"Moving forward," the letter says, "it will be even more challenging to perform meaningful inter-state comparisons, and to understand which COVID-19 mitigation strategies were successul (or failed)."
When asked by CNN, HHS did not confirm if it had received the letter. Members of the committee said that the CDC, which is part of HHS, was informed of the letter.
The Trump administration said the change would streamline the data collection process, but it swiftly drew criticism from public health officials.
"It's another example of CDC being sidelined. Not only should the data be coming to CDC, but CDC should be talking to the public through the media every day," Besser told CNN.
This recent letter shared similar concerns.
"We are extremely concerned about this abrupt change in Covid-19 reporting," the letter said. Retiring the CDC system that was in operation would have "serious consequences on data integrity."
By removing the data collection from the CDC, the country would lose decades of expertise in interpreting and analyzing information about infectious disease and it would jeopardize the department's goals of developing interventions that would improve public health, the letter said.
Hospitals have extensive experience sending crucial data to this system and trust that it appropriately tracks and analyzes the data, the letter said.
Since hospitals now have to change the way they report the data, they have had to rely on local public health experts or hospital associations to change reporting and management of data. Making the shift during a pandemic puts this important data at risk, the letter writers argue.
"As past and present HICPAC members, we are troubled by the Administration's unexpected decision to divert Covid-19 data reporting from CDC to DHHS," the letter said. "We strongly advise that the CDC's DHQP data experts be allowed to continue their important and trusted work in their mission to save lives and protect Americans from health threats."
During the pandemic, the University of Michigan accepted the most inter-hospital transfers of patients compared to any other hospital in the state, Chopra said; the NHSN data served as an important warning system that helped the hospital understand how the pandemic was unfolding in real time.
"We knew how to input data, how to extract data, and we know how to access it for prediction purposes," Chopra said in an email. "In contrast, the new data system has many inconsistencies," including with cases reported, bed occupancy numbers and that data itself is often out of date.
Many hospitals, he said, have struggled to understand how to us the new system and aren't entering data consistently.
"In other words, the new system has made intelligent calculations to inform real time decisions almost impossible," Chopra wrote.
Chopra said the committee and many of his colleagues felt pushed to write the letter.
"I think the core problem that bothers many of us is it's unclear why this change was made," Chopra wrote. "The system as we knew it worked very well and did inform us in the height of the pandemic. We see no real reason to change it and certainly no good appears to have come from it."
In a statement to CNN, an HHS official said the CDC system "was unable to keep up" with the demands of the pandemic.