In these first lumbering weeks of the largest vaccination campaign in U.S. history, Dr. Julie Vaishampayan has had a battlefront view of a daunting logistical operation.

Vaishampayan is the health officer in Stanislaus County, an almond-growing mecca in California’s Central Valley that has recorded about 40,000 cases of covid-19 and lost 700 people to the illness. Her charge is to see that potentially lifesaving covid shots make it into the arms of 550,000 residents.

And like her dozens of counterparts across the state, she is improvising as she goes.

From week to week, Vaishampayan has no idea how many new doses of covid vaccines will be delivered until just days before they arrive, complicating advance planning for mass inoculation clinics. The inoculation clinics themselves can be a bureaucratic slog, as county staffers verify the identities and occupations of people coming in for shots to ensure strict compliance with the state’s multitiered hierarchy of eligibility. In these early days, the county also has provided vaccines to some area hospitals so they can inoculate health care workers, but the state system for tracking whether and how those doses are administered has proven clumsy.

With relatively little help from the federal government, each state has built its own vaccination rollout plan. In California, where public health is largely a county-level operation, the same departments managing testing and contact tracing for an out-of-control epidemic are leading the effort. That puts an already beleaguered workforce at the helm of yet another time-consuming undertaking. A lack of resources and limited planning by the federal and state governments have made it that much harder to get operations up and running.

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“We are flying the plane as we are building it,” said Jason Hoppin, a spokesperson for Santa Cruz County. ”All of these logistical pieces are just a huge puzzle to work out.”

It’s a massive enterprise. Counties must figure out who falls where in the state’s multitiered system for eligibility, locate vaccination sites, hire vaccinators, notify workforce groups when they are eligible, schedule appointments, verify identities, then track distribution and immunizations administered.

Some of that burden has been eased by a federal program that is contracting with major pharmacies Walgreens and CVS to vaccinate people living in nursing homes and long-term care facilities, as well as a California mechanism that allows some large multicounty health care providers to order vaccines directly. As of this week, some smaller clinics and doctors’ offices also can get vaccine directly from the state.

But much of the job falls on health departments, the only entities required by law to protect the health of every Californian. And they are doing it amid pressures from the state to prevent people from skipping the line and a public eager to know why the rollout isn’t happening faster.

As of Monday, only a third of the nearly 2.5 million doses allocated to California counties and health systems had been administered, according to the most recent state data available. Gov. Gavin Newsom has acknowledged the rollout has “gone too slowly.” Health directors counter it’s the best that could be expected given the short planning timeline, limited vaccine available and other strictures.

“I would not call this rollout slow,” said Kat DeBurgh, executive director of the Health Officers Association of California. “This isn’t the same as a flu vaccine clinic where all you have to do is roll up your sleeve and someone gives you a shot.”

It has been one month since the first vaccines arrived in California, and just over five weeks since the state first outlined priority groups for vaccinations, then passed the ball to counties to devise ways to execute the plan.

Like most states, California opened its rollout with strict rules about the order of distribution. The first phase prioritized nursing home residents and hospital staffs before expanding to other broad categories of health care workers. In the weeks after the vaccines first arrived, state officials made clear that providers could be penalized if they gave vaccinations to people not in those initial priority groups.

Multiple counties said there had been little in the way of line-skipping, but stray reports in the media or complaints sent directly to community officials need to be chased down, wasting precious public health resources. The same goes for reports of vaccine doses being thrown away. One of the vaccines in circulation, once removed from ultra-cold storage, must be used within five days or discarded.

State officials have since loosened their rules, telling counties and providers to do their best to adhere to the tiers, but not to waste doses. On Jan. 7, California officials told counties they could vaccinate anyone in “phase 1a,” expanding beyond the first priority group of nursing homes and hospitals to nearly everyone in a health-related job. Once that wide-ranging category is finished, counties were supposed to move to “phase 1b,” which unfolds with its own set of tiers, starting with people 75 and older, educators, child care workers, providers of emergency services, and food and agricultural workers before expanding to all people 65 and older.

Mariposa and San Francisco both said they would be vaccinating people in the first 1b categories this week. That means residents will start seeing inequities among counties, said DeBurgh, noting that some counties had not yet received enough vaccine doses to cover health care workers while others are nearly finished. Stanislaus County, for example, had received approximately 16,000 first doses as of Jan. 9, but estimates it has between 35,000 and 40,000 health care workers for phase 1a.

And the orders are changing yet again, forcing counties to pivot. On Tuesday, U.S. Health and Human Services Secretary Alex Azar said the Trump administration would begin releasing more of its vaccine supply, holding onto fewer vials for second doses; and he encouraged states to open up vaccinations to everyone age 65 and older. In response, California officials said Wednesday that once counties are done with phase 1a, people 65 and older are in the next group eligible for vaccines.

Some local health directors expressed dismay at the prospect, saying they welcome the influx of vaccines but need to prioritize people 75 and older who represent the bulk of hospitalizations. They also noted that states already offering broader access have had their own challenges, including flooded health department phone lines, crashed websites and fragile seniors camping out overnight in hopes of securing their place in line.

While sensible in theory, California’s phased approach to the rollout has proved cumbersome when it comes to verifying that people showing up for shots fall under the umbrella groups deemed eligible. In Stanislaus, for example, 6,600 people qualify as in-home support workers. Someone from another county department has to sit with health department staffers to verify their eligibility, since the health department doesn’t have access to official data on who is a qualified member of the group.

Complicating matters, about half the county’s in-home workers are caring for a family member, and many are bringing that person with them to get vaccinated. The county is required to turn those family members away if they don’t meet the eligibility criteria, Vaishampayan said.

A range of other hiccups hampered the rollout. Across the state, uptake of vaccination slowed to a crawl from Christmas to New Year’s. Health workers, particularly those who do not work in hospitals, were on vacation and enjoying a few days off with family after a tough year, several county officials said. Many chose not to get vaccinated during that time.

Others are choosing not to get vaccinated at all. Across the state, health care workers are declining vaccinations in large numbers. The health officer for Riverside County has said 50% of hospital workers there have declined the vaccine.

And in Los Angeles and Sonoma, officials described software challenges that prevented them from quickly enrolling doctors’ offices to receive vaccines and perform injections.

Still, statewide, officials said they were confident that the pace would pick up in the coming days, as more doses arrive, data snags get sorted out and more vaccination sites come on board. Los Angeles County announced this week it would convert Dodger Stadium and a Veterans Affairs site from mass testing sites into mass vaccination clinics. Similar plans are underway at Petco Park in San Diego and the Disneyland Resort in Orange County. Officials hope Dodger Stadium alone can handle up to 12,000 people a day.

The move solves one problem, but potentially exacerbates another: The two Los Angeles sites have been testing 87,000 people a week, according to Dr. Christina Ghaly, Los Angeles County Department of Health Services director. That will put new constraints on testing, even as covid cases in the nation’s most populous county continue to rise and hospitals are beyond capacity.

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