Short thread on case growth in Gauteng province, SA.

I compiled daily reported cases in November from… 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
Doing a *rough* fit of 2 exponentials to first and second half of Nov gets this. The bit that really matters is 2nd half of purer growth - this estimated growth is 25% a day, just over 3 day doubling. 4/7
They've been actively case finding in Gauteng & there've been superspreader events. So this is may be an overestimate. In UK, population much more vaxxed & boosted & loads of Delta around.

Also, this is pure Omicron growth - overall growth lower while Delta still there. 5/7
But even if growth is half of what has been observed so far in Gauteng (same chart as before on linear scale) if Omicron becomes dominant in UK (so 6 day doubling) that is still potentially very problematic.

Trick is to boost & vax as many as possible before then. 6/7
The more we slow growth of Omicron now, the more people we can protect. A few weeks makes a BIG difference and it's MUCH easier to do earlier rather than later.

Unfortunately, this means not waiting until we have vax experiment results in a few weeks. 7/7
PS Exactly what needs doing now depends on how widespread Omicron is here and how much community transmission. I don't that have info but govt, UKHSA & SAGE will have the best available knowledge.

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More from @chrischirp

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
25 Nov
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
Read 17 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.
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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