Neighbour joining phylogenetic tree of nucleotide sequences of selected Flavivirus isolates and reference sequences. The sequences of the isolates under study (highlighted in yellow) were compared to other Flaviviruses from database [GenBank: HM147822.1, GenBank: JF834580.1, GenBank: GQ165810.1, GenBank: FJ644291.1, GenBank: AY149905.1, GenBank: JQ068102.1, GenBank: HM582101.1, GenBank: JX898869.1, GenBank: AY632545.2, GenBank: JX236040.1]. The NSP5 coding regions of the sequences and of selected Flaviviruses under study were aligned using clustalW and the phylogenetic tree constructed using MEGA v5.05. Numbers on internal branches indicate bootstrap values for 1000 replicates. The Flaviviruses have originated from a common ancestor. The West Nile viruses isolates under study have all clustered together while the Ntaya virus is an outgroup. The insect flaviviruses seems to have recently emerged as compared to other Flaviviruses and they have formed a clade except Chaoyang virus which has fallen to a different clade. Usutu virus is related to West Nile, Dengue and Yellow Fever viruses. GSA: Garissa; KSM: Kisumu; RAB: Rabai; S: site; CYV: Chaoyang virus; QBV: Quang Bihn virus; CFA: Cell fusing agent; WN: West Nile.