Incomplete sanitation in the Metropolitan Region of Sao Paulo results in detection of SARS-CoV-2 in headwater streams

Among the largest metropolitan regions in the world, the Metropolitan Region of Sa similar to o Paulo (MRSP) represents an important case study for the COVID-19 respiratory disease pandemic because it is home to >20 million people, making it one of the largest metropolitan regions in the global south. Besides the high population density, the MRSP has several problems related to social and economic aspects, which may reflect in the dynamics of SARS-CoV-2 virus, such as low income, lack of sanitation and social vulnerability in the peripheral regions of MRSP. In these regions, the input of untreated sewage on the streams and rivers can be frequently observed, which may represent an indicator of poor sewer system. Therefore, this study aimed to identify if streams draining urbanized regions without appropriate sanitation are prone to receive higher loads of detectable SARS-CoV-2 in its waters. For this, we collected water samples from 45 headwater streams distributed across an urbanization gradient (0-100 % of urbanization) in the MRSP, with three replicates in each stream and analyzed the concentrations of SARS-CoV-2 RNA targeting the nucleocapsid N1 and N2 genomic regions. In addition, we analyzed the relationship between the concentrations of SARS-CoV-2 RNA and sanitation and social variables. Our results showed that the concentrations of SARS-CoV-2 RNA were higher in the streams draining medium to high urbanizedcatchments, especially because of the lack of sanitation and the higher probabilities to detect SARS-CoV-2 RNA in the stream water was associated with households without a septic tank or sewage system within the catchment, followed by per capita household income. These results reflect the lack of urbanization planning and the lack of sanitation, especially in the poor regions from the MRSP, adding another risk for the already vulnerable population in a metropolitan region from the global south during a pandemic disease.