U.S. tracking of virus variants has improved after a slow start


After a slow start, the United States has improved its surveillance system for tracking new coronavirus variants (such as omicron), and has added tens of thousands of samples per week since the beginning of this year.

The virus keeps mutating. In order to discover and track the new version of the coronavirus, scientists analyzed the genetic makeup of some samples that tested positive.

They are studying the chemical letters of the viral genetic code to find new and worrying mutants, such as omicron, and to track the spread of known variants (such as delta).

This is a global effort, but until recently, the United States’ contribution was small. Due to uncoordinated and scattered testing, the United States sequenced less than 1% of positive samples earlier this year. Now it is running these tests on 5% to 10% of the samples.

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

Contributing to this work are nearly 70 state and local public health laboratories, which sequence 15,000 to 20,000 samples every week. Other laboratories, including those operated by the Centers for Disease Control and Prevention and its contractors, total 40,000 to 80,000 per week.

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

Kenny Beckman of the University of Minnesota said: “We are in a much better situation than a year ago or even six or nine months ago,” he believes that federal funds are allocated to public and private laboratories. He leads the university’s genomics laboratory, which now sequences approximately 1,000 samples from Minnesota, Arkansas, and South Dakota every week. A year ago, the laboratory did not perform sequencing.

Relying on President Joe Biden’s $1.7 billion Coronavirus Relief Act, the United States has been building a national network to better track mutations in the coronavirus.

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Dr. William Moss of the Bloomberg School of Public Health at Johns Hopkins University said that there are still about 20 countries that have a higher rate of sequencing of positive samples than the United States. The emergence of Omicron may “spur the United States to do better in this regard.”

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

In addition to monitoring, a standard PCR test using nasal swabs sent to the laboratory can detect signs that someone may have an omicron variant. If the PCR test only tests positive for two of the three target genes—the so-called S-dropout test result—even before an additional gene sequencing step is performed to prove it, it is a marker for omicron.

“It was accidental,” said Trevor Bedford, a biologist and genetics expert at the Fred Hutchinson Cancer Research Center. “If you need to sequence to identify mutations, you will always lag a little bit, and the cost will be higher. If you just rely on this S-dropout for identification, then it will be easier.”

He said that other variants also caused this quirk in PCR test results, but not delta variants. Bedford said that because delta is currently so dominant in the United States, the S-dropout results will attract attention. (Bedford received funding from the Howard Hughes Medical Institute, which also supports the Associated Press Department of Health and Science.)

Dr. Anthony Fauci, a top US infectious disease expert, said that omicron’s entry into the United States is “inevitable.”

Many experts said that it may already be here and will soon be discovered by the surveillance system. But the question is, what then?

David O’Connor, an AIDS researcher at the University of Wisconsin, points out: “We don’t have the kind of interstate travel restrictions that can control the virus anywhere.”

He said, instead, genomic monitoring will tell officials whether omicron is spreading abnormally fast somewhere and whether more resources should be sent to those places.

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When omicron emerges, public health authorities will have to consider other variables in their classification work, such as the level of infection and vaccination rates that already exist in the community. Severe outbreaks in highly vaccinated areas are particularly worrying.

Nonetheless, Beckman of the University of Minnesota believes that there is no benefit in substantially increasing sequencing.

He said: “You don’t need to rank more than a few percent of the positive cases to feel the growth rate.”

Unlike some other countries, US government officials have not exercised their power to force people to quarantine if they test positive for the worrying variant. In view of this, sequencing is mainly a surveillance tool to track the spread of mutations.

“I think tracking variants is important, but I think it is impractical to think that we will be able to quickly and extensively sequence to prevent the tracking of variants,” Beckman said.



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