Lymphocytic choriomeningitis virus (LCMV) is a neglected rodent-borne zoonotic virus primarily infecting house mice. The virus can be highly pathogenic, particularly in immunocompromised individuals and in congenital infections. LCMV is distributed worldwide but shows local clustering, probably due to the highly structured populations of its hosts and the vertical transmission of the pathogen. These factors should also promote long-term virus persistence in wild populations, yet this aspect remains largely unexplored. To investigate this, we resampled a transect in the western Czech Republic that was primarily studied more than a decade ago. Additionally, we analyzed a sample collection from Buškovice, a locality where LCMV was first detected in 2008, to trace virus presence back to the year 2000. Positive samples underwent whole-genome characterization to assess the virus’s genetic structure over space and time. We detected intermittent presence over 24 years in a geographically limited area, where LCMV was already present in 2000 and remained detectable in 2023. Phylogenetic analysis showed no clear spatio-temporal clustering, suggesting that virus persistence in Buškovice is a dynamic process involving mouse dispersal between neighboring villages. Given LCMV’s zoonotic potential and house mouse synanthropy, these findings highlight the need for continuous monitoring in the region.

Parasites are expected to hybridise in similar ways to free living organisms, although this may be modified by their reduced genome architecture. Recombinant strains and taxa of hybrid origin can be studied in nature where hosts come into secondary contact. Here we apply genome-wide analysis to parasites from a contact previously characterised for many individuals using classical markers. The host contact is the European house mouse hybrid zone; the parasites are lung fungus Pneumocystis and gut pinworm Syphacia. The multilocus and multi-individual datasets are broadly consistent in scale and centering. Whole mitogenome comparisons confirm earlier suggestions that parasite divergence is low compared to their hosts, perhaps due to reduced genome stabilising selection. In the recombining genome we are able to show blocks of parasite genome of alternating host origin, including one Pneumocystis strain which appears to be an F3+ cross and one recombinant Syphacia strain found over multiple localities. Functional analyses of introgressing genes show enrichment for genes likely important for parasitic lifestyle.