Enteric viruses and SARS-CoV-2 in environmental water in rural communities of Osun State, Nigeria

Abstract

Background: Understanding water pollution risks in rural communities is crucial, especially during the coronavirus disease (COVID-19) pandemic’s trough phase, when concerns about exposure to enteric virus remains heightened. The study investigated environmental water of rural communities in Osun State, Nigeria for presence of certain enteric viruses and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Methods: Using the grab method, water sampling which prioritized potential viral contamination sources was done during the rainy season from April to June 2023. Water samples were concentrated using an aqueous two-phase partitioning system (ATPS). In addition, a positive control (Coxsackievirus B3) was employed to verify the efficiency of the sample treatment. Viral nucleic acid extraction was performed on all viral concentrates using QIAamp Viral RNA Mini Kit (QIAGEN, Germany). The detection of the targeted enteric viruses (norovirus, rotavirus, poliovirus, and hepatitis E virus) and SARS-CoV-2 in viral nucleic acid was done by RT-PCR and RT-qPCR, respectively. Results: On gel electrophoretic analysis of the primer-mediated RT-PCR amplicons, hepatitis E virus (HEV) was detected in 2 (9.09%) of the 22 environmental water samples, the positive control was also detected. No SARS-CoV-2 gene was detected using RT-qPCR (Ct value ≥ 37.4). Conclusions: Detection of HEV RNA in the study water bodies, to the best of our knowledge, appeared to be the first of such documentation. While HEV circulated at a low rate, there was no evidence of circulating SARS-CoV-2 in the study areas.