Labs hunting for omicron start their search with a clue in positive coronavirus tests
The hunt for the omicron coronavirus variant is on at 68 state and local public health labs across the country, and it begins with a process of elimination.
The Centers for Disease Control and Prevention told lab directors this week to begin searching for omicron in COVID-19 test results that come back positive, but with one specific part of the test having failed. If the results don’t identify the specific gene that produces the coronavirus’ iconic spike protein, that would be a sign that it could be the omicron mutation.
A test produced by Thermo Fisher Scientific is being used to detect what lab scientists are referring to as the “S-gene target failure.” The Food and Drug Administration is reviewing whether other available tests can be used in the search for omicron using a similar process.
The test searches for three signatures of the coronavirus. While the ‘S’ gene of omicron does not show up on these tests, the other two signatures are still detected, producing a positive result.
Even before omicron was first detected in South Africa, state and local labs were collecting the genetic sequences of 15,000 to 20,000 diagnostic tests each week, allowing scientists to keep track of what COVID-19 variants were circulating in communities across the country. Thousands more are collected by private labs and academic institutions.
Those labs are now being told to increase their use of Thermo Fisher’s tests for the next few weeks to search for the new omicron variant — and to prioritize those that come back with “S-gene target failure” for genomic sequencing, which is the process of documenting the full genetic makeup of the virus.
While the test by itself does not confirm it is omicron, labs would follow up on the clue that it might be the new variant by conducting the genomic sequencing process, Kelly Wroblewski, director of infectious diseases at the Association of Public Health Laboratories, told reporters this week.
“The S-gene target failure does not mean that omicron is present. It is a useful screening tool, though, and allows us to prioritize those specimens for sequencing,” Wroblewski said. “This ability to prioritize is really, really helpful.”
In a flurry of calls this week, health officials with the Biden administration have asked lab directors to target these unique test results as a top priority, and to share sequences that match omicron with the Centers for Disease Control and Prevention, a CDC official told McClatchy.
Once an omicron sequence has been identified, federal officials are asking labs to coordinate closely with CDC leadership on the announcement of any confirmed case.
The first case of the omicron variant in the United States was identified on Wednesday. It has also been detected in over 20 countries including Canada, the United Kingdom, Germany, Belgium, Australia and Israel.
The White House says that one in seven PCR tests that come back positive, and roughly 5% to 10% of all total cases, are being examined for variants. But not all of them use Thermo Fisher’s test kits, which are the only tests known to identify the S-gene dropout clue that labs are looking for in the search for omicron.
In regions where COVID-19 testing is still infrequent, state and local labs have fewer samples to test. That could delay their identification of omicron in communities where the coronavirus is spreading.
“What more can be done? The more you test, the more and more quickly you will find something,” said John Moore, professor of microbiology and immunology at Weill Cornell Medical College.
PCR testing has been expanded at four major U.S. airports, including two — Newark-Liberty International Airport in New Jersey and Hartsfield-Jackson Atlanta International Airport — that continue to receive direct flights from South Africa.
“I do think the U.S. government is doing what it can. It is very likely the omicron variant is already here,” said Dr. Eric Toner, senior scholar at the Johns Hopkins Center for Health Security. “The key thing the government can do, and is doing, is to ramp up testing as much as possible — and not just travelers — and communicate the seriousness of the threat to the public so that they are more likely to get vaccinated and wear masks.”
Omicron has a significant number of mutations from the original strain of SARS-CoV-2 that scientists say could make it more transmissible and resistant to vaccines.
“The plan outlined by the Biden administration will increase our ability to detect and monitor the omicron variant. However, there’s quite a bit more we can, and should, be doing,” such as post-arrival testing of travelers at U.S. borders, said Sam Scarpino, managing director of pathogen surveillance at the Rockefeller Foundation’s Pandemic Prevention Institute.
In addition to helping labs confirm the omicron variant, the CDC wants labs to share their data to bolster its own investigation into the contagiousness and severity of the mutant strain.
“Our variant surveillance system has demonstrated we can reliably detect new variants, from Alpha in the start of 2021 to Delta over this past summer,” CDC Director Rochelle Walensky told reporters this week. “We are actively putting systems in place with local and state laboratories to make detection and sequencing even faster.”
This story was originally published December 1, 2021 at 10:34 AM.
