Danger in the dirt

A fungus that lurks in desert soil makes thousands of Americans sick every year with a condition known as Valley Fever. Thanks to climate change, it’s spreading north.

Jesse Abair wasn’t all that alarmed when he started to feel oddly tired in the summer of 2019.

He had moved to Arizona the year before, and was still adjusting to the desert heat, which regularly hits 40 C. After playing competitive soccer for more than a decade, Abair considered himself a healthy 27-year-old. Yet his extreme fatigue kept getting worse.

“It was almost like what you imagine feeling like if you hadn’t eaten in several days,” he said.

One night in August, Abair let out a deep-chested cough — and hacked up blood.

His mind began flitting between grim possibilities. Were his symptoms linked to having asthma as a child? Or to his vaping habit? Could it be lung cancer? When he went to a local hospital to get answers, doctors promptly put him in an isolation room and raised yet another possibility: tuberculosis.

The real culprit was something far stranger.

What’s scary for me when I think about it is how subtly this came on.

At some point after moving from nearby Colorado to the drier climate of Arizona, Abair had inhaled a fungus that lurks in the desert soil. On dry, windy days, spores of coccidioides — or “cocci,” as scientists call it — can float through the air and find their way into human lungs. From there, they multiply, spread and cause chaos, leading to an infection known as Valley Fever.

Many people never know they’ve caught it, but for others it causes symptoms ranging from a cough to exhaustion to dangerous swelling around the brain. In rarer cases, when the fungus spreads throughout the body, it can take up residence for months, years, even indefinitely. Treatments can also last a lifetime, restraining the threat without curing the patient.

“What’s scary for me when I think about it is how subtly this came on,” Abair said, “and how serious it can get.”

What Abair experienced is not just a freak fungal infection, but a pernicious pathogen that is adapting to our changing climate. It’s now venturing further north, putting millions more people at risk, and is poised to become a bigger health issue in the decades ahead, alongside a slate of other evolving fungal threats. Most are becoming adept at dodging our best drug treatments — and there’s no vaccine to protect against any of them.

They’re also getting tougher to avoid.

“We all have to breathe,” said Dr. Andrej Spec, who leads a consortium of researchers tackling fungal infections at Washington University. “And there is no getting away from mold spores.”

Fungi exist everywhere. Scientists estimate there are roughly five million species — outnumbering plants at least six to one — and they thrive in soil, on tree bark, in the water and in places as far-flung as the International Space Station. Mold, mycologists know well, can grow just about anywhere. Even inside the human body.

Late last year, the World Health Organization (WHO) released a sweeping report on the top global fungal threats, noting many are also becoming increasingly resistant to the few drugs that exist to combat fungal infections. The challenge, scientists say, is that humans and fungi are so genetically similar that treatments capable of killing these pathogens can also kill their hosts.

“Despite the growing concern,” the WHO report notes, “fungal infections receive very little attention and resources.”

Listed among the WHO’s roundup of priority pathogens, coccidioides is considered one of the most virulent fungal invaders on the planet, given its capacity for wreaking havoc inside its human hosts. It can infect anyone, but it often hits people with compromised immune systems the hardest — causing severe disease that kills roughly one in 10 people. And like many other species, it begins by lurking underground.

Cocci is known for living in the soil in its mycelial phase, as a network of fungal threads that absorb nutrients from the environment. People who disturb the dry desert soil — whether it’s workers digging in the dirt or ATV riders kicking up dust — are more vulnerable to catching it.

The fungus has sparked outbreaks during military training sessions, armadillo hunting expeditions, construction work and model airplane competitions, and sickened more than 100 archeology students in California who inhaled cocci while excavating Indigenous ruins back in the 1970s.

Though invisible to the naked eye, its spores are potent and hardy. Dr. Isaac Bogoch, a clinician-scientist with the University Health Network in Toronto, recalled treating one elderly, immunocompromised Valley Fever patient in Boston who became “extraordinarily ill” after rifling through old boxes in an attic — they were previously stored in the southwestern U.S. — and unknowingly breathing in cocci hiding among the dust particles.

In 2019, 20,000 infections were reported across the United States, mainly in the longtime hotbeds of California and Arizona, and there are around 200 annual deaths. But the U.S. Centers for Disease Control says that’s likely an undercount, with tens of thousands more infections left untested or misdiagnosed.

The numbers officials do have suggest rates of infection are rising dramatically, while the fungus keeps appearing in new areas.

California’s annual incidence of reported infections, for example, increased nearly fivefold between 2001 and 2021, jumping from a rate of around four cases per 100,000 to more than 20. The number of new cases reported in 2019 was also the highest in a single year since reporting began in the mid-1990s, notes a report released last year by the state government.

Patients have also popped up in Nebraska, Oregon and Colorado, said Dr. George Thompson, a professor of clinical medicine at the University of California, Davis, who specializes in the care of patients with invasive fungal infections. The fungus was even spotted a decade ago in the soil of Washington state, unsettlingly close to British Columbia.

WATCH | A scientist at Northern Arizona University on looking for cocci in soil:

Scientists suspect multiple factors may be fuelling the rise of Valley Fever, ranging from booming population growth to a larger number of vulnerable older and immuno-compromised individuals to spores hitching a ride on jet streams. What unites all those theories: the impact of our changing climate.

A headline-making study published in the journal GeoHealth in 2019 used climate projections to model the range of Valley Fever in the decades ahead. It found rising temperatures and shifting rainfall patterns could allow the fungus to keep spreading north, all the way to the Canadian border, before the end of the century.

“Generally, the disease is limited to areas that are hot and dry,” wrote the research team, led by Morgan Gorris of the University of California, Irvine. “Climate change will cause the western United States to become hotter and may change the location, timing and amount of rain.”

By 2100, the team’s model predicts that the area affected by Valley Fever will more than double, and the number of people who become sick will increase by 50 per cent.

Snapshot of 2007: Valley Fever cases are mainly in southern California, Nevada, Arizona, New Mexico and western Texas, as well as in areas of Oregon and Washington state.

Projection for 2035: Valley Fever cases spread to Utah, Colorado and Kansas, as well as Idaho.

Projection for 2065: Valley Fever cases spread to Wyoming, Montana, Nebraska and South Dakota.

Projection for 2095: Valley Fever cases intensify in existing states and spread to North Dakota, showing up in areas close to the Canadian border.

What’s concerning, scientists warn, is that while the climate shifts and cocci spreads, the medical field might not keep up, at a time when fungal infections are already tough to track and even tougher to treat.

Marieke Ramsey, a research associate at Northern Arizona University, said there’s not enough awareness or surveillance even in many parts of the United States, which leaves many Valley Fever patients in the dark about what’s causing their illness. Symptoms — which range from flu-like to more severe — can also mimic a host of other conditions.

“If people are unaware that this is happening and it’s not being monitored, individuals who don’t live in the defined endemic region, like Canada, when they go to the doctors or to the hospital with these symptoms, those clinicians and doctors might not know what they’re treating,” Ramsey said.

Research backs up those concerns. One American study showed patients often struggle to get a diagnosis, typically waiting around five weeks from the time they first seek medical care. Seven in 10 of them receive another diagnosis, before ever getting tested for cocci.

In Canada, there is no national surveillance of coccidioidomycosis, though cases typically imported through travel are diagnosed and monitored by provincial labs, the Public Health Agency of Canada told CBC News in a statement. Patients, however, still slip through the cracks.

WATCH | Northern Arizona University researcher explains what the fungus looks like in human lungs:

Last year, Vivek Patel, a 30-year-old metallurgist from Brampton, Ont., went through a months-long ordeal trying to figure out what was causing the crippling headaches and severe weakness he developed after visiting Phoenix, Ariz., for a job interview.

He spent a week in the city, going on day trips with his wife to visit the sweeping red rock formations of Sedona and the iconic Grand Canyon. After he came back home, Patel bounced between doctors in Toronto and faced a battery of tests, from blood work to a CT scan to a spinal tap, but nothing led to an official diagnosis.

It wasn’t until Patel landed the job, and officially moved to Arizona that September, that he finally got an answer. During an eye check-up in Tucson, an ophthalmologist noticed Patel’s optic nerve, which connects the eyes to the brain, was squished into an oval shape because of pressure inside his head. Patel spent one night in an emergency room, and later collapsed at work.

Finally, his Arizona medical team raised the possibility of Valley Fever, which he learned had caused both meningitis, the potentially deadly swelling of the brain and spinal cord’s protective membranes, and hydrocephalus, a build-up of fluid in cavities deep within the brain itself.

“It wasn’t until the doctors started showing me the MRIs and CT scans that I realized, this is extremely serious,” Patel said.

He is still taking medication to keep his symptoms at bay, and brain scans taken earlier this year showed both his headaches and general weakness were improving — though not totally gone — thanks to his treatment.

“It’s an anti-fungal,” he said, “but it doesn’t kill the fungus.”

How humans can get Valley Fever

Spores enter the lungs.

Spherule

Each spore inflates like a beach ball filled with Ping-Pong balls.

Once the large spheres rupture, the smaller balls are released.

Endospores

The cycle repeats, over and over again, aggravating the lungs and leading to fatigue, fever and other flu-like symptoms.

(CBC)

How humans can get Valley Fever

Spores enter the lungs.

Spherule

The cycle repeats, over and over again, aggravating the lungs and leading to fatigue, fever and other flu-like symptoms.

Each spore inflates like a beach ball filled with Ping-Pong balls.

Endospores

Once the large spheres rupture, the smaller balls are released.

(CBC)

How humans can get Valley Fever

Spores enter the lungs.

Spherule

The cycle repeats, over and over again, aggravating the lungs and leading to fatigue, fever and other flu-like symptoms.

Each spore inflates like a beach ball filled with Ping-Pong balls.

Endospores

Once the large spheres rupture, the smaller balls are released.

(CBC)

How humans can get Valley Fever

Spores enter the lungs.

Spherule

The cycle repeats, over and over again, aggravating the lungs and leading to fatigue, fever and other flu-like symptoms.

Each spore inflates like a beach ball filled with Ping-Pong balls.

Endospores

Once the large spheres rupture, the smaller balls are released.

(CBC)

The insidious nature of this fungal infection, which slowly, stealthily invades various bodily systems, is a major source of concern for researchers.

Usually, the human body’s high internal temperature of 37 C keeps hazardous fungal organisms at bay, thwarting their ability to thrive and spread. It’s the reason most run-of-the-mill yeast infections or toenail fungi don’t explode into full-body diseases. But again, thanks to global warming, that’s all changing.

“As you increase temperatures in the environment, you sort of pre-adapt these infectious diseases to be able to tolerate higher and higher temperatures,” said longtime Valley Fever researcher Bridget Barker, speaking to CBC News inside her lab at Northern Arizona University in Flagstaff, Ariz.

The lab is where Barker’s team analyzes soil samples to better understand a fungus that, when seen on a petri dish, looks like harmless white fuzz.

But when it’s breathed in, it has a higher rate of infection in otherwise perfectly healthy people compared to other types of fungal disease, Barker said.

Cocci gets this uncanny ability from its dual personalities. It’s classified as a dimorphic fungus, meaning it can exist in two forms — as both a mold and a yeast, depending on the temperature of its surroundings.

Once spores become airborne — lifted, perhaps, by a gust of wind into someone’s lungs — they form large spherules that spew out dozens of smaller endospores, which turn into more spherules, allowing the fungus to proliferate within the warm confines of the human body.

Barker likens it to what it would look like if you inflated a beach ball filled with Ping-Pong balls, and let them loose, over and over again.

“If you’re lucky, it will stay in the lung environment,” she said. “Once it moves beyond the lungs, then you’re in for a very rocky ride.”

In the early stages of infection, Valley Fever symptoms such as fever, coughing or night sweats can mimic other types of respiratory disease like influenza or tuberculosis. Then, as spores disseminate through the body, spreading into other organs, people can take a turn for the worse.

Dr. Fariba Donovan, a physician working at the Valley Fever Center for Excellence at Arizona University in Tucson, said a preventative approach is crucial, given the limited treatment options for patients suffering from the disease. Some people respond well to anti-fungal medications, but others face a host of new side effects, from vomiting to kidney issues to decreased libido.

And when infections have spread through the body, Donovan said it can be an endless battle.

“Treatment for life means several pills a day, every day, for life,” she said.

One of Donovan’s patients, Tucson resident Renee Benoit, has been living with the effects of Valley Fever for more than a decade. While living on a ranch in California in 2011, she rode horses regularly and would often come back inside the house covered in dust. That year, she started having lower back pain and fatigue, and was hospitalized after her symptoms kept getting worse. She ended up losing 16 pounds in 16 days.

“Valley Fever will mess with you,” Benoit said. “But you don’t want to mess with it.”

A daily anti-fungal regime now keeps the symptoms at bay, but one of the medications she tried gave her debilitating joint pain. Benoit also wants to make it clear: she’s not cured. The fungus is still living in her lungs. And if her immune system ever falters — because of another infection, like COVID-19, or if she needs chemotherapy or an organ transplant — she knows the cocci could come roaring back.

“I probably won’t ever be cured, unless something can change in the research field,” she said.

With millions more at risk, scientists are in a race against time to find better ways to prevent Valley Fever infections. Both Barker and Donovan’s universities are striving to develop vaccines that could protect against cocci infection, with the Valley Fever Center for Excellence currently testing an option for dogs, who can also die from inhaling spores released from below ground.

But Spec at Washington University worries anyone trying to produce a fungal vaccine is “starting from scratch.” These infections simply aren’t a global priority, and funding is limited, he warned. And since no working vaccine exists yet for any fungal infection, research teams also lack a foundation to build on — a stark contrast, for example, to the rapid-fire production of shots to fight COVID-19, a coronavirus.

“How long would it take us to develop a fungal vaccine? Maybe we’ll get lucky and get it in 18 months,” Spec said. “Or maybe it’ll take us two decades.”

We could have agricultural collapse while at the same time dealing with a brand new pandemic that’s spread by breathing.

As the global climate shifts rapidly and dramatically, with new heat records being broken every summer, Spec worries the world is teetering closer to a nightmare scenario, where pathogens like cocci adapt faster than we can contain them.

Already, Candida auris, a type of yeast that first appeared in a patient’s ear in Japan in 2009, is being identified around the world. It preys on people with weakened immune systems, can often be multi-drug-resistant and is tough to eradicate once it appears in hospitals or care facilities. It also kills up to half of those it infects. (Canada has a country-wide surveillance program in place for it, unlike for cocci.)

Then there’s Histoplasma, a family of pathogens found in bird and bat droppings, which can cause a condition called histoplasmosis. Symptoms can range from mild and flu-like to severe conditions that can spread to nearly any part of the body, including the mouth, skin and central nervous system.

“They could infect us, they could infect our pets, they could infect our livestock. We could have agricultural collapse while at the same time dealing with a brand new pandemic that’s spread by breathing,” Spec said.

WHO fungal priority pathogens list

Critical

High

Medium

Cryptococcus

neoformans: Critical priority

Aspergillus

fumigatus: Critical priority

Candida auris,

Candida albicans: Critical priority

Nakaseomyces

glabrata

(Candida glabrata): High priority

Histoplasma

(several species): High priority

Eumycetoma: High priority

Mucorales: High priority

Fusarium

(several species): High priority

Candida tropicalis,

Candida parapsilosis: High priority

Scedosporium

several species: Medium priority

Lomentospora

prolificans: Medium priority

Coccidioides

several species: Medium priority

Pichia

kudriavzeveii

(Candida krusei): Medium priority

Cryptococcus

gattii: Medium priority

Talaromyces

marneffei: Medium priority

Pneumocystis

jirovecii: Medium priority

Paracoccidioides

several species: Medium priority

Source: World Health Organization (CBC)

WHO fungal priority pathogens list

Critical

High

Medium

Cryptococcus

neoformans: Critical priority

Aspergillus

fumigatus: Critical priority

Candida auris,

Candida albicans: Critical priority

Nakaseomyces

glabrata

(Candida glabrata): High priority

Eumycetoma: High priority

Histoplasma

(several species): High priority

Fusarium

(several species): High priority

Mucorales: High priority

Scedosporium

(several species): Medium priority

Candida tropicalis,

Candida parapsilosis: Medium priority

Lomentospora

prolificans: Medium priority

Coccidioides

(several species): Medium priority

Cryptococcus

gattii: Medium priority

Pichia

kudriavzeveii

(Candida krusei): Medium priority

Talaromyces

marneffei: Medium priority

Pneumocystis

jirovecii: Medium priority

Paracoccidioides

(several species): Medium priority

Source: World Health Organization (CBC)

WHO fungal priority pathogens list

Critical

High

Medium

Cryptococcus

neoformans: Critical priority

Aspergillus

fumigatus: Critical priority

Candida auris,

Candida albicans: Critical priority

Eumycetoma: High priority

Nakaseomyces

glabrata

(Candida glabrata): High priority

Histoplasma

(several species): High priority

Fusarium

(several species): High priority

Mucorales: High priority

Candida tropicalis,

Candida parapsilosis: High priority

Lomentospora

prolificans: Medium priority

Coccidioides

(several species): Medium priority

Scedosporium

(several species): Medium priority

Cryptococcus

gattii: Medium priority

Pichia

kudriavzeveii

(Candida krusei): Medium priority

Talaromyces

marneffei: Medium priority

Pneumocystis

jirovecii: Medium priority

Paracoccidioides

(several species): Medium priority

Source: World Health Organization (CBC)

WHO fungal priority pathogens list

Critical

High

Medium

Cryptococcus

neoformans: Critical priority

Aspergillus

fumigatus: Critical priority

Candida auris,

Candida albicans: Critical priority

Nakaseomyces

glabrata

(Candida glabrata): High priority

Eumycetoma: High priority

Fusarium

(several species): High priority

Histoplasma

(several species): High priority

Mucorales: High priority

Lomentospora

prolificans: Medium priority

Candida tropicalis,

Candida parapsilosis: High priority

Scedosporium

(several species): Medium priority

Coccidioides

(several species): Medium priority

Cryptococcus

gattii: Medium priority

Pneumocystis

jirovecii: Medium priority

Pichia

kudriavzeveii

(Candida krusei): Medium priority

Talaromyces

marneffei: Medium priority

Paracoccidioides

(several species): Medium priority

Source: World Health Organization (CBC)

It’s a grim prognosis, the stuff of science fiction. But for those already living it, it doesn’t feel all that far off.

Abair, who caught Valley Fever at the age of 27, told CBC News he was on an anti-fungal treatment for nine months, and now wonders whether or not cocci is still hiding somewhere inside his body. While standing on a steep trail as the sun set over Scottsdale, Ariz., he recalled letting out another bloody cough two years after his initial illness, but it went away. He tries not to think about it.

What Abair can’t shake is the feeling that cocci is hiding throughout his desert home, invisible in the soil, floating through the air and capable of living farther and farther away from its usual range in the American Southwest — just waiting for new human hosts to breathe it in.

“It’s everywhere. It’s super easy to inhale,” he said. “That’s kind of a scary thing.”

WATCH | See the full National item on Valley Fever:

Top image: Lauren Pelley | Editing: Andre Mayer

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