US tracking of virus variants has improved after slow start

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 per 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 chemical letters of 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 U.S. was contributing very little. With uncoordinated and scattershot testing, the U.S. was sequencing fewer than 1% of positive specimens earlier this year. Now, it is running those tests on 5% to 10% of samples.

“Genomic surveillance is strong,” said Kelly Wroblewski, director of infectious diseases at 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 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 each 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. He directs the university’s genomics laboratory, which now sequences about 1,000 samples a week from Minnesota, Arkansas and South Dakota. A year ago, the lab did no sequencing.

Relying on $1.7 billion in President Joe Biden’s coronavirus relief bill, the U.S. has been setting...