Come fall, the rise of influenza and other seasonal respiratory infections could exacerbate already staggering delays in coronavirus testing, making it easier for the virus to spread unnoticed, experts said.

In typical years, doctors often don’t test for flu, simply assuming that patients with coughs, fevers and fatigue during the winter months are probably carrying the highly infectious virus. But this year, with the coronavirus bringing similar symptoms, doctors will need to test for both viruses to diagnose their patients — further straining supply shortages in an already overwhelmed testing system.

A handful of manufacturers have begun making tests that can screen for several pathogens at once. But these combo tests are expensive and will likely make up only a fraction of the market. Some researchers are trying to make their own multi-virus tests as well, but they almost certainly won’t fill in the gaps.

“The flu season is a bit of a ticking time bomb,” said Amanda Harrington, medical director of microbiology at Loyola University Medical Center. “We are all waiting and trying to prepare as best we can.”

Flu viruses and coronaviruses differ in many ways, including how they spread, how long they linger in the body and the groups they affect most severely. Food and Drug Administration-approved antivirals and vaccines exist for the flu, but no such treatments yet exist for the coronavirus, which has killed about 800,000 people worldwide in less than a year.

Being infected with one virus doesn’t preclude contracting the other. And researchers also don’t yet know how risky it is for a person to harbor both viruses at the same time.

Those differences make it essential to tease the two pathogens apart, as well as rule out other common wintry infections like respiratory syncytial virus, or R.S.V., which hits the very young and very old especially hard.

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But testing for individual viruses poses many challenges for doctors and laboratory workers already fighting their way through supply shortages. Several of these tests use similar machines and chemicals, and require handling and processing by trained personnel.

What’s more, many flu and R.S.V. tests vanished from the market this spring as the companies that make them rapidly pivoted to address the coronavirus.

Late summer is typically when laboratories start stockpiling flu tests, R.S.V. tests, and flu-R.S.V. combo tests in anticipation of the autumn surge, said Susan Butler-Wu, clinical microbiology lab director with the University of Southern California’s Keck School of Medicine, whose lab purchases thousands of these tests every winter. But the supply chain shake-up has left shelves empty just weeks ahead of one of the busiest times of the year.

“Many people are legitimately concerned about the winter because we’re not able to squirrel away our nuts right now,” Dr. Butler-Wu said. “Every lab is fighting to get what they need for their system.”

A few test manufacturers are trying to maximize efficiency by developing tests that can spot several pathogens at once. BioFire and Qiagen, for instance, have already made tests that can simultaneously screen for more than 20 bacterial and viral pathogens, including influenza viruses, R.S.V. and the new coronavirus.

“The beauty of these panels is: it’s everything,” said Esther Babady, director of the clinical microbiology service at Memorial Sloan Kettering Cancer Center.

But the bigger the panel, the bigger the price tag — and “those costs can add up really quickly,” Dr. Babady said. These ultra-comprehensive tests will probably only be used in the sickest patients, which means health workers can’t rely exclusively on them. And while coronavirus testing in the United States has largely been comped, federal funding sources like the CARES Act haven’t explicitly addressed the issue of combo diagnostics, leaving ambiguous how much patients might have to pay.

Cheaper options do exist, including some that can screen patient samples for only the most likely microbial culprits.

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Credit…Erin Schaff/The New York Times

California-based Cepheid, which received emergency approval for a coronavirus-only test earlier this year, is putting the final touches on a new test for four pathogens — two types of flu, R.S.V. and the coronavirus — which will deliver results in about half an hour. Pending emergency authorization from the F.D.A., the company expects to roll the test out sometime in the next couple of months. Almost all of the roughly 2,000 American labs currently running Cepheid’s stand-alone Covid-19 test probably will be buyers.

“We do expect strong demand for this,” said Dr. David Persing, the company’s chief medical and technology officer.

But Cepheid is small, and it has already maxed out its production lines at about 2 million coronavirus tests per month. Production is ramping up, Dr. Persing said, but slowly, and in the meantime, the company will need to phase out coronavirus-only testing to make room for its new product.

Another company, Hologic, is working on a three-virus test for two types of flu and the coronavirus, which will be available in time for flu season, according to a representative. But Hologic declined to specify a more concrete timeline or estimate production volume for its new panel.

Dozens of public health laboratories run at the state and county level — which process hundreds of thousands of samples from hospital patients, health workers and nursing homes every week — will soon be using a new test for three viruses, coronavirus, influenza A and influenza B. The combo test was designed by the Centers for Disease Control and Prevention and cleared for use by the F.D.A. in July.

The C.D.C.’s test is a boon for efficiency, said William Glover, assistant director of infectious diseases at North Carolina’s state public health lab. It will also help labs search for flu cases by sampling large swaths of the general population, a process called surveillance. But in order to meet local testing demand, Dr. Glover’s team will likely need to supplement that test with a combination of commercial panels. Given the supply shortages that have thwarted testing thus far, he said, “my plan is to have as much diversity in platforms as we possibly can.”

Some labs are trying DIY combo tests, including some loosely based on the C.D.C.’s original three-virus recipe. “That’s always an option for us,” said Dr. Laurel Glaser, director of the clinical microbiology lab at the University of Pennsylvania. “It could loosen up the supply chain.”

These laboratory-developed tests can now be deployed without seeking F.D.A. review, the Trump administration announced on Wednesday. That could make it easier for big testing companies like Quest Diagnostics to make a proprietary combo panel, which is in the works, according to a company representative.

Still, most labs don’t have the time or resources to tinker with new tests, and the DIY versions often end up being more labor-intensive than their industry counterparts, said Jennifer Dien Bard, director of the clinical microbiology and virology laboratory at Children’s Hospital Los Angeles.

Preparing for this year’s flu season has become an onerous process of layering contingency plans atop contingency plans, Dr. Babady said. “Figuring out all those pieces before November is what’s keeping us up at night.”

There has been at least one tentative glimmer of hope: The flu season this year may be milder than in the past. Countries in the southern hemisphere, like Australia, which get hit with the flu six months before the U.S. does, have experienced an unusually tempered flu season, due in part to concerted efforts in physical distancing and sheltering in place.

“Distancing should also keep other viruses at bay,” Dr. Harrington said. “It might just be a completely atypical season.”

Dr. Butler-Wu offered a less rosy view. Adherence to public health measures in the U.S. has been patchy at best, she said: “If people aren’t going to mask, aren’t going to distance, we can anticipate there’s going to be high demand for testing.”