NEW: today’s update from Gauteng, now on a log scale to better show current trajectories.

Steepness of lines shows how much faster the growth in cases and positivity is now vs past waves, and hospital admissions are now steepening too as the acceleration in cases feeds through.
Here’s same thing back on linear scale.

The eagle-eyed among you may spot something here: hospital admissions were tracking the Beta wave and first wave in yesterday’s chart, but today they’re slightly steeper. How is that possible, since it still shows data for the same dates?
This is why:

South Africa’s weekly hospital admission counts are back-filled every day as new patient data comes in, so the figure for the week ending Nov 28 has been rising in recent days, from 580 in the data published on the 29th, to 788 in today’s report.
In other words we need to be cautious in interpreting admissions data for two reasons:
1) It lags cases by ~ a week, so admissions line now is reflecting cases line a week ago, not today
2) It’ll be revised upwards, steepening even before including admissions in last 5 days
And that’s only the quantitative reasons.

We also need to be aware that Omicron wave in Gauteng currently skews very young, as @tomtom_m shows here, which would push case-hospitalisation rate down [but only while cases remain concentrated among young]:
And of course the other possibility, the one we’re hoping for, is that immunity could be reducing the share of cases that end up in hospital, much as we saw in Europe recently where vaccination greatly weakens the link between cases and severe disease
But a clear warning on that from data published earlier today: researchers in South Africa find that the risk of re-infection is much higher with Omicron than with past variants, suggesting some evasion of immunity from prior infection (no data on vax)
Final points:
1) Vax-induced immunity works differently to prior-infection, and there’s reason to believe that with a heavily mutated variant, vax may fare better due to vax-induced antibodies’ ability to bind to more parts of the virus than infxn-induced Abs. BUT don’t know yet.
2) Some people are making the mistake of comparing deaths *today* to cases and concluding low severity. Current wave of cases is so steep it’s climbed as high in 20 days as Delta got in 42. If you compare deaths over a short period to a much longer one, of course they’re lower.
Please let me know if you have any questions, feedback, things I’ve missed etc, and thank you to everyone who has pointed out new data that I’ve been incorporating into these threads.

Please also follow experts on the ground in SA including @tomtom_m @SACEMAdirector @Tuliodna

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More from @jburnmurdoch

30 Nov
NEW: we know cases rising fast in South Africa, but what about severe outcomes?

I spent yesterday pulling together hospitalisations for Gauteng province, so we can compare the fledging Omicron wave to those that preceded it.

So far admissions following ~same path as past waves.
Quick notes (1/2):
• For cases to be rising faster while admissions are on same pace may hint at a lower proportion of severe disease
• But this may also simply be the result of more infection-acquired immunity and vax
• Or of cases so far being predominantly younger people
And 2/2:
• Share of patients in ICU currently much lower than same stage of Delta wave, but may change if cases spread from being mainly young. Or may not, which would suggest T and B cells kicking in 🤞
• Please follow people on the ground incl @Tuliodna @tomtom_m @rjlessells
Read 6 tweets
25 Nov
Five quick tweets on the new variant B.1.1.529

Caveat first: data here is *very* preliminary, so everything could change. Nonetheless, better safe than sorry.

1) Based on the data we have, this variant is out-competing others *far* faster than Beta and even Delta did 🚩🚩
2) This is coinciding with a wider rise in cases in South Africa.

Again, currently we’re talking about small numbers (both of B.1.1.529 and of cases in SA overall), but there’s a clear upward trend. This may be a blip, but this is how waves start.
3) Aside from its rapid rise in South Africa, the other key reason for concern here is that the specific mutations that B.1.1.529 has are — based on what we’ve seen with other variants — known to be associated with greater transmissibility & immune evasion
Read 9 tweets
24 Nov
NEW: detailed thread on Europe’s winter wave and the contrast vs UK

What’s happening? Why the difference? Can boosters help?

First, the wave itself: cases, hospitalisations & deaths surging in Europe, several western countries shooting past UK 📈

Story: ft.com/content/974487…
The situation is even clearer when plotted on a log scale:

UK is broadly a flat line, with European countries cutting up steeply through it. France, Italy & Spain all on course to pass UK for cases. Germany now above UK for daily deaths and Netherlands set to follow.
So why these exponential surges across Europe but not in the UK?

There’s increasingly little difference in social mixing behaviour between the countries, and where we do see differences e.g in mask-wearing, they’re generally more virus-friendly in the UK 🤔
Read 24 tweets
18 Nov
The good thing about this story is that any time I see someone sharing it as evidence that wearing masks cuts Covid incidence by 53%, I know they haven’t read the paper it’s based on and aren’t fussed about the quality of evidence as long as it produces the right number 🙃
What do I mean by this?

Let’s start by saying that yes, we have good evidence that masks reduce Covid incidence 😷🦠📉😀

BUT it points to nowhere near a 53% reduction. As today’s @bmj_latest states, the best evidence — randomised controlled trials — point to more like a 10% cut
Indeed, here is the BMJ’s take on today’s paper:
• Most of the studies included in the meta-analysis from the Guardian story are poor quality and subject to major biases
• We need more & better research [like the mask-wearing RCTs which have consistently found a smaller effect]
Read 6 tweets
15 Nov
NEW: @UKHSA study finds Pfizer booster is extremely effective against symptomatic infection, both compared to the unvaccinated and to those with 2 doses ft.com/content/8330da…

Whether first 2 doses were AZ or Pfizer, a Pfizer booster sends vaccine efficacy up to 93-94% 💪 Image
Study was on people aged 50+, comparing those boosted ~5+ months after dose 2, to those @ 5+ months unboosted.

AZ efficacy was 61% after dose 2, waning to 44% @ 5 months.

Pfizer was 82% after dose 2, waning to 63% @ 5 months.

2 wks after Pfizer booster, both groups -> 93-94%!
Best way to think about booster impact is not to look at going from 44 to 93 with AZ, i.e roughly doubling, but invert the numbers and go from (100-44) to (100-93), i.e from relative risk vs unvaxxed of 56% to just 7%

That’s an 87% increase in protection *relative to two doses!* Image
Read 8 tweets
11 Nov
NEW: England has recorded 18 successive days of week-on-week declines in cases, its longest sequence of declines since February, suggesting its autumn/winter wave may have peaked ft.com/content/e11add…
Crucially, hospital admissions, patient numbers and deaths are now also trending downwards, as the fall in case numbers has shifted from being youth-driven into all age groups.

These acute indicators look to be topping out at 10-20% of last winter’s peak levels.
A key factor here has been England’s booster rollout.

Antibody levels in the oldest groups (vaccinated the earliest) had been slowly eroding as the months passed, but in the last 5 weeks they have shot back up as third doses have gone into arms 💉💉💉💪💪💪
Read 18 tweets

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