Monitoring SARS-CoV-2 in wastewater in Kisumu, Kenya: Association with COVID-19 case numbers

While wastewater-based surveillance (WBS) has proven to be effective as an early warning system for SARS-CoV-2 monitoring in high-income countries (HICs), its feasibility in low- and middle-income countries (LMICs) is challenging due to limited sewer infrastructure, particularly outside major cities. This study evaluated SARS-CoV-2 in community-based wastewater sampling locations in addition to centralized wastewater treatment plants in Kisumu, Kenya from March 29, 2022, to March 8, 2023. The results of wastewater analysis were evaluated in relation to documented COVID-19 case counts. Wastewater samples (n = 161) were collected from centralized wastewater treatment sites (n = 41) and from decentralized sites: hospitals (n = 50), public toilets in markets (n = 31), and public toilets at transportation hubs (n = 39). Twenty-three samples (14.3%) tested positive for SARS-CoV-2 RNA. Epidemiological data were obtained from official sources. The odds of detecting one or more COVID-19 cases within 4–7 days after a positive WBS sample were 9 times higher than on days with negative WBS samples. Rates of viral RNA detection were similar for centralized and decentralized sampling sites. On five of the 32 days (15.6%) on which both centralized and decentralize samples were tested, SARS CoV-2 was detected only in the samples from decentralized sites. Centralized WBS can be supplemented with public toilet monitoring to increase the sensitivity of COVID-19 surveillance in areas with limited sewer infrastructure to enhance early detection of new cases.