Characterizing environmental surveillance sites in Nigeria and their sensitivity to detect poliovirus and other enteroviruses

Background Environmental surveillance (ES) for poliovirus is increasingly important for polio eradication, often detecting circulating virus before paralytic cases are reported. The sensitivity of ES depends on appropriate selection of sampling sites, which is difficult in low-income countries with informal sewage networks. Methods We measured ES site and sample characteristics in Nigeria during June 2018 - May 2019, including sewage physicochemical properties using a water-quality probe, flow volume, catchment population and local facilities such as hospitals, schools and transit hubs. We used mixed-effects logistic regression and machine-learning (random forests) to investigate their association with enterovirus isolation (poliovirus and non-polio enteroviruses) as an indicator of surveillance sensitivity. Results Four quarterly visits were made to 78 ES sites in 21 states of Nigeria, and ES site characteristic data matched to 1,345 samples with an average enterovirus prevalence among sites of 68% (range 9% to 100%). A larger estimated catchment population, high total dissolved solids and higher pH were associated with enterovirus detection. A random forests model predicted ‘good’ sites (enterovirus prevalence >70%) from measured site characteristics with out-of-sample sensitivity and specificity of 75%. Conclusions Simple measurement of sewage properties and catchment population estimation could improve ES site selection and increase surveillance sensitivity