Inside Louisiana's battle to control the Delta variant

Eighteen months after the pandemic began, Louisiana and more than 20 other states are still trying to fill important data gaps while tackling the most aggressive version of the virus to date. With the ongoing snowball of new cases, schools reopening, and the holidays yet to come, state health officials are preparing for a tough case – and the possibility that a new, even more dangerous variant could emerge in the coming months.

“It’s a bit like we’re back to the beginning because the cases are increasing so quickly. Hospital admissions have increased so quickly … tests have increased so quickly, “Lee Mendoza, director of health informatics for the Louisiana Department of Health, said in a recent interview. “The demands on our time, both in terms of data requests, information and additional reporting, are really increasing at a very difficult pace.”

Contact tracing efforts have declined in Louisiana and across the country over the past year due to a large number of cases and staff shortages. Thousands of laboratories are still not submitting test results electronically, slowing health authorities’ surveillance operations – a disastrous delay in the face of Delta two to three times more contagious than the original version of the coronavirus.

Health officials in at least 20 states told POLITICO that their data systems and patchwork monitoring process would never withstand Delta.

Louisiana – now grappling with the aftermath of Hurricane Ida – has handled the flood of data better than most states. These are dedicated resources to break down data on Covid infections by race and ethnicity, as well as to study breakthrough infections and dwindling vaccine immunity. The state health department has also taken steps to streamline data collection, hire providers, and put in place ad hoc systems to close reporting holes.

While the health department is still unable to perform genome sequencing of virus samples in-house, it has partnered with academic institutions to increase the number of samples it sends out for sequencing each month. In June, the state sequenced 418 copies of Covid-19. By the end of July, that number had risen to 1,672.

But Louisiana still isn’t sequencing as many samples as it would like, and that, along with lab glitches and errors in hospitalization information, has created blind spots in critical records. Because of this, and the fact that most adults in Louisiana skip Covid-19 vaccines, state health officials predicted that cases would rise uncontrollably as Delta prevailed.

And they did.

Delta’s anger

At the beginning of July, Louisiana had reported just over 10,700 Covid-19 deaths and about 482,000 cases. About 30 percent of the population has been vaccinated.

By the end of August, another 1,550 people had died and 194,000 infected, according to the CDC. More than 14,200 of these cases were among the most fully vaccinated, Louisiana health officials said. During this time, around 500,000 people received the first vaccination.

These numbers reflect a reality that Louisiana public health officials and doctors find difficult to talk about. Realizing that their data systems are stalling, case investigations are slowing down, and Delta is rampant around them, means admitting that despite their best efforts, they have not been able to keep up with the variant.

When asked about their efforts to collect data, streamline reporting, and analyze the data, health officials often responded with a sigh. Worst of all, they said, the glitches in the collection and processing of this information were largely avoidable.

Health officials have been calling on the federal government for years to allocate more resources to rebuilding the country’s crumbling public health infrastructure. States often track disease in different ways, their systems don’t communicate with each other, and they don’t always allow officials to automatically load case data from one outbreak investigation to the next.

Warnings of harmful data gaps have been loud and consistent across the public health world. But apparently no one in the federal government has responded with any urgency, dozen of health officials told POLITICO. So if cases Started to rise again earlier this summer, Louisiana public health officials prepared for another devastating surge.

When Delta arrived, the state Department of Health was still grappling with a major problem: getting test labs to report results electronically, in a format that Louisiana’s government systems could understand and synthesize.

The health department had spent months fixing the problem, Louisiana senior epidemiologist Theresa Sokol said. But when summer started, her team was still working with labs to dissuade them from delivering results by mail or fax – options that delayed government investigations of cases and outbreaks and overwhelmed staff, Sokol said.

“It would have been nice to have everything in place for electronic lab reporting that could accommodate the amount of lab reports we received, and also to be able to have staff and be ready to accommodate the number of new reporters we’ve seen, ”said Sokol. “Nobody is prepared for that.”

Louisiana has spent more time and resources making sure the non-electronic test results get through the department as soon as possible. However, this required employees to spend extra hours in the office trying to find new and better ways to ensure that the data they had in front of them was as current as possible.

“When you look at the amount of data we have to process … it’s like building an airplane while it’s flying,” Mendoza said.

Confusion mounts

As Louisiana health officials looked for better ways to control the spread of Delta and the bluntly increasing number of cases, federal health officials were only just beginning to understand the threat posed by the variant.

Studies in Israel and the United Kingdom showed that Delta was much more transmissible than previous versions of the virus and greatly increased hospitalization rates in undervaccinated communities. but At the time, the Biden government health officials were still suspicious of the accuracy of these reports. They wanted to study Delta domestically.

CDC officials called the Louisiana Health Department over the summer to inquire about rising case numbers. To Louisiana health experts, it appeared that the federal government did not understand the danger Delta posed. There were no reliable national statistics showing how quickly delta was expanding and where it was prevalent. 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, seeking answers from the federal government on whether to consider recommending mask mandates and closing or restricting certain types of businesses.

By mid-July, summer camps and large indoor gatherings had boosted the cases in Louisiana, Sokol said. Contact tracing 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 find out,” said a senior Biden health official. “We had never seen anything like Delta and had to pull up a lot of different data streams to prepare for further surges.”

But the CDC’s infectious disease reporting network was untidy – disjointed and cumbersome. The agency regularly relies on state health officials to provide data on disease outbreaks, including Covid-19. But the state health departments don’t have the resources or data systems to do it on a regular basis Submit CDC quality and current case and outbreak data.

And not every health department has access to the vaccination cards of their federal state. Others cannot match vaccination registries with hospital stay data, which limits the CDC’s ability to understand the full extent of Delta’s impact on vaccinated and unvaccinated individuals.

In July, the CDC asked states to submit reports from hospitals on the number of Covid cases they treated. It has also started a study with Louisiana and other states to investigate all breakthrough infections, not just the infections that led to hospitalization. The results are still pending.

The rise

As July stretched into August, hospitalizations in Louisiana rose again. It was clear to doctors and state health officials that the Delta variant was easier to transmit than previous strains. Hospitals began to see younger people seeking care – a change from earlier waves when older people with other health problems that made them more susceptible to the virus needed the most urgent attention.

“There was an eye test when you got Covid. If you look at a patient who has diabetes and obesity and has these risk factors, you are not going to do well,” said Tonya Jagneaux, an intensive care doctor at Our Lady of the Lake Regional Medical Center in Baton Rouge during an interview in July. “We can’t say that now. I can’t look at the person and say that they are going to die or do badly because Delta is there. And Delta is not only contagious but also more aggressive. And it’s about people who would never see themselves as potential victims of the disease. “

Without rigorous contact tracing, it was impossible to locate clusters of transmission and know exactly what made people more susceptible to serious illness beyond their vaccination status.

Communication between the federal government and the states had also decreased, according to interviews with dozens of state health authorities. The Biden government’s regular briefings with governors’ offices became less frequent, and health officials said they were having a hard time reaching out to high-ranking CDC officials, many of whom were busy starting or running their own national Delta studies analyze. Several state health officials said they only learned of the CDC’s deliberations 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 individuals return to wearing masks indoors. The evidence suggested that fully vaccinated people infected with Delta had virus levels similar to infected and unvaccinated people. However, the data could not answer one critical question: whether infected, vaccinated people without symptoms could transmit the virus just as easily as those who had symptoms.

By the time the CDC announced its new mask guidelines, Delta had invaded much of Louisiana. Many state residents failed to follow federal government recommendations on masking and social distancing.

Our Lady of the Lake doctors were few and far between. Dozens of nurses and doctors quit last year because they were burned out from treating Covid-19 patients. Others had left for better-paying medical trips. And the need for treatment once again pushed the facility to its limits.

“We have 68 Covid patients here today,” said the hospital’s medical director, Catherine O’Neal, in an interview at the end of July. O’Neal said she only slept a few hours and that her husband, also a doctor, had been called to care for seriously ill Covid-19 patients at Lafayette General Medical Center.

She and her staff were looking for ways to make room for more Covid-19 patients. The intensive care unit was full, and so was the hospital across the street. And there weren’t enough doctors to treat the patients who already had beds.

“The scariest thing is just the sheer number of cases and the speed with which they come,” said O’Neil. “They all get infected very quickly.”

Breakthroughs

As the number of cases continued to rise in August, federal health officials insisted that the risk of infection after vaccination was rare. Cases in which fully vaccinated people ended up in hospital are even rarer.

But state health officials began to see increasing numbers of infections among people who had been vaccinated. Unlike many other states, Louisiana had the option of comparing the state’s vaccination registry with its Covid-19 laboratory results. The health department has set up a team to track breakthrough infections.

However, this team was unable to match laboratory results with hospital stay data, which would show how many people vaccinated with Covid-19 needed this level of care. Instead, health officials relied on hospitals to report breakthrough infections to the state. And the information received was often out of date and incomplete.

Local hospitals like Our Lady of the Lake worked to get real-time data on which patients were fully vaccinated and infected at admission. The hospital uses the EPIC medical system, an electronic platform that thousands of healthcare networks across the country rely on to digitize records. But EPIC didn’t have a feature that would allow doctors to easily track breakthrough infections.

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

Despite patchy hospital records across the country, the CDC decided in May to only track breakthrough infections that resulted in hospitalization. At the time, the agency said it wanted to investigate the most serious cases to get a better understanding of whether and how the vaccine’s effectiveness requires overtime.

As of August, Louisiana had recorded 14,000 breakthrough infections. But the CDC, with its close follow-up, counted only 8,000 breakthrough cases in the hospital nationwide.

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

In the meantime, Sokol said her team is doing their best to find new ways to improve data-gathering efforts with children in schools, more offices to reopen, and the possibility of new and dangerous variants emerging.

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

Right now, Louisiana health officials are keen to keep state residents informed of important changes in coronavirus behavior. But they and other states are constrained by deep flaws in the country’s public health infrastructure that make it difficult or even impossible to collect accurate and reliable Covid-19 data.

“We know the importance of having the right information and being able to do it as quickly as possible,” said Mendoza. “But there will always be a tradeoff between the speed we can report and the accuracy of the information we report.”

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