A study reveals the evolutionary history of the Flaviviridae family through the mapping of glycoprotein structures. The Flaviviridae is a large family of enveloped positive-sense RNA viruses, including pathogens such as dengue, Zika, and hepatitis C viruses. The study combines phylogenetic analysis with protein structure prediction to survey glycoproteins across the entire family. It identifies class II fusion systems in most species, including highly divergent jingmenviruses and large genome flaviviruses. However, the E1E2 glycoproteins of hepaciviruses, pegiviruses, and pestiviruses are structurally distinct and may represent a novel class of fusion mechanism, strictly associated with infection of vertebrate hosts. Mapping glycoprotein distribution onto the phylogeny reveals a complex evolutionary history marked by the capture of bacterial genes and potential inter-genus recombination. The study also identifies that glycoproteins follow ecological niches, with E1E2 strictly correlated with vertebrate hosts. The findings suggest that the gain of E1E2 and the loss of E and MTase represent a molecular commitment to the vertebrate niche. The study highlights the importance of glycoproteins in determining host range, tissue tropism, and pathogenesis. The research provides insights into the evolutionary history of the Flaviviridae family, revealing the events that have shaped its diverse virology and ecology. The study also identifies novel proteins in large genome flaviviruses and suggests that these proteins may have been acquired through horizontal gene transfer. The findings have implications for understanding viral evolution and the development of interventions such as vaccines.A study reveals the evolutionary history of the Flaviviridae family through the mapping of glycoprotein structures. The Flaviviridae is a large family of enveloped positive-sense RNA viruses, including pathogens such as dengue, Zika, and hepatitis C viruses. The study combines phylogenetic analysis with protein structure prediction to survey glycoproteins across the entire family. It identifies class II fusion systems in most species, including highly divergent jingmenviruses and large genome flaviviruses. However, the E1E2 glycoproteins of hepaciviruses, pegiviruses, and pestiviruses are structurally distinct and may represent a novel class of fusion mechanism, strictly associated with infection of vertebrate hosts. Mapping glycoprotein distribution onto the phylogeny reveals a complex evolutionary history marked by the capture of bacterial genes and potential inter-genus recombination. The study also identifies that glycoproteins follow ecological niches, with E1E2 strictly correlated with vertebrate hosts. The findings suggest that the gain of E1E2 and the loss of E and MTase represent a molecular commitment to the vertebrate niche. The study highlights the importance of glycoproteins in determining host range, tissue tropism, and pathogenesis. The research provides insights into the evolutionary history of the Flaviviridae family, revealing the events that have shaped its diverse virology and ecology. The study also identifies novel proteins in large genome flaviviruses and suggests that these proteins may have been acquired through horizontal gene transfer. The findings have implications for understanding viral evolution and the development of interventions such as vaccines.