Wastewater-based Surveillance for SARS-CoV-2 in rural northern South Africa: Implementation and Observations from 2021 – 2022

Globally, wastewater-based epidemiology (WBE) is employed to assess the distribution and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19. This study reports SARS-CoV-2 trends, circulating variants of concern (VOCs), and predicted prevalence of infections in the rural Vhembe and Mopani districts, in northern South Africa between January 2021 and June 2022, using WBE. Weekly, a grab sample of wastewater influent was collected from seven wastewater treatment plants and one waste sedimentation pond and analyzed for viral genetic material. The trends showed three periods of increased detection of SARS-CoV-2 viral RNA in wastewater which corresponded to the third and fourth waves during the COVID-19 pandemic in South Africa. From the wastewater surveillance reported herein, VOCs detected in the study sites were Delta (in January 2021) and Omicron (in February 2021). These detections from wastewater were earlier than what had been reported from clinical surveillance in South Africa and in other parts of the world. Therefore, WBE has the potential to serve as an early warning system for rural parts of South Africa, and in similar settings as well. Consequently, making possible nation-wide surveillance systems for pathogens capable of causing widespread epidemics. The absence of municipal sewerage systems is common in African communities. Thus, studies to strengthen pandemic preparedness measures, as well as improvement in wastewater treatment infrastructure in the study communities, are also needed. Finally, wastewater-based surveillance as part of long-term strategy is relevant for early detection of novel SARS-CoV-2 variants.