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.

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.

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.

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.

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.

Household Air Pollution and Respiratory Symptoms a Month Before and During the Stringent COVID-19 Lockdown Levels 5 and 4 in South Africa.

Background: Household air pollution (HAP) is associated with adverse human health impacts. During COVID-19 Lockdown Levels 5 and 4 (the most stringent levels), South Africans remained at home, potentially increasing their exposure to HAP. Objectives: To investigate changes in fuel use behaviours/patterns of use affecting HAP exposure and associated HAP-related respiratory health outcomes during COVID-19 Lockdown Levels 5 and 4. Methods: This was a cross-sectional online and telephonic survey of participants from an existing database. Logistic regression and McNemar's test were used to analyse household-level data. Results: Among 2 505 participants, while electricity was the main energy source for cooking and heating the month before and during Lockdown Levels 5 and 4, some households used less electricity during Lockdown Levels 5 and 4 or switched to "dirty fuels." One third of participants reported presence of environmental tobacco smoke in the home, a source of HAP associated with respiratory illnesses. Prevalence of HAP-related respiratory health outcomes were <10% (except dry cough). Majority of households reported cooking more, cleaning more and spending more time indoors during Lockdown Levels 5 and 4 - potentially exposed to HAP. Conclusion: Should South Africa return to Lockdown Levels 5 or 4, awareness raising about the risks associated with HAP as well as messaging information for prevention of exposure to HAP, including environmental tobacco smoke, and associated adverse health impacts will be necessary.

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.

Cohort profile: A Prospective Household cohort study of Influenza, Respiratory syncytial virus and other respiratory pathogens community burden and Transmission dynamics in South Africa, 2016-2018.

PURPOSE: The PHIRST study (Prospective Household cohort study of Influenza, Respiratory Syncytial virus, and other respiratory pathogens community burden and Transmission dynamics in South Africa) aimed to estimate the community burden of influenza and respiratory syncytial virus (RSV) including the incidence of infection, symptomatic fraction, and to assess household transmission. PARTICIPANTS: We enrolled 1684 individuals in 327 randomly selected households in a rural and an urban site over three consecutive influenza and two RSV seasons. A new cohort of households was enrolled each year. Participants were sampled with nasopharyngeal swabs twice-weekly during the RSV and influenza seasons of the year of enrolment. Serology samples were collected at enrolment and before and after the influenza season annually. FINDINGS TO DATE: There were 122 113 potential individual follow-up visits over the 3 years, and participants were interviewed for 105 783 (87%) of these. Out of 105 683 nasopharyngeal swabs, 1258 (1%) and 1026 (1%) tested positive on polymerase chain reaction (PCR) for influenza viruses and RSV, respectively. Over one third of individuals had PCR-confirmed influenza each year. Overall, there was influenza transmission to 10% of household contacts of an index case. FUTURE PLANS: Future planned analyses include analysis of influenza serology results and RSV burden and transmission. Households enrolled in the PHIRST study during 2016-2018 were eligible for inclusion in a study of SARS-CoV-2 transmission initiated in July 2020. This study uses similar testing frequency to assess the community burden of SARS-CoV-2 infection and the role of asymptomatic infection in virus transmission.

COVID-19 and a temporary ban on tobacco sales in South Africa: impact on smoking cessation.

OBJECTIVE: To evaluate the impact of COVID-19 plus a temporary ban on the sale of tobacco and vaping products, on smoking cessation in South Africa, by reviewing research surveys conducted while the prohibition was in place. METHOD: An internet search was conducted on 20 August 2020, using the key words: 'South Africa', 'survey', 'poll', 'smoking', 'cigarettes', 'tobacco", 'vaping', and 'COVID-19'. There were no language restrictions. Additional studies were identified through press reports. Only studies conducted between March and August 2020 were included. RESULTS: Four surveys which reported on smokers quitting behaviour were included. None had been published in a peer reviewed journal. The heterogeneity of the data did not allow pooling. Support for the ban on tobacco sales amongst smokers varied from 6% to 36%. Similarly, there were inconsistent findings about quitting behaviour. Nationally, between 16% to 49% of smokers reported not smoking during the ban. CONCLUSIONS: Cigarette smoking in SA dropped during the 2020 COVID-19 lockdown, but the estimates were inconsistent, probably because of survey design. There was evidence that the lockdown achieved the fastest rate of decline in smoking prevalence in the country's history. The true extent of the fall though is uncertain. Prevalence studies post lockdown, using probability sampling, may more accurately show how many people quit smoking.

Wastewater surveillance for Covid-19: An African perspective.

The COVID-19 pandemic has once again highlighted the importance of access to sufficient quantities of safe water and sanitation in public health. In the current COVID-19 pandemic, an early warning wastewater system has been proposed as a platform for SARS-CoV-2 surveillance, and a potentially important public health strategy to combat the disease. This short communication on wastewater surveillance in sub-Saharan Africa highlights challenges, opportunities and alternatives taken into account the local context.

COVID-19 Statement: The unanticipated costs of COVID-19 to South Africa's quadruple disease burden

As of early Jul 2020, the full force of COVID-19 has yet to strike in South Africa, though it has already impacted the economy further and disrupted the healthcare system. While much has been said about the former, with few exceptions, little has been discussed about the disruption to routine, essential healthcare services. The pandemic brings threats previously unknown and has reordered priorities for health. Hospitals have reprogrammed care units to accommodate COVID-19 patients, while others have temporarily closed. To date, government leadership has done a remarkable job of trying to limit the spread of SARS-CoV-2 infection by promoting the most effective prevention toolkit currently available--social-behavioral measures such as social distancing, handwashing and ensuring that transportation and workplaces apply safety protocols. Here, Ataguba et al discuss the challenges in addressing South Africa's quadruple disease.