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

1 Dec
Short thread on case growth in Gauteng province, SA.

I compiled daily reported cases in November from sacoronavirus.co.za/category/daily… and had a look at growth...

TLDR pure omicron growth there looks pretty scary. We do NOT yet know how it will translate here. 1/7
Just plotting daily reported cases (dots) and the rolling centred average shows rapid increase in cases last few weeks of November. Blue dots are weekend reporting effects (Sundays and Mondays).

But for exponential growth we really need log scales... 2/7
Same chart on log scale looks like 2 periods of exp growth - one slower in 1st half Nov & then faster in 2nd half. Can interpret as period when Omicron gaining dominance over Delta (so smaller % of cases) & from 15th purer Omicron growth (now considered >90% of Gauteng cases) 3/7
Read 8 tweets
26 Nov
Very quick thread on UK covid situation:

TLDR: boosters going well now, cases rising particularly in children, admissions & deaths dropping 1/5
First vaccination: boosters now in about quarter of population - NI is a bit behind other nations.

Very good booster coverage in over 70s - would be great to get it higher.

Significantly lower uptake in more deprived areas.

Teen vax ongoing (slowly). 2/5
Second cases: cases climbing in UK. Over 50K again today. By date of test, climbing in NI & England and falling (a little) in Wales & Scotland. But positivity rates falling in NI so could be more testing.

Slightly diff picture from ONS with nations either rising or flattish. 3/5
Read 5 tweets
26 Nov
Some thoughts about Nu and bad timing, benefit of delaying spread & what we should do... 1/5
First timing: a new dangerous variant arrives just before millions of people across world start travelling internationally for Christmas holiday period - not good.

Millions of people travelling within and to US this week for Thanksiving just as variant announced - not good. 2/5
Second: Delaying spread: UK won't keep it out forever. But delaying has large benefits.

We're currently boosting almost 2.5 million people every week. Even a few weeks delay is millions more vulnerable adults with extra protection. That matters. 3/5
Read 5 tweets
24 Nov
THREAD on Europe and whether UK is a good position for winter...

TLDR: Much of Europe in v difficult circumstances.
But UK has been in difficult circumstances since June with much more total illness and death, and still is. 1/17
Concentrating on W Europe where vax rates & context are more similar - E Europe is in its own world of pain, mainly due to population with high existing health problems and low vax, particularly in vulnerable. 2/17
Many countries in W Europe going through bad Covid surges - in both cases and deaths - each for their own combo of reasons of measures, behaviours, vax rates, waning.

They have similar vax rates to UK but are later in boosting (but also vaxxed later so waning later). 3/17
Read 18 tweets
21 Nov
Some personal thoughts:

Husband and I have just recovered (mostly) from Covid... no idea how we got it since we've been super careful and not done much. Shopping or swimming we think.

I am left grateful for masks & vaccines - here's why: 1/8
Firstly vaccines: having Covid sucked but I am sure it would have sucked much worse without being vaccinated. I am grateful that I had the chance to get that protection first.

I'm annoyed that I got sick a few weeks before my booster was due, but that's life. 2/8
Secondly masks: the first symptoms were so innocuous it was only obvious later what they were. I was 100% convinced we didn't have Covid cos we'd been so careful.

The weekend before symptoms and 1st day of, we were in *a lot* of shops.
3/8
Read 10 tweets
15 Nov
🧵The line from Boris Johnson that Europe's Covid wave might come here is *arrant nonsense* - just convenient cover if cases climb this winter.

We've been having this wave ever since end of June.

It's driven here - as elsewhere in Europe - by local context not importation 1/5
National Covid trajectory is determined by combo of:
1. public health measures (masks, ventilation, which venues are open, vax passports, testing, isolation etc) & behaviours,
2. vax rates (inc boosters)
3. levels of prev immunity

If it's spreading, combo not enough. 2/5
England relied basically on 2 since June and it's not been enough. We've now got 2 and (sadly!) 3 & it's still not bring cases down.

E Europe has nowhere near enough 2 (hence high deaths too).

Germany & Austria are lower on 2 and 3. NL, Belgium stopped 1 (esp in schools). 3/5
Read 5 tweets

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