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

If you’re tracking the virus in San Francisco these days, don’t expect big changes. Hospitalizations, infections, positivity rates and R Number estimates appear to be in a holding pattern with hospitalizations still on a relatively high plateau.

The pandemic has been a master class on the relationship between politics and science. “When used correctly, science is the greatest lighthouse for human endeavors, but if misused, science has led to some of the greatest errors in our history.” So writes UCSF doc Vinay Prasad in a piece on how politics infects and inhibits covid science.

Speaking of scientific errors, let’s take another look at the safety issues in virology labs dealing with potentially pandemic pathogens.

A Trumpless White House unfortunately doesn’t mean politics has ceded primacy to science as we’ve seen in the booster debate as well as the debate over the existence and durability of natural infection.

Is it politics or science or something else that accounts for the low rate of vaccination among nursing home staff, why some nursing homes have resisted vaccine mandates, and have even lobbied against them? Note that nonprofit nursing homes have a better record in this regard.

Congrats to the Giants for making the playoffs. Unfortunately, winning baseball, like politics and science, seems to have nothing to do with the corporate club’s covid policies. Will you get a ticket refund if workers go on strike?

Note: There are new population figures out after the last census showing about 20,000 fewer San Franciscans in 2020 than were here in 2010. For the being, we will continue to use figures supplied by SFDPH.

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 Sept. 16, DPH reports over 87 percent of San Francisco residents over 12 have received at least one dose, and more than 81 percent are completely vaccinated. On Sept. 16, the seven-day rolling average of shots per day dropped again to 228. For information on where to get vaccinated in and around the Mission, visit our Vaccination Page.

Our hospital graph has been slow to update (as the numbers have been slow in coming down). On Sept. 13, DPH reports there were 78 hospitalizations. or about 8.9 per 100,000 (based on an 874,000 population). There were 60 in acute care, 18 in the ICU, . The latest update from DPH says as of Sept. 10, 77 fully vaccinated San Franciscans had been hospitalized (a rate of 12.6 per 1,000 cases compared to 85.1 per 1,000 cases for those not fully vaccinated) . According to the CDC, there were 51 new admissions for the week ending Sept. 14  (+8.51 percent from the previous week). For the week ending Sept. 14, covid patients accounted for 4.26 percent of hospital beds (-.71 percent from previous week) and 7.43 percent of ICU beds (-3.07 percent from previous week). As of Sept. 7, the CDC says that, of more than 176 million vaccinated U.S. residents, 14,115 patients with a covid vaccine breakthrough infection were hospitalized or died. Of that number 25 percent either had no covid symptoms or their hospitalization or death was not COVID-related

The latest report from the federal Department of Health and Human Services shows Zuckerberg San Francisco General Hospital with 19 covid patients and 79 percent ICU occupancy, while across the Mission, CPMC had 9 covid patients and 54 percent ICU occupancy. Of 99 reported covid patients, 56 were at either SFGH or UCSF.

Case numbers have begun to ease off, slightly, in the neighborhood. Between July 14 and Sept. 12, the Mission had  801 new cases (a rate of 136 new cases per 10,000 residents), while Bayview Hunters Point had 928 cases for a rate of 245 new cases per 10,000 residents. Of 38 SF neighborhoods, 23 had case rates over 100 per 10,000 residents, of which 15 were in the east and southeast sectors of the City.

The daily average number of new infections rose again above 100. DPH reports  for the week ending Sept. 9, the seven-day rolling average of daily new cases in the city was 103 new cases, or approximately 11.7 new cases per day per 100,000 residents (based on an 874,000 population).  According to the latest from DPH on Sept. 10, the 7-day average case rate among fully vaccinated residents was 8.5 per 100,000 fully vaccinated residents  and  19.8 per  not fully vaccinated 100,000 residents.  

No new data from DPH but the graph shows clearly the Delta surge has been fueled primarily by infections in the White community. Since the pandemic began, based on the group’s San Francisco population, Latinx residents have a case rate of 1,304 cases per 10,000 residents, while Blacks have a rate of 868; Whites, 351; and Asians, 268 cases per 10,000 residents. DPH estimates the rate of Pacific Islanders to be 2,120 and Native Americans to be 961 cases per 10,000 residents but concedes these numbers are “less reliable.”

Although the overall rate in the City has been static for most of the month, it still gets a “low trnasmission” designation from the CDC. In August, the Mission had a positivity rate of 4.4 percent (down from 5 percent in July), Bayview Hunters Point 6.2 percent (down from 8 percent), SOMA had 5.0 percent (down from 6.6 percent in July), the Castro had 4.6 percent (down from 6.2 percent), Presidio Heights had 2.9 percent (down from 3 percent) and Seacliff had 2.9 percent (up from 1.1 percent)

Covid-related deaths in San Francisco are always difficult to ascertain. Another September death has been recorded, bringing the September toll to 3, and the cumulative covid-related death toll to 607. Of those, approximately 3 percent had no underlying conditions.

Covid R Estimation has taken its estimate of the San Francisco R Number to below .80 at  .79 while again slightly raising  its estimate for the California R number to .96. All models in the ensemble  estimate the San Francisco R Number below 1, with an average of .81, while the average California R Number is .88. The ensemble average estimate for San Francisco has been below 1 since Aug. 3.

The overall population percentages have changed due to the 2020 Census. For the time being, we will continue to use use the figures provided by SFDPH. In August DPH report 123 infections among the SF unhoused population for a total of 922 infections and 6 deaths recorded since the pandemic began.

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Mark Rabine has lived in the Mission for over 40 years. "What a long strange trip it's been."

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