‘It Is Embarrassing’: CDC Struggles To Track COVID Cases As Omicron Looms

As the world experiences new, more transmissible Covid-19 variants, scientists and health officials in the U.S. are still struggling to gather accurate and timely domestic data to help inform policy decisions to safeguard Americans.

Continuing gaps in the CDC’s data collection program, which almost two years into the pandemic still relies on state health departments who use a mix of often incompatible and outdated state systems to identify cases, impedes the nation’s understanding of where and how fast the virus is spreading, according to more than a dozen state and federal officials involved in tracking cases.

The fact that the data gaps have been apparent since the start of the pandemic makes the lack of substantial improvement particularly galling to many infectious disease specialists.

“I think we’ve done a horrible job from day one in data tracking for the pandemic,” said Eric Topol, a professor of molecular medicine at Scripps Research and former advisory board member of the Covid Tracking Project, a team that worked to collect and synthesize local Covid-19 during the peak of the pandemic. “We’re not tracking all the things that we need to to get a handle on what’s going on. It is embarrassing.”

Meanwhile, other Western countries have tapped into their modern health systems that can easily track patient data and seamlessly share epidemiologic information across a broad spectrum of health care facilities and public health departments. Because of the lack of accurate and timely domestic data, Biden health officials over the last eight months have increasingly relied on international sources to respond to domestic surges in part because they believe the information is more reliable, the officials said.

The administration’s dependence on international data underscores the extent to which the U.S. public health data infrastructure is still failing to produce real-time data on not only the spread of the virus but also the degree to which the virus evades the vaccine and the degree to which it impacts various American populations. It also raises questions about whether the American public health system, supported by state health departments, will be able to sustain itself under the inevitable deluge of Omicron cases that will pop up across the U.S. in the coming months.

With the emergence of Omicron, public health officials across the country told POLITICO that the current level of investment by the federal government to improve the country’s data systems is not enough to overhaul their existing surveillance systems to a degree that they can handle another massive surge or another pandemic like Covid-19.

In an interview with POLITICO, Dan Jernigan, the deputy director of the CDC’s Public Health Science and Surveillance office, acknowledged that the CDC had not yet secured additional future funding to improve state data collection — funding supplemental to the money it earmarks for data modernization annually.

“It will be very important that we identify ways to have sustainable support for these non-categorical activities like data modernization,” Jernigan said. “That’s something that we look to our partners in Congress to identify how best to support the ongoing need for maintaining a good data infrastructure.”

Lacking comprehensive domestic data, U.S. scientists and health officials have in recent months examined information from Israel, the United Kingdom and India to understand how the Delta and Omicron variants are transmitted, how they impact both the vaccinated and unvaccinated communities and which public health policies work best at stopping their spread.

Two top Biden health officials said they often look overseas for answers because the newer variants have spread more quickly in other regions of the world first and data from those areas are critical in helping the U.S. prepare for future surges.

Anthony Fauci, the president’s chief medical adviser, told POLITICO the administration is primarily using South Africa data to study the transmissibility of the Omicron variant as well as its infectious nature.

“There’s a lot of data that’s coming in from a lot of different places. It’s coming in from the U.K., it’s coming in from Israel, it’s coming in a lot from South Africa, which is ahead of the rest of the world in the experience they’re having with Omicron,” Fauci said. “We’ve gotten virus either in the live virus form or in the pseudo virus form. But we don’t have enough of this in the United States to be able to bank on our own clinical experience which is in contrast to the South Africans who are in real time experiencing the clinical impact of Omicron.”

But even as the Delta variant spread across the U.S. over the summer and the country gathered more information about cases and hospitalizations, the administration continued to rely on data from other countries, according to the two senior health officials and another individual with direct knowledge of the matter.

In interagency health and high-level White House meetings, health and White House Covid-19 officials have lamented that U.S. epidemiological data is lacking in speed and accuracy and have advocated that the administration use data collected by international allies while considering policies on vaccinations and booster shots, those sources said.

“We’re relying on everyone else’s data. We should be providing data to the world and we are not,” said Zeke Emanuel, a bioethicist and former member of President Biden’s transition Covid-19 advisory board. “We started [the pandemic] with a serious problem of not enough data and bad data infrastructure. We have not made the structural investments we need. The ideal is that we have real time data. And we don’t have that. We’re not even close to that.”

Health advocates, scientists, doctors and health officials have long highlighted the importance of improving U.S. public health data systems and ensuring they more accurately predict and manage the spread of diseases and viruses. But with diminishing federal funding, state health officials said they have struggled to make the necessary improvements to their data systems — improvements that would withstand the crush of a pandemic. When Covid-19 emerged in the U.S., those data systems failed.

State and local public health departments and the CDC have tried to gather information on Covid-19 cases, investigate outbreaks and translate epidemiological data to the public as quickly as possible. But outdated data systems that require significant manual data entry, slow laboratory reporting and a dwindling local public health workforce have hampered those efforts.

Jernigan, of the CDC’s surveillance office, said the agency has allocated billions of dollars in funding to provide upgrades to those systems.

“What we’re focusing on is really changing how the data gets collected, changing where that data lands, like what kind of platform you put that data into, and then really changing the way that CDC gets the data and uses that data … to help make the work better and make investigations faster,” Jernigan said.

The CDC has allocated funding to states and public health labs across the country to ramp up genomic sequencing efforts. That effort seems to be paying off. With the outbreak of the Omicron variant in the U.S. this month, state health departments in Washington and New York received samples and detected the variant in less than 48 hours — a far shorter period of time than the weeks it took some labs during the height of the pandemic.

And in August, days after a POLITICO investigation revealed pandemic data gaps, the CDC announced it was using $29 million to create a new data forecasting center that will speed the delivery of critical public health data to federal decision makers.

The agency also ramped up its efforts to support states in improving their data systems and hire new, skilled employees to manage those systems by providing health departments with significant new funding, he said. State health officials from Wyoming, Arkansas, Vermont and the state of Washington all said they are finally working with teams that have the technical knowledge and depth to be able to make all the necessary changes needed to prepare for the next pandemic.

Specifically, those officials said, they are working with Jernigan and his team to find ways to create new platforms through which health care facilities, physicians and state health departments can electronically share patient case information, allowing health officials to quickly open new case investigations for specific viruses and diseases.

But it could take several years to implement, state officials said, which will require a level of federal funding that matches that which they’ve been receiving during the pandemic. The big question is whether Congress will make the necessary funds available to the CDC for disbursement. Without additional investment, local officials worry the funding will disappear in the coming year, reversing some of the progress they have made in fixing the country’s public health data problems.

“We have been a hole in public health and under invested in over the decades, we cannot delude ourselves to think that one time investments will be enough to regain the footing for public health across the country,” said Umair Shah, secretary for health in the state of Washington. “We must have strategic, smart, sustainable funding. Whether it’s Covid-19 today, or whether it’s the next emergency or pandemic tomorrow, we have to have significantly better capacity across the system otherwise we’re going to repeat what we saw previously.”

Confronting years of neglect

Before the Covid-19 pandemic hit, scientists and health officials warned that the U.S. public health system’s data infrastructure was crumbling and in need of revitalization.

Not only were the computer and data systems health departments rely on failing, but state health offices were losing experienced staff — dwindling state budgets over the previous ten years had forced many health departments to downsize.

Under the Obama administration, former CDC Director Tom Frieden used $40 million in federal funding to set up programs to improve and modernize U.S. public health data systems. The agency began doling out more money to states to improve their local surveillance systems. During the Ebola outbreak, it created a program called CCIPHER that allowed the agency, states and other federal partners to share vital epidemiological data.

Since then, states have continued to receive funding for data modernization purposes, but many public health officials said the money isn’t enough to make quick and substantial changes to their programing. States are still relying on the same systems they used close to a decade ago. Limited in part by the HIPAA privacy law, hospitals and public health departments continue to struggle to find ways to share data electronically.

State health departments have improved one piece of their surveillance process by setting up a system whereby labs could send in results electronically to state health offices, allowing officials there to crunch data more efficiently. But that effort could not withstand the deluge of Covid-19 cases.

At the height of the first surge in 2020, public health workers across the country scrambled to detect, investigate and track Covid-19 cases. As numbers quickly multiplied, officials drowned underneath a mountain of paperwork, sifting through lab reports and conducting contact tracing for individuals who had received positive results. And thousands of smaller labs that did not normally work with state health departments opened testing operations, sending results to health officials for review via fax and snail mail.

The sheer number of cases overwhelmed health departments where officials were used to investigating and tracking a few thousand cases of viruses and diseases a year. With Covid-19, departments had to process thousands of cases a week.

Outdated data systems routinely crashed and health officials were forced to manually enter information into systems that could not automatically download patient information from labs and hospitals. Significant lag times between when a laboratory detected a positive result, when the department could investigate the case and when the state reported it to the CDC hampered health officials’ ability to contain the virus.

At the federal level, the CDC could not visualize how Covid-19 was spreading across the country because it relied almost entirely on the states to provide it with epidemiological data. The CDC requires every state to report specific virus and disease information to its scientists who then study the data, track trends and create policy recommendations based on their analyses. But with state data backlogged and missing critical components, the CDC simply could not get a clear picture of how the virus was spreading.

Mapping the boundaries of the pandemic

When the Biden administration took office in 2021, CDC Director Rochelle Walensky set out to improve the way in which the agency gathered data by directing states to submit more timely Covid-19 data. But without significant funding to overhaul the existing, piecemeal approach the U.S. took to surveilling diseases, the country still lagged behind its international allies.

By May, the lack of clear-cut federal data on Covid-19, genomic sequencing and the state of vaccinations prompted tense conversations inside the upper echelons of the administration. Senior Biden health officials urged the CDC to do more to not only illicit better data from states, but to work more swiftly in completing its own epidemiological investigations — probes that often took months to complete.

Frieden appeared on Capitol Hill that same month and told lawmakers that the crumbling U.S. data infrastructure was one of the main reasons Covid-19 spread uncontrollably throughout the country, infecting millions of people.

“As Covid-19 spread through the country a year ago, we saw the devastating result of decades of underinvestment,” Frieden said in his May 2021 testimony. “Our nation had a patchwork of underfunded, understaffed, poorly coordinated health departments and decades out-of-date data systems — none of which were equipped to handle a modern-day public health crisis.”

In the weeks and months that followed, the Biden administration attempted to mitigate the fallout from the Delta variant. When it arrived in the U.S., the majority of the country had not received their first dose of the vaccine. Vaccine demand fell off, and health officials desperately tried to convince the hesitant to sign up for the shot.

By the summer, cases began to tick up again and hospitals quickly became overwhelmed with patients seeking medical care. Medical facilities and state health departments once again grappled with how to investigate new cases, issue quarantine orders and identify outbreaks in restaurants and other large-scale indoor facilities. States across the U.S. had implemented strict mask and testing guidelines, but Americans living in more conservative states, including those in the southern part of the country, refused to adhere to them. Cases multiplied and thousands died.

It wasn’t just the unvaccinated Americans who were getting sick — fully vaccinated individuals were testing positive, too. With scientists and epidemiologists already overwhelmed by normal Delta surveillance, the breakthrough infections added an extra layer of panic — particularly because they raised questions about the extent to which the vaccine was waning among the vaccinated community. Health officials worried that Americans would begin to think the vaccines did not work.

Despite the uncertainty about the vaccine’s effectiveness and the future severity of breakthrough infections, the CDC made the decision to stop tracking all breakthrough infections and instructed state health departments to do the same.

CDC officials decided in internal meetings that the agency would only track breakthrough infections that led to severe disease and hospitalization — the cases that would give them the most insight into how the virus impacted the vaccine’s effectiveness. Health advocates and scientists lambasted the decision, advocating the CDC use more data points to understand the full scope of breakthrough infections and to determine if Americans would eventually need booster shots. But even after the CDC tried to cut down on the number of infections states were responsible for reporting, local health officials still struggled to report on breakthrough hospitalizations, citing an inability to match hospital admission data with their immunization records.

During the same time, top Biden health officials including Fauci began relying heavily on data from Europe and Israel. Other countries were experiencing similar Delta surges but had begun not only tracking all breakthrough infections but launching investigations into the vaccine’s effectiveness.

“The U.S. system has real disadvantages, when compared with, for example, the Israeli or U.K. system. And it’s not strictly for public health. It’s about our whole healthcare system,” Frieden said in an interview of the administration’s recent reliance on international data. “We have health care facilities and laboratories, and they don’t easily talk with each other.”

Senior health officials and White House Covid-19 officials debated for weeks whether Americans needed booster shots and when the administration should advocate for their authorization.

The debate split officials, with some advocating that the U.S. did not yet possess clear data that showed Americans needed boosters. Those officials acknowledged that it would take time for the CDC to gather the necessary data from states to analyze the issue, but that the administration should allow the agency to move forward with its research before making any policy announcements.

Others, including Fauci and officials on the White House Covid-19 task force, presented data from Israel that showed fully vaccinated individuals were beginning to contract the Delta variant and that some of those individuals, particularly the elderly, needed hospital medical care. Fauci pushed the president and his top aides to consider moving forward with a broad booster strategy, one that would allow the disbursement of boosters to all age groups on a rolling basis as soon as they were authorized and approved by the Food and Drug Administration.

The administration decided instead to create an eligibility system, one that would provide a pathway for vaccine makers to submit booster applications to the FDA for approval for specific age groups. The administration decided the priority should be given to nursing-home residents and frontline health workers before expanding access to other groups based on their vulnerability. In the meantime, White House and health officials pushed the CDC to quickly complete and release its ongoing investigations into breakthrough infections and vaccine hesitancy — investigations health officials believed would prove that America should begin distributing booster shots.

In mid-September, months after the Delta variant had begun gaining ground in the U.S., the CDC finally released vaccine efficacy studies that showed breakthrough infections in vaccinated people were rare but that fully vaccinated Americans’ immunity to Covid-19 was waning as the Delta variant spread across the country. And, the studies showed, the vaccine’s effectiveness was waning against hospitalization in the elderly.

Now, as more Americans begin to receive their booster shot, state health officials say they are still trying to find a way to match immunization records with patient case data. And with the spread of the Omicron variant, officials are raising questions with the CDC about whether the agency will continue to distribute funds that would allow health departments to carry on with their modernization efforts into 2022 and beyond.

Can the data crisis be fixed in time?

Since the beginning of 2020, the federal government has allocated hundreds of millions of dollars to each state across the country for the specific purpose of helping public health departments fight Covid-19.

Some of those federal dollars have gone directly toward data modernization efforts — for the improvement and strengthening of the data systems so state and local officials can more accurately detect and contain infectious diseases. The efforts to, for example, create national and state systems for electronic case management, existed well before Covid-19 emerged in the U.S. But the CDC ramped up funding during the pandemic to cut down the time it would take for states and healthcare providers to integrate new approaches to sharing data.

Jernigan said the CDC data modernization team has created what he calls a “strategic implementation plan” with five “priority areas” that focus on improving the way health care facilities, health departments and the CDC collect and process data.

The CDC is currently working on creating a system in coordination with the Association of Public Health Laboratories whereby health care facilities and labs collect patient data and input it into a computer program using the same kind of electronic messaging. The system is intended to allow state health departments to synthesize data easily and track trends. Jernigan said state health departments can connect with immunization and laboratory data that will allow them to see if a patient has tested positive, if they received care and if they died.

The only problem: State health officials have not yet found a way to connect their existing data platforms with that new system, which could take years and significant more funding to complete.

“It is an enormous effort,” said Theresa Sokol, lead epidemiologist in the Louisiana health department. “We think we have the funding to support at least starting to get it off the ground, but with all of these data modernization efforts you really need continued funding to be able to support the continued operation.”

With the funding that the federal government has made available to Louisiana, Sokol said, her office has focused on contracting with laboratories to expand their genomic sequencing capacity. The health department does not currently have the capacity to sequence, but it is working on building that infrastructure. Louisiana has also used the funding to work with new labs that entered the Covid-19 testing space over the last year and could only send test results through faxes and snail mail to begin reporting electronically.

In Arkansas, the health department has spent the past year boosting their surveillance efforts, hiring new employees to expand case investigations and contact tracing. In the state of Washington, Shah said his department has spent money upgrading its platforms so epidemiologists do not have to enter as much manual data before opening a case investigation and tracking an outbreak. Washington has also stopped trying to investigate every case, concentrating instead on individuals associated with superspreader events, or who have recently tested positive for Omicron, in order to prevent additional surges.

Dozens of states have also spent CDC money to hire skilled employees, to replace old data systems and to work to ensure the entire surveillance process, from data collection to contact tracing, is completed electronically.

“I was an epidemiologist that wore a lot of hats. I did electronic lab reporting, did database management for surveillance systems and did the surveillance itself and analysis for different outbreaks. And with Covid, it was very clear that that needed to change and I couldn’t do it all,” said Veronica Fialkowski, Vermont’s health surveillance epidemiologist. “With that funding, we were actually able to establish a team that now I lead.” Fialkowski said that team has several different employees who work on electronic lab reporting, electronic case management and surveillance.

While the allotment of money from the federal government amounts to more than what state health departments receive in normal times, local and state officials worry the funding will disappear in the coming years, reversing some of the progress they’ve made.

“I don’t expect to have a yearly budget of $300 million,” said Mike Cima, the lead epidemiologist at the Arkansas health department. “I understand that that’s probably unrealistic. But the investment in public health at the state and local level is imperative. That lesson could not be any more clear from what we have experienced throughout this pandemic.”

States are still waiting to see whether Congress will pass the Build Back Better bill, which includes $7 billion to support the improvement of public health infrastructure across the country and whether some of that funding will be earmarked specifically for modernizing the nation’s data systems.

Jernigan said the CDC is in contact with lawmakers on Capitol Hill about securing more funding to ensure states have what they need to continue to build on their current data modernization programs.

“The data modernization initiative is a multi-year program,” Frieden told POLITICO. “The fact is that our data systems don’t talk well to each other and aren’t well standardized — that is not the CDC’s fault. That is the reality of healthcare in the United States. It’s very hard to collect effective data, and public health is tired.”


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