Genomic evidence for phylogenetic congruence with sporadic host shifts in leishmaniaviruses and their parasite hosts

The association between Leishmania parasites and the double-stranded RNA virus, Leishmaniavirus (LRV), significantly impacts human health by modulating disease severity. Despite its clinical importance, the evolutionary history of this symbiosis remains largely unknown. This study presents one of the first formal investigations of their co-phylogenetic history across different taxonomic hierarchical levels; based on total RNA sequencing of cultivated isolates, simultaneously capturing the parasite`s transcriptome and the viral genome. We found strong support for phylogenetic congruence between Leishmania and LRV at both the subgenus and species level; based on genetic distance correlations and formal co-phylogenetic statistics. Focusing on the interactions of L. (V.) braziliensis and L. (V.) guyanensis with LRV1, we observed weaker co-phylogenetic signals though frequent instances of intraspecific host switching. Together, our findings indicate that LRV has been a persistent evolutionary partner of Leishmania, providing a framework for understanding the emergence and maintenance of virus-mediated disease phenotypes.