Texas has a problem with its COVID-19 vaccination data, and the stakes are high. Now the state is scrambling to solve it.

After the staff at Austin’s Tarrytown Pharmacy hustled to vaccinate 500 vulnerable Texans and front-line workers over the holidays, pharmacist Rannon Ching logged into an online state system used to track the vaccines.

Then he panicked.

According to the system, his Tarrytown pharmacy hadn’t vaccinated anyone. The numbers on his screen indicated all 500 doses were still sitting on his shelf.

“I freaked out thinking, ‘Oh my gosh, they’re not going to give me any [more] doses because they think I’m not giving anything,’” Ching said.

As the state began the massive undertaking of distributing the coronavirus vaccine, its early rollout was beset by data problems that left state officials with immunization and dose information that was outdated, incomplete and sometimes misleading.

Health care providers feared those inaccurate numbers, collected by the state’s immunization registry, ImmTrac2, and another system were being used by the state to decide who would get the weekly allotment of vaccine — and by others to decide who would get blamed for moving too slowly as a desperate public clamored for shots.

Health officials say the registry data were not used to dole out vaccines in the early weeks of the rollout — that’s a misconception, they said — but added that the data they’re collecting with ImmTrac2 could soon become a central factor in how many vaccine doses Texas gets from the federal government going forward.

In the first six weeks of the vaccine rollout, the federal government allocated doses based largely on population, but will likely start using the vaccination rate — how fast doses are going into arms — as “at least a piece of their allocation process,” said Lara Anton, a spokesperson for the Texas Department of State Health Services, which runs the registry.

“We haven't been using the data that's in ImmTrac for allocation, but it sounds like we are going to need to place greater emphasis on that,” Anton said. “Because if they think we're not using up all of their vaccines, they're not going to send us additional vaccine. You know, they'll send it somewhere else that's using more.”

As Texas tries to vaccinate its roughly 29 million residents during its worst surge in COVID-19 cases, hospitalizations and deaths since the onset of the pandemic, the stakes attached to accurately reporting and tracking vaccinations could not be higher.

“The fear is that with delayed reporting, if you can't see [vaccination distribution] in real time ... you’re hindering [vaccine providers’] availability to get future batches, because nobody wants to send a scarce resource and put it in the hands of people who can't move it,” said Carrie Kroll, an ad hoc member of the state’s Expert Vaccine Allocation Panel and the director of advocacy for the Texas Hospital Association.

Designed years ago to help consenting Texans keep track of their inoculation records, ImmTrac2 was chosen last year by the Texas Department of State Health Services to be the state’s main avenue for tracking the COVID-19 vaccine rollout — and a vehicle to transmit required immunization data to the federal government.

Using the system, some users say, is time-consuming, can require providers to alter their own software to transfer data, and sometimes — as in Ching’s case — did not reflect reality days after the exhaustive data on each patient had been entered into the registry.

“This has been such a pain,” said Dr. Lane Aiena of Huntsville Family Medicine, who estimates that his clinic could vaccinate people at least three times faster if not for the cumbersome system. “I just wish they would streamline it. It’s so important to get the shot out. It’s just so frustrating that I have to dedicate staff to this.”

A delay of up to 48 hours in publicly posting the vaccination rate can also be troublesome at a time when officials and the public are looking for up-to-the-minute progress reports on where the vaccine is available.

To address that, right before New Year’s Eve, the Texas Division of Emergency Management — charged with managing the state’s response to declared disasters — pushed out its own system to collect “near-real-time” data about the number of doses that each provider has on hand every day, based on a simpler daily reporting system that only takes a few keystrokes. The numbers can update on the TDEM dashboard as quickly as 15 minutes after the provider has reported them, which is required by 8 a.m. each day.

“The goal here with this, the reason TDEM stepped in with this, was to ensure that daily, we're getting a live-feed update in as near as real time as possible,” said Seth Christensen, spokesperson for TDEM, adding that the system isn’t intended to replace ImmTrac2 or serve as the state’s official health statistics reporting system.

Kroll sees another benefit to TDEM’s efforts: It should deter politicians and the public from claiming hospitals and other providers are slow-walking the vaccine while Texans are contracting COVID-19 at record rates.

“It's frustrating for our hospitals that are obviously moving [the vaccines] and doing a great deal in our community to prevent the disease, and nobody can tell that,” Kroll said. “So getting the clarity and speed fixed is super important because we want the vaccine to continue to flow.”

Anton said the state health department recognizes that it’s a “huge undertaking” for the vaccine providers to immunize large numbers of people and get the required information into online systems on an abnormally tight turnaround. They have seen errors happen when vaccine providers input bad data, like an incorrect number denoting the batch of the vaccine, and are working to help fix data entry and technical problems contributing to the gaps in data, she said.

“I think they always kind of knew that there were going to be some data issues … as with anything — when you have a whole bunch of [new users] adopting a new system all at the same time, [and] everybody’s got to learn it, there's always going to be issues with it as far as just making sure everybody understands how it works, and what information to put into it,” Anton said.

Experts and health officials acknowledge that the Department of State Health Services has a Herculean task on its hands as it manages both the pandemic response and the vaccine rollout.

To help providers, the agency has undertaken massive training efforts to teach the system to the thousands of workers who, before the pandemic, had little to no experience with the registry. And Anton said DSHS also moved the ImmTrac system onto new servers before the vaccines arrived, to get ahead of any “memory or storage issues.”

Texas is the first state to have given more than 1 million doses of the vaccine, crossing that milestone a month after the first batch arrived Dec. 14 in UPS and FedEx trucks. This month, the state began turning to large “hubs” in urban areas to distribute a large portion of the state’s vaccine doses, rather than relying on networks of pharmacies and other small providers.

Dr. John Zerwas, a member of the vaccine allocation panel who has advised Gov. Greg Abbott on the pandemic, said tracking different facets of the virus and vaccine rollout has challenged the state’s data systems.

They “were never structured or developed with the idea that this massive amount of information would need to be ingested,” said Zerwas, a former state lawmaker. “Now, it's been something that has been addressed on the fly throughout the whole pandemic.”

A crush of calls but no vaccine

On Dec. 29, the day Ching noticed his numbers hadn’t been recorded by the state, Abbott admonished health care providers to speed it up, suggesting that doses may be “sitting on hospital shelves” while Texans clamored for vaccines.

The next morning, Ching’s pharmacy was bombarded with calls from people anxious to be vaccinated. He had no shots left.

Ching initially blamed himself. He’d worked hard — hurriedly calling nursing homes and doctors’ offices to offer them vaccines when they arrived with little notice — and had kept his staff until the evening tapping information about each dose they gave into their own electronic health records system.

But Ching quickly discovered a problem. His pharmacy’s electronic records weren’t syncing with ImmTrac2.

He emailed state health officials to tell them. Ultimately, four of his employees had to re-enter all the information by hand, a task that took six hours on Dec. 30 — the day after Abbott’s tweet.

“The system that they had in place to supposedly log which facilities had given how many doses wasn't working properly,” Ching said. “I think that played into some of that pandemonium.”

Other providers were having problems too. A Brazos County state lawmaker said “an error in the system” made it seem like less than half the vaccines given to that county had been used, which was false. The head of the Dallas-Fort Worth Hospital Council called the state’s reporting process “laborious'' and said it had a “significant lag time.”

“The problem has been the bookkeeping,” he told a television station in December.

A "perfect storm" of data problems

When the pandemic hit, ImmTrac2 was in the process of being upgraded to let it more seamlessly work with pharmacies’ and hospitals’ vaccine recording systems, which were also being adjusted.

Its functionality has been heavily influenced by anti-vaccine and pro-privacy activists who have lobbied to keep Texas’ immunization registry one of the nation’s only opt-in registries, critics say — meaning adults must consent to have their immunization records retained, a step they have said is inefficient and complicated.

As a result, standard software used by health care providers “doesn’t come out of the box” ready to address Texas’ unique consent requirement, said Nora Belcher, executive director of the Texas e-Health Alliance, an advocacy organization that represents digital health companies. Unlike other states, Texas also has a separate consent process for first responders, further complicating the reporting process.

The coronavirus vaccine poses an added complication: The usual consent process is being bypassed because of the pandemic and because the federal government requires that states send it statistics about vaccine doses.

Because it’s classified as a disaster vaccine, records about the coronavirus vaccine must be stored for five years — a requirement at odds with the rest of Texas’ opt-in registry.

Software used by health care providers can be configured to work with Texas’ opt-in registry and to report COVID-19 vaccine data, but trying to make the adjustments in the middle of a pandemic has been like building a plane and flying it at the same time, Belcher said.

Those factors combined with the ongoing upgrade created the “perfect storm,” Belcher said.

There’s “no malicious intent on anybody’s part,” she said, “[with] all of these things converging to where it cracked.”

Rebecca Hardy, director of state policy for Texans for Vaccine Choice, said her group is not against immunization or a state registry, but lobbied against efforts to make the system an opt-out system to protect patients’ privacy rights. ImmTrac2, she said, is unreliable enough when there isn’t a pandemic — much less when it is being used to record millions of doses in a short amount of time.

State works on solutions

In Huntsville, Aiena’s clinic recently had its third-party records system try to create a patch solution to link his system to ImmTrac2 and automate the process, but it didn’t work.

The system needs to work in a timely manner — without getting in the way of the ultimate mission, which is vaccinating the people, he said.

“If it’s not working, we don’t get more shots, and that's what the state keeps dangling over our heads,” Aiena said. “I understand that, you know, they only want to get shots to people who are giving the shots out, that makes perfect sense to me. But unfortunately that means if we don’t update ImmTrac and TDEM within 24 hours, we don’t get the shots.”

Meanwhile, he’s involved in the planning of a potential mass-vaccination program in Huntsville — located in a county of 74,000 people — and says organizers are considering recruiting nearby medical students to help update records in ImmTrac2.

In an email sent to providers on New Year’s Eve, state health officials wrote that the TDEM workaround, deployed in late December, was “an interim step until we can get all the data flowing consistently in ImmTrac2. … Please know that the teams are working hard to quickly resolve the data submission issues for some providers.”

Some of the state’s larger health systems, like University Health in San Antonio, have automated their processes and were able to sync their electronic records to the immunization registry, said spokesperson Leni Kirkman.

“Our process is automated. It uploads each evening,” Kirkman said. “I’m not sure we have any recommendations for other organizations other than to see if there is a way to configure their medical records system to batch these records into a file that can be sent to the state.”

Anton said the issues with the data and allocation would become less of a problem as more vaccines become available, smaller providers have less need for it, and the state moves to larger vaccination hubs, many of which have the resources or systems to quickly handle the ImmTrac2 demands.

For now, state Rep. Donna Howard, D-Austin, said the onus seems to be on local providers to “jump through all kinds of hoops” — a responsibility that was “totally overwhelming” them as they also tried to “deliver the vaccines, get people signed up and do whatever else they have to do,” she said.

But she’s not surprised there have been problems with ImmTrac2. She’s filed several bills trying to make the immunization registry an opt-out system, a change she said was needed “because of the inevitable possibility of an epidemic.”

“I did think there would be hang-ups because I knew that the system had not been upgraded and was not meant to be a system that would allow for an opt out vaccination,” Howard said. “This is exactly what we were trying to anticipate, though, and correct before it actually happened.”

Alana Rocha contributed to this report.

Disclosure: Texas Hospital Association has been a financial supporter of The Texas Tribune, a nonprofit, nonpartisan news organization that is funded in part by donations from members, foundations and corporate sponsors. Financial supporters play no role in the Tribune's journalism. Find a complete list of them here.