At least 35 states are lifting stay-at-home orders or other restrictions, even though the CDC says the U.S. is still in the "acceleration" phase of the pandemic and many regions are seeing caseloads rise. That requires enhanced real-time surveillance of how the disease is spreading before it gets out of control in a state or community.

Congress approved more than $500 million for health data in a relief package last month but for now disease trackers say they’re drowning in paper reports and using outdated spreadsheets for critical tasks like contact tracing, or determining how many people were exposed to an infected individual.

“Our ability to do the detection work we need to do is hampered,” said Raquel Bono, the coordinator of Washington state’s coronavirus response. “We don’t have a single data repository for tracing per se,” she said, adding that record-keeping and reporting is “primarily manual.”

That’s playing out nationwide. And even when officials can tap data, like cell phone location tracking, they can’t connect the dots for an up-to-the-minute picture of disease spread.

So they comb over unconnected, at times incomplete, bundles of information — including health provider reports of symptoms like respiratory distress or lab test results. One in four hospitals don't feed information to federal websites on how many patients have flu-like symptoms. With more investment in technology, experts think health departments could do disease surveillance better and faster.

The situation was causing alarm even before the coronavirus arrived. Health officials frequently hit dead ends investigating reports of food-borne illness that came days after the fact. "If they come to you [and] ask say, what was in your refrigerator 14 days ago, you can guess" how useful the response is, said Laura Conn, a CDC official working on a project to create seamless, electronic case reports.

But the pandemic has dramatically elevated the concern. In Congress, more than 100 Republicans and Democrats from both houses have pressed CDC over the past two weeks for details on how the agency plans to spend the more-than-half billion dollars of data money — and are urging congressional leaders to approve more.

“Public health departments are unable to share data on cases, persons under investigation, laboratory tests and person-to-person transmission with the CDC seamlessly — instead they are forced to rely on a combination of methods: antiquated pen and paper, faxes, excel spreadsheets, phone calls, and manual entry,” a group of nine senators led by Richard Blumenthal (D-Conn.) wrote to Senate leaders.

The CDC says it will detail its spending plans in the coming weeks, with some of the money going toward upgrading its own data systems and hiring personnel. The agency also intends to announce a first wave of grants for local health agencies, focused on improving reporting and surveillance.

“Virtually every health department’s affected by this, in some fashion,” said Chesley Richards, the agency's deputy director for public health science and surveillance.

Balky data collection and gaps in reporting have already bedeviled efforts to identify who's sick and where after a surge of coronavirus testing early this spring.

Experts say a lack of investment in public health surveillance and a jumble of sometimes conflicting reporting mandates set the nation up for trouble even before the pandemic. The coronavirus crisis has only brought the problems into stark relief, with officials easily overwhelmed and struggling to size up the situation on the ground.

“You get to the county level, and we’re talking Excel and paper,” said Sondra Renly, of the University of California, San Francisco’s Center for Digital Health Innovation.

That means officials have to work long hours just to establish family histories of patients or other medical conditions they may have. The delays often leave investigators flying blind, without a clear sense of how sick patients are or how quickly the disease took hold.

Lawmakers worry the situation is leading to critical information gaps about details like how the disease is weighing on minority communities and people with disabilities. And they’re worried the Trump administration isn’t being transparent about its plans going forward.

“We have no idea what they are doing,” said Aaron Fritschner, a spokesperson for Rep. Don Beyer (D-Va.). “The big worry being expressed here is that as states start ‘reopening’ they just don’t have the resources and coordination that you need for a real surveillance program to prevent another flare-up.”

The heart of the problem is a cumbersome, paper-based system that contact tracers rely on to find infected people and that health authorities scrutinize to gauge how fast disease is spreading and where.

Doctors are supposed to flag public health departments when they see patients diagnosed with certain conditions. But the need to fill out paper forms means cases slip through the cracks: the CDC's Conn told a federal health IT advisory committee that about one in 10 Lyme Disease cases don’t get reported.

Reporting standards also vary from county to county. And doctors often have to report to more than one jurisdiction if a patient lives in one county, works in a second and is diagnosed in a third.

The big northern California health system Sutter Health has a “complex matrix” to guide its doctors and lab technicians on what to report when, said Steven Lane, an emergency department physician leading an effort to digitize the system. The “manual process is really fraught with getting the right data to the right place.”

Many providers simply don’t fill out reports — though it’s difficult to tell how often. And the potential for information gaps not only plagues individual case reports but “syndromic surveillance,” an important public health tool that can, for example, lumps anonymized data on how many patients had flu-like symptoms in an emergency department.

Reporting is “just a menu item” and not a requirement for the federal electronic health records program, said John Loonsk, a former CDC official who’s now with the Association of Public Health Laboratories. That designation slowed down the adoption of key technology for disease tracking.

Even when reports do filter back, public health officials still have to sort through mountains of paper. That’s already slowed down the response to the pandemic: Emails obtained by ProPublica show the CDC put out a call in February for employees to comb through forms describing suspected cases of the coronavirus.

Before the pandemic, the CDC and selected providers like Sutter Health were testing a new system, dubbed eCR Now, to replace manual reporting with digital records.

The system, which has been rolled out in selected sites around the country, pulls data out of providers’ electronic health systems and formats them as case reports to a central hub, which is then programmed to dispatch the reports to appropriate agencies.

It’s a big efficiency gain, said Paul Matthews, the chief technology officer with OCHIN, a nonprofit working with federally qualified health centers and other low-resourced providers in 19 states. The organization recently rolled out the eCR Now app with its providers, who sent some 13,000 reports over the first week-and-a-half.

“Instead of us having to build case reporting for each organization, you submit once,” he said. “No longer do I have to build case reports for 19 states, however many jurisdictions.”

It's also leading to more complete data submissions. Civil rights groups and congressional Democrats have repeatedly asked for racial and ethnic breakdowns of coronavirus patients, to assess how communities of color are holding up under the burdens of the disease.

CDC says about 53 percent of reports come back without racial or ethnic data. Conn, however, says electronic case reporting returns racial and ethnic data almost 92 percent of the time.

But the product she's developing has yet to be adopted. While Epic, the dominant electronic health vendor, has embraced the system, its rival Cerner is taking a different approach tailored just to the coronavirus cases. That system may take weeks to roll out, Conn said, with a version for more widespread use forthcoming. The time lag could lead to continued reliance on old records.

It’s possible doctors and other providers won’t rush to the new tools, at least in the short run. Chief information officers contacted by POLITICO indicated that, amid all the coronavirus tumult, there are a lot of tech tasks on their to do lists.

Experts anticipate the pandemic will unleash yet more funding for data systems — an opportunity to address existing problems but one that can come with strings attached.

“A whole bunch of money is going to come in, it’s going to be earmarked for Covid-19, it’s going to be two years, three years, and then it’s going to be gone,” Renly said. “We don’t think of public health in a holistic way.”