Originally Published: 05 MAY 23 11:01 ET

Updated: 05 MAY 23 14:19 ET

By Brenda Goodman, CNN

(CNN) -- When the US public health emergency ends May 11, the US Centers for Disease Control and Prevention will have to change some of the ways it tracks Covid-19 in the United States, but the agency says it won't lose its sightlines on the infection as it continues to be part of American life.

On Thursday, for the first time in three years, the CDC will stop posting a national count of Covid-19 cases. The agency's color-coded maps of county-level transmission and disease burden will be retired, the CDC will no longer track variants down to the state level, and it will update its genomic surveillance estimates every two weeks instead of weekly.

"Though our data going forward will be different, they will continue to provide timely insights for CDC, for local health officials, as well as for the public to understand Covid-19 dynamics," CDC Principal Deputy Director Dr. Nirav Shah said.

"In short, we will still be able to tell that it's snowing, even though we're no longer counting every snowflake."

Instead of following Covid-19 cases, the agency will track the burden and spread of disease primarily through hospitalizations and deaths.

The move to stop posting a national case count is largely symbolic. The number of Covid-19 cases known to public health officials has long been undercounted. The percent of detected cases has only fallen further as people have turned to rapid home testing for a diagnosis. At some points in the pandemic, experts estimated that the true number of cases was more than 14 times higher than official counts.

Other metrics that people are used to seeing on the CDC's Covid Data Tracker are also going to go away. As CNN previously reported, the CDC will stop publishing detailed, color-coded Covid-19 Transmission Levels and Covid-19 Community Level maps that have been tied to recommendations about when to wear masks, when it's a good idea for people to test to prevent the spread of disease and when to avoid large indoor public gatherings.

When the public health emergency ends, more states are expected to stop reporting Covid-19 cases to CDC. Iowa, for example, has already stopped. So the CDC says it won't be feasible to maintain a national count or update its maps.

Future recommendations for precautions like masking will instead be tied to hospitalization levels.

Covid-19 will retain its designation as a nationally notifiable disease, but that's just a recommendation, says Dr. Brendan Jackson, who leads the CDC's Covid-19 response. It doesn't carry any authority for required reporting. When the public health emergency ends, it will be a state-by-state decision whether to share those numbers, Jackson said Thursday.

The CDC says it will still publish the case counts it gets from states, but that will be in a different section of its website, and the numbers won't be totaled.

Some experts say they're disappointed to see that the CDC will have to go back to an older, fragmented system of having to ask states to share data.

"We're kind of reverting back to a system where the CDC kind of independently negotiates all these data sharing agreements with the states and they make it more voluntary," said Beth Blauer, associate vice provost for public sector innovation at Johns Hopkins University.

"I think having the states do this all independently doesn't make a ton of sense because it doesn't help us understand, in the aggregate, the impact that disease is having on our communities," Blauer said.

She also said it will be very difficult to scale this system back up should another large, immediate public health threat emerge.

Data changes ahead

Starting next week, vaccination counts will become discretionary. Jackson said that most, but not all, of the 64 jurisdictions that report to the CDC have signed data use agreements to share their vaccine administration numbers. They may not share as much as they have in the past about who is getting vaccinated or do it as frequently, which may limit the nation's ability to spot widespread racial, ethnic or socioeconomic disparities for future vaccination campaigns. Starting in June, the CDC says, it will update its vaccination data on a monthly basis.

Laboratories will no longer be required to send testing data to the CDC, which will hamper the ability to understand test positivity rates, a metric that, early in the pandemic, helped public health officials know whether they were doing enough testing or if transmission in a community was going up or down. Positivity rates were used in the transmission maps but also for the CDC's tracking of variants.

The CDC will still get some lab testing data from another system called the National Respiratory and Enteric Virus Surveillance System, a network of about 450 labs that help it track illnesses like influenza and respiratory syncytial virus, or RSV.

Variant tracking will continue, but the CDC will have to adjust some of the metrics it uses to model variant proportions. State-level estimates of variant proportions with go away, but regional levels will remain. Those will be updated twice a month going forward instead of weekly, as they are now.

The way the CDC will collect data on deaths will change, too. Instead of scraping numbers from state website and getting direct reports from states, which counted deaths based on the date they were reported, the CDC will switch to a national system that counts deaths based on death certificate data. The agency says this system has become much more timely and will be a more stable way to count Covid-19 deaths going forward. It will also add a new metric to its death reporting: the percentage of all deaths reported that week that are caused by Covid-19.

Hospitals will still have to report Covid-19 data through April 2024, but they won't track as many metrics or submit that information as frequently. Hospitals have shared information daily through most of the pandemic, but now that reporting will be weekly.

Hospitalizations and deaths are known as lagging indicators because they increase only after people have gotten sick. Studies released Friday from CDC epidemiologists show that hospitalizations may not lag behind cases as much as we once thought they did.

The new studies, published in the CDC's Morbidity and Mortality Weekly Report, show that Covid-19 hospitalizations lagged one day behind increases in reported cases and four days behind increases in emergency room visits.

The research also shows that the new system the CDC will be using to track deaths will show trends 13 days earlier than data collected from states, the system that's being discontinued.

Covid-19 data needs are changing

With case levels low across most of the country, the need for these kinds of insights has gone away, or scientists have found other ways to get the information, such as testing of wastewater, which begins to increase about a week before testing data reflects an uptick in spread. Wastewater testing is available in some places, but not all areas have this capability.

The CDC will also maintain traveler surveillance, testing wastewater on airplanes in an effort to spot new incoming threats.

The CDC will also maintain what it calls sentinel systems: smaller, but nationally representative networks of hospitals and laboratories that will feed in more detailed data. This is much the same way the agency tracks patterns in other respiratory diseases, such as the flu and RSV. The CDC says recent investments in these sentinel systems will help it maintain eyes on Covid-19.

Instead, it will be using hospitalizations and emergency room visits as the primary ways it tracks Covid-19 and as the basis for its recommendations. When hospitalization rates in an area are high, for example, it will be recommending that people wear masks, said Jackson.

CDC Director Dr. Rochelle Walensky acknowledged some of these data changes in a Senate committee hearing this week, although she emphasized that the CDC was not "changing the steam" of its work on Covid-19.

"As the public health emergency is set to end next week, I do want to just reiterate that we at CDC are not changing the steam at which we are working through resolving this public health emergency," Walensky said at a hearing of the Senate Committee on Health Education, Labor and Pensions.

"It is the case at the end of the public health emergency, we will have less window as to the data," she said. "We won't get laboratory reporting. We won't get case reporting. So we'll lose some of that."