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

Like an uninvited guest who comes to dinner and won’t stop talking or leave, the Delta variant continues to hang around San Francisco. R Number models continue to show relatively low transmissibility but hospitalizations and infections continue their fitfully slow decline.

Throughout the pandemic, hospitalizations have been seen as a key, if not the key, metric for understanding how the virus was affecting the community. Seen as more reliable than infections (cases) and more timely than deaths, some have proposed, like in Germany, that hospitalizations should be the key to imposing more or fewer restrictions. A new study casts some shade on the hospitalization metric, finding that a substantial number of patients in the hospital for covid are actually patients with covid (generally asymptomatic).

As schools are opening in SF and around the country, there have been some articles referencing covid hospitalizations of children. A new pre-Delta study of two California hospitals suggest reported hospitalization rates “greatly overestimate the true burden of Covid-19 disease in children,” says UCSF doc Monica Gandhi.

Another study demonstrates why children may be less susceptible to covid than adults.

It’s Women in Medicine month and this earlier report from Mission Local notes the debt we owe to UCSF’s Covid 19 women warriors. The only problem? Not enough of them.

Note: There are new population figures out after the last census showing about 20,000 fewer San Franciscans in 2020 than were here in 2010. For the being, we will continue to use figures supplied by SFDPH.

Scroll 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. Here, the vaccination picture has been relatively static for at least a month or more. As of Sept. 14, DPH reports over 79 percent of all San Francisco residents have received one dose, and more than 73 percent are completely vaccinated. Despite the proven protection, the City’s unvaccinated have been less than enthusiastic about embracing The Vaccine. On Sept. 14, the seven-day rolling average of shots per day was 326. For information on where to get vaccinated in and around the Mission, visit our Vaccination Page.

Our hospital graph has been slow to update. On Sept. 11, DPH reports there were 74 hospitalizations. or about 8.5 per 100,000 (based on an 874,000 population). There were 55 in acute care, 19 in the ICU. The latest update from DPH says, as of Sept. 3, 76 fully vaccinated San Franciscans had been hospitalized (a rate of 14.3 per 1,000 cases compared to 84.8 per 1,000 cases for those not fully vaccinated) . According to the CDC, there were 53 new admissions for the week ending Sept. 12  (no change from the previous week). For the week ending Sept. 12, covid patients accounted for 4.41 percent of hospital beds (-.82 percent from previous week) and 8.43 percent of ICU beds (-3.06 percent from previous week). As of Sept. 7, the CDC says that, of more than 176 million vaccinated U.S. residents, 14,115 patients with a covid vaccine breakthrough infection were hospitalized or died. Of that number, 25 percent either had no covid symptoms or their hospitalization or death was not covid-related.



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 12 and Sept. 10, the Mission had  809 new cases (a rate of 138 new cases per 10,000 residents), while Bayview Hunters Point had 939 cases for a rate of 248 new cases per 10,000 residents. Of 38 SF neighborhoods, 24 had case rates over 100 per 10,000 residents, the second-highest in SOMA with 190 cases per 10,000 residents.

The daily average number of new infections have dropped below 100 for the first time since July 14. DPH reports, for the week ending Sept. 7, the seven-day rolling average of daily new cases in the city was 95 new cases, or approximately 10.8 new cases per day per 100,000 residents (based on an 874,000 population).  According to the latest from DPH on Sept. 3, the 7-day average case rate among fully vaccinated residents was 6.8 per 100,000 fully vaccinated residents  and  19.7 per  not fully vaccinated 100,000 residents.  

No new data from DPH, but the graph shows clearly the Delta surge has been fueled primarily by infections in the White community. Since the pandemic began, based on the group’s San Francisco population, Latinx residents have a case rate of 1,304 cases per 10,000 residents, while Blacks have a rate of 868; Whites, 351; and Asians, 268 cases per 10,000 residents. DPH estimates the rate of Pacific Islanders to be 2,120 and Native Americans to be 961 cases per 10,000 residents but concedes these numbers are “less reliable.”

In August, the Mission had a positivity rate of 4.4 percent (down from 5 percent in July), Bayview Hunters Point 6.2 percent (down from 8 percent), SOMA had 5.0 percent (down from 6.6 percent in July), the Castro had 4.6 percent (down from 6.2 percent), Presidio Heights had 2.9 percent (down from 3 percent) and Seacliff had 2.9 percent (up from 1.1 percent).


Covid-related deaths in San Francisco are always difficult to ascertain. In the last few days, DPH reports  31 August deaths, and 1 death in September, bringing the cumulative covid-related death toll to 605. Of those, approximately 3 percent had no underlying conditions.


Covid R Estimation has kept it estimate of the San Francisco R Number below .90  at .86 and slightly raised  its estimate for the California R number to .94. All models in the ensemble  estimate the San Francisco R Number below 1, with an average of .82, while the average California R Number is .83. The ensemble average estimate for San Francisco has been below 1 since Aug. 3.


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. For the month of August, men had 3,159 new cases (or 54.2 percent), women had 2,608 (44.8 percent), trans women had 3, trans men had 2, others had 28 and folks whose gender was unknown had 27

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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