Evolution and divergence of the genetic lineage of Rabies Virus Desmodus rotundus/Artibeus lituratus in São Paulo State

Abstract Since 1998, with the occurrence of the last case of rabies in dogs or cats in São Paulo State related to the dog-specific rabies virus (RABV) lineage, 55 cases of rabies in these animals have been reported until 2021, and the vast majority (51) have been genetically characterized as belonging to the Desmodus rotundus/Artibeus lituratus lineage of RABV, However, it has not been demonstrated so far if there is the possibility to infer which of these bats acted as a source of infection in these cases through the genetic sequencing of isolated RABV. In order to characterize the Desmodus rotundus/Artibeus lituratus lineage aiming at the possibility of differentiating its isolates in RABV associated with each of these reservoirs, this research performed the DNA sequencing technique by amplification on the Illumina Miseq platform in 70 RABV isolates from the State of São Paulo, sent to the virology laboratory of the Pasteur Institute of São Paulo between 2006–2015, being 33 related to the hematophagous bat D. rotundus and 37 to the fruit bat A. lituratus. A genomic approach using phylogenetic and nucleotide identity analyses demonstrated that the isolates investigated in this study can be considered as belonging to the same genetic lineage of RABV and that in São Paulo State the D. rotundus/A. lituratus lineage is subdivided into at least four phylogenetic sub lineages, two associated with D. rotundus and two with A. lituratus, and that these results can be practically applied to the epidemiological surveillance of rabies in this state.