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

Hospitalizations are down and infections are up, while the average positivity rate and R Number remain low.

University of California at San Francisco’s Bob Wachter thinks the risk in SF is way down from where it was earlier in the summer. He bases his view on data from UCSF hospitals, showing less than 1 percent positivity among patients who are asymptomatic.

A dearth of stats

During the pandemic, we’ve heard a lot about public distrust of government and public health officials. But it’s a two-way street: the authorities also seem to have little trust in the public.

Over the weekend, we got a little closer to one of the enduring mysteries of the delta surge. Bayview Hunters Point is the San Francisco neighborhood which, according to San Francisco’s Department of Public Health, has both the highest rate of vaccination and the highest rate of infection. For many, the contradiction seemed to cast shade on the efficacy of the vaccine (though DPH does not report hospitalizations by neighborhood, only infections). For others, it represented a relatively high rate of testing.

Thanks to Noah Arroyo at SF Public Press, we found out that although the neighborhood has high rates of vaccination, there are census tracts within the Bayview that have rather low rates. Arroyo didn’t have any easy time prying the information loose from DPH, but disturbingly, neither did the community groups working with DPH to promote vaccination.

If DPH has the information on census tracts, and if this information gives clearer, more targeted, information on vaccination rates, why has it been withheld from community groups who are trying to convince residents to get vaccinated? Early in the pandemic, epidemiologists across the country warned against a failure to share data.

The problem here continues. In addition to vaccination rates in census tracts, DPH provides no geographic or demographic information regarding hospitalizations, no information whatsoever on workplace outbreaks (even though mandated by the state) and has provided no information for a year on what it has learned through whatever contact tracing program it has. (Does the city still do contact tracing?)

DPH seems to think the information it gathers is proprietary, which it is not. It is paid for by the public and is public information. By withholding what it knows, DPH not only demonstrates its distrust of the public, it also undermines the information it does provide and opens the door for even more “misinformation” to circulate.

Scoll down for today’s covid numbers.

The U.S. Centers for Disease Control data used for the chart lags behind the data supplied from the San Francisco Department of Public Health. As of Sept. 19, DPH reports that more than 87 percent of San Francisco residents over 12 have received at least one dose, and more than 81 percent are completely vaccinated. On Sept. 19, the seven-day rolling average of shots per day dropped again to 286. For information on where to get vaccinated in and around the Mission, visit our Vaccination Page.

Hospitalizations have been falling, though relatively slowly compared to other surges. Whether it’s the virus or an artifact of the reporting, for the past month, numbers have fallen about 10 a week, plateaued, then fallen again.

On Sept. 16, DPH reports there were 65 hospitalizations. or about 7.4 per 100,000 (based on an 874,000 population). There were 41 in acute care, 24 in the ICU. The latest update from DPH says that, as of Sept. 10, 77 fully vaccinated San Franciscans had been hospitalized (a rate of 12.6 per 1,000 cases compared to 85.1 per 1,000 cases for those not fully vaccinated). According to the CDC, there were 51 new admissions for the week ending Sept. 17  (-3.77 percent from the previous week). For the week ending Sept. 17, covid patients accounted for 3.89 percent of hospital beds (-.74 percent from previous week) and 7.33 percent of ICU beds (-1.87 percent from previous week). As of Sept. 13, the CDC says that, of more than 178 million vaccinated U.S. residents, 15,790 patients with a covid vaccine breakthrough infection were hospitalized or died (though not all of those died or were hospitalized due to covid, or displayed covid symptoms). 



The latest report from the federal Department of Health and Human Services shows Zuckerberg San Francisco General Hospital with 19 covid patients and 79 percent ICU occupancy, while across the Mission, CPMC had 9 covid patients and 54 percent ICU occupancy. Of 99 reported covid patients, 56 were at either SFGH or UCSF.


Between July 17 and Sept. 15, the Mission had  783 new cases (a rate of 133 new cases per 10,000 residents), while Bayview Hunters Point had 906 cases for a rate of 239 new cases per 10,000 residents. Bayview Hunters Point is the only neighborhood with a rate of over 200. Of 38 SF neighborhoods, 23 had case rates over 100 per 10,000 residents, of which 13 were in the east and southeast sectors of the City.

DPH reports that, for the week ending Sept. 12, the seven-day rolling average of daily new cases in the city was 103 new cases, or approximately 11.7 new cases per day per 100,000 residents (based on an 874,000 population).  According to the latest from DPH on Sept. 10, the 7-day average case rate among fully vaccinated residents was 8.5 per 100,000 fully vaccinated residents  and  19.8 per  not fully vaccinated 100,000 residents.  

So far in September, Whites have had almost twice as many infections recorded by DPH than other groups with 510. Asian residents had 312, Latinxs 284, Blacks 129, Multi-racials 31, Pacific Islanders 18 and Native Americans 6 new recorded infections.

So far in September, the Mission has a positivity rate of 2.0 percent (down from 4.4 percent in August), Bayview Hunters Point 3.3 percent (down from 6.2 percent), SOMA  2.9 percent (down from 5.1 percent), and the Castro had 1.5 percent (down from 4.6 percent). The Inner Sunset has the lowest September rate so far with 1.3 pecent (down from 2.2 percent) and Lakeshore the neighborhood least vaccinated  had 1.7 percent (down from 5.2 percent).


Covid-related deaths in San Francisco are always difficult to ascertain. Another September death has been recorded, bringing the September toll to 3, and the cumulative covid-related death toll to 607. Of those, approximately 3 percent had no underlying conditions.


Covid R Estimation has taken its estimate of the San Francisco R Number back up to .85 while slightly lowering  its estimate for the California R number to .91. All models in the ensemble  estimate the San Francisco R Number below .9, with an average of .74, while the average California R Number has fallen to .77. The ensemble average estimate for San Francisco has been below 1 since Aug. 3 and for California below 1 since August 30.


The overall population percentages have changed due to the 2020 Census. For the time being, we will continue to use use the figures provided by SFDPH. So far in September, DPH has recorded 46 new cases among SF residents between 0-4, 89 for those between 5-10, 30 for those 11-13, 24 for those between 14-17, 34 for those between 18-20, 124 for those between 21-24, 211 for those between 25-29, 325 for those between 30-39, 201 for those between 40-49, 159 for those between 50-59, 114 for those between 60-69, 56 for those between 70-79 and 35 new cases for those 80 and above.

Mark Rabine

Mark Rabine has lived in the Mission for over 40 years. "What a long strange trip it's been."

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2 Comments

  1. Bob Wachter’s tweet said that the risk that a person who has no symptoms has COVID and doesn’t realize it is lower than it was in the summer. So less worry specifcally about that. But plenty of people run around thinking they have allergies or a cold rather than COVID (like the teacher in Marin who spread it to her students) . When I am going to be in close contact with someone and I have allergy symptoms, I double check with at least a home test

  2. Can you do an full-on investigative report on SF DPH? Something is terribly wrong there and has been since the beginning of the pandemic. Is it Colfax? Is it corruption? Is it incompetence? What??? And how can we get the State to enforce its mandate of sharing data on workplace outbreaks? Furthermore, the NY Times reports a total of 21 deaths in Sept. Why doesn’t the DPH?

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