Higher COVID-19 mortality in low-income communities in the City of Cape Town - a descriptive ecological study

SARS-CoV-2 seroepidemiology in Cape Town, South Africa, and implications for future outbreaks in low-income communities

In low- and middle-income countries where SARS-CoV-2 testing is limited, seroprevalence studies can help describe and characterise the extent of the pandemic, as well as elucidate protection conferred by prior exposure. We conducted repeated cross-sectional serosurveys (July 2020 -November 2021) using residual samples from patients from Cape Town, South Africa, sent for routine laboratory studies for non-COVID-19 conditions. 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. Among the subset sampled, seroprevalence of SARS-CoV-2 in Cape Town increased from 39.19% (95% confidence interval [CI] 37.23-41.19) in July 2020 to 67.8% (95%CI 66.31-69.25) 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. Using COVID-19 hospital admission and death data at the Provincial Health Data Centre, 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). The 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 disease. In low-income communities, where diagnostic testing capacity is often limited, surveillance systems dependent on them will underestimate the true extent of an outbreak. Rapidly conducted seroprevalence studies can play an important role in addressing this.

How do new crises impact HIV risk behaviour - exploring HIV risk behaviour according to COVID-19-related orphanhood status in South Africa?

The COVID-19 pandemic resulted in high death rates globally, and over 10.5 million children lost a parent or primary caregiver. Because HIV-related orphanhood has been associated with elevated HIV risk, we sought to examine HIV risk in children affected by COVID-19 orphanhood. Four hundred and twenty-one children and adolescents were interviewed, measuring seven HIV risk behaviours: condom use, age-disparate sex, transactional sex, multiple partners, sex associated with drugs/alcohol, mental health and social risks. Approximately 50% (211/421) experienced orphanhood due to COVID-19, 4.8% (20/421) reported living in an HIV-affected household, and 48.2% (203/421) did not know the HIV status of their household. The mean age of the sample was 12.7 years (SD:2.30), of whom 1.2% (5/421) were living with HIV. Eighty percent (337/421) reported at least one HIV risk behaviour. HIV sexual risk behaviours were more common among children living in HIV-affected households compared to those not living in HIV-affected households and those with unknown household status (35.0% vs. 13.6% vs.10.8%, X2 = 9.25, p = 0.01). Children living in HIV-affected households had poorer mental health and elevated substance use (70.0% vs. 48.5%, X2 = 6.21, p = 0.05; 35.0% vs. 19.9%, X2 = 4.02, p = 0.1306, respectively). HIV-affected households may require specific interventions to support the health and well-being of children and adolescents.

COVID-19 among adults living with HIV: correlates of mortality among public sector healthcare users in Western Cape, South Africa

INTRODUCTION

While 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 of mortality with characteristics of HIV severity and management, and vaccination, among adult PWH.

METHODS

We 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 evidence of antiretroviral therapy (ART) collection, time since first HIV evidence, CD4 cell count, viral load (among those with evidence of ART collection) and COVID-19 vaccination, adjusting for demographic characteristics, comorbidities, admission pressure, location and time period.

RESULTS

Mortality 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 and recent first HIV evidence, differentially by age. Vaccination was protective. The burden of comorbidities was high, and tuberculosis (especially more recent episodes of tuberculosis), chronic kidney disease, diabetes and hypertension were associated with higher mortality, more strongly in younger adults.

CONCLUSIONS

Mortality was strongly associated with suboptimal HIV control, and the 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 optimized.

Socioeconomic disparities associated with mortality in patients hospitalized for COVID-19 in Colombia

Socioeconomic disparities play an important role in the development of severe clinical outcomes including deaths from COVID-19. However, the current scientific evidence in regard the association between measures of poverty and COVID-19 mortality in hospitalized patients is scant. The objective of this study was to investigate whether there is an association between the Colombian Multidimensional Poverty Index (CMPI) and mortality from COVID-19 in hospitalized patients in Colombia from May 1, 2020 to August 15, 2021. This was an ecological study using individual data on hospitalized patients from the National Institute of Health of Colombia (INS), and municipal level data from the High-Cost Account and the National Administrative Department of Statistics. The main outcome variable was mortality due to COVID-19. The main exposure variable was the CMPI that ranges from 0 to 100% and was categorized into five levels: (i) level I (0%−20%), (ii) level II (20%−40%), (iii) level III (40%−60%), (iv) level IV (60%−80%); and (v) level V (80%−100%). The higher the level, the higher the level of multidimensional poverty. A Bayesian multilevel logistic regression model was applied to estimate Odds Ratio (OR) and their corresponding 95% credible intervals (CI). In addition, a subgroup analysis was performed according to the epidemiological COVID-19 waves using the same model. The odds for dying from COVID-19 was 1.46 (95% CI 1.4–1.53) for level II, 1.41 (95% CI 1.33–1.49) for level III and 1.70 (95% CI 1.54–1.89) for level IV hospitalized COVID-19 patients compared with the least poor patients (CMPI level I). In addition, age and male sex also increased mortality in COVID-19 hospitalized patients. Patients between 26 and 50 years-of-age had 4.17-fold increased odds (95% CI 4.07–4.3) of death compared with younger than 26-years-old patients. The corresponding for 51–75 years-old patients and those above the age of 75 years were 9.17 (95% CI 8.93–9.41) and 17.1 (95% CI 16.63–17.56), respectively. Finally, the odds of death from COVID-19 in hospitalized patients gradually decreased as the pandemic evolved. In conclusion, socioeconomic disparities were a major risk factor for mortality in patients hospitalized for COVID-19 in Colombia.

Cardiac manifestations in children with the multisystem inflammatory syndrome (MIS-C) associated with SARS-CoV-2 infection: Systematic review and meta-analysis

According to the World Health Organisation, as of October 2022, there have been 55,560,329 reported cases of SARS-COV-2 in patients under 19 years old. It is estimated that about 0.06% of these patients may develop MIS-C, representing more than 2 million children worldwide. This systematic review and meta-analysis examined the pooled prevalence of cardiovascular manifestation and cardiac complications in children hospitalised with MIS-C. The PROSPERO register number is CRD42022327212. We included case-report studies, case-control studies, cohort studies, and cross-sectional studies, as well as clinical trials or studies describing cardiac manifestations of MIS-C and its sequelae in a paediatric population. Initially, 285 studies were selected, but there were 154 duplicates, and 81 were excluded because they did not fit the eligibility criteria. Thus, 50 studies were selected for review, and 30 were included in the meta-analysis. A total sample size of 1445 children was included. The combined prevalence of myocarditis or pericarditis was 34.3% (95% CI: 25.0%-44.2%). The combined prevalence for echocardiogram anomalies was 40.8% (95% CI: 30.5%-51.5%), that of Kawasaki disease presentation was 14.8% (95% CI: 7.5%-23.7%), and that of coronary dilation was 15.2% (95% CI: 11.0%-19.8%). The rate of electrocardiogram anomalies was 5.3% (95% CI: 0.8%-12.3%), and the mortality rate was 0.5% (CI 95%: 0%-1.2%). Furthermore, 186 children still had complications at discharge, with a combined prevalence of such long-lasting manifestations of 9.3% (95% CI: 5.6%-13.7%). Studies that assess whether these children will have an increased cardiovascular risk with a greater chance of acute myocardial infarction, arrhythmias, or thrombosis will be essential for healthcare planning.

Epidemiology and outcomes of SARS-CoV-2 infection associated with anti-nucleocapsid seropositivity in Cape Town, South Africa

Background

In 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.

Methods

We 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.

Findings

Among 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).

Interpretation

The 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.

Funding

Wellcome Trust, National Health Laboratory Service, the Division of Intramural Research, NIAID, NIH (ADR) and Western Cape Government Health.

COVID-19 mortality and deprivation: pandemic, syndemic, and endemic health inequalities

COVID-19 has exacerbated endemic health inequalities resulting in a syndemic pandemic of higher mortality and morbidity rates among the most socially disadvantaged. We did a scoping review to identify and synthesise published evidence on geographical inequalities in COVID-19 mortality rates globally. We included peer-reviewed studies, from any country, written in English that showed any area-level (eg, neighbourhood, town, city, municipality, or region) inequalities in mortality by socioeconomic deprivation (ie, measured via indices of multiple deprivation: the percentage of people living in poverty or proxy factors including the Gini coefficient, employment rates, or housing tenure). 95 papers from five WHO global regions were included in the final synthesis. A large majority of the studies (n=86) found that COVID-19 mortality rates were higher in areas of socioeconomic disadvantage than in affluent areas. The subsequent discussion reflects on how the unequal nature of the pandemic has resulted from a syndemic of COVID-19 and endemic inequalities in chronic disease burden.

COVID-19 among adults living with HIV: Correlates of mortality in a general population in a resource-limited setting

Introduction

While 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.

Methods

We 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.

Results

Mortality 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.

Conclusions

Mortality 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.

How the COVID-19 Pandemic Alters the Landscapes of the HIV and Tuberculosis Epidemics in South Africa: A Case Study and Future Directions

South Africa has long grappled with one of the highest HIV and tuberculosis (TB) burdens in the world. The COVID-19 pandemic poses challenges to the country's already strained health system. Measures to contain COVID-19 virus may have further hampered the containment of HIV and TB in the country and further widened the socioeconomic gap. South Africa's handling of the pandemic has led to disruptions to HIV/TB testing and treatment. It has, furthermore, influenced social risk factors associated with increased transmission of these diseases. Individuals living with HIV and/or TB also face higher risk of developing severe COVID-19 disease. In this case study, we contextualize the HIV/TB landscape in South Africa and analyze the direct and indirect impact of the COVID-19 pandemic on the country's efforts to combat these ongoing epidemics.

SARS-CoV-2 Infection Is Associated with Uncontrolled HIV Viral Load in Non-Hospitalized HIV-Infected Patients from Gugulethu, South Africa

In South Africa, high exposure to SARS-CoV-2 occurs primarily in densely populated, low-income communities, which are additionally burdened by highly prevalent Human Immunodeficiency Virus (HIV). With the aim to assess SARS-CoV-2 seroprevalence and its association with HIV-related clinical parameters in non-hospitalized patients likely to be highly exposed to SARS-CoV-2, this observational cross-sectional study was conducted at the Gugulethu Community Health Centre Antiretroviral clinic between October 2020 and June 2021, after the first COVID-19 wave in South Africa and during the second and beginning of the third wave. A total of 150 adult (median age 39 years [range 20−65 years]) HIV-infected patients (69% female; 31% male) were recruited. 95.3% of the cohort was on antiretroviral therapy (ART), had a median CD4 count of 220 cells/µL (range 17−604 cells/µL) and a median HIV viral load (VL) of 49 copies/mL (range 1−1,050,867 copies/mL). Furthermore, 106 patients (70.7%) were SARS-CoV-2 seropositive, and 0% were vaccinated. When stratified for HIV VL, patients with uncontrolled HIV viremia (HIV VL > 1000 copies/mL) had significantly higher odds of SARS-CoV-2 seropositivity than patients with HIV VL < 1000 copies/mL, after adjusting for age, sex and ART status (p = 0.035, adjusted OR 2.961 [95% CI: 1.078−8.133]). Although the cause−effect relationship could not be determined due to the cross-sectional study design, these results point towards a higher risk of SARS-CoV-2 susceptibility among viremic HIV patients, or impaired HIV viral control due to previous co-infection with SARS-CoV-2.

Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa

OBJECTIVES

The objective was to compare COVID-19 outcomes in the Omicron-driven fourth wave with prior waves in the Western Cape, assess the contribution of undiagnosed prior infection to differences in outcomes in a context of high seroprevalence due to prior infection and determine whether protection against severe disease conferred by prior infection and/or vaccination was maintained.

METHODS

In this cohort study, we included public sector patients aged ≥20 years with a laboratory-confirmed COVID-19 diagnosis between 14 November and 11 December 2021 (wave four) and equivalent prior wave periods. We compared the risk between waves of the following outcomes using Cox regression: death, severe hospitalisation or death and any hospitalisation or death (all ≤14 days after diagnosis) adjusted for age, sex, comorbidities, geography, vaccination and prior infection.

RESULTS

We included 5144 patients from wave four and 11,609 from prior waves. The risk of all outcomes was lower in wave four compared to the Delta-driven wave three (adjusted hazard ratio (aHR) [95% confidence interval (CI)] for death 0.27 [0.19; 0.38]. Risk reduction was lower when adjusting for vaccination and prior diagnosed infection (aHR: 0.41, 95% CI: 0.29; 0.59) and reduced further when accounting for unascertained prior infections (aHR: 0.72). Vaccine protection was maintained in wave four (aHR for outcome of death: 0.24; 95% CI: 0.10; 0.58).

CONCLUSIONS

In the Omicron-driven wave, severe COVID-19 outcomes were reduced mostly due to protection conferred by prior infection and/or vaccination, but intrinsically reduced virulence may account for a modest reduction in risk of severe hospitalisation or death compared to the Delta-driven wave.

Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa

OBJECTIVES

We aimed to compare COVID-19 outcomes in the Omicron-driven fourth wave with prior waves in the Western Cape, the contribution of undiagnosed prior infection to differences in outcomes in a context of high seroprevalence due to prior infection, and whether protection against severe disease conferred by prior infection and/or vaccination was maintained.

METHODS

In this cohort study, we included public sector patients aged ≥20 years with a laboratory confirmed COVID-19 diagnosis between 14 November-11 December 2021 (wave four) and equivalent prior wave periods. We compared the risk between waves of the following outcomes using Cox regression: death, severe hospitalization or death and any hospitalization or death (all ≤14 days after diagnosis) adjusted for age, sex, comorbidities, geography, vaccination and prior infection.

RESULTS

We included 5,144 patients from wave four and 11,609 from prior waves. Risk of all outcomes was lower in wave four compared to the Delta-driven wave three (adjusted Hazard Ratio (aHR) [95% confidence interval (CI)] for death 0.27 [0.19; 0.38]. Risk reduction was lower when adjusting for vaccination and prior diagnosed infection (aHR:0.41, 95% CI: 0.29; 0.59) and reduced further when accounting for unascertained prior infections (aHR: 0.72). Vaccine protection was maintained in wave four (aHR for outcome of death: 0.24; 95% CI: 0.10; 0.58).

CONCLUSIONS

In the Omicron-driven wave, severe COVID-19 outcomes were reduced mostly due to protection conferred by prior infection and/or vaccination, but intrinsically reduced virulence may account for an approximately 25% reduced risk of severe hospitalization or death compared to Delta.