COVID-19 and all-cause mortality in South Africa – the hidden deaths in the first four waves

Changes in the medical admissions and mortality amongst children in four South African hospitals following the COVID-19 pandemic: A five-year review

Vulnerable children from poor communities with high HIV and Tuberculosis(TB) burdens were impacted by COVID-19 lockdowns. Concern was raised about the extent of this impact and anticipated post-pandemic surges in mortality. Interrupted time series segmented regression analyses were done using routinely collected facility-level data of children admitted for medical conditions at four South African referral hospitals. Monthly admission and mortality data over 60 months from 01 April 2018 to 31 January 2023 was analysed using models which included dummy lockdown level variables, a dummy post-COVID period variable, Fourier terms to account for seasonality, and excess mortality as a proxy for healthcare burden. Of the 45 015 admissions analysed, 1237(2·75%) demised with significant decreases in admissions during all the lockdown levels, with the most significant mean monthly decrease of 450(95%, CI = 657·3, -244·3) p<0·001 in level 5 (the most severe) lockdown. There was evidence of loss of seasonality on a six-month scale during the COVID periods for all admissions (p = 0·002), including under-one-year-olds (p = 0·034) and under-five-year-olds (p = 0·004). No decreases in mortality accompanied decreased admissions. Post-pandemic surges in admissions or mortality were not identified in children with acute gastroenteritis, acute pneumonia and severe acute malnutrition.During the COVID-19 pandemic, paediatric admissions in 4 hospitals serving communities with high levels of HIV, TB and poverty decreased, similar to global experiences; however, there was no change in in-hospital mortality. No post-pandemic surge in admissions or mortality was documented. Differences in the impact of pandemic control measures on the transmission of childhood infections and access to health care may account for differing outcomes seen in our setting compared to the global experiences. Further studies are needed to understand the impact of pandemic control measures on healthcare provision and transmission dynamics and to better inform future responses amongst vulnerable child populations.

A cost-effectiveness analysis of South Africa's COVID-19 vaccination programme

BACKGROUND

COVID-19 vaccines were rolled out in South Africa beginning in February 2021. In this study we retrospectively assessed the cost-effectiveness of the vaccination programme in its first two years of implementation.

METHOD

We modelled the costs, expressed in 2021 US$, and health outcomes of the COVID-19 vaccination programme compared to a no vaccination programme scenario. The study was conducted from a public payer's perspective over two time-horizons - nine months (February to November 2021) and twenty-four months (February 2021 to January 2023). Health outcomes were estimated from a disease transmission model parameterised with data on COVID-19-related hospitalisations and deaths and were converted to disability adjusted life years (DALYs). Deterministic and probabilistic sensitivity analyses (DSA and PSA) were conducted to assess parameter uncertainty.

RESULTS

Incremental cost-effectiveness ratio (ICER) was estimated at US$1600 per DALY averted during the first study time horizon. The corresponding ICER for the second study period was estimated at US$1300 per DALY averted. When 85% of all excess deaths during these periods were included in the analysis, ICERs in the first and second study periods were estimated at US$1070 and US$660 per DALY averted, respectively. In the PSA, almost 100% of simulations fell below the estimated opportunity cost-based cost-effectiveness threshold for South Africa (US$2300 DALYs averted). COVID-19 vaccination programme cost per dose had the greatest impact on the ICERs.

CONCLUSION

Our findings suggest that South Africa's COVID-19 vaccination programme represented good value for money in the first two years of rollout.

Covid-19 demography in France and South Africa: A comparative study of morbidity and mortality in 2020-2022

BACKGROUND

Covid-19 epidemics raged around the world in years 2020-2022. The dynamics of the epidemics and their mortality varied by country depending on prevention, treatments, vaccination and health status of the population.

OBJECTIVE

The study compares Covid-19 morbidity and mortality in South-Africa and in France, two countries with similar population size and with reliable reporting systems, in order to better understand the dynamics and impacts of the epidemics and the effects of health policies and programs.

DATA AND METHODS

Data on cases, deaths, hospitalizations, vaccinations were drawn from national statistics. Published data on cases and deaths were corrected for undercount.

RESULTS

Results show a different epidemiology in the two countries in the first three years of the epidemic (2020-2022). Incidence was higher in South Africa, and some 44% more people were infected by December 2022 than in France. Mortality and case-fatality were also higher in South Africa despite a favourable age structure. The age pattern of mortality showed higher values in South Africa among the young adults. Young women appeared somewhat disadvantaged in South Africa. Lastly, vaccination appeared to have had no effect on incidence, but a large effect on case-fatality in France.

CONCLUSIONS

Despite about the same population size and the same crude death rate at baseline, South Africa exhibited more cases and more deaths from Covid-19 over the 2020-2022 period. Prevention strategies (lockdown and vaccination) appear to have had large impacts on morbidity and mortality.

The importance of including manner of (injury) death on the death notification form

-

Undiagnosed Pulmonary Tuberculosis (TB) and Coronavirus Disease 2019 (COVID-19) in Adults Dying at Home in a High-TB-Burden Setting, Before and During Pandemic COVID-19: An Autopsy Study

BACKGROUND

Missing or undiagnosed patients with tuberculosis (TB) or coronavirus disease 2019 (COVID-19) are of concern. Identifying both infections in patients with no diagnosis prior to death contributes to understanding the burden of disease. To confirm reports of global reduction in TB incidence, a 2012 autopsy study of adults dying at home of natural causes in a high-TB-burden setting was repeated, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) assessments after the first COVID-19 surge in South Africa.

METHODS

Adult decedents who died at home with insufficient information to determine cause of death, no recent hospitalization, and no current antemortem TB or COVID-19 diagnosis were identified between March 2019 and October 2020 with a 4-month halt during lockdown. A standardized verbal autopsy followed by minimally invasive needle autopsy (MIA) was performed. Biopsies were taken for histopathology from liver, bilateral brain and lung; bronchoalveolar lavage fluid was collected for Xpert (MTB/RIF) and mycobacterial culture, and blood for human immunodeficiency virus (HIV) polymerase chain reaction (PCR) testing. After the start of the COVID-19 pandemic, a nasopharyngeal swab and lung tissue were subjected to SARS-CoV-2 PCR testing.

RESULTS

Sixty-six MIAs were completed in 25 men and 41 women (median age, 60 years); 68.2% had antemortem respiratory symptoms and 30.3% were people with HIV. Overall, TB was diagnosed in 11 of 66 (16.7%) decedents, and 14 of 41 (34.1%) in the COVID-19 pandemic were SARS-CoV-2 positive.

CONCLUSIONS

Undiagnosed TB in adults dying at home has decreased but remains unacceptably high. Forty percent of decedents had undiagnosed COVID-19, suggesting that estimates of excess deaths may underestimate the impact of SARS-CoV-2 on mortality.

Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa

South Africa was among the first countries to detect the SARS-CoV-2 Omicron variant. However, the size of its Omicron BA.1 and BA.2 subvariants (BA.1/2) wave remains poorly understood. We analyzed sequential serum samples collected through a prospective cohort study before, during, and after the Omicron BA.1/2 wave to infer infection rates and monitor changes in the immune histories of participants over time. We found that the Omicron BA.1/2 wave infected more than half of the cohort population, with reinfections and vaccine breakthroughs accounting for > 60% of all infections in both rural and urban sites. After the Omicron BA.1/2 wave, we found few (< 6%) remained naïve to SARS-CoV-2 and the population immunologic landscape is fragmented with diverse infection/immunization histories. Prior infection with the ancestral strain, Beta, and Delta variants provided 13%, 34%, and 51% protection against Omicron BA.1/2 infection, respectively. Hybrid immunity and repeated prior infections reduced the risks of Omicron BA.1/2 infection by 60% and 85% respectively. Our study sheds light on a rapidly shifting landscape of population immunity in the Omicron era and provides context for anticipating the long-term circulation of SARS-CoV-2 in populations no longer naïve to the virus.

Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa

South Africa was among the first countries to detect the SARS-CoV-2 Omicron variant. Propelled by increased transmissibility and immune escape properties, Omicron displaced other globally circulating variants within 3 months of its emergence. Due to limited testing, Omicron's attenuated clinical severity, and an increased risk of reinfection, the size of the Omicron BA.1 and BA.2 subvariants (BA.1/2) wave remains poorly understood in South Africa and in many other countries. Using South African data from urban and rural cohorts closely monitored since the beginning of the pandemic, we analyzed sequential serum samples collected before, during, and after the Omicron BA.1/2 wave to infer infection rates and monitor changes in the immune histories of participants over time. Omicron BA.1/2 infection attack rates reached 65% (95% CI, 60% - 69%) in the rural cohort and 58% (95% CI, 61% - 74%) in the urban cohort, with repeat infections and vaccine breakthroughs accounting for >60% of all infections at both sites. Combined with previously collected data on pre-Omicron variant infections within the same cohorts, we identified 14 distinct categories of SARS-CoV-2 antigen exposure histories in the aftermath of the Omicron BA.1/2 wave, indicating a particularly fragmented immunologic landscape. Few individuals (<6%) remained naïve to SARS-CoV-2 and no exposure history category represented over 25% of the population at either cohort site. Further, cohort participants were more than twice as likely to get infected during the Omicron BA.1/2 wave, compared to the Delta wave. Prior infection with the ancestral strain (with D614G mutation), Beta, and Delta variants provided 13% (95% CI, -21% - 37%), 34% (95% CI, 17% - 48%), and 51% (95% CI, 39% - 60%) protection against Omicron BA.1/2 infection, respectively. Hybrid immunity (prior infection and vaccination) and repeated prior infections (without vaccination) reduced the risks of Omicron BA.1/2 infection by 60% (95% CI, 42% - 72%) and 85% (95% CI, 76% - 92%) respectively. Reinfections and vaccine breakthroughs had 41% (95% CI, 26% - 53%) lower risk of onward transmission than primary infections. Our study sheds light on a rapidly shifting landscape of population immunity, along with the changing characteristics of SARS-CoV-2, and how these factors interact to shape the success of emerging variants. Our findings are especially relevant to populations similar to South Africa with low SARS-CoV-2 vaccine coverage and a dominant contribution of immunity from prior infection. Looking forward, the study provides context for anticipating the long-term circulation of SARS-CoV-2 in populations no longer naïve to the virus.