This study uses wastewater-based epidemiology (WBE) to rapidly and, through targeted surveillance, track the geographical distribution of SARS-CoV-2 variants of concern (Alpha, Beta and Delta) within 24 wastewater treatment plants (WWTPs) in the Western Cape of South Africa. Information obtained was used to identify the circulating variant of concern (VOC) within a population and retrospectively trace when the predominant variant was introduced. Genotyping analysis of SARS-CoV-2 showed that 50% of wastewater samples harbored signature mutations linked to the Beta variant before the third wave, with the Delta variant absent within the population. Over time, the prevalence of the beta variant decreased steadily. The onset of the third wave resulted in the Delta variant becoming the predominant variant, with a 100% prevalence supporting the theory that the Delta variant was driving the third wave. In silico molecular docking analysis showed that the signature mutations of the Delta variant increased binding to host proteins, suggesting a possible molecular mechanism that increased viral infectivity of the Delta variant.

Recent scientific trends have revealed that the collection and analysis of data on the occurrence and fate of SARS-CoV-2 in wastewater may serve as an early warning system for COVID-19. In South Africa, the first COVID-19 epicenter emerged in the Western Cape Province. The City of Cape Town, located in the Western Cape Province, has approximately 4 million inhabitants. This study reports on the monitoring of SARS-CoV-2 RNA in the wastewater of the City of Cape Town’s wastewater treatment plants (WWTPs) during the peak of the epidemic. During this period, the highest overall median viral RNA signal was observed in week 1 (9200 RNA copies/mL) and declined to 127 copies/mL in week 6. The overall decrease in the amount of detected viral SARS-CoV-2 RNA over the 6-week study period was associated with a declining number of newly identified COVID-19 cases in the city. The SARS-CoV-2 early warning system has now been established to detect future waves of COVID-19.

This study was one of the first to detect Omicron sublineages BA.4 and BA.5 in wastewater from South Africa. Spearman rank correlation analysis confirmed a strong positive correlation exists between SARS-CoV-2 viral RNA in wastewater samples and clinical cases (r = 0.7749, p < 0.0001). SARS-CoV-2 viral load detected in wastewater, resulting from the Delta-driven 3rd wave, was significantly higher than during the Omicron-driven 4th wave, p < 0.005. Whole-genome sequencing confirmed the presence of Omicron lineage defining mutations in wastewater with the first occurrence reported on 23 November 2021 (BA.1 predominant). The variant rapidly spread, with the prevalence of Omicron positive wastewater samples rising to >80% by 10 January 2022 with BA.2 as the predominant sub-lineage by 10 March 2022, whilst on 18 April 2022 BA.4 and BA.5 were detected in selected wastewater sites. Taken together, these findings demonstrate the value of WBE to monitor the spatiotemporal spread and potential origination of new Omicron sub-lineages of SARS-CoV-2.

Background: South Africa is characterised by high levels of biodiversity and species endemism alongside critical levels of socio-economic vulnerability, demonstrating potential for conservation practices that provide both environmental and social benefits. It is argued that communitybased conservation (CBC) practices can be strategically positioned to achieve environmental conservation objectives as well as promote local-level socio-economic development. The KwaZulu-Natal Sandstone Sourveld (KZNSS) vegetation type is classified as endemic (to KZN, South Africa), and is at present listed as endangered. Additionally, one of the KZNSS grassland patches occurs adjacent to the low-income peri-urban community of iNanda. The study examined local community uses and perceptions of the vegetation type. Objectives: To examine the uses, perceptions and attitudes displayed by the iNanda community towards the KZNSS grassland patch. Furthermore, it is hoped that the results of this study can be utilised to inform the potential use of CBC strategies within socio-economic contexts such as iNanda. Method: A mixed methodological approach was adopted, focusing on iNanda as the case study. One hundred households were purposively interviewed. Descriptive and chi-square statistical tests were carried out to examine main data trends. Results: Respondents displayed alarming levels of unemployment (61%) and 34% relied on state grants as a source of household income. Households used the grassland for subsistence (51%), grazing (14%), recreational (13%) and cultural purposes (12%). Respondents displayed limited awareness of conservation and the ecological importance of the grassland. However, respondents recognised the need to conserve the grassland based on their perception of changes to the adjacent patch. Conclusion: Potential grassland conservation plans should consider the current use displayed by respondents. Participatory approaches to conservation such as CBC initiatives could provide much-needed socio-economic and conservation benefits.

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