How A Glitchy Computer System Skewed Texas’ Coronavirus Data And Hampered Its Pandemic Response

Texas’ coronavirus positivity rate was higher than reported

In September, Texas health officials changed the way the state calculates the positivity rate — the share of tests that yield positive results — to account for the date on which a coronavirus test was administered. The rate previously relied on the date a test was reported to health officials. The new calculation reveals that the state’s positivity rate was higher in June than originally disclosed.

An Abbott spokesman did not respond to questions for this story.

One reason for the data inaccuracies was that the old NEDSS system could not process lab results fast enough, leading to a backlog of some 350,000 tests. The disclosure of the logjam sent some local health departments scrambling to sort through cases and explain the seeming sudden spike of infections to the public.

Some of the test results were so outdated by the time officials recorded them that follow-up efforts to trace the contacts of infected people were nearly pointless, local health officials said.

Laboratories also struggled to upload test results into NEDSS because of precise formatting requirements.

“We are optimistic that the state will modernize their data reporting system and support it with the right resources,” said CHRISTUS Health spokesperson Katy Kiser, when asked about a delay importing 95,000 test results this summer.

Texas health officials have faced the herculean task of assembling data — including negative test results as well as positive ones — from hundreds of different laboratories and testing sites and publishing it in near real-time. The health services agency hired a contractor to minimize problems getting lab results imported to NEDSS.

The state “has done what they can under a trying situation,” said Eduardo “Eddie” Olivarez, the chief administrative officer for Hidalgo County’s health and human services division. The pandemic “just has astronomically increased the amount of work in things that we’ve never had to do in the past.”

“Very, very outdated”

Even before the pandemic, the version of NEDSS used in Texas was “very, very outdated,” health commissioner Dr. John Hellerstedt told lawmakers in 2019. It was prone to blinking on and off, required a lot of maintenance, and sometimes lost information that had been entered, he said.

In a plea for funding around that time, the health agency said NEDSS was “at risk of failure due to aging infrastructure” and was delayed in getting lab reports and other information vital to start disease investigations or inform treatment for affected patients. The delays would worsen as the system continues to deteriorate, they wrote in a 2018 appropriations request — and would “increasingly threaten the timeliness of public health’s infectious disease response.”

The agency received $3.5 million from lawmakers to upgrade NEDSS. The agency is also hiring seven people to help its four-person NEDSS team. Federal funding will pay for 18 more people for two years.

State and local authorities use NEDSS to collate information about public health threats from foodborne illnesses to diseases like mumps and measles and share it with the U.S. Centers for Disease Control and Prevention. Used in Texas since the 2000s, the system is meant to serve as a central, electronic repository of crucial disease information.

All 50 states and the District of Columbia have an electronic system that works with NEDSS, many using commercially or custom built systems and about 20, including Texas, relying on the free base system developed by the CDC — but those states may have to buy software licenses, hardware or pay for staff to tend to the technology.

The version Texas now uses looks like something out of the 1990s: gray, boxy graphics and sometimes lagging response times. Even after the August improvements, the state is not using the latest version of NEDSS, though Van Deusen said the state health department plans to upgrade and that other states aren’t using the latest version, either.

The upgrade had to be carefully planned so that it didn’t cause information in the system to be lost, he said.

NEDSS is meant to collect standard data on each case, including things like race, age, and date of onset, to ensure that “what I’m calling a confirmed COVID case in Tarrant County is the same as somebody in Wisconsin or Nevada,” said Cervantes, the epidemiologist at the UNT Health Science Center. Local health officials can also use NEDSS to access COVID-19 test results that laboratories send to the state.

But NEDSS isn’t robust enough for real-time tracking — like tracing an infection to a local restaurant, Cervantes said. For that, health departments often turn to separate tools to organize complicated data about an infection and to trace clusters of cases, she said. National public health groups have criticized that trend as inefficient.

The state paid Deloitte more than $1.1 million in federal funds to create a separate program, Texas Health Trace, to help track coronavirus cases, and let local health officials draw on a statewide call center of contact tracers. But by the time it was rolled out in late May, some health departments had already created their own systems to investigate cases and have not merged them with Health Trace. Others decided not to switch over.

Harris County Public Health built a program it calls CRP, or COVID-19 Response Program, after finding NEDSS and other computer systems were “overwhelmed and not nimble enough” to handle an influx of coronavirus data, said Dr. Umair Shah, the department’s executive director.

The department had already hired 300 contact tracers who were using the home-grown program — which collects laboratory data and allows workers to document progress on case investigations and contact tracing — before the state introduced Texas Health Trace. Shah said the department has no intention of switching to the state’s new system.

Austin Public Health turned to a Salesforce tool — similar to Health Trace — because NEDSS was a “legacy system that was running really, really slow,” said Chief Epidemiologist Janet Pichette. It “just was not performing to meet the case demands” of the department, she added.

Such pricey solutions are out of reach for other health departments, like Cameron County on the state’s southern tip, which has been among the hardest hit regions in Texas.

The local health department lacks the resources of some of its urban counterparts that can afford to hire contractors, buy specialized software or create polished maps, said Esmeralda Guajardo, health administrator for Cameron County Public Health.

They turned to Excel.

“I can’t afford to utilize NEDSS and then in the middle … be told that they’re going to have to take it down for a few days for maintenance,” as has happened before, Guajardo said.

Her department has begun to submit case information to the state through Health Trace instead of NEDSS, an improvement in her eyes even though they initially had to manually input the data.

The state is now trying to merge local systems with Health Trace and is “actively importing data from jurisdictions on the back end,” Van Deusen said.

The patchwork of local systems used to investigate infections before the pandemic did not “allow for the kind of easy information sharing necessary to let state contact tracers augment work at the local level when needed,” he said, adding that Excel and other simple tools are constrained by “how many records they can store and are subject to corruption.”

At Northeast Texas Public Health District, based in Tyler, officials said NEDSS was plagued by slowdowns and errors in the spring and that it was unrealistic to migrate to the Texas Health Trace application in the middle of a pandemic.

Though NEDSS’ responsiveness has improved since the pandemic began, epidemiologists said, they have no plans to abandon their strategy of working in Excel spreadsheets and other databases they consider more reliable.

“In my 12 years of experience with [NEDSS], it crashes all the time and you just can’t rely on it,” said Russell Hopkins, the district’s director of public health preparedness.

Paper faxes, missing information complicates investigations

Compounding the state’s problems in getting ahead of the virus are complicated reporting chains that can make gathering raw information a nightmare. State and local officials often receive duplicate tests or case information from hospitals, medical providers, and laboratories.

A host of new players — particularly nursing homes and other long-term care providers — have begun to test for the virus and aren’t familiar with how to report results to state and local health officials, a process that can have exacting requirements. Health officials say crucial information is often missing, requiring them to track down additional detail or eyeball addresses to determine whether a case falls within their jurisdiction.

With so many people involved in collecting and transmitting information, there are data entry and translation errors. Olivarez, the Hidalgo County health official, has seen “Hidalgo” spelled with an “E,” or “Donna” written down as “donut.”

That has left health workers to spend hours sifting out duplicates, manually copying data into different data systems and being bombarded with faxes, particularly in the early days of the pandemic. Doctors’ and labs’ lingering reliance on faxes — which are relatively cheap and comply with federal privacy standards — is in part due to lack of government funding.

“It’s appalling that in 2020 we’re still dealing with so many of these paper faxes and having to hand enter lab data because we can’t just automatically upload this sort of data,” said Dr. Philip Huang, health authority for the Dallas County Health and Human Services Department.

Local and state officials have advocated for a federal fix, including $1 billion in new funding to the CDC to improve its public health surveillance systems.

In Cameron County, Guajardo said the pressure to get the data cleaned up and entered quickly is immense. Sixty percent of her public health preparedness staff has left since the pandemic began after having to work up to seven days a week, sometimes 14 hours a day, to manually input data and contact people who may have been infected. Some have sought better paying jobs.

The county has had to take an “all hands on deck” approach, drafting nutritionists and environmental health inspectors to track down information or sift through backlogged test results, Guajardo said. Each case is tied to a person who may be waiting to go back to work or be told what to do next if they test positive for COVID-19, she said.

The state temporarily sent staff and epidemiologists to help, and Guajardo said they’re grateful. But she worries that the backlogs, data errors, and corrections will erode the public’s confidence in her profession.

“Because we don’t have a technology in place, we’re losing credibility overnight over this,” she said. “When you’re in public health for 21 years, this is not the legacy you want.”

Epidemiologists and other experts say they hope the public frustration over incomplete or delayed data during the pandemic will spur greater investment in public health technology.

Many have championed efforts to streamline the reporting process so that it can move seamlessly from medical providers to health authorities. But that goal has remained elusive.

“That’s going to be one of the critical things that we’ve got to improve as a result of this whole situation,” said George Roberts, chief executive of the Northeast Texas Public Health District. “Local public health, state public health — they all realize that we need to make vast improvements.”

Guajardo is more blunt.

“You don’t put a Band-Aid on a broken leg. You don’t. You have to figure out what the problem is and fix it,” she said. “That’s what needs to happen here. We need to fix it.”

This story originally published by the Texas Tribune.