After a slow start, the United States has improved its surveillance system to track new variants of the coronavirus


After a slow start, the United States has improved its surveillance system to track new coronavirus variants such as omicron, increasing its capacity to tens of thousands of samples per week since the start of this year.

Viruses are constantly mutating. To find and track new versions of the coronavirus, scientists are analyzing the genetic makeup of some of the samples that test positive.

They examine chemical letters in the virus’s genetic code to find disturbing new mutants, such as omicron, and track the spread of known variants, such as delta.

It’s a global effort, but until recently the United States contributed very little. With uncoordinated and scattered testing, the United States sequenced less than 1% of positive samples earlier this year. Now he runs these tests on 5-10% of the samples. It’s more in line with what other countries have sequenced and shared with global disease trackers during the pandemic.

“Genomic surveillance is strong,” said Kelly Wroblewski, director of infectious diseases at the Association of Public Health Laboratories.

Nearly 70 national and local public health laboratories, which sequence 15,000 to 20,000 samples each week, are contributing to this effort. 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 per week.

Nine months ago, approximately 12,000 samples per week were analyzed in this way.

“We’re in a much better position than a year 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 runs the university’s genomics lab, which now sequences about 1,000 samples per week from states such as Minnesota, Arkansas and South Dakota. A year ago, the laboratory did not do any sequencing.

Relying on $ 1.7 billion from President Joe Biden’s coronavirus relief bill, the United States has established a nationwide network to better track coronavirus mutations.

Still, about two dozen countries sequence a greater proportion of positive samples than the United States, said Dr William Moss of the Johns Hopkins Bloomberg School of Public Health. The emergence of Omicron could “spur the United States to do better.” “

“I think we still have a long way to go,” Moss said.

Some states only sequence about 1% of samples while others are in the order of 20%, noted Dr. Phil Febbo, chief medical officer of Illumina, a San Diego-based company that develops technologies for detection. genomic sequencing.

“We could be more systematic about this and more consistent to make sure that there aren’t any genomic surveillance deserts where we could miss the emergence of a variant,” Febbo said.

To aid in the surveillance effort, standard PCR tests that use nasal swabs sent to labs can pick up a sign that someone likely has the omicron variant. If a PCR test is positive for just two of the three target genes – a so-called S drop test result – it’s a marker for omicron even before the extra step of genetic sequencing to prove it.

“It’s fortuitous,” said Trevor Bedford, biologist and genetics expert at the Fred Hutchinson Cancer Research Center. “If you have to do sequencing to identify the variant, you will always be a little late and it will cost more. If you just rely on this S-dropout for identification, it’s easier.

He said other variants triggered this quirk in PCR test results as well, but the delta variant did not. With the Delta so dominant in the United States right now, an S dropout result will be noticed, Bedford said. (Bedford receives funding from the Howard Hughes Medical Institute, which also supports the Associated Press’s Department of Health and Science.)

Dr Anthony Fauci, the nation’s foremost infectious disease expert, said it was “inevitable” that omicron would make its way to the United States.

Many experts said it was probably already there and would soon be detected by the surveillance system. But the question is, so what?

University of Wisconsin AIDS researcher David O’Connor noted, “We don’t have the kind of interstate travel restrictions that would keep the virus in one place. “

Instead, genomic surveillance will tell authorities if omicron is spreading abnormally quickly somewhere and whether more resources need to be sent to those locations, he said.

When omicron emerges, public health authorities will need to consider other variables in their triage efforts, such as the level of infection already present in that community and the vaccination rate. Serious epidemics in heavily vaccinated areas would be of particular concern.

Still, Beckman of the University of Minnesota sees little benefit from dramatically speeding up sequencing.

“You don’t need to sequence more than a few percent of positive cases to get a feel for how quickly it grows,” he said.

Unlike some other countries, U.S. government officials have not wielded the power to force people to self-quarantine if they test positive for disturbing variants. In view of this, sequencing is primarily a surveillance tool to track the spread of mutations.

“I think it’s important to follow the variations, but I don’t think it’s practical to think that we’re going to be able to sequence quickly and broadly enough to stop a variation in its tracks,” Beckman said.

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