Prof. Christina Pagel Profile picture
Nov 25, 2021 17 tweets 5 min read Read on X
THREAD on the new variant B.1.1.529 summarising what is known from the excellent South African Ministry of Health meeting earlier today

TLDR: So much uncertain but what *is* known is extremely worrying & (in my opinion) we should revise red list immediately.

This is why: 1/16
The South African Ministry of Health had a live streamed briefing today on the new variant detected there.



The variant was identified this week and has been found in three countries so far: Botswana, South Africa and Hong Kong (returning traveller). 2/16
In South Africa it has been detected in Guateng province - positivity rates in Tshwane (part of Guateng) have increased massively in the last 3 weeks from less than 1% to over 30%.

3/16 Image
Because of this increase, COVID sequencing has been concentrated on samples from Guateng.

Almost all recent samples from there (77) have been this new variant (blue dots) - taking over from a background of Delta (red) and C.1.2 (also a concerning variant, yellow). 4/16 Image
SA had a big Delta surge over June and July but recent rates were very very low. Most recent days have seen early surge, mainly driven by Guateng.

SA has high levels of prev infection from 3 very large waves but relatively low levels of vaccination (~24% fully vaxxed). 5/16 Image
The bias of sequences towards Guateng means that it looks as if B.1.1.529 is rapidly taking over from Delta (red) and C.1.2 (yellow) on chart of sequenced cases - but few samples.

BUT there is one stroke of luck - it also has "S-gene dropout" like Alpha did, which means... 6/16 Image
...that we can track it across all PCR positive cases that used a specific type of test (TaqPath). This means much better real time data.

BUT that's where the good news stops - because S-gene drop out data suggests it's rapidly increasing across S Africa. 7/16 Image
And in a regional breakdown, you see the same vertical spike in almost all regions. This + traveller from SA case in Hong Kong suggests B.1.1.529 already widespread in SA and that other regions might follow Guateng's rise soon. 8/16 Image
The sheer increase on these charts is very worrying and suggests that B.1.1.529 might have significant advantages over Delta and C.1.2. What exactly this advantage is and how it breaks down between immune escape and transmissibility is not yet known.

BUT 9/16
We do know that B.1.529 has many more mutations than other variants *and* has mutations seen in other variants that are associated with BOTH higher transmissibility AND immune escape.

It's the number and type of mutations that are worrying the virologists & immunologists 10/16 Image
The SA science establishment & Ministry of Health transparency are doing *a global service* - we *cannot* underestimate how important their work and transparency are this week.

They are urgently doing lab experiments to understand it more & continuing to track spread 11/16
A new UKHSA technical briefing on variants is due tomorrow - I am sure they will at least mention this variant. WHO are meeting about it today as well.

People working in this field in England at the highest levels are very concerned 12/16 ImageImage
Given the speed with which this variant has spread & mutations which *might* mean signifcant vaccine escape, in my opinion the UK should get ahead of this *right now*.

As far as we know, it's not here yet.

*Adding SA and close neighbours to the red list seems sensible* 13/16
Because of UK status as international travel hub, v few restrictions in UK and the worrying signs from SA, we must act now or risk it being too late.

Regardless of travel restrictions, supporting S African response as Barrett suggests is the right thing to do. 14/16 Image
If it's a false alarm, then we can step down response in a few weeks. But this is our window to act. As with Delta (and B.1.1.529 seems to spreading as or more quickly), waiting for certainty risks waiting too long.

15/16
Finally, this is just my opinion.

It's hopefully not here yet. We don't have definitive evidence on transmission advantage or immune escape but we have plenty of cause to suspect both.

Let's be super protective of our vaccine programme and take precautionary action. 16/16
NB they reported a big backlog yesterday so recent increase artificially big! I don't think it affects the other charts though which are directly from the ministry presentation

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More from @chrischirp

Aug 28
THREAD: I asked what the point of Public Inquiries is for @bmj_latest

We've spent hundreds of millions of £ on Inquiries over last decades, generating deep understanding of failures & 1000s of recommendations.

But v few recommendations get implemented!
What is going on?

1/12 Image
E.g. Covid-19 Inquiry has cost £94 million so far - and is projected to cost over £200m by its end (it still has years to go).

1st report published (out of at least 9) found major flaws and proposed 10 recommendations.

Chances are low that they will be implemented :-( 2/12


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Inst for Government looked at 68 Inquiries from 1990-2017.
The Inquiries cost over £630 million and made 2,625 recommendations.

Only 6/68 Inquiries have received full scrutiny by a parliamentary select committee on implementation of recommendations. 3/12 Image
Read 12 tweets
Aug 9
🧵War causes direct civilian deaths but also indirect deaths over the following years.

Recent paper estimates eventual total direct & indirect deaths in Gaza attributable to the war - 10% of entire pop'n.

I want to explain these estimates and why deaths must be counted. 1/13 Image
Why count casualties from war anyway? For moral, legal and strategic reasons.

1 - owe it to those who have died
2 - International law says must count & identify dead as far as possible
3 - monitor progress of war & learn from tactics

2/13 Image
There are direct and indirect casualties of war. Direct deaths include those who killed by fighting or bombs.

Indirect deaths are those that die when they would otherwise have lived because of one or more of: lack of food, healthcare, housing, sanitation, income, hope. 3/13 Image
Read 14 tweets
Aug 1
THREAD: the summer Covid wave in the UK continues.
Basically, there is a LOT of Covid around and not a lot of other respiratory viruses.

If you have cold or flu symptoms, it's probably Covid.

The latest hospital data from England shows steady, quite high levels. 1/8 Image
But admissions don't tell us how much virus is circulating more generally. The best (but imperfect) measure we have is wasterwater measurements, and only in Scotland and not England.

Scotland's wastewater is showing a huge July peak - highest since Omicron's 1st yr in 2022 2/8 Image
Because different people shed different amounts of virus and variants can matter too, you can't for sure infer how many people were infected between different wasterwater peaks. BUT given the size, I'd say it's pretty likely this is the largest peak since 2022 in Scotland 3/8
Read 8 tweets
Jul 23
THREAD:
I wrote about Baroness Hallett's Inquiry Module 1 report for @bmj_latest .

She found that there was *never* a plan to keep a pandemic death toll down - I discuss this and what it means going foward.

Main points below: 1/14 Image
The headline most seen is that the UK planned for the wrong pandemic.

While it is true that was far too narrow a focus on a flu pandemic, that is not the most telling bit.

To me the most telling bit, is what the plan did NOT do 2/14


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The issue is less the wrong disease, but that there was never a plan to prevent one at all – of any disease type.

The plan was *never* about reducing the number of pandemic deaths. 3/14 Image
Read 14 tweets
Jul 19
Quick thread on current Covid situation in England and Long Covid.

I have Thoughts about the Inquiry Report published yesterday but am still trying to organise them.

TLDR: high Covid levels remain, Long Covid remains 1/11
This wave is not over. While the number of admissions with Covid remains lower than the autumn/winter waves, it has now remained highsh for several weeks.

This means there are a lot of people out there getting sick - and having their work, plans and holidays disrupted. 2/11 Image
Scottish wastewater data to 9 July shows a sharp decrease, suggesting that prevalence might be on its way down.

Obviously Scotland and England can have different dynamics, but it’s the best we’ve got as long as England refuses to analyse its own wastwater. 3/11 Image
Read 12 tweets
Jul 3
THREAD: Given tomorrow's election, I've been thinking about our nation's (poor) health, the wider determinants of health and how these have worsened and what it means for policy....

TLDR: worrying only about NHS & social care is missing the point

let's dive in... 1/25
The UK has a health problem. After steady gains in life expectancy for decades, it flatlined during the austerity years and fell for the first time this century with the Covid pandemic.

The number of people out of work for long term sickness is near record levels. 2/25
There are huge inequalities between rich & poor. Boys born in the most deprived areas can expect to die almost 10 years earlier than their peers in the least deprived areas.

Even worse, they can expect to spend 18 fewer years of their life in good health (52 vs 70 years) 3/25 Image
Read 38 tweets

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