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COVID in California: Bay Area wastewater samples show big surge is under way

San Francisco Chronicle 12/2/2022 Aidin Vaziri, Matt Kawahara

UPDATE: Here are the latest updates on COVID in the Bay Area and California.

The numbers are in and another winter COVID surge is clearly getting underway. Case counts and hospitalizations are jumping in California and the Bay Area, albeit from lower levels and not yet to the peaks seen last winter or summer. L.A. County’s figures are rising so fast it might re-impose a mandatory indoor mask mandate. And nationwide, post-Thanksgiving hospitalizations are climbing. Small inconveniences, such as the temporary closure of famed San Francisco restaurant Zuni Café due to a COVID outbreak, are starting to multiply. All in all, it’s a moment for caution and concern — and perhaps for putting back on your mask when you go out, if you don’t already.

Latest updates: 

Bay Area wastewater samples show big COVID surge is under way

Surveys of coronavirus levels in Bay Area wastewater suggest another COVID-19 surge is not only under way but may top last summer’s omicron BA.5 wave in the number of people infected. While official case counts show a sharp rise, they do not capture the true scale of the virus in the community because a majority of people use home tests, the results of which are not reported to county or state public health authorities. State data on viral counts in wastewater collected from the Oceanside sewer shed in San Francisco shows virus gene copies per gram of waste solids rising sharply — already reaching the same level they hit in July, near the peak of the summer surge. Samples from the Alameda and Central Contra Costa county sewer sheds show similar spikes, with a near-vertical rise on the graph between Nov. 1 and Dec. 1.

Virus can live on certain groceries “for several days,” report finds

The SARS-CoV-2 virus that causes COVID-19 can live on some groceries for days, according to new laboratory tests by the U.K.’s Food Standards Agency. The research, conducted at the University of Southampton, was commissioned by the FSA as a follow-up to a 2020 study measuring the risk of surface transmission. For this report, the researchers deliberately smeared the virus on the surface of various ready-to-eat foods and packaging that people may not routinely wash.

For most of the food tested, they found the overall risk to consumers fell quickly. But on some foods, such as cheese, broccoli and ham, the virus survived for several days. Despite the findings, they said the overall risk to consumers from coronavirus via food remains very low since the risk level did not reflect real-world contamination levels found in grocery stores and other settings. Nevertheless, it reinforces “the need to rigorously follow the guidance on maintaining appropriate hygienic handling measures and display of unpackaged foods,” they said.

“This research gives us additional insight into the stability of coronavirus on the surfaces of a variety of foods and confirms that assumptions we made in the early stages of the pandemic were appropriate and that the probability that you can catch COVID via food is very low,” said Anthony Wilson, microbiological risk assessment team leader at the FSA, in a statement.

China fines former Warriors star for “inappropriate” comments

Former NBA star Jeremy Lin, who was born in California to parents from Taiwan, has been fined 10,000 yuan ($1,400) for criticizing quarantine facilities in China, according to a report from CBS News. The country’s strict COVID-19 restrictions have sparked huge protests in numerous cities, in the biggest show of opposition to the ruling Communist party in decades. Lin played for the Bay Area’s Golden State Warriors in 2010 before joining the New York Knicks in the 2011-12 season and becoming the first Asian American to win an NBA championship with the Toronto Raptors in 2019. He now plays for the Loong Lions Basketball Club in China. Lin allegedly made “inappropriate remarks about quarantine hotel-related facilities” where the team stayed Wednesday ahead of a game, the China Basketball Association said, adding that his words “caused adverse effects on the league and the competition area.” Lin reportedly posted a video complaining about hotel workout facilities in Zhuji, a city south of Shanghai. “Can you believe this is a weight room?” Lin said on the popular Sina Weibo social media platform. “What kind of garbage is this?” The video was later deleted.

42% of U.S. adults infected but nearly half didn’t know it

About 42% of people in the U.S. have antibodies indicating previous coronavirus infection, according to a study published Friday in the CDC’s Morbidity and Mortality Weekly Report. (That’s much lower than the total number showing signs of either vaccination or infection.) But of these individuals, 44% said they had never experienced COVID-19, suggesting the prevalence of asymptomatic infection in the population. Researchers from the U.S. Centers for Disease Control and Prevention analyzed serologic testing data from a sample of 1,574 participants in the National Health and Nutrition Examination Survey from August 2021 to May 2022.

The researchers also observed that seropositivity patterns among adults who were younger or belonged to racial and ethnic minority groups suggested exposure more linked to past infection and less to vaccination than among seropositive white adults. “Younger adults and Black adults with unidentified infections might have been more likely to lack access to testing and to have unknowingly exposed others, resulting in disparities in community transmission,” the study authors wrote. “In this way, undiagnosed infections could have amplified disparities in infection rates and outcomes.”

WHO chief says conditions are ripe for a deadly new variant

A failure to effectively contain the coronavirus this year has created conditions for a deadly new variant to emerge, the head of the World Health Organization said at a briefing on Friday. Director-General Tedros Adhanom Ghebreyesus has changed his once-optimistic tone, saying the end of the COVID-19 pandemic is no longer in sight. “Gaps in testing and vaccination are continuing to create the perfect conditions for a new variant of concern to emerge that could cause significant mortality,” he said, noting that cases are rising again in China and in the U.K. after months of improving trends. According to WHO data, there are now more than 500 immune-evasive omicron sub-lineages in circulation. Tedros added that more than 8,500 people worldwide lost their lives to COVID-19 last week, “which is not acceptable three years into the pandemic when we have so many tools to prevent infections and save lives.”

“We’re already seeing cases start to go up,” says U.S. surgeon general

U.S. Surgeon General Dr. Vivek Murthy says that federal officials are preparing for an expected rise in COVID-19 cases over the next few weeks. “We’re already seeing cases start to go up,” he told ABC News on Friday. “But I do think that we will be in a better place than we were in the last two winters when we had surges.” He said high levels of vaccination and prior infection among the U.S. population should blunt the swell, with the added benefit of treatments such as Paxlovid reducing the worst outcomes of the disease. “But we need people to use these tools,” Murthy said. He noted that between 300 to 400 people still die every day due to COVID-19. “Most of those deaths are actually preventable if you’re up to date with your vaccines; if you reach for medications like Paxlovid,” he said.

Abysmal bivalent booster uptake rate in U.S. falls by 46%

The already sluggish pace of people receiving the updated bivalent COVID-19 boosters in the U.S. has fallen from a daily peak of 608,676 in mid-October to 330,827 as of Nov. 23, according to data updated Friday by the Centers for Disease Control and Prevention. That marks a 46% decline, and preliminary data from the health agency shows that figure likely to fall further over the next few weeks despite repeated pleas from public health officials for Americans to get the new shots before the holidays. Nearly 40 million people, or 12.7% of those eligible over the age of 5, have received the dose, according to the CDC. At least 9,000 U.S. residents died of COVID-19 in November, and the rate of new cases and hospitalizations is again on the rise.

“There’s no doubt that if you look at the data — and there is now copious data of the morbidity and mortality of individuals who are unvaccinated versus those who are vaccinated, boosted, and particularly with an updated, upgraded, more recent boost — the differences in morbidity and mortality are profound,” said Dr. Anthony Fauci, the nation’s top infectious disease expert in a Washington Post Live interview this week. “If there was any advice, it’s pretty simple — and it’s not just coming from me, it’s coming from any of a number of people involved in this outbreak — is do whatever you can to get your people vaccinated and boosted with a highly effective vaccine.”

Community virus levels rise across the U.S.

After steadily improving for months, COVID-19 community levels in the U.S. have reversed course. More than a third of counties nationwide moved out of the “low” tier on Friday, based on hospitalization and case metrics used by the Centers for Disease Control and Prevention. Two weeks ago, about 81% were in that tier. About 25% of counties are now in the “medium” category — up by half in the past two weeks — and 6% are categorized as having “high” community levels, double the rate in mid-November. California, which reported “low” COVID-19 community levels across the whole state two weeks ago, has seen most of its urban centers shift into the “medium” category. But a majority of the nine Bay Area counties still have “low” community levels.

The agency’s community transmission map, based on a separate metric that tracks the rates of new cases and positive tests, also shows a major shift, with 54% of U.S. counties now in the “high” virus transmission category, 27% in the “substantial” tier, 15% in “moderate,” and less than 4% of all counties with “low” virus transmission. California counties are all over the map on transmission, but Bay Area counties are all either “high” (Santa Clara and Solano) or “substantial” (the other seven).

Immune evasive BQ and XBB variants make up 7 out of 10 cases

The immune evasive omicron subvariants BQ.1, BQ.1.1, and XBB made up a combined 69% of the total coronavirus cases circulating in the United States last week, according to data published Friday by the Centers for Disease Control and Prevention. BQ.1.1 accounted for 32% of circulating variants, and BQ.1 made up an estimated 31% for the week ending Nov. 27. XBB, which the public health agency began tracking last week, jumped to 5.5% of cases, followed by a “variant soup” that includes BN.1, BA.5.2.6, BA.4.6, BA.2.75, BA.2.75.2, BA.4, BA.1.1.529 and several other strains that are circulating. The once dominant BA.5 accounted for less than 14% of cases sequenced. Earlier this week, researchers at Columbia University published a preprint study that noted the emerging coronavirus omicron BQ and XBB subvariants have additional spike mutations that give them “alarming antibody evasion.”

Wachter warns of rise in asymptomatic cases in S.F.

Bob Wachter, UCSF’s chair of medicine, on Friday said the asymptomatic COVID-19 test positive rate has more than doubled in his hospitals over the past month, reaching 5%. “While not a perfect sample, implies that (about) 1 in 20 people in SF who feels well would test pos. for COVID,” Wachter said in a tweet. That means in a crowd of 10 people, the odds that at least one person is positive for the coronavirus in greater than 40%, he said, and on an airple with 150 passenger, the odds are “99.9%.”

Marin, Santa Clara counties move into CDC’s “medium” COVID-19 Community Level

Marin and Santa Clara counties are now in the “medium” COVID-19 community level as defined by the U.S. Centers for Disease Community Prevention. Both moved into “medium” tier Thursday due to averaging more than 10 new COVID-19 hospital admissions per 100,000 residents over the previous week. Marin averaged 11.2 new hospitalizations and Santa Clara averaged 10.2 in that time. Sonoma County (11.2) also moved into the “medium” tier. All other Bay Area counties remained in the “low” level. The CDC COVID-19 Community Levels factor in both case and hospital metrics. Counties also move up from “low” if they record a rate of more than 200 new weekly cases per 100,000 residents; Marin (86.1), Santa Clara (101.9) and Sonoma (68.9) counties remained well below that threshold in the 7-day window prior to Thursday.

Pandemic accelerated aging in teenagers’ brains, Stanford study finds

Teenagers’ brains showed physical signs of accelerated aging after experiencing pandemic-related lockdowns and other stresses, a new Stanford University study found. Researchers compared MRI brain scans of two groups of teens from the Bay Area, about 16 years old on average, before and after COVID-19 shutdowns. Brains of teens amid the pandemic showed physical features “more typical of individuals who are older or who experienced significant adversity in childhood,” according to the study published in Biological Psychiatry: Global Open Science. Those teens “not only had more severe internalizing mental health problems, but also had reduced cortical thickness, larger hippocampal and amygdala volume, and more advanced brain age,” lead author Ian Gotlib, a Stanford professor of psychology, said in a news release.

Gotlib added it is “not clear” if those changes are permanent or linked to changes in mental health. Study authors noted that the pandemic “appears to have been particularly difficult” on the mental health of children and adolescents who experienced school closures, social restrictions and other disruptions. They noted the Stanford study involved teens of high socioeconomic status from the Bay Area and that research has shown “more severe” psychosocial and health consequences of the pandemic among people in socially marginalized groups.

What will the latest surge in cases and hospitalizations mean this time?

California is seeing a sustained rise in coronavirus cases and hospitalizations, with numbers climbing at the same alarming rate that the state experienced ahead of previous COVID-19 surges. Nearly a year to the day the first case of the omicron variant in the United States was identified in a San Francisco resident, the daily number of newly reported cases in the state has climbed to 5,466, up 157% from a month earlier. More worrisome, new hospital admissions of patients with confirmed COVID are at 3,793, up 133% over the same period, according to health department data published Thursday. Bay Area public health experts say they can’t predict how bad things will get, given the high level of overall immunity in the population from vaccination or prior infection. Read more about the new winter surge and how it could affect us during the holidays and beyond.

L.A. County poised to bring back indoor mask mandate as cases rise 180%

Los Angeles County officials on Thursday said they will bring back an indoor mask mandate if COVID-19 community levels rise to the “high” category, which could happen as early as next week but more likely by the end of the month. During a public briefing, the county’s Health Director, Barbara Ferrer, said that during the past week an average of 2,700 cases were reported per day — an 85% increase over the 1,500 daily cases reported in the prior week and a 180% increase since Nov. 1. Daily hospital admissions have increased 200% since the beginning of the month with 192 per day, she added. The numbers are “significantly higher than what we saw this time last year,” she said. “There is this common line of thinking that the pandemic is over and COVID is no longer of concern. But these numbers clearly demonstrate that COVID is still with us,” Ferrer said.

Los Angeles County currently falls under the “medium” community tier, according to metrics from the U.S. Centers for Disease Control and Prevention. But at the current pace of rising cases, it could soon meet the criteria for “high” transmission. “If both hospital indicators — the new COVID-19 admissions and the proportion of staffed in-patient beds occupied by COVID patients — surpasses the threshold for ‘high,’ and our case rate is at or above 200 new cases per 100,000 people, L.A. County will follow the CDC guidance for communities designated at the ‘high’ community level, including universal indoor masking.”

She clarified later in the briefing that she did not expect the county to meet both those metrics next week but more likely around Christmastime. “I anticipate that it could get there later in the month of December but I don’t think it’ll be there next week,” she said. “I’d be very surprised. it would mean that hospitalizations are really going up very, very quickly — much more quickly than we usually see.”

U.S. men’s soccer team promotes updated COVID vaccines

With World Cup fever in full swing, the Department of Health and Human Services has partnered with the U.S. national men’s soccer team to promote the bivalent COVID-19 boosters, which only 12% of Americans have received. Starting Thursday, the team will post messages on its social media channels encouraging people to get the updated shots, Axios reports. The debut clip features defender Walker Zimmerman telling the team’s fans that the vaccine will protect them from “COVID’s worst possible outcome.” HHS Secretary Xavier Becerra said in a statement, “Our message is simple: Don’t wait. Get the updated COVID-19 vaccine this fall. It’s safe and effective.”

Famed S.F. restaurant closes due to virus outbreak

San Francisco’s renowned Zuni Café has temporarily shut its doors until Dec. 7 due to “an upsurge of COVID cases within our team members,” according to a note on its website. “We have decided to take preventive measures to prioritize the health and safety of our team, guests, and community,” Zuni wrote. “We apologize for any inconvenience and appreciate your understanding. We look forward to welcoming you back on Wednesday, December 7th.”

Long COVID may cost the U.S. economy $3.7 trillion

About 23 million Americans are living with long COVID, which could cost the U.S. economy trillions of dollars, according to estimates by the U.S. Centers for Disease Control and Prevention analyzed by CNBC. Up to 30% of Americans who have gotten COVID-19 have developed long-haul symptoms, according to the U.S. Department of Health and Human Services. The aggregate cost could be $3.7 trillion, based on a report released earlier this year by Harvard University economist David Cutler that highlighted medical expenses, lost earnings and the cost of insurance benefits. “Long COVID will be around long after the pandemic subsides, impacting our communities, our health-care system, our economy and the well-being of future generations,” a November HHS report said. “We can reduce the severity and breadth of that impact, however, if we act collectively and urgently.”

Hospitalizations growing nationwide post-Thanksgiving holiday

New admissions of patients with confirmed COVID-19 in the U.S. have increased substantially since the Thanksgiving weekend, with a 20% jump among older adults compared to the week prior, according to numbers updated overnight by the U.S. Centers for Disease Control and Prevention. The overall seven-day average of new daily admissions for all age groups is 4,126, up from the prior average of 3,503. The agency’s national ensemble predicts that the number of new daily confirmed COVID-19 hospital admissions will likely increase, with 1,600 to 11,000 additional patients likely to be reported on Dec. 23. California is likely to see up to 1,000 new admissions in that time, based on state-level forecasts.

What Bay Area health experts say about masking amid rising COVID cases

Some people may be wondering how to navigate a period in the pandemic where precautions are largely up to the individual. As the holidays arrive and COVID numbers show signs of climbing again — albeit not so far to previous surge levels — what are currently the best practices to stay healthy? How much safety is needed? We spoke to Bay Area public health experts for their perspectives on masking and other precautions heading into the holidays, and the verdict was to be as careful as you need to be, for yourself and the people around you. Read more about the latest advice on whether to don a mask again when you go shopping and how to prepare for big family gatherings during the festive season.

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