Testing labs brace for first U.S. cases of Omicron

Public health officials said Tuesday they expect to uncover the first U.S. cases of the Covid-19 Omicron variant within days and are making contingencies to activate a testing network that fell short tracking earlier strains of the virus.

Public health labs are prioritizing sequencing of positive samples that exhibit what is known as an “s-gene dropout” — a telltale characteristic Omicron shares with other variants but not the Delta strain.

“I am expecting it any day now, I’ve said that for the last two days,” Association of Public Health Laboratories CEO Scott Becker said at a briefing. “Given what we've seen in southern Africa, and certainly in Europe, we do expect that it is here.”

White House chief medical adviser Anthony Fauci told reporters Tuesday the Omicron variant has not yet been detected in the U.S.

The U.S. surveillance system is in a far stronger position than when the Covid-19 Alpha variant emerged last year. At the beginning of this year fewer than 1 percent of positive tests were being sequenced and subsequently reported to the Centers for Disease Control and Prevention before the agency pushed to expand its network of public, private and university labs contributing data.

The current surveillance effort in the U.S. is comparable to the European Union, said Phil Febbo, chief medical officer of DNA sequencing company Illumina, which is working with the CDC.

“What we have to keep our eye on is consistency and making sure there aren't pockets where we're not getting any input," Febbo said.

The U.S. is now sequencing between 5 to 10 percent of positive cases — a level that can detect any variant that accounts for a hundredth of a percent of total cases, according to Becker. CDC Director Rochelle Walensky told reporters the number of positive tests being sequenced — approximately 80,000 samples per week — represents one in seven lab-based PCR positive cases.

The popularity of at-home antigen tests poses one challenge for public health officials working to understand the emergence of new variants because many of the results aren't reported to authorities.

“Unfortunately, we don't have a system in place in our country yet to automatically triage some of those rapid tests — positive samples — to get sequenced,” former Biomedical Advanced Research and Development Authority Director Rick Bright told POLITICO.

Another challenge is ensuring the country is testing and sequencing a representative number of positive results from patients with mild or no symptoms.

“We might find that this Omicron variant has been circulating for a while just under the radar because it wasn't causing as severe illness, and we weren't sequencing or doing enough surveillance in those populations,” said Bright, who is now the CEO of The Rockefeller Foundation’s Pandemic Prevention Institute.

CDC is expanding one surveillance effort to test travelers at some international airports to more rapidly detect Covid-19 cases among those arriving in the U.S., according to Walensky.

“CDC is evaluating how to make international travel as safe as possible, including pre-departure testing closer to the time of flight and considerations around additional post-arrival testing and self quarantine,” Walensky said.