NAU researchers, computers contribute to study of Valley Fever origins

Paul Keim in his lab.

Using the latest in genomic analysis technologies, scientists at the Translational Genomics Research Institute with ties to Northern Arizona University have tracked the likely origins and dispersal of the fungus that causes Valley Fever, according to a study published today in the journal mBio.

In a story that spans 2 million years and includes the effects of glaciation and the pre-historic movements of animal hosts, the study sets the stage for tracking future outbreaks of this potentially deadly dust-bound disease as it spreads across arid regions of North and South America.

Valley Fever is an infection caused by the microscopic fungus Coccidioides, which lives in desert soils and typically enters the body through the lungs. An estimated 150,000 Americans are infected annually by Valley Fever, and as many as 500 die each year.

“The combination of whole genome sequencing and advanced statistical analysis provides for an understanding of the possible ancestry and dispersal pathways of this fungus,” said David Engelthaler, director of Programs and Operations for TGen’s Pathogen Genomics Division—also known as TGen North—and the study’s lead author.

According to NAU Regents’ Professor Paul Keim, director of TGen North and one of the study’s senior authors, “These data and analysis enhance our ability to conduct genomic epidemiology today, and give us a better understanding of the changing distribution of this disease moving forward.”

Keim is also director of NAU’s Center for Microbial Genetics and Genomics, where Engelthaler is an affiliate researcher. Their analysis was supported by the Monsoon high-performance computing cluster at NAU.

Nearly 60 percent of infected people—and other mammals, especially dogs—develop no significant symptoms from exposure to Valley Fever.

However some infected patients develop highly debilitating symptoms, such as cough, fever and fatigue. These symptoms are similar to other respiratory diseases caused by bacteria or virus, and often lead to delayed diagnoses and inappropriate treatment. Very severe Valley Fever can require lifelong treatment with antifungal drugs, and even death.

There are two distinct species of the fungus Coccidioides that cause Valley Fever: C. posadasii, the oldest species, which originated in the Sonoran Desert of southern Arizona and northern Mexico; and C. immitis, which is the species found in California’s Central Valley, as well as parts of southern California and Baja Mexico.

Using the genetic data derived from 86 Coccidioides genomes, the study’s analysis estimates that C. posadasii diverged, forming Arizona and non-Arizona subpopulations, between 820,000 and 2 million years ago.

The Arizona subtype today is found throughout central and southern Arizona. Within Arizona, TGen researchers identified multiple distinct genetic groups originating in the Tucson region, one of which also includes all the Phoenix isolates, where the largest concentrations of Valley Fever occur.

The study’s authors also estimate that the fungus spread to Mexico and Texas as many as 675,000 years ago, to South America about 527,000 years ago, and to Guatemala in Central America less than 190,000 years ago.

The geographic range of the fungus is expanding. New clusters of C. immitis have been identified in eastern Washington state, which likely emerged from California. Valley Fever also is also known to occur in Argentina, Paraguay, Brazil and Honduras.