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

Infections and positivity rates are going through the roof, while the R number remains high. Hospitalizations are increasing, but not anywhere near what might be expected.

Twenty-one months into the pandemic and I’ve never felt so vulnerable, or so protected.

Want to know what exponential growth means? Local data scientist Peter Khoury notes that humans tend to think linearly, not exponentially.

How much have your chances of getting infected changed during this wave? National covid celeb Andy Slavitt gives a sense of your odds, along with recommendations for staying uninfected. Why don’t these guys ever talk about what hospitals, or public health institutions, should do? I have yet to read a word about hiring more workers, contact tracing or isolation support. Without such measures, won’t we be facing the same situation over and over again?

Here’s the latest thread from UCSF’s Bob Wachter on the local situation. He worries about hospitals getting overwhelmed. So, besides worrying, what are the hospitals (and the City hospital system, if such thing exists) doing about it?

And here are some good graphs on the local scene from the Chron, which demonstrate a decoupling of hospitalizations from number of infections. Similar reports have been coming from South Africa and London. Despite the lack of public restrictions, the UK is preparing a Plan B. Is San Francisco?

Will the pandemic ever end? Probably. But it does raise the question: How do pandemics end?

Note: Covid Tracker may not publish Monday, due to delays in data reporting over the New Years weekend. It will be a game-time decision.

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. 30, DPH reports more than 87 percent of all San Francisco residents have received one dose, and over 81 percent have received two. For residents 5 and older, DPH reports the figures rise above 90 percent and above 85 percent and over 90 percent of those 65 and older have received two doses. SFDPH reports that as of Dec. 30, approximately 379,148 residents (54 percent of all residents) have received a COVID-19 booster dose including 75 percent of residents 65 and over, 63 percent for those 50-64, 57 percent for those 35-49 and 43 percent for those 16-34. For information on where to get vaccinated in and around the Mission, visit our Vaccination Page.

On Dec. 27, DPH reports there were 52 covid hospitalizations, or about 5.9 per 100,000 (based on an 874,000 population). The increase appears entirely to be in Acute Care. Note: DPH does not break out how many are in the hospital for covid, and how many are in the hospital for another reason and tested positive upon entrance. At a time when hospitalization data is more important for the public than ever, 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, and Seattle 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 7 covid patients and 6 ICU beds available, while across the Mission, CPMC had 5 covid patients and 6 ICU beds available. Of 49 reported covid patients, 32 were at either SFGH or UCSF, with at least 52 ICU beds available among reporting hospitals (which does not include the Veterans Administration). The California DPH currently reports 68 covid patients and  114 ICU beds available in San Francisco.

Note: DPH uses dated population figures for neighborhoods. As of Dec. 29, DPH estimates 50 percent of Mission residents have been boosted. Castro leads with 69 percent while Treasure Island and Bayview Hunters Point are the only City neighborhoods with less than 40 percent of its resident population boosted. Between Oct. 27 and Dec. 26, the Mission recorded a City high of 680 infections, or a rate of approximately 116 per 10,000 residents. Sunset/Parkside is the only other City neighborhood with more than 600 recorded infections. The Marina, with 57 percent of boosted, continues to lead by infection rate, with a rate of 205 per 10,000 residents, the only neighborhood in excess of 200.

On Dec. 23, the 7-day average of daily new infections in the City soared to 608 or approximately 69.5 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 68.5 per 100,000 vaccinated residents and for unvaccinated residents,  96.6 per 100,000 unvaccinated residents. Though the unvaxxed are clearly at more individual risk of infection, the great majority have been recorded by those who have received two doses of The Vaccine. Perhaps it’s time to stop calling them “breakthrough infections”. There is no data on infections among those boosted.

As of Dec. 26, 63 percent of SF White residents had received a booster, Asians 57 percent, Blacks 40 percent, Native American 39 percent, Latinxs 37 percent, and 35 percent of Pacific Islanders have received the booster.

With omicron in control, the average city-wide positivity rate has reached levels not recorded since March 2020. Right, there’s a lot of virus currently in circulation.

Four new covid-related deaths have been recorded so far in December. DPH does not provide monthly demographic data on deaths. Though San Franciscans 65 and older account for 10 percent of the total infections, they account for 70.6 percent of the total number of covid-related deaths. Of those San Franciscans who died covid-related deaths, approximately 3.1 percent had no underlying conditions.

R Number models continue to suggest more exponential growth in our near future.  Covid R Estimation raised its San Francisco R Number to a very high 2.3 (still highest in the state but no longer the only county at or above 2) and estimates the California R Number at 1.96. The ensemble raised its average for the  San Francisco R Number to 1.73, while posting an average California R Number of 1.59. Almost all models in the ensemble show SF over 1.6.

As of Dec. 26, DPH reports men accounted for 51.7 percent of December infections, while women accounted for 46.8 percent, trans women .1 percent, trans men 0 percent while “other” (?) accounted for nearly 1 percent. Men account for 60 percent of total covid-related deaths, while women account for 39.7 percent.

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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. The hospitals and healthcare systems within SF do talk to each other and DPH is part of that. DPH set up a field hospital in 2020 that luckily wasn’t needed. They wouldn’t be starting from scratch.

  2. I really appreciated the thread from Dr. Murray on how pandemics end.

    So um, am I the only one to see that Ellie Murray Sc.D. has a remarkable resemblance in appearance and tone to Ellie Arroway, Ph.D?

  3. When you say “men” and “women” in your last section, do you mean cis men and women? It’s unclear if you’re referring to all men and women or just cis people because then you specify trans women and men after that. Btw, “other” would refer to non-binary and possibly intersex people.

  4. The Twitter thread about outdoor activities is from January 2021 and using data/study from 2020. This is pre delta and most importantly pre omicron.

    I’m not sure it’s wise to use it in the current context.

  5. Sorry, I have another question that others might have as well.

    “43 percent for those 16-34,” have been boosted — that age range is really, really diverse in needs and experiences.

    Is there any data for those who are 16-18 years old, or maybe under 22, namely, those who are still in high school, college in the city, or home for the holidays?

    This kind of information would be really useful for families, schools, and outside-of-school activities.

    Thanks so much for your continued reporting. Our family really appreciates your diligence.

    1. No, sorry, don’t think they’ve done any kind of breakout within that age group. There has been some discussion about the wisdom and/or need to boost teenagers, but so far not clear how many have received it. And again no data on prevention of infection.