The R number.

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

Hospitalizations decline as infections and positivity rates surge. R Number models continue to show substantial and increasing transmission rates.

I wasn’t going to publish the Covid Tracker today, because of expected delays in reporting around the Christmas weekend. But the hospitalization numbers, if nothing else, are worth checking out. The New York Times continues to show much higher infection numbers (almost double the average number below). From the beginning, we’ve known that in covid world, time is relative, and there are no reliable “absolute” numbers. Numbers are useful to identify trends. Today, whether the Times, the State, or Johns Hopkins University, it is evident the infection trend line is climbing a vertical slope. We will continue to publish numbers supplied by San Francisco’s Department of Public Health, as the Department (theoretically) is accountable to the residents of the City, and should (theoretically) supply the most accurate figures.

Covid Tracker will next publish on Friday.

Decoupling infections from hospitalizations? It appears so. Whether it is due to less severity of omicron, or the power of The Vaccine, not really clear (to me), but the numbers, which reflect trends elsewhere, are mildly hopeful.

Here is University of California, San Francisco doctor Bob Wachter’s thread on local conditions (from a couple days ago).

On the one hand, there’s the pandemic. On the other, there’s pandemic protocols, particularly isolation after a positive test. Almost everyone is wrestling with the questions of isolation/quarantine after testing positive. Although there is no “official” guidance, a consensus seems to be developing around a minimum of five days (including negative test) after testing positive. Note: the thread cited is based in delta characteristics, not omicron.

Want some “cautiously optimistic” holiday cheer, not based (I assume) on drinking or smoking? Try this.

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 Dec. 26, DPH reports more than 87 percent of all San Francisco residents have received one dose, and over 80 percent have received two. For residents 5 and older, DPH reports the figures rise above 90 percent and above 84 percent and over 90 percent of those 65 and older have received two doses. SFDPH reports that as of Dec. 26, approximately 358,427 residents have received a COVID-19 booster dose including 73 percent of residents 65 and over, 60 percent for those 50-64, 54 percent for those 35-49 and 39 percent for those 16-34. For information on where to get vaccinated in and around the Mission, visit our Vaccination Page.

On Dec. 20, DPH reports there were 33 covid hospitalizations, or about 3.7 per 100,000 (based on an 874,000 population). For over two months, DPH has failed to report on hospitalizations among those who used to be considered “fully vaxxed”. In New York City not only are hospitalizations broken out by vaxxed and unvaxxed, but also by age and race/ethnicity. If New York can do it, why can’t SF?

The latest report from the federal Department of Health and Human Services shows Zuckerberg San Francisco General Hospital with 6 covid patients and 5 ICU beds available, while across the Mission, CPMC had 5 covid patients and 4 ICU beds available. Of 45 reported covid patients, 28 were at either SFGH or UCSF, with at least 60 ICU beds available among reporting hospitals (which does not include the Veterans Administration). The California DPH currently reports  84 ICU beds available in San Francisco. SFDPH won’t say.

Note: DPH uses dated population figures for neighborhoods. Between Oct. 23 and Dec. 21, DPH recorded 410 infections in the Mission or a rate of approximately 70 per 10,000 residents. No other neighborhood in the City recorded more than 400 infections. The Marina continues to lead by infection rate, with a rate of 143 per 10,000 residents. During this time, 6 City neighborhoods had infection rates in excess of 100, and 13 in excess of 80 infections per 10,000 residents.

On Dec. 18, the 7-day average of daily new infections in the City was 219 or approximately 24.9 new cases per day per 100,000 residents (based on an 874,000 population). The 7-day average infection rate among vaccinated (not boosted) residents was 22.6 per 100,000 vaccinated residents and for unvaccinated residents,  44.8 per 100,000 unvaccinated residents.

As of Dec. 26, 60 percent of SF White residents had received a booster, Asians 54 percent, Blacks 38 percent, Native American 36 percent, Latinxs 35 percent, and 32 percent of Pacific Islanders have received the booster.

With the average city-wide positivity rate over 4 percent for the first time since August 17, as of Dec. 21, Native Americans had a positivity rate of 5 percent for the month, Whites 4.4 percent, Multi-racials 4.3 percent, Latinxs 4.2 percent, Pacific Islanders 3.6 percent, Blacks 3.1 percent and Asians had a positivity rate of 2.9 percent so far in December.

Of those San Franciscans who died covid-related deaths, approximately 3.1 percent had no underlying conditions.

R Number models reflect the higher transmission rates for omicron.  Covid R Estimation raised its San Francisco R Number to a very high 2.2 (still the only county in the state at or above 2) and estimates the California R Number at 1.5. The ensemble raised its average for the  San Francisco R Number to 1.6, while posting an average California R Number of 1.37. All models in the ensemble show SF over 1.48.

As of Dec. 12, DPH has recorded 81 December infections among those SF residents 0-4 years old, or 2.0 percent of the December totals so far, 5-11 101 infections, 2.5 percent, 12-17 66 infections, 1.6 percent, 18-20 88 infections, 2.2 percent, 21-24 456 infections, 11.4 percent, 25-29 956 infections, 23.8 percent, 30-39 1285 infections, 32 percent, 40-49 509 infections, 12.2 percent, 50-59 260 infections, 6.5 percent, 60-69 135 infections, 3.4 percent, 70-79 50 infections, 1.2 percent, and those 80 and above have had 27 recorded infections so far in December, .7 percent of the total recorded December infections.

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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. Mark, do those percentages for boosted people refer to *all* SF residents, or just those who are eligible (over 16? Over 17?)? Thanks.

    1. Miriam: My quote is from Wachter’s thread above. He doesn’t specify the demographics of the people he is talking about. Also, I notice that he later modified his comment thus:

      “A few of my more astute readers have pointed out (thanks!) I got the math wrong (sorry): if crowd is 25 people & the probability of each having Covid is 4.6%, then the probability of someone having Covid is 69%, not a near certainty. Don’t reach >90% chance until ~45 in crowd. ”

      So 25 non-symptomatic people in the room: 69% chance someone has COVID.
      45 non-symptomatic people in the room: 90% chance someone has COVID.

      Any way you cut it, if you hang out in crowded rooms (restaurants, bars, movie theaters, concerts, you-name-it) you are going to be hanging out with somebody with COVID. You roll the dice and you take your chances.

      Of course, the real solution is not for all of us to hide somewhere, but for the powers-that-be to institute a real program of mass testing, serious contract-tracing, and isolation — and I don’t mean a voluntary program. That said, the US laissez-faire capitalist system with an emphasis on “individual” rights (as distinguished from the “collective” right to a healthy and safe environment) makes this impossible in this country.

  2. From Dr. Robert Wachter’s thread (see above):
    “…if you find yourself in a closed space in SF with 25 other people who feel fine, it’s a near certainty that one of them has Covid. And since it’s likely they have Omicron, their virus is about twice as transmissible as it would have been last month.”
    Think about it.

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