Analysis: Why Didn't the U.S. Detect Omicron Cases Sooner?

Why Didn't the U.S. Detect Omicron Cases Sooner? Last Friday, just a day after South African scientists first announced the discovery of the omicron variant, Europe reported its first case: The new coronavirus variant was in Belgium. Before the weekend was out, Australia, Britain, Canada, Denmark, Germany, Israel, Italy and other countries had all found cases. But in the United States, scientists kept searching. “If we start seeing a variant popping up in multiple countries across the world, usually my intuition is that it’s already here,” sai YahooNews

Last Friday, just a day after South African scientists first announced the discovery of the omicron variant, Europe reported its first case: The new coronavirus variant was in Belgium. Before the weekend was out, Australia, Britain, Canada, Denmark, Germany, Israel, Italy and other countries had all found cases.

But in the United States, scientists kept searching.

“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, U.S. 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.

Scaling 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 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 Centers for Disease Control and Prevention 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 CDC’s dashboard, far less than 1% of reported cases. (Experts recommend sequencing at least 5% 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. ...