Omicron could have spread in New York before it even received a name

They wore fluorescent wigs and capes with gold tassels. They arrived in knee-high white platform boots, and with feathered wings affixed to their backs. Dressed like their favorite characters, or just wearing street clothes, they packed into Manhattan’s main convention hall — some 53,000 of them — over three days in November to celebrate their love of Japanese animation shows known as anime.

In the crowd was Peter McGinn, a 30-year-old health care analyst in town from Minneapolis. He attended discussion panels, chatted with strangers about his anime podcast and, at night, sang karaoke with friends. After flying home, he learned that one friend from the convention — an anime fan from North Carolina — had just tested positive for the coronavirus. In the days to come, many more of his friends from the convention would test positive, as well. Coughing and feeling tired, Mr. McGinn also took a test. He had the virus, too.

That was Nov. 23, a day before most scientists had even heard of the new variant that was tearing across southern Africa. The World Health Organization had not yet even given the variant a name — Omicron. But it was already present in the United States, undetected.

That became apparent this past week, when health authorities in Minnesota examined the virus samples in a batch of recent tests. One of them — from Mr. McGinn — showed Omicron’s telltale mutations.

His infection, which was announced by the Minnesota health authorities on Dec. 2, is the first known instance of Omicron spreading within the United States. “I’m essentially patient zero,” he said in an interview from Minneapolis on Friday, though he wonders how he contracted it. “It’s still a mystery.”

He may never know. The announcement came more than 10 days after the anime convention ended, leaving health authorities far behind, even before they realized the race against Omicron had begun.

New York City health officials have sent tens of thousands of emails and text messages to the convention attendees, urging them to get tested. But so far the authorities have yet to confirm any transmission of Omicron at the Anime NYC convention, which was held Nov. 19-21.

It is possible that the convention contributed little to Omicron’s spread. But it appears more likely that the virus is once again outpacing a public health response that is simply unable to keep up. (On Saturday, Connecticut officials said that a man in his 60s from their state fell sick with the Omicron variant in late November, days after a family member had returned from attending the anime convention.)

In the nearly two years since the novel coronavirus first began circulating in this country, the United States has built enough capacity to test more people than any other country. It is now sequencing some 14 percent of positive P.C.R. tests, searching for mutations and identifying variants.

Some municipalities, like New York City, and states, like Massachusetts, built out large-scale contact tracing organizations. Most of the U.S. population — 60 percent — are vaccinated. Just a few weeks ago, before Omicron was identified, there was widespread hope that the pandemic, in this country at least, was easing. People felt safe as they flashed their proof of vaccination — as was required for entry — and streamed into the Javits Center for the convention.

But amid tens of thousands of new Delta infections in the United States each day, Omicron’s landfall and spread are easily hidden. Many coronavirus infections are asymptomatic or have only minor symptoms, slipping under the radar.

Indeed, it remains unclear if the anime convention was a super spreader event. “We haven’t found evidence of widespread transmission at the convention,” Adam Shrier, a spokesman for New York City’s contact tracing program, Test and Trace Corps, wrote in an email.

It is also unclear whether Mr. McGinn was infected at the convention or by a fellow attendee. But he spent successive days at the convention, and evenings with other convention goers.

Of the roughly 30 people he recalls socializing with in New York City, about half have since tested positive for the coronavirus, Mr. McGinn said. However, none of the states where they live have announced whether those people also had the Omicron variant.

Much remains unknown about Omicron, including how deadly it is or the degree of protection that Covid vaccines provide against it. But epidemiologists are once again talking about flattening the curve, through mask wearing and more cautious behavior. And they are urging action now, to avoid a repeat of the mistakes made in March 2020, when New York officials were slow to understand just how quickly the virus was spreading throughout the city.

Over the past four days, New York’s genome sequencing program has detected seven Omicron cases among residents in New York City, although health authorities have provided little information about the cases. “All of these cases are believed to be unrelated to the recent Anime NYC convention at the Javits Center,” the governor’s office said in a news release on Saturday morning.

New York’s surveillance program for screening variants is relatively robust, but it comes with a lag, as do similar programs elsewhere. It typically takes between four and eight days from the time a sample is swabbed to identify which variant caused the infection. That means any alarming increase in new cases that is noticed today may already be a week old.

Dr. Jay Varma, an epidemiologist who helped guide New York City’s pandemic response as a City Hall adviser, said in an interview that he believed the city should distribute N95 masks to households in the neighborhoods that were hardest hit by Covid-19 last year and start opening more testing sites in response to Omicron. And he said it was time to tighten New York City’s vaccination requirement for indoor venues like restaurants and bars. Rather than requiring only one dose, he suggested that it was time to require three.

“We don’t know how effective that is going to be,” said Dr. Varma, who said he shared these and other ideas with top city health officials this past week. “But as far as I can tell, there is no downside to basically forcing the issue: Full immunity now means three doses of a vaccine, so go ahead and get it.”

Mr. McGinn’s experience illustrates the difficulties of contact tracing. He flew into La Guardia Airport on Nov. 18, excited to link up with other anime fans and soak up New York. He went out for dinner and drinks, stayed with two friends in an Airbnb in Hell’s Kitchen and sang karaoke in Koreatown on a Saturday night. During the day, he attended the anime conference at the Javits Center.

The atmosphere was joyous, with the feel of a huge reunion. The “Artist Alley,” which showcased anime artists, was so clogged and chaotic that one attendee, Lucy Camacho, 23, described it as “Penn Station during rush hour.”

Tian Chang, 29, one of the artists, said she felt safe from Covid-19 at first, with many attendees wearing masks, as the convention required. Still, her worries grew, as the crowds did. She recalled “an explosion of attendees,” with “crowds shoulder to shoulder in some areas.” From her table, she watched as masks came off while people ate, chatted with friends or found an empty corner to take a nap.

Organizers said Mr. McGinn might have contracted Omicron elsewhere. “He was just one person who was at our event,” said Kelly Comboni, president of Left Field Media, which organized Anime NYC. “There have been no other mass cases reported from our event.”

Returning to Minnesota a few days before Thanksgiving, Mr. McGinn felt unusually tired. His slight cough was probably his asthma, he figured. After a long sleep — some 14 hours — he felt fine.

Then Mr. McGinn heard from a friend from the convention who lived in North Carolina and had tested positive for the virus.

On Nov. 23, he took an at-home Covid test, which came up positive. He also went to a large testing site for a P.C.R. test.

Other friends from the convention, all vaccinated, reported that they too had been infected.

“One guy had a bad day, but for the most part, mild symptoms for everyone,” Mr. McGinn said. “It was a stay home, get a blanket and watch a movie kind of thing.”

Mr. McGinn said he had no idea who infected whom, or where.

By the evening of Dec. 1, Minnesota health officials were convinced that a batch of samples they had recently analyzed for mutations included their first case of Omicron. A case investigator, Kathy Como-Sabetti, called Mr. McGinn to learn whom he might have exposed to the new variant. Mr. McGinn told her about the anime convention, with its crowds. “I kind of went, ‘Wow, well, this changes our story,’ ” she said.

Minnesota officials immediately called the New York City Health Department with the bad news. “They took it very much in stride,” Ms. Como-Sabetti said.

Dr. Ted Long, who oversees New York City’s Test and Trace Corps, said he was aware of five New York City residents who attended the anime convention and had also tested positive. These five had sought out testing, received positive test results and mentioned the anime convention when contact tracers called. But he did not know whether they had been infected with the new Omicron variant or the Delta variant, which is infecting some 1,500 people a day and driving a new surge of cases in the city.

The Centers for Disease Control and Prevention is assisting the Minnesota and New York City Health Departments track the outbreak, a spokeswoman said, and it held a conference call Saturday morning with officials from local health departments.

But with so many people in attendance, and a lag of two weeks, public health experts said it was not realistic to try to untangle precisely who infected whom. “I don’t think there needs to be an individual phone interview with the 53,000 people who attended,” said Dr. Wafaa El-Sadr, an epidemiology professor at Columbia University.

Professor El-Sadr added that all individuals should follow C.D.C. guidelines, which instruct fully vaccinated people who have been exposed to wear a mask for up to 14 days — a period that ends this weekend — and get tested. “I think the pragmatic way to do contact tracing in this context is that everyone should consider themselves a close contact,” she said.

Sophie Kasakove contributed reporting.