Category Archives: San Francisco Bay Area

Coronavirus, Covid 19, COVID-19 Purple Tier, Delta variant, San Francisco Bay Area, Solano County CA, Vaccine

Counties see alarming infection rates – Solano would be in purple if tiers were still used

Northern California counties, including Solano, have new alarming infection rates

If tier system in place, at least a dozen would be in purple

Northern California counties, including Solano, have new alarming infection rates

Vallejo Times-Herald, by John Woolfolk & Harriet Rowan, July 20, 2021

How bad is California’s Delta COVID-19 surge?

If the Golden State was still using its four-color reopening blueprint for ranking counties by infection rates, at least a dozen, including Los Angeles, Alameda, Contra Costa and Solano now would be in the most-restrictive purple tier, and many businesses would not be fully open.

And that’s using new metrics introduced in March that made it easier for counties with higher case rates to move into lower-restriction tiers once the state reached what it considered equitable vaccination rates. Using the state’s original tier definitions, 29 counties, including San Francisco, now would be purple, which meant that the virus was widespread, a Bay Area News Group analysis found.

This map is interactive at TimesHeraldOnline.com.

The dire picture comes a little over a month since California authorities on June 15 dropped the reopening blueprint and its color-coded restrictions on gatherings and business activities and eased requirements for face masks in public to slow the virus’ spread. Since then, sports venues, bars and amusement parks have fully reopened, and people throughout the state gathered for July Fourth barbecues and parties.

“We’ve all forgotten about the tier system because we wanted to,” said Dr. John Swartzberg, clinical professor emeritus of infectious diseases and vaccinology at UC Berkeley’s school of public health. “We’re not in a very good place compared to where we were a month ago.”

California was one of the slowest states to reopen its economy during the pandemic and has one of the highest vaccination rates, especially among large states, with almost 52% of its population fully inoculated against the virus compared with 56% in New York, nearly 48% in Florida and 43% in Texas.

But like much of the United States, California is seeing rapid spread of COVID-19 driven by the highly infectious Delta variant, nearly all of it among those who haven’t been vaccinated.

On Monday, Napa, Santa Cruz, San Benito and Monterey counties became the latest to urge people who are both vaccinated and unvaccinated to wear masks while indoors in public places to slow the virus’ spread, joining most other Bay Area counties as well as Sacramento, Fresno and Yolo. Los Angeles made that an order Saturday.

According to the California Department of Public Health, the virus is spreading statewide at a 7-day average daily rate of 6.3 cases per 100,000 people among the unvaccinated, but at a rate of 1.1 per 100,000 people among the vaccinated. The department did not have those figures by county.

“Vaccines remain the best protection against COVID-19, including the highly infectious Delta variant,” the CDPH said in a statement Friday. “As we continue to see the real and aggressive impact of the Delta variant in rising case rates, we cannot stress enough how critical it is for eligible individuals to get vaccinated.”

California introduced its color-coded reopening blueprint last August amid a summer surge in cases after the state eased its March 2020 stay-home order to curb the coronavirus.

Under the original blueprint, counties in which the 7-day average of daily COVID-19 cases was 7 per 100,000 people or more were assigned the most restrictive purple tier.

At those rates, middle and high schools, and at some levels even elementary schools, couldn’t begin opening campuses to students. Bars were closed, and restaurants, theaters and gyms could only operate outdoors, where the virus doesn’t easily spread.

The blueprint allowed for progressively more gatherings and activities once counties’ case rates fell, putting them into the “substantial” red, “moderate” orange and “minimal” yellow tiers.

At the January peak of California’s deadly winter COVID-19 case spike, all but four rural counties were in the purple tier.

In March, as vaccines became more widely available and more people were getting the shots, state officials revised the tier metrics to account for the protection offered by immunization, making it easier for counties with high vaccination rates to move out of the restrictive tiers and reopen more businesses. Under the revised rules, the purple tier applied to counties with 7-day average daily case rates of 10 per 100,000 people or more.

On June 15, when the state ended its tier system, no California counties remained in the purple tier, and just one was in the red, while 29 were in the yellow tier.

The breathtaking pace of the virus’ resurgence already has led many local health authorities to at least recommend measures such as wearing masks indoors in public for all, vaccinated or not. But state officials for now have not changed their guidance, including allowing the vaccinated to go without masks inside.

Swartzberg noted that given how low infections had fallen since the spring, the sharp rise in new case rates still involves relatively small numbers. Statewide, the 7-day average daily case rate as of Sunday was 7 per 100,000 people, up significantly from 2 per 100,000 in early June but far lower than the 109.3 per 100,000 Jan. 9. And hospitalizations and deaths, which tend to lag new cases by a few weeks, remain on a downward slope. The 7-day average daily death rate as of Sunday was 0.01 per 100,000, down from 1.7 per 100,000 Jan. 9.

But given the Delta variant’s high transmissibility and rapid spread, even in the highly vaccinated Bay Area where many people continue wearing masks, new restrictions may be in order.

“The Delta variant’s transmissibility is so much greater than anything we’ve encountered,” Swartzberg said. “I think the Bay Area was wise in recommending masks indoors for everyone. If things continue on the trajectory we’re seeing, the Bay Area will probably have to mandate it and hope it’s sufficient to flatten the curve.”

Marshes, San Francisco Bay Area, Sea level rise, Wastewater

One Bay Area city may surrender land to the rising sea

A $900 million plan outlines how Hayward is preparing its sewage plants, natural gas power plant and 1,899 acres of marshes and tidelands for  a rising San Francisco Bay.

San Francisco Chronicle, by John King, July 2, 2021
LINKS TO THE SERIES: Mission Creek, Foster City, Hayward

By 2100, we may need to let rising waters cover portions of today’s shoreline, once and for all.

“You’ve got to be forward-thinking,” said Al Mendall, who served on the Hayward City Council from 2012 until December. “As a layperson, it seems obvious to me that we’re going to have to consider some form of retreat at some point. Not just in Hayward, but all around the Bay.”

Before San Francisco Bay’s shoreline was recognized as an irreplaceable resource, it was where cities put garbage dumps, highways and industrial zones. Out of sight, out of mind.

That’s why the west edge of Hayward north of Highway 92 includes two sewage plants and the natural gas power plant that opened in 2013. The white toll booths of the San Mateo-Hayward Bridge shimmer in the haze of automobile exhaust. Two stumpy hillocks conceal long-closed dumps.

But there also are 1,800 acres of protected marshes and tidelands, along with the Hayward Shoreline Interpretive Center built in 1986. Even as new warehouses and research parks are built next to such preserves, populations of species like the snowy plover and salt water harvest mouse continue to increase.

A group of pelicans rest in a channel near the Hayward Shoreline Interpretive Center last month.

Three pelicans rest in a channel near the Hayward Shoreline Interpretive Center last month. Carlos Avila Gonzalez / The Chronicle

It’s a juxtaposition that feels oddly timeless, but the placid scene can be deceptive. Already, several times each year, the combination of high tides and strong winds send sheets of water fanning across the trail from the interpretive center. Factor in the likelihood of significant sea level rise and the rare could become commonplace.

Sea level rise is fueled by higher global temperatures that trigger two forces: Warmer water expands oceans while the increased temperatures hasten the melting of glaciers on Antarctica and Greenland and add yet more water to the oceans.

Variations of this forecast — inconvenience followed by upheaval — are found all along the edges of San Francisco Bay. The difference is that Hayward worked out a detailed plan for what might lie ahead.

In February, Hayward’s City Council approved a set of strategies on how to adapt the shoreline zone to what climate change might bring between now and 2070. In some areas, the city would restore marshes or relocate trails. In others, new levees would shield industrial functions that cannot be moved, like the wastewater treatment facility.

John Blanchard/The Chronicle | GIS data from ART Bay Shoreline Flood Explorer, Hayward Area Shoreline Planning Agency, Scape and Hayward Regional Shoreline Adaptation Master Plan

The effort was led by Scape, a New York landscape architecture firm that has been active in sea-level-rise planning since Hurricane Sandy laid waste to coastal New York and New Jersey in 2012.

Unlike some bay settings — such as San Francisco’s heavily developed Mission Creek or Foster City, where a levee already protects homes — Hayward’s shoreline area offers room to maneuver. The area studied by Scape extends 3¼ miles from Highway 92 past the city’s northern border, while extending inland as much as 2 miles, past the power plant and research buildings to modest older homes.

Bicyclists are in the foreground riding along the Hayward Regional Shoreline. In the background the San Francisco skyline is visible amid fog and clouds.
San Francisco rises in the distance as cyclists ride through the Hayward Regional Shoreline last month. Carlos Avila Gonzalez / The Chronicle

Scape’s team of designers and engineers was selected in 2018 by the Hayward Area Shoreline Planning Agency, which includes representatives from the city, the East Bay Regional Park District and the Hayward Area Recreation and Park District.

The scale of the area captured the firm’s notice. So did the scale of Hayward’s ambitions.

“Plenty of cities and agencies are beginning to study risks. Hayward is one of the few places taking the next step and trying to offer solutions,” said Gena Wirth, who led the Scape team.

The 244-page plan lays out steps that can be taken in coming decades to stay ahead of the changes that would accompany daily tides 4 feet above current levels. Another 3.3 feet were added to account for the waves that could be triggered by a once-in-a-century storm.

“You want to look for how you can restore natural systems in a way that magnifies the overall benefits,” Werth said. “It’s all about establishing a vision and then breaking it down into bite-size components.”

None of this is easy — or cheap.

The combined price tag for everything in the plan tops $900 million, and there is no funding yet. But the recommendations are split into 26 projects of varying size — the idea being that pilot programs and smaller initiatives can kick off within the next few years, building momentum for larger projects in later decades.

“We have a lot of work ahead of us, definitely,” said Erik Pearson, the environmental services manager for Hayward’s Public Works department. “This is something we can use as a guide.”

The approach is applauded by scientists and officials wrestling with the challenge of a future in which the old danger — developers wanting to fill in the bay — is replaced by the need to keep the bay from reclaiming the low-lying lands at its edge.

“The level of sophistication and thoughtfulness is rare,” said Jessica Fain, the head planner of the Bay Conservation and Development Commission, a state agency created in 1967 to watch over the health of the bay. “There’s a range of solutions spelled out, and also a real dedication to pursuing them.”

This includes what potentially is the most controversial solution of all.

After it describes various natural methods to enhance and protect the shoreline, the plan devotes two pages to “managed retreat.” Or as Scape puts it, “a management strategy for retreating from vulnerable coastal areas” and “adapting to sea level rise over time.”

In one design scenario, Scape went so far as to study moving the Interpretive Center from the south end of the area, near Highway 92, to the top of one the hillocks that hide a former dump. Besides protecting the center from flooding, this option “maintains visibility of the structure and offers expansive views of the Bay.”

Al Mendall, who served on Hayward’s City Council from 2012 until last year, has been an advocate for Hayward’s planning efforts along its shoreline. Carlos Avila Gonzalez / The Chronicle

The final plan doesn’t include this move. But it emphasizes that if sea level rise matches current projections, the relocation of buildings and services “would likely be needed … long-term.”

That topic rarely is discussed, except in coastal areas that routinely flood or suffer dangerous levels of erosion. But Hayward officials inserted it deliberately.

“It’s important to mention that the concept exists” within the larger discussion, Pearson said. “At 4 feet, it doesn’t make sense to look at retreat. But at some point after that, it may be the best approach.”

Experts familiar with bay’s potential reach welcome the willingness of Hayward and the design team to acknowledge this.

“We need to stop thinking, ‘This is going to be here forever,’” said Letitia Grenier. She leads the resilient landscapes program at the San Francisco Estuary Institute, which advised Scape on the Hayward shoreline’s environment. “That’s not the way the world works. We need to learn to live with that.”

Will Travis, who was the executive director of the bay commission when it released its first sea level projections in 2007, has a similar view.

“The hard decisions will be what not to protect,” he said. “How you prioritize where to put your (limited) resources.”

The plan went to Hayward’s City Council on Feb. 16. It passed on a 5-0 vote.

Mendall, the former council member, was excited to see the council act in unison — and with no public opposition.

“We wanted something doable, not pie-in-the-sky,” he said. “It’s a tool for the next generation to preserve and protect the shoreline.”

An aerial view of the Hayward Regional Shoreline. In addition to restored marshes, it includes wastewater storage ponds and a field of solar panels. Carlos Avila Gonzalez / The Chronicle

CREDITS

REPORTING – John King

EDITING – Mark Lundgren

VISUALS – John Blanchard, Carlos Avila Gonzalez,
Guy Wathen, Alex K. Fong, Drawings animated in Mental Canvas

DESIGN AND DEVELOPMENT – Paula Friedrich

GIS DATA – BCDC (2017). Adapting To Rising Tides Bay Area Sea Level Rise Analysis & Mapping Project: SF Bay [spatial data file]. SF Bay Conservation and Development Commission

Coronavirus, Covid 19, Re-opening, San Francisco Bay Area, Solano County CA

Solano County COVID infections up by 49% since re-opening, 2nd highest jump in Bay Area

COVID cases up more than 20% in Bay Area, California since June 15 reopening

San Francisco Chronicle, by Catherine Ho, July 1, 2021
A worker walks along Stockton Street in San Francisco on June 15, the day California lifted most of its pandemic restrictions. Stephen Lam/The Chronicle

New coronavirus cases have jumped more than 20% in California and the Bay Area since the state’s June 15 reopening — a sign that even as residents embrace a return to normalcy, the virus can still spread among unvaccinated people and will likely linger for months to come.

Statewide, new cases crept up from about 900 on June 15 to nearly 1,100 on June 30, according to seven-day averages of new daily infections. In the Bay Area, cases ticked up from 187 to 225 during the same period, according to Chronicle data.

State and local health officials had predicted a rise in new cases after June 15, when California lifted nearly all pandemic restrictions on public life. Case rates are still considered low, at fewer than 3 new infections per 100,000 people statewide and in the Bay Area. In January, during the worst of the winter surge, there were nearly 100 new cases a day per 100,000 people statewide.

In the Bay Area, the biggest jump in new cases is in Alameda County, which has seen a 55% increase since June 15. New cases are up 22% in San Francisco, 27% in Contra Costa County and 35% in Marin County, according to Chronicle data.

In some counties, though, the number of new cases is relatively small. San Francisco went from averaging 11 cases a day to 13. Marin went from four cases a day to five.

COVID-19 hospitalizations are also increasing statewide and in the Bay Area, but at a slower rate than new cases. The number grew 11% statewide and 9% in the Bay Area from June 15 to 30, according to state data.

Deaths are largely flat statewide and dropping in the Bay Area. There is usually a lag time of several weeks between new cases and hospitalizations and deaths.

The rise in new cases can be attributed to three factors: the reopening, the fact that nearly a third of people eligible to be vaccinated have not received a shot and the spread of the more contagious delta variant, said local health officials and infectious disease experts.

Most of the new cases are among people who have not been vaccinated, including young adults and teenagers, and in areas that have lower vaccination rates, health officials said.

“It’s a good argument that the vaccine is helping to protect residents,” said Dr. Nicholas Moss, health officer for Alameda County. “And people who have not had the opportunity to get vaccinated yet, we strongly encourage to do that.”

In neighboring Contra Costa County, the city of Antioch — which has significantly lower vaccination rates than the county overall — accounted for 25% of new cases over the past two weeks, even though it has just 10% of Contra Costa’s population, said county Health Officer Dr. Chris Farnitano.

unvaccinated people in Contra Costa are 16 times more likely to get COVID than vaccinated people, according to county data. The COVID vaccines also do a better job of preventing serious symptoms in the handful of vaccinated people who do test positive.

“With the lifting of the business restrictions, more people getting out and doing things, a lot of people not wearing masks, it’s kind of a recipe for increased infections in people who are unvaccinated,” Farnitano said.

unvaccinated people mingling indoors is especially concerning, now that most venues go by the honor system when it comes to masking, said Dr. George Lemp, a former University of California epidemiologist.

“The problem is because they’ve changed the mask mandate, particularly indoors, there’s no way for proprietors of stores or any other facilities to know whether a person who’s maskless indoors is vaccinated or not,” Lemp said. “The large crowds of people who are unvaccinated who gather together indoors in places like Disneyland and other venues around the state are going to spread coronavirus to each other.”

The Bay Area as a whole has one of the highest vaccination rates in the country, led by San Mateo and and Marin counties, where more than 80% of eligible residents are fully vaccinated. More than 70% of residents are fully vaccinated in Santa Clara, San Francisco and Contra Costa counties. But even in those highly vaccinated counties, there are pockets where vaccination rates are less than 50%.

The spread of the delta variant prompted Los Angeles County health officials to urge even vaccinated people to resume wearing masks in indoor public spaces — one of the pandemic restrictions that the state lifted June 15. Local counties have not issued similar advice, but health officials say the growing number of delta infections could mean that the Bay Area’s already impressive vaccination numbers may have to get even better to check the disease’s spread.

“Delta might be transmissible enough, infectious enough, that you just need to push your vaccination rates a little higher,” said Moss of Alameda County. “A more transmissible virus is more likely to get to those susceptible (unvaccinated) people. And even just a small increase in the ability of the virus to pass from one person to another, when you multiply that over millions of people, you can start to see these changes in the pandemic.”

Catherine Ho is a San Francisco Chronicle staff writer.
Coronavirus, Coronavirus variant, Covid 19, San Francisco Bay Area, Vaccine

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.