Covid-19 Tracker: Omicron moves into the Mission

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

Hospitalizations, infections and positivity rates move up while R Number models for San Francisco continue to show mixed estimates on the currrent rate of local transmission.

Covid Tracker will not publish on Wednesday.

Although the numbers show only a modest increase, that could be changing soon as omicron has been spotted in the Mission.

Data from South Africa continues to show a high rate of contagion, but lesser virulence. The latter may be due to the nature of the variant.

Adding to the holiday spirit of dismay and confusion, Vice President Kamala Harris said that the Biden Administration and the scientists advising them did not see delta or omicron coming. Wow! What planet are they on? The warnings have been loud and explicit for at least a year or more.

Rapid tests can helpful and recommended to be used frequently this season, like before and after parties and travel. Assuming you can find them and/or afford them in bulk.

Of course, rapid tests raise an obvious question. If you test positive with the sniffles or no symptoms, how many days should you quarantine/isolate? There’s no easy answer. As out Annika Hom reports, Joe DeRisi, who runs the Chan Zuckerberg BioHub, says the virus’s most infectious stage is during days 3 to 5, which is the time one needs to isolate and prevent spread. Here’s the standard, somewhat dated, advice. Here’s University of California, San Francisco doctor Bob Wachter trying to figure it out. And here’s a graph by rapid test apostle Michael Minna, which might be helpful (assuming you know when you were exposed). But no matter what the “science” says, without adequate support for isolating, and without paid time off work, the practical answer for many, especially our “essential(ly screwed) workers” will be 0. Not to mention how much isolation for infected healthcare workers will affect the hospitals.

Finally, some advice from national covid celeb, Ashish K. Jha in The Atlantic: Don’t panic, but don’t be dismissive.

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. 19, 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. 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. 16, DPH reports there were 38 covid hospitalizations, or about 4.3 per 100,000 (based on an 874,000 population), and ICU patients rose to 12. 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. Let’s hope DPH has more complete hospital data than they make available to the public. 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  98 ICU beds available in San Francisco. SFDPH won’t say.

Note: DPH uses dated population figures for neighborhoods. Between Oct. 16 and Dec. 15, DPH recorded 275 infections in the Mission or a rate of approximately 47 per 10,000 residents. During that period, four San Francico neighborhoods had more than 200 infections including Sunset/Parkside (277), the Marina (211) and Bayview Hunters Point (205). The Marina continues to lead by infection rate, with a rate of 83 per 10,000 residents. The only other neighborhood with a rate above 70 is Mission Bay at 72 per 10,000 residents

On Dec. 12, the 7-day average of daily new infections in the City was 85 or approximately 9.7 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 8.5 per 100,000 vaccinated residents and for unvaccinated residents,  19.3 per 100,000 unvaccinated residents.

As of Dec. 15, DPH recorded 619 infections in December among Whites, 42.5 percent of the total December infections, Asians 312, 21.4 percent, Latinxs 224, 15.4 percent, Blacks 85, 5.8 percent, Muti-racials 21, 1.4 percent, Native Americans 9, .6 percent, and Pacific Islanders recorded 9 December infections or .6 percent of the total December infections.

As of Dec. 15, Native Americans have a 3.3 percent December positivity rate, Whites 2.6 percent, Latinxs 2.5 percent, Pacific Islanders 2.5 percent, Multi-racials 2.3 percent, Blacks 2.1 percent and Asians so far in December have a 1.7 percent positivity rate. With rates like these, it’s difficult for me to understand why the Citywide average positivity rate is only 2 percent.

Of those San Franciscans who died covid-related deaths, approximately 3.7 percent had no underlying conditions. The formal infection fatality rate 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 raised its San Francisco R Number to 1.35 (still among the highest in the state) and lowered its California R Number estimate to 1.03. The ensemble raised its average for the  San Francisco R Number back above 1 to 1.05, while posting an average California R Number of .96.

As of Dec. 15, DPH has recorded 29 December infections among those SF residents 0-4 years old, or 2.0 percent of the December totals so far, 5-11 61 infections, 4.2 percent, 12-17 35 infections, 2.4 percent, 18-20 32 infections, 2.2 percent, 21-24 147 infections, 10.1 percent, 25-29 324 infections, 22.3 percent, 30-39 451 infections, 31 percent, 40-49 174 infections, 12 percent, 50-59 101 infections, 6.9 percent, 60-69 54 infections, 3.7 percent, 70-79 30 infections, 2.1 percent, and those 80 and above have had 17 recorded infections so far in December, 1.2 percent of the total December infections.