First case of Omicron coronavirus variant identified in the U.S.

U.S. health officials on Wednesday reported the country’s first case of the Omicron variant of the coronavirus, in a person in California.

The Covid-19 case was identified by the California and San Francisco health departments in a person who had traveled to South Africa and returned on Nov. 22, the Centers for Disease Control and Prevention said in a release. The individual, who was fully vaccinated with the Moderna shot but had not received a booster, had mild symptoms and has since recovered, federal and local officials said. The person has been isolating since testing positive on Nov. 29. All close contacts have tested negative thus far.

The discovery of Omicron in the United States is not a surprise. Upon characterizing the mutations in the variant, scientists in South Africa last week quickly raised the world’s alarms about the potential threat it posed, but it had already started to circulate silently. Some two dozen countries, from the United Kingdom to Australia to Israel, have already reported cases, many in travelers. 

This newly identified case is not necessarily the first one in the United States, just the first to be detected. Genomic sequencing was conducted at the University of California, San Francisco, and the sequence was confirmed at CDC.

Omicron is bringing renewed attention to the problems and piecemeal nature of the U.S. surveillance network. The country’s genetic sequencing infrastructure has grown during the pandemic, and at a briefing Tuesday, CDC Director Rochelle Walensky said that the number of positive tests being sequenced in the U.S. is now 80,000 samples per week, or between 5% and 10% of confirmed cases. That’s up from the beginning of the year, when the agency and its partners were sequencing just a few thousand samples per week. But progress has been uneven. Over the past three months, a number of states were sequencing and reporting just 3% of their confirmed infections. 

California has a comparatively robust sequencing network, with some 12% of infections sequenced over the past three months.

Without stronger surveillance, it’s difficult to know which iterations of the virus are circulating.

Health officials praised the person who tested positive for Omicron, noting that they got tested upon developing symptoms. “They did the right thing and got tested and reported their travel history,” said Grant Colfax, San Francisco’s health director.

On Monday, U.S. travel restrictions went into effect on South Africa and Botswana — where early cases of Omicron were identified — and six other countries in the region. Many other countries have imposed their own travel restrictions, and some have halted international arrivals.

With a pathogen like the coronavirus, travel restrictions can slow, but not generally block, the arrival of new variants, research has shown. 

Viruses generally follow travel patterns as they spread to new areas, and San Francisco is a major U.S. travel hub. But what happens next is subject to a lot of randomness. Many imported infections don’t result in any other infections, but some set off new chains of transmission. The more imported cases, the higher the likelihood that some cause subsequent infections.

Scientists are racing to better understand the threat posed by Omicron. Preliminary epidemiological evidence in South Africa suggests it may have a transmission advantage even over the highly transmissible Delta variant, and its genome indicates it may be able to evade at least some immune protection. But it will take time for scientists to run the studies and gather the evidence that can confirms whether or not those concerns will be realized. 

Even apart from Omicron, the U.S. in recent weeks has seen a resurgence of spread, in states in the Mountain West, Midwest, and Northeast, driven largely by the Delta variant, the arrival of colder temperatures, and pockets of unprotected people. According to the latest CDC data, more than 80,000 Americans are still being being infected every day.

Megan Molteni contributed reporting.