Covid-19 Tracker: Rising R Number estimates

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

R Number estimates for San Francisco and California have been generally below 1 for most of November. They appear to have taken a recent jump (see below) as hospitalizations tick upwards, though case numbers and positivity rates remain static.

Almost all the Covid-19 news over the weekend were panic reports on omicron. No reason for panic, says UCSF researcher Diane Havlir.

Even though very little is known about the new variant, Big Pharma, the FDA and CDC are not only pushing boosters, about which very little is known, but planning for a new vaccine to be “fast-tracked” (the Wall Street Journal article is behind a paywall, but don’t dismay, all the “news” you need is in the headline). If this comes about, it will be the fourth vaccination for many of us within a year.

In its last days, the de Blasio administration in New York City has announced it will require at least one dose of The Vaccine for all employees who work in-person at private companies. Other than driving Republicans crazy, it’s not clear exactly what science de Blasio is following.

All the mandates, restrictions, etc. are supposed to save our understaffed, under-resourced, underfunded hospitals from getting overwhelmed. One hospital chain, the Catholic Ascension network, has taken a novel approach to funding. According to an article in STAT, the hospital moonlights as a private equity fund. That’s right, a “nonprofit” private equity fund. The article in STAT is behind a paywall, but it’s definitely worth a 30-day free trial. Alternatively, you can check out a summary here.

I cannot vouch for the politics of the author, who states “The organization of the hospital system in the United States and its funding is unique, complicated and a mess. No other country has such a hodgepodge.” As a private equity fund, the hospital network does not have to disclose how its profits are spent on improving patient care. According to the STAT article, Ascension invested in “a beleaguered medical debt collection company, [which] faced a lawsuit over aggressive debt collection tactics that included pressuring patients to pay bills while they were, in some cases, still in the emergency room.” Soon after Ascension began playing the private equity game in 2015, it started “gutting services at a hospital in Washington, D.C., that served low-income patients. Ascension shuttered the hospital’s maternity ward, then all hospital services including its emergency room and intensive care unit. The same year, it pursued similar cuts at a hospital in Milwaukee.” Nothing illegal about it. Since 1998, nonprofit hospitals have been allowed to profit tax-free from partnerships with for-profit companies.

While covid mitigation policies may have protected hospitals, they also fueled a “pandemic of violence against women and girls.” Here’s a review and mitigation policies and some recommendations for the future. The authors state “maintaining a constant state of emergency is not viable. A more realistic public health approach is to adjust current mitigation goals to be more data-driven and to minimize unintended harms associated with unfocused or ineffective control efforts.”

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. 5, DPH reports more than 85 percent of all San Francisco residents have received one dose, and 78 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. 2, DPH reports there were 27 covid hospitalizations, or about 3.1 per 100,000 (based on an 874,000 population). Although cases declined or remained somewhat stable, hospitalizaitons rose by 6 since last Friday’s report. 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.

The latest report from the federal Department of Health and Human Services shows Zuckerberg San Francisco General Hospital with 4 covid patients and 6 ICU beds available, while across the Mission, CPMC had 4 covid patients and 2 ICU beds available. Of 30 reported covid patients, 19 were at either SFGH or UCSF, with at least 67 ICU beds available among reporting hospitals (which does not include the Veterans Administration). The California DPH currently reports  78 ICU beds available in San Francisco. SFDPH won’t say.

Note: DPH uses dated population figures for neighborhoods. Between Oct. 2 and Dec. 1, DPH recorded 238 cases in the Mission or a rate of 40 per 10,000 residents. During that period, although Bayview Hunters Point had the most cases (178), it’s rate of 47 per 10,000 residents was outpaced by the Marina, Mission Bay, FiDi/South Beach, Hayes Valley, Tenderloin, Presidio Heights (?!), Russian Hill, Twin Peaks, SOMA. Haight Ashbury and Potrero Hill. The Marina leads with a rate of 65 per 10,000 residents.

On Nov. 28, the 7-day average of daily new cases in the City was 44, or approximately 5 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 4 per 100,000 vaccinated residents and for unvaccinated residents,  10.3 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.

As of Nov. 28, the City’s 7-day rolling average tests per day dropped to less than half the number of tests reported on Sept. 20. There is no explanation for the decline.

The total of Delta surge covid-related deaths (August through November) so far is 98 and the cumulative covid-related death toll stands at 675. DPH has not updated deaths among those “fully vaxxed” since September. Of those San Franciscans who died of covid-related deaths, approximately 3 percent had no underlying conditions.

Covid R Estimation keeps its San Francisco R Number over 1 at 1.08, and its California R Number estimate at 1.03. The ensemble continues to estimate rising R Numbers around the state, raising its average for the  San Francisco R Number to 1.07  and the average California R Number at 1.14. For most of November, the ensemble had San Francico below 1.

For the month of November, DPH reports only 1 case the City’s nursing homes (“Skilled Nursing Facilities”) and 0 covid-related deaths. In Single Room Occupancy hotels (SROs) 30 cases were reported during the month, and 0 new covid-related deaths. Among thosed unhoused, 11 new cases were reported and 0 new covid-related deaths.