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Prof. Christina Pagel Profile picture
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10 May, 7 tweets, 3 min read
THREAD on latest data on B.1.617.2 (an "India" Variant) in England.

The Sanger Institute released its latest sequencing data for variants in England today
covid19.sanger.ac.uk/about

TLDR: it's not looking good at all. 1/6
Sanger removes cases from travellers to England & from surge testing to get a picture of what is happening in the community.

In England, within TWO weeks to 1 May, B.1.617.2 (the new variant of concern) went from 1% to 11% of cases. Other variants <1%.

A massive increase. 2/6
This is concentrated in a few regions: London, the NW (quickest rise), East of England and then E Midlands & SE.

PHE also highlighted London and NW as particularly concerning in its Friday report
assets.publishing.service.gov.uk/government/upl… 3/6
In the NW cases are concentrated in a few towns with v high proportion B.1.617 w/e 1 May: highest are Blackburn with Darwen (75%), Bedford (73%), Bolton (69%).

These are obv low numbers of cases. But what is happening to overall covid cases here? 4/6
Downloading data from coronavirus.data.gov.uk/details/downlo… for each local authority shows that, compared to week before, cases in week to 5th May have increased by 43% (Blackburn), 58% (Bedford) and 91% (Bolton).

It's not more tests - tests look flat & all 3 have growing PCR positivity. 5/6
Under *current* restrictions, within a context of v infectious B117 ("Kent" variant) and *high population immunity* B.1.617.2 seems to be spreading quickly.

Numbers still low(ish) but for how much longer? What will happen after 17th May when so much more opens? 6/6
PS this is not about returning to lockdown, it's about taking this seriously & strengthening public health measure such as contact tracing, support for isolation, testing, masks in indoor spaces (inc schools). it's about getting on top of situation *now*

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Prof. Christina Pagel Profile picture
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
Prof. Christina Pagel Profile picture
7 May
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
Read 16 tweets
Prof. Christina Pagel Profile picture
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
Prof. Christina Pagel Profile picture
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
Prof. Christina Pagel Profile picture
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
Prof. Christina Pagel Profile picture
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

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