Phylogeography of rabies virus transmitted by the hematophagous bat Desmodus rotundus in the state of São Paulo, Brazil.

Rabies is a zoonosis primarily transmitted through bites from infected animals. The rabies virus (RABV) remains a significant public health concern in some countries and causes substantial economic losses in livestock farming. In Brazil, around 45,000 cattle die annually due to rabies, resulting in an estimated economic impact of up to 15 million dollars. Phylogeographic analysis is a valuable tool for tracking viral dispersion over time and space and is commonly used to monitor RABV's molecular epidemiology. This study aimed to characterize the dispersion of RABV isolated from cattle infected by hematophagous bats Desmodus rotundus in São Paulo state. Seventy-nine RABV samples collected between 2018 and 2020 were genetically characterized, focusing on the nucleoprotein gene, followed by sequencing and phylogenetic reconstruction. The analysis revealed four distinct lineages of RABV circulating among cattle in São Paulo. Phylogeographic inference traced the time to the most recent common ancestor (TMRCA) for two clades: SP Endemic (Clade 01) emerged around 1977, likely introduced from Minas Gerais, while Pan-American (Clade 03) dates to 1972, originating from viruses already circulating in São Paulo. Pan-American persisted for years and spread to Goiás, Tocantins, and Rio de Janeiro. These findings indicate that multiple RABV lineages co-circulate in São Paulo, with Campinas identified as a key initial hotspot for viral dissemination within the state.