Was Coccidioides a Pre-Columbian Hitchhiker to Southcentral Washington?

Abstract

Coccidioides immitis, a pathogenic environmental fungus that causes Valley fever (coccidioidomycosis) primarily in the American Southwest and parts of Central and South America, has emerged over the past 12 years in the Columbia River Basin region, near the confluence with the Yakima River, in southcentral Washington state, USA. An initial autochthonous Washington human case was found in 2010, stemming from a wound derived from soil contamination during an all-terrain vehicle crash. Subsequent analysis identified multiple positive soil samples from the park where the crash occurred (near the Columbia River in Kennewick, WA), and from another riverside location several kilometers upstream from the park location. Intensified disease surveillance identified several more cases of coccidioidomycosis in the region that lacked any relevant travel history to known endemic locales. Genomic analysis of both patient and soil isolates from the Washington cases determined that all samples from the region are phylogenetically closely related. Given the genomic and the epidemiological link between case and environment, C. immitis was declared to be a newly endemic fungus in the region, spawning many questions as to the scope of its presence, the causes of its recent emergence, and what it predicts about the changing landscape of this disease. Here, we review this discovery through a paleo-epidemiological lens in the context of what is known about C. immitis biology and pathogenesis and propose a novel hypothesis for the cause of the emergence in southcentral Washington. We also try to place it in the context of our evolving understanding of this regionally specific pathogenic fungus.

Keywords: Coccidioides; genomics; paleo-epidemiology.

FIG 1

Maximum parsimony whole genome phylogenies of (A) Coccidioides immitis and (B) C. immitis strains from South Central WA. SNP distances are represented on numbered line. Adapted from Oltean et al. 2019 (6) and Monroy-Nieto et al. 2023 (9).

FIG 2

Coccidioides spp. soil habitat suitability in United States, including outbreak locations outside the classic endemic zone. Stars represent locales of archeological outbreak sites in California (CA) and Utah (UT), and locales of positive soils in southcentral Washington (WA). Lightly shaded area represents classic endemic zone. Adapted from Dobos et al. 2021 (15).