Sequence analysis of nucleoprotein gene reveals the co-circulation of lineages and sublineages of rabies virus in herbivorous in Rio Grande do Sul state, Brazil

An unprecedented outbreak of rabies occurred in Rio Grande do Sul state (RS) from 2012 onward, resulting in thousands of bovine deaths, important economic losses, and posing risk to human health. This article describes a genetic analysis of 145 rabies viruses (RABV) recovered from herbivorous from RS between 2012 and 2017, based on partial sequence analysis of the nucleoprotein (N) gene. High nucleotide ( nt ) identity (95.5 to 100%) and amino acid ( aa ) similarity (96.7 to 100%) were observed among the analyzed sequences. These sequences displayed a high sequence nt identity/ aa similarity with bovine RABV sequences (96.4–97.9%; 98.1–100%, respectively) and vampire bat RABV sequences (96.3–97.5%; 97.8–99.5%). Phylogenetic analyzes based on the N sequence allowed for the segregation of viruses into two distinct clusters . Cluster 1 comprised RABV sequences covering the whole studied period, whereas cluster 2 grouped a lower number of viruses from 2013, 2014, 2015, to 2017. In some cases, viruses obtained from the same region within a short period of time grouped to distinct clusters or sub-clusters, indicating the co-circulation of distinct virus lineages in these outbreaks. The segregation into sub-clusters was also observed for viral sequences obtained from the same region at different times, indicating the involvement of distinct viruses. In summary, partial sequence analyses revealed a high conservation of N protein and the circulation of two lineages and different sublineages of RABV in the region. In addition, our results confirm the suitability of N gene to study the genetic relationships among RABV isolates.