A series of mini-thoughts for a Sunday afternoon. South Africa vs. Rest of the World - the Omicron Edition.
1) We are pretty confident that Gauteng, the province at the South African Omicron epicentre is past its peak in terms of proportion of tests returning positive.
2) Despite massive number of cases (and incredibly high PTP: in the week to 11Dec, in Gauteng an ALL-TIME high of 38.7% - and an intra-week daily high of 41% when looking at PCR tests only), we have seen relatively few hospitalisations and deaths.
3) It really *does seem* as if South Africa, my country, will escape relatively unscathed in this wave.

None of that is particularly new. But other things gnaw at me.
4) Excess natural deaths as of 11 Dec were 278 000 as per our weekly @MRCza report.
We have also been of the view that between 85 and 95% of these ED, over the entire course of the epidemic, are related to Covid (genus.springeropen.com/articles/10.11…)
5) So that means, perhaps 250 000 Covid deaths since Autumn 2020. (cf: the official number of barely 90 000). Expressed per million, that is an 'unofficial Covid deaths' of around 4 200.
6) From Worldometer (yes, I *know* - I am pulling approximates here), the UK is around 2 150 -- roughly HALF the unofficial SA number
7) I am struck by this comparison from OWID. Their SA data are ours (but all-cause not natural-only).
And we can see towards of the beta wave, excess deaths in the two countries were of a kind.
8) But the UK had begun to vaccinate extensively by then. Our programme only got going in July, by which time Delta was on us.
9) SO. WHAT IF ... South Africa's 'light escape' (in the context of a QUARTER OF A MILLION excess natural deaths) is _in no small measure because_ we 'bought' that present at horrendous cost during past waves.
10) No, I do not have the answers. Yes, I am deeply grateful by what we are seeing here. But, I am appalled by how the South African Experience (TM) is being used to weaponise against unfolding events in other countries ("don't intervene, it's a nothingburger" says my bete noire)
11) Until we have a better sense of the issues raised here (esp in #9), premature celebration is uncalled for outside of SA; and in SA, perhaps we should spare a thought for the families of 250 000 of our fellow citizens whose loved ones will not be joining them for Christmas.
11) Careful data analysis, and a deep appreciation of local knowledge and specificities, coupled with global action (as argued with @GYamey and @BillHanage last week: time.com/6128506/omicro…) may yet get us through this.

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More from @tomtom_m

16 Dec
More on the turn in proportions testing positive in Gauteng (mentioned in last night's thread: ).
1. While we had suspected that the daily PTP had maxed out on 1 Dec, the clear periodicity in the data means that we had to wait to confirm
1b. We also had crashed into data problems of loaded data from public facilities, so had to split by public/private to be more certain that PTP in each had turned before calling it.
On top of that, the known issues with loading of Ag test results means focus must be on PCR tests.
1c. Weekly periodicity means that it's preferable to use a 7day centred moving average, and to wait until the daily peaks had moved out of the 7DCMA window to confirm. Adding another day's data (covering to 14/12) confirms the trend. NB! GAUTENG PCR ONLY
Read 9 tweets
15 Dec
Latest @MRCza and @UCT_news report on excess deaths in South Africa released, covering the period to 11Dec2021. A total of 277 700 excess natural deaths since 3May20. Full report available here: samrc.ac.za/reports/report…
(2/) 1 887 excess natural deaths in the week to 11Dec, up from 1 726 in the preceding week. The p-score this week is 23%, up slightly from 21% the previous week.
(3/) Still no strong excess natural mortality signal from Gauteng or its metros. The p-score in Gauteng in the most recent week is 19% (the fourth lowest of the 9 provinces). Highest in the Eastern Cape (45%) and Mpumalanga (25%).
Read 21 tweets
12 Dec
Given the comedic misinterpretation of the South African testing data offered by @BallouxFrancois (and many others!) last night ... I offer some tips having contributed to the analysis of the testing data for the @nicd_sa since April last year. (1/6)
1. The daily tests announced are those that are LOADED that day. The test may have been conducted several days/weeks earlier. What those daily reports mean is pretty hard to interpret. (2/6)
2. The VOLUME of daily tests is highly periodic, low on weekends, for example. The count of CASES is also highly periodic. But the proportion testing positive is ALSO periodic - so it's not a case of the two periodicities in cases and tests cancelling each other out. (3/6)
Read 6 tweets
8 Dec
Latest @MRCza and @UCT_news report on excess deaths in South Africa released, covering the week to 4Dec21. 276 000 excess natural deaths since 3May20. 191k in 2021. Report here: samrc.ac.za/reports/report…
There is no clear signal yet of W4 mortality yet in the provinces and metros with the highest numbers of cases to date.
Measured by the p-score, excess natural deaths increased slightly to 25% this week (just over 2000 deaths), highest in Eastern Cape (46%), lowest in Northern Cape (9.4%).
Read 8 tweets
1 Dec
Latest @MRC and @UCT_news report on excess mortality in South Africa released, covering the period through 27Nov21. 273k estimated excess natural deaths since 3May2020, 647 in the last week. Report here: samrc.ac.za/reports/report…
At present, no sign of increased natural mortality in South Africa, Gauteng, or indeed Tshwane metro.
p-scores for natural deaths are at interwave lows (8.3% nationally, ranging from -4.5% in Gauteng to 39% in the Northern Cape.
By age, p-scores fell in all age-groups other than 5-19. Deaths are few in this age band, so the p-score inherently unstable. #NotToBeOverInterpreted
Read 13 tweets
29 Nov
On developed country privilege, and the marginalisation of the global South in much of what passes as Covid public science: a view from the South. A thread. 1/20
I do not intend to engage on the topic of the disproportionate and hypocritical treatment meted out by countries of the North to Southern Africa and Southern Africans stemming from the identification of the omicron variant. 2/20
I, and many others far more erudite than I, have already expressed those views (see, for example @tuliodna @_HassanF; @gregggonsalves; @GYamey) 3/20
Read 21 tweets

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