Despite New York City getting hit hard this winter by the initial omicron wave, its case rates are climbing back into danger zones.

On Monday, New York City health officials raised the COVID alert level from low to medium — citing a persistent uptick in cases that has pushed the collective risk above the limits defined by the Centers for Disease Control and Prevention.

This upgrade happened even though the city’s alert level and the CDC’s rankings prioritize hospital burden rather than community transmission. Citywide case rates are now, on average, over 200 cases per 100,000 (100k) residents over the past seven days — the threshold needed to automatically qualify as medium risk by the CDC.

A new study from epidemiologists at City University of New York can help explain why cases are still rising — even while hundreds of thousands of residents are carrying immunity from omicron due to winter infections.

The report, released last Thursday on the preprint database Medrxiv, estimates that only about a quarter of New York City adults caught omicron during the first three months of 2022. That was just after the variant began accounting for more than 90% of cases in the region.

Based on these findings, a majority of adults — about 72% — would still be susceptible to catching omicron and its ever-expanding bouquet of subvariants. These estimates also help pinpoint which communities and demographics were least hit during the winter wave.

“We're able to make generalizable estimates among people by age, by gender, by race, ethnicity, by education, status, income, and borough. We also looked at vaccination status as well,” said Dr. Denis Nash, an epidemiology professor at City University of New York, who led the study. “We can look at the extent to which vulnerable New Yorkers were infected during the surge, the people that we're trying to protect.”

The report also gives clues to how many infections are being missed due to city officials not collecting the results of most at-home tests. The CUNY team said only about 5% of adults who tested positive during those early months exclusively used at-home tests, while about three times as many opted for testing with a health provider.

“Our worry was that changes in testing behaviors and practices — one big example of which is the exclusive use of at-home testing — could kind of undermine our understanding of what the routine testing data on cases really means over time,” Nash said.

How the study was done

To glean these patterns, Nash and his colleagues conducted a representative survey of about 1,000 New York City adults in mid-March. They asked the respondents about their testing history since January 1st, which is right about the peak of the omicron surge in New York City. Questions included: How many tests had they taken since New Year's Day? How many were positive? How many were negative? Where did they test: at home or at clinic? And given cases also happen among some folks who never get tested, people were asked if they ever experienced a range COVID symptoms.

From there, the CUNY team built weighted averages for how many infections occurred, estimating that 27% of city adults — about 1.8 million — caught the BA.1 omicron subvariant during those opening months of the year. Last week, the CDC came to a similar conclusion in a study about the nationwide prevalence of omicron infections.

“If you look at the CDC data, they estimate between 10% and 30% of people in the U.S. were infected during the omicron surge,” Nash said. “Our estimates are kind of in line and suggest it's a bit higher. That makes sense to me because we're in New York City, and our surge was pretty significant.”

CUNY’s estimates also mirror analyses from other local epidemiologists who’ve tried to extrapolate the full burden of infections based on the official record of cases, which only accounts for tests taken at clinics. Official tallies only found about 552,000 cases of all ages between January 1st and March 16th of this year.

“Our estimate was 1.8 million New Yorkers,” said Dr. Anna Bershteyn, an assistant professor in the department of population health at the NYU Grossman School of Medicine. "So it's in the same ballpark, and it just reflects the extreme amount of under-diagnosis that was happening during the wave.”

People ages 25-34 had the highest prevalence, with 37% estimated to have been infected with BA.1 omicron.

Breaking down CUNY’s results by demographics shows who caught omicron the most often during the winter surge. People ages 25-34 had the highest prevalence, with 37% estimated to have been infected with BA.1 omicron. They were followed closely by adults ages 45-54. People without high school diplomas had the highest estimated rate (34%) in terms of education level.

Males were more likely than females and non-binary people. Hispanic groups had the biggest ethnic prevalence with 41% infected, followed by Asian/Pacific Islanders at 27%, white New Yorkers at 21% and Blacks at 20%.

Vaccinated people also had a higher infection rate than the unvaccinated, which, on the surface, may seem counterintuitive. But the majority of the city’s population had had at least one shot during omicron’s early months, and vaccine mandates were still in place — meaning if a person was exposed, they were more likely to be vaccinated.

Why are so many New Yorkers still susceptible to omicron infection?

When the omicron variant emerged in November, it reset the field on who is susceptible to catching the coronavirus. Its mutations are so dramatic that immunity tuned to earlier variants cannot stop the virus from entering our bodies. This rule applies to vaccinated people, too, because the vaccines were designed based on early variants.

The bright side is that if you were one of 1.8 million adults infected BA.1 omicron, it's very likely that you're protected against BA.2 and BA.3 as well, said Dr. Ned Landau, a microbiology professor at New York University Grossman School of Medicine, who studies coronavirus antibodies.

“If you got vaccinated, boosted and then got BA.1 or any omicron, I think you're very strongly protected against getting infected again — or certainly against getting sick,” Landau said. “But those 75% [or so] that you're talking about would still be susceptible to BA.1, BA.2 or BA.3.”

New York City Health Commissioner Dr. Ashwin Vasan said Monday that as a practical matter, moving from low to medium risk means that New Yorkers must exercise even greater caution than they have the last few weeks. He said vaccination and boosters are as critical as ever, and that eligible people should go get their booster doses now.

“We moved into medium this morning on the basis of our case transmission rate. We also look at our hospitalization rate and our bed occupancy rate,” Vasan said at a press conference on Monday. “On hospitalizations, we see a slight increase. On bed occupancy, we’re relatively stable. Both of those would have to jump up to a higher a significantly higher level for us to move into a higher risk category."

But the city stopped short of reinstating mask requirements, even though health department guidance says that the mayor's office should consider requiring masks in schools and other crowded settings when the alert level reaches medium. They opted for a “strong” recommendation, instead.”

“With the rising risks, we need to take rising precautions. New Yorkers, mask up when you're indoors,” Vasan said. “Regardless of whether you know the vaccination status of the people around you, mask up, it's the safe thing to do."

The city health department also wants all New Yorkers to think about getting tested before and after any gatherings, and if they test positive, call their doctor or 212-COVID19 to get evaluated for treatment like antiviral pills or monoclonal therapies.

Landau added that it is important to distinguish between protection from infection and protection from disease. The vaccines and immunity from pre-omicron cases don't protect well against infection now, but those defenses still work against severe outcomes, such as hospitalization and death, for the majority of people, especially if they get their first boosters.

The exceptions are senior citizens or anyone with a moderate or severe immunocompromising condition — both of which struggle to maintain their immune defenses. That’s why second boosters are recommended for these groups, which comprise millions of people nationwide.

Landau wondered if the public discussion has become too focused on the emergence of new omicron subvariants — and if the message on people’s actual risk is getting lost in the confusion.

“This idea of just naming these viruses, giving them a different name, scares people to some extent,” Landau said. “It's all omicron. If you're vaccinated and boosted, you're going to be in good shape.”

Jaclyn Jeffrey-Wilensky and Elizabeth Kim contributed to reporting.