We characterised hantaviruses circulating in different
Akodon rodent species collected in midwestern Santa Catarina (SC), southern Brazil, where the Jabora hantavirus (JABV) strain was first identified in
Akodon montensis
. Genetic and phylogenetic analyses based on a partial S segment indicated that, in SC,
Akodon paranaensis
and
A. montensis carried the same type of hantavirus. Additionally, we conducted the first genomic characterisation of the complete S segment from the Brazilian JABV strain. This is the first report of
A. paranaensis infected with the JABV.