The extent of interruptions to primary care medical officers' consultations in the Western Cape.

BACKGROUND:  Administrative tasks are an increasing burden for primary care doctors globally and linked to burnout. Many tasks occur during consultations. They cause interruptions with possible effects on patients' and doctors' experiences and care. The burden and typology of interruptions of doctors in primary care consultations have not been studied in South Africa. Given the link between administrative loads and burnout, describing the extent of these interruptions would help. This study's aim was to assess the extent of interruptions on primary care doctors in the Western Cape. METHODS:  This was a descriptive cross-sectional survey. Doctors from rural and urban primary care clinics in the Western Cape answered an online self-administered survey on the types of interruptions experienced during consultations. Interruptions were categorised and their prevalence calculated. Clinical and non-clinical interruption categories were compared. RESULTS:  There were 201 consultations from 30 doctors. Most interruptions were from retrieving and recording the current patient's information (93.0%), paperwork for other patients (50.7%), and telephone calls about the current patient (41.8%). Other prevalent interruptions were for emergencies (39.8%) and acquiring consumables (37.3%). The median (interquartile range [IQR]) of four (2-4) interruption types per consultation was higher than global settings. CONCLUSION:  Doctors experienced many interruptions during consultations. Their wide range included interruptions unrelated to the current patient.Contribution: This study adds insights from the global south on clinicians' administrative burden. It elaborates on the types of activities that interrupt consultations in an upper-middle income primary care setting. Exploration of interventions to decrease this burden is suggested.

Molecular characterisation of hepatitis A in the Western Cape province, South Africa in 2023.

In 2023, passive laboratory-based surveillance showed an increase in hepatitis A virus (HAV) infection. We investigated hepatitis A incidence using the notifiable medical condition surveillance system (NMCSS) data and molecularly characterised positive blood samples from the Western Cape province for 2023. All HAV IgM seropositive cases from the NMCSS from 1 January to 31 October 2023 in South Africa were investigated. HAV RNA from blood samples that had tested positive for HAV IgM from Western Cape was amplified in the VP1/P2B junction and sequenced (3500Xl Genetic Analyser). Sequences were assembled, aligned (Sequencher) and analysed (Aliview 1.27 and MEGA11). Statistical analysis was performed using Excel and the CuSum2 Threshold to determine suspected outbreaks. In 2023, the incidence of HAV IgM was 6.28/100,000 in South Africa, with the highest incidence in Western Cape province (15.86/100,000). Children aged 5 to 14 years were affected the most in the Western Cape. The positive cases in the Western Cape were above the CuSum2 threshold from January to May 2023, with the highest incidence observed in the City of Cape Town Metropolitan (14.8/100,000). Genotyping was successfully performed on 92.7% (139/150) of serum samples, for which the IB sub-genotype was detected. Three primary mutations R63K, R71S and M104I were observed in more than 49% of the samples. Most of the samples sequenced belonged to patients residing in areas close to each other within the City of Cape Town Southern, Western, and Mitchells Plain sub-districts. The CuSum2 threshold method allowed the identification of suspected HAV outbreaks in the districts within the Western Cape in 2023 while genotyping identified clusters of sub-genotype IB. Genotyping could assist with determining the common source of infection during an outbreak, especially if coupled with epidemiological and geographical data. Further active surveillance can assist in investigating the HAV risk factors for targeted public health responses.

The profile of people undergoing lower limb amputations at Groote Schuur Hospital.

Background: The annual incidence of lower limb amputations (LLA) at Groote Schuur Hospital is rising gradually. However, little is known about the sociodemographic and clinical profiles of people undergoing these limb amputations. Objectives: To collect and analyse data to describe the sociodemographic, health and amputation profiles of people who have undergone LLA at Groote Schuur Hospital. Method: A descriptive retrospective chart review was conducted using a sample of 107 participants who had undergone LLA at Groote Schuur Hospital between January 2019 and July 2020. A customised assessment tool was used to extract data on the sociodemographic, health and amputation profiles of patients who had LLA. Data were analysed descriptively. Results: Sixty per cent of the patients who had undergone LLA at Groote Schuur Hospital were women. Most of the patients were over the age of 60 years and had not completed school and were pensioners or unemployed, with very low income and multiple co-morbidities including poorly controlled diabetes. Conclusions: Complications because of uncontrolled diabetes were the primary indication for LLAs at Groote Schuur Hospital. Therefore, health literacy projects are indicated to address chronic diseases of lifestyle, which, in turn, may reduce the overall burden of LLA, particularly on the South African under-resourced healthcare system. Contribution: The results of this study may help us identify key factors that predispose patients to LLAs. Consequently, this may help us identify key areas for prevention and better management of diseases that can result in complications that indicate the need for amputation.

Forensic taphonomic experimental design matters: a study assessing clothing and carrion biomass load on scavenging in Cape Town, South Africa.

The identification of unknown human remains is a significant and ongoing challenge in South Africa, worsened by the country's high murder rate. The rate of decomposition in South Africa is significantly influenced by vertebrate scavenging, which, if not considered, can impede the accurate estimation of the post-mortem interval. Scavenging patterns vary greatly depending on the environment and ecological region, and there is limited data for the Western Cape province. To address this gap, two clothed and uncaged pig carcasses weighing 60 kg each were placed in the field in July 2021 and January 2022, respectively. Motion-activated infrared-capable trail cameras were used to observe decomposition, scavenger species, and their activities. Additionally, a comparative sample of 16 unclothed carcasses deployed between 2014 and 2016 in the same habitat were analyzed to assess the impact of clothing and biomass load. The study found three main results: (1) Regardless of habitat or biomass load, it took significantly less time to reach decomposition milestones (25%, 50%, and 75%) during the summer season; (2) the presence of mongoose scavengers had a greater impact on the time required to reach milestones during winter compared to summer; and (3) single carcass deployments reached the milestones faster than multi-carcass deployments in both seasons. This research highlights the potential inaccuracy of current methods for estimating the post-mortem interval when scavenging activity is not considered or documented in the underlying experimental data, particularly for environments or ecological biomes where scavengers actively impact decomposition rates.

The Impact of COVID-19 on the Utilization of Public Sector Radiological Services in the Western Cape Province of South Africa.

Background Coronavirus (COVID-19) was officially declared a pandemic in March 2020 and has had a major impact on global healthcare services, including radiology. However, little is known about the full impact of COVID-19 on the utilization of diagnostic imaging in Africa's public healthcare sector. Objectives The objective of this study was to compare public sector diagnostic imaging utilization by modality for the whole Western Cape Province (WCP) of South Africa (SA), as well as its metropolitan and rural areas, in 2019 and 2020 in terms of the absolute number of investigations and investigations per 1000 people. Method We performed a retrospective analysis of Western Cape Government Department of Health and Wellness and Stats SA District Council 2021 Mid-Year Population Estimates data. All diagnostic imaging investigations performed in 2019 and 2020 were collated and stratified by imaging modality, geographic region (metropolitan/rural), and calendar year. Data are presented as the total number of investigations and investigations per 1000 people. We calculated mammography utilization for women aged 40-70 years and compared data for 2019 and 2020. Results Between 2019 and 2020, the provincial population increased by 1.9%, while total imaging investigations and investigations per 1000 people decreased by 19% (1,384,941 vs. 1,123,508, -261,433) and 20% (262/103 vs. 208/103), respectively. Total numerical decline was highest in plain radiographs (1,005,545 vs. 800,641, -204,904), accounting for more than three-quarters (78%) of the total reduction. Percentage decline was most pronounced for mammography, as utilization was almost halved (15.7/103 vs. 8.9/103, -43%), whereas computed tomography was the least impacted (17.9/103 vs. 16.7/103, -12%) with the remaining modalities decreasing between approximately one-quarter and one-fifth (magnetic resonance imaging = 26%, fluoroscopy = 25%, general radiographs = 23%, ultrasound = 16%, chest radiographs = 18%). Proportional metropolitan (-18.7%) and rural decreases (-19.3%) were similar. Conclusion COVID-19 had a substantial impact on WCP imaging services, decreasing overall radiological investigations by almost one-fifth. The greatest impact was on elective investigations, particularly mammography. Although the proportional impact was similar for the metropolitan and rural areas, COVID-19 nonetheless exacerbated existing discrepancies in imaging utilization between the geographical regions. The medium- and long-term clinical impacts of decreased imaging are still to be defined.

Complementary Feeding in Western Cape, South Africa: Identifying Suboptimal Practices and Potential Targets for Intervention.

Introduction Appropriate complementary feeding is important for the normal growth and development of children. This study aimed to describe the complementary feeding practices and identify suboptimal practices that would be possible targets for intervention to improve practices among mothers of infants aged six weeks to one year in Western Cape Province, South Africa. Methods This hospital-based cross-sectional study was conducted at the emergency unit of the Department of Paediatrics and Child Health of Tygerberg Academic Hospital, Cape Town, South Africa, between May 2017 and June 2017 among 110 mothers and their infants. Infants with minor ailments were included in the study. Patients requiring hospital admissions or severely ill infants requiring oxygen or ventilation, premature babies, and children with congenital anomalies were excluded from the study. The relationship between sociodemographic variables and the time of commencement of complementary food was described. Results The mean age of infants was 6.4±3.2 months, while the mean age of mothers was 27.6±5.5 years. On average, the age at introduction of complementary food to infants was 2.17±1.50 months. Among the complementary foods given to infants less than six months of age, cereals were the most commonly introduced (76.5%), while the least were sweet beverages (5.9%). Maternal age ≤ 34 years and first-born infant were significantly associated with early commencement of complementary food before six months of age (p=0.042 and p=0.032, respectively). Conclusion This study indicated that commencement of complementary food as early as two months of age with the use of non-nutritious and inappropriate food remains a significant problem in the region. There is a need for further education of mothers on appropriate complementary feeding practices given the importance of complementary feeding practices to the optimum growth and development of children.

Bone histology of Neogene angulate tortoises (Testudines: Testudinidae) from South Africa: palaeobiological and skeletochronological implications.

Here we examine the tibial microstructure of modern and fossil angulate tortoises to assess the histology and growth from the late Miocene-early Pliocene, Pleistocene through to modern forms. The cross-sections of all the tibiae sampled revealed highly vascularized, uninterrupted, fibrolamellar bone tissue during early ontogeny, which suggests that early growth was fast. However, later in ontogeny, growth was slower, as indicated by the deposition of parallel-fibred bone tissue in the outer cortex, and even ceased periodically, as indicated by lines of arrested growth. Comparative analyses of the growth rates of the tortoises from different time periods showed that the tortoises from the late Miocene-early Pliocene Langebaanweg locality and from Diepkloof Rock Shelter had relatively slower growth rates under less optimal growth conditions. Additionally, these prehistoric specimens show extensive remodelling, and several generations of secondary osteons further suggest functional and/or metabolic stresses on the skeleton. Palaeoenvironmental reconstructions suggest that it was mostly cooler and drier with seasonal fluctuations in late Miocene-early Pliocene, and it is likely that Chersina responded to these conditions by having a lower rate of growth as compared with their modern counterparts, which thrive in the current prevailing more favourable Mediterranean type of climate.

Parasite diversity and community structure of translocated Clarias gariepinus (Burchell) in South Africa: Testing co-introduction, parasite spillback and enemy release hypotheses.

Clarias gariepinus (Burchell) is one of several freshwater fish species that have been translocated beyond its natural geographic range in South Africa. The present study investigated the parasitic communities of two translocated populations (one in the Riviersonderend River, Western Cape and the other from the Great Fish River, Eastern Cape) as well as its native source population from Gariep Dam, Free State. A total of nine, seven, and eight parasitic taxa were found to parasitise various organs of C. gariepinus from the three populations, respectively. The diversity and abundances of parasitic species in the two translocated populations were similar, but distinct community assemblages were observed. Parasite community composition from the Great Fish River was similar to that of the source population from Gariep Dam, whereas the parasitic community from C. gariepinus in the Riviersonderend River was distinct from that of Gariep Dam. This, together with the introduction history into the Western Cape, suggests that translocated C. gariepinus is sourced from various systems across South Africa, or that suitable intermediate hosts are present in the recipient ecosystems to sustain host-specific co-introduced parasitic taxa of C. gariepinus. In total, the resilience of 11 specialist parasite species of C. gariepinus is demonstrated in their persistence upon co-introduction into the two novel environments with their host, and support for the enemy release hypothesis is confirmed in the loss of known parasite taxa in translocated populations. The presence of the co-invasive fish lice Argulus japonicus Thiele, 1900 is reported from C. gariepinus in Gariep Dam and the Asian tapeworm Schyzocotyle acheilognathi (Yamaguti, 1934) was found from translocated C. gariepinus in the Riviersonderend River, Western Cape and lastly, a suspected case of parasite spillback from an unknown native host is reported.

Evaluation of a public COVID-19 dashboard in the Western Cape, South Africa: a tool for communication, trust, and transparency.

BACKGROUND: Public health dashboards have been used in the past to communicate and guide local responses to outbreaks, epidemics, and a host of various health conditions. During the first year of the COVID-19 pandemic, dashboards proliferated but the availability and quality differed across the world. This study aimed to evaluate the quality, access, and end-user experience of one such dashboard in the Western Cape province, South Africa. METHODS: We analysed retrospective aggregate data on viewership over time for the first year since launch of the dashboard (30 April 2020 - 29 April 2021) and conducted a cross-sectional survey targeting adult users of the dashboard at one year post the initial launch. The self-administered, anonymous questionnaire with a total of 13 questions was made available via an online digital survey tool for a 2-week period (6 May 2021 - 21 May 2021). RESULTS: After significant communication by senior provincial political leaders, adequate media coverage and two waves of COVID-19 the Western Cape public COVID-19 dashboard attracted a total of 2,248,456 views during its first year. The majority of these views came from Africa/South Africa with higher median daily views during COVID-19 wave periods. A total of 794 participants responded to the survey questionnaire. Reported devices used to access the dashboard differed statistically between occupational status groups with students tending toward using mobile devices whilst employed and retired participants tending toward using desktop computers/laptops. Frequency of use increases with increasing age with 65.1% of those > 70 years old viewing it daily. Overall, 76.4% of respondents reported that the dashboard influenced their personal planning and behaviour. High Likert score ratings were given for clarity, ease of use and overall end-user experience, with no differences seen across the various age groups surveyed. CONCLUSION: The study demonstrated that both the availability of data and an understanding of end-user need is critical when developing and delivering public health tools that may ultimately garner public trust and influence individual behaviour.

Pressing need for national governmental recognition of forensic anthropology in South Africa as illustrated in a medico-legal case.

Forensic anthropology in South Africa is well developed in the higher education sector, with advanced training and research programmes. Despitethis and decades of academic involvement in casework, forensic anthropology still lacks a defined framework and mandate ata governmentallevel. Therefore, the involvement of forensic anthropologists' expertise varies markedly between cases, provinces, and among various stakeholderswithinthe country, to the detriment of dispensation of social and criminal justice. The lack ofclearly defined guidelines for the renderingof the service was exemplified and demonstrated through a recent forensic case. Here,contextual information was absent, and the remains posed a challenge to analyse, ostensibly due tomissing information. Numerous questions were raised during the analysis of the remains, and broader concerns about the investigative involvement of a forensic anthropologist within South African casework were brought to the fore. Through the analysis of this case, we describe the deductive processes that led to the formation of an opinion that the skeletal linear defects were the result of taphonomic changes. In addition, we highlighthow these efforts where constrained and each step in theprocess unnecessarily hindered. Finally, we demonstrate the capacity andwillingness offorensic anthropology practitioners to be involved, and how, withoutgovernmentalsupport, it is a great potential lamentably untapped.

Child and adolescent mental health services in the Western Cape Province of South Africa: the perspectives of service providers.

BACKGROUND: Current work in the field point to the need to strengthen child and adolescent mental health services (CAMHS) globally, and especially in low- and middle-income countries (LMICs). Policy development, planning and service provision must be relevant to the needs of stakeholders at grassroots level, and should include their perspectives. This study set out to explore the perspectives and lived experiences of service providers, including their recommendations to strengthen CAMHS in South Africa. METHODS: Using focus group discussions (FGDs) and semi-structured individual interviews (SSIIs), qualitative data were collected from 46 purposefully selected multidisciplinary health service providers across the Western Cape, one of the nine provinces of South Africa. Audio-recorded data were entered into NVivo 11 (QSR), and thematic analysis was performed by two independent raters. RESULTS: Results highlighted a significant lack of CAMH resources, poor intersectoral collaboration, limited access to training, absence of consistency and uniformity in service delivery, weak support for staff, and high rates of negative attitudes of staff. External factors contributing to poor CAMHS identified by service providers included poor socioeconomic circumstances, high rates of HIV/AIDS, substance use and stigma. The eight recommendations to strengthen CAMHS included a need to (1) increase CAMH staffing, (2) provide dedicated CAMHS at secondary care and child-friendly infrastructure at primary care, (3) review current service focus on number of patients seen versus quality of care provided to children, (4) formalise intersectoral collaborations, (5) increase learning opportunities for trainees, (6) employ a lead professional for CAMHS in the province, (7) increase support for staff, and (8) acknowledge staff initiatives. CONCLUSIONS: Findings underlined the need for quality improvement, standardisation and scale-up of mental health services for children and adolescents in South Africa. Whilst we used the Western Cape as a 'case study', we propose that our findings may also be relevant to other LMICs. We recommend that the perspectives of service users, including children and adolescents, be sought to inform service transformation.

Factors that influence regional resilience planning in Central Karoo, South Africa.

Applied in various disciplines, the concept of resilience has become a catchword in academic and policy discourse across the world. Despite the rapidly growing interest, there is a dearth of literature on resilience in the context of rural areas. To contribute towards extending the existing knowledge, this article analyses factors that influenced the low levels of incorporation of regional resilience in the plans (spatial development frameworks [SDFs]) that guide planning and development in a rural region of Central Karoo, South Africa. The study that the article draws upon revolved around qualitative interviews conducted with seven key informants who were knowledgeable about social, economic and environmental challenges as well as planning and development in the Central Karoo region. The semi-structured interviews were conducted through the online platform of Microsoft Teams. Against the background of low levels of incorporation of regional resilience in the plans that have a bearing on planning and development in the Central Karoo region, it was discovered that the lack of knowledge, financial and human resource constraints and a lack of synergy between different stakeholders were the main reasons for the inadequate incorporation of regional resilience in the subject SDFs. To improve this state of affairs, it is recommended that the stakeholders in the region be empowered on matters pertaining to regional resilience. In terms of empirical research, it is recommended that future studies go beyond the analysis of the content of plans in the manner of this article and analyse the actual regional resilience of rural areas.

A situational analysis of child and adolescent mental health services and systems in the Western Cape Province of South Africa.

BACKGROUND: Even though child and adolescent mental health is a global health priority, services are very limited, particularly in low- and middle-income countries (LMIC), and therefore need comprehensive strengthening. This requires knowledge of the hardware elements of the system (human resources, financing, medicines, technology, organisational structure, service infrastructure, and information systems). This study sought to examine these elements of child and adolescent mental health (CAMH) services and systems in the Western Cape Province of South Africa. METHODS: The World Health Organization Assessment Instrument of Mental Health Systems (WHO-AIMS) version 2.2 of 2005 was adapted to identify key variables of interest in CAMH. Data were collected for the calendar year 2016 and focused on the public health sector. We outlined findings based on best available data across the six domains of the WHO-AIMS. RESULTS: In domain 1, we found no provincial CAMH policy or implementation plans to support the national CAMH policy and were unable to identify a CAMH-specific budget. In domain 2, there was no dedicated provincial leadership structure for CAMH, and no dedicated or 'child- and adolescent-friendly' mental health services at primary or secondary care levels. At tertiary level, there were only three specialist CAMH teams. The majority of CAMH resources were based in the City of Cape Town, with limited resources in the rural districts. Essential medicines were available in all facilities, and the majority of children and adolescents had access to free services. In domain 3, data were limited about the extent of training offered to primary healthcare staff, and little or no psychosocial interventions were available in primary care. Domain 4 identified a small and variable CAMH workforce across all levels of care. In domain 5, few public health campaigns focused on CAMH, and little evidence of formal intersectoral collaboration on CAMH was identified. Domain 6 identified significant limitations in health information systems for CAMH, including lack of child- and adolescent-specific and disaggregated data to establish baselines for policy development, monitoring, evaluation and CAMH research. CONCLUSIONS: This study identified significant structural weaknesses in CAMH and presents a clear call for action to strengthen services and systems in the province and in South Africa. it would be important to expand research also to include provider and user perspectives for service strengthening.

Youths' Perceptions Of The Relation Between Alcohol Consumption And Risky Sexual Behaviour in the Western Cape, South Africa: A Qualitative Study.

The purpose of this study is to explore the factors that youth identify as contributing to alcohol consumption, and more specifically its relation to risky sexual behaviour among youth. We employed an exploratory qualitative method using focus group discussions with 34 young people between the ages of 18-25-years-old in low socio-economic status communities in the Western Cape province of South Africa. Data were analyzed thematically utilizing Braun and Clarke's (2006) six-step thematic analysis process. We identified two thematic domains pertaining to alcohol consumption and risky sexual behaviour, namely individual and social factors, each comprising three themes. The individual factors thematic domain comprises intrapersonal influences, employment and educational attainment; while the social factors thematic domain includes interpersonal influences, social influences, and hope for the future. Youth living in low socio-economic status communities were thought to be at greater risk of alcohol misuse and subsequent risky behaviour, given the political and social history of marginalisation, systematic oppression, and social inequality. To address alcohol use and risky sexual behavior among youth, we recommend interventions with adolescents, parents or guardians, and the community. More specifically, interventions aimed at adolescents should focus on the transition to young adulthood. Interventions with parents should focus on their role in modelling and potentially regulating alcohol consumption. Finally, community interventions should centre on drinking behaviors, levels of drinking, what constitutes harmful drinking, and how to identify when treatment and recovery support is likely to be required.

Seasonal variations in air concentrations of 27 organochlorine pesticides (OCPs) and 25 current-use pesticides (CUPs) across three agricultural areas of South Africa.

For decades pesticides have been used in agriculture, however, the occurrence of legacy organochlorine pesticides (OCPs) and current-use pesticides (CUPs) is poorly understood in Africa. This study investigates air concentrations of OCPs and CUPs in three South African agricultural areas, their spatial/seasonal variations and mixture profiles. Between 2017 and 2018, 54 polyurethane foam-disks passive air-samplers (PUF-PAS) were positioned in three agricultural areas of the Western Cape, producing mainly apples, table grapes and wheat. Within areas, 25 CUPs were measured at two sites (farm and village), and 27 OCPs at one site (farm). Kruskal-Wallis tests investigated area differences in OCPs concentrations, and linear mixed-effect models studied differences in CUPs concentrations between areas, sites and sampling rounds. In total, 20 OCPs and 16 CUPs were detected. A median of 16 OCPs and 10 CUPs were detected per sample, making a total of 11 OCPs and 24 CUPs combinations. Eight OCPs (trans-chlordane, o,p'-/p,p'-dichlorodiphenyldichloroethylene (DDE)/dichlorodiphenyltrichloroethane (DDT), endosulfan sulfate, γ-hexachlorocyclohexane and mirex) and two CUPs (carbaryl and chlorpyrifos) were quantified in all samples. p,p'-DDE (median 0.14 ng/m3) and chlorpyrifos (median 0.70 ng/m3) showed the highest concentrations throughout the study. Several OCPs and CUPs showed different concentrations between areas and seasons, although CUPs concentrations did not differ between sites. OCPs ratios suggest ongoing chlordane use in the region, while DDT and endosulfan contamination result from past-use. Our study revealed spatial and seasonal variations of different OCPs and CUPs combinations detected in air. Further studies are needed to investigate the potential cumulative or synergistic risks of the detected pesticides.

Flooding trends and their impacts on coastal communities of Western Cape Province, South Africa.

Climate change-induced extreme weather events have been at their worst increase in the past decade (2010-2020) across Africa and globally. This has proved disruptive to global socio-economic activities. One of the challenges that has been faced in this regard is the increased coastal flooding of cities. This study examined the trends and impacts of coastal flooding in the Western Cape province of South Africa. Making use of archival climate data and primary data from key informants and field observations, it emerged that there is a statistically significant increase in the frequency of flooding and consequent human and economic losses from such in the coastal cities of the province. Flooding in urban areas of the Western Cape is a factor of human and natural factors ranging from extreme rainfall, usually caused by persistent cut off-lows, midlatitude cyclones, cold fronts and intense storms. Such floods become compounded by poor drainage caused by vegetative overgrowth on waterways and land pollution that can be traced to poor drainage maintenance. Clogging of waterways and drainage systems enhances the risk of flooding. Increased urbanisation, overpopulation in some areas and non-adherence to environmental laws results in both the affluent and poor settling on vulnerable ecosystems. These include coastal areas, estuaries, and waterways, and this worsens the risk of flooding. The study recommends a comprehensive approach to deal with factors that increase the risk of flooding as informed by the provisions of both the Sustainable Development Goals framework and the Sendai Framework for Disaster Risk Reduction 2015-2030 in a bid to de-risking human settlement in South Africa.

Primary care nurses' preparedness for COVID-19 in the Western Cape province, South Africa.

INTRODUCTION: The novel coronavirus 2019 or COVID-19 pandemic has brought about a global public health crisis. Primary care (PC) nurses render first line care, or refer for more specialised services. AIM: To investigate the preparedness of PC nurses for COVID-19 in the Western Cape. SETTING: The Western Cape province of South Africa. METHODS: We administered an online survey, with closed and open-ended questions, to 83 Stellenbosch University postgraduate PC nursing students and alumni working in the Western Cape, between 03 July and 01 September 2020. RESULTS: The results indicated that 43.3% of participants were confident about the infection, prevention, and control (IPC) training they received and 56.7% felt prepared to provide direct care to suspected cases of COVID-19. Primary care nurses were more comfortable to triage (78.3%) than to manage persons with COVID-19 (42.2%), indicating that they may not be functioning to the full capacity of their education and training. Adequate infrastructure was reported by less than a third of the participants (30.1%) and 59.1% reported that personal protective equipment (PPE) was always available. Primary care nurses needed support in coping with stress (57.8%) although few (14.5%) reported access to mental health services. CONCLUSION: Primary care nurses were not prepared optimally for the COVID-19 pandemic. Challenges included adequate training, infrastructure, the availability of personal protective equipment, COVID-19 testing of health care workers and management support. Primary care nurses need comprehensive support to manage stress and anxiety.

Molecular characterisation and epidemiology of enterovirus-associated aseptic meningitis in the Western and Eastern Cape Provinces, South Africa 2018-2019.

BACKGROUND: Enteroviruses are amongst the most common causes of aseptic meningitis. Between November 2018 and May 2019, an outbreak of enterovirus-associated aseptic meningitis cases was noted in the Western and Eastern Cape Provinces, South Africa. OBJECTIVES: To describe the epidemiology and phylogeography of enterovirus infections during an aseptic meningitis outbreak in the Western and Eastern Cape Provinces of South Africa. METHODS: Cerebrospinal fluid samples from suspected cases were screened using a polymerase chain reaction targeting the 5'UTR. Confirmed enterovirus-associated meningitis samples underwent molecular typing through species-specific VP1/VP2 primers and pan-species VP1 primers. RESULTS: Between November 2018 and May 2019, 3497 suspected cases of aseptic meningitis were documented in the Western and Eastern Cape Provinces. Median age was 8 years (range 0-61), interquartile range (IQR=4-13 years), 405/735 (55%) male. 742/3497 (21%) cases were laboratory - confirmed enterovirus positive by routine diagnostic PCR targeting the 5'UTR. 128/742 (17%) underwent molecular typing by VP1 gene sequencing. Echovirus 4 (E4) was detected in 102/128 (80%) cases. Echovirus 9 was found in 7%, Coxsackievirus A13 in 3%. 10 genotypes contributed to the remaining 10% of cases. Synonymous mutations were found in most cases, with sporadic amino acid changes in 13 (12.7%) cases. CONCLUSION: The aseptic meningitis outbreak was associated with echovirus 4. Stool samples are valuable for molecular typing in CSF confirmed EV-associated aseptic meningitis.

Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa.

Cape Town was the first city in South Africa to experience the full impact of the coronavirus disease 2019 (COVID-19) pandemic. We acquired samples from all suspected cases and their contacts during the first month of the pandemic from Tygerberg Hospital. Nanopore sequencing generated SARS-CoV-2 whole genomes. Phylogenetic inference with maximum likelihood and Bayesian methods were used to determine lineages that seeded the local epidemic. Three patients were known to have travelled internationally and an outbreak was detected in a nearby supermarket. Sequencing of 50 samples produced 46 high-quality genomes. The sequences were classified as lineages: B, B.1, B.1.1.1, B.1.1.161, B.1.1.29, B.1.8, B.39, and B.40. All the sequences from persons under investigation (PUIs) in the supermarket outbreak (lineage B.1.8) fall within a clade from the Netherlands with good support (p > 0.9). In addition, a new mutation, 5209A>G, emerged within the Cape Town cluster. The molecular clock analysis suggests that this occurred around 13 March 2020 (95% confidence interval: 9-17 March). The phylogenetic reconstruction suggests at least nine early introductions of SARS-CoV-2 into Cape Town and an early localized transmission in a shopping environment. Genomic surveillance was successfully used to investigate and track the spread of early introductions of SARS-CoV-2 in Cape Town.

Estimating qualification and factors associated with third-line antiretroviral therapy referral in the Western Cape.

BACKGROUND: South Africa's antiretroviral therapy (ART) programme is the largest globally and the universal test-and-treat policy is expected to increase the numbers on ART. This may have implications for treatment failure rates implying a greater future need for third-line regimens. South Africa initiated a third-line programme in 2013. However, there is little evidence quantifying the third-line need in this setting and the programme itself has not been formally evaluated. OBJECTIVES: The study evaluated the third-line ART referral process in the Western Cape. METHOD: Routinely collected data were analysed to derive an estimate of patients meeting criteria for third-line referral and compared with patients who were referred. Factors associated with referral were identified. RESULTS: In the study period, 947 patients met criteria for third-line referral and 167 patients were referred. Comparison revealed a poor overlap of only 42 patients. In multivariate analysis, factors associated with referral included receiving care at a hospital rather than a primary healthcare facility (adjusted odd ratios [aOR] = 2.15, 95% confidence interval [CI] 1.1-4.2), a higher number of viral load [VLs] ≥ 1000 copies/mL whilst on a protease inhibitor (PI) (aOR = 1.2, 95% CI 1.01-1.42) and a greater number of years on a PI (aOR = 1.25, 95% CI 1.07-1.46). Patients with a 6-month gap in dispensing were less likely to be referred (aOR = 0.37, 95% CI 0.17-0.81). CONCLUSION: This study adds to a limited body of knowledge regarding third-line ART programmes. The findings indicate missed opportunities for and inappropriate referral of patients. Factors associated with referral were largely health system related. Clinician awareness and compliance with referral remain unknown and may be contributory.