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
Where is it spreading? Sanger lets you download data by local authority - I aggregated into region and combined together B.1.617 & its sub-lineages (B.1.617.1, B.1.617.2 and B.1.617.3).

It's mainly in the South & East of England. In London it was 11% of cases w/e 17 April! 4/10
Looking just at London, you can see how the dominance of B.1.1.7 ("Kent") has reduced over last few weeks. 5/10
YES, overall London numbers have dropped A LOT since Feb & there is no indication (yet) that they are rising.

BUT we've seen rising variants masked by overall case drop / plateau before all over the world (esp spread of B.1.1.7 ("Kent")) ...
... and that this has caused complacency as everything looks fine, until, one day, it's not as new variants gain dominance.

Now - best case is that we will vaccinate people fast enough & vax effective enough to prevent B.1.617 gaining dominance in London (or elsewhere) 7/10
a worse case is that B.1.617 dominates in London and then elsewhere like B.1.1.7 did before it and causes a new, limited, surge in cases until vaccination (and new local restrictions?!) can suppress 8/10
worst case is that vaccines less effective against B.1.617 and we need booster vaccines. I stress that this is *unlikely* - we need more evidence urgently but so far, looks as if our vaccines should work against it.

BUT - should we wait around to take the risk? 9/10
I think this data is saying "Take B.1.617 very seriously and surge test, contact trace, support isolation of cases & contacts, ring vaccinate - NOW".

Then we can head off any potential trouble and have the summer we all want. 10/10
PS sanger website here:

PPS we should also keep doing all we can to help India and its neighbours cope with their ongoing horrendous surges. The situation out there is not getting any better even if it's dropped off the headlines. ditto S America

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More from @chrischirp

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
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
30 Apr
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
29 Apr
THREAD update on variants:

Today PHE released more variant data (& split the B1617 ("Indian") variant into 3 subtypes).

Big increase with 400 overall cases in UK - closing in on B1351 (S.African variant).

Guardian article:…

The COVID-19 Genomics UK Consortium (COG) release specimen data by date of test taken - so we can track numbers over time.

NOTE: COG specimen data contain some duplicates (ie. more than 1 test per person) but nums consistent w PHE & trends still evident. England data only below
655 spotted tests of S.African & 497 of Indian variant(s) - but clear v rapid increase in Indian variant in 3 wks to 17 Apr

Most are travellers (PHE), but each carries a risk of onward transmission if traveller infects houshold or doesn't isolate…
Read 9 tweets
27 Apr
Short THREAD on Covid-19 Variants in ENGLAND:

The Sanger Institute has just released webpages that let you explore genomes that they sequences every week...

I had a look - two variants are currently growing "S Africa" and "India" but v small numbers. 1/7
This chart show the numbers of potentially worrying variants sequenced each week.

The recent rapid growth of the India variant (B1617) & the highish, steadier, numbers of S African variant (B1351) are clear (not great).

Brazil variant (P1) almost negligible (good!). 2/7
These are small numbers.

But S African & Indian variants are growing in the context of overall numbers going down. So the *proportion* of sequenced cases that are these two variants is going *up* - and for the Indian variant - going up A LOT.

Should we be worried? 3/7
Read 9 tweets
26 Apr
In Dec, SAGE behavioural subgroup warned that people might reduce adherence to measures once vaccination programme under way and recommended a govt communication strategy to pre-empt this...… 1/3
However, this has not happened. Govt messaging around a cautious opening has been counterbalanced by the focus on the dates of the roadmap, lack of emphasis on protective behaviours & (partial!) vax numbers.

And sure enough, adherence is dropping - particularly in over 50s. 2/3
Yes, numbers are ok here right now - but soon we open up a LOT more indoor mixing.
Chile shows how opening too fast, even with high vax, can cause bad surges requiring new lockdown.

We need better communication - esp after THAT daily express letter.… 3/3
Read 4 tweets

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