REPORT ON WEEKLY DEATHS IN SOUTH AFRICA

17 - 23 JANUARY 2021

(WEEK 3)

Debbie Bradshaw, Ria Laubscher,

Rob Dorrington, Pam Groenewald, Tom Moultrie

Burden of Disease Research Unit South African Medical Research Council

26 January 2021

Glossary:

Actual number of deaths: The actual number of deaths in South Africa have been estimated from the numbers recorded on the National Population Register using weighting factors set to produce results consistent with those of the annual Rapid Mortality Surveillance Report to account for deaths of persons who are not on the National Population Register as well as those that have not been registered with the Department of Home Affairs. The adjustments to account for incompleteness of recording of deaths on the NPR have been re-estimated for the 2021 reports taking into account the 2017 cause-of-death data released by Stats SA in 2020. A methodological note briefly outlining the changes can be downloaded with this report from the SAMRC website: https://www.samrc.ac.za/reports/report-weekly-deaths-south-africa.

Epi-week: The Weekly Death Reports in 2020 used weeks from 1 January and ran from Wednesday to Tuesday. In setting up the monitoring for 2021, we recast the data to report by an ‘Epi-week’ consistent with CDC and many NICD reports which run from Sunday to Saturday, ensuring continuity of weeks from one year to the next. Each week is aligned with the ‘Epi-year’ that has 4 of more days in that week. Week 53 of 2020 is from 27 December 2020 to 2 January 2021 and Week 1 of 2021 is 3 January – 9 January 2021.

Excess deaths: There is no universal definition of, or understanding of what is meant by, “excess mortality”. It is a term used in epidemiology and public health that refers to the number of deaths that are occurring above what we would normally expect. The WHO uses the term to describe “Mortality above what would be expected based on the non-crisis mortality rate in the population of interest. Excess mortality is thus mortality that is attributable to the crisis conditions. It can be expressed as a rate (the difference between observed and non-crisis mortality rates), or as a total number of excess deaths.”

Excess natural deaths associated with COVID-19: Generally, the number of excess deaths per week is calculated as the number of all-cause deaths in that week less the number that might be assumed to have occurred had there not been the epidemic (i.e. the counterfactual number), provided that the counterfactual is lower. However, this approach has generally only been applied to countries where deaths have been tracking the counterfactual before the onset of significant numbers of COVID-19 related deaths. The method provides a poor estimate of the numbers of COVID-19 and collateral deaths in the early stages of the epidemic when this is not the case. Thus, we estimated the numbers of COVID and collateral deaths, once a clear upward trend is evident, as the number of actual deaths less a baseline number determined as a proportion of the predicted number. By the end of the 1st wave of the pandemic, the predicted values have been used as the counterfactual.

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Warning: The Department of Home Affairs has faced sporadic temporary office closures, particularly in areas that are more affected by COVID-19. This may affect our allocation of a death to a metro area. For example, a death that occurred in the City of Cape Town might have been registered at an office outside of the City because of a temporary closure. Closure may also cause a delay in the processing of the death registration which would result in an underestimate of the deaths in the most recent week. This accounts for the kinks in what should otherwise be a smooth increase in numbers of deaths in Cape Town and Buffalo City, for example.

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Background

This report provides estimates of the weekly number of deaths of person 1+ years in South Africa for epidemiological Week 3 of 2021, covering the period 17-23 January 2021.

While preparing predicted numbers of weekly deaths for 2021, enhancements have been made to the estimation process. The estimates now take into account the release of vital registration data to include registrations up to the close of 2017. They also ensure that the national estimate of excess deaths is consistent with the sum of the estimates for the provinces. Reporting has changed to ‘Epi-weeks’ that run from Sunday to Saturday which will align with other weekly reports and enable us to lessen the lag in reporting.

The main methodological change introduced in the 2021 reporting is that death data for the period 2014-2019 have been used to estimate the trend in mortality and the weekly variations to provide predicted values for 2020 and 2021, rather than using data for 2018 and 2019 as was done for 2020 estimates. After reviewing trends in the data, separate negative binomial models have been fitted to the unnatural deaths, the natural deaths for KwaZulu-Natal, the natural deaths for Western Cape and for natural deaths for the 7 other provinces to provide estimates by age, sex and epi-week for each year.

A prediction interval has been estimated on the basis of the variability in the observed weekly data for each reported domain. The data for both 2020 and 2021 have been recast and both years will be reported with a cumulative total of excess deaths taken from the 3 May 2020, considered to be the starting point of excess deaths associated with the COVID-19 pandemic in South Africa. Except for KwaZulu-Natal (and eThekwini in particular) the impact of the changes is relatively small. The time-series approach using data from 2018 and 2019 is used for the metropolitan areas as the trends in the sub-provincial data need further investigation to develop a comprehensive district-level model.

A brief methodological note outlining the changes that have been made for monitoring deaths during 2021 can be downloaded with this report from the SAMRC website as well as a spreadsheet with estimated values: https://www.samrc.ac.za/reports/report-weekly-deaths-south-africa.

Trends

The rapid increase in the weekly numbers of deaths of persons 1+ years of age from all causes throughout the months of December and January reached a peak of 23,879 in Week 2 (10 -16 Jan 2021). This dropped to 21,787 in the Week 3 (17 – 23 Jan 2021).

The number of excess deaths of persons 1+ years from natural causes also dropped to 13,474 in Week 3 (17

–  23 Jan 2021) after reaching a peak of 15,486 in Week 2 (10 -16 Jan 2021), which was more than double the highest number of excess natural deaths of 6,673 experienced during the 1^st wave of the pandemic in Week 30 (19 -27 Jul 2020).

By the end of Week 3, spanning the period 3 May 2020 – 23 Jan 2021, there had been a total of 125,744 excess deaths from natural causes of persons 1+ years of age. The estimated cumulative total by the of Week 2 (16 Jan 2021) was 112,270.

For people 1-59 years the excess natural deaths since 3 May 2020 is 30,745 and 94,754 for people 60+ years by the end of Week 3 (23 Jan 2021).

The number of deaths 1+ years from natural causes in the Eastern Cape has decreased for the 3^rd consecutive week and the province has experienced a total excess of 30,501 excess deaths by the end of Week 3 (23 Jan 2021). The peak number of weekly deaths in the 2^nd wave occurred in Week 53 (27 Dec 2020

–  2 Jan 2021) and was considerably higher (2,627) than the number of excess natural deaths that occurred in the peak of the 1^st wave in the province (1,436). Natural deaths in 2^nd wave in Nelson Mandela Bay and Buffalo City have also decreased but are still above the upper prediction bounds.

The number of deaths from natural causes in the Western Cape peaked during Week 53 of 2020 (27 Dec 2020-2 Jan 2021) with 1,502 excess deaths and has started decreased for a 2^nd consecutive week. During Week 3 (17 – 23 Jan 2021), the province experienced 940 excess deaths resulting in a cumulative total of 14,108 excess deaths of person 1+ years and older from natural causes in the period 3 May 2020 – 23 Jan 2021. The natural deaths in the City of Cape Town has also started to decrease rapidly with the peak in the 2^nd wave being about 40% higher than the peak in the 1^st wave.

The number of deaths from natural causes in the KwaZulu-Natal appears to have peaked ) at 6,370 during Week 2 (11 – 16 Jan 2021 and has reduced to 5,725 excess natural deaths during Week 3 (17-23 Jan 2021) resulting a cumulative total of 30,694 since 3 May 2020. The number of deaths from natural causes in eThekwini peaked during Week 1 (3 – 10 Jan 2021) with a cumulative total of 7,999 excess deaths from 3 May 2020 – 23 Jan 2021.

During Week 3 (17 -23 Jan 2021), the number of deaths from natural causes in the Gauteng decreased to 1,854 after reaching a high during Week 2 (10 -16 Jan 2021) of 2,018, similar to the numbers during the peak of the 1^st wave. During Week 3 (17 -236 Jan 2021), the number of excess deaths in Johannesburg plateaued while Ekurhuleni and Tshwane decreased. By the end of Week 3 (23 Jan 2021), the province had experienced an excess of 18,934 deaths.

The extremely sharp increases in the number of natural deaths in Limpopo and Mpumalanga during December and January have turned. During Week 3, Limpopo experienced an excess of 2,270 deaths and Mpumalanga an excess of 1,305 natural deaths.

Deaths from natural causes have been increasing in all the other provinces.

The weekly number of deaths from unnatural causes in Week 2 (10 -16 Jan 2021) has dropped below the prediction interval.

Table 1: Number of excess natural deaths of persons 1+ years by province and metro relative to revised predicted number based on the observed drop during lockdown, South Africa 2020

Note: Period has been determined based on when an upturn in the number of natural deaths became apparent. Parts do not sum to the whole because office closures due to Covid-19 may have led to registration of deaths at other offices which may not be in the same area, and random fluctuation at the point at which the baseline is determined.