“The thing I’m concerned about is continuity of our surveillance data while this protest is playing out,” said Chad Gubala, a wastewater official in Juneau, Alaska.

After an open bidding process earlier this year, the CDC decided to replace its longtime contractor, Biobot, with Verily, a subsidiary of Google’s parent company, starting in September.

But the transition is on pause. And while the Government Accountability Office hears Biobot’s appeal, Verily can’t do its work, according to a company email obtained by POLITICO. A GAO decision is due in January.

Bradley White, the principal scientist for the Verily wastewater lab, said that the company is ready to go, with much of its infrastructure already built.

“We are committed to working with the CDC to advance the goals of the … testing program, initiate testing on the samples already delivered when allowed to resume work, and make wastewater data available as quickly as possible,” White said.

In an interview, CDC Director Mandy Cohen declined to comment on the specifics of the dispute, saying it was a “contracting situation.”

The CDC has not explained why it decided to change contractors, though its deal with Verily is considerably less expensive.

Verily’s contract is for $38 million over five years. Biobot’s most recent contract was for about $31 million over less than a year and a half.

Cohen said the agency does see wastewater surveillance as an important “tool to add to our toolbox in terms of early detection,” adding that she wants to expand the testing through the new contract.

Wastewater testing was particularly helpful during the pandemic in detecting Covid surges. And with fewer people than before testing themselves for the disease or reporting results when they do, it’s one of the best remaining ways to see where the virus is spreading.

Public health officials have also used wastewater to find Mpox and spikes in opioid use.

A quarter of the nation’s testing sites — some 400 in “a handful of states and territories” — are shut down because of the dispute, the CDC said, while the remaining 1,200 sites are not covered under the contract and can continue work.

A CDC spokesperson said the agency felt that was enough to maintain a “pretty comprehensive” picture of Covid and Mpox spread, but others are skeptical.

“The existing gap in the wastewater data will continue for possibly several months as we head into flu season and another Covid surge,” said one state health department epidemiologist who wasn’t authorized to speak publicly. “It’s not as easy as just handing the keys to Verily.”

A second state health department official who wasn’t authorized to speak publicly, agreed that changing vendors — protest aside — could harm Covid surveillance efforts this fall and winter. “It’s the time that it takes to turn the ship to get it done,” the official said.

Even if Verily is able to begin work soon, some foresee problems related to the continuity of the data.

“The loss is the loss of historical comparability. It’s like starting from day zero with a new surveillance system,” said David Larsen, chair of the public health department at Syracuse University and a wastewater surveillance researcher. “It’s not ideal to change methods.”

A CDC spokesperson said the issue will be addressed but declined to say how.

Biobot declined to comment on the protest, citing the “ongoing legal review.”

CEO Mariana Matus wrote in a LinkedIn post that the company had already laid off 35 percent of its staff because of the contract decision.

“We know that this decision had nothing to do with our past performance,” Matus wrote.

Chelsea Cirruzzo contributed to this report.