Identification of lymphocytic choriomeningitis mammarenavirus in house mouse (Mus musculus, Rodentia) in French Guiana

•We identified a new LCMV strain in Mus musculus in French Guiana.•We characterized its complete genome sequence, the first from South America.•This strain is phylogenetically related to ones inducing severe diseases in humans.•Its identification offers the possibility to investigate its presence in humans.

Thirty-seven house mice (Mus musculus, Rodentia) caught in different localities in French Guiana were screened to investigate the presence of lymphocytic choriomeningitis mammarenavirus (LCMV). Two animals trapped in an urban area were found positive, hosting a new strain of LCMV, that we tentatively named LCMV “Comou”. The complete sequence was determined using a metagenomic approach. Phylogenetic analyses revealed that this strain is related to genetic lineage I composed of strains inducing severe disease in humans. These results emphasize the need for active surveillance in humans as well as in house mouse populations, which is a rather common rodent in French Guianese cities and settlements.