Phylogeny of the genus Flavivirus using complete coding sequences of arthropod-borne viruses and viruses with no known vector

Attempts to define the evolutionary relationships and origins of viruses in the genus Flavivirus are hampered by the lack of genetic information parti cularly amongst the non-vectored flaviviruses. Using a novel protocol for s equence determination, the first complete coding sequence of St Louis encep halitis virus and those of two representative non-vectored flaviviruses, pi e Brave (isolated from bat) and Apoi (isolated from rodent), are reported, The encoded polyproteins of Rio Brave and Apoi virus are the smallest descr ibed to date within the genus Flavivirus, The highest similarities with oth er flaviviruses were found in the NS3 and NS5 genes. The proteolytic cleava ge sites for the viral serine protease were highly conserved among the flav iviruses completely sequenced to date. Comparative genetic amino acid align ments revealed that p-distance cut-off values of 0.330-0.470 distinguished the arthropod-borne viruses according to their recognized serogroups and Ri o Brave and Apoi virus were assigned to two distinct non-vectored virus gro ups. Within these serogroups, cladogenesis based on the complete ORF sequen ce was similar to trees based on envelope and NS5 sequences. In contrast, b ranching patterns at the deeper nodes of the tree were different from those reported in the previous study of NS5 sequences. The significance of these observations is discussed.