COVID-19 monitoring in rural communities: First comparison of lagoon and pumping station samples for wastewater-based epidemiology

Abstract

Wastewater-based epidemiology is a topic of significant interest over the last year due to the application of SARS-CoV-2 surveillance to track incidence rates of COVID-19 in communities. Although SARS-CoV-2 surveillance has been applied in more than 50 countries to date, the application of this surveillance has been largely focused on relatively affluent urban and peri-urban communities. As such, there is a lack of knowledge regarding the implementation of reliable wastewater surveillance in small and rural communities for the purpose of tracking rates of incidence of COVID-19 and other pathogens or biomarkers. This study examines the correlations between SARS-CoV-2 RNA signal from wastewater samples harvested from the access port at a lagoon (waste-stabilization pond), a wastewater pumping station and the regional COVID-19 rate of incidence (measured as percent test positivity) in a small, rural community in Ontario, Canada. Real-time quantitative polymerase chain reaction (RT-qPCR) targeting the N1 and N2 genes of SARS-CoV-2 of lagoon samples demonstrate that 80% of 24-hr composite samples collected across a period of 5.5 weeks were below the limit of quantification (5 gene copies/microliter). However, 100% of the 24-hr composite samples collected on the same days from the upstream pumping station were capable of not only yielding strong viral signal but once normalized for PMMoV, also predicted the increase in viral signal approximately 10-14 days prior to an increase in community s COVID-19 reported test percent positivity. RNA concentration and integrity of samples harvested from the lagoon was both lower and more variable than from RNA harvested from the upstream pumping station that were collected on the same date, indicating a higher overall stability of SARS-CoV-2 RNA and hence a stronger viral signal that correlates to community incidence of COVID-19. In sewered small and rural communities operating wastewater lagoons, WBE samples should therefore be harvested from pumping stations or the sewershed as opposed to lagoons.