As Congress lurches toward passing a final deal to keep the government running until January 15, researchers across the nation say their work—some of it already compromised by the budget sequestration–will suffer lasting damage as a result of the 16-day shutdown.

Some of that damage will be tangible. Researchers were reportedly slated to euthanize scores of lab mice and revamp budget plans to accommodate the delay. Other impacts will be more subtle. “Research is an iterative process, and quite often something happens that is an ‘aha’ moment,” says Georges Benjamin, executive director of the American Public Health Association. “We will never know how many of those ‘aha’ moments were missed.”

Health surveillance may take some time to recover. Every fall the U.S. Centers for Disease Control and Prevention begin monitoring the flu, identifying emerging flu strains and figuring out their vaccination game plan. The shutdown forced the agency to furlough 8,754 people—some two thirds of its staff—weakening the agency’s ability to monitor flu and support state and local monitoring efforts. The CDC should now expect a deluge of requests from states, says William Schaffner, a flu expert at the Vanderbilt University School of Medicine and former president of the National Foundation for Infectious Diseases. “When the government reopens there will be a splurge of requests because [states] held back and there will be a backlog that will have to be evaluated.”

Basic lab operations came to a screeching halt for a host of projects attempting to make headway against blood cancer, pediatric cancers and HIV during the shutdown, with potential ripple effects as the government opens back up for business. Juan Bonifacino’s lab at the National Institute of Child Health and Human Development, for one, had discovered the role a certain protein plays as asymptomatic infection progresses to AIDS but testing of a new class of potential HIV medications had to be stopped due to the shutdown. A trial of a new treatment for blood cancer also could not be initiated because of the shutdown.

Impacts of the shutdown also threaten to skitter across national borders. The closure left many federally funded scientists unable to attend international meetings, says Caroline Smith DeWaal, director of the food safety program for the Center for Science in the Public Interest. A Brussels-based meeting with the Trans Atlantic Consumer Dialogue, which brings consumer organizations from both sides of the Atlantic together to discuss food and intellectual property, was slated for the end of the month, but no U.S. representatives are committed to being there, she says. “It is not clear we will get representation from the U.S. government,” she says.

With the threat of another government shutdown looming once the current deal lapses in January, some researchers may be hesitant to start their work anew, Benjamin says. The concern, he says, is that researchers might need to yet again leave their work during a critical stage, resulting in loss of data and soaring costs. “Your research grant won’t increase just because it’s going to cost you x more to do the project,” he says. “In some cases, having to spend more money than anticipated for the project may actually totally change the way in which research will get done.”