Delays as State Officials Face Deluge of COVID-19 Reporting Data

State health officials say there have now been more than 10,000 deaths from the novel coronavirus in California. This comes as Health and Human Services Secretary Dr. Mark Ghaly gave an update Friday on a technical glitch with the electronic lab reporting system for COVID-19 cases.

Ghaly said a server outage on July 25 led to an extensive backlog of unreported COVID-19 tests results. The state reporting system, known as CalREDIE, suffered another hiccup between July 31 and Aug. 4, during which it failed to receive test results from a major commercial lab.

Ghaly said the CalREDIE reporting system has been challenged by the cascade of COVID-19 data — that it was not built to handle such a high volume. He said the state is accelerating development of a new laboratory reporting system for COVID-19, but he did not indicate when it would be online. New protocols and notifications have been put in place, and servers now have larger capacity. In addition, he said Gov. Gavin Newsom has directed an investigation of what went wrong.

The state plans to sort through the backlog of 250,000 - 300,000 test records — most of them COVID — in the next few days.

Ghaly said the unaccounted-for lab results could be positive or negative and he remains confident the number of new cases is stabilizing.

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The backlog has created difficulties for some county public health departments, where officials have described the reliability of COVID-19 data as “flying blind” and hindering their contact tracing abilities.

— Peter Arcuni (@peterarcuni)

10 More COVID-19 Deaths in California Prisons in Last Week

Ten inmates in California state prisons have died from complications from COVID-19 in the last week, bringing the total number of prisoner deaths related to the coronavirus to 184. Nineteen staff members for the California Department of Corrections and Rehabilitations have also died from the virus.

The number of active cases in custody has been dropping since a high of nearly 11,000 on Dec. 20.

Still, as of Jan. 18, infections in state prisons were about six times those of California as a whole when adjusted for population.

Just over 3,000 incarcerated people have gotten their first dose of the vaccine, which takes a few weeks to offer protection. But even inoculation won't prevent the virus from spreading in pentitentaries, says Dr. Peter Chin-Hong, an infectious disease specialist at UCSF.

“It doesn’t matter if you vaccinate a zillion people, if they are crowded together they are going to spread COVID very efficiently,” he said.

While the vaccine is a helpful tool, it needs to be coupled with other safety measures like physical distancing of inmates, masks and proper ventilation, says Chin-Hong.

Prison facilities “are ancient for the mass majority of locations," he said. "They are overcrowded ... It seems really surprising, disappointing and heartbreaking that we haven’t cared for inmates as we have for the general population.”

He warns that the arrival of new, more infectious variants of the virus may already be circulating in California prisons. A more transmissible virus, combined with an aging prison population, can spell disaster, he says

“The risk of these individuals after contracting COVID in terms of doing poorly and dying is higher than your general population.”
In a statement, a spokesperson for the California Department of Corrections and Rehabilitation said approximately 18,640 people have had their release date sped up due to the pandemic.. CDCR has released 24,000 inmates overall since March, it said.

Marco Siler-Gonzales

Kaiser Limits Vaccinations for Seniors to Members Over 74

Kaiser Permanente says it is not yet able to give COVID-19 vaccinations to all seniors under the age of 75, due to a lack of supply.

On the heels of the federal government and then the state expanding vaccine eligibility to people 65 and over, the health care giant opened up its phone lines last week for seniors to make vaccination appointments. But slots for those under 75 were only briefly available, according to the company, as the limited supply has forced it to prioritize older seniors, along with continuing to vaccinate health care workers.

Vaccine supply permitting, the company expects to honor existing appointments made by those under 75 when they were available.

Members should no longer attempt to proactively make vaccine appointments, the company says.

"There is no need for members to contact us by email, phone, or on the website until they first hear from us," Kaiser said.

With more than 1.5 million members age 65 and older, Kaiser received a first-dose vaccine supply last week of just 20,000 doses, it said.

"At the current rate, we are looking at vaccine distribution that is much slower than any of us find acceptable," a company statement said. "We are doing all we can to get additional vaccine supply as soon as possible."

Kaiser says that as of Jan. 16, it had administered more than 170,000 doses in California, including the second shots that people must receive to complete their inoculation.

Polly Stryker and Jon Brooks

Don't Worry So Much About the California Variant, Says Infectious Disease Specialist

During a press conference on Sunday, Bay Area health officials said they are “concerned” about the rising number of coronavirus cases identified with a California variant of COVID-19. This variant is different from others identified in the UK, South Africa and Brazil.

The California variant was first discovered in May and simmered in the population over the summer and fall, when the number of cases was much lower than it is now.

Known by virologists as L452R, the variant grew from 4% of the samples scientists sequenced in the first half of December to roughly a quarter in the second half of the month.

Virologists are still trying to determine if the variant is more infectious than the original coronavirus strain.

Dr. Sarah Cody, Santa Clara County’s health officer, says it’s too early to draw conclusions about the variant, which has been identified in a number of outbreaks.

“We need to lean in and do more investigation,” she said. “And that’s what we’re doing.”

Dr. Monica Gandhi, an infectious disease specialist at UCSF, talked about the variant with KQED's Tara Siler on Tuesday. Gandhi says she is not worried about the effectiveness of the vaccines on the variants. Here is an excerpt from that interview, edited for length and clarity:

How concerning are these variants in terms of California's current surge?

Dr. Monica Gandhi: We only know, so far, that the so-called UK variant B117 is more infectious, and we don't know if the L452R, the California strain, is more infectious. It just happened to be the strain that is being sequenced and coming out in our latest Bay Area surge. But it may have just gotten lucky; it doesn't mean it's more infectious. It may have just been the one that was spreading as things were opening up.

How effective will the vaccines be in protecting us from these new virus variants?

Gandhi: I think it's really important to feel hopeful about the vaccines and not start getting really concerned that [the variants] are going to evade them. The reason I say that is because the two authorized vaccines we have, from Pfizer and Moderna, have the entire spike protein that you code for when the vaccine is put in your system, and you make a very complex antibody response to that spike protein.

These variants have little point mutations along the spike protein, but that doesn't mean the spike protein is totally changed. In fact, there are three mutations on the L452R variant along the spike protein, but that doesn't mean the vaccine won't work. I think that is total speculation, and we'll worry a lot of people if we stress that too much.

On that front, do you think we're underselling the vaccines?

Gandhi: I am really concerned about that. These vaccines could not be better. We thought that if we got a 50% efficacy rate, we would probably still approve it in this country, and these vaccines are 95% effective at preventing COVID-19 infection that's symptomatic, and almost 100% effective in preventing severe outcomes. These vaccines are amazing. Instead of worrying that these variants are going to evade the vaccine response, I'm not worried about that at all. In fact, Pfizer's done some studies with B117, and it looks like the UK variant is just fine in terms of the vaccine working. So I wouldn't speculate. I think when we keep focusing too much on the negatives, it actually could prevent people from getting the vaccine. We are lucky to have these vaccines, and we've got to get them out.

More on coronavirus variants:

Polly Stryker, Kevin Stark and Jon Brooks

Poor Food Quality, Sanitation Add to COVID-19 Risk at Santa Rita Jail, Advocates Say

Last week, advocates hosted a virtual press conference to discuss what they say is a growing outbreak of COVID-19 in Alameda County's Santa Rita Jail in the wake of an alarming spike in cases at the facility in late December.

Legal advocates and family members with loved ones detained inside have specifically highlighted poor food quality and sanitation issues as COVID-19 risk factors for those incarcerated.

"Namira," who wished to remain anonymous for fear of retribution against her or her husband who is incarcerated at Santa Rita Jail, told KQED that conditions are jam-packed.

“I’d say that there are shelters for animals that are way cleaner and better,” she said. “As soon as he entered Santa Rita Jail, he started feeling sick. Initially, I said no, it’s just the environment."

But then, on the phone, she heard her spouse coughing. After talking to him, she called the main Santa Rita Jail number asking for medical attention. They told her to wait until the next morning, but she called again after a few hours.

"If there is nobody outside to be there for you — to speak on your behalf, they are very casual,” Namira said.

Read the full story.

Lakshmi Sarah

California Hospitalizations, Positivity Rate Trending Down

The dreaded post-New Year's COVID-19 surge has not been as bad as California health officials had feared.

State hospitalizations are down 8.5% over 14 days, with the number of intensive care patients also easing, Health and Human Services Secretary Dr. Mark Ghaly said Tuesday. 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,” said Ghaly, who also said he’s hoping things improve with the new Biden administration. "I think we're seeing that statewide, not just in certain parts that often have seen that decrease first, but (also) in some of those most heavily impacted areas like Southern California and San Joaquin Valley."

He warned that hospitals will likely experience a slight bump in patients in the coming week, but a drop by the end of the month.

The recent decreases all indicate that the state's wave of winter coronavirus cases and deaths may be beginning to crest, Ghaly said.

State officials, including Gov. Gavin Newsom, have referred to the winter spike in cases as the "last wave" of the virus before vaccines become widely available to the public.

Even so, California this week surpassed 3 million COVID-19 cases since the pandemic began last January. More than 34,000 people have died in the state, including more than 6,700 people in the last two weeks.

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.

To date, roughly 3.2 million vaccine doses have been shipped to the state's local health departments and health care systems, with roughly 1.5 million doses administered.

On Friday, counties across California administered the largest number of vaccine doses in one day to date, 110,505, ultimately helping the state meet its goal of doling out 1 million doses by Friday.

Delays in data reporting also mean the state's total number of administered vaccine doses is likely even higher than 1.5 million, Ghaly said.

—KQED News and wire services

Here's Where San Franciscans Can Sign Up to Receive Notifications When They're Eligible for Vaccine

San Francisco’s text message service to alert city workers and residents when it is their turn to get the vaccine is now live, along with a dashboard that details the latest statistics about how many people have been vaccinated.

City residents can sign up to receive a vaccine notification at sf.gov/vaccinenotify.

After it launched, the website went down for a short period in the afternoon. Supervisor Matt Haney, who has been critical of the city’s vaccine rollout, called the launch of the site a “mess” on Twitter.

The city hopes to open vaccine hubs at the Moscone Center, City College of San Francisco’s Ocean Campus, and the San Francisco Produce Market in Bayview, sites where the city says it can administer as many as 10,000 doses per day when they are available.

Mayor London Breed said the city’s biggest obstacle is a critical shortage of doses, and residents will still likely have to wait months before receiving their shot in the arm.

City leaders say they will use up their vaccine allotment by the end of the week. San Francisco’s system has received 102,825 doses from the federal government.

In Oakland, a Moment of Remembrance for COVID Victims

Health care workers joined community leaders and Oakland Mayor Libby Schaaf Tuesday in a nationwide moment of remembrance for those who have died of COVID-19.

The memorial was one of many inaugural events leading up to the swearing-in Wednesday of President-elect Joe Biden and Vice President-elect Kamala Harris, who was born in Oakland.

Schaaf offered condolences to the loved ones of the more than 760 victims of COVID-19 in Alameda County. She also expressed gratitude for essential workers

“Community leaders, volunteers, educators, health care workers, these are the people we celebrate today and who deserve to be part of this ceremony as we join in this national moment,” Schaaf said.

The bells of Our Lady of Lourdes church near Lake Merritt in Oakland rang out at 2:30 p.m., as the mayor and other community leaders released white doves. Similar ceremonies were held simultaneously in cities and towns across the country as Biden and Harris presided over the lighting of 400 lights on the National Mall in recognition of the lives lost.

Biden has outlined an ambitious COVID-19 response that includes a $1.9 trillion relief package. The plan sets aside $400 billion to directly address the virus, including funding for additional public health workers, support for states and an expansion of people eligible for the vaccine. Biden hopes to deliver 100 million doses of the vaccine in his first 100 days in office.

The U.S. death toll from COVID-19 reached 400,000 Tuesday.

Alice Woelfle