Genomic evidence for co-evolution and sporadic host shifts in leishmaniaviruses

The evolutionary relationships between hosts and their symbionts offer valuable insights into the origins, maintenance, and consequences of biological interactions. While co-divergence and host-switching have been extensively explored in systems, such as Wolbachia –arthropod symbioses or viruses infecting vertebrates, similar investigations in protistan parasites remain scarce. The Leishmania–Leishmaniavirus (LRV) association offers a rare opportunity to study co-divergence in a medically relevant symbiotic system, in which the virus modulates the parasitic disease severity in humans. Here, we used total RNA sequencing to capture both the Leishmania transcriptome and the LRV genome simultaneously, enabling the first comprehensive investigation of the co-evolutionary history of Leishmania and LRV across different hierarchical levels (subgenus, species and population). We found significant positive correlations between the parasite and viral genetic distances at both the subgenus (R ² = 0.89; F = 10,913.49; p < 0.001) and species level (focusing on L. ( Viannia ) spp.; R ² = 0.59; F = 1,254; p < 0.001). This was corroborated by additional co-phylogenetic methods (global-fit and event-based), indicating a strong pattern of phylogenetic congruence between Leishmania and LRV up to the species level. Only at the population level, focusing on the interactions of L. ( V. ) braziliensis and L. ( V. ) guyanensis with LRV1, we found weaker co-phylogenetic signals accompanied by more instances of intraspecific host switching. Overall, our findings provide, for the first time, analytical evidence for the co-evolution between Leishmania and LRV, with co-speciation as the predominant process, while also shedding light on how such symbioses were maintained over larger time scales.