In-Depth: The flaw with U.S. efforts to track coronavirus variants

In-Depth: The flaw with U.S. efforts to track coronavirus variants

By Derek Staahl

May 25th, 2021

SAN DIEGO (KGTV) — The announcement of $1.75 billion in federal funding has rapidly expanded efforts to sequence genetic information from COVID-19 viral samples in search of troublesome variants, but scientists say more work needs to be done to address a key limitation in the nation’s early warning system.

Across the country, labs are now sequencing about 35,000 viral samples each week, or about 10 percent of all confirmed cases, according to Mary Lee Watts of the American Society for Microbiology.

That’s up from just 0.3 percent in early February, when U.S. labs were sequencing about 8,000 genomes per week.

It’s an encouraging sign of progress, but researchers say the work to modernize the nation’s genomic surveillance infrastructure is just getting underway. The bulk of the $1.75 billion allocated in the American Rescue Plan began rolling out this month, and the money will be distributed for the next few years.

“It’s an extremely important investment that has the ability to transform how we bring that genomic technology to the front lines of public health,” she said.

Here in San Diego County, health officials have detected more than 280 people infected by variants in the last month thanks to a collaboration with Scripps Research Institute and UC San Diego.

The data they collect can reveal which mutations are becoming more prevalent and where certain variants are spreading. But the numbers don’t answer some important questions.

“Is a certain variant causing a difference in the type of infection? Is the infection longer or shorter? Is there more mortality or lower mortality? Is it causing more ICU or less ICU admissions?” said Karthik Gangavarapu, a researcher at Scripps.

Gangavarapu can see the genetic code from each sample, but he can’t see how sick those patients got. Those two pieces of information are not linked together, and scientists say that’s a big flaw with our nation’s genomic surveillance system.

Having the full electronic health record linked to the viral sequence would be “extraordinarily powerful,” said Dr. Gary Firestein, UC San Diego’s Associate Vice Chancellor for Health Sciences.

The combination would help “determine which variants we should worry about, which ones should be the ones that we’re going to make the next generation of vaccines, and so on,” he said.

There are some complicated, but not insurmountable, issues standing in the way involving privacy laws and data portability, Firestein said.

For example, how do you convert a doctor’s written notes about an X-ray or a pathology report into usable data? Exactly which health outcomes matter?

“There’s really no standardized way, not just in the U.S. but anywhere, for really being able to transfer that sort of information in a consistent way,” he said.

The $1.7 billion for genomic surveillance in the American Rescue Plan will be divided up into three buckets. One billion will go to the Centers for Disease Control and Prevention and states to bolster their existing surveillance efforts.

Another $400 million will be used to establish six Centers of Excellence in Genomic Epidemiology. These centers will operate as partnerships between state health departments and academic institutions, according to the White House, to “fuel cutting-edge research into genomic epidemiology.”

The final $300 million will be used to build a National Bioinformatics Infrastructure. “This investment will support bioinformatics throughout the U.S. public health system, creating a unified system for sharing and analyzing sequence data in a way that protects privacy but allows more informed decisionmaking,” the White House said in a statement.

The funding for genomic surveillance in the American Rescue Plan was originally proposed in legislation co-sponsored by Rep. Scott Peters (D-San Diego).

He said the money will improve many aspects of the U.S.’s early warning system against viral threats, but he acknowledged it won’t fully solve the problem of data sharing.

“I’ve been banging this drum since last year before there was a Biden administration,” he said. “The problem is we have too many data silos that don’t talk to each other. In the federal government alone, there were 13 different agencies that touch your COVID health data. It’s a patchwork and it doesn’t make any sense.”

Rep. Peters has proposed a separate bill to help link health records with other information, including sequence data, to help stay ahead of this virus and the ones to come.