THREAD on latest Covid situation in the UK:

TLDR things are looking pretty good right now. Caveat is variants (which is a whole other thread). 1/16
Overall UK cases are hoevering at just over 2K a day and back to levels back at the end of last summer. We can see drop over Easter hols (partly due to less testing) - but clear that opening outdoor spaces & shops has not caused an uptick (good!!). 2/16
Looking at types of tests done, clear upticks in twice weekly rapid LFDs when schools are open.

The drop off in LFDs over last few weeks also obv. School kids doing them less? other people? no idea. But clearly govt aim for loads of people to do them not happening. 3/16
Worryingly, the proportion of positive cases that are rapid tests *unconfirmed* by PCR tests has gone up (70% of LFD +ves!) - even though confirmatory PCR is available. Why? Who? Means it's hard to know how to interpret case numbers. 4/16
Still, looking at positivity rates for each nation (PCR tests only), clear that positivity is reducing and back at levels last seen summer 2020. ONS infection survey has same picture.

This is a good thing. 5/16
Regionally in England, Yorks & Humber still has highest rates (ONS agrees). Slight increase in NW. Everywhere else flat or declining. ONS says similar but says London, Yorks, East of England might not be declining. 6/16
Hospitalisations and deaths are both back at levels last seen in the summer. This is a combination of low case rates after months of lockdown *and* highly effective vaccines in over 90% of our most vulnerable people. Excellent. 7/16
We're steady at around 3m jabs a week for vax and still mainly on second doses. Expect this to continue for a few more weeks but we are on track to offer 1st jab to all adults by end July and 2 jabs to all by end Sept. 8/16
Currently we're doing first jabs in the 40s - 75% of 45-49 yr olds already have one. For second jabs we're on the 65-74 yr olds and hopefully finding the last few % of older groups. All good. 9/16
That said, ONS released a comprehensive breakdown by different demographics. Similar to what we've seen from before, lower take up in black & minority ethnic populations, more deprived communities. There seem to be some language barriers too. 10/16
Let's have a closer look at schools... From public health england data, although 10-19 year olds have highest case rates, we have not (yet?) seen the increase in cases we saw in March.

ONS says cases in school age kids falling. 11/16
PHE also show a small increase in school outbreaks but levels much lower than in March and massively lower than last winter.

This is all good and shows that low levels of Covid in communities + mitigations such as masks can and do make schools safer. 12/16
Finally the international picture... Cases globally remain very high. The last week saw the most cases ever recorded. 13/16
Although US is doing ok (although they still have rates 2x ours), Europe is high (even if coming down) & S. America & Asia (driven by India & neighbours) are experiencing terrible Covid surges.

They also have much lower vax rates. Helping vaccinate the globe is crucial! 14/16
(NB I've not put on same plot cos denominators not really comparable - Asia looks v low cos such a large pop inc China which is basically zero Covid, S America also has very large and very geographically spread pop). Both also have worse testing. 15/16
Anyway, to sum up everything going in right direction.

I wish I knew who was doing LFDs and why (eg are symptomatic using them instead of PCR cos quicker?)

The fly in the ointment is variants - but that's the next thread...

Thx as ever to Bob Hawkins for his help. 16/16

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More from @chrischirp

7 May
THREAD on new Variant of Concern (VOC), B.1.617.2:

PHE released its report on B.1.617.2. It has loads of info - some quite disturbing.

I'll try to go through the key bits in this thread.

Full doc is here: assets.publishing.service.gov.uk/government/upl…

all graphs use their data. 17 tweets.
It's become a VOC because it's been spreading so fast - and in the community.

PHE are pretty sure (MODERATE) it's *at least* as transmissible as our dominant "Kent" variant (B117) (RED rating). They are worried (AMBER) it might have some immune escape but don't know yet (LOW)
First, note that as overall cases have come down, we're sequencing *more* community cases - since early March about 50% of all postive PCR cases. This means estimates of spread are pretty good. And less bias from traveller data (all traveller +ves sequenced).
Read 18 tweets
5 May
The Maldives have similar vax rates to us & the Seychelles much higher (full) vaccination rates

Below is fully vaccinated & then at least one dose of vaccine.
Both Maldives & Seychelles are using a mix of the Chinese vaccine (Sinopharm) and Astrozeneca.
Israel used Pfizer.
Both Seychelles and Maldives are currently experiencing huge Covid surges.

The Seychelles has just locked down for two weeks. bloomberg.com/news/articles/…
I don't know why the Seychelles experience is so different from Israel.

One difference is that Israel has had longer with a high percentage of fully vaxxed people. It also used a different vaccine.
Read 4 tweets
4 May
THREAD on B1617 from COG data:

Yesterday I did some tweets about the growth of B1617 ("India") and its subtypes in the community using data from the Sanger Inst (England only).


Here is the recent data from England from COG (genetics consortium for covid)
2.This includes data from travellers & surge testing

BUT overall picture is the same as for community cases from Sanger yesterday.

B1617 growing very fast & has overtaken all other variants of concern / under investigation (except B117 ("Kent") which is still >90% of cases). Image
3.Look at the number each week, you can see that the other main variants are hardly growing. B117 cases ("Kent") are also going down (which is why our overall case numbers are falling).

But this variant, B1617 ("India"), is still shooting up. Image
Read 7 tweets
4 May
THREAD:
New paper led by @SarahESeaton from the @DEPICT_Study team - we analysed over 9,000 transports of critically sick children from local hospitals to paediatric intensive care units...

DEPICT, led by @pic_pram , has been such a great study to work on. 1/6
There are two main ways you can do this: "scoop and run" where you get the child to PICU as fast as possible or "stabilise first" where you spend some time (often hours) at the local hospital treating the child there before transport. 2/6
Of course it's not quite that simple - for very sick children you just *have* to stabilise at the local hospital before transport, so patients with longer stabilisation times tend to be sicker.

Once you account for that there is no significant difference in mortality 3/6
Read 6 tweets
3 May
THREAD:
Update on B.1.617 ("India") variant in England using latest data from the Sanger institute.

This data *excludes* sequenced cases from travellers & surge testing so "should be an approximately random sample of positive tests in the community"

TLDR: warning signs! 1/10
Data is available up to week ending 17th April.

Firstly raw counts (excluding B.1.1.7 ("Kent") which is dominant) shows rapid growth of B.1.617 ("India") over last 4 weeks.

S Africa (B.1.351) and B.1.525 variants are not growing in absolute numbers. 2/10
Looking at each variant as a proportion of all sequenced cases the rapid rise of B.1.617 ("India") is crystal clear. Remember this data *excludes* traveller and surge test data.

In week to 17 April it was almost 4% of all sequenced cases! 3/10
Read 11 tweets
30 Apr
FRIDAY GOOD NEWS THREAD:
how about some positivity?

Here's a brief overview of state of Covid in UK right now.

TLDR: pretty good, couple of things to keep an eye on. 1/13
Case rates are below 50/100,000 people/week in all nations (orange), dropping from prev week (grey) and approaching levels last seen Sept 1 last year (green). 2/13
England is the flattest in terms of case rates and this is reflected regionally (orange and grey dots close together). Yorks & Humber still highest region, confirmed by the ONS infection survey too. 3/13
Read 13 tweets

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