The flaviviruses can be divided into 2 clades: one with the vector borne viruses and the other with no known vector.[25] The vector clade in turn can be subdivided into a mosquito borne clade and a tick borne clade. These groups can be divided again.[26]
The mosquito group can be divided into two branches: one branch contains the neurotropic viruses, often associated with encephalitic disease in humans or livestock. This branch tends to be spread by Culex species and to have bird reservoirs. The second branch is the non-neurotropic viruses which are associated with haemorrhagic disease in humans. These tend to have Aedes species as vectors and primate hosts.
The tick-borne viruses also form two distinct groups: one is associated with seabirds and the other - the tick-borne encephalitis complex viruses - is associated primarily with rodents.
The viruses that lack a known vector can be divided into three groups: one closely related to the mosquito-borne viruses which is associated with bats; a second, genetically more distant, is also associated with bats; and a third group is associated with rodents.
It seems likely that tick transmission may have been derived from a mosquito borne group.[27]
A partial genome of a flavivirus has been found in the sea spider Endeis spinosa.[28] The sequences are related to those in the insect specific flaviviruses. It is not presently clear how this sequence fits into the evolution of this group of viruses.