Expanding access to wastewater surveillance beyond sewered networks: Effectiveness of active and passive sampling of waste effluent streams in Côte d’Ivoire

In response to COVID-19, wastewater surveillance rapidly expanded in high-income sewered settings. However, little is known about sampling in at-risk areas without sewerage infrastructure. We developed a method to test waste effluent streams, including: identifying environmental virus detection and waste effluent locations for testing; determining appropriate sampling methods; and, safely collecting and analyzing samples. In Côte d’Ivoire, we identified waste canals from urban slum areas and liquid waste streams in chicken slaughtering markets as high risk for SARS-CoV-2 and Influenza A Virus (IAV), respectively. For 12 weeks, we sampled once per week for SARS-CoV-2 using active and passive sampling at two canals downstream of urban slum areas containing primarily human wastewater; and IAV using passive sampling at one site containing animal slaughtering wastes (in duplicate). Samples were prepared, extracted, and processed using RT-PCR in Côte d’Ivoire. Of 48 SARS-CoV-2 samples, 22 (13 active, 9 passive) tested positive (Ct values 28.2-35.1). Of 24 IAV passive samples, three (12.5%) tested positive (Ct values 29.3-32.4). We successfully used our methods to identify relevant viral pathogens with diverse host ranges and provide proof-of-concept for sampling priority pathogens in waste effluent streams. Our work provides a pathway to democratize and extend gains of wastewater surveillance to at-risk populations in non-sewered contexts without wastewater infrastructure. Further research is needed to develop waste effluent surveillance in non-sewered settings along the entire chain of understanding high-risk viral pathogens in waste effluent, including: laboratory research to understand pathogen survivability in various media; understanding where in the environment high-risk pathogens might be; determining how to sample and test various waste effluent streams; and, in establishing the collaborative partnerships and training to complete high-quality research and expand these results to additional pathogens.