Category Archives: San Francisco Bay Area

South Africa coronavirus variant that reduces vaccine efficacy found in two Bay Area counties

A worker is seen at a coronavirus testing site in San Francisco in November. The city has had no known cases of the South Africa variant, but elsewhere in the Bay Area two cases have been recorded.
A worker is seen at a coronavirus testing site in San Francisco in November. The city has had no known cases of the South Africa variant, but elsewhere in the Bay Area two cases have been recorded. Lea Suzuki / The Chronicle 2020
San Francisco Chronicle, by Erin Allday, Feb. 10, 2021

Two cases of a coronavirus variant first found in South Africa that reduces the effectiveness of some vaccines have been identified in the Bay Area, in Alameda and Santa Clara counties, Gov. Gavin Newsom said Wednesday.

They are the first two cases of this variant, called B.1.351, to be found in California. They were identified by scientists at the Stanford Clinical Virology Laboratory Tuesday night and reported to the state Wednesday morning.

Variants that are more infectious or reduce vaccine effectiveness pose a threat to the state’s ability to control and quickly end the pandemic, public health officials have said. More than 150 cases of a variant first identified in the United Kingdom that is known to be more infectious have been found in California, including Alameda and San Mateo counties.

Another pair of closely related variants identified in California have been spreading quickly in the Bay Area and Southern California. Scientists believe those variants respond to vaccines but they are running tests now to determine if they reduce effectiveness. They’re also studying whether the variants are more infectious.

The variant from South Africa is considered particularly concerning because studies have found that it is able to partially evade the body’s immune response, whether it’s generated from a vaccine or previous infection with the coronavirus. So far the vaccines appear to prevent severe disease and death from the variant.

“The British variant, it’s still susceptible to vaccines and it’s going to spread anyway. But let’s get this one back in the box,” said Dr. George Rutherford, an infectious disease expert at UCSF.

As of Tuesday, nine cases of the variant from South African had been identified in three states, according to the Centers for Disease Control and Prevention. That number did not include the new California cases.

“These variants are here,” Dr. Nicholas Moss, the Alameda County health officer, said at a press event on Wednesday. “We should prepare and plan accordingly.” Because relatively few coronavirus cases are genomically sequenced, he said, “we only have a very limited picture of their spread locally.”

Dr. Benjamin Pinsky, who heads the Stanford lab that found the variants, said they are identified through a process that first screens positive coronavirus samples for specific mutations. Samples that have those mutations then go through genomic sequencing to confirm the variant.

The two cases announced on Wednesday were from samples sent to the lab about a week to ten days ago, Pinsky said. His lab also identified the first cases of the variant from the United Kingdom found in the Bay Area.

The two vaccines currently available in the United States, made by Pfizer and Moderna, provide some protection against B.1.351, but perhaps less than the initial virus from China for which they were designed.

The Moderna vaccine induced an immune response six times lower against the variant from South African compared to earlier variants, the company said in late January after conducting a small study. But even this lower level of immune response, or neutralizing antibodies, is likely enough to protect against COVID-19, the company said.

Still, Moderna is testing a booster vaccine to see if it can provide more immunity.

Similarly, the Pfizer vaccine also induced a slightly lower level of neutralizing antibodies against the variant but it should still be enough to protect against COVID-19, according to studies by Pfizer and the University of Texas Medical Branch. The difference is “unlikely to lead to a significant reduction in the effectiveness of the vaccine,” Pfizer said.

Pfizer and Moderna are both made using messenger RNA, a type of technology that allows vaccine manufacturers to tweak vaccines quickly to account for variants. So the companies could essentially “plug in” a slightly adjusted genetic sequence into the vaccine. This could still be concerning, though, because even though the vaccine itself could be tweaked fast, it would take time to produce and distribute.

Also concerning is whether other vaccines in the pipeline, particularly one made by AstraZeneca and Oxford University, will work against emerging variants. South Africa recently stopped using the AstraZeneca vaccine because of reduced effectiveness. That vaccine is not yet approved for use in the United States. South Africa switched to the Johnson & Johnson vaccine, which has yet to be authorized in any country but in clinical studies was shown to be 57% effective at preventing moderate to severe disease caused by B.1.351.

Scientists in South Africa also have said that people who were previously infected with other coronavirus variants appear to be susceptible to reinfection with the new one.

Moss of Alameda County expressed optimism about vaccines. But meanwhile, he said, “We have to stick with the things we know work for the time being. That means, face coverings, distancing, and limiting gatherings.”

“The most important thing with variants is to just limit the amount of COVID that is out there,” he added.


San Francisco Chronicle staff writers Aidin Vaziri and Catherine Ho contributed to this report.  Erin Allday is a San Francisco Chronicle staff writer.

COVID-19: As deaths spike, other curves begin to bend

Coronavirus: Near-record deaths in California, but cases keep going down

California averaging 543 deaths per day, but almost half the cases from 2 weeks ago
Source: Mercury News, Coronavirus Tracker
Vallejo Times-Herald, by Evan Webeck, January 27, 2021
[See also Benicia Independent: Solano deaths on January 26, 2021]

As California begins to turn the corner in the latest wave of the COVID-19 pandemic, fewer Californians are testing positive or hospitalized with the virus — but deaths, which can lag cases by up to four weeks, continue to come at a record pace.

On Tuesday, county health departments around the state combined to report California’s second-largest death toll on any single day of the pandemic — 735, according to data compiled by this news organization — but also half the infections from two weeks ago. With 22,247 new cases Tuesday, California is now averaging approximately 23,200 per day over the past week, 48% fewer than its peak just over two weeks ago. At 7.9%, the positivity rate over the past week in California fell to its lowest point since the first week of December, down from a high of over 14% earlier this month.

For interactive chart, see graph on Vallejo Times-Herald article, timesheraldonline.com/2021/01/27/coronavirus-near-record-deaths-in-california-but-cases-keep-going-down/

Now out from under the stay-at-home order, every region in the state has seen a decrease in cases, as well as hospitalizations, though Southern California and the San Joaquin Valley continue to report higher numbers on a per-capita basis than elsewhere in the state. Only four small counties have progressed beyond the purple reopening tier, though, and the statewide infection rate is still almost 10 times higher than anything past the “widespread” tier.

Across California, the number of COVID-19 patients receiving care in hospitals has fallen 20% in the past two weeks, and the number of those in ICUs is down 11%. Hospital capacity remains strained throughout much of the state — ICUs are still at surge capacity in Southern California and the San Joaquin Valley and only 8.2% and 9.9% capacity in the Bay Area and Greater Sacramento, respectively — though every region is now projected to exceed 15% capacity in four weeks, according to the state’s models.

For now, though, the state is experiencing its deadliest period of the pandemic.

The only deadlier day in California than Tuesday came just five days earlier, and the total over the past week is higher than any other seven-day period of the pandemic. January alone has already accounted for a third of the casualties in California over the course of the entire pandemic.

The weekly death toll in California grew over 3,800 — an average of 543 per day — and the total for January rose over 12,000, on pace to double the previous monthly record, set the month prior. Over the course of the pandemic, 38,234 Californians have lost their lives to the virus. More than two in every three of those deaths have come in Southern California, but on Tuesday, the region was responsible for more than three in every four of the fatalities in California.

Seven counties in Southern California reported a combined 577 fatalities on Tuesday: 289 in Los Angeles, 113 in Riverside, 64 in Orange, 46 in San Diego, 41 in San Bernardino, 21 in Ventura and three in San Luis Obispo. The Bay Area on Tuesday totaled 72 fatalities between 10 counties within the region, including three with double-digit tallies: 30 in Santa Clara, 16 in San Mateo and 10 in Alameda.

On a per-capita basis, Southern California is still reporting cases at a rate that would still rank among the worst states, nationally, while the Bay Area, Greater Sacramento and Northern California have reduced their case loads to less than half that level.

Statewide, at about 58 daily cases per 100,000 residents over the past week, California has cut its infection rate nearly in half and now ranks below 12 other states. In Southern California, however, the daily infection rate over the past week was approximately 71.5/100K, and in the Bay Area, it was approximately 33.7/100K.


Evan Webeck, Reporter | Evan Webeck covers high-school sports on the field and beyond — and a little bit of everything else — for the Bay Area News Group. A Pacific Northwest native and graduate of Arizona State, Evan has previously worked for The Seattle Times, MLB.com and Sports Illustrated.

Newsom reopens California, with most counties going to ‘purple’ tier. Here’s what it means

Elias Gambaccini brings in a propane heater as he shuts down his restaurant's outdoor seating at Pizzeria Trattoria in North Beach in San Francisco. Across California, some counties will begin allowing some business activities to resume, including outdoor dining, after Gov. Gavin Newsom rescinded regional stay-home orders.
Elias Gambaccini brings in a propane heater as he shuts down his restaurant’s outdoor seating at Pizzeria Trattoria in North Beach in San Francisco. Across California, some counties will begin allowing some business activities to resume, including outdoor dining, after Gov. Gavin Newsom rescinded regional stay-home orders. Photo: Carlos Avila Gonzalez / The Chronicle
Vanessa Arredondo and Michael Williams Jan. 25, 2021 Updated: Jan. 25, 2021 9:18 a.m.

Gov. Gavin Newsom lifted mandatory stay-home orders across California Monday as the surge of coronavirus cases that followed the holiday season begins receding.

The move will shift counties back into the color-coded reopening system and reopening will no longer be tied strictly to the number of available beds in intensive care units.

Now, with most counties statewide poised to reenter the purple tier, some activities like outdoor dining and personal-service businesses like nail salons will be allowed to resume. Individual counties can still impose stricter requirements, despite the relaxed mandate from the state.

“California is slowly starting to emerge from the most dangerous surge of this pandemic yet, which is the light at the end of the tunnel we’ve been hoping for,” said California Health and Human Services Secretary Dr. Mark Ghaly.

“Seven weeks ago, our hospitals and front-line medical workers were stretched to their limits, but Californians heard the urgent message to stay home when possible and our surge after the December holidays did not overwhelm the health care system to the degree we had feared,” he said.

Mayor London Breed tweeted Monday morning that she expects San Francisco to return to the state’s purple tier. “We will be moving forward with some limited re-openings, including outdoor dining and personal services,” she said. More details on San Francisco’s reopening plans were expected to emerge during a news conference Monday afternoon.

Following a post-holiday surge, coronavrirus cases and hospitalizations have been decreasing across the state. ICU capacity in regions that remained under the stay-at-home orders as of Sunday — including the Bay Area and Southern California — are projected to rise above the 15% threshold that triggered the lockdown measures.

The decision comes more than six weeks after the Bay Area and nearly all of the state was placed under stringent stay-at-home orders due to the explosive spread of the virus in late November and early December.

Though the Dec. 3 stay-at-home order was statewide, it was not triggered unless ICU projections fell below 15%. Because of this, the state’s northernmost counties were never affected. Most Bay Area counties voluntarily moved into the lockdown condition on Dec. 6. But as of Saturday’s report from the state, the Bay Area’s ICU capacity was 23.4%.

News of the change first began circulating Sunday evening after the California Restaurant Association sent a letter to members saying it had received word from Newsom’s administration that the stay-at-home orders would be lifted. Several members passed the letter along to media outlets including The Chronicle.

Vanessa Arredondo and Michael Williams are San Francisco Chronicle staff writers.

Surge: Some ambulances forced to wait hours as Bay Area ICU availability plunges

California, Bay Area hospitals strain amid crush of ICU patients

San Francisco Chronicle, By Jill Tucker, January 2, 2021
A COVID-19 patient who has had a stroke is prepared to be flown from one hospital to another on Dec. 22. Hospitals across California are straining to keep up with the surge.
A COVID-19 patient who has had a stroke is prepared to be flown from one hospital to another on Dec. 22. Hospitals across California are straining to keep up with the surge. Photo: Francine Orr / Los Angeles Times

The Bay Area’s intensive care unit availability dipped to 5.1% — its lowest figure yet — on the second day of the new year, even as the state braces for a further surge from Christmas and New Year’s celebrations.

The situation has gotten so difficult in Santa Clara County that some ambulances are sitting outside emergency rooms for up to seven hours waiting for a bed to open up for the patients they are carrying, county health officials said.

The delays — which mean the waiting ambulances cannot respond to other calls — have caused the San Jose Fire Department to transport people to emergency rooms at least a half-dozen times in the past week, the county officials said.

It’s a problem that’s already well known to the hard-hit Los Angeles area, where ambulances have waited for up to eight hours outside a hospital before patients could be moved inside, according to the Associated Press. In some cases, doctors started treating cases inside the vehicles.

Across the state, the outlook remained bleak, with a record 4,531 coronavirus patients in California intensive care units on Friday and the number of cases continuing to rise. The state recorded 53,341 new coronavirus cases on Friday, the second highest single-day figure, and another 386 deaths.

Available intensive care unit capacity in the Greater Sacramento region dropped sharply on Saturday, from 11.5% on Friday to 6.9%. The region, which includes the California side of Lake Tahoe, remains under a stay-home order, as do the Bay Area, the San Joaquin Valley and Southern California. The latter two regions are drawing heavily on hospital surge capacity, since their regular ICUs have zero availability.

Experts fear it’s unlikely to get better anytime soon, because it’s still too early for hospitals to see the effects from a Christmas surge.

“Admission to the ICU is often 10 to 12 days after exposure,” said Dr. Robert Siegel, a Stanford virologist. “The number of deaths may continue to increase for another week or more.”

Siegel also expects spikes from Christmas gatherings “will merge with, and contribute to surges” from New Year’s gatherings.

The ambulance wait times in Santa Clara County could be an alarming sign of things to come. The county saw a record number of COVID-19 deaths Friday — 38.

Santa Clara County Supervisor Joe Simitian, who co-chairs the Health and Hospital Committee at the Board of Supervisors, said wait times for ambulances are not uncommon during busy times of the week or during holidays. But they typically last no more than an hour — not seven.

“Whatever the period of time is, it’s always a concern because by definition you have folks you want to have admitted as soon as possible, and you want to have an ambulance crew on the road as quickly as possible,” Simitian said.

The combination of New Year’s Eve and COVID may have added stress on the county’s emergency system, he said.

“When you put together New Year’s Eve compounded by the COVID crisis, there are going to be some outliers that are troubling,” he said. “My understanding is they were relatively few in number — but obviously that’s cold comfort if you’re the one waiting for an ambulance.”

James Williams, the Santa Clara County counsel, said the county’s hospital system has been “teetering on the edge,” since a post-Thanksgiving surge in virus hospitalizations. He fears that another, similar surge, would greatly exacerbate what is already a problem with wait times at hospitals.

“If we have another surge now, anything like what we had after Thanksgiving — it’s going to cause collapse,” Williams said. Unlike March, the county cannot just make room by transporting patients to other facilities in California or another state. Santa Clara County has contingency plans for how to provide “some level of support” to those who may need it during a potential surge. But, Williams warned, those contingency plans would not be “providing everyone with the level of medical care that we take for granted in the United States.”

The virus continued its indiscriminate path through the population, infecting the young, old, famous and infamous. Talk show host Larry King, 87, was hospitalized with the virus, according to reports Saturday, while Dawn Wells, who played Mary Ann on “Gilligan’s Island,” died Wednesday. And at least one person was hospitalized after a New York Republican club’s Christmas party featuring an unmasked conga line.

Between pandemic fatigue and the holidays, the current surge will probably continue well into January, with hospitals, funeral homes and nursing homes continuing to see the fallout. State prisons also continued to see a surge, with 6,510 reported cases in the last two weeks — a sizable portion of the 40,985 incarcerated people who have had COVID-19 at some point.

Across Southern California, where the virus has hit the hardest, mortuaries have had to turn away families due to lack of space for all the bodies — and with funeral homes filling up, there’s a backup of bodies at hospitals, Los Angeles County Director of Health and Human Services Dr. Christina Ghaly told the Associated Press. The county medical examiner is looking for alternatives to store the bodies, she said.

Although thousands of California front-line workers have received vaccines, there is no impact yet on case counts. But the idea of a vaccine may be having something of behavioral impact, for good or for bad, according to Stanford’s Siegel.

“Some people have increased their precautions with the realization that it would be tragic to be infected when their turn to be vaccinated may be just around the corner,” he said. “Other people have increased their risk behavior knowing they will soon be protected or knowing that other people around them are vaccinated.”


Chronicle staff writer Michael Williams contributed to this report.  Jill Tucker is a San Francisco Chronicle staff writer.