Data and analysis thread, started 12 November

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Data and Analysis Thread, started Oct 29 www.mumsnet.com/Talk/coronavirus/4064113-Data-and-Analysis-Thread-started-Oct-29

Regular lurker but I frequent poster, didn't want to lose the threads.

I don't think I understand one research point, why do they say it's cross immunity? It was done in June, so there's a chance that those people were asymptomatic, had a mild infection, or had an atypical set of symptoms. I can't see anything that explains the assumption that it must be cross immunity rather than a much earlier infection that was entirely fought off by T-cells, or where the antibodies degraded but not the T-cells?

That’s a good question and they only say ‘probably’. It might just be that they can’t prove it one way or the other. There’s this PDF www.medrxiv.org/content/10.1101/2020.11.02.20222778v1 linked that I haven’t had time to read yet but I would think the most important finding is that those with higher levels of T-cells didn’t catch Covid in the four months following the study.

I'd clicked through to that and tried reading it, but it just looks like assumptions layered onto assumptions to me, e.g.
"To divide individuals based on T-SPOT results, we identified a subgroup of cases with proven SARS-CoV-2 infection before study recruitment (PCR positive, Stream C, n=154), and a subgroup at low risk of prior SARS-CoV-2 infection before recruitment (n=1,126; see Supp. Methods Fig. S4, and results)."
And
"The absence of epidemiological risk factors for SARS-CoV-2 in this population argues against, but does not completely exclude, an alternative scenario involving T cell priming by minimally symptomatic SARS-CoV-2 infection without antibody generation/ persistence."
Then the antinucleoprotein immunity looks to mostly only apply from known previous infection. (Which also makes me wonder, which vaccine targets nucleus protein rather than the spike, surely more effective based on this? T-spot structural & envelope on the other hand more likely to be useless.)

It also suggests highest T-cells in under-20s who aren't known to have been infected and over-65s who are known to have been infected. Which perhaps supports cross- immunity at younger ages, plus harsher infection.are older ages.

Sadly my lack of knowledge means I'm just not grasping the detail on this one.

Aaargh, I'm falling down a rabbit-hole of too much reading, by this looks really interesting on what the vaccines target and why: www.nature.com/articles/s41577-020-00434-6.

I’d agree with the hypothesis that if we are to start seeing a plateau and fall the next few days numbers will start to give a real sense of possible direction.

I don’t however think we can read too much into Monday 16th spec date yet if we look at the last few Mondays and how the case total for each has built up. So showing the figures each day oldest first, Monday 26 0ct, 2nd November, 9th and finally 16th for which only two reporting days so far. The Monday with the highest total each day is in bold

D1. 565 / 1305 / 448 / 2162

D2. 14947 / 18826 / 12957 / 15412

D3. 21068 / 25829 / 24612

D4. 22301 / 27150 / 26233

D5. 22571 / 27400 / 27857

D6. 22640 / 27463 / 27950

D7. 22661 / 27499 / 27983

D8. 22676 / 27525 / 28013

D9. 22706 / 27590 / 28018

D9 is the most recent for Monday 9th spec date, however the other two Mondays now stand at 22758 and 27878 respectively.

The above just relates to cases in England

This might be an interesting watch:
“'Lockdown 1.0 - Following The Science?' is on BBC2 at 21:00 GMT on Thursday 19 November and on the BBC iPlayer afterwards.”

Thanks, boys3, it is very impressive that you have got history of how the numbers for different Mondays built up over time.

My back of the envelope calculation has been much simpler. I think over past few days the reporting lag has been shrinking so about 60% of cases seems to now get reported by the second day. I have therefore assumed 15,412 cases reported for Dec 16th as of yesterday represents about 60% of the total cases. As a result, my crude estimate for Monday was around 26,000 positives.

@wintertravel1980 I think that is why today’s number for Monday will be key. A further 5-7k cases and it would seem likely it will end up 10% or more lower when the reporting fully plays out.

A bigger increase and it will likely be in a similar place still to the last two Mondays - bearing out the argument that there was that last minute pre lockdown I must see everyone / go everywhere / do everything . Certainly that seemed the case where I am.

Let’s hope for the former in terms of numbers which might set us up for a more positive —granted not the best word— week numbers wise.

Surveillance data out. This stands out rather for me:

NeurotrashWarrior Interesting. What constitutes an outbreak though? Is one confirmed case, the same as 100 confirmed cases, as it would seem the university blocks are far too small for the numbers that we know have been confirmed as covid positive.

I'm not sure. But one onward transmission event has the potential to spread to other families.

We sadly have a teacher off with it as her partner caught it in another school. (That school has fully closed temporarily.)

Does anyone know what it takes to close a school? We have 4/9 bubbles self isolating atm after confirmed cases

That's a big and sudden jump @Neuro. Suggests the theories we had about a recent hike being down to everyone going out in advance of the looming lockdown may not be all of the story, and a hike in school cases might be more to blame. Why so sudden though so you think? Post half term?

Could you post the link to the surveillance report? I can't seem to find out via usual googling.

@NeurotrashWarrior
Hope you don't mind me re-posting a link to your image on another thread. Credited to you!

We've been told by PHE that it would take 15+ cases in a year group to be considered an outbreak. Had no cases before half term, have had six since!

20291 cases added in England today, 6954 with a Monday 16th specimen date, so Monday overall this week looks likely come out below the circa 28000 cases from the last two Mondays in England.

Early days for Tuesday but that is also lower than the figure at this time for Tuesday last week

@Cantaloupeisland

We've been told by PHE that it would take 15+ cases in a year group to be considered an outbreak. Had no cases before half term, have had six since!

15 in a year group? In many village primary schools that could be over half the year group to have to get it!

We've been told by PHE that it would take 15+ cases in a year group to be considered an outbreak.

No, of course, it is not 15+ cases. The official definition of an outbreak is “two or more more laboratory confirmed cases linked to a particular setting” (page 19 of the weekly surveillance report).

boys3, you are ahead of me! Yes, the numbers for Monday look pretty good. North West has gone down a lot.

Sorry, how rude of me!

www.gov.uk/government/statistics/national-flu-and-covid-19-surveillance-reports

assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/936672/Weekly_COVID-19_and_Influenza_Surveillance_Graphs_w47.pdf

Here are the graphs.

There's so many factors I imagine.

In my area I've noticed the darker purple areas slowly spread outward from young professionals and student areas to the outer areas of the city, where it's mostly families, local communities etc. So more contact from community to school and back and forth.

Observational comments: Dh said the city shopping centres were heaving just before lockdown. Certainly bonfire night was v noisy.

My nephew has it after catching from his teacher step father who apparently caught it from school. And has now possibly passed on to his dad and step mum. (Both also teachers) (I feel like I suddenly know of a lot of teachers and some children ill with this right now.)

22915
501

Cases down 2.4% in the last 7 days

I've popped this on another thread, but am wondering:

Week 46 is 9th November I think - so this is a full week after half term. Does this mean infections came in from half term week off? It doesn't really matter in terms of spread, but is interesting in terms of where it originated.