Assessing the clinical severity of the Omicron variant in the Western Cape Province, South Africa, using the diagnostic PCR proxy marker of RdRp target delay to distinguish between Omicron and Delta infections: a survival analysis

Background Emerging data suggest that SARS-CoV-2 Omicron variant of concern (VOC)is associated with reduced risk of severe disease. The extent to which this reflects a difference in the inherent virulence of Omicron, or just higher levels of population immunity, is currently not clear. Methods RdRp target delay (RTD: a difference in cycle threshold value of RdRp - E > 3.5) in the Seegene AllplexTM 2019-nCoV PCR assay is a proxy marker for the Delta VOC. The absence of this proxy marker in the transition period was used to identify suspected Omicron VOC infections. Cox regression was performed for the outcome of hospital admission in those who tested positive for SARS-CoV-2 on the Seegene AllplexTM assay from 1 November to 14 December 2021 in the Western Cape Province, South Africa, public sector. Vaccination status at time of diagnosis, as well as prior diagnosed infection and comorbidities, were adjusted for. Results 150 cases with RTD (proxy for Delta) and 1486 cases without RTD (proxy for Omicron) were included. Cases without RTD had a lower hazard of admission (adjusted Hazard Ratio [aHR] of 0.56, 95% confidence interval [CI] 0.34-0.91). Complete vaccination was protective of admission with an aHR of 0.45 (95%CI 0.26-0.77). Conclusion Omicron has resulted in a lower risk of hospital admission, compared to contemporaneous Delta infection in the Western Cape Province, when using the proxy marker of RTD. Under-ascertainment of reinfections with an immune escape variant like Omicron remains a challenge to accurately assessing variant virulence.

Change in profile of COVID-19 deaths in the Western Cape during the fourth wave

Fewer COVID-19 deaths have been reported in this fourth wave, with clinicians reporting less admissions due to severe COVID-19 pneumonia when compared to previous waves. We therefore aimed to rapidly compare the profile of deaths in wave 4 with wave 3 using routinely collected data on admissions to public sector hospitals in the Western Cape province of South Africa. Findings show that there have been fewer COVID-19 pneumonia deaths in the Omicron-driven fourth wave compared to the third wave, which confirms anecdotal reports and lower bulk oxygen consumption by hospitals in the province.

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.

Drought: A Common Environmental Disaster

Droughts have been identified as an environmental hazard by environmentalists, ecologists, hydrologists, meteorologists, geologists, and agricultural experts. Droughts are characterised by a decrease in precipitation over a lengthy period, such as a season or a year, and can occur in virtually all climatic zones, including both high and low rainfall locations. This study reviewed drought-related impacts on the environment and other components particularly, in South Africa. Several attempts have been made using innovative technology such as earth observation and climate information as recorded in studies. Findings show that the country is naturally water deficient, which adds to the climate fluctuation with the average annual rainfall in South Africa being far below the global average of 860 mm per year. Drought in South Africa’s Western Cape Province, for example, has resulted in employment losses in the province’s agriculture sector. According to the third quarterly labor force survey from 2017, the agricultural industry lost almost 25,000 jobs across the country. In the Western Cape province, about 20,000 of these were lost which has a direct impact on income generation. Many of these impacts were linked to drought events.

Incidence and distribution of human leptospirosis in the Western Cape Province, South Africa, (2010-2019): A retrospective study.

Background Leptospirosis is an emerging zoonosis of global importance. In South Africa, the infection is an underreported public health concern, with limited information on its incidence and distribution. This study aimed to determine the incidence of human leptospirosis from 2010 to 2019 in Western Cape Province (WPC), and to compare the incidence based on seasonal and demographic factors. Methods A retrospective study was conducted with data on leptospirosis diagnoses by sex, age, season, and year in WCP obtained from the National Health Laboratory Services. With the provincial population sizes as the denominator, the incidence of leptospirosis was estimated and expressed as cases per 100,000 population. Negative binomial regression was used to estimate the effect of sex, season, and year on the incidence of leptospirosis. Results A total of 254 cases of leptospirosis were reported between 2010 and 2019, with the highest number of cases being in 2015. The annual incidence ranged between 0.15 and 0.66/100,000 population with a 10-year average incidence of 0.40/100,000 population. The incidence was higher among males than in females (0.55 vs. 0.25/ 100,000 population; incidence rate ratio (IRR) 2.2, 95% CI: 1.66,3.03). The 18-44 age cohort and had the highest average incidence (0.56/100,000 population), while the less or equal to 17 age cohort had the lowest incidence (0.07/100,000 population). The 18-44 (IRR 8.0, 95% CI: 4.65,15.15) and the greater or equal to 45 (IRR 7.4, 95% CI: 4.17,14.17) age cohorts were more at risk of infection compared to the less or equal to 17 age cohort. The average incidence of the infection was similar among seasons and there was no significant association between season and incidence of leptospirosis. Conclusions The results highlight that leptospirosis is an important zoonosis within the province disproportionately affecting males and the productive age demographic groups. These findings should enhance targeted prevention and provoke further investigation on the importance of environmental and socioeconomic factors on leptospirosis burden.

Enhancing Public Participation in Public Health Offerings: Patient Preferences for Facilities in the Western Cape Province Using a Discrete Choice Experiment

Understanding patients’ preferences for health facilities could help decision makers in designing patient-centered services. Therefore, this study aims to understand how patients’ willingness to trade for certain attributes affects the choice of public health facilities in the Western Cape province of Cape Town, South Africa. A discrete choice experiment was conducted in two community day centers (CDCs). Patients repetitively chose between two hypothetical health facilities that differed in six attributes: distance to facility, treatment by doctors vs. nurses, confidentiality during treatment, availability of medication, first visit (drop-in) waiting times, and appointment waiting times. The sample consisted of 463 participants. The findings showed that availability of medication (50.5%), appointment waiting times (19.5%), and first visit waiting times (10.2%) were the most important factors for patients when choosing a health facility. In addition, respondents preferred shorter appointment and first visit waiting times (<2 h). These results identified important characteristics in choosing public health facilities in Cape Town. These public health facilities could be improved by including patient voices to inform operational and policy decisions in a low-income setting.

Cooperative Governance and Local Economic Development in Selected Small Towns: A Case Study of the Western Cape Province, South Africa

This article reports on a study based on cooperative governance and Local Economic Development (LED) in selected small towns in the Western Cape Province. The dearth of an integrative institutional framework to promote collaborative participation negatively influences local municipalities ability to successfully manage LED cooperatively with relevant stakeholders. Promoting such inclusive representation and participation of all relevant stakeholders provides a viable and complementary alternative to the traditional bureaucratic governance mechanism. The study investigated the specific factors involved in designing and implementing cooperative governance for LED in selected, comparable municipalities in the Western Cape. Specifically, the study aims to determine the push and pull factors for the successful functioning of cooperative governance aimed at promoting LED in those municipalities. Data were collected through three data collection instruments, namely, document review, interviews, and focus group discussions. The document review is complemented by data from interviews and focus groups discussion. The study contributes to the body of knowledge on cooperative governance by identifying the specific cooperative governance factors, enabling the efficacy and governance of LED in small towns, aimed at positively influencing municipalities ability to successfully manage LED cooperatively with relevant stakeholders. An in-depth understanding of the relationship and dynamics of these variables helps to offer recommendations as to how to improve the management and responsiveness to socio-economic concerns within the municipalities through improved LED governance.

Quantifying clinic transfers among people living with HIV in the Western Cape, South Africa: a retrospective spatial analysis

ObjectivesFor persons living with HIV (PLWH) in long-term care, clinic transfers are common and influence sustained engagement in HIV care, as they are associated with significant time out-of-care, low CD4 count, and unsuppressed viral load on re-entry. Despite the geospatial nature of clinic transfers, there exist limited data on the geospatial trends of clinic transfers to guide intervention development. In this study, we investigate the geospatial characteristics and trends of clinic transfers among PLWH on antiretroviral therapy (ART) in the Western Cape Province of South Africa.DesignRetrospective spatial analysis.SettingPLWH who initiated ART treatment between 2012 and 2016 in South Africa’s Western Cape Province were followed from ART initiation to their last visit prior to 2017. Deidentified electronic medical records from all public clinical, pharmacy, and laboratory visits in the Western Cape were linked across space and time using a unique patient identifier number.Participants4176 ART initiators in South Africa (68% women).MethodsWe defined a clinic transfer as any switch between health facilities that occurred on different days and measured the distance between facilities using geodesic distance. We constructed network flow maps to evaluate geospatial trends in clinic transfers over time, both for individuals’ first transfer and overall.ResultsTwo-thirds of ART initiators transferred health facilities at least once during follow-up. Median distance between all clinic transfer origins and destinations among participants was 8.6 km. Participant transfers were heavily clustered around Cape Town. There was a positive association between time on ART and clinic transfer distance, both among participants’ first transfers and overall.ConclusionThis study is among the first to examine geospatial trends in clinic transfers over time among PLWH. Our results make clear that clinic transfers are common and can cluster in urban areas, necessitating better integrated health information systems and HIV care.

Trends in public sector radiological usage in the Western Cape Province, South Africa: 2009–2019

Background: Although global use of medical imaging has increased significantly, little is known about utilisation trends in low- and middle-income countries (LMICs).Objectives: To evaluate changes over a decade in public sector diagnostic imaging utilisation at provincial level in a middle-income country.Method: A retrospective analysis of medical imaging utilisation in the Western Cape Province of South Africa in 2009 and 2019. Use of conventional radiography, ultrasonography (US), fluoroscopy, CT, MRI, digital subtraction angiography (DSA) and whole-body digital radiography was assessed by total studies and studies/103 people, for the whole province, the rural and metropolitan areas. Mammography utilisation was calculated for every 103 females aged 40–70 years.Results: The provincial population and total imaging investigations increased by 25% and 32%, respectively, whilst studies/103 people increased by 5.5% (256 vs 270/103), with marked variation by modality. Provincial US, CT and MRI utilisation/103 people increased by 111% (20 vs 43/103), 78% (10 vs 18/103) and 32% (1.9 vs 2.5/103) respectively, whilst use of fluoroscopy (3.6 vs 3.7/103) and mammography (14.2 vs 15.9/103 women aged 40–70 years) was steady and plain radiography decreased by 20% (216 vs 196/103). For CT, mammography and fluoroscopy, percentage utilisation increases/103 people were higher in the rural than metropolitan areas.Conclusion: Population growth is the main driver of overall imaging utilisation in our setting. The relatively constant imaging workload per 1000 people, albeit with increasing ultrasound, CT and MR utilisation, and decreasing use of plain radiography, reflects improved provincial imaging infrastructure, and appropriate use of available resources.