CDC invested $1.75B to improve coronavirus variant data, but it could be going to waste

The widespread COVID-19 infection rates, genetic diversity and high number of people vaccinated against COVID-19 makes the U.S. an ideal place to study the genetic evolution of the novel coronavirus. However, experts with firsthand genomic sequencing experience during the pandemic told MIT Technology Review the country's legal and infrastructural obstacles make it almost impossible to turn genomic surveillance data on coronavirus variants into insightful takeaways.

The CDC and WHO set a goal of sequencing 5 percent of COVID-19 cases to track the spread of variants and quickly reached that goal, mostly through private testing labs. The $1.9 trillion COVID-19 relief package President Joe Biden signed into law March 11 allocated $1.75 billion for genomic sequencing of diseases and infections, including COVID-19. 

However, the CDC's surveillance sequencing program does not link sequences back to the people they originated from, their vaccination status or their clinical outcome. Understanding  when variants escape immune systems can inform researchers on how to redesign vaccine formulas, but that information cannot be obtained because all sequences the U.S. collects from labs are de-identified due to patient privacy and other regulatory requirements.

Duncan MacCannell, PhD, chief science officer of the CDC's Office of Advanced Molecular Detection, told MIT Technology Review the agency does plan on contextualizing the de-identified data with clinical information. "Those contracts are set up to give us the 10,000-foot view," he said.

Even if the CDC set out to connect its surveillance sequences with patient information, most patient records are spread throughout many disparate databases. It is up to the owners of that information whether they share it with the government, so obtaining consent from each entity would be time-consuming and inefficient.

"It's insanely difficult to do this well in the United States," Lane Warmbrod, PhD, senior analyst at the Johns Hopkins Center for Health Security told MIT Technology Review. "I would be very disappointed if all this money just went to getting a whole bunch of covid sequences, and no thought went toward building something that lasts."


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