Wastewater-based SARS-CoV-2 airport surveillance: key trends at the Cape Town International Airport.

Monitoring of SARS-CoV-2 RNA in wastewater has revealed the role of mobility in the transmission of coronavirus disease (COVID-19), and the surveillance of airport wastewater in cities across the world has demonstrated how travel entry points can give an indication of trends in transmission. This study undertook wastewater surveillance at the Cape Town International Airport (CTIA) to assess the use of a WBE approach to provide supplementary information on the presence of COVID-19 at a key air travel entry point in South Africa. Grab wastewater samples (n = 55) were collected from the CTIA wastewater pump station and analysed using quantitative real-time polymerase chain reaction (qRT-PCR) method. The study found a correlation between the wastewater data and clinical cases reported in the City of Cape Town during various time periods and during the peak of a COVID-19 wave. Highly elevated viral loads in the wastewater were observed at times there was increased mobility through the airport. The study also revealed elevated viral load levels at the airport despite the stricter restrictions and through the lower restrictions. The study findings indicate wastewater surveillance and airports can provide supplementary information to airport authorities to assess the impacts of imposed travel restrictions.

Delineating the Spread and Prevalence of SARS-CoV-2 Omicron Sublineages (BA.1-BA.5) and Deltacron Using Wastewater in the Western Cape, South Africa.

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 between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA in wastewater samples and clinical cases (r = 0.7749, P < .0001). SARS-CoV-2 viral load detected in wastewater, resulting from the Delta-driven third wave, was significantly higher than during the Omicron-driven fourth wave. Whole-genome sequencing confirmed presence of Omicron lineage defining mutations in wastewater with the first occurrence reported 23 November 2021 (BA.1 predominant). The variant spread rapidly, with prevalence of Omicron-positive wastewater samples rising to >80% by 10 January 2022 with BA.2 as the predominant sublineage by 10 March 2022, whilst on 18 April 2022 BA.4 and BA.5 were detected in selected wastewater sites. These findings demonstrate the value of wastewater-based epidemiology to monitor the spatiotemporal spread and potential origin of new Omicron sublineages.

Using Wastewater Surveillance to Compare COVID-19 Outbreaks during the Easter Holidays over a 2-Year Period in Cape Town, South Africa.

Wastewater surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown to be an important approach to determine early outbreaks of infections. Wastewater-based epidemiology (WBE) is regarded as a complementary tool for monitoring SARS-CoV-2 trends in communities. In this study, the changes in the SARS-CoV-2 RNA levels in wastewater during Easter holidays in 2021 and 2022 in the City of Cape Town were monitored over nine weeks. Our findings showed a statistically significant difference in the SARS-CoV-2 RNA viral load between the study weeks over the Easter period in 2021 and 2022, except for study week 1 and 4. During the Easter week, 52% of the wastewater treatment plants moved from the lower (low viral RNA) category in 2021 to the higher (medium to very high viral RNA) categories in 2022. As a result, the median SARS-CoV-2 viral loads where higher during the Easter week in 2022 than Easter week in 2021 (p = 0.0052). Mixed-effects model showed an association between the SARS-CoV-2 RNA viral loads and Easter week over the Easter period in 2021 only (p < 0.01). The study highlights the potential of WBE to track outbreaks during the holiday period.

Heavy Metal Contamination of Soil in Preschool Facilities around Industrial Operations, Kuils River, Cape Town (South Africa).

The contamination of soil by heavy metals is a potential health risk, especially among susceptible populations. The aim of this study was to measure the levels of heavy metals, identify the contamination levels and possible sources of heavy metals, and evaluate the health risk caused by heavy metals to the children living in Kuils River. Composite samples of soil were collected at 34 preschools. A portable X-ray fluorescence spectrometer was used to measure the levels of metals. Contamination levels were evaluated using a geoaccumulation index (Igeo), enrichment factor (EF), contamination factor (CF) and pollution load index (PLI). The spatial distribution of the Igeo contamination levels was assessed using ArcGIS. Sources of heavy metals and the correlation among metals were assessed using factor analysis and Pearson correlation, respectively. The measured concentrations of metals were used to estimate the health risk for children. The average levels of the metals were 16, 4469, 137, 30, 176, 1547 and 232 mg/kg for arsenic (As), iron (Fe), manganese (Mn), lead (Pb), strontium (Sr), titanium (Ti) and zinc (Zn), respectively. According to Igeo, EF, CF and PLI contamination exist in the study area. The health index (HI) for non-carcinogenic effects showed the ingestion route as the main contributor to the total risk, with the accumulative carcinogenic risk exceeding the maximum acceptable level. To protect the affected communities, and children in particular, this study provides evidence of the need for action, including the institution of mandatory buffer zones between pollutant-generating activities and human settlements.

Sewage surveillance of SARS-CoV-2 at student campus residences in the Western Cape, South Africa.

The current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic capacity is limited in defined communities, posing a challenge in tracking and tracing new infections. Monitoring student residences, which are considered infection hotspots, with targeted wastewater surveillance is crucial. This study evaluated the efficacy of SARS-CoV-2 targeted wastewater surveillance for outbreak mitigation at Stellenbosch University's student residences in South Africa. Using torpedo-style passive sampling devices, wastewater samples were collected biweekly from manholes at twelve Stellenbosch University Tygerberg (SUT) campus and Stellenbosch University-Main (SUM) campus student residences. The surveillance led to an early warning detection of SARS-CoV-2 presence on campus, followed by an informed management strategy leading to restriction of student activities on campus and a delay in the onset of the third wave that was experienced throughout the country. Moreover, the study highlighted the extent of possible infections at defined locations even when a low number of confirmed coronavirus disease 2019 (COVID-19) cases were reported. The study also tracked the surge of the Delta and Omicron variants in the student residences using the Thermo Fisher TaqMan® RT-qPCR genotyping assay.

Tracking the circulating SARS-CoV-2 variant of concern in South Africa using wastewater-based epidemiology.

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.

Spatial and Temporal Trends of SARS-CoV-2 RNA from Wastewater Treatment Plants over 6 Weeks in Cape Town, South Africa.

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.

Household Fuel Use for Heating and Cooking and Respiratory Health in a Low-Income, South African Coastal Community.

In low-income communities, non-electric fuel sources are typically the main cause of Household Air Pollution (HAP). In Umlazi, a South African coastal, informal settlement, households use electric- and non-electric (coal, wood, gas, paraffin) energy sources for cooking and heating. The study aimed to determine whether respiratory ill health status varied by fuel type use. Using a questionnaire, respondents reported on a range of socio-demographic characteristics, dwelling type, energy use for cooking and heating as well as respiratory health symptoms. Multivariate Poisson regression was used to obtain the adjusted Odds Ratios (ORs) for the effects of electric and non-electric energy sources on prevalence of respiratory infections considering potential confounding factors. Among the 245 households that participated, Upper Respiratory Tract Infections (URTI, n = 27) were prevalent in respondents who used non-electric sources compared to electric sources for heating and cooking. There were statistically significant effects of non-electric sources for heating (adjusted OR = 3.6, 95% CI (confidence interval): 1.2⁻10.1, p < 0.05) and cooking (adjusted OR = 2.9, 95% CI: 1.1⁻7.9, p < 0.05) on prevalence of URTIs. There was a statistically significant effect of electric sources for heating (adjusted OR = 2.7, 95% CI: 1.1⁻6.4, p < 0.05) on prevalence of Lower Respiratory Tract Infections (LRTIs) but no evidence for relations between non-electric sources for heating and LRTIs, and electric or non-electric fuel use type for cooking and LRTIs. Energy switching, mixing or stacking could be common in these households that likely made use of multiple energy sources during a typical month depending on access to and availability of electricity, funds to pay for the energy source as well as other socio-economic or cultural factors. The importance of behaviour and social determinants of health in relation to HAP is emphasized.