U.S. to spend $1.7 billion to detect, monitor coronavirus variants

By Tyler Pager and Joel Achenbach,

The Biden administration announced Friday that it is allocating $1.7 billion to detect and monitor mutations in the coronavirus that have led to the emergence of more transmissible and potentially more deadly variants.

The White House said a central goal of the effort will be to increase the country’s capacity for genomic sequencing, in which virus samples are scrutinized in laboratories for their genetic makeup.

The funding, which comes from the American Rescue Plan and will be allocated through the Centers for Disease Control and Prevention, includes $1 billion to expand genomic sequencing; $400 million to support innovation, including establishing six Centers of Excellence in Genomic Epidemiology; and $300 million to build and support a national bioinformatics infrastructure.

The money will be distributed to states in two batches. The first will be sent in early May, and the second round will be invested over the next several years.

“At this critical juncture in the pandemic, these new resources will help ensure states and the CDC have the support they need to fight back against dangerous variants and slow the spread of the virus,” White House coronavirus testing coordinator Carole Johnson said in a statement.

An earlier investment of $200 million from the White House helped U.S. laboratories scale up genomic sequencing from 8,000 coronavirus samples a week in early February to 29,000 samples a week. The latest round of funding will help the CDC and states identify variants and monitor their circulation.

The new centers will operate as partnerships between state health departments and academic institutions, and could focus on developing surveillance tools to better track pathogens. The national bioinformatic infrastructure will create a unified system for sharing and analyzing data.

More than 565,000 Americans have died of covid-19, and the country has seen an upturn in infections in the past month. But the United States has made significant strides in its vaccination drive, with more than 198 million doses administered.

The funding announced Friday “is unquestionably a good move that will likely help with the pandemic and potentially many other infectious diseases as well,” said William Hanage, an epidemiologist at the Harvard T.H. Chan School of Public Health. “On paper the plans look great, including innovation and funding targeted to states to help them. As ever, the impact will depend on the implementation, but this is an opportunity for the country to level up.”

The initially feeble capacity for genomic sequencing hampered the battlefield awareness of U.S. officials as new variants began to spread. In December, the CDC reported that only about 3,000 positive test samples were being scrutinized for their genetic makeup each week, at a time when more than 1 million cases a week were being reported and the true infection numbers, including undiagnosed cases, were believed by experts to be several times as high.

With the bombshell announcement in Britain on Feb. 15 that a new, more transmissible variant, named B.1.1.7, was responsible for a sudden spike in cases there, U.S. officials realized they needed to ramp up sequencing. That build-out of capacity involved not only federal researchers but also partners in private labs and academic institutions.

Even as the sequencing improved in scale, the variants — and particularly the one seen first in Britain — gained traction in the United States.

The B.1.1.7 variant is now the dominant strain of the virus in the United States, according to the CDC.

Two other worrisome variants, first seen in South Africa and Brazil, have had less success in spreading in the United States. But scientists are watching them closely because they contain a mutation known as E484K, nicknamed “Eek,” that can reduce — though not entirely eliminate — the efficacy of vaccines. And there are other variants spreading rapidly, including one seen first in California and one common in New York City.

“In this ecosystem of variants, we don’t know how they’re going to compete against one another in the same space,” said Nicholas Gilpin, an infectious-disease doctor with Beaumont Health, which runs eight hospitals in the Detroit area.

The coronavirus continues to mutate as it circulates through the global population. With millions of infections worldwide each day, the virus has plenty of chances to improve its ability to spread or evade immunity.

“You can have accumulation of additional mutations that promote immune evasion,” said Mark Zeller, a virologist with the Scripps Research Institute, noting that variants could emerge from immunocompromised patients who are treated for coronavirus infections over protracted periods.

There is no evidence that the variants are a driving force behind the tiny number of “breakthrough infections” that have occurred among fully vaccinated people. Most experts believe those breakthrough cases are due to poor immune system response, not to mutations in the virus.