Persistence, spillover, and evolution of co-occurring lineages of lymphocytic choriomeningitis virus

Lymphocytic choriomeningitis virus (LCMV) is a neglected zoonotic arenavirus primarily transmitted by house mice (<i>Mus musculus</i>). In humans, LCMV infection can cause encephalitis, meningitis, or severe birth defects. In New World (NW) primates, LCMV causes acute and fatal callitrichid hepatitis (CH). We detected a continuous occurrence of LCMV lineages I and II in the house mouse population of a zoo, with the first occurrence of lineage II in 2014 and lineage I in 2021. Although the total LCMV RNA prevalence tended to increase between 2021 and 2023, this was primarily associated with lineage I, while the occurrence of lineage II tended to decrease. Despite both lineages I and II being present in house mice in the same building where NW primates are housed, only lineage II was detected in NW primates with CH, and a wild wood mouse (<i>Apodemus sylvaticus</i>). Genomic assignment detected exclusively <i>M.m. domesticus</i> ancestry in the house mouse population of the zoo, in keeping with a natural origin of house mice from the study region. Therefore, the origin of lineage I is most likely explained by the occurrence of this house mouse subspecies. The origin and incursion mode of lineage II still remain elusive. The detection of three or four LCMV genome segments in several house mice was interpreted as LCMV co-infections, and the emergence of a reassortant virus containing an S-segment of lineage II and an L-segment of lineage I. Full genome sequences showed limited diversity of the 2014 LCMV sequences from NW primates, consistent with a recent introduction of lineage II. LCMV sequences from 2021 to 2023 diverged, not only from those from 2014 but also from each other, which suggests long-term evolution in a large host population and/or potential repeated introductions of LCMV lineage II. In conclusion, the presence of two LCMV lineages within the house mouse population of the zoological garden not only poses a potential health threat for employees and visitors of the zoological garden, and potentially other zoo animals, but also provides a unique opportunity to advance our understanding of arenavirus evolution.