First Identification and Genomic Characterization of Mammalian Orthoreovirus Type 1 in a Heavily Polluted Stream from an Underserved Urban Settlement in Brazil

Mammalian orthoreovirus (MRV), a member of the family Spinareoviridae within the order Reovirales, has a ten-segmented double-stranded RNA genome and is known for its environmental stability and broad host range, including humans. Although human MRV infections are usually asymptomatic or mild, occasional severe MRV-associated disease has been reported. Despite the widespread presence of MRV, particularly in contaminated water, genomic data from South America are limited, especially from environmental sources in underserved urban settlements. In this study, we isolated a virus from a heavily polluted stream running through an underprivileged, underserved, urban settlement in São Paulo, Brazil. The causative agent was identified as a novel MRV strain (MRV1_SP/BR) by whole-genome Illumina sequencing, and its presence was subsequently confirmed by RT-qPCR. This analysis revealed a complex mosaic genome architecture indicative of genetic reassortment. Based on phylogenetic analysis of the S1 segment, the strain was genetically classified as MRV-1, whereas its remaining segments showed high nucleotide identity to sequences previously detected in humans and bats. These findings provide the first genomic characterization of a reassortant MRV detected in an urban stream in South America and expand the available information on MRV diversity in sewage-impacted aquatic environments.