Good morning, Mission, and welcome to Virus Village, your (somewhat regular) Covid-19 data dump.

With a long way to go, hospitalizations, positivity rates and recorded infections continue trending downward, while recent R Number models show San Francisco well below 1.

Through most of 2020 and into 2021, lockdowns, masking and other public health non-pharmaceutical interventions were predicated upon protecting hospitals from getting overwhelmed. Has the experience of the past two years changed matters? It does not appear so. “Wealthier hospitals with the capacity to take patients from safety-net and rural hospitals crushed by Covid aren’t incentivized to do so. It makes more sense for them to keep more lucrative elective surgeries and other procedures going.”

We are lucky to have the University of California, San Francisco, one of the best hospitals in the country with a core of outstanding doctors and healthcare workers, which treats most local covid patients. It seems very likely that the relatively low number of covid-related deaths in SF is due, in part, to the outstanding work of UCSF, which has also generously lent its expertise to San Francisco’s Department of Public Health.

Yet we know next to nothing about how UCSF operates, even less about the City’s for-profit hospitals, and much less what it has learned over the past two years and what changes need to be made. Unfortunately, instead of leading a community-wide discussion on our hospitals, one of the country’s (world’s?) leading “hospitalists” regularly tweets about individual risk-taking.

In any case, individual risk evaluations like these can be problematic.

The Centers for Disease Control and Prevention has released a new report on two-dose and three-dose effectiveness of mRNA vaccines. Perhaps this report was prompted by criticism that the agency has withheld critical data on boosters, hospitalizations and, until recently, wastewater analyses. As the article points out, “timely data on hospitalizations by age and race would help … identify and help the populations at highest risk.”

Update on the Fourth Shot: Some say it won’t be necessary. The UK is now offering a fourth shot to those over 75 and those who are immunocompromised. What will happen in the U.S. this fall, when Big Pharma has a new vaccine ready?

Multiple vaccine doses and annual “boosters” are not uncommon.

Here’s a critical review of the Biden Administration’s first year in response to the virus. It reminds me of the title of the Joan Didion book, “The Year of Magical Thinking.”

Scroll down for today’s covid numbers.

As of Feb. 20, DPH reports 782,785 residents have been vaccinated, more than 89 percent of all San Francisco residents have received one dose, and over 83 percent have received two. For residents 5 and older, DPH reports the figures rise above 90 percent and above 87 percent while for those 65 and older over 90 percent have received two doses. SFDPH reports that as of Feb. 20, approximately 467,833 SF residents (65 percent of all residents, 82 percent of residents 65 and older) have received a COVID-19 booster dose.

For information on where to get vaccinated in and around the Mission, visit our Vaccination Page.

On Feb. 17, DPH reports there were 138 covid hospitalizations, or about 15.7 covid hospitalizations per 100,000 residents (based on an 874,000 population). ICU patients have dropped to their lowest level since Jan. 8. Today, the California Department of Public Health reports 133 covid patients in SF hospitals and 26 ICU patients. Much like the CDC, DPH does not make public information as to vaxxed and unvaxxed hospitalizations nor any demographic data whatsoever making it impossible for the public to know the degree to which populations and neighborhoods have been affected.

The latest report from the federal Department of Health and Human Services shows Zuckerberg San Francisco General Hospital with 25 covid patients and 6 ICU beds available, while across the Mission, CPMC had 20 covid patients and 2 ICU beds available. Of 225 reported covid patients, 96 were at either SFGH or UCSF, with at least 67 ICU beds available among reporting hospitals (which does not include the Veterans Administration). The California DPH currently reports 79 ICU beds available in San Francisco. Note: The Government Accountability Office (GAO) has issued a scathing report for sustained public health crisis failures at HHS. The failures cited include “collecting and analyzing data to inform decisionmaking.”

Omicron revived SF’s “normal” pandemic pattern, hitting the lower socioeconomic sectors of the City the hardest. Between Dec. 18 and Feb. 16, DPH recorded 4406 new infections among Mission residents or 750 new infections per 10,000 residents. Bayview Hunters Point had the highest number of recorded new infections (4621) with a rate of 1219 new infections per 10,000 residents. Of 38 neighborhoods, 14 had rates above 700 per 10,000 residents, 13 in the east and southeast sectors of the City. Seacliff had the lowest rate with 383 new infections per 10,000 residents and Lakeshore, the only neighborhood in the City with a vaccination rate below 50 percent, had the second-lowest rate at 433 new infections per 10,000 residents.

DPH reports on Feb. 13, the 7-day average of daily new infections recorded in the City dropped to 256 or approximately 29.2 new infections per day per 100,000 residents (based on an 874,000 population). According to DPH, the 7-day average infection rate among vaccinated residents was 26.1 per 100,000 “fully vaccinated” residents and 62.8 per 100,000 unvaccinated residents. It is unclear whether “fully vaccinated” includes boosters or the infection rate among those vaccinated with 2 doses.

As of Feb. 16., DPH reports Asians had 1,272 newly recorded infections in Februrary or  28.5 percent of the month’s total so far; Whites had 1,041 or 23.3 percent; Latinxs had 736 or 16.5 percent; Blacks had 271 or 6.1 percent; Multi-racials had 62 or 1.4 percent; Pacific Islanders had 31 or .7 percent; and Native Americans had 8 newly recorded infections or .2 percent of the Februrary total so far.

As of Feb. 16, DPH reports that so far in Februrary San Francisco’s Latinx residents have had a positivity rate of 7.7 percent, ; Multi-racials 7.7 percent; Blacks 7.4 percent; Asians 6.5 percent; Native American 6.2 percent; Pacific Islanders 6.1 percent; and White San Franciscans have had a February positivity rate so far of 4.9 percent.

Another covid-related death has been recorded in Februrary. There have been 69 covid-related deaths since the beginning of the year. Probably most are related to omicron. DPH won’t say how many were vaxxed and how many unvaxxed. Nor does it provide information on the race/ethnicity or socio-economic status of those who have recently died. Note: According to DPH, the highest monthly SF covid-related death total was 165, recorded in January 2021. According to DPH “COVID-19 deaths are suspected to be associated with COVID-19. This means COVID-19 is listed as a cause of death or significant condition on the death certificate.” Using a phrase like “suspected to be associated with” indicates the difficulty in determining a covid death. The ambiguity is heightened when currently it is unknown whether or not 34.5 percent of the deaths had one or more underlying conditions. As of Feb. 16, DPH continues to report only 21 of the 762 deaths are known to have had no underlying conditions, or comorbidities.

Covid R Estimation has not updated its San Francisco R Number since Feb. 8. It is still at 1.07. I will try to find out why the delay. On Feb. 19, it estimates the California R Number at a remarkably low .39. The ensemble lowered its average San Francisco R Number to .67 and slightly raised its average California R Number to .57. All ensemble models currrently reporting estimate the SF R Number well below 1.

As of Feb. 16, DPH reports San Franciscans aged 0-4 had 192 newly recorded infections or 4.3 percent of the Februrary total so far; 5-11 had 300 or 6.7 perecnt, 12-17 had 184 or 4.1 percent, 18-20 had 110 or 2.5 percent, 21-24 had 276 or 6.2 percent, 25-29 had 501 or 11.2 percent, 30-39 had 979 or 22 percent, 40-49 had 605 or 13.6 percent, 50-59 had 507 or 11.4 percent, 60-69 had 424 or 9.5 percent, 70-79 had 207 or 4.6 percent, and those San Franciscans 80+ had 170 newly recorded infections or 3.8 percent of the Februrary total so far.

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Mark Rabine has lived in the Mission for over 40 years. "What a long strange trip it's been." He has maintained our Covid tracker through most of the pandemic, taking some breaks with his search for the Mission's best fried-chicken sandwich and now its best noodles. When the Warriors make the playoffs, he writes up his take on the games.

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  1. > Also I don’t think it’s a contradiction for ML to provide summaries of UCSF Grand Rounds, which I hope you will agree have been a useful community service for understanding the virus, and for me to link to issues with the logic of a tweet from a doctor who organizes and participates in those presentations.

    It’s a tremendous service! I seek them out!

    > I am frustrated there has been no public discussion about the state of SF and CA hospitals after two pandemic years, especially what needs to be done now so we don’t have to worry about getting overwhelmed by the next wave or the next virus.

    I am very frustrated by this as well. Early on, in the pandemic, and then again with vaccines, and then again with our logistics problem I was hoping for a daily briefing, I hate to say it, but similar to Norman Schwarzkopf in 1991, describing what was going on, and what we were doing.

    (One of my biggest regrets is thinking we should have a Mythbusters like program weekly, just addressing pandemic issues, doing real simple experiments. My regret is not realizing Adam Savage lives in San Francisco and between Savage and UCSF such a show would have been a possibility)

    Or that Trump/Biden or Newsom didn’t lead publicly aired panels each week with scientists and government officials talking about what was going on, what the research was showing, where we were possibly going.

    Man o man did we drop the ball.

    Once more back to Bar-Yam, I think his logic about gambler’s ruin is just wrong.

    Gambler’s ruin must assume that the gambler treats each visit to the gambling hall as an independent event, repeated frequently (wiki suggests it’s really a theorem about an infinite number of repeated eventS), and never stopping to consider current events.

    Wachter going out to dine once a week or so, or my going out to buy groceries (versus having Safeway deliver them) are not independent events, they are well considered events dependent on current conditions..

    I may be blowing smoke up my own ass, but I don’t think an occasional well-considered visit to a restaurant is very much like the gambler’s ruin at all, until a pandemic becomes uniform in time and space, lasting forever.

    (For that scenario, see the 1971 Charlton Heston documentary, The Omega Man, (I am legend))

  2. Your characterization of Wachter speaking about individual risk and not community risk is complete and utter bullshit coming from Mission Local that goes out of its way to summarize the Grand Rounds at UCSF led by Wachter and given all his many media appearances discussing the state of covid as well as his spending four months hosting the In the Bubble podcast.

    WRT individual risk, several times a week you post R numbers that are so vapid you have to use an ensemble to make sense of them. And you post week old numbers from DPH without examining or mentioning the NYTimes findings which are often less than 24 hours old.

    So what is an individual left with in the face of a pandemic where information changes daily wrt rate counts, variants, test cases, and conflicting research on immunity waning.

    We are left with heuristics and preferences regarding how we judge the danger to ourselves and how we want to live our lives.

    What is it Bar-Yam wants? He tears Wachter’s logic apart while providing no alternative of his own.

    Wachter has been clear, for many older people like Wachter, with parents even older and still alive, there comes a time when locking down 24×7 as Bar-Yam clearly recommends is no way to live their life.

    And we see that in the protests against mask mandates.

    When I have spoken to my PCP, and my cardiologist, about my situation, where I appear to be mostly healthy but have some severe congenital birth defects that may or may not make me high risk wrt covid, they all say exactly as Wachter does: they cannot give me any sort of answer as to how much risk covid gives me, all they can do is provide information that may allow me to make my own personal decision about my own personal risk.

    Wachter tells no one ever that what he decides is what they should do. He lays out his methodology which everyone should consider and decide how their own conditions change that methodology.

    It’s very helpful.

    One thing Bar-Yam never considers, is that our knowledge of the virus changes and how much the virus circulates in the community changes on a weekly basis, so his “gambler’s ruin” problem is not accurate, especially since Wachter describes his process as taking local conditions into account each and every time.

    What a weird take!

    1. Thanks for your comments Jay. I will re-read both threads with your comments in mind. To be clear, I am frustrated there has been no public discussion about the state of SF and CA hospitals after two pandemic years, especially what needs to be done now so we don’t have to worry about getting overwhelmed by the next wave or the next virus. There are many in town, like your PCP and cardiologist who can talk with your about your individual risk and there is no end to articles, tweets, digital risk evaluators and and videos available to help guide us, as individuals, in this period. I have linked to some in the past. But there are very few who have the expertise and knowledge of the City’s hospital network to inform conversation on a topic which has been almost entirely absent from public discourse (especially SF hospitals in particular). Also I don’t think it’s a contradiction for ML to provide summaries of UCSF Grand Rounds, which I hope you will agree have been a useful community service for understanding the virus, and for me to link to issues with the logic of a tweet from a doctor who organizes and participates in those presentations. I find both threads provide a lot to think about. Finally, I’m generally with you on the whole numbers thing. It often drives me crazy (as readers will attest) and I know I’m not alone. Again, ML chose DPH data because the virus is both global and hyperlocal and DPH is a data source that is accountable to the people of this City. We pay for that data. Whether we read the New York Times or Fox News, we all have a common interest in our City providing timely, credible, comprehensive and quality local data.