Case Study - Vaal River


Virus Forensic Services: Covid-19 Sewerage Surveillance




Statement of the Project Objectives

Problem Statement

Vaal River Catchment

The Vaal River catchment contains South Africa’s economic heartland, the Pretoria-Witwatersrand-Vereeniging (PWV) complex. Although the catchment only produces eight percent of the mean annual runoff of the country, it has the highest concentration of urban, industrial, mining and power generation development in South Africa (Braune and Rogers, 1987).

Water pollution problems have attracted considerable attention. Notable amongst this is the steady increase of salinity of the Vaal River and eutrophication in dams within the catchment area.

The following are reported in the past studies in the catchment (Braune and Rogers, 1987; DWS, 2009):

  • Increased levels of organic contaminants load from both industrial and agricultural sources

  • Effluents from urban, industrial and mining activities have resulted in an increase total salinity of the Vaal River

  • Irrigation return flow are regarded as a major contributor to the increased levels of salinity

  • Eutrophication on the other hand is a looming threat, and the system is considered to be a high risk from eutrophication

The urban areas are reported to contribute sewage return flows to Vaal River. These return flows also carry significant pollution loads.

Wastewater Treatment Works

Sewage pollution and improper disinfection of treated sewage effluents have in the past been blamed for increased nutrients load in surface water resources in the Vaal River Catchment. The effects of the presence of COVID-19 viruses in wastewater treatment works is currently not understood. Wastewater Treatment works in the Vaal River Catchment are available here.

impact on the receiving water resources, including the presence of coronaviruses.

City of Tshwane Metropolitan Municipality

Wastewater treatment works located within the City of Tshwane Metro are listed in Table 2-3 below. The list provided has been extracted from the unpublished Green Drop report of 2014.

Eleven (11) WWTW’s in the Green Drop report and listed below are reported to be in poor condition and in digress.

In 2018 the DWS took the City of Tshwane Metro to court to stop pollution of water resources emanating from some of the wastewater treatment works. At the time of publishing1 on the 21 December 2018, the following wastewater treatment works were identified as the most polluters: Rooiwal Waste Water Treatment Works, Klipgat Waste Water Treatment Works, Baviaanspoort Waste Water Treatment Works and Sunderland Ridge Waste Water Treatment Works. 

List of Waste Water Treatment Works here

 The majority of the WWTW’s are polluting the water resources within the Tshwane Metro, at this stage, the impact of coronaviruses is not fully understood.

Project Area

A map showing rivers and dams in the Vaal River Catchment provided is provided in figure 2-1 below:

Figure 21: Vaal River Catchment Area

Maps showing the wastewater treatment plants in the catchment are showed in Annexure E.

Purpose of the Project

The purpose of the project is to enable a Virus Risk Forensic Service: COVID-19 sewerage surveillance in the Vaal River System and City of Tshwane Wastewater Treatment Works catchment.

Project Objectives

The following objectives will be achieved during the implementation of the project:

  • Assess the condition of wastewater infrastructure and establish infrastructure needs for the study e.g. accurate flow measurement;

  • Improved flow measurement at all wastewater treatment works mentioned above either through the installation of new equipment or restoring existing equipment to full functionality

  • Installation of automatic samplers capable of composite sampling for a 24hr cycle;

  • Sample preservation consistent with the KWR protocols and transport to a highly specialised water quality laboratory; and

  • Analysis of composite samples received from WWTWs according to the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel for Emergency Use Only, as per KWR recommendations, as the most appropriate and cost-effective international standard readily available.

  • Interpretation of the analysis results to identify trends and sampling strategy.

 The project approach is presented in the next section

     Approach and Scope of Services

    Our overall approach is presented in Figure 2-1 below.

    Figure 22: Overall project approach

    Our project approach is enunciated in the sections below

    Stakeholder’s Engagement and Communication

    The stakeholder’s engagement and communication will be conducted throughout the project implementation. The envisaged stakeholders are listed, but not limited to, the below:

    • Department of Water and Sanitation;
    • National and Provincial Department of Health (DoH);
    • Department of Environment, Forestry and Fisheries;
    • Ekurhuleni Metro Municipality;
    • City of Tshwane Metropolitan Municipality;
    • Respective Local and District Municipalities;
    • Mining and Industries within the Vaal River Catchment and City of Tshwane; and
    • Consulting and contractors currently implementing projects at the WWTW’s.

    Shown in Table 2-4 is a matrix which will be adopted to identify to conduct stakeholders profiling and mapping.

    Condition-performance of existing flow measurement devices

    As part of the sampler installation process, a high-level condition-performance assessment will be completed for the existing WWTW flowmeters, where such meters are installed. This will include, but not be limited to the, assessment of the existing Primary Device and associated open-channel flowmeters, confirmation that the Primary Device is correctly installed and/or correctly manufactured, no downstream obstructions exist and the accompanying flowmeter is set up correctly and measuring accurately.

    Assuming the Primary Device is correct and the flowmeter is programmed correctly and functioning, all such flowmeters will be calibrated every six months including an initial upfront calibration.

    Recommendations, where applicable, will be submitted detailing what requires attention and how to restore the respective WWTW flow measurement(s) to the correct standards. The rectification and completion of these items will be handled within the A-4-A team without the need for additional consultants and / or costly studies.

    Installation of samplers to collect composite samples
    Critical to the success of this project is the installation of reliable and sophisticated automatic bulk sampling machines (‘auto-samplers’). The auto-sampler generates a composite and representative sample over a predetermined period of time, generally 24 hours’ time step. Combined with the accurate flow measurement explained above, the composite sample obtained will fully represent the volume of flow passing by the sampling point.

    This is a key departure from the ‘grab sampling’ approach which only represents a single point in time, the time of the grab sample does not include any important data before or after that single sample.

    The samplers to be deployed are equipped with remote-connectivity, enabling off site maintenance and trouble-shooting, where required, as well as transmitting the sampler data for each day of sampling – number of samples taken, site conditions, error messages and sampler status. This same data can also be transmitted to a central dashboard and / or other reporting system of relevance to the project stakeholders.

    A GPS module is also fitted to the auto-sampler, allowing all stakeholders to track the location and / or movement of the samplers in the field.

    Samples preservation and transportation to the laboratory
    The sample transport protocol has been based on the KWR method and adapted for South African conditions. The pilot study that was conducted was used to develop and test the methodology that will be used. The methodology ensured the samples were kept cool between (2-8 °C) during transport and all necessary steps were taken to deliver the samples as fast as possible to the testing laboratory.

    The resulting transport protocol was demonstrated to retain the forensic integrity of the samples. This same protocol will be used to transport samples from the sampling sites to the testing laboratory.

    The sample preservation and transportation protocol includes the following steps:

    • Bottles were sterilised prior to filling
    • Bottles sealed with tamper-proof closures
    • Sample bottles placed into zip-loc or other appropriate sealable plastic bags
    • Bottles placed into a cooler box with ice packs.
    • Delivery to a courier service for overnight delivery to the laboratory .
    • Sample temperature checked and verified on arrival at laboratory to be less than 8 °C
    • Each sample bottle is barcoded and tracked from time of sample collection on site to lab receipt + results generation to ensure and track the forensic chain of evidence

    The data stored above, from point of sample retrieval to lab testing and final results, is stored online and available for subsequent interrogation and/or spot tests. Each collected sample can only be signed off as complete once all predetermined steps have been completed and verified. The integrity of the chain of forensic evidence is preserved at all times to ensure reliability of the data yield and subsequent decision-making.

    Analysis of composite samples

    Analysis of samples was performed as per KWR protocol (Medema et al., 2020) and CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel for Emergency Use Only. This panel is manufactured in the USA and licensed for IVD use in South Africa by SAHPRA. Briefly, the wastewater sample is clarified, followed by concentration of any viral particles through 10 kDa ultrafiltration. Resultant concentrate is subjected to viral RNA extraction using an approved commercial kit. Process automation is available in case of high demand. RNA quality checked via nanospectrophotometer, followed by amplification of viral RNA using suitable, approved RT-qPCR mastermix. Genes amplified include N1 and N2, with process controls in place. Qualitative and quantitative analysis is automatic via defined algorithms.

    All initial, intermediate and final processing volumes are recorded to effect accurate extrapolation back to the original sample.

    Modeling Sewer Flow

    Sewer models will be interpreted, and results combined with measured flow patterns to understand the sewer flow domain at each sampling point, as well as to perform volumetric calculations for the purpose of performing quantitative trend analysis. The models and flow measurements will also be used to determine optimal upstream sampling strategies.

    GIS Mapping

    Spatial information such as shapefiles for catchment areas, rivers, places and population figures per catchment areas will be obtained from various credible and trustworthy sources. Shapefiles for dams and wastewater treatment works will be created by the project team. GIS will also be used to optimise travel routes for sampling and delivery to the laboratory. 

    Pollution transport within the catchment areas will be simulated and presented in the report through mapping.

    Furthermore, results from the laboratory will also be presented in a form of GIS mapping for visualisation and better presentation. This output may end up being the ‘dashboard’ which may be developed as part of this process, this is would be determine by the Client.

    Statement of describing how the proposal is innovative

    The COVID-19 pandemic is an accelerator of economic distress in South Africa, acting as a fundamental driver of economic decline. Therefore, unless the COVID-19 pandemic is rapidly brought under control, investor confidence will remain low and the prospects of an economic rejuvenation elusive. For this reason A-4-A pioneered the Virus Risk Forensic Service, as an enabler for the restoration of confidence in government, in order that private capital can be brought into play as part of the Public Private Growth Initiative (PPGI) for post-pandemic rejuvenation.

    The A-4-A approach to the COVID-19 pandemic is to recognize all existing initiatives, including the Water Research Commission (WRC) and National Institute of Communicable Diseases (NICD) efforts at improving the science of wastewater surveillance. A-4-A has led the way by closing the gaps in those two initiatives (WRC and NICD) by developing the bulk sampling and logistics value chain feeding into the laboratories. In this regard A-4-A is unique, because no other entity has focussed on the complexity of regular sampling from multiple sites, using sophisticated bulk sampling machines, and then preserving the custodial chain intrinsic to all forensic investigation as those samples are delivered to laboratories, wherever they might be.

    This model recognizes the political risk to government by failing to act decisively, as it waits for the WRC and NICD to provide the next generation science. The A-4-A model accepts that the best available science will be used by rapidly deploying bulk samplers, until such time as the next generation science can be delivered by the NICD and WRC. As improved science becomes available, it will merely be onboarded into the existing logistical networks needed to sustain any national surveillance program. This approach is consistent with the A-4-A objective to unlock the full value of water as an economic enabler, by mitigating the risk faced by the government as it grapples with an existential threat to the very viability of the state as we know it. A-4-A therefore supports the government in a two phased approach.

    Firstly by providing a viable Virus Risk Forensic Service to restore confidence in South Africa as an investment destination. Secondly by applying its blended finance model to assist the state in recapitalising the water sector as a key element of post-pandemic economic rejuvenation. In this regard A-4-A is unique.

    It must be noted that this process is not just about now with COVID-19, but also for future possible outbreaks, mutations of the current disease and sampling for other pathogens as and when required. If the majority of WWTW are brought up to spec, and all the correct equipment installed, this should just become the ‘norm’ of monitoring going forwards. Even the narcotics aspect can eventually be included, to help SAPS clamp-down on drug hotspots.

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