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

How much is the virus circulating around San Francisco after three months of the Delta surge? Recorded infections and hospitalizations declined quickly, but have fluctuated at relatively high levels for the past two months, while the citywide average positivity rate is low and, though some disagree, most R number models show San Francisco at or below 1.

A U.S. Food and Drug Administration committee has not taken a position on Moderna boosters. In its report, it says the data shows the two-shot regimen for Moderna has continued to prove effective against delta. Note: In applying for a booster, Moderna ran a clinical trial with 170 people.

In addition to the data, logic and morality argue against mass boosterism.

Here’s the latest on vaccine efficacy out of Canada. Needless to say, these kinds of mass studies can’t be done in the United States. Getting data continues to be an issue with our own Department of Public Health’s reporting on vaccinated hospitalizations and deaths to be “temporarily” paused for close to a month.

An understanding of math helps to understand the risks of covid. Since the beginning of the pandemic, it’s been more than abundantly clear that those facing the greatest risks are the elderly (say, over 65, but really, much older).

Vaccine mandates have been the rage this summer and fall, both to protect people and to get more people to get vaccinated. Will they end, or will we continue to show our cards 20 years from now like we take off our shoes in airport “security” lines? Without a clear commitment including clear metrics when to end covid-related mandates and restrictions, we may be providing political opportunities for hucksters and charlatans who will make Donald Trump look like Albert Einstein.

Lack of tests and lack of testing was a popular horror show 18 months ago. Grab the popcorn. A sequel is in the works and should be out in time for the holidays.

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. As of Oct. 12, DPH reports more than 80 percent of all San Francisco residents have received one dose, and 75 percent are completely vaccinated. For those over 12, 88 percent have received one dose and 83 percent are fully vaccinated. New vaccinations, though low, keep on truckin’. On Oct. 12, the seven-day rolling average of shots per day was 199. For information on where to get vaccinated in and around the Mission, visit our Vaccination Page.

On Oct. 9, DPH reports there were 54 covid hospitalizations, or about 6.2 per 100,000 (based on an 874,000 population).  ICU numbers have dropped below 20 for the first time in almost a month. DPH says it has “temporarily pausing our reporting of breakthrough hospitalizations and deaths to conduct a thorough review of data quality and completeness.”   According to the CDC, there were 36 new admissions for the week ending Oct. 10  (-29.4 percent from the previous week). For the week ending Oct. 10, covid patients accounted for 3.16 percent of hospital beds (no change from the previous week) and 6.65 percent of ICU beds (– 2.2 percent from the previous week).   As of Oct. 4, the CDC says that, of more than 185 million vaccinated U.S. residents, 30,177 patients with a covid vaccine breakthrough infection were hospitalized or died (though 15 percent of deaths  and  hospitalizations did not have symptoms of covid, 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 9 covid patients and 7 ICU beds available, while across the Mission, CPMC had 4 covid patients and 3 ICU beds available. Of 71 reported covid patients, 39 were at either SFGH or UCSF, with at least 74 ICU beds available among reporting hospitals. The California DPH says there are 90 ICU beds available in San Francisco. The SF DPH won’t say.


Between Aug. 9 and Oct. 8, DPH recorded 484 new cases in the Mission for a rate of 82 new cases per 10,000 residents. Over that period, DPH recorded 620 new cases in Bayview Hunters Point or 164 new cases per 10,000 residents. In addition to Bayview Hunters Point, SOMA, Western Additon, Japantown and Hayes Valley had new case rates above 100 per 10,000 residents. Presidio and Seacliff had 34 new cases between them.

After rising a bit, cases are falling a bit.  For the week ending Oct. 5, the seven-day rolling average of daily new cases in the City was 78, or approximately 9 new cases per day per 100,000 residents (based on an 874,000 population).  The 7-day average case rate among vaccinated residents was 7.6 per 100,000 fully vaccinated residents  and for unvaccinated residents  14.2 per unvaccinated 100,000 residents.  

As noted before, the data which show racial and ethnic “disparities” in covid numbers, are often place holders for socio-economic inequality which is rarely tracked (never reported by SFDPH). Instead of “bringing us together,” responses to the virus may have made things worse.

As of Sept. 30, Pacific Islanders had a September testing rate of 525 tests per 1000 residents with a positivity rate of 2.9 percent, Native Americans 337 tests with 2.4 percent positivity, Blacks 254 with 2.2 percent positivity, Whites 170 with 2 percent positivity  Asians 161 with 1.6 percent positivity and Latinxs 148 tests per 1000 residents with a positivity rate of 3.3 percent.  Since Sept. 21, DPH has reported a Citywide 7 day test positivity average of less than 2 percent.

Covid-related deaths in San Francisco are always difficult to figure. DPH added 1 more death in September, bringing the delta total (August and September) to 69 so far, and the cumulative covid-related death toll to 645. According to DPH, over half the deaths were among persons over the age of 80 with 87 percent over the age of 60. Less than 3 percent had no known underlying condition. For the time being, DPH has stopped reporting the vaccination status of covid-related deaths.

Covid R Estimation put its most recent San Francisco R Number back over 1 at 1.01 and raised its current estimate for the California R number to .93. According to this model, SF has the second highest R Number in the state. In contrast, the ensemble lowered its average  San Francisco  R Number to .79 while putting its California average at .8. No model in the ensemble shows the SF rate of transmission  currently above 1.

Though 4.5 percent of all recorded infections, 55.4 percent of all covid-related deaths were among those 80 and older. Those 30-39 have had 23.7 percent of all recorded infections and 1.6 percent of all deaths. Those 17 and younger have had approximately 12 percent of all recorded infections and 0 deaths. DPH does not provide demographic (including age) information on hospitalizations.

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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1 Comment

  1. Mark, is there any indication of how SFDPH, or anyone for that matter, is accounting for at-home testing? Are we just on the ever reliable honor system?

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