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:…
(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%).
(4) Some uncertainty re what’s driving the pattern in Eastern Cape.
(5/) p-scores by age have risen slightly for ages 60 and over.
Unnatural deaths have kept uncannily close to the predicted levels for an extended period of time.
(6/) The @nicd_sa released their weekly testing summary today, covering the week to 11Dec2021. The report is available here:….
(7/) Proportions testing positive increased steeply in all provinces, other than Gauteng (which also increased in the week to 11Dec. Nationally, PTP was 35%.
(7b) By age, still testing highest among adolescents and young adults, but has spread to older age groups
(7c) Nationally, the country is shade of Christmas red. More than half of all districts recorded PTP > 30% last week
(8/) BURIED LEDE #1. The proportion testing positive, measured on a daily (as opposed to weekly) basis, has turned in the last few days.
BL#1/2 (This analysis uses only PCR tests (as it is known, see threads passim, that there are delays and problems with loading of antigen results), and split by public-private testing (as known IT problems last week).
BL#1/3 The lower PTP in private is likely due to greater volumes of worried-well testing in private, as well as other selection effects.
(9/) But we can also combine the data from the testing and excess deaths reports, lagging the excess deaths a week behind the testing data.
(10/) BURIED LEDE #2. The pattern in wave 4 is materially different from that in previous waves. A story in 3 graphs
BL#2/2: First. Case and (lagged) excess deaths: in W4, cases have rocketed, but excess deaths? Not so much. Not even in Gauteng.
BL#2/3: Second. Normalised cases and normalised (lagged) excess deaths: in the previous 3 waves, these metrics moved almost perfectly in sync. Not so much. Not even in Gauteng (where cases are > 80% of the peak in W3, yet excess deaths not even 10% of the W3 peak.
BL#2/4: Third. Same plot as the previous, but now presented as a correlation plot between PTP and (lagged) excess deaths. Generally a very stable relationship. Except the red dot for Gauteng, being the most recent week's data.
(11/) OK. So LOTS of people are going to go wild on here shouting about this. Here’s my not-so-hot take. These data are really important. They STRONGLY suggest that the Omicron wave in South Africa will be different.
(12/). But this is NOT definitive proof. We need another week or two data. And this is NOT clinical or virological evidence. And it MAY still be confounded (not least of all by age; we don't think so but still working on that).
(13/) All round the most positive news in weeks. This is cause for optimism. Let's now amass the rest of the data to (hopefully) show that this is all good!
Stay well; stay safe; vaccinate!
(in case clarification required for this and the next few tweets: _IN GAUTENG_; although the figure makes that clear)

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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 Image
Read 9 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:…
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:…
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
28 Jul
Latest @MRCza and @UCT_news report out on excess deaths, covering the period to 24 July 2021. 10 500 excess deaths in the week to 24 July 2021, bringing the total excess natural deaths since 3 May 2020 to 214 000. 130 000 of those in 2021. Report here:…
20 000 natural deaths this week, still below the peak of 24 000 at the top of wave 2. Complex pattern may emerge in the next few weeks as Gauteng and its metros decrease, while other provinces (and metros) increase.
Nationally, natural deaths this week 119% of expected. Gauteng 181% (down from 210% last week). P-scores in other provinces increasing: NW (165%); LP (157%); MP (138%). Big increase in KZN to 100% (2x expected deaths), up from 51% last week.
Read 5 tweets

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