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

Hospitalizations and case counts stayed are more or less where they’ve been for the week. Positivity rates have risen, and R Number models for San Francisco are mixed on the current rate of spread.

The local numbers may have not increased much over the past week, but the noise around omicron has become almost deafening.

First, the good news. The numbers coming out of South Africa continue to be hopeful, with respect to hospitalizations. Recent studies also show little change when the numbers are controlled for age.

Now, the bad news.

Speakers at yesterday’s UCSF Grand Rounds pointed to data indicating omicron is highly contagious, meaning we need to get ready for some big case numbers this winter. Del Rio had other data on hospitalizations and deaths, but it’s still too soon to say how severe omicron is compared to delta and previous variations. The doctors agreed it’s time, past time really, to get vaccinated and boosted.

With a wave of omicron infections on the horizon, vaccinated (and boosted) individuals are better off than last year. What is not better, as Ed Yong of The Atlantic has chronicled throughout the pandemic, is the dreadful state of public health. Omicron may not be as severe, but it won’t take much to overwhelm the hospital system in the U.S. Even if the political will existed (which it doesn’t), what took decades to destroy cannot be rebuilt in a year or two.

The Vaccine may be effective, but the one from Johnson & Johnson, which UCSF Dr. Kim Rhoads has argued against for months, has been formally downgraded (or in CDCese, “not preferred”).

New York City has begun to make rapid tests and K95 masks widely available for free. With a fraction of the population, why can’t SF do the same?

Before scrolling down for today’s data, check out this open letter from National Health Service workers in the UK to the Conservative Party. Much the same can be said in this country.

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. 16, DPH reports more than 86 percent of all San Francisco residents have received one dose, and 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. 13, approximately 296,921 residents have received a COVID-19 booster dose including 68 percent of residents 65 and over, 50 percent for those 50-64, 44 percent for those 35-49 and 29 percent for those 16-34. For information on where to get vaccinated in and around the Mission, visit our Vaccination Page.

On Dec. 13, DPH reports there were 32 covid hospitalizations, or about 3.6 per 100,000 (based on an 874,000 population), more or less where it’s been for most of this month. For over two months, DPH has failed to report on hospitalizations among those who used to be considered “fully vaxxed”. In a recent email, DPH Communications Director Alison Hawkes writes “Our hospitalizations page is more of a deep time into the cases, specifically verifying them clinically to be caused by covid, and other analysis that is done.” I’m not sure exactly what that means. For September data see the latest from DPH.

The latest report from the federal Department of Health and Human Services shows Zuckerberg San Francisco General Hospital with 5 covid patients and 6 ICU beds available, while across the Mission, CPMC had 5 covid patients and 5 ICU beds available. Of 44 reported covid patients, 29 were at either SFGH or UCSF, with at least 70 ICU beds available among reporting hospitals (which does not include the Veterans Administration). The California DPH currently reports  80 ICU beds available in San Francisco. SFDPH won’t say.

Note: DPH uses dated population figures for neighborhoods. Between Oct. 13 and Dec. 12, DPH recorded 253 cases in the Mission or a rate of approximately 43 per 10,000 residents. During that period, the only other neighborhood with more than 200 cases was Sunset/Parkside (264), but it’s rate was 32 per 10,000. The Marina leads with a rate of 73 per 10,000 residents. Hayes Valley, Mission Bay and Potrero Hill are the only other neighborhoods with rates of 60 or above per 10,000 residents

On Dec. 9, the 7-day average of daily new cases in the City was 82 or approximately 9.4 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 8.2 per 100,000 vaccinated residents and for unvaccinated residents,  18.5 per 100,000 unvaccinated residents.

We won’t have December figures until the 20th at the earliest, and DPH stubbonly refuses to tell us who has been hospitalized. Instead of providing socio-economic data, DPH only reports on race, ethnicity, age, gender and sexual preference. As of Dec. 12, pandemic case rates for population groups based on their population numbers were Pacific Islanders 2,324 per 10,000 residents, Latinxs 1,410, Native American 1,108, Blacks 967, Whites 429, and Asians 339 per 10,000 residents.

Between Oct. 13 and Dec. 12, DPH reports a 1.5 percent positivity rate in the Mission. During that time, the Marina had a rate of 3.3 percent, and 13 neighorhoods, including Pacific Heights and Seacliff, had rates of 2 percent or higher. Glen Park, Japantown and the Outer Mission had positivity rates of 1.1 percent.

Two more December covid-related death has been reported, which should raises total to 682. Of those San Franciscans who died of covid-related deaths, approximately 3.7 percent had no underlying conditions. The formal case fatality rate (CFR) is currently 1.2 percent for the City. It may be lower as there are probably many more infections which have not been reported.

  Covid R Estimation has kept its San Francisco R Number at a relatively high 1.30 (among the highest in the state) and kept its California R Number estimate around 1.15. The ensemble has lowered its average for the  San Francisco R Number below 1 to .98, while posting an average California R Number of 1.01.

With 3.1 percent of the cases (1,693) and 54.8 percent of the deaths, (374), the Case Fatality Rate for those San Franciscans 80 and older is 22.1 percent, for those 60-79 3.7 percent, for those 21 – 59 .22 percent, and for those 0-20 percent 0.0 percent (like in 0 total deaths).

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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. in looking at the chart for vaccination by county, is there any correlation between higher percentage of vaccination and higher percentage of people with regular access to quality health care providers through full time employment or making enough money to afford personal health insurance? could this be an argument for universal health care?

  2. I agree, Mark, that it’s entirely reasonable to ask SF DPH to provide us with that basic Covid data. It’s some of the most important data they could be making available to the public.

  3. The digs at DPH sprinkled into these covid update posts serve mainly as clutter that distract from the updates and charts.

    The energy spent copy-pasting the same complaints about DPH into every post might be better directed toward writing a separate piece in which Mark details how he thinks DPH has failed and what he’d like to see done about it.

    For example, why is it unreasonable for them to withhold some data until they can ensure its quality? That would be a great thing to answer in a dedicated post instead of passive-aggressively whining about it here.