In an aerial view, traffic crosses the San Francisco-Oakland Bay Bridge on June 14 in San Francisco.

SAN JOSE – Even as the Bay Area celebrates high COVID vaccination rates, the region is falling drastically short in efforts to inoculate thousands of people living on the street, in vehicles and in homeless shelters.

In some counties, unhoused people are getting vaccinated at close to half the rate of the general population. Other counties aren’t even tracking vaccination rates in homeless communities, making it all but impossible to gauge their success and target areas for improvement.

Experts worry low vaccination rates, combined with the continued spread of the highly contagious Delta variant and the end of some hotel programs that protected unhoused people, are putting homeless communities at risk. A major outbreak at a Santa Rosa homeless shelter this month has infected dozens of people, while Alameda County and San Francisco have reported smaller outbreaks in their unhoused communities.

“Our vaccination rates in shelters are definitely not where we would like them,” said Lucy Kasdin, director of Alameda County’s Health Care for the Homeless Program. “I think there is definitely concern about that.”

Her agency estimates between 25% and 40% of people in homeless shelters in the county are vaccinated — a far cry from the county’s goal of 60%. About 70% of the general population age 12 and older is vaccinated. The agency isn’t tracking rates in encampments.

Meanwhile, case rates are going up in some places. During the week of July 5, Alameda County reported 20 new COVID infections among its unhoused residents — the most the county has seen in one week since early February.

Bay Area health agencies have created pop-up vaccination clinics and sent mobile teams with coolers full of shots to homeless shelters and encampments, but it can be difficult to reach everyone. Shelters have transitory populations and encampments often form in out-of-the-way areas, where it’s easy for health care workers to miss people.

“It is a concern for us, so much so that we are not releasing any of the PPE (personal protective equipment) restrictions at any of our congregate shelter sites,” said Andrea Urton, CEO of HomeFirst Services, which runs Santa Clara County’s largest shelter. “We’re keeping all of it in place. Because we just don’t know what’s going to happen right now.”

San Francisco estimates it has fully vaccinated 38% of its homeless residents, compared to 76% of its general population 12 and older. In Contra Costa County, an estimated 33% of unhoused residents are fully vaccinated, compared to 74% of the general public 12 and older.

The data is spotty, and some counties, including San Mateo and Sonoma, were unable to provide estimates. The California Immunization Registry doesn’t track a vaccine recipient’s housing status, so county officials piece information together from multiple databases. Complicating matters, officials don’t have a current base count of the Bay Area’s homeless population. Counts that were supposed to happen this year were canceled because of COVID precautions.

Santa Clara County’s Valley Homeless Healthcare Program surveyed 1,800 of its unhoused patients and found 70% were vaccinated, according to spokeswoman Joy Alexiou. But at encampments, only between 30% and 40% of people offered a vaccine have accepted.

“You have to be able to trust science, you have to be able to trust the health care system, you have to be able to trust the people you’re around,” said Dr. Margot Kushel, professor of medicine and director of the UCSF Center for Vulnerable Populations. “And I think people who are homeless often have had a lot of trauma and a lot of reasons to not trust those systems.”

Santa Rosa reported a major outbreak earlier this month at Samuel Jones Hall, where about half of the shelter’s 156 residents had COVID or were suspected of catching the virus. Many of the infected residents had been vaccinated — including six who were hospitalized despite having had their shots.

Experts say in a shelter setting where dozens of people eat and sleep in close quarters and many people are unvaccinated, the virus is likely to spread more easily — even to vaccinated people.

As did much of the Bay Area, Sonoma County largely relied on the Johnson & Johnson vaccine to protect its homeless communities. The one-shot approach means outreach workers don’t have to worry about tracking people down for a second dose. But the Johnson & Johnson shot has struggled with acceptance because it’s a bit less effective at preventing COVID than the Pfizer and Moderna vaccines and comes with warnings that recipients have suffered Guillain-Barré syndrome and blood clots in very rare cases.

While vaccination rates may be low in the rest of the Bay Area, Leland Wells, manager of the St. Vincent de Paul shelter in Oakland, is proud of his numbers. When county health workers began showing up with vaccines, Wells made it his mission to convince everyone to get a shot. Now, just about all of the shelter’s roughly 45 regular guests have been vaccinated, he said.

“I think a lot of it is about trust and relationships,” Wells said. “I’m here and they know that I’m here. And I know that they believe that I’m not going to have them do something that’s not for their good.”

Carlos Dubose is his most recent success story. The 51-year-old came to St. Vincent de Paul for a free lunch Tuesday and ended up leaving with a sandwich and a Johnson & Johnson shot.

It was the first time Dubose, who had been sleeping outside before getting a shelter bed about three weeks ago, was offered a vaccine. He’s not worried about catching COVID, but he feared his unvaccinated status would prevent him from functioning in society.

“As much as you agree or disagree, you may as well get it over with as soon as you can,” he said.

Not everyone feels that way. When a health care worker offered a shot, David Stevens, 53, shook his head.

“Not right now,” he said as he walked away.

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