Wastewater-Based Surveillance of Sars-Cov-2 and Description of Variants of Concern in Northern South Africa: Observations from 2021 – 2022

Globally, wastewater-based epidemiology (WBE) has been utilized to assess and manage the COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study reports SARS-CoV-2 trends, circulating variants of concern (VOCs), and predicted prevalence of infections in Vhembe and Mopani districts, in Limpopo Province of South Africa between January 2021 and June 2022 using WBE. Grab sampling was employed in weekly collection of wastewater influents from seven wastewater treatment plants and one waste sedimentation pond. This WBE served as an early warning prior to increased infections reported at the district level prior to the third and fourth waves. Towards the end of the surveillance period, increased SARS-CoV-2 viral load detected were not reflected in the reported clinical cases. This could be explained by decreased disease severity of the dominantly circulating Omicron variant, especially with increased vaccine uptake, leading to fewer reported clinical cases. Delta and Omicron VOCs were detected in the study sites by 03 May 2021, earlier than what has been reported by other studies, emphasizing the necessity for community surveillance. Comparing the reported number of cases per district to the predicted prevalence revealed more cases in the Vhembe district compared to the Mopani district. The latter could be attributed to predominant utilization of non-sewered sanitation systems, thus missing important shedding events of infected inhabitants. WBE application for SARS-CoV-2 surveillance and VOC monitoring have been reported from more urbanized regions in South Africa; we show the usefulness of surveillance in a rural setting. This is relevant for genomic surveillance, since early detection of variants can contribute to vaccine development efforts to potentially mitigate the detrimental impact of disease. Challenges of poorly managed or non-existent sewerage systems are predominant worldwide; more studies from rural areas, like the one reported here are needed to strengthen pandemic preparedness measures.