not to clean hands after that at the best of times), but could it not also also be a fog of viral particles hanging in the air in that corridor? I don't understand how they ruled that out?

Very good point @MRex .

@MRex

That's not good *@Bifflepants*, I've merrily quoted the research that most fomite risk is basically theoretical and will have to rethink. I have a question; if they were sharing a bin, then they were also in the same physical space at different times. Yes, perhaps it was from touching the bin lid (pretty gross not to clean hands after that at the best of times), but could it not also also be a fog of viral particles hanging in the air in that corridor? I don't understand how they ruled that out?

Yes, aerosol transmission was exactly my thought too! Besides... who touches a bin, unless they are emptying it? Doesn't one just chuck the rubbish in from above?

Not sure if this has been posted as a link before Cambridge MRC Biostatistics Unit modelling of Covid deaths using nowcasting and forecasting model.

www.mrc-bsu.cam.ac.uk/tackling-covid-19/nowcasting-and-forecasting-of-covid-19/

The NZ article also mentions a lift button, and I recall multiple comments when China blamed an outbreak on a lift button that it was more likely air particles.
This was the Chinese case:
www.independent.co.uk/news/world/asia/coronavirus-super-spreader-woman-lift-infections-china-heilongjiang-a9615886.html.
Here's some data to ponder.
Fomite low risk article says fomites die within an hour on surfaces: www.ncbi.nlm.nih.gov/pmc/articles/PMC7333993/.
UK gov paper says aerosols die off after a little over an hour, especially in poorly ventilated environments:
www.gov.uk/government/publications/transmission-of-sars-cov-2-and-mitigating-measures-update-4-june-2020.
So, equally likely to be either unless they have evidence of ventilation or actual droplets? It is good to reduce touch points and increase cleaning, but ventilation matters as much or more and should be addressed too.

who touches a bin, unless they are emptying it? Doesn't one just chuck the rubbish in from above?

depends on the type of bin.
cheap swing lid bins require touching it somewhat.
or those bucket type bins with a tight lid.

Ah ha - There you are!

Not caught up with the previous 9 pages.... so I don't know whether there is any opinion on whether a full lockdown was justified in low transmission areas. I am on the fence. However, interesting stats for my local town Guildford, including university.

Surrey University, 17,000 students (smallish), but only 95 positive cases, and that's total including staff, who must be an extra 1,000 or so. Guildford already trending down 5% from last week. DD's secondary school only one case early in Sept, and very few local schools have had cases, certainly not mass outbreaks.

So what does this illustrate? Not sure, other than a very pronounced North/South divide.

@Sunshinegirl82

I've been looking at RP131's chart of cases by specimen date and it does look to me as though things are levelling off a bit. I'd even say it seems more like a trend than a blip but happy to be Corte ted! There is a part of me that wishes they'd held their nerve with the Tier approach for another week...

I understand why they've pulled the lockdown trigger, no one wants to be responsible for the collapse of the health service after all but given that they only finished arguing with Andy Burnham about financial support for going up a Tier a few days ago it does seem a bit like they panicked.

Sunshine I always appreciate this chart. The red in the background was Vallance Whitty projection?

Is there any thinking on why deaths have surpassed their initial 200 by Nov but cases see to be far below (if I’m reading it correctly)

I think when community spread is as high as at the moment, national measures make sense. even if some areas seem to be affected less.

When Greater Manchester was put in restrictions in July, infection rates were around 35/100k.
Looking at the interactive rates map, even the "green" areas have higher rates than that now.
I think a nationwide lockdown is necessary to stop all the edge effects, as we are a densely populated nation with boundaries across streets and people living and working across boundaries.

I'm comfortable that there are enough cases in every borough for a limited period lockdown to be of benefit. There were a lot of rumblings in the NW about disinclination to follow rules, perhaps they might be more inclined if they see everyone else in the country has to do the same.
What really needs to happen though is stamping down on illegal parties, the number and huge size of these events is startling. www.theguardian.com/world/2020/nov/01/police-in-england-fear-flouting-of-lockdown-rules-after-breaking-up-weekend-raves:
Just this weekend: 1000 at one rave in Tottenham, 500 at another in Bristol, 300 in Wigan, 200 at a bloody Christening (just redo it next year FFS, it's hardly something that can only be done once). Then there are loads more smaller events. Are police actually fining every attendee? They should be.