Divergent Rabies Virus Variant of Probable Bat Origin in 2 Gray Foxes, New Mexico, USA

Abstract

In the Western Hemisphere, bat-associated rabies viruses (RABVs) have established independent transmission cycles in multiple mammal hosts, forming genetically distinct lineages. In New Mexico, USA, skunks, bats, and gray foxes are rabies reservoir hosts and represent a public health risk because of encounters with humans. During 2015 and 2019, two previously undescribed RABVs were detected in 2 gray foxes (Urocyon cinereoargenteus) in Lincoln County, New Mexico. Phylogenetic analysis of the nucleoprotein gene indicated that the isolates are a novel RABV variant. These 2 cases probably represent repeated spillover events from an unknown bat reservoir to gray foxes. Molecular analysis of rabies cases across New Mexico identified that other cross-species transmission events were the result of viral variants previously known to be enzootic to New Mexico. Despite a robust rabies public health surveillance system in the United States, advances in testing and surveillance techniques continue to identify previously unrecognized zoonotic pathogens.

Keywords: New Mexico; United States; bat origin; bats; divergent virus variant; gray foxes; lyssavirus; phylogenetic analysis; rabies; rabies virus; spillover; viruses; zoonoses.

Figure 1

Phylogenetic tree based on partial nucleoprotein gene (348 bp) sequences and geographic distribution of rabies virus (RABV) variants, New Mexico, USA. The tree was constructed by using representative isolates and only posterior values leading to the RABV variants are included on the tree nodes. Three major clades were identified in New Mexico. The RABV variants are displayed in distinct colors in the tree and map according to the legend included in the figure. Blue indicates novel RABV isolates collected from gray fox in Lincoln County. Accuracy of the location in the map is at city level; for samples that did not have city information, the location was randomly assigned within the county. Numbers along branches are bootstrap values. Scale bar indicates nucleotide substitutions per site.

Figure 2

Maximum clade credibility tree using full nucleoprotein gene sequences of RABV variants identified in New Mexico, USA, and representative sequences from RABV variants in the Western Hemisphere. Values in the nodes indicate estimates for the posterior clade probability for each RABV variants. Branch in blue indicates novel RABV variant that includes the 2 isolates from Lincoln County, and branch in green indicates RABV associated with Nyctinomops macrotis bats. Scale bar indicates nucleotide substitutions per site. RABV, rabies virus.