After a slow start, the United States has improved its surveillance system for tracking new coronavirus variants such as omicron, boosting its capacity by tens of thousands of samples a week since early this year.
Viruses mutate constantly. To find and track new versions of the coronavirus, scientists analyze the genetic makeup of a portion of samples that test positive.
They’re looking at the virus’s genetic code to find new worrisome mutants, such as omicron, and to follow the spread of known variants, such as Delta.
It’s a global effort, but until recently the United States was contributing very little. With uncoordinated and scattershot testing, the U.S. government was sequencing fewer than 1% of positive specimens earlier this year. Now, it’s running those tests on 5% to 10% of samples — which is more in line with what other nations have sequenced and shared with global disease trackers over the course of the pandemic.
“Genomic surveillance is strong,” said Kelly Wroblewski, director of infectious diseases for the Association of Public Health Laboratories.
Contributing to the effort are nearly 70 state and local public health labs, which are sequencing 15,000 to 20,000 specimens each week. Other labs, including those run by the federal Centers for Disease Control and Prevention and its contractors, bring the total to 40,000 to 80,000 weekly.
Nine months ago, about 12,000 samples a week were being analyzed in this way.
“We’re in a much, much better place than a year ago or even six or nine months ago,” said Kenny Beckman of the University of Minnesota, who credited federal dollars distributed to public and private labs.
Beckman directs the university’s genomics laboratory, which now sequences about 1,000 samples a week. A year ago, the lab did no sequencing.
Relying on $1.7 billion in President Joe Biden’s coronavirus relief bill, the United States has been setting up a national network to better track coronavirus mutations.
Still, about two dozen countries are sequencing a larger proportion of positive samples than the United States, said Dr. William Moss of the Johns Hopkins Bloomberg School of Public Health. Omicron’s emergence could “stimulate the United States to do this better.”
“I think we still have a long way to go,” Moss said.
Some states are sequencing only about 1% of samples while others are in the range of 20%, noted Dr. Phil Febbo, chief medical officer for Illumina, a San Diego company that develops genomic sequencing technologies.
“We could be more systematic about it and more consistent so we ensure there are no genomic surveillance deserts where we could miss the emergence of a variant,” Febbo said.