Vaccine supply issues continued to plague California on Tuesday even as other indicators about the spread of the coronavirus showed what the top health official called “rays of hope” amid the deadliest days of the pandemic.

San Francisco’s public health department said it’s likely to run out of vaccine Thursday, in part because the state pulled back on administering a batch of Moderna shots after several health workers in San Diego had a bad reaction.

The county health department received 12,000 doses last week and had expected the same amount this week, but it received only 1,775.

“This unreliable source makes it very hard to plan,” public health director Dr. Grant Colfax said.

Even with the lagging supply, California in the last week greatly expanded both the number of people cleared to get a vaccine and its capacity for administering shots. A center that can handle as many as 12,000 shots a day opened Friday at Dodger Stadium in Los Angeles as other cities also opened stadiums and fairgrounds.

Yet Yolo County Public Health Officer Dr. Aimee Sisson said the state is “creating unreasonable expectations” by pushing to inoculate those age 65 and up when the county still lacks enough vaccines even for health care workers.

Sacramento County Public Health has just 975 doses allocated for this week, leading Public Health Officer Dr. Olivia Kasirye to call for patience.

Meanwhile, Los Angeles County Board of Supervisors Chairwoman Hilda Solis directed the county Department of Public Health to make vaccination appointments available starting Thursday to an estimated 1.3 million county residents 65 and older, despite the shortage.

“This is about equity. Older adults have been unfairly impacted by the virus,” Solis said, also urging patience.

The nation’s most populous county opened five large-scale coronavirus vaccination sites Tuesday, with the capacity to inoculate 4,000 people at each location daily.

LA County Department of Public Health Director Barbara Ferrer said there is currently enough vaccine “to get through this week,” with an uncertain future supply. The county’s vaccination hotline and website were getting thousands of calls and users, so many that it was having what officials called technical difficulties.

Fresno County could inoculate 30,000 people each week, but it has been getting between 8,000 and 10,000 weekly vaccine doses. This week officials there sought an additional 20,000 doses but were allotted 5,100 doses, preventing them from running out but forcing the county to reduce its vaccination goal.

Hospitals also said they are running short.

The Kaiser Permanente health care consortium said it received 20,000 doses last week — far too few for its 1.5 million members 65 and older and forcing a rollout it said “is much slower than any of us find acceptable.”

The University of California, San Francisco Medical Center could run out of vaccine by Friday, but it hopes additional doses will arrive in time.

“The vaccine supply has been erratic, but we are opening as many appointments as possible as supply comes in,” spokeswoman Elizabeth Fernandez said.

California officials from state Health and Human Services Secretary Mark Ghaly on down said they are counting on the federal distribution network speeding up once President-elect Joe Biden takes office Wednesday.

So far 3.2 million doses have been shipped to California and 1.5 million have been administered, Ghaly said. That exceeds Gov. Gavin Newsom’s goal of getting an additional 1 million shots in arms over a 10-day period, but Ghaly could not say if the state met Newsom’s self-imposed Friday deadline for doing so, citing lagging reports.

The delay in administering the remaining 1.7 million doses may be because some have not actually arrived in the state yet, and some have been earmarked for those needing second doses or for the mass vaccination sites, he said.

Meanwhile, infection indicators are “all showing trends in the right direction,” Ghaly said. A surge following Christmas and New Year’s had been feared on top of the surge after Halloween and Thanksgiving that drove case levels and hospitalizations to record levels.

Only a couple of weeks ago, it was feared some hospitals in Los Angeles and other hard-hit areas might have to begin rationing care as they ran out of surge capacity that was tapped when regular beds were filled.

But statewide hospitalizations are down 8.5% over 14 days, with the number of intensive care patients also easing. Hospitals that had been seeing 3,500 new patients each day are now seeing 2,500 to 2,900 daily admissions — still distressingly high, but “quite a significant reduction,” Ghaly said.

The statewide positivity for the virus fell below 10% for the first time in weeks, and each infected individual is now infecting less than one other person — a recipe for an eventual decline in cases.

“These are rays of hope shining through,” Ghaly said.

Skilled nursing homes that bore the brunt of the virus in the early months of the pandemic and then again during the latest surge have seen cases drop by half in the last month.

Deaths continue at a frightening pace, however. More than 6,700 people have died in the last two weeks. In Los Angeles County, so many people have died that the air quality board temporarily amended its rules to allow for more cremations.

Health officials are in a race against time, not only as patients continue to become sick and die but as the virus mutates into forms that can spread much more easily.

An L452R variant has been found in at least a dozen counties and identified in several large outbreaks in Northern California’s Santa Clara County.

The variant is one of five recurring mutations that made up a strain called CAL.20C found in more than one-third of Los Angeles County infections, researchers at Cedars-Sinai said.