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

Dec 2
THREAD: update on Covid (UK) & the NHS Crisis (England) more broadly

TLDR: could be at start (just) of a new Covid wave but don't know if it will be high. Long Covid continues to be problem

Flu & RSV causing problems

NHS in v bad state - latest data sad & frightening. 1/xx
Vaccination: we're only really doing is autumn boosters which are tailing off. Uptake in 50-64 year olds is a disappointing 54%. Govt should be pushing this!

Also - most younger adults have not had a vaccine dose in almost a year. Why aren't we offering them a booster? 2/xx Image
ONS infection survey (testing ~50K people at random every week) shows that in England and Scotland infections have risen a little bit but are still falling in NI & Wales.

Over last year, minimum level of infections we've reached seems stuck at @ 1.5% which is still q high. 3/xx Image
Read 17 tweets
Dec 1
Govt tech Covid report. 🤬🧵:

This seems to be a pre-emptive response to the Covid Inquiry.

Much of it is useful & fair reflection. Some seems more intended to justify policy decisions.

BUT reflections on interventions in schools is - in my opinion - totally outrageous. 1/7
In contrast to other chapters, ALL the reflections on schools are basically saying "don't bother with mitigations in schools".

gov.uk/government/pub…

2/7
Impact on kids' education is cited; cases in the community are cited

Missing school through out of control covid a BIG issue! 10% teachers off sick is big issue!

Mitigations in schools *can* work very well, keeping schools OPEN even with high community transmission. 3/7 Image
Read 7 tweets
Nov 29
UKHSA published their findings of the Immensa Scandal - reminder back in Sept 2021, the Immensa Lab wrongly reported about 40K positive tests as negative - and ongoing chains of transmission resulted in massive spikes in cases.

The timeline in the Appendix is quite damning 1/3 Image
Local teams *repeatedly* raised suspicious negative PCR tests from 8 Sept onwards - little action taken. *3* spikes over 3 wks in daily positivity from Immensa were missed.

Not until 7 October when UKHSA epi team got their hands on it were PCR errors looked at in detail! 2/3 ImageImageImageImage
Immensa should not have made the errors & should have had qual control in place to notice.

PHE / UKHSA def should have procedures to pick this automatically MUCH sooner. AND should have responded much faster to local concerns.

Instead 1000s more got sick and some died. 3/3 Image
Read 4 tweets
Nov 25
THREAD state of Covid in the UK:

TLDR prevalence falling (but flattening?), hospitalisations flat, flu rising, if Covid starts rising again in Dec, v grim for NHS alonside flu (and RSV). 1/9
The proportion of people testing positive fell in all nations except NI. We are close to the lowest level in over a year - which is good news, except will it last...? 2/9
Hospital admissions with Covid have now been flat for a week with rates (possibly?) increasing in the very oldest groups and in Midlands, SE and London.

This suggests that we've reached the bottom of the dip and might start to go up again over the next month. 3/9
Read 10 tweets
Nov 10
Doesn't this plan misunderstand why most people are on Twitter? ie NOT to post loads but to get up to date content from trusted others (news, journos, celebs, politics, science, arts) + some random fun content (cats! heartwarming stories, outtakes, random grammar facts). 1/3
It's *not* usually about producing loads of content. Most tweeps tweet a few times a week at most. Why would they pay $8 a month?

All the new scheme does is make it *harder* to find good content either cos it's not verified or the interesting verified are harder to find 2/3
The bit of Twitter that is about building community is in fact possible to do elsewhere whether that's mastodon or whatsapp or something else entirely.
Read 4 tweets
Nov 4
QUICK THREAD on Covid in the UK:
TLDR: cases falling everywhere except NI, admissions falling everywhere, Long Covid high but falling, boosters going well, BQ.1* growing, deaths (and non Covid Excess deaths) going up. 1/7
Prevalence remains high but is falling everywhere except N Ireland. 2/7 Image
The Omicron subvariant soup seems to be coalescing around BQ.1 and BQ.1.1 which are now the main growing ones. Currently 30% of sequenced cases. They are definitely growing but not as rapidly as once feared - and they *might* not cause a big wave after all given boosters... 3/7 Image
Read 8 tweets

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