N.Y. Today: Where Omicron could have spread

What you need to know for Monday.

It's Monday. Today we'll meet the person with the first case of the Omicron variant identified in the United States. We'll also look at the latest supply-chain hiccup, a shortage of cream cheese for bagel shops.

Attendees at the Anime NYC convention in Manhattan last month.Kena Betancur/Agence France-Presse — Getty Images

"I'm essentially patient zero," Peter McGinn said — the first person in the United States found to have contracted the new Omicron variant of the coronavirus.

McGinn, a 30-year-old health care analyst from Minneapolis, may never know how he caught the virus. The test that showed he had it came back 10 days after he had attended an anime convention in Manhattan that became so chaotic that another person who was there — Lucy Camacho, 23 — described it as "Penn Station during rush hour."

By the time McGinn found out he had been infected, the virus had once again outrun the public health system. It typically takes between four and eight days from the time a sample is swabbed to identify which variant caused the infection. With such a lag, public health experts said it was unrealistic to try to untangle precisely who had infected whom, considering that some 53,000 people had attended the convention at the Javits Center.

Still, New York City health officials have sent tens of thousands of emails and text messages to convention attendees, urging them to get tested.

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Four of my colleagues — Joseph Goldstein, Julie Bosman, Kimiko de Freytas-Tamura and Roni Caryn Rabinwrite that much remains unknown about Omicron, including how deadly it is or how much protection Covid vaccines provide against it. But there is a troublingly familiar drumbeat, with epidemiologists once again talking about flattening curves, wearing masks and practicing social distancing.

Nationally, several dozen cases of the Omicron variant have been identified in at least 17 states. Dr. Rochelle Walensky, the director of the Centers for Disease Control and Prevention, said on the ABC News program "This Week" that the caseload is "likely to rise."

It is possible that the anime convention contributed little to the spread of Omicron. Of the roughly 30 people McGinn recalls socializing with in New York City, about half have since tested positive for the coronavirus, he said. None of the states where they live has announced that they have the Omicron variant. But on Saturday, Connecticut officials said that a man in his 60s from their state became sick with the Omicron variant in late November, days after a family member had returned from attending the anime convention.

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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 convention and had tested positive. 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 organizers of the convention said McGinn might have contracted Omicron elsewhere.

McGinn's experience illustrates the difficulties of contact tracing. He flew into La Guardia Airport on Nov. 18, a Thursday, excited to link up with other anime fans and soak up New York. He stayed with two friends in an Airbnb rental in Hell's Kitchen and sang karaoke that Saturday night. During the day, he attended the convention.

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. Her worries grew as the crowds did. She watched as masks came off while people ate, chatted with friends or found an empty corner to take a nap.

McGinn went home to Minnesota and felt unusually tired. He attributed a slight cough to asthma. Then he heard from a friend at the convention who lived in North Carolina and had just tested positive for Covid-19. On Nov. 23, he took an at-home test. The result was positive. He also went to a large testing site for a P.C.R. test.

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Other friends who had attended the convention, all vaccinated, told him that they too had been infected.

By Dec. 1, Minnesota health officials were convinced that a batch of samples they had analyzed for mutations included their first case of Omicron. A case investigator, Kathy Como-Sabetti, called McGinn to learn whom he might have exposed to the new variant. McGinn told her about the anime convention.

"I kind of went, 'Wow, well, this changes our story,' " Como-Sabetti said. Minnesota officials immediately called the New York City Health Department with the bad news.

WEATHER

It's a cloudy day, New York, with temps in the low 60s and wind gusts and showers in the late afternoon persisting through the night. In the evening, temps will drop to the mid-30s.

ALTERNATE-SIDE PARKING

In effect until Wednesday (Immaculate Conception).

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The latest supply-chain headache: Not enough cream cheese for bagels

Adam Friedlander for The New York Times

Just when you thought you'd heard everything about supply-chain problems, the schmear shortage hit New York.

That's why, behind the counter, frustrated and frazzled bagel shop owners are hoarding cream cheese.

As my colleague Ashley Wong wrote, Zabar's estimated on Friday that it had enough cream cheese to last only 10 days. Absolute Bagels, also on the Upper West Side, reported that its usual supplier in Queens had run out.

New York bagel sellers go through thousands of pounds of cream cheese every few weeks. Many shops start their mixes with Philadelphia cream cheese, a Kraft Heinz brand.

The pallets for bagel shops are not filled with the Philadelphia cream cheese sold in grocery stores. What goes to bagel shops is unprocessed and unwhipped, said bagel makers, who use it as a base for their own creations. Without that base, they said, their spreads just won't taste or feel the same.

Dairy suppliers say that in the last three weeks, cream cheese orders placed with manufacturers have come up short.

Phil Pizzano, a sales representative at Fischer Foods, a large distributor, said problems have popped up at every point along the supply chain that carries cream cheese from factories to the morning bagel, including a labor shortage in the manufacturing sector that began at the height of the coronavirus pandemic, a lack of truck drivers because of resistance to vaccine mandates and a scarcity of packaging supplies.

"If someone like us orders 1,000 cases, maybe you only get a portion," Pizzano said. "Or maybe you order a truckload, and you only get a few pallets."

A spokeswoman for Kraft Heinz said demand for several of the company's products had spiked. "As more people continue to eat breakfast at home and use cream cheese as an ingredient in easy desserts, we expect to see this trend continue," she said. To accommodate the increases, the company has been shipping 35 percent more of its product, she said.

But Christopher Pugliese, the owner of Tompkins Square Bagels, said his dairy supplier had called on Thursday night to say that the 800-pound order due the following day was not coming. After calling four other distributors, he finally got his hands on a case — except that instead of the usual giant container, the box was full of individually wrapped three-pound sticks, he said.

"It sounds kind of silly, talking about this like it's some kind of huge crisis," Pugliese said. But a bagel with cream cheese is a New York institution — and a "big deal," he said.

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METROPOLITAN DIARY

Five lights at dawn

Dear Diary:

Monday mornings, a boy of four
stands in grass by the stoop
and clasps his mother's hand,
raises his left arm and fist
and pumps the air to see if
the driver of the garbage truck
will toot his horn, which he does,
with a grin, drawing smiles from
mother and son and the two men
who've paused at the curb before
tossing more bags in the bin.

— Tom Furlong

Glad we could get together here. See you tomorrow. — J.B.

Melissa Guerrero, Rick Martinez and Olivia Parker contributed to New York Today. You can reach the team at nytoday@nytimes.com.

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