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

Covid hospitaliztions have jumped from 21 to 35 in a week as infections and positivity rates have also begun rising again and R Number estimates show increased virus spread.

Early reports on omicron are preliminary, fragmented, self-interested or sketchy. The latest from the European Union (where there are almost as many cases as in Southern Africa, but no travel ban) shows all cases were either asymptomatic or mild. Dr. Fauci interprets the data to mean the variant “might” be less severe, “certainly not more severe” than delta.

Most of the reporting on omicron data, especially from Pfizer, reads like an infomercial for boosters. It won’t be long before three shots are considered “fully vaccinated,” which will further complicate mandates and venue requirements.

Biden’s vaccine mandates are running into conservative courts. However effective The Vaccine, it won’t work if people don’t get it. The U.S. Centers for Disease Control says only 60 percent of U.S. residents are now “fully vaccinated.”

The mandate complications may not be as complicated or expensive as changing ventilation standards in big venues like the San Francisco Opera House, ACT, Davies Symphony Hall and the Chase Center.

The Chan Zuckerberg Initiative has announced a major biotech play to support observation and new ways of measuring human biology. With substantial and sustained financing, the biotech industry will become an even more significant force in the City.

If you’re “fully vaccinated” and asymptomatic, must you quarantine for 10 days if you test positive?

Despite the recent jump in hospitalizations, the Phoenix Data Project has some good news on local hospitalizations during the delta surge.

Finally, this article from Vox, calling for the need for clear endgame goals in fighting covid, underlines not only the current lack of goals, but also the difficulty in setting them.

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. 7, DPH reports more than 85 percent of all San Francisco residents have received one dose, and 79 percent have received two. For residents 5 and older, DPH reports the figures rise to 89 percent and 82 percent. SFDPH reports that as of Nov 29, approximately 201,871 residents have received a COVID-19 booster dose including 53 percent of residents 65 and over. For information on where to get vaccinated in and around the Mission, visit our Vaccination Page.

On Dec. 4, DPH reports there were 35 covid hospitalizations, or about 4 per 100,000 (based on an 874,000 population). The increase comes in acute care patients as the number of ICU patients remains in single digits. DPH has released no information on hospitalizations among what used to be considered “fully vaxxed” for two months, saying it halted reports “because we are analyzing the data to ensure accuracy.” For September data see the latest from DPH. Why doesn’t DPH have the same problem in breaking out vaccinated and unvaccinated positive tests (see below)?

The latest report from the federal Department of Health and Human Services shows Zuckerberg San Francisco General Hospital with 3 covid patients and 6 ICU beds available, while across the Mission, CPMC had 5 covid patients and 5 ICU beds available. Of 31 reported covid patients, 19 were at either SFGH or UCSF, with at least 77 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. 4 and Dec. 3, DPH recorded 248 cases in the Mission or a rate of 42 per 10,000 residents. During that period, although Bayview Hunters Point had the most cases (191), it’s rate of 50 per 10,000 residents was outpaced by the Marina, Mission Bay, FiDi/South Beach, Hayes Valley, Tenderloin, Pacific Heights (!), Russian Hill, Twin Peaks, SOMA and Potrero Hill. The Marina leads with a rate of 69 per 10,000 residents.

On Nov. 30, the 7-day average of daily new cases in the City was 54, or approximately 6.2 new cases per day per 100,000 residents (based on an 874,000 population). The 7-day average case rate among vaccinated (not boosted) residents was 5.3 per 100,000 vaccinated residents and for unvaccinated residents,  11.4 per 100,000 unvaccinated residents.

For the month of November, DPH reports Whites have recorded 829 infections, 45 percent of the total; Asians 363 infections, 19.7 percent, Latinxs 284 infections, 15.4 percent, Blacks 95 infections, 5.1 percent, Multi-racial residents 37 infections, 2 percent, Pacific Islanders 15 infections, .8 percent and Native Americans recorded 11 infections in November, .6 percent of the total.

For the month of November, Whites and Multi-racials recorded 2 percent positivity, Latinxs 1.6 percent, Blacks and Native Americans 1.4 percent, Asians 1.2 percent and Pacific Islanders had a November positivity rate of 1.1 percent.

DPH reports the first December covid-related death and adds 2 new November deaths for a total of 678. To “ensure accuracy,” DPH has not updated deaths among vaccinated and unvaccinated since September. Of those San Franciscans who died of covid-related deaths, approximately 3 percent had no underlying conditions.

Covid R Estimation now puts its San Francisco R Number at an alarming 1.38, and its California R Number estimate at 1.3. Somewhat less alarmist, the ensemble average for the  San Francisco R Number is 1.06  and the average California R Number at 1.12. Now all models in the ensemble show California over 1 and all but one model show SF over 1.

In November, males accounted for 52.1 percent of infections and females accounted for 46.9 percent of reported infections, while .6 percent were “other” and .4 percent were “unknown.” No cases were reported among trans males or trans females. Though the City doesn’t ask test takers to report, or display, their vaccination status, they do ask sexual orientation. In November, straights accounted for 33.6 percent of the cases, Gays or Lesbians accounted for 2.7 percent, Bisexuals 1.6 percent and almost 60 percent were “unknown”.

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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. It’s too early to tell if omicron is milder. Many of those cases are in people who’ve already been vaccinated (vaxxed *and* boosted, in the majority of cases from the recent cluster of Kaiser employees) and/or are younger and/or have had previous exposure. Doesn’t yet show us how it will affect the elderly, the immunocompromised, or other vulnerable populations.

  2. “It won’t be long before three shots are considered “fully vaccinated” which will further complicate mandates and venue requirements.”

    It’s really not that complicated to check for three shots on a vaccine card instead of two* (with the obvious exception of J&J recipients, but that’s already an issue).