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‘This Time We Got Lucky': Virus Variants Reveal Gaps in Tracking

Jan. 19, 2021, 6:47 PM

New Covid-19 variants that appear to spread easier than the original strain are sparking concerns that the U.S. system for tracking the virus isn’t keeping pace with mutations.

Some scientists say that even though testing works now, health officials need to be better prepared for variants down the road or risk not being able to properly detect the SARS-Cov-2 virus. They’re calling on the Biden administration to invest more in genomic sequencing, a process that involves collecting the DNA blueprint of an organism.

A new mutation that can hide from a common testing procedure, like the variant that surfaced in the U.K. does—albeit not significantly—marks a “serious tremor before a quake,” Fyodor Urnov, a professor in the University of California, Berkeley’s Molecular and Cell Biology Department, said. While the variant does hide from one part of the test, most tests use multiple procedures to look for different parts of the SARS-Cov-2 virus, which for now negates the variant’s ability to avoid detection.

But without a national sequencing effort, the U.S. leaves itself vulnerable to more serious mutations down the line. Not just of SARS-Cov-2, but of any virus.

Sequencing Covid-19 variants is a piecemeal process in the U.S., typically happening in academic institutions or local labs. Some labs are forwarding suspected variant samples to the Centers for Disease Control and Prevention for sequencing. The CDC says it’s working to “expand its ability” to track Covid-19 and new variants.

“This is a preview of what will be a recurrent problem,” Urnov said. “The United States of America has to have a federally supported effort to sequence a lot more virus, collect the data in a national database, and make those data available to all who work on molecular test development.”

‘Most Wanted’

Urnov equates virus mutations to an outlaw changing their appearance and requiring law enforcement officials to update the sketch on their “Most Wanted” poster.

In this case, the poster is a molecular test. From a virus standpoint, the way to create the sketch is through genomic sequencing. That’s how scientists detect when a virus has mutated.

Right now, it doesn’t appear the mutation seriously impacts Covid-19 tests used in the U.S. The Food and Drug Administration warned this month that three tests “may be impacted by genetic variants” of the virus, but that “the impact does not appear to be significant.” Covid-19 vaccines will still work too, doctors say.

But there’s no way of knowing exactly what will come down the variant pipeline, and some scientists want to be better prepared so the nation isn’t caught flat-footed.

“This time, we got lucky,” Urnov said.

Why Tests Still Work

The mutation that was originally detected in the U.K. is found on the virus’s “spike gene,” Kimberly Hanson, a physician and professor at the University of Utah School of Medicine, said on a Covid-19 testing panel in early January.

Many tests that do target that gene, like a widely-used test by Thermo Fisher Scientific, typically also target two other parts of the SARS-Cov-2 virus.

Thermo Fisher’s test has three gene targets, and scientists only need to hit two out of three targets to determine a test is positive and that person has Covid-19, Hanson said. So even though one testing procedure doesn’t pick up the new variant, there are two others that do and act as a safety net.

Antigen tests, or rapid tests, typically target something besides the spike protein, “so the vast majority of our tests should be in good shape,” Angela Caliendo, a physician and professor at Alpert Medical School at Brown University, said. She spoke at the Infectious Diseases Society of America panel with Hanson.

Eric Blank, the chief program officer for the Association of Public Health Laboratories, doesn’t expect major Covid-19 variants to knock the U.S. testing strategy off kilter.

He said current tests will likely still be able to detect future variants, but it remains to be seen how much the virus will mutate.

“We expect we’ll see more and more of this over time and it’ll be a more prevalent thing as time goes on,” Blank said of virus mutations. From a public health standpoint, that means “we have got to get better about getting vaccines in arms.”

Biden’s Testing Plan

The incoming administration says it supports a nationwide testing effort that includes genomic sequencing. Part of the president-elect’s pandemic strategy is to “build better preparedness,” according to his pandemic response outline released Jan. 14.

Biden wants to use $11 billion for a variety of pandemic preparedness efforts, including global efforts to “build the capacity required to fight COVID-19, its variants, and emerging biological threats.”

Scientists hope that means that going forward, the U.S. will see a more robust, nationwide sequencing system than the current piecemeal approach.

The new administration is “perfectly positioned to have might of federal government to support the integration of the might of American science,” Urnov said.

To contact the reporter on this story: Jacquie Lee in Washington at

To contact the editors responsible for this story: Fawn Johnson at; Alexis Kramer at

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