Emergence of a Deadly Coronavirus

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Every day, the state releases the percentage of different groups of New Yorkers who are vaccinated against COVID-19, sometimes accompanied by statements trumpeting the achievement of major milestones.

But those percentages — such as the more than 91% of adults the state says are at least partially vaccinated — are probably inaccurate and inflated because of double-counting, population shifts and other factors, experts say.

Some vaccination rates are mathematically impossible to achieve. For example, the state says 153,621 Nassau County residents 65 to 74 had been vaccinated by Friday, even though, according to a state website, only 132,862 people in that age group live in Nassau. That would mean a vaccination rate of 116%. Rates for residents 55 to 64, and 75 and older, also exceed 100%.

Denis Nash, a professor of epidemiology at the CUNY School of Public Health in Manhattan, noted that under former Gov. Andrew M. Cuomo, the state released COVID-19 numbers that were later found to downplay the severity of the pandemic in New York.

The 2018 projections are often lower than the populations in the Census Bureau’s 2019 American Community Survey estimates, which are based on an annual survey of more than 3.5 million households nationwide. Detailed population data is not yet available for 2020.

Using a lower population estimate leads to a higher vaccination rate.

Silk said the state doesn’t use the American Community Survey because it incompletely counts "congregate settings." But, according to the Census Bureau, the survey has been counting people in congregate settings such as nursing homes, student housing, prisons and homeless shelters since 2006.

Nash said accurate numbers are especially important as COVID-19 case numbers climb with the arrival of colder weather and the holiday season.

"It’s the proportion of people who are vaccinated that we’re really relying on to know how well we’re going to be able to weather another surge this winter," he said. "If that is not reliable, if it’s wildly underestimated or overestimated, and especially overestimated, the consequences are dire."

The vaccination rates over 100% for groups such as seniors and Asians suggest that other vaccination rates the state releases likely are inflated, Nash said.

But the discrepancies in numbers are not limited to New York. Across the Hudson River, multiple New Jersey municipalities report rates of more than 100%.

And the Centers for Disease Control and Prevention currently reports that 99.9% of adults 65 and older have at least one dose — despite individual states that report numbers well below 90%.

Nash said some overcounting likely is from incorrect names and birth dates being entered.

Sean Clouston, an associate professor of public health at Stony Brook University, said people who received booster shots before they were officially authorized by the federal government may have said they were getting their first shot, to evade scrutiny. "They would be listed as a first vaccine," he said.

Likewise, in the first few months of vaccination, when there was far more demand for vaccines than there were appointment slots, some people trying to get a shot at a vaccination site with a residency requirement gave an incorrect address, said Stephanie Silvera, an epidemiologist and professor of public health at Montclair State University in New Jersey.

Goodman said population estimates that are different from the actual, current population likely are the main cause of the discrepancies and of numbers that exceed 100%.

Discrepancies also might stem from the Census Bureau and state using different terminology in asking for demographic data, such as for multiracial people, Goodman said.

He said a 99.9% vaccination rate for seniors seems "implausibly high" because of widespread vaccine resistance and because of the large number of older unvaccinated people who have been dying of COVID-19.

Silvera said she doubts nationwide and statewide vaccination rates "are ever going to be accurate.

Even before the arrival of Omicron, the winter months were going to be tough for parts of the United States. While COVID transmission rates in the South caught fire over the summer, the Northeast and Great Plains states were largely spared thanks to cyclical factors and high vaccination rates. But weather and the patterns of human life were bound to shift the disease burden northward for the holidays—and that was just with Delta. Enter a new variant that appears better able to evade immunity, and that seasonal wave could end up a tsunami.

Back in July, CDC Director Rochelle Walensky announced that COVID had become “a pandemic of the unvaccinated,” an unfortunate turn of phrase that was soon picked up by the president. Now the flaws in its logic are about to be exposed on what could be a terrifying scale. Unvaccinated Americans will certainly pay the steepest price in the months to come, but the risks appear to have grown for everyone. The pandemic of the vaccinated can no longer be denied.

The 60 percent of Americans who are fully vaccinated could soon find their lives looking very different. For much of the summer and fall, those who had received two Pfizer or Moderna doses or one Johnson & Johnson shot were told that they were essentially bulletproof, especially if they were young and healthy. But preliminary data from South Africa and Europe now suggest that two vaccine doses alone might still allow for frequent breakthrough infections and rapid spread of the disease—even if hospitalization and death remain unlikely. Getting three shots, or two shots plus a previous bout of COVID, seems to offer more protection. For Saad Omer, the director of the Yale Institute for Global Health, that’s enough evidence to justify changing the CDC’s definition of full vaccination.

At this point, the CDC has recorded that less than a quarter of adults who are fully vaccinated under the existing definition have gotten a third shot. That leaves about 150 million people who are vaccinated but unboosted. Given that the people in this group are less protected against infection, they’re at greater risk of passing on the disease to unvaccinated or partially vaccinated kids, as well as to unvaccinated or immunologically vulnerable adults. They will also pass the coronavirus more readily among themselves. Settings that might have previously seemed safe for vaccinated folks—say, a restaurant or performance venue that strictly checks vaccination status—could become fertile ground for transmission, because the people inside them are more likely to catch and spread the virus. Indeed, anecdotal reports already suggest that large indoor gatherings of fully vaccinated people can become super-spreader events in the age of Omicron.

Population-level immunity could suffer in another way too, Omer said: People who were previously protected because of a prior infection could now be quite vulnerable to getting reinfected and passing on the disease. In fact, it’s possible that the only parts of the country where community transmission might be blunted are those that faced devastating early waves of the virus and subsequently had strong vaccination rates—mostly a handful of areas in the Northeast. “It’s really very, very challenging to consider how those differences might play out,” Joshua Schiffer, a disease-modeling expert at the Fred Hutchinson Cancer Research Center, told me.

Here’s the upshot: Each fully vaccinated person might still be at minimal risk of getting seriously ill or dying from COVID this winter, but the vestiges of normalcy around them could start to buckle or even break. In the worst-case scenario, highly vaccinated areas could also see “the kind of overwhelmed hospital systems that we saw back in 2020 with the early phase in Boston and New York City,” Samuel Scarpino, a network scientist at the Rockefeller Foundation’s Pandemic Prevention Institute, told me.

Such a scenario would be especially dangerous if those millions of people all needed a bed at the same time. Omicron is so transmissible that cases could peak across the country more or less in tandem, Schiffer and Scarpino both said, which would make it harder for the U.S. to shuffle personnel and ventilators to particularly hard-hit regions. ICU capacities in some states are already stretched thin and health-care workers are resigning en masse, so the harms could be even worse.

“If we don’t get serious, if we don’t get the masks on, if we don’t get testing up, we’re going to be back into lockdown again because people will be dying in the hallways of hospitals,” Scarpino said.

This all would be mitigated if Omicron turns out to cause significantly milder disease than Delta—still a possibility, but far from confirmed—and if the vaccines’ protection against severe disease holds strong. But even in that sunnier version of the future, cases are almost certain to increase in highly vaccinated areas and undervaccinated ones alike, and bring with them a host of disruptions to daily life.

Whatever the effects on vaccinated Americans, the Omicron fallout is going to be much more severe for everyone else. In places with low vaccine coverage and strong anti-shutdown politics, inconvenience could be replaced by mass death and even greater grief. And the devastation will almost certainly be greater, on average, in rural communities, poor communities, and communities of color.

None of these futures are yet written in stone. The scope of the coming hardship will depend on how capable Omicron is of causing severe disease and death. And though Omicron seems likely to overtake Delta, “cases are still low enough with Omicron that we can have a big effect if [we] act early,” Scarpino said—though “acting early was last week.” A month ago, one could still pretend that burden fell on those who lived in some other place, far away from vaccinated people in vaccinated communities. Now that delusion looks shakier than ever.

A lot of people are suffering," says Jennifer Frontera, a neurology professor at the NYU Grossman School of Medicine.

Frontera led a study that found that more than 13% of hospitalized COVID-19 patients had developed a new neurological disorder soon after being infected. A follow-up study found that six months later, about half of the patients in that group who survived were still experiencing cognitive problems.

The current catalog of COVID-related threats to the brain includes bleeding, blood clots, inflammation, oxygen deprivation and disruption of the protective blood-brain barrier. And there's new evidence in monkeys that the virus may also directly infect and kill certain brain cells.

Studies of brain tissue suggest that COVID-related changes tend to be subtle, rather than dramatic, says Geidy Serrano, director of the laboratory of neuropathology at Banner Sun Health Research Institute. Even so, she says, "Anything that affects the brain, any minor insult, could be significant in cognition."

Some of the latest insights into how COVID-19 affects the brain have come from a team of scientists at the California National Primate Research Center at UC Davis.

Neurons are the brain cells that make thinking possible. But studies of human brains have produced conflicting evidence on whether these cells are being infected by the virus.

The monkey brains offer an opportunity to learn more because they come from a close relative of humans and are easier to study and scientists know precisely how and when each animal brain was infected.

And, similar to monkeys, the virus seemed to have entered through the nose, says Serrano, the study's lead author.

"There's a nerve that is located right on top of your nose that is called the olfactory bulb," she says. That provides a potential route for virus to get from the respiratory system to the brain, she says.

Serrano says the virus appears able to infect and kill nerve cells in the olfactory bulb, which may explain why many COVID patients lose their sense of smell — and some never regain it.

In other brain areas, though, the team found less evidence of infection.

That could mean that the virus is acting in other ways to injure these areas of the brain.

COVID-19 can also damage the brain by causing blood clots or bleeding that result in a stroke. It can damage the protective cells that create what's known as the blood-brain barrier, allowing entry to harmful substances, including viruses. And the disease can impair a person's lungs so severely that their brain is no longer getting enough oxygen.

These indirect effects appear to be a much bigger problem than any direct infection of neurons, Frontera says

My breakthrough infection started with a scratchy throat just a few days before Thanksgiving. Because I’m vaccinated, and had just tested negative for COVID-19 two days earlier, I initially brushed off the symptoms as merely a cold. Just to be sure, I got checked again a few days later. Positive The result felt like a betrayal after 18 months of reporting on the pandemic. And as I walked home from the testing center, I realized that I had no clue what to do next.

I had so many questions: How would I isolate myself in a shared apartment? And why for 10 days, like the doctor at the testing site had advised? Should I get tested again? Following the doctor’s orders, my partner—who had tested negative—dragged a sleeping bag to the couch. Masks came on, windows went up, and flights were canceled. I ate flavorless dinners on my side of the apartment. One by one, the symptoms I knew so well on paper made their real-life debut: cough, fever, fatigue, and a loss of smell so severe, I couldn’t detect my dog’s habitually fishy breath.

Turns out I wasn’t the only one feeling baffled about what to do. “Oh yeah, people are very confused about breakthrough cases,” Peter Chin-Hong, an expert on infectious diseases at UC San Francisco, told me.

At least for now, Omicron shouldn’t change how Americans act when they get a breakthrough infection.

If only the official guidance were this straightforward. Rebecca Wurtz, an infectious-disease expert at the University of Minnesota, told me that people are perplexed “partly because, I think, the guidance is confusing.” The CDC’s guidelines are limited: Isolate if you’ve either tested positive in the past 10 days or are experiencing symptoms, and end your isolation after 10 days only if you’ve gone 24 hours with no fever (without the use of Tylenol or other anti-fever drugs) [i]and[/] your other symptoms are improving—not counting the loss of taste and smell, which could take a couple of weeks to return. “They’re unclear as they’re stated, and they’re a little too complicated in any case,” Wurtz said.

If you start feeling anything that resembles COVID symptoms or learn that you’ve been exposed to someone who has tested positive, some experts told me, the first thing to do is to get tested. “If you’re not sure, you have to get tested,” Chin-Hong said. That’s especially true now that we’re heading into the winter, when all sorts of non-COVID illnesses are also circulating. It can be impossible to differentiate between the early symptoms of a cold, the flu, and COVID, and getting tested is the only way to confirm a breakthrough infection. The bottom line is that knowing whether you’re positive is important not just for you, but also for anyone who you’ve been in contact with recently—especially those who are unvaccinated or immunocompromised.

PCR tests are still considered to be the gold standard, but they take much longer to generate results than rapid tests, which you can buy at a pharmacy and take at home. A test is merely a snapshot in time, and because Omicron appears to have a shorter incubation period than past variants, a result from a few days ago may not mean much.

Wurtz said that if you start to feel sick but haven’t been in contact with anyone and don’t plan to be, the best recourse is to stay home, minimize exposure to other people, and rest. “

If you do test positive, you should alert your local public-health authority so they can initiate contact tracing, Chin-Hong said. Many testing sites do this automatically, but at-home tests, of course, do not. The CDC advises that after confirming your infection, you should start isolating right away, but unless you are asymptomatic, the first day of symptoms is technically what counts as the start of your 10 days of isolation. I learned the hard way that you aren’t supposed to “test out” of isolation, when a physician assistant yelled at me for getting tested after feeling better on day seven. She said I was putting others at risk, although the CDC guidance didn’t specifically say not to get tested. Explaining that I would have to isolate regardless of the outcome, she never told me my result.

Isolating can be especially tricky if, like many Americans, you don’t get paid sick leave, or if you live with people who have tested negative. That’s a common situation with breakthrough infections: While a positive test in a household full of unvaccinated people may soon lead everyone to test positive, that’s not necessarily the case in a home where everyone is vaccinated. “At the minimum, don’t be in the same room,” Javaid said. “If you have to interact with each other, you should always wear masks.” Considering Omicron’s contagiousness, it’s worth wearing more protective masks, such as N95s or KN95s, in lieu of the cloth masks that are common across the U.S. And even if it’s cold, opening windows four to six inches, Kissler said, can help with ventilation. If people you live with start having symptoms, the same guidelines apply: They too should self-isolate, and test if they’re going to see others.

But as The Atlantic’s Katherine Wu has written, not all public-health experts agree that those with breakthrough infections really need to isolate for 10 days, given recent research suggesting that they clear the virus more quickly than the unvaccinated, for whom the 10-day window was designed. Wurtz said that the 10-day isolation period is “somewhat arbitrary,” but she acknowledged that the cautiousness can be reassuring with a new, less understood variant.

Thankfully, most breakthrough infections tend to be mild cases, and that seems likely to hold true with Omicron too (especially for those with booster shots). If you’re feeling unwell, the usual treatment for respiratory infections—cold-and-flu medications, anti-fever drugs, liquids, and rest—are sufficient for most people with breakthrough COVID, Wurtz said.

the best thing vaccinated people can do is make sure they’re ready for a breakthrough infection before it strikes. Stock up on rapid tests so you’re not in a bind if any COVID symptoms suddenly appear. Talk to your family or roommates about where the best place to isolate is in your home. Be prepared to miss 10 days of work if you’re in person.

It's propaganda designed to instill fear and to induce control by the authorities. People who listen to this stuff have no self respect in my view.

It's like hitting download on a file infected with malware. It'll slow you down & has no discernible benefit to a persons wellbeing.

If this disease is so deadly - why am I not dead yet? I am a vulnerable group according to the NHS. Real plagues have people face down in the street by the numbers.

Almost exactly one month after Mayor Bill de Blasio triumphantly announced tens of thousands of fully vaccinated people could return to Times Square to celebrate New Year's Eve in person this year, the state saw it's highest single-day reporting of new COVID infections.

The previous record, set 11 months ago on Jan. 14, crumbled when Gov. Kathy Hochul announced 21,027 new positive cases statewide Friday. The old record for most reported cases in a single day was 19,942, when reported hospitalizations were on the brink of 9,000. Now, the number of people admitted is down by more than half.

New York reported close to the same number of tests taken last Friday, but of that batch (over 260,000), there were 10,000 less positive cases one week ago. Also, when you compare hospitalizations to one week ago, the number of people in hospitals for COVID-19 has risen by about 300, reflecting an increase of 8%.

And in New York City, where testing lines have wrapped around blocks and people report wait times well over an hour, 10,286 positive cases were reported Friday. That total is up 20% from the previous day, and 100% from two days earlier. It's also the highest reported testing day for the city since the beginning of the pandemic, and the first time the city saw more than 10,000 cases in a single day.

In an effort to combat rising cases of either variant, the state is rushing to acquire millions of at-home tests for New Yorkers living in communities with lower vaccine rates. On CNN Friday, the governor confirmed 1 million cases were already in hand with another 2 million on the way.

The city's rolling daily case average is up almost 57% over the rolling averages for the previous four weeks and COVID hospitalizations are up nearly 31%. Delta is the variant believed to be fueling the spike in more severe cases, while omicron is thought to be behind the surge in infections. Both are called "variants of concern."

Soaring COVID-19 case numbers, long testing lines and event cancellations might feel a bit like déjà vu, but so far New York City hospitals aren’t seeing a repeat of the surges that swamped emergency rooms early in the pandemic

The Rockettes on Friday canceled remaining performances of the Radio City Christmas Spectacular, citing “increasing challenges from the pandemic,” lines at some testing sites in the city stretched around the block and at-home tests remained hard to come by, or pricier than usual.

But new hospitalizations and deaths — so far — are averaging well below their spring 2020 peak and even where they were this time last year, during a winter wave that came as vaccinations were just beginning, city data show.

Mount Sinai Health System’s emergency rooms are seeing about 20% more patients — with all conditions — in recent days, according to Dr. Eric Legome, who oversees two of the network’s seven ERs. But at least so far, “we’re seeing a lot more treat-and-release” coronavirus patients than in earlier waves, he said.

Hospital admissions and deaths tend to rise and fall weeks after cases do. But Dr. Fritz François, the chief of hospital operations for NYU Langone Health, says so far, “we’re actually seeing something different” than in previous surges.

For one thing, COVID-19 patients are going home a bit quicker, he said.

NYU Langone has seen a small uptick in patients with COVID-19, now totaling about 80 in its several hospitals in New York City and nearby Long Island. That’s about 80% less than the tally at the top of last winter’s wave, François said

Northwell, the state’s largest private healthcare system with nearly two dozen hospitals in and around New York City, had about 400 COVID-19-positive patients as of Friday — up from around 300 a few weeks ago, but a fraction of the 1,350 at one point last January, to say nothing of the 3,500 in early spring 2020.

About a quarter are vaccinated, up from about 10-15% a month ago, mostly people with underlying health problems, D’Angelo said.

The biggest spikes in COVID-19 cases on Long Island during the past month have been in majority-white communities, a dramatic shift from the beginning of the pandemic, when Black and Latino communities were impacted much more heavily, a Newsday analysis found.

The rise in cases led the percentage of people testing positive for the coronavirus to surge from just over 2% in late October to more than 9% now.

Health experts said less adherence to mask-wearing, social distancing and other precautions in communities with surging caseloads are some of the key reasons for the shift.

"If you weren’t as heavily impacted [early in the pandemic], you may feel the virus is not that serious an issue, and you may not be engaging in all those [precautionary] activities," said Brian Harper, chief medical officer and vice president for equity and inclusion at the New York Institute of Technology in Old Westbury, and a former Suffolk County health commissioner.

All 69 communities with the largest per capita number of cases over the 30 days ending Dec. 13 are majority white, according to Nassau and Suffolk county data, as compared with U.S. Census Bureau population estimates.

On May 1, 2020, 14 of the 20 communities with the highest cumulative COVID-19 rates were majority Black and Latino, including the five hardest hit communities

As of Dec. 13, the eight communities with the highest cumulative rates — counting all cases since the beginning of the pandemic — were at least 85% white, non-Hispanic.

Michael Ryder, the clerk for Hewlett Harbor, said he was "shocked" his village topped the list. Ryder said he doesn’t know why the village has such a high rate.

Harper said people in communities with high coronavirus rates early in the pandemic "felt the impact, whether it be hospitalizations or deaths, very directly of friends or family, such that they may have taken the community mitigation efforts a little bit more seriously, things like social distancing and mask-wearing

He said the biggest challenge public health officials face is the politicization of the virus, including on masking.

Among communities that have seen the most recent COVID-19 cases are some with relatively high vaccination rates. Others have low vaccination rates.

Clouston said that in part might be because "the view was that if you’re vaccinated, you’re safe."

Even though vaccinated people are much less likely to get severely ill than unvaccinated people, "You’re still at risk, and many people who are vaccinated don’t wear masks," Clouston said. "In essence, they offset some of the benefit of the vaccine."

Dr. Aaron Glatt, chairman of medicine at Mount Sinai South Nassau hospital in Oceanside, said people in high-vaccination areas were more likely to get inoculated early on, meaning their immunity often is lower than those who got shots more recently.

"Unless they have the booster dose, they’re going to be somewhat susceptible" to contracting the virus, he said.

The community with the most cases per capita over 30 days, Point Lookout, has a high vaccination rate, but it also has a much older population than the rest of Nassau.

Senators Elizabeth Warren and Cory Booker said on Sunday they both tested positive for Covid-19 and were experiencing mild symptoms amid a nationwide surge in coronavirus cases.

Warren, a Massachusetts Democrat, 72, said on Twitter she is vaccinated and boosted and regularly tested for Covid-19, and “while I tested negative earlier this week, today I tested positive with a breakthrough case.”

Booker, 52, a New Jersey Democrat, said on Twitter he had learned Sunday of his positive test “after first feeling symptoms on Saturday.” He added he had “relatively mild” symptoms and recently had received a vaccine booster. “I’m certain that without them I would be doing much worse,” he said.

There were long lines at a Capitol Hill Covid-19 testing location last week. The Senate adjourned early Saturday until Jan. 3.

On Friday, Southwest Airlines said its Chief Executive Gary Kelly tested positive for Covid-19 after appearing at a U.S. Senate Commerce hearing on Wednesday alongside other airline industry executives. Southwest said Kelly was vaccinated and recovering at home.

Warren and Booker are not members of the Commerce Committee.