Molecular evolution of the insect-specific flaviviruses

Abstract

There has been an explosion in the discovery of 'insect-specific' flaviviruses and/or their related sequences in natural mosquito populations. Herein we review all 'insect-specific' flavivirus sequences currently available and conduct phylogenetic analyses of both the 'insect-specific' flaviviruses and available sequences of the entire genus Flavivirus. We show that there is no statistical support for virus-mosquito co-divergence, suggesting that the 'insect-specific' flaviviruses may have undergone multiple introductions with frequent host switching. We discuss potential implications for the evolution of vectoring within the family Flaviviridae. We also provide preliminary evidence for potential recombination events in the history of cell fusing agent virus. Finally, we consider priorities and guidelines for future research on 'insect-specific' flaviviruses, including the vast potential that exists for the study of biodiversity within a range of potential hosts and vectors, and its effect on the emergence and maintenance of the flaviviruses.

Fig. 1.

Bayesian phylogenies of (a) the NS5 and (b) the NS3 ‘insect-specific’ focus nucleotide datasets. Only posterior probabilities of ≥0.9 are included. Both trees are midpoint-rooted. Bars, 0.2 substitutions per site.

Fig. 5.

Simple topology used for mosquito species included in co-divergence tests. The two Culex species are sister species, which are sometimes regarded as subspecies of Cx. pipiens. Their sister relationship is not in doubt. Cx. tritaeniorhynchus is placed as sister to the pipiens+quinquefasciatus clade (St John, 2007; Rossi & Harbach, 2008).

Fig. 2.

Bayesian phylogeny of the NS5 ‘global genus’ amino acid dataset. Only posterior probabilities of ≥0.9 are included. The tree is midpoint-rooted. Bar, 0.09 substitutions per site. Red, ‘insect-specific’ flaviviruses; brown, NKV flaviviruses; blue, mosquito-borne flaviviruses; light blue, secondary loss flaviviruses; green, tick-borne flaviviruses.

Fig. 3.

Bayesian phylogeny of the E gene ‘insect-specific’ focus amino acid dataset. Posterior probabilities of ≥0.9 for major nodes only are included for clarity. The tree is midpoint-rooted. Bar, 0.09 substitutions per site.

Fig. 4.

Bayesian phylogeny of the ORF ‘global genus’ amino acid dataset. Only posterior probabilities of ≥0.9 are included. The tree is rooted on GB virus C. Bar, 0.2 substitutions per site. Red, ‘insect-specific’ flaviviruses; brown, NKV flaviviruses; blue, mosquito-borne flaviviruses; light blue, secondary loss flaviviruses; green, tick-borne flaviviruses; purple, TABV.