Latest @MRCza and @UCT_news report on excess deaths in South Africa released, covering the period to 18Dec21. 280 000 excess natural deaths (471/100 000) since 3May2020.
Report available here:…
2/ Nationally, natural deaths were 33% above expected (the p-score), compared to 18% the previous week. 2 600 excess natural deaths in the most recent week (12-18Dec), up from 1500 the previous week.
70% of excess deaths were among those aged 60+.
3/ By province, excess deaths increased in Gauteng over the week (p-score up from 16 to 44%). Limpopo up from 19% to 47%. Deaths in Johannesburg was 53% above expected (last week 27%). But still FAR below the peaks in previous waves
4/ Unnatural deaths follow the expected weekly pattern very closely.
5/ I recorded earlier this week that the official death numbers are both laggy and complete. The figure below shows the reported deaths (by reporting date) and excess natural deaths (by occurrence).
6/ The differential quality of reporting in a devolved healthcare system is evident. While the Western Cape reporting captures most of the quantity of the excess deaths and is consistent with the temporal pattern, other provinces do not do as well (e.g. Mpumalanga).
7/ With such differences in reporting within a single country (where we have an idea of a counterfactual), the potential scale of under-reporting in many other sub-Saharan African countries becomes apparent.
/8 The @nicd_sa testing report has yet to be released ... will append comments to this thread when it is. But in the meantime
9/ Combining the data from testing and excess deaths. The pattern previously described persists, with a substantial decoupling of deaths from cases: the figure below shows the cases and (lagged) excess deaths normalised to their historical peaks
10/ The same data, looked at differently: lagged p-score plotted against PTP, by wave. (Definitions of when a wave ends and the next begins are somewhat arbitary; here based on when National PTP turns upwards –for W4, on 7Nov21).
11/ This also shows much lower excess natural mortality for a given PTP across the board (red dots).
12/ So again – overwhelmingly positive news. It really does look like this wave will not be as bad as previous ones. Here’s hoping this is true in other parts of the world too. In the meantime, stay safe, be safe, vaccinate.
13/ lastly (for now, until comments on the testing data are added): the next report on excess deaths is scheduled for 5 Jan 2022.
14/ At last! The @NICD_sa has released its weekly testing report, covering testing through 18Dec21. Proportion testing positive (PTP), nationally, increased from 35.7% to 36.7%, but fell sharply in Gauteng (from 28.6% to 29.1%)…
15/ Provincial PTP exceeded 40% in 7 provinces. By age, PTP highest among those aged 10-19, but PTP exceeded 30% in every age group other than those under 5. PTP increased in each age group other than those aged 10-39, where small declines were observed.
16/ 195 of 262 districtis in the country showed a PTP greater than 30% in the week to 18Dec21
17/ For Gauteng (daily data; PCR only) - cases are falling faster than PTP as testing volumes fall. (Thus: looking at trends in cases exaggerates the pace of decline, although evidently a decline has been under way for some time now on either metric)
18/ Nationally (PCR tests only), the 7day centred moving average is falling consistently. The national pattern APPEARS to have stalled at a high peak, but that is a compositional effect of PTP falling in the northern provinces, rising in the coastal provinces ...
19 (end)/ ... and changing volumes by province over time.

That said, it feels very odd to be celebrating the decline in PTP in Gauteng. In recent days, it's STILL around 20-25%. It has a LONG way to fall before this wave is over.
@nicd_sa Aaargh! *38.6%**.
Addition to thread reflecting release of NICD testing report...

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More from @tomtom_m

19 Dec
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.
Read 12 tweets
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:…
(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:…
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

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