Why Omicron cases in US got detected late

“If we start seeing a variant popping up in multiple countries across the world, usually my intuition is that it’s already here,” said Taj Azarian, a genomic epidemiologist at the University of Central Florida. On Wednesday, American officials announced that scientists had found it — in a California patient who had recently returned from South Africa. By then, Canada had already identified six cases; Britain had found more than a dozen.

On Thursday, additional cases were identified in Minnesota, Colorado, New York and Hawaii, and a second case was found in California, indicating that more are almost certainly lurking, scientists said. Why wasn’t the variant detected sooner?

There are various potential explanations, including travel patterns and stringent entrance requirements that may have delayed the variant’s introduction to the United States. But there are also blind spots and delays in the country’s genomic surveillance system. With many labs now conducting a targeted search for the variant, the pace of detection could quickly pick up.

Since the beginning of the pandemic, scientists have been sequencing the genetic material from samples of the virus, a process that allows them to spot new mutations and identify specific variants. When done routinely and on a large scale, sequencing also allows researchers and officials to keep tabs on how the virus is evolving and spreading.

In the United States, this kind of broad genomic surveillance got off to a very slow start. While Britain quickly harnessed its national health care system to launch an intensive sequencing program, early sequencing efforts in the United States, based primarily out of university laboratories, were more limited and ad hoc. Even after the C.D.C. launched a sequencing consortium in May 2020, sequencing efforts were stymied by a fragmented health care system, a lack of funding and other challenges. In January, when cases were surging, the United States was sequencing fewer than 3,000 samples a week, according to the C.D.C.’s dashboard, far less than 1 percent of reported cases. (Experts recommend sequencing at least 5 percent of cases.) But in recent months, the situation has improved dramatically, thanks to a combination of new federal leadership, an infusion of funding and an increasing concern about the emergence and spread of new variants, experts said.

“Genomic surveillance really has caught up in the U.S., and it is very good,” said Dana Crawford, a genetic epidemiologist at Case Western Reserve University. The country is now sequencing approximately 80,000 virus samples a week and 14 percent of all positive P.C.R. tests, which are conducted in labs and considered the gold standard for detecting the virus, Dr. Rochelle P. Walensky, the director of the Centers for Disease Control and Prevention, said at a White House briefing on Tuesday. The problem is that the process takes time, especially when done in volume. The C.D.C.’s own sequencing process typically takes about 10 days to complete after it receives a specimen.

“We have really good surveillance in terms of quantity,” said Trevor Bedford, an expert on viral evolution and surveillance at the Fred Hutchinson Cancer Research Center in Seattle. He added, “But by nature, it lags compared to your case reporting. And so we’ll have good eyes on things from two weeks ago.”

Anthes is a journalist with NYT©2021