Discovery of a novel lymphocytic choriomeningitis virus strain associated with severe human disease in immunocompetent patient, New Mexico

Lymphocytic choriomeningitis virus (LCMV) is an underreported emerging pathogen and was recently included as a National Institute of Allergy and Infectious Disease (NIAID) priority pathogen. LCMV is an important cause of aseptic meningitis and has high morbidity and mortality during congenital and organ-transplant transmission. The house mouse, <i>Mus musculus</i>, is a reservoir for LCMV, and human infection occurs through exposure to aerosolized virus from the mouse excreta. In 2023, an immunocompetent patient in Albuquerque, New Mexico (NM), became infected with LCMV and experienced severe disease, representing a unique disease presentation as LCMV rarely causes disease in immunocompetent individuals. We trapped 20 <i>Mus musculus</i> in the patient's home and tested for LCMV prevalence using PCR and ELISA. We found that 17/20 mice had LCMV RNA in their livers, while 3/20 had detectable anti-LCMV antibodies. We sequenced the complete coding region of the LCMV genome, revealing a novel strain, LCMV-ABQ. This represents the first documented LCMV strain from New Mexico. The S segment nucleotide sequence of LCMV-ABQ was 87.28% homologous to the closest related LCMV (strain 201102714), and the L segment was 82.03% homologous to strain Traub. Phylogenetic analysis revealed that LCMV-ABQ falls into lineage I. We surveyed 69 additional <i>Mus musculus</i> across four distinct sites in New Mexico, none of which were PCR-positive for LCMV. Thus, the patient's home represents a hot spot for LCMV prevalence in New Mexico. This work informs the distribution and genetics of LCMV, which is increasingly recognized as an emerging pathogen of public health concern.