US tracking of virus variants improved after slow start

After a late start, the United States has improved its surveillance system to track new coronaviruses Variants such as Omicron has been increasing capacity with tens of thousands of samples per week since the beginning of this year.

The virus constantly mutates. To find and track new versions of the coronavirus, scientists analyze the genetic makeup of some of the samples that test positive.

They examine the chemical letters of the virus’s genetic code to find new and interesting variants such as Omicron and track the spread of known variants such as Delta.

This is a global initiative, but until recently the United States made little contribution.Unadjusted scatter shot test, U.S.A. It was sequencing Less than 1% of positive specimens earlier this year. We are currently running these tests on 5% to 10% of our samples. This is more consistent with what other countries have sequenced, Share with global disease trackers In the process of a pandemic.

“Genome surveillance is powerful,” said Kelly Broblevsky, Head of Infectious Diseases at the Institute of Public Health.

Approximately 70 state and local public health laboratories contribute to this effort, sequencing 15,000 to 20,000 specimens each week. In other laboratories, including those operated by the Centers for Disease Control and Prevention and its contractors, the total is 40,000 to 80,000 per week.

Nine months ago, about 12,000 samples were analyzed this way each week.

“We are in a much better place than a year ago, and even six or nine months ago,” said Kenny Beckman of the University of Minnesota. He directs the University’s Genomics Institute and currently sequences about 1,000 samples per week from states such as Minnesota, Arkansas, and South Dakota. A year ago, the lab didn’t run the sequence.

Depends on $ 1.7 billion President Biden’s Coronavirus Relief Bill, The United States has established a national network to better track coronavirus mutations.

Still, about 20 countries are sequencing more positive samples than the United States, says Dr. William Moss of the Johns Hopkins Bloomberg School of Public Health. The advent of Omicron could “stimulate the United States to make this better.”

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

Dr. Phil Febbo, Illumina’s chief medical officer who is based in San Diego and developing genomic sequencing technology, has sequenced only about 1% of samples in some states and 20 in others. It states that it is in the range of%.

“We guarantee that there are no genomic surveillance deserts that could miss the emergence of mutants, as we are more systematic and more consistent about it,” Febbo said.

Standard PCR tests using a nasal swab sent to the laboratory to support monitoring efforts can detect signs that someone probably has the Omicron variant. If the PCR test is positive for only two of the three target genes, the results of the so-called S dropout test are Omicron markers, even before additional steps in gene sequencing to prove it. ..

“It’s a coincidence,” said Trevor Bedford, a biologist and genetics expert at the Fred Hutchinson Cancer Research Center. “Whenever you need to run a sequence to identify a variant, there is always a slight delay and cost. It’s easy if you just use this S dropout as an identification.”

He said other variants also caused this habit in PCR test results, but not the delta variant. According to Bedford, Delta Air Lines is currently so dominant in the United States that the results of the S dropout will be noticeable. (Bedford is funded by the Howard Hughes Medical Institute, which also supports the Associated Press’s Department of Health Sciences.)

Dr. Anthony Fauci, a leading infectious disease expert in the United States, said Omicron’s entry into the United States is “unavoidable.”

Many experts have stated that it is probably already here and will soon be picked up by surveillance systems. But what’s the question then?

David O’Connor, an AIDS researcher at the University of Wisconsin, said: “There is no interstate travel ban that can contain the virus in one place.”

Instead, genome surveillance will tell authorities if Omicron is spreading abnormally fast somewhere, and if more resources should be sent to those locations.

When Omicron surfaced, public health authorities need to consider other variables in their triage efforts, such as the level of infection and vaccination rates already present in the community. Serious outbreaks in highly vaccinated areas will be of particular concern.

Still, Beckman of the University of Minnesota believes that there is little benefit to significantly enhancing the sequence.

“You don’t have to sequence more than a few percent of positive cases to feel how fast it’s growing,” he said.

Unlike some other countries, US government officials do not exercise the power to force people to quarantine if they test positive for the variant they care about. With that in mind, sequencing is primarily a monitoring tool for tracking the spread of mutations.

“I think it’s important to track the variant, but I don’t think it’s feasible to think that the sequence can be run fast and wide enough to stop the variant on that track,” Beckman said. I am saying.