Population genetic analyses of Phytophthora cinnamomi reveals three lineages and movement between natural vegetation and avocado orchards in South Africa

Phytophthora cinnamomi is the causal agent of root rot, canker and dieback of thousands of plant species around the globe. This oomycete not only causes severe economic losses to forestry and agricultural industries, but also threatens the health of various plants in natural ecosystems. In this study, 380 isolates of P. cinnamomi from four avocado production areas and two regions of natural vegetation in South Africa were investigated using 15 microsatellite markers. These populations were found to have a low level of genetic diversity and consisted of isolates from three lineages. Shared genotypes were detected between isolates from avocado orchards and natural vegetation, indicating the movement of isolates between these areas. The population from the Western Cape natural vegetation had the highest genotypic diversity and unique alleles, indicating this could be the point of introduction of P. cinnamomi to South Africa. Index of association analysis suggested that five out of six populations were under linkage disequilibrium suggesting a clonal mode of reproduction whereas genotypes sampled from a recently established avocado orchard in the Western Cape were derived from a randomly recombined population. This study provided novel insights on the genetic diversity and spread of P. cinnamomi in South Africa. It also reported on the predominance of triploidy in natural occurring populations and provided evidence for recombination of P. cinnamomi for the first time. The presence of two dominant genotypes in all avocado production areas in South Africa highlight the importance of considering them in disease management and resistance breeding programmes.

Knotted memories of a betrayed sacrifice: Rethinking trauma and hope in South Africa

Different groups within South African society express disillusionment with the present through a discourse of betrayal in relation to the liberation movement-cum-governing-party of the African National Congress. This article focuses on a particular articulation of this discourse within two memory communities in the Western Cape (Bonteheuwel and Crossroads) who were embroiled in violence and political struggle during apartheid and continue to suffer conditions of structural violence in the post-apartheid era. It analyses the shared memory narrative of a ‘betrayed sacrifice’ to demonstrate a proposed theoretical concept of ‘knotted memories’ which describes the way in which past and present memories of suffering knot together to produce a lived affective condition of despair. It further considers what these everyday experiences of ‘knotted memories’ mean for re-thinking the nature of trauma and hope in relation to post-apartheid despair.

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.

Challenges experienced by community health workers and their motivation to attend a self-management programme

Background: Community health workers (CHWs) are change agents expected to assist in decreasing the global burden of disease in the communities they serve. However, they themselves have health risk behaviours, which predispose them to non-communicable diseases and thus need to be empowered to make better health choices. There is a gap in literature detailing the challenges faced by CHWs in addressing their own health risk behaviours.Aim: This study aimed to explore the challenges experienced by CHWs in carrying out their daily duties and the motivating factors to join a self-management programme.Setting: The study was conducted in a low socio-economic urban area of the Western Cape, South Africa.Methods: This study used a qualitative exploratory design using in-depth interviews to obtain rich data about the personal and professional challenges that CHWs experience on a daily basis.Results: Five themes emerged with regard to professional challenges (social conditions, mental health of patients, work environment, patient adherence and communication). This cadre identified ineffective self-management as a personal challenge and two themes emerged as motivation for participating in a self-management programme: empowerment and widening perspective.Conclusion: The challenges raised by the CHWs have a direct impact on their role in communities. This study therefore highlights an urgent need for policymakers and leaders who plan training programmes to take intentional strategic action to address their health challenges and to consider utilising a self-management intervention model to improve their overall health status.

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.

Postharvest Losses in Quantity and Quality of Pear (cv. Packham’s Triumph) along the Supply Chain and Associated Economic, Environmental and Resource Impacts

Approximately one third of the food produced globally is lost or wasted along the supply chain. Reducing this would be an important measure to increase the global food supply as the world continues the struggle to feed its people sustainably. Not merely a waste of food, these losses also represent a waste of human effort and agricultural inputs from expensive fertilizers to natural resources as well as contributing to global greenhouse gas emissions. Measuring the extent of, and understanding the reasons for, these losses can assist in developing appropriate measures required to prevent or reduce such losses. Therefore, the objective of this research was to quantify postharvest losses in quantity and quality of ‘Packham’s Triumph’ pears at farm and simulated retail levels. Pears were sampled from two farms in the Western Cape Province of South Africa, the largest deciduous fruit production and export region in Southern Africa. The greatest losses measured along the supply chain were on-farm immediately after harvest, with 18% recorded. The main reasons for on-farm losses were small size (65%), deformity (26%), and chafed peel (9%). After 14 days in cold storage (−0.3 ± 0.7 °C, 81.3 ± 4.1% RH), mean pear losses were 0.86% which increased to 1.49% after 28 days. After 10 days of further storage under simulated market conditions (5.4 ± 0.6 °C, 83.7 ± 2.9% RH), fruit losses were 1.52% during retail marketing and 2.09% during export. Storing pears under ambient conditions (25.1 ± 1.3 °C and 46.6 ± 6.0% RH) resulted in a higher incidence of losses, increasing from 0.90 to 1.55 and 2.25% after 3, 7, and 10 days, respectively. The socio-economic impacts of these postharvest losses amounted to financial losses of between ZAR 492 million (USD 34.1 million according to the conversion rate of 14 April 2021) to over ZAR 831 million annually, and this was associated with the loss of 301 million MJ of fossil energy, 69 million m3 of fresh water and contributed to the emission of approximately 19,690 tons of CO2 equivalent. The fresh water lost could sustain 3.7 million individuals daily for a whole year at a daily minimum usage rate of 0.05 m3 per day while it will require planting 0.5 million trees to sink the 19,690 tons GHG emissions of the pear losses (0.039 metric ton per urban tree planted). Decreasing postharvest losses will conserve resources as well as improve food security and nutrition, objectives of the post-2015 sustainable development agenda led by the United Nations.