‘We’re in the dark’: The U.S. is way behind on testing for dangerous COVID variants

Other countries, such as the U.K., have established robust, nationwide surveillance programs to identify new COVID genomes and track the spread of existing ones. But the U.S. has not: It ranks 32nd in the world for the number of sequences completed per 1,000 COVID cases, according to data from GISAID, a global database where researchers share new genomes.

While the Biden administration is promising to boost the country’s sequencing efforts, it won’t be easy. The U.S. system now in place includes a scattered constellation of academic, commercial and public health labs that typically are both underfunded and under-resourced. This amounts to a gaping hole in national security at a time when at least three dangerous global variants have already been identified and others are yet to be unearthed.

“The problem is that this was never a public-health lab priority,” said Michael Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota, and an adviser to U.S. President Joe Biden. ”Most of the sequencing was going on in private labs.”

Moving forward, he said, is about “making it a priority and getting it done.”

Over the past week, federal health officials promised to increase the U.S. ability to track variants. “We are now scaling up both our surveillance of these and our study of these,” said Rochelle Walensky, the new director of the U.S. Centers for Disease Control and Prevention, on “Fox News Sunday.” But the administration has yet to outline concrete steps to turn the current effort into a cohesive and efficient national program.

In the U.S., about 200,000 Americans test positive for COVID-19 weekly. But only about 3,000 of those tests are sequenced to hunt for mutations, according to the CDC. The low rate is behind not only nations known for their genomic prowess, such as the U.K. and Iceland, but also behind Gambia, Senegal and Latvia, according to the GISAID listings.

Effective tools

Creating a viral surveillance network “is a public health need, but also a defense need,” said Francis deSouza, chief executive officer of the sequencing giant Illumina Inc., which has been working with partners to help monitor the virus’s evolution.

“Understanding how the virus is mutating will tell you whether the tools you’re using to combat the virus will continue to be effective,” deSouza said.

The three variants that have raised concerns among scientists and public health experts were identified in the U.K, South Africa and, most recently, Brazil. The Brazil variant was identified in a Minnesota resident who had recently traveled to that country, the Minnesota Department of Health said. That suggests the variant may not yet be widely circulating in the U.S.

The highly transmissible U.K. variant has already been found in more than 20 American states. The Brazil variant, meanwhile, was identified for the first time in the U.S. this week, in a Minnesota resident who recently returned from a trip to that country.

Moderna Inc. on Monday expressed concern that the South Africa variant may cause vaccination immunity to wane more quickly. The Cambridge, Massachusetts-based company said in a statement that it plans human studies of a booster shot for its vaccine because of that concern.

“When you have something that maybe is twice as readily transmitted than something else, that alone is going to cause a problem because the more people that get infected, the more people are going to get hospitalized,” said Anthony Fauci, the top U.S. infectious-disease doctor, referring to the U.K. variant.

Frequent mutations

SARS-CoV-2, the cause of COVID-19, mutates frequently, though not as often as the virus that causes influenza, scientists have said.

While most mutations will have no significant impact on COVID-19’s ability to infect, the U.K. and South Africa variants appear to have the ability to infiltrate the bodies’ cells better than the original form of the virus. That could make them more contagious.

The B.1.1.7 variant that emerged in southeast England in September, for example, contributed to a surge in cases that in January sent the U.K. back into a lockdown. By early January, cases caused by this variant had also been identified in some 50 countries or territories, including the U.S., Australia, Canada, Germany, Italy, Japan, Lebanon, the Netherlands, Singapore and South Korea.

The effort to advance the U.S. sequencing efforts began in May, when the CDC established a consortium of sequencing labs known as the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance consortium, or SPHERES.

Spotty efforts

But within the U.S., sequencing efforts have been spotty at best. As of January, California — with 3 million COVID-19 cases — had sequenced more than 9,000 cases. Texas, with more than a million cases, sequenced nearly 15,000. But Virginia, where cases are approaching a half-million and on the rise, has sequenced just 7 viral genomes.

Eric Topol, the director of Scripps Research Translational Institute, says that existing sequencing programs are in part the result of serendipity and sweat. Scripps is a participant in the SPHERES program and does receive some funding from it, he said, but not nearly enough to cover the cost of significantly scaling up its sequencing operation.

The institution’s pre-existing relationship with San Diego County, where Scripps is based, allows them to get hold of patient samples to sequence. But he added, “it requires resources to do this, and there has been no formal system put in place.”

Generally, he said, “there hasn’t been respect for genomic surveillance. The U.K. variant was a wake up call for how pathetic things are here.”

Policy decisions

Sequencing can be extremely important to understanding how the virus is spreading, and whether mutations might be able to interfere with the effectiveness of newly developed vaccines. But Topol said sequencing can also help inform other aspects of public health policy.

“We see case rates go up and we don’t know if that’s because people aren’t doing the right things in terms of staying home and masking and social distancing, or whether it’s a variant,” he said. “We’re in the dark.”

At Illumina, deSouza said his company hasn’t maxed out its sequencing capacity. “What we need” he said, “is a centrally-led government program.”

The U.K. sequences about 10% of its positive COVID-19 cases. In stressing how much work the U.S. needs to do to catch up, deSouza said the U.S. is sequencing around 0.3%.

Ramping up

Illumina’s own lab is ramping up in hopes of sequencing 3,000 samples per day, according to the company. Illumina has partnered in its sequencing efforts with DNA testing firm Helix and the CDC. Helix recently launched a public-facing dashboard to track variants. So far they have found 130 cases of the U.K variant in the U.S.

Such a program is needed not just in response to the current pandemic, he said, but to track over time other emerging zoonotic diseases as well, including so-called superbugs and potential bioterror threats.

Even the type of sequencing done in the U.S. has been lacking, some experts say, with much of the effort focused on finding cases of the U.K. variant, rather than casting a wider net for any variant, including ones not previously identified, said Jeremy Kamil, a virologist at Louisiana State University Health Sciences Center Shreveport.

“It’s the Wild West,” he said. “Every state, city, county is doing its own thing. It’s a bunch of random cats and no one is trying to herd them.”