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Background The quality of cause of death (COD) statistics in South Africa has room for improvement. It is possible that supplementary use of verbal autopsy (VA) interviews for the deaths that occur outside of health facilities might be useful. This study describes the challenges and successes of collecting a national sample of VA interviews. Methods We recruited next of kin who registered deaths in 27 randomly sampled sub-districts across South Africa between September 2017 – April 2018. Trained fieldworkers (84) conducted face-to-face interviews using the WHO2016 verbal autopsy (VA) instrument. A team of physicians (51), trained in medical certification of cause of death and reading VAs, certified the underlying causes of death. Feasibility was assessed considering response rates, participation and quality of data. Cause specific-mortality fractions (CSMF) based on physician reviews and InterVA-5 automated software were compared with 2017 Statistics South Africa (Stats SA) data and assessed for plausibility against burden of disease estimates. Results Only 26% of the 36,976 total deaths registered in the sample area were identified during recruitment and 65% of the next of kin agreed to be contacted. A total of 5,375 VA were conducted (overall response rate of 55%) and 83% of physician reviewed VAs were judged to have good quality data for assigning underlying cause of death. Fifty-nine percent of the VAs occurred in the 27 sampled sub-districts, with the remainder ones coming from adjacent areas. Comparing the CSMFs, the physician reviewed VA identified 22.3% HIV/AIDS and InterVA-5 18.5% deaths, in line with burden of disease estimates, while Stats SA identified 4.9% HIV/AIDS deaths. Conclusions The study demonstrated feasibility of using VA on a national scale, but immense challenges in identifying and recruiting next of kin highlights the importance of formalising VAs within the country’s death notification system.

BackgroundIn low- and middle-income countries where SARS-CoV-2 testing is limited, seroprevalence studies can characterise the scale and determinants of the pandemic, as well as elucidate protection conferred by prior exposure.MethodsWe conducted repeated cross-sectional serosurveys (July 2020 – November 2021) using residual plasma from routine convenient blood samples from patients with non-COVID-19 conditions from Cape Town, South Africa. SARS-CoV-2 anti-nucleocapsid antibodies and linked clinical information were used to investigate: (1) seroprevalence over time and risk factors associated with seropositivity, (2) ecological comparison of seroprevalence between subdistricts, (3) case ascertainment rates, and (4) the relative protection against COVID-19 associated with seropositivity and vaccination statuses, to estimate variant disease severity.FindingsAmong the subset sampled, seroprevalence of SARS-CoV-2 in Cape Town increased from 39.2% in July 2020 to 67.8% in November 2021. Poorer communities had both higher seroprevalence and COVID-19 mortality. Only 10% of seropositive individuals had a recorded positive SARS-CoV-2 test. Antibody positivity before the start of the Omicron BA.1 wave (28 November 2021) was strongly protective for severe disease (adjusted odds ratio [aOR] 0.15; 95%CI 0.05-0.46), with additional benefit in those who were also vaccinated (aOR 0.07, 95%CI 0.01-0.35).InterpretationThe high population seroprevalence in Cape Town was attained at the cost of substantial COVID-19 mortality. At the individual level, seropositivity was highly protective against subsequent infections and severe COVID-19.FundingWellcome Trust, National Health Laboratory Service, the Division of Intramural Research, NIAID, NIH (ADR) and Western Cape Government Health.Research in contextEvidence before this studyIn low- and middle-income countries where SARS-CoV-2 testing is limited, seroprevalence studies can help describe the true extent of the pandemic.Infection from Omicron was associated with less severe disease in South Africa, but it is unclear whether this was due to a decrease in virulence of the variant or if prior infection provided protection.Added value of this studyThe seroprevalence data nested within a population cohort enabled us to assess differential case ascertainment rates, as well as to examine the contribution of both natural and vaccine-induced immunity in protecting communities against infections and severe disease with different SARS-CoV-2 variants.Implications of the available evidenceInequality and differential access to resources resulted in poorer communities having higher seroprevalence and COVID-19 death rates, with lower case ascertainment rates. Antibody positivity provided strong protection against an immune escape variant like Omicron but came at a high mortality cost.

IntroductionWhile a large proportion of people with HIV (PWH) have experienced SARS-CoV-2 infections, there is uncertainty about the role of HIV disease severity on COVID-19 outcomes, especially in lower income settings. We studied the association between mortality and characteristics of HIV severity and management, and vaccination, among adult PWH.MethodsWe analysed observational cohort data on all PWH aged ≥15 years experiencing a diagnosed SARS-CoV-2 infection (until March 2022), who accessed public sector healthcare in the Western Cape province of South Africa. Logistic regression was used to study the association of mortality with CD4 cell count, viral load, evidence of ART, time since first HIV evidence, and vaccination, adjusting for demographic characteristics, comorbidities, admission pressure, location and time period.ResultsMortality occurred in 5.7% (95% CI: 5.3,6.0) of 17 831 first diagnosed infections. Higher mortality was associated with lower recent CD4, no evidence of ART collection, high or unknown recent viral load (among those with ART evidence), and recent first HIV evidence, differentially by age. Vaccination was protective. The burden of comorbidities was high, and tuberculosis, chronic kidney disease, diabetes and hypertension were associated with higher mortality, more strongly in younger adults.ConclusionsMortality was strongly associated with suboptimal HIV control, and prevalence of these risk factors increased in later COVID-19 waves. It remains a public health priority to ensure PWH are on suppressive ART and vaccinated, and manage any disruptions in care that occurred during the pandemic. The diagnosis and management of comorbidities, including for tuberculosis, should be optimised.

Background Retreatment tuberculosis (TB) disease is common in high-prevalence settings. The risk of repeated episodes of recurrent TB is unknown. We calculated the rate of recurrent TB per subsequent episode by matching individual treatment episodes over a period of 13 years. Methods All recorded TB episodes in Cape Town between 2003 and 2016 were matched by probabilistic linkage of personal identifiers. Among individuals with a first episode notified in Cape Town and who completed their prior treatment successfully we estimated the recurrence rate stratified by subsequent episode and HIV status. We adjusted person-time to background mortality by age, sex, and HIV status. Results A total of 292 915 TB episodes among 263 848 individuals were included. The rate of recurrent TB was 16.4 per 1000 person-years (95% CI, 16.2–16.6), and increased per subsequent episode (8.4-fold increase, from 14.6 to 122.7 per 1000 from episode 2 to 6, respectively). These increases were similar stratified by HIV status. Rates among HIV positives were higher than among HIV negatives for episodes 2 and 3 (2- and 1.5-fold higher, respectively), and the same thereafter. Conclusions TB recurrence rates were high and increased per subsequent episode, independent of HIV status. This suggests that HIV infection is insufficient to explain the high burden of recurrence; it is more likely due to a high annual risk of infection combined with an increased risk of infection or progression to disease associated with a previous TB episode. The very high recurrence rates would justify increased TB surveillance of patients with >1 episode., Tuberculosis treatment episodes over a period of 13 years were linked. Rates of recurrence increased 9-fold between episode 2 and 5 and did not differ by HIV status or previous treatment outcome, suggesting an underlying mechanism not mediated by HIV infection.

Background Cape Town, a South African city with high levels of economic inequality, has gone through two COVID-19 waves. There is evidence globally that low-income communities experience higher levels of morbidity and mortality during the pandemic. Methods Age-standardized COVID-19 mortality in the eight sub-districts of Cape Town was compared by economic indicators taken from the most recent Census (unemployment rate, monthly income). Results The overall Standardized Death Rate (SDR) for COVID-19 in Cape Town was 1 640 per million, but there was wide variation across the different sub-districts. A linear relationship was seen between sub-districts with high poverty and high COVID-19 SDRs. Conclusions Low-income communities in Cape Town experienced higher levels of COVID-19 mortality. As we continue to contend with COVID-19, these communities need to be prioritized for access to quality health care.

Introduction The Western Cape Provincial Health Data Centre (PHDC) consolidates person-level clinical data across government services, leveraging sustained investments in patient registration systems, a unique identifier, and maturation of administrative and clinical digital health systems. Objectives The PHDC supports clinical care directly through tools for clinicians which integrate patient data or identify patients in need of interventions, and indirectly through supporting operational and epidemiological analyses. Methods The PHDC is housed entirely within government. Data are processed from a range of source systems, usually daily, through distinct harmonisation and curation, beneficiation, and reporting processes. Linkage is predominantly through the unique identifier which doubles as a pervasive folder number, augmented by other identifiers. Further data processing includes triangulation of multiple data sources for enumerating health conditions, with assignment of certainty levels for each enumeration. Outputs include patient-specific email alerts, a web-based consolidated patient clinical viewing platform, filterable line-listings of patients with specific conditions and associated characteristics and outcomes, management reports and dashboards, and data releases in response to operational and research data requests. Strict architectural, administrative and governance processes ensure privacy-protection. Results In the past decade 8 million unique people are recorded as having sought healthcare in the provincial public sector health services, with current utilisation at 15 million attendances or admissions a year. Cross-sectional enumeration of health conditions includes over 430 000 people with HIV, 500 000 with hypertension, 235 000 with diabetes. 110 000 pregnancies and 54 000 patients with tuberculosis are enumerated annually. Each year over 50 data requests are processed for internal and external requesters in accordance with data request and release governance processes. Conclusions The single consolidated environment for person-level health data in the Western Cape has created new opportunities for supporting patient care, while improving the governance around access to and release of sensitive patient data.

Objectives educing child mortality requires good information on its causes. Whilst South African vital registration data have improved the quality of cause-of-death data remains inadequate. To improve this data from death certificates were linked with information from forensic mortuaries in Western Cape Province. Methods A local mortality surveillance system was established in 2007 by the Western Cape Health Department to improve data quality. Cause-of-death data were captured from copies of death-notification forms collected at Department of Home Affairs Offices. Using unique identifiers additional forensic mortuary data were linked with mortality surveillance system records. Causes of death were coded to the ICD-10 classification. Causes of death in children under five were compared with those from vital registration data for 2011. Results Cause-of-death data were markedly improved with additional data from forensic mortuaries. The proportion of ill-defined causes was halved (25% to 12%) and leading cause rankings changed. Lower respiratory tract infections moved above prematurity to rank first accounting for 20.8% of deaths and peaking in infants aged 1-3 months. Only 11% of deaths from lower respiratory tract infections occurred in hospital resulting in 86% being certified in forensic mortuaries. Road traffic deaths increased from 1.1% to 3.1% (27 to 75) and homicides from 3 to 28. Conclusions The quality and usefulness of cause-of-death information for children in the WC was enhanced by linking mortuary and vital registration data. Given the death profile interventions are required to prevent and manage LRTI diarrhea and injuries and to reduce neonatal deaths.

Information systems designed to support health promotion in pregnancy, such as the MomConnect programme, are potential sources of clinical information which can be used to identify pregnancies prospectively and early on. In this paper we demonstrate the feasibility and value of linking records collected through the MomConnect programme, to an emergent province-wide health information exchange in the Western Cape Province of South Africa, which already enumerates pregnancies from a range of other clinical data sources. MomConnect registrations were linked to pregnant women known to the public health services using the limited identifiers collected by MomConnect. Three-quarters of MomConnect registrations could be linked to existing pregnant women, decreasing over time as recording of the national identifier decreased. The MomConnect records were usually the first evidence of pregnancy in pregnancies which were subsequently confirmed by other sources. Those at lower risk of adverse pregnancy outcomes were more likely to register. In some cases, MomConnect was the only evidence of pregnancy for a patient. In addition, the MomConnect records provided gestational age information and new and more recently updated contact numbers to the existing contact registry. The pilot integration of the data in the Western Cape Province of South Africa demonstrates how a client-facing system can augment clinical information systems, especially in contexts where electronic medical records are not widely available.

To identify the leading causes of mortality and premature mortality in Cape Town, South Africa, and its subdistricts, and to compare levels of mortality between subdistricts.Cape Town mortality data for the period 2001-2006 were analysed by age, cause of death and sex. Cause-of-death codes were aggregated into three main cause groups: (i) pre-transitional causes (e.g. communicable diseases, maternal causes, perinatal conditions and nutritional deficiencies), (ii) noncommunicable diseases and (iii) injuries. Premature mortality was calculated in years of life lost (YLLs). Population estimates for the Cape Town Metro district were used to calculate age-specific rates per 100,000 population, which were then age-standardized and compared across subdistricts.The pattern of mortality in Cape Town reflects the quadruple burden of disease observed in the national cause-of-death profile, with HIV/AIDS, other infectious diseases, injuries and noncommunicable diseases all accounting for a significant proportion of deaths. HIV/AIDS has replaced homicide as the leading cause of death. HIV/AIDS, homicide, tuberculosis and road traffic injuries accounted for 44% of all premature mortality. Khayelitsha, the poorest subdistrict, had the highest levels of mortality for all main cause groups.Local mortality surveillance highlights the differential needs of the population of Cape Town and provides a wealth of data to inform planning and implementation of targeted interventions. Multisectoral interventions will be required to reduce the burden of disease.