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

By any measure — infections, hospitalizations, positivity rates and R Numbers — San Francisco appears to be still in the thick of the omicron woods.

First, the good news. Local data scientist Peter Khoury reports the number of new infections seems to decelerating. Not decreasing, mind you, but not rising as fast as it has been.

So much for the good news.

Hopefully, you’ve read Anlan Cheney’s piece on the lack of protection provided to workers in local restaurants. In it, Dr. Susan Philip, San Francisco’s “health officer,” said that, instead of providing protection, the City provides “information.” She explained that the city is encouraging people to upgrade protection with more “easily obtainable” masking options, thereby “prioritizing our healthcare workforce for [N95s] to make sure they remain available and essential workers have access to those around the city.” Is she saying that almost two years into the pandemic, the City has to hoard “easily attainable” high-quality masks to prioritize healthcare workers? Really? What local hospitals are not supplying their workers with sufficient personal protective equipment? Does Phillip mean to say restaurant workers, particularly cooks, (who were among the hardest hit in 2020) are no longer considered “essential?”

The lack of personal protective equipment may have been one of the “dire working conditions” which provoked workers at Kaiser to threaten to strike a couple of months ago. In 2020, a new analysis shows Kaiser Permanente logged the most complaints on workers’ safety, over double the number from the next highest establishment.

Covid, and now especially omicron, has graphically displayed the understaffing, underpay and dangerous working conditions for workers in hospitals.

Members of the Biden transition COVID-19 Advisory Board have been speaking out about the failure of the Administration to do little beyond pushing The Vaccine. Much of what they have to say relates to creating a functional public health system. Though they make a number of good points, including community healthcare workers, they make no mention of improved working conditions, increased pay and increased staffing at hospitals and across the industry.

Time for a joke. Remember Biden’s plan to have your insurance provider reimburse you for the outrageously expensive rapid tests (assuming you could find one)? Here’s a tale from someone who tried.

I can’t leave you to the numbers without getting back to Dr. Phillip’s assertion that DPH provides information. At a time when improved hospitalization data is required, especially on how many patients are being treated for covid, and how many came to the hospital for something else and subsequently tested positive, DPH provides the absolute minimum. Actually, we get less information on hospital conditions than we did in 2020. In addition, DPH provides limited, ambiguous or opaque information on covid in schools, and no information on outbreaks around the City, contact tracing, or resources available for isolation (if any). Seems like the “information” is waning.

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 Jan. 6, DPH reports more than 88 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 Jan. 6, approximately 400,395 residents (56 percent of all residents) have received a COVID-19 booster dose including 77 percent of residents 65 and over, 66 percent for those 50-64, 61 percent for those 35-49 and 46 percent for those 16-34. For information on where to get vaccinated in and around the Mission, visit our Vaccination Page.

Despite fewer than last winter, hospitalizations are rising quickly. On Jan. 3, DPH reports covid hospitalizations jumped to 112, or about 12.8 per 100,000 (based on an 874,000 population), including 23 now in ICU. The California Department of Public Health currently reports 113 covid patients in SF hospitals with 24 in ICU. Note: SFDPH refuses to provide (or is incapable of providing) demographic information about covid patients, how many are in the hospital for covid, and how many are in the hospital for another reason and tested covid positive upon entrance, or the number of vaxxed and unvaxxed covid patients.

The latest report from the federal Department of Health and Human Services shows Zuckerberg San Francisco General Hospital with 11 covid patients and 10 ICU beds available, while across the Mission, CPMC had 3 covid patients and 6 ICU beds available. Of 52 reported covid patients, 37 were at either SFGH or UCSF, with at least 91 ICU beds available among reporting hospitals (which does not include the Veterans Administration). The California DPH currently reports 114 covid patients and  97 ICU beds available in San Francisco.

Note: DPH uses dated population figures for neighborhoods. Between Nov. 3 and Jan. 2, DPH recorded 1242 infections among Mission residents or 211 infections per 10,000 residents. The high number (highest in the City) may be in part due to continuous testing at 24th Street. Only Sunset/Parkside has over 1000 infections. The Marina continues to have the highest rate, with 291 infections per 10,000 residents. Along with the Mission and the Marina, 13 other neighborhoods have rates over 200 per 10,000 residents, including Mission Bay, Russian Hill, Hayes Valley, FiDi/South Beach, Potrero Hill, Pacific Heights, SOMA, Haight Ashbury, North Beach, Bayview Hunters Point, Western Addition, Lone Mountain/USF, and Twin Peaks.

On Dec. 30, the 7-day average of daily new infections recorded in the City was 1140 or approximately 130.43 new infections per day per 100,000 residents (based on an 874,000 population). The 7-day average infection rate among vaccinated residents was 126.4 per 100,000 vaccinated residents and for unvaccinated residents, 186 per 100,000 unvaccinated residents.

For the month of December, DPH reports 5,640 infections among White SF residents, 37.9 percent of the total, Latinxs, 2,891 infections, 19.4 percent, Asians 3,386 infections, 22,7 percent, Blacks 844 infections, 5.7 percent, Multi-racials 246 infections, 1.7 percent, Pacific Islanders 172 infections, 1.2 percent, and Native Americans had 50 infections, .3 percent of December totals.

Between Nov. 3 and Jan. 2, DPH recorded a 6.8 percent positivity rate in the Mission. The Marina had a positivity rate of 10.5 percent, the only neighborhood above 10 percent. Twelve neighborhoods had rates above 7 percent. The neighborhood with the lowest rate was Glen Park (4.3 percent), and Lakeshore, the only neighborhood in the City with less than 50 percent of its residents vaccinated, recorded a rate of 4.7 percent.

One more December covid-related death and 2 new January deaths have been recorded.

Covid R Estimation has lowered its San Francisco R Number below 2 to 1.96 and slightly lowered its California R Number at 2.03. The ensemble raised its average for the  San Francisco R Number to a doubtful 1.27, while posting an average California R Number of 1.53. The ensemble includes one model which shows a .69 number and LEMMA (a collaborative effort between individuals mainly from UC Berkeley and UCSF) which posts a 1.01 number.

One reason why hospitalization numbers may have “decoupled” from infection numbers is that we don’t see the outbreaks in nursing homes we saw in 2020. In December, DPH has recorded only 9 infections and 2 covid-related deaths in 19 “skilled nursing facilities”. Single Room Occupancy hotels (SROs) recorded 182 infections and 0 covid-related deaths in December. One more death was added in January. Among those unhoused, 121 December infections and a pandemic total of 7 covid-related deaths have been reported.

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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. government worker – that’s upsetting. it’s shot in the dark, but try asking if they can get decertified N95s or medical grade surgical masks.

  2. Staff in my department recently asked whether City of San Francisco will provide N95 masks, since we work directly with the public, sometimes in enclosed spaces. The official line is that they won’t give us N95s – “those are for healthcare workers” – but we are allowed, if it makes us feel more comfortable(!) to wear the paper surgical masks we provide to the public under our cloth masks.

  3. Thanks again, Mark.

    So much local coverage seems to be saying only, “don’t worry; it’s milder.”

    I wish there were more focus on the huge risks that omicron still poses to many people who fall into a high-risk category.

    As Mar Hicks recently put it on Twitter:

    “ ‘It is very encouraging news,” said the government, ‘that only people like you will die.’

    ‘Excuse me?’ I said.

    ‘Very encouraging news,’ they repeated.”

  4. Seems like the city is always trying to take resources away from covid response, shutting down important services because they want the pandemic to be over. What # surge is this and it’s still a surprise to them… is there anybody left in local gov working full time on COVID?? Or is ti just press conferences?

  5. It’s difficult to see the latest trends both in part because well, the graphs here are usually for totals over the past two years, but also because sigh, between Christmas, New Years and weekends, there is so many days missing that get lumped into the following Monday.

    The financial times coronavirus charts (, zoomed in, are showing recent peaks in the US and the UK, but sigh, that’s almost certainly missing data

    1. Thanks Jerry. I will pass along your comments to our visualizers. In terms of recent trends, could also seem harder to see because it’s just, unfortunately, one long vertical line.