Genetic lineage characterization and spatiotemporal dynamics of classical insect-specific flaviviruses: outcomes and limitations

HIGHLIGHTS

• Complete and partial cISF sequences were characterized using multiple analyses.

• cISF sequences show low diversity and entropy, and evolve under purifying selection.

• Recombination does not seem to impact the evolution of cISF extensively.

• Different datasets displayed high phylogenetic, but mostly low temporal signals.

• Spatiotemporal dispersal analyses suggested cISF distribution is recent and dynamic.

ABSTRACT

The genus Flavivirus incorporates bona fide arboviruses, as well as others viruses with restricted replication in insect cells. Among the latter, a large monophyletic cluster of viruses, known as cISF (classical insect-specific flaviviruses), has been sampled in many species of mosquitoes collected over a large geographic range.

In this study, we investigated nucleotide and protein sequences with a suite of molecular characterization approaches including genetic distance, Shannon entropy, selective pressure analysis, polymorphism identification, principal coordinate analysis, likelihood mapping, phylodynamic reconstruction, and spatiotemporal dispersal, to further characterize this diverse group of insect-viruses. The different lineages and sub-lineages of viral sequences presented low sequence diversity and entropy (though some displayed lineage-specific polymorphisms), did not show evidence of frequent recombination and evolved under strong purifying selection. Moreover, the reconstruction of the evolutionary history and spatiotemporal dispersal was highly impacted by overall low signals of sequence divergence throughout time but suggested that cISF distribution in space and time is dynamic and may be dependent on human activities, including commercial trading and traveling.

KEYWORDS

Flavivirus; Insect-specific viruses; Genetic diversity; Phylogenetic analysis; Phylogeography; Phylodynamics; BEAST.