Genome sequencing identifies “Limestone Canyon virus” as Montaño virus (Hantaviridae: Orthohantavirus montanoense) circulating in brush deermice in New Mexico

Orthohantaviruses infect distinct eulipotyphlan and rodent reservoirs throughout the world; some rodent orthohantaviruses can cause disease in humans. In the United States, a primary rodent reservoir for the human-pathogenic Sin Nombre virus (SNV) is the western deermouse (Peromyscus sonoriensis; formerly included in Peromyscus maniculatus). Deermice (rodents of genus Peromyscus) carry presumably distinct orthohantaviruses but, although deermice of ten species have been recorded in New Mexico, only SNV has been reported in rodents from that state. Using a set of pan-orthohantavirus primers, we discovered a non-SNV orthohantavirus in a brush deermouse (P. boylii), trapped in central New Mexico in 2019. Sequencing enabled the generation of a consensus coding-complete genome sequence, revealing similarity to the known partial sequences of the unclassified “Limestone Canyon virus (LSCV)” in GenBank and aligning with the information in an unpublished study of wild-caught brush deermice trapped in southwestern New Mexico in 2006. Phylogenetic analysis of these combined data revealed geospatial clades and overall identity of “LSCV”, uncovering its association with the classified Montaño virus (MTNV), which is known to infect Aztec and Orizaba deermice in central Mexico. Our work emphasizes the importance of determining coding-complete viral genome sequences as a framework for rigorous virus classification as the basis for epidemiological studies.