Flaviviruses (Flaviviridae) are primarily arthropod-borne, positive-sense RNA viruses causing significant human and animal diseases (e.g., dengue, yellow fever, Zika, West Nile). Their evolutionary history is substantially deeper and more complex than previously recognised, with flaviviruses now identified in diverse taxa including cnidarians, cephalopods, and crustaceans. Our research, integrating virus discovery, genomic analysis of endogenous viral elements, and virological characterisation, has fundamentally recalibrated this timeline. Recent collaborative phylogenomic analyses establish flavivirus origins at >100 million years ago (Mya), with sea spider and arachnid-associated flaviviruses basal to tick-borne, and subsequently mosquito-borne lineages, directly linking their emergence to the evolution of blood-feeding in acarids.
To more robustly test this "out of arachnids" hypothesis for vector-borne flaviviruses (VBFs), we conducted a comprehensive analysis of 10,230 Chelicerata transcriptomes from the NCBI SRA database, performing de novo assembly and viral screening. We identified five novel flaviviruses in spiders and horseshoe crabs that form a distinct clade basal to tick-borne flaviviruses. Phylogenetic analysis demonstrated terrestrial chelicerate-associated flaviviruses are ancestral to the tick-only lineages, firmly anchoring VBF origins to the evolution of blood-feeding in acarids.
This evolutionary transition is further exemplified by our discovery of Xinyang flavivirus (XiFV), identified in Haemaphysalis flava ticks in China. XiFV defines a basal, likely tick-only Flavivirus clade representing a crucial intermediate between arachnid-specific viruses and vertebrate-infecting flaviviruses. By generating recombinant XiFV chimera virus particles and in silico structural analyses, we identified distinctive adaptations to arthropod hosts, including the absence of a furin cleavage site in the prM protein and a nucleotide composition similar to insect-only flaviviruses, which may explain its host restriction.
These discoveries reveal a dynamic evolutionary history shaped by host switching and structural adaptation across diverse ecological niches. The Flavivirus 100-million-year journey from aquatic chelicerates, to terrestrial spiders and ticks, to mosquito and tick-vectored human pathogens reveals fundamental principles of viral emergence that will help predict and counter future pandemic threats.