Monitoring SARS-CoV-2 variants in wastewater during periods of low clinical case surveillance in Ethiopia

Abstract

This study highlights the critical role of wastewater monitoring in detecting and tracking severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks, particularly in regions with limited clinical reporting. Using genomic analysis tools like Freyja enables the detection and monitoring of SARS-CoV-2 variants by untangling mixed signals to track viral evolution and mutations. This unbiased method offers a comprehensive assessment of virus prevalence, including asymptomatic cases, making it a key supplement to clinical surveillance. By addressing gaps and biases in testing, the detection of two distinct viral waves in Addis Ababa, including one missed by patient-based surveillance, underscores the effectiveness of this approach. The shifting dominance of Omicron sub-lineages, such as XBB.1.5 and XBB*, and their spike protein mutations provide essential insights into viral evolution and transmission dynamics. The connection between specific mutations and increased viral loads further suggests potential impacts on viral fitness and transmissibility. These results reinforce the need to integrate wastewater surveillance into public health strategies to support clinical surveillance, enable early detection of emerging variants, and support timely interventions. Moreover, wastewater surveillance can be extended to monitor other pathogens and antimicrobial resistance, making it an essential tool for pandemic preparedness and ongoing public health management.