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.
4.Looking at absolute weekly sequenced numbers, the rapid increase of B.1.617.2 compared to other variants (including its sibling B.1.617.1) is obvious.

And clear why SAGE worried it could be ~50% more transmissible than B.1.1.7 (our "Kent" variant).
assets.publishing.service.gov.uk/government/upl…
5.This data might still over-represent B.1.617.2 & there are ways it is could increase rapidly without being more transmissible.
But I think the simplest explanation is that it is more transmissbile & we are right to be worried. Precautionary principle suggests action now. /END

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More from @chrischirp

18 May
1 THREAD on latest COG data on B1.617.2 (so called "India" variant) in England

COG sequences positive tests from the community (~50% of them), all travellers to UK & from surge testing. Data is updated almost every day.

What does it tell us about spread?
sars2.cvr.gla.ac.uk/cog-uk/#shiny-…
2 COG data is not entirely representative because it over-represents surge and traveller cases.

Sanger data removes traveller and surge cases to try to get a picture of community transmission, but Sanger only updates once a week.

What if we compare the two?
3 This compares the number of sequenced tests of B.1.617.2 that appear in COG (black) and Sanger (blue).

Over time there is much more overlap between the two showing that community cases are growing and that COG is becoming more representative of community cases (Sanger). Image
Read 11 tweets
17 May
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?
Read 13 tweets
16 May
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
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
Read 6 tweets
13 May
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
Read 5 tweets
12 May
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
Read 18 tweets
10 May
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
Read 7 tweets

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