The National Institute for Communicable Diseases (NICD) takes pride in its pivotal role as the national public health institute tasked with disease surveillance in South Africa. The Wastewater Genomics Syndicate, situated within the Centre for Vaccines and Immunology at NICD, spearheads wastewater and environmental surveillance (WES) for communicable diseases.
Environmental surveillance commenced in 2018 as part of the global effort to eradicate polio. Samples from wastewater treatment plants (WWTP) across the country are tested for polio. In 2020, amidst the challenges posed by the COVID-19 pandemic, the NICD swiftly built on the polio surveillance network to commence WES for SARS-CoV-2. Through meticulous observations and analyses, we demonstrated the efficacy of wastewater analysis as an early detection tool for changes in transmission dynamics and population disease burden. In addition to this, with the incorporation of cutting-edge bioinformatics tools, such as Freyja, it has become possible to identify SARS-CoV-2 variants within wastewater samples. This breakthrough not only reinforces the utility of wastewater surveillance in combating COVID-19 but also provides invaluable insights into population-level disease dynamics and variant circulation. As clinical case numbers decline, wastewater surveillance has become a cornerstone for disease surveillance.
SARS-CoV-2 quantitative and genomic findings from wastewater are a complementary surveillance tool. Interpretation of wastewater data must always be done together with data from clinical surveillance programmes. Wastewater surveillance builds on the findings from the NICD’s Centre for Respiratory Disease and Meningitis weekly surveillance data reports (to be found here). Wastewater has the added advantage of giving sight to disease burden and population transmission without needing to rely on health-seeking by patients or laboratory testing by doctors. Wastewater testing also includes the transmission dynamics of asymptomatic infections. We are pleased to announce the launch of publicly available resources to support monitoring of the virus’s trajectory.
NICD Wastewater Dashboard:
Access real-time data and visualisations tracking SARS-CoV-2 transmission dynamics nationwide in wastewater. The dashboard is built using Plotly Dash, a Python package for building interactive visualisations. It provides a summary of the number of clinical cases of SARS-CoV-2 per epidemiological week reported to the NICD notifiable medical conditions register. Additionally, it incorporates viral loads and sequencing results from the Freyja-outputs repository described below.
NB: The significance of SARS-CoV-2 levels in wastewater should always be interpreted together with clinical SARS-CoV-2 surveillance data, as reported on our weekly wastewater surveillance report page.
NICD-Freyja-outputs Repo:
Explore Freyja analysis outputs for ongoing reporting and research endeavours. This repository serves as a central hub for all Freyja analyses, providing data outputs for regular reports, dashboards, and publications. It includes outputs from the Freyja variants and Freyja demix commands, with SNV variant information, site-specific sequencing depth information, and demixed outputs stored for further analysis and reporting. Automatic Freyja demix re-runs with updated barcodes, exports into formats for reporting, and automatic pushes to corresponding GitHub repositories are also facilitated.
Wastewater Documentation Repo:
Gain comprehensive insights into our methodologies and procedures for wastewater analysis. This page serves as a reference guide, outlining procedures routinely performed in our reporting and publications. Whether you are a researcher, healthcare professional, or policymaker, this guide provides insights into the methodologies employed by the Wastewater Genomics Syndicate.
We are also pleased to share that CVI’s efforts in wastewater surveillance extend beyond COVID-19, with the planned inclusion of other vaccine-preventable diseases such as hepatitis A, hepatitis E, measles, rubella, and influenza A and B onto our surveillance platform throughout the course of the year. This expansion reflects our commitment to comprehensive disease monitoring to support proactive public health interventions based on evidence from clinical and wastewater surveillance.
In conclusion, the NICD remains steadfast in its mission to safeguard public health through innovative surveillance strategies. Our integration of epidemiological and genomic data sets a precedent for future endeavours, fostering a resilient framework for monitoring emerging pathogens and guiding evidence-based interventions.
