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

Hospitalizations and positivity rates have gone up, as recorded infections took a big dive. Wastewater monitoring shows less covid than two weeks ago, and R Number models are generally below one.

Ed Yong has a new piece in The Atlantic on “brain fog,” a common symptom in the list of long covid symptoms. It’s not your run-of-the-mill exhaustion from work and modern-day life.

It is a part of the contribution that high levels of covid transmission and long covid are believed to be making to the general labor shortage.

Brain fog in Washington, D.C., is nothing new, but it has gotten worse since covid. Today’s version of “The Best and the Brightest” can’t wait to declare covid finished (again).

In robotic unison, they have already begun to flog the new booster. As we don’t know yet whether the new booster will be a trick or treat, it is fitting Halloween has been announced as the due date for getting a shot. Here are more nuanced views, which hardly dissipate the fog, with respect to efficacy and timing.

Should the official brain fog clear (unlikely) after a new variant, or virus, strikes, companies and academics are already lining up with their hands out.

Here’s a long thread on the upcoming variants.

New research on the virus has yielded some interesting clues as to why some people don’t get the virus or don’t get symptoms. The constellation and interaction of an individual’s T-cells may also be a defense mechanism.

Along with these, a study on covid in immunocompromised individuals.

The research activity regarding the nature of the virus (more, much more, is badly needed) has not been matched (to put it badly) by research into non-pharmaceutical interventions to curb transmission. Unfortunately, this year’s conference of the American Public Health Association may be dominated by finger-pointing and a variety of ad-hominem attacks.

The last two-plus years of covid have left most Americans disgusted, or “dissatisfied” with the U.S. healthcare system, especially public health.

Even the U.S. Centers for Disease Control and Prevention admits its widespread failure to meet the covid challenge. Dr. Tom Frieden, a previous director, agrees that changes are needed at the CDC, what’s needed and what’s not. A rational society would pay attention and make the necessary changes.

One of the common responses to the claims that supplements like vitamin D and zinc don’t do anything to prevent covid or ameliorate the symptoms has been a lack of clinical trials. Here’s a report on two large (somewhat flawed) trials with vitamin D.

And, finally, an actual peer-reviewed study showing the protection against long covid provided by The Vaccine.

Scroll down for today’s covid numbers.

Hospitalizations are up from last week. On September 10, the San Francisco Department of Public Health reported 73 covid hospitalizations, or about 8.4 covid hospitalizations per 100,000 residents (based on an 874,000 population). This represents a 12.4 percent increase from last week. Over the week, hospitalizations had climbed to 83. ICU patients rose to 15 before falling back to 14, an increase of 2 over last week. The California Department of Public Health reports on September 9, that there were 79 covid patients in SF hospitals with 14 patients in ICU. For the week ending September 11, the CDC says there were 56 new covid admissions, a 6.4 percent increase from the previous week. According to the New York Times, on September 13, there were 77 covid hospitalizations. Neither the CDC, NYT or the CaDPH say which hospitals are included in their survey. When the brain fog lifts at SFDPH, it may report how many covid positive patients have been vaccinated and how many are hospitalized “for” covid, and how many “with” covid.

The latest report from the U.S. Department of Health and Human Services shows Zuckerberg San Francisco General Hospital with 9 covid patients and 8 ICU beds available, while across the Mission, CPMC had 9 covid patients and 4 ICU beds available. Of 78 reported covid patients in the City, 31 were at either SFGH or UCSF. At least 63 ICU beds are available among reporting hospitals (not including the Veterans Administration or Laguna Honda). The California DPH reports that as of September 9, SF had 66 ICU beds available. Whether those beds are actually “staffed” neither the city nor the state will say.

Between July 11 and September 9, DPH recorded 730 new infections among Mission residents (a decrease of 16.5 percent from last week) or 124 new infections per 10,000 residents. During that period, Bayview Hunters Point had the highest rate at 214 new infections per 10,000 residents. Of 38 neighborhoods, 8 had rates at or above 150 per 10,000 residents, 6 in the east and southeast sectors of the City.

DPH reports on September 6, the 7-day average of daily new infections recorded in the City dropped to 56 or approximately 6.4 new infections per 100,000 residents (based on an 874,000 population), a decrease of approximately 55 percent from last week. According to DPH, the 7-day average infection rate among vaccinated residents was 6.1 per 100,000 “fully vaccinated” residents and 15.4 per 100,000 unvaccinated residents. It is unclear whether “fully vaccinated” means 2, 3 or 4 doses. The New York Times said the 7-day average on September 6 was 143. On September 13, the Times says the 7-day average was 66, a 61 percent decrease over the past two weeks. Wastewater monitoring shows covid continuing to decline in the City’s southeast sewers (below where it was two weeks ago). This report comes from the Stanford model.

Over the course of the pandemic, San Francisco’s Pacific Islander population has a case rate of 5,252 per 10,000 Pacific Islander residents; Latinxs 2,910; Native Americans 2,497; Blacks 2,284; Asians 1,387; and San Francisco’s White population has a case rate of 1,207 per 10,000 White residents.

On September 6, the 7-day rolling Citywide average positivity rate rose 1.6 percent from last week to 6.5 percent. Since last week, the average daily testing dropped approximately 15.8 percent to the lowest it’s been since May 30, 2020. Between July 11 and September 9, the Mission had a positivity rate of 9.4 percent (based on 9,694 tests) a 10.5 percent drop from last week’s report. For the month of August, San Francisco’s Asian population had a 9.5 percent positivity rate; Latinxs 9.4 percent; Pacific Islanders 8.4 percent; Whites 6.9 percent; Native Americans 6.7 percent; Muliti-racials 6.3 percent and San Francisco’s Black population had a positivity rate of 6.2 percent during the month of August.

Between September 6 and September 13, 411 San Francisco residents received their first or second shot; 130 got a booster. Vaccination rates in SF show virtually no change over the past three or four months: 90 percent of all San Franciscans have received one shot, 85 percent two shots and 64 percent have received at least one booster. As of September 13, DPH estimates 70 percent of the City’s Asian residents have received at least one booster; White’s 59 percent; Latinxs 57 percent; Pacific Islanders 55 percent; Native Americans 52 percent; Blacks 51 percent; and the percentage of the City’s multi-racial population which has received at least one booster is “not calculated.”

For information on where to get vaccinated in and around the Mission, visit our Vaccination Page.

Ten new covid-related deaths have been reported since our last report, bringing the total since the beginning of the year to 334. The case (recorded infections) fatality rate so far in 2022 is .3 percent. Between March and August this year there have been 187 recorded covid-related deaths. During the same time period in 2021 there were 93 recorded deaths and in 2020 94 deaths. DPH refuses to report how many were vaccinated. It only provides cumulative information on race, ethnicity or socioeconomic status. According to DPH “COVID-19 deaths are suspected to be associated with COVID-19. This means COVID-19 is listed as a cause of death or significant condition on the death certificate.” Using a phrase like “suspected to be associated with” indicates the difficulty in determining a covid death. The fog gets denser as DPH reports, as it has for months, only 21 of the deaths are known to have had no underlying conditions, or comorbidities. DPH only supplies cumulative demographic numbers on deaths.

The lack of reliable infection numbers makes R Number estimates very uncertain. Covid R Estimation on September 7 estimated the San Francisco R Number at a surprising .50 while its estimate for the California R Number on September 12 was .64. The ensemble, on September 11, estimated the San Francisco R Number at .97 and the California R Number at .74. Note: Only one model in the ensemble shows SF above 1 (and one model shows it at .33).

For the month of August, DPH recorded 1,064 new infections and 4 new covid-related deaths among residents in nursing homes (“skilled nursing facilities). DPH doesn’t say whether Laguna Honda is included.

In Single Room Occupancy hotels (“SROs”), DPH recorded 88 new infections and 3 new covid-related deaths.

Among the City’s unhoused residents, DPH recorded 90 new infections and 1 new covid-related death for the month of August.

Follow Us

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.

Join the Conversation


  1. Thanks for linking to that excellent study about COVID and immunocompromised individuals.

    China now has a higher average life expectancy than the United States, now that our average life expectancy has plunged due to COVID. I don’t know why that’s not a bigger story.

    All dentists, all medical providers should be wearing N95s or equivalent. It’s completely reasonable to expect *medical facilities* to be places of zero transmission.

    votes. Sign in to vote
  2. I had a dentist appointment scheduled this week, but it was cancelled because my dentist got COVID. The staff wanted to reschedule my appointment in short order, but I told them I would wait a week or two before rescheduling to see if COVID is running around the office. It never ends…

    votes. Sign in to vote
  3. Perhaps, it’s time to stop focusing on these numbers? They may have been useful at one time, but it seems like they don’t serve any useful purpose except to stoke fear and anxiety now:
    For the never-ending-restrictions crowd, it’s great, but for the other 99% of us, not so much. To that crowd, (I ask again and expect the usual silence in reply):
    “When should the restrictions (or any specific restriction) end? What metric do you need to see at what level to feel safe again?”
    I have sympathy for you up to a point; there’s still a lot of scare mongering from official sources out there. (In the US, anyhow. Not at all the case in Europe where, presumably everyone is dying and the hospitals are over capacity and morgues are filled, and everyone is permanently disabled, and they don’t care about immune compromised folks etc. ?) And, since you all are currently just waging the (so far) losing battle to reinstate mask mandates, you are not causing TOO much harm for the rest of us, my sympathy extends far. And I am open as ever to being persuaded by folks I disagree with acting in good faith; they might be right. But I mostly hear random stats and insults accompanying an absolutely unflinching certainty in the rightness of their arguments. Sounds more like religion and less like science every day.
    Perhaps you could turn your attention to the severe harms inflicted on school age children by denying them a couple of years of critical development as a substitute for your current obsessions
    or at least balancing the downsides of interventions vs. the upsides:

    votes. Sign in to vote
Leave a comment
Please keep your comments short and civil. Do not leave multiple comments under multiple names on one article. We will zap comments that fail to adhere to these short and very easy-to-follow rules.

Your email address will not be published. Required fields are marked *