Klaps, J. | Search bioRxiv

bioRxiv2025

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

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.

evolutionary biology↗

bioRxiv2025

nf-core/viralmetagenome: A Novel Pipeline for Untargeted Viral Genome Reconstruction

MotivationEukaryotic viruses present significant challenges for genome reconstruction and variant analysis due to their extensive diversity and potential genome segmentation. While de novo assembly followed by reference database matching and scaffolding is a commonly used approach, the manual execution of this workflow is extremely time-consuming, particularly due to the extensive reference curation required. Here, we address the critical need for an automated, scalable pipeline that can efficiently handle viral metagenomic analysis without manual intervention. ResultsWe present nf-core/viralmetagenome, a comprehensive viral metagenomic pipeline for untargeted genome reconstruction and variant analysis of eukaryotic DNA and RNA viruses. Viral-metagenome is implemented as a Nextflow workflow that processes short-read metagenomic samples to automatically detect and assemble viral genomes, while also performing variant analysis. The pipeline features automated reference selection, consensus quality control metrics, comprehensive documentation, and seamless integration with containerization technologies, including Docker and Singularity. We demonstrate the utility and accuracy of our approach through validation on both simulated and real datasets, showing robust performance across diverse viral families in metage-nomic samples. Availabilitynf-core/viralmetagenome is freely available at https://github.com/nf-core/viralmetagenome with comprehensive documentation at https://nf-co.re/viralmetagenome Contactjoon.klaps@kuleuven.be Supplementary informationSupplementary data are available at https://github.com/Joon-Klaps/nf-core-viralmetagenome-manuscript online.

bioinformatics↗