Flaviviruses have been known due their complex biological cycle and their relevance in public health and global economy. The ecologic aspected and
clinic pictures are related with phylogeny and evolution of flaviviruses. This work aims the molecular characterization of Bussuquara (BSQV), Iguape (IGUV),
Ilheus (VILH) e Rocio (VROC) flaviviruses genomes, determining their phylogenetic relationships with others members of genus Flavivirus. The study
included: the full-length sequencing of the four Brazilian flaviviruses; analyzes of the predictive secondary structure of RNA and conserved sequences in the 3’NCR; determination of cleavage and glicosilation sites, cisteine residues and conserved motifs in the polyprotein; and similarity and phylogenetic analyzes. The BSQV, IGUV, VILH and VROC genomes present 10815 nt, 10922 nt, 10775 nt, and 10794 nt, respectively. The conserved standard sequences in 3’NCR of BSQV was RCS2-CS2-CS1, while to IGUV, ILHV and ROCV were CS3-RCS2-CS2-CS1. The secondary structure of RNA obtained for the
Brazilian flaviviruses were similar to the other flaviviruses. The numbers of the glicosilation sites to PrM, E and NS1 proteins were distinct among the studied Brazilian flaviviruses, therefore the pattern 6,12,12 Cis residues and the cleavage sites were conserved. In the E protein, some singles mutations were observed in fusion peptide of BSQV, IGUV and ROCV, and the RGD motif were distinct for the flaviviruses under study. The motif that determines the MTase-SAM activity in NS5, as well as the helicase and protease activity in NS3 were conserved. Among the eight polimerase motifs in NS5, only the V, VI and VII
motifs were observed single mutations in ILHV and ROCV. The similarity analyzes showed that BSQV presents high relationship with VIGU, while ILHV
and ROV were more related among themselves, however those viruses were considerated distincts species. Based in the phylogenetic analyzes, molecular
and biological characteristics, it was proposed the establishment of three distinct genetic groups: the Rocio group, grouping ILHV and ROCV, Bussuquara group formed by BSQV and Naranjal virus; and Aroa group, that include Aroa virus and IGUV.
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