Dr. Peter Meacher expected to receive just a small supply of Moderna’s coronavirus vaccine to inoculate his staff at a network of clinics that he oversees in New York City. Instead, 600 doses arrived late last month, far more than he needed.

For two weeks, more than half of the supply sat in freezers. At other clinics in the city, small numbers of unused doses have even been thrown out.

Dr. Meacher said he would like to give the extra vaccine to high-risk patients, but had not for fear of violating strict eligibility rules from the state about who can receive it.

“It’s stressful and frustrating to have vaccine and to be unable to start giving it to our patients as quickly as we would like,” said Dr. Meacher, chief medical officer for the Callen-Lorde Community Health Center in Manhattan, which serves some 18,000 L.G.B.T.Q. New Yorkers.

“There are very vulnerable patients who come to us for their care, and we want to get them the vaccine,” he said.

In New York City and many places around the country, the mass vaccination campaign is off to a dispiriting start, with public health experts voicing concerns about how few people have been vaccinated so far, even as coronavirus cases soar and a more contagious variant of the virus has been detected.

It initially seemed that the main bottleneck would be scarcity of the vaccine. But in New York City, health experts said the problem was that officials have been slow to make use of vaccine doses already distributed. As of early Friday, only 167,949 of 489,325 doses had been administered — about 34 percent, which was lower than the rate across New York State, which was about 50 percent.

Elsewhere, governors are relaxing protocols because of criticism over the pace of inoculations and growing demand. For their part, federal officials have asked states to expand eligibility.

In New York, Gov. Andrew M. Cuomo had stuck to rigid guidelines that prioritize health care workers, and residents and staff of nursing homes and group homes. But on Friday, after repeated criticism from Mayor Bill de Blasio and local officials around the state, Mr. Cuomo announced that New York would allow a broad group of essential workers and New Yorkers who are over 75 to begin scheduling vaccinations as soon as Monday — one month after New York City received its first doses.

The slow pace has touched off new tensions between Mr. Cuomo and Mr. de Blasio. The two men, Democrats with a history of feuding, have frequently clashed over the response to the pandemic.

The governor had resisted expanding eligibility, saying that it was important to first vaccinate as many health care workers as possible. On Friday, he again called for the prioritization of those workers, and he recently signed an executive order threatening fines of up to $1 million for health care providers who violate his system.

City officials said it would be easier to speed things up when far more people were eligible. On Friday, Mr. de Blasio said on Twitter that New York City would begin vaccinating city workers and older adults on Monday.

Alex M. Azar II, the secretary of the federal Department of Health and Human Services, urged states this week to not allow rigid prioritization lists to slow things down.

“There is no reason that states need to complete, say, vaccinating all health care providers before opening up vaccinations to older Americans or other especially vulnerable populations,” Mr. Azar said.

He said states should not “leave vaccines sitting in freezers.”

But that is exactly what has been happening in New York City. As a result, some community clinics, like those in the Callen-Lorde system, feel they are caught in the middle of a haphazardly planned vaccine rollout. While many vaccine doses have gone to hospitals, a substantial amount have gone to smaller, nonprofit community health networks that typically treat low-income and underserved people.

At first, the clinics in these networks were limited to vaccinating their own staff. But this week, as officials tried to clear the logjam, the clinics were tasked with trying to find other eligible health care workers they could vaccinate.

On Tuesday evening, the Family Health Center of Harlem stayed open late after scheduling vaccination appointments between 6 p.m. and 8 p.m. with more than 20 workers at a neighboring community health agency, said Dr. Neil Calman, president of the Institute for Family Health, a nonprofit health network that includes the Harlem clinic.

But some workers did not show and others decided against getting the vaccine at the last moment, Dr. Calman said. That left just 12 people willing to be vaccinated.

Vials of the Moderna vaccine generally yield 10 doses, which must be used within six hours after a vial is punctured. Not wanting to turn away two people, the clinic opened a second vial. After a quick search, the staff found three other eligible people, leaving five unused doses, Dr. Calman said.

The nurse at the clinic called her supervisor at home asking what to do with the remainder. From her home, the supervising nurse called her contact at the city’s health department for guidance. She was told to try to find people who fit the eligibility criteria and was encouraged to contact a nearby nursing home, an urgent care center and a women’s shelter.

Covid-19 Vaccines ›

Answers to Your Vaccine Questions

While the exact order of vaccine recipients may vary by state, most will likely put medical workers and residents of long-term care facilities first. If you want to understand how this decision is getting made, this article will help.

Life will return to normal only when society as a whole gains enough protection against the coronavirus. Once countries authorize a vaccine, they’ll only be able to vaccinate a few percent of their citizens at most in the first couple months. The unvaccinated majority will still remain vulnerable to getting infected. A growing number of coronavirus vaccines are showing robust protection against becoming sick. But it’s also possible for people to spread the virus without even knowing they’re infected because they experience only mild symptoms or none at all. Scientists don’t yet know if the vaccines also block the transmission of the coronavirus. So for the time being, even vaccinated people will need to wear masks, avoid indoor crowds, and so on. Once enough people get vaccinated, it will become very difficult for the coronavirus to find vulnerable people to infect. Depending on how quickly we as a society achieve that goal, life might start approaching something like normal by the fall 2021.

Yes, but not forever. The two vaccines that will potentially get authorized this month clearly protect people from getting sick with Covid-19. But the clinical trials that delivered these results were not designed to determine whether vaccinated people could still spread the coronavirus without developing symptoms. That remains a possibility. We know that people who are naturally infected by the coronavirus can spread it while they’re not experiencing any cough or other symptoms. Researchers will be intensely studying this question as the vaccines roll out. In the meantime, even vaccinated people will need to think of themselves as possible spreaders.

The Pfizer and BioNTech vaccine is delivered as a shot in the arm, like other typical vaccines. The injection won’t be any different from ones you’ve gotten before. Tens of thousands of people have already received the vaccines, and none of them have reported any serious health problems. But some of them have felt short-lived discomfort, including aches and flu-like symptoms that typically last a day. It’s possible that people may need to plan to take a day off work or school after the second shot. While these experiences aren’t pleasant, they are a good sign: they are the result of your own immune system encountering the vaccine and mounting a potent response that will provide long-lasting immunity.

No. The vaccines from Moderna and Pfizer use a genetic molecule to prime the immune system. That molecule, known as mRNA, is eventually destroyed by the body. The mRNA is packaged in an oily bubble that can fuse to a cell, allowing the molecule to slip in. The cell uses the mRNA to make proteins from the coronavirus, which can stimulate the immune system. At any moment, each of our cells may contain hundreds of thousands of mRNA molecules, which they produce in order to make proteins of their own. Once those proteins are made, our cells then shred the mRNA with special enzymes. The mRNA molecules our cells make can only survive a matter of minutes. The mRNA in vaccines is engineered to withstand the cell’s enzymes a bit longer, so that the cells can make extra virus proteins and prompt a stronger immune response. But the mRNA can only last for a few days at most before they are destroyed.

The nurse at the clinic set out on foot. She was turned away at a few places, including a nursing home and fire station, although she did finally find one eligible health care worker willing to be vaccinated, Dr. Calman said.

He said the nurse eventually threw out the remaining doses after the health department told the clinic that it could only vaccinate members of eligible groups.

Dr. Calman said the lesson was clear: Eligibility categories are too narrow, and it is time to open up vaccinations to more people.

“People don’t hold hands in blocks of 10 to come over to get immunized,” he said. “We just need to enable providers to use their professional judgment to give it to people at their highest risk.”

A spokesman for New York City’s health department, Patrick Gallahue, said that when the clinic reached out for guidance, “we shared nearby facilities where they could find eligible individuals.”

“Nevertheless, if a single dose was indeed discarded, it is a vivid illustration of why the categories of eligible people must be broadened,” Mr. Gallahue said in an email.

Early on, Mr. Cuomo decided to largely bypass local health departments and send the initial shipments of the vaccine directly to hospitals and health clinics.

The state initially instructed these health care centers to vaccinate their employees in specific order, according to risk. The result was a system that put pressure on organizations to proceed cautiously, representatives for several clinics said.

Centers had to evaluate every single employee according to a complex matrix that included job description, the environment in which the employee worked and age, among other factors.

“It’s just a very bureaucratic process,” Charles King, chief executive of Housing Works, a nonprofit organization which offers social services and health care to homeless people and people with H.I.V. and AIDS.

Housing Works’s chief operating officer, Andrew Greene, said he spent Christmas Eve at his kitchen table pulling up employee pay records on his laptop in an attempt to gauge how many days his regular employees typically worked on site — one of the inputs for the risk assessment matrix.

“The federal government pushed this down to the state or municipalities, and they pushed it down to the people with no choice but to get the job done from the kitchen table on Christmas Eve,” he said.

Additionally, health care facilities had to consider employee schedules, the risks of too many simultaneous adverse reactions within a unit and the availability of staff to administer the vaccine, which could all slow down the process.

Even the guidelines caused considerable uncertainty about whom to vaccinate. The state has told organizations to prioritize the highest risk employees, but it has been unclear how far down the risk matrix they should go.

Every week, the state issues guidance expanding the eligible groups of employees. But the criteria are often vague, health care providers say.

One recent document from the state Department of Health said that hospitals could begin vaccinating employees who “have the potential for direct or indirect exposure to patients or infectious materials,” noting that riding elevators or eating in cafeterias both count as potentially risky activities.

“We interpreted the maintenance team was eligible,” Dr. Vaty Poitevien, Housing Works’s chief medical officer, said. “It wasn’t completely clear. I hope I’m right.”

She added, “I don’t want Dr. Zucker to come and pull my operating license,” referring to the state health commissioner, Dr. Howard Zucker, and the state’s escalating warnings against vaccinating people out of order.

“The threats have made you extra cautious,” Dr. Poitevien said.

On Friday, the state’s Department of Health told The Journal News, a newspaper in the lower Hudson Valley, that a hospital was under investigation for vaccinating city and school system employees in New Rochelle, a suburb north of New York City. Those groups are not yet eligible, and the mayor of New Rochelle told The Journal News that Montefiore New Rochelle Hospital had “misinterpreted the state guidelines.”

Just days earlier, Governor Cuomo had singled out several hospitals, including Montefiore New Rochelle, for taking too long to administer its doses.

The state Department of Health was “investigating this egregious violation of the state’s clearly defined guidelines for the Covid-19 vaccine,” a department spokesman told the newspaper.

The threats of investigations and fines have slowed the pace of vaccinations, according to interviews with doctors and health care administrators.

Dr. Rachael Piltch-Loeb, an associate research scientist at New York University’s School of Global Public Health who studies emergency preparedness, said some of these issues could have been avoided by setting up mass vaccination sites independent of employers, or by having health departments play a more direct role in the vaccination campaign.

“The answer is setting up the points of distribution and scaling up capacity independent of any given employer,” she said.

This week, the city started vaccinations at the first two of 125 small pop-up sites that are expected to open up by the end of January. The city said that in the coming weeks, it would also open up five mass vaccination sites that would run round the clock.

That should eventually relieve some of the burden that community clinics face. But for now, several clinics said, they will move forward with whatever vaccinations they can give.

A day after the state Health Department gave the green light for vaccination of a wider range of health care workers, a team of nurses at Callen-Lorde’s health center in Manhattan’s Chelsea neighborhood prepared to vaccinate a handful of addiction counselors and other employees from the Greenwich House, a nearby social service agency.

Dr. Meacher said on Thursday night that the clinic had so far administered about 300 doses — half of what Callen-Lorde received more than two weeks ago.

Michael Gold contributed reporting.

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