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The genus Flavivirus (family Flaviviridae) presently comprises around 70 single-strand positive-sense RNA viruses. These replicate in a range of vertebrate and invertebrate cells and may be mosquito-borne, tick-borne or have no-known-vector. Since transmission mode correlates strongly with phylogeny, the flaviviruses constitute a valuable model for the evolution of vector-borne disease. Attempts to resolve the higher-level taxonomic relationships of the flaviviruses through molecular phylogenetics have thus far proved inconclusive because of conflicting positions for the three main transmission groups. We conducted the most comprehensive phylogenetic study to date, involving maximum likelihood analyses of the NS3 and NS5 genes and the entire genome sequences available at present. For the first time, we use and test a variety of more robust methods of sequence alignment and appropriate models of amino acid replacement to study these highly divergent sequences, and explicitly test specific hypotheses of tree topology. We show that (i) the NS5 gene contains insufficient phylogenetic signal to choose between competing topological hypotheses, (ii) the NS3 gene and whole genome data indicate that the mosquito-borne flaviviruses represent an outgroup to the remaining flaviviruses, and (iii) that tick-borne transmission is probably a derived trait within the genus.

A multigene analysis of the phylogenetic relationships among the flaviviruses (Family: Flaviviridae) and the evolution of vector transmission