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

@upthewolves

Article on testing here:
www.nature.com/articles/s41564-020-00818-3.epdf?sharing_token=C6YEQDu8Uwbqs7IlQkG7KdRgN0jAjWel9jnR3ZoTv0O7pUvtK2qsU1-hV2BOfaTXGH9vzaXX2n-I5jmBIXEa9e9UYSe5sWelyLBJNJGJkrn4lHD5izupMI1i5QzxhyGqc2Wbg438Edd-HNWSSUIe1ZlimNq75PlYhERYEVQYtHY%3D

Would suggest Alan McNally and Rupert Beale on twitter as they have answered similar questions in their replies:

mobile.twitter.com/alanmcn1/with_replies

As for respiratory admissions, see:
mobile.twitter.com/BristOliver/status/1322255390793498629

mobile.twitter.com/bealelab/with_replies

Hi, apologies as I know it will already have been posted on here but I can’t find it. I’m after the latest ons data on where outbreaks are occurring? I’m sure I’ve seen a pie chart showing this but cannot find it now.

Many thanks!

@MarcelineMissouri - in the surveillance report: www.gov.uk/government/news/weekly-national-flu-and-covid-19-surveillance-reports-published

Figures today
18950 cases
136 deaths

Very encouragingly, number of people in hospital is down for the first time in not sure how long
Yesterday 9077
Day before 9313

also daily admissions is showing signs of stabilising at the 1100-1300 mark.

Cases in most regions currently coming down a bit if you look at the 7 day rolling average - but not in West mids, south east or south west.

Cases in most regions currently coming down a bit if you look at the 7 day rolling average - but not in West mids, south east or south west

Suggesting that tier 2 and tier 3 is effective?

I wonder if half term has had any effect on the slight decline?

As much as I think schools should remain open the government really need to get some systems in place to reduce transmissions (although I guess it might be easier said than done)

Easier said than done without any willpower or funding ...

I know I should know this but those are UK figures, right?

So the downward figure might include NI and Wales actually having little circuit breakers? Or possibly too early to include that?

@Pertella

I wonder if half term has had any effect on the slight decline?

As much as I think schools should remain open the government really need to get some systems in place to reduce transmissions (although I guess it might be easier said than done)

i think too early to tell as it's only just finished. I am worried about cases going up again after HT though.

Agree I think closing secondaries at least temporarily would surely help.

Harder to do for Primaries as difficult for parents to keep working and also transmission seems to be lower.

@Piggywaspushed

I know I should know this but those are UK figures, right?

So the downward figure might include NI and Wales actually having little circuit breakers? Or possibly too early to include that?

Yes, but England's number is also the lowest announced number it's been since 18th Oct. Rate of growth by specimen date has definitely slowed.

NI's is the lowest since 4th Oct, and cases by specimen date there are definitely on the decline.

Wales's is not low, but yesterdays was so it's not possible to see any real impact there at the moment either by date reported or specimen date.

Thanks patricia.

I have been watching Elmbridge as a South East “case” (I don’t live there, just noticed the increasing numbers a while back and decided to watch it).

The number of cases per 100,000 for the 7 days ending
27 Sept 26 cases
4 Oct. 108 cases
11 Oct. 132 cases
18 Oct. 153 cases. - tier 2 was introduced 18 Oct
Peak per 100,000 was for the 7 days ending 20 Oct - 159
They have gone down since (149, 146, 137, 132, 127, 126, 113) and the latest is 116 per 100000 for the 7 days ending 28 Oct.

This would appear that even the limited Tier 2 have some effect if introduced early enough.

However, I think that the point Whitt’s & Valence made at the press conference was that it is no good stabilising at the high level they are now (in the North), they need to come right down otherwise a reproduction number of even just over one means a lot of people being infected, then hospital and death.

One of the big benefits of doing the lockdown over halfterm would have been stopping travelling. I live in south Devon, near coast and we have been full of visitors over the last ten days. I'm not one to normally moan about people having holidays and bringing the virus here but we were rising anyway, the weather was horrible all week and I can't imagine many people thought it was a wonderful holiday as they wandered round looking for something to do out of the weather.

I'd be amazed if our figures don't increase due to how crowded everything has been, shops, restaurants, arcades,softplay etc. I know the businesses need the income but for infection control it didn't seem like a good idea.

I do wonder about the humidity. I've begun tracking it where I live as interested on how if affects local numbers.

@Hmmph

I have been watching Elmbridge as a South East “case” (I don’t live there, just noticed the increasing numbers a while back and decided to watch it).

The number of cases per 100,000 for the 7 days ending
27 Sept 26 cases
4 Oct. 108 cases
11 Oct. 132 cases
18 Oct. 153 cases. - tier 2 was introduced 18 Oct
Peak per 100,000 was for the 7 days ending 20 Oct - 159
They have gone down since (149, 146, 137, 132, 127, 126, 113) and the latest is 116 per 100000 for the 7 days ending 28 Oct.

This would appear that even the limited Tier 2 have some effect if introduced early enough.

However, I think that the point Whitt’s & Valence made at the press conference was that it is no good stabilising at the high level they are now (in the North), they need to come right down otherwise a reproduction number of even just over one means a lot of people being infected, then hospital and death.

If the tier 2 was introduced on 18th October, I don't think it really would have effect for a good few days, 5 at least, and probably more like 7, so it looks like they were going to go down anyway. There's got to be time for people to pick it up, go through incubation period and develop symptoms, decide they need a test and order a test and receive that test.

Maybe through self regulating as people saw the figures go up?

Today's figures look hopeful overall though.

Also Elmbridge was one of the most likely "wrong postcodes for uni students" so it may have been an artificial increase in any case.

There's definitely a lot more green "falling" arrows on littleowls covid messenger data table than there were previously!

Humidity's definitely helpful, isn't it, am sure have read somewhere advice to humidify rooms etc. I think because it means virus particles attach to the water droplets and fall to the floor rather than stay in the air? Not sure though.

1. Understanding cycle threshold (Ct)

in SARS-CoV-2 RT-PCR - both links government documents and relatively easy to understand.

<a class="break-all" href="https://www.google.com/url?sa=t&source=web&rct=j&url=www.gov.uk/government/publications/cycle-threshold-ct-in-sars-cov-2-rt-pcr&ved=2ahUKEwis0LOLt-TsAhUit3EKHWpIC6IQFjAAegQIARAB&usg=AOvVaw0xjMR6jRzOupe-VQ8C0du-" rel="nofollow" target="_blank">www.google.com/url?sa=t&source=web&rct=j&url=www.gov.uk/government/publications/cycle-threshold-ct-in-sars-cov-2-rt-pcr&ved=2ahUKEwis0LOLt-TsAhUit3EKHWpIC6IQFjAAegQIARAB&usg=AOvVaw0xjMR6jRzOupe-VQ8C0du-

<a class="break-all" href="https://www.google.com/url?sa=t&source=web&rct=j&url=assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/895843/S0519_Impact_of_false_positives_and_negatives.pdf&ved=2ahUKEwilm46ltuTsAhWXThUIHYBnA7EQFjAAegQIARAB&usg=AOvVaw09SwJFWA4XgwYBHC_2lA7i" rel="nofollow" target="_blank">www.google.com/url?sa=t&source=web&rct=j&url=assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/895843/S0519_Impact_of_false_positives_and_negatives.pdf&ved=2ahUKEwilm46ltuTsAhWXThUIHYBnA7EQFjAAegQIARAB&usg=AOvVaw09SwJFWA4XgwYBHC_2lA7i

Good visual way of seeing how false positives and negatives can be affected by likelihood of patients being positive and test sensitivity/specificity from BMJ.

<a class="break-all" href="https://www.google.com/url?sa=t&source=web&rct=j&url=www.bmj.com/content/369/bmj.m1808/infographic&ved=2ahUKEwi_qvK8t-TsAhWKRhUIHfmTBVgQFjAAegQIARAB&usg=AOvVaw1iSvLcGYjgfSXPKxgEhitl" rel="nofollow" target="_blank">www.google.com/url?sa=t&source=web&rct=j&url=www.bmj.com/content/369/bmj.m1808/infographic&ved=2ahUKEwi_qvK8t-TsAhWKRhUIHfmTBVgQFjAAegQIARAB&usg=AOvVaw1iSvLcGYjgfSXPKxgEhitl

Basically if a patient is symptomatic and cycle threshold low then more likely Covid, if asymptomatic and cycle threshold higher then less likely, grey area in between and more than one test might be required for these patients to rule out false results.

1. Weekly flu reports for the last year if you want to check numbers, hospital admissions someone linked to above I think.

www.gov.uk/government/statistics/weekly-national-flu-reports-2019-to-2020-season

1. Cancer referrals research from Cancer Research UK

www.google.com/amp/s/scienceblog.cancerresearchuk.org/2020/09/11/whats-happened-to-cancer-services-during-the-covid-19-pandemic/amp/

Definitely looks a positive direction for the NW from the top level numbers. But looking at the very detailed (and very large) file for cases by 5 yr age bands it seems to be largely driven, at the moment, by a big fall in the numbers of cases in the 15-19 age group. This is based on a superficial look, just filtering the region and cases since start October, as opposed to a proper analysis. However the same quick look for the SE suggested cases in that age group continuing to rise there.

Must look at Elmbridge to see if that level of detail gives any more weight to the home rather than uni postcode argument. Although I have limited belief that postcode mix ups have caused a truly material difference.

Hello, not sure if relevant but here in the north west we have had wild weather this last 6 days . My local testing centre had to close for a day due to the wind blowing the tents. Our positive rates are dropping like a stone. Not sure if its a coincidence or wether poorly people would choose not to get tested during bad weather

I wonder if that affected people choosing to have postal tests rather than drive-ins? I guess it depends if it was communicated clearly or not.

1. John Burn Murdoch hospital admissions graph again (see his Twitter for more details)

Processed tests over the last 7 days are down by 5%, positives up 3.7%.

Cautiously hoping we're levelling off a bit.