Inside Louisiana’s battle to control the Delta variant

Eighteen months into the pandemic, Louisiana and more than 20 other states are still trying to fill key gaps in data while fighting the most aggressive version yet of the virus. With new cases continuing to snowball, schools reopening and the holidays still to come, state health officials are bracing for a rough fall — and the possibility that a new, even more dangerous variant could emerge in the coming months.

“It is a little bit like we’re back at the beginning because cases are going up so quickly. hospitalizations have gone up so quickly … testing has gone up so quickly,” said Lee Mendoza, director of Health Informatics in the Louisiana health department, in a recent interview. “The demands on our time, both in terms of data requests, information and additional reporting is just really increasing at a pace that’s very difficult.”

Contact tracing efforts have dwindled in Louisiana and across the country over the last year, under a crush of cases and staff shortages. Thousands of labs are still not sending in test results electronically, slowing health departments’ surveillance operations — a catastrophic delay in the face of Delta, which is two to three times more contagious than the original version of the coronavirus.

Health officials in at least 20 states told POLITICO their data systems and the patchwork surveillance process were never going to hold up against Delta.

Louisiana — which is now struggling with the aftermath of Hurricane Ida — has managed the data deluge better than most states have. It’s dedicated resources toward breaking down Covid infection data by race and ethnicity as well as studying breakthrough infections and waning vaccine immunity. The state’s health department has also implemented measures to help streamline data collection, hiring vendors and creating ad hoc systems to fill reporting holes.

While the health department still cannot perform genomic sequencing in-house on virus samples, it has partnered with academic institutions to ramp up the number of samples it sends for sequencing each month. In June, the state had sequenced 418 Covid-19 specimens. By the end of July that number jumped to 1,672.

But Louisiana is still not sequencing as many samples as it wants, and that along with lab glitches and errors in hospitalization information have created blind spots in key data sets. Because of that, and the fact that most Louisiana adults are forgoing Covid-19 vaccines, state health officials predicted cases would spike uncontrollably as Delta took hold.

And they did.

Delta’s wrath

As July began, Louisiana had reported a little more than 10,700 Covid-19 deaths and about 482,000 cases. Roughly 30 percent of its population was vaccinated.

By the end of August, another 1,550 people had died and 194,000 had become infected, according to the CDC. More than 14,200 of those cases were among the fully vaccinated, Louisiana health officials said. During that period, roughly 500,000 people received the first shot of the vaccine.

Those numbers reflect a reality that is difficult for public health officials and physicians in Louisiana to talk about. To recognize their data systems faltering, case investigations slowing and Delta surging around them is to admit that they were unable to keep up with the variant despite their best efforts.

When asked about their efforts to collect data, streamline reporting and analyze the data, health officials often replied with a sigh. The worst part, they said, is that the breakdowns in gathering and processing that information were largely avoidable.

Health officials have for years called for the federal government to devote more resources to rebuilding the country’s crumbling public health infrastructure. States often track diseases in different ways, their systems do not talk to one another and they do not always allow officials to load case data automatically from one outbreak investigation to the next.

The warnings of damaging data gaps were loud and consistent across the public health world. But seemingly no one in the federal government responded with urgency, dozens of health officials have told POLITICO. So, when cases began rising again earlier this summer, Louisiana public health officials geared up for another devastating surge.

The state health department was still struggling with a major issue as Delta arrived: Getting testing labs to report results electronically, in a format the Louisiana government systems could understand and synthesize.

The health department had spent months trying to fix the problem, said Louisiana’s lead epidemiologist, Theresa Sokol. But as summer began her team was still working with labs to wean them off delivering results by mail or fax — options that delayed state investigations of cases and outbreaks, and strained staff, Sokol said.

“It would have been nice to have had everything in place for electronic laboratory reporting that could accommodate the volume of lab reports that we’re getting, and also to be able to have staff and be prepared to onboard the number of new reporters that we’ve seen,” Sokol said. “There’s nobody who was prepared for that.”

Louisiana dedicated more time and resources to ensuring the non-electronic test results arrived at the department as quickly as possible. But that required staffers spending extra hours in the office to find new and better ways to ensure the data they had in front of them was as up to date as possible.

“When you look at the amount of data that we’re having to process … it’s like building a plane as it flies,” Mendoza said.

Confusion mounts

As health officials in Louisiana sought better ways to control Delta’s spread and blunt rising case numbers, federal health leaders were only just beginning to understand the threat posed by the variant.

Studies in Israel and the United Kingdom showed Delta was much more transmissible than earlier versions of the virus and caused hospitalization rates to spike sharply in under-vaccinated communities. But at the time, Biden administration health officials were still wary about the accuracy of those reports. They wanted to study Delta domestically.

CDC officials called the Louisiana health department over the course of the summer to inquire about rising case numbers. To Louisiana’s health experts, it seemed that the federal government didn’t understand the danger Delta presented. There were no reliable national statistics to show how quickly Delta was spreading and where it predominated. And the CDC was still trying to understand how easily the variant infected people, including those who were fully vaccinated.

That left Louisiana and other states in the dark, grasping for answers from the federal government about whether they should consider recommending mask mandates and closing or limiting certain types of businesses.

By mid-July, summer camps and large indoor gatherings had sent cases soaring in Louisiana, Sokol said. Contact tracers and case investigations couldn’t keep up. And hospitals in New Orleans, Baton Rouge and Lafayette were overwhelmed by the constant influx of patients.

“Everyone was just trying to figure it out,” one senior Biden health official said. “We’d never seen anything like Delta and we had to pull on a lot of different data streams to try and prepare for more surges.”

But the CDC’s infectious disease reporting network was messy — disjointed and cumbersome. The agency regularly relies on state health departments to send in data on disease outbreaks, including Covid-19. But state health departments do not have the resources or data systems in place to regularly send the CDC quality and up-to-date case and outbreak data.

And not every health department has access to its state’s vaccination records. Others cannot match immunization registries with hospitalization data, limiting the CDC’s ability to understand the full scope of how Delta affected vaccinated and unvaccinated people.

In July, the CDC asked states to send in hospitals’ reports on the number of Covid cases they were treating. It also launched a study with Louisiana and other states to study all breakthrough infections, not just those infections that led to hospitalization. The results are still pending.

The surge

As July stretched into August, hospitalization numbers in Louisiana jumped again. To physicians and state health officials, it was clear the Delta variant was transmitted more easily than previous strains. Hospitals began to see younger individuals arrive seeking care — a change from past surges when older people with other health problems that increased their vulnerability to the virus needed the most acute attention.

“There was a visual test if you get Covid, looking at a patient who is diabetic and obese and they have these risk factors, they’re not going to do well,” said Tonya Jagneaux, a critical-care doctor at Our Lady of the Lake Regional Medical Center in Baton Rouge, during a July interview. “Now we can’t say that. I can’t look at the person and say you’re going to die or do poorly because there’s Delta. And Delta is not only infectious, but is more aggressive. And it’s coming after people who would never see themselves as a potential victim of the disease.”

Without rigorous contact tracing operations, it was impossible to pinpoint clusters of transmission and to know exactly what made people more susceptible to severe disease, beyond their vaccination status.

Communication between the federal government and states had also dwindled, according to interviews with dozens of state health officials. The Biden administration’s regular briefings with governors’ offices became less frequent, and health departments said they had a difficult time reaching senior CDC officials, many of whom were consumed with launching or analyzing their own national Delta studies. Several state health officials said they only learned about the CDC’s thinking on the variant through the press or White House press conferences.

It wasn’t until July 28 that the CDC released data backing up its recommendation that fully vaccinated people should again wear masks indoors. The evidence suggested that fully vaccinated people who are infected with Delta carry similar levels of the virus to those seen in infected and unvaccinated people. But the data failed to answer one critical question: whether infected, vaccinated people without symptoms could transmit the virus as easily as those who had symptoms.

By the time the CDC announced its new mask guidelines, Delta had invaded large swaths of Louisiana. Many residents of the state did not adhere to the federal government’s recommendations on masking and social distancing.

Physicians at Our Lady of the Lake were stretched thin. Dozens of nurses and physicians had quit over the past year, burned out from treating Covid-19 patients. Others had left for better paying traveling medical jobs. And the demand for treatment was once again pushing the facility to its limits.

“We have 68 Covid patients here today,” the hospital’s medical director, Catherine O’Neal, said in an interview in late July. O’Neal said she was running on only a few hours of sleep and her husband, also a doctor, had been called in to help attend to critically ill Covid-19 patients at Lafayette General Medical Center.

She and her staff were scrambling to find ways to make room for more Covid-19 patients. The ICU was full and so was the hospital across the street. And there were not enough doctors to treat the patients who already had beds.

“What’s most startling is just the sheer number of cases and the speed with which they’re coming,” O’Neil said. “Everybody’s getting infected super fast.”

Breakthroughs

As case rates continued to spike throughout August, federal health officials insisted that the risk of infection after vaccination was rare. Even rarer, they said, were cases that landed fully vaccinated people in the hospital.

But state health officials were beginning to see rising numbers of infections in vaccinated people. Louisiana, unlike many other states, had the ability to match the state’s vaccination registry with its Covid-19 lab results. Its health department dedicated a team to tracking breakthrough infections.

But that team did not have the ability to match lab results with hospitalization data, which would reveal how many vaccinated people with Covid-19 required that level of care. Instead, health officials relied on hospitals to report breakthrough infections to the state. And the information that arrived was often outdated and incomplete.

Local hospitals like Our Lady of the Lake were laboring to get a hold of real-time data on which patients were fully vaccinated and infected when admitted. The hospital uses the EPIC medical system, an electronic platform that thousands of health care networks across the country rely on to digitize records. But EPIC didn’t have a function that allowed physicians to easily track breakthrough infections.

“EPIC didn’t necessarily have a solution right away. Some of that was manual in the beginning,” O’Neal said. “We do the manual entry through our infection control and prevention department which reviews every case anyway. We added that to their list of things to do.”

Despite the patchy hospital data across the country, the CDC had decided in May to only track breakthrough infections that resulted in hospitalization. At the time, the agency said it wanted to study the most severe cases to get a better understanding of whether and how vaccine effectiveness wanted overtime.

By August, Louisiana had recorded 14,000 breakthrough infections. But the CDC, with its narrower tracking, counted only 8,000 hospitalized breakthrough cases nationwide.

The agency is still reviewing data from the subset of states participating in its study looking at all breakthrough infections, not just those that have been hospitalized. The results could help states better understand whether they need to change their policies on issues like masks and social distancing to safeguard their residents in the coming months.

In the meantime, Sokol said her team is doing their best to find new ways to improve its data collection efforts with children back in schools, more offices reopening, and the possibility than new and dangerous variants will emerge.

While the CDC has begun to dole out millions of dollars to help states better their staffing and data collection, health officials in Louisiana and elsewhere say the improvements require more money and will take years to implement.

For now, Louisiana’s health officials are dedicated to keeping residents of the state informed about any important changes in how the coronavirus is behaving. But they and other states are limited by deep flaws in the country’s public health infrastructure that make it hard or even impossible to collect accurate and reliable Covid-19 data.

“We know how important it is to have the right information and be able to do that as quickly as possible,” Mendoza said. “But there’s always going to be a trade-off between how rapidly we can report and the accuracy of the information that we report.”