1.THREAD on latest Sanger data on B.1.617.2 (new variant of concern).

Remember Sanger use all sequenced cases for England (about 50% all cases) and remove data from travellers and surge testing - so approx community cases.

covid19.sanger.ac.uk/about

TLDR: nothing encouraging.

2.Continued rapid increase of B.1.617.2 (a so-called "India" variant) to week ending 8 May. Other variants not doing much.

But B.1.617.2 now almost 30% of sequenced cases in England (!).

3.Regionally, it almost dominant now in North West and getting there (but more slowly) in London.

High proportions in SW and SE, but overall cases here v low. Need to keep an eye on the Midlands & East of England.

1. THREAD on vaccines, "Indian" variant, Bolton and the summer.

Bolton currently has 18 patients in hospital with Covid, 12 no jab, 5 one jab, 1 both jabs (who was frail).

What are the implications?
bbc.co.uk/news/uk-571341…

11 tweets.

2. Hancock apparently said the "vast majority" of unvaccinated patients were eligible. I don't know what "vast majority" of 12 is, but let's say it's 11.

About 95% of over 50s have had 1 dose and about 90% of over 70s have had 2 doses in England.

3. Eligible is over 40s and health care workers - so can't say too much *precise* about vax efficacy without knowing more (inc exposure).

We also don't know which variant but >70% of cases in Bolton from recent Sanger data were new variant (B.1.617.2).

so what can we say?

THREAD:
Spread of B.1.617.2 ("India") variant could have been prevented.

It's not "Captain Hindsight" @MattHancock to highlight our leaky border policy & red list delay in particular. thetimes.co.uk/article/indian…

Here are some early warnings from SAGE, @IndependentSage & me! 1/6

https://twitter.com/PippaCrerar/status/1393853362739859461

SAGE on *21 January* said red list countries would not prevent importation of new variants. If used, they'd need to be imposed quickly.

Most effective would be quarantine for all arrivals (as AUS & NZ).

Israel closed its borders while vaccinating.
assets.publishing.service.gov.uk/government/upl… 2/6

@IndependentSage called for comprehensive border measures on 24 January (independentsage.org/independent-sa…)

@GabrielScally of @IndependentSage wrote that comprehensive quarantine was needed to prevent importation of new variants on 28th January

theguardian.com/world/commenti… 3/6

SHORT THREAD:
I was on Sky News earlier where I explained why I thought test 4 (new variant test) for the next stage of the roadmap had not been met, because of B.1.617.2 (the so called "Indian" variant of concern). 1/5

I then also said what I, personally, thought that meant for next steps.

Added to these must be much more support for local teams to beat outbreaks *and* proper financial & practical support for those who test positive & contacts. Once in place, could enable safer opening. 2/5

@markaustintv pointed out that people would be shouting at the telly hearing me suggest delaying Monday's opening... this is what I said about that. 3/5

THREAD - my thoughts on variant situation:

I've been tweeting about it a lot but much has happened in last day.

@guardian today quoted me saying that my personal feeling was we should delay next stage of Roadmap.

theguardian.com/world/2021/may…

Let me explain why... 1/18

The govt set out 4 tests for proceeding each stage of the roadmap. Tests 1 & 2 relate to vaccination, test 3 is hospitals in no danger of being overwhelmed and test 4 is that there are no new variant concerns.

Test 1-3 have been (easily) met, but I don't think Test 4 has. 2/18

Last Friday, Public Health England designated B.1.617.2 (an "Indian" variant) as a variant of concern because of worries that it was more transmissible than B.1.1.7 ("Kent") and cos we didn't know much about its response to vaccines.

What has happened since? 3/18

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

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).

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

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.

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).

https://twitter.com/chrischirp/status/1389349904770813957?s=20

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).

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.

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

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

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

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:
theguardian.com/world/2021/apr…

PHE
gov.uk/government/pub…

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

herefordtimes.com/news/national/…

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

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...

assets.publishing.service.gov.uk/government/upl… 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.

theguardian.com/world/2021/apr… 3/3

SHORT THREAD on JAPAN / OLYMPICS:

Japan is going through a major new Covid wave and this potentially puts the Olympics later this summer at real risk... (and of course Japan's large population!) 1/4

The sequencing data for Japan is sparse, but it does seem as if B117 (the "Kent, UK" variant) has become dominant there over last couple of months and that this might be behind the recent increase. 2/4

reuters.com/business/healt…

The other thing is that Japan is being very slow to vaccinate compared to other high income regions - Just over 1% of its population has received one dose of Covid vaccine so far.

This leaves it more exposed to surges from B117 (vaccines work brilliantly against B117). 3/4

THREAD on VARIANTS, VACCINES & POTENTIAL FUTURES:

I’ve been looking at data on sequenced variants. I’ve also been thinking about our vax programme & India.

TLDR: the Indian variant needs to trigger surge testing in England. And India needs to be on red list. 1/23

Some dates: while over 60% of adults have had 1 dose of vax, we've got another ~15 weeks before *all* adults could have immunity from at least 1 dose.

And another 20+ weeks before all adults could be fully vaxxed. And we don't yet know what uptake will be in younger adults. 2/23

So what can variants do while we are vaxxing people?

We already know that B117 can infect some partially vaccinated people and (far far) fewer but still some fully vaccinated. edition.cnn.com/2021/04/14/hea… 3/23

The latest PHE variant of concern update is out...

TWO KEY things:

1) B1351 ("South African") variant continuing to spread (as we've seen in the headlines!)

2) 77 cases (!) of the new B1617 "double mutant" variant discovered in India .

B1617 is worrying because... 1/3

https://twitter.com/Dr_D_Robertson/status/1382717740012687367

It has some potentially worrying mutations NOT seen in SA, Kent or Brazil strains.
forbes.com/sites/williamh…

This variant *might* escape both T-cell and antibody action. India going through a big surge - mix of B117 & new B1617 (location dependent)
science.thewire.in/health/sars-co… 2/3

As I tweeted yesterday, India should be on the red list (as should many other countries that currently aren't btw) *and* Johnson should *not* go on a trip to Delhi this month! madness!

https://twitter.com/chrischirp/status/1382316137225027595?s=20

THREAD on VACCINATION & EQUITY in ENGLAND:

I know I've tweeted about this before, but now we can look at how gaps by deprivation and ethnicity change with age groups and what that might mean...

TLDR: widening gaps but access and communication will be key I suspect 1/5

By deprivation:
Vax coverage gaps *widen* markedly as we move to young ager groups. This is not just a time effect - coverage has flattened off for all these age groups.

Access (able to leave work to get vaccinated, travel, internet access) & communication likely issues 2/5

By ethnicity:
Much larger gaps for all age groups by ethnicity but less impact by age.

Different but overlapping reasons driving ethnicity gaps compared to deprivation gaps? 3/5

THREE TWEETS:

1. The situation in India is very bad and worsening.
theguardian.com/world/2021/apr……

It is frankly insane that Bangladesh and Pakistan are on the UK travel red list countries but India is not.

gov.uk/guidance/trans…

2. Globally we are back in a pandemic that is as bad as it has been and no sign of peaking yet.

Deaths are trailing cases by a few weeks as expected but they are also rising steeply - this isn't just more testing or ok because we have vaccines & better treatments.

3. Out of control covid anywhere is a danger everywhere.

We need to address vaccine inequality ASAP. This is urgent - morally for global fairness & self-interestedly to stop future UK waves.

We'll be covering this in Friday's @IndependentSage
briefing - join us!