New updated dashboard to support wastewater surveillance for SARS-CoV-2
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 Center 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, incorporation of cutting-edge bioinformatics tools, such as Freyja, it has become possible to identiy of 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 at https://www.nicd.ac.za/diseases-a-z-index/disease-index-covid-19/surveillance-reports/weekly-respiratory-pathogens-surveillance-report-week/). 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 transmission dynamics of asymptomatic infectious.
Access real-time data and visualizations tracking SARS-CoV-2 transmission dynamics nationwide in wastewater. The dashboard is built using Plotly Dash, a Python package for building interactive visualizations. 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 at https://www.nicd.ac.za/diseases-a-z-index/disease-index-covid-19/surveillance-reports/weekly-respiratory-pathogens-surveillance-report-week/