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

Recorded infections, positivity rates and hospitalizations remained mostly flat. Wastewater has also been somewhat flat (above where it was two weeks ago) and R Number models show a rising local transmission.

Has the virus decided to forego its fall vacation (worried about inflation)? We’ll see.

No change is an exaggeration. There are always some changes, but fundamental change, serious change? In 2019, the U.S. was rated number one in pandemic preparedness. In hindsight, this report could not have been more wrong. One of the hopes of the covid crisis was that governments at all levels would be forced to deal with the inadequacies of the nation’s (and the City’s) public healthcare infrastructure. As Ed Yong points out in his latest installment, this hasn’t happened, and it appears that it won’t.

Don’t worry, say the celebrity experts who pad their careers with preprints and tweets, we’ve got it under control.

Should we blame Putin? Trump?The Proud Boys? There’s enough blame to go around, but don’t leave the Best and Brightest (2.0) off the list. For example, Gov. Gavin Newsom’s new healthcare inititative is heavy on the propaganda and light on the healthcare, especially for those who need it most.

Whatever the “experts” and officials say, the real “no worries” message has been clear as the fog. Which is why only about 4 percent of those eligible in the country have gotten the latest booster. San Francisco’s Department of Public Health hasn’t even bothered to keep track yet.

Here is a summary of the current situation by Dr. Peter Hotez, a vaccine scientist who has helped create a patent-free vaccine available to the world. Note #5 where he says “Not enough Americans are aware that protection vs. hospitalization declines 4-5 months after your last booster . . .” Really? I knew that protection against infection wanes, but also against hospitalization? How much? If that’s true, don’t we need three, or at least two, boosters each year?

And where is the San Francisco DPH? What changes have been made on a local level so we don’t have to shut down the City for a year when the next pandemic comes?

Is another world possible? In contrast to the U.S., Japan has actually controlled the virus without lockdowns and mandates. “Avoiding the Three C’s” is a simple, clear, intelligent and non-polarizing message. No wonder the Centers for Disease Control and Prevention never adopted it.

The World Heath Organization has called for a determined effort to “tackle” long covid. Good luck. If we only knew what “long covid” is and what causes it. Here is an accompanying article showing the impact of some of the associated symptoms.

A preprint claims vaccination reduces the risk of long covid (whatever it is). For how long?

Another preprint shows the effectiveness of a booster in preventing infection and hospitalization during last year’s omicron surge.

A “determined effort” to deal with long covid would be welcome, but what about medium covid, which might be even more dangerous? Oh, well; no worries.

The “no worries” policy wonks usually accompany their ideas for doing nothing with a very pious pronouncement of “protecting the elderly and the infirm.” Although the life-enhancing properties of propaganda have yet to be studied, here is what we can expect. More Zoomcasts on the way.

Finally, the White House is known as a place where good ideas go to die. Recently there was a forum on indoor air quality (ventilation), one of the many things that could be done to improve the current situation and prepare for future pandemics. Here is a long tweet thread covering the discussion, which seemed to have been very intelligent. Whether any meaningful policies will come from it is unlikely. Though no one attacks public officials for providing clean air in schools, it’s a choice that requires more political will than seems available at the White House and SF City Hall.

Scroll down for today’s covid numbers.

Hospitalizations are slightly down from last week. On October 8, the San Francisco Department of Public Health reported 47 covid hospitalizations, or about 5.3 covid hospitalizations per 100,000 residents (based on an 874,000 population). This represents an 4.4 percent rise from our last report. ICU patients remained single digits. The California Department of Public Health reports on October 6, there were 60 covid patients in SF hospitals (the same as last report) with 7 patients in ICU. For the week ending October 9, the CDC says there were 47 new covid admissions, a 7.4 percent decrease from the previous week. In addition, the CDC says 2.8 percent of staffed ICU beds were occupied by confirmed covid patients (a .1 percent drop from the previous week). According to the New York Times, on October 11, the daily average of covid hospitalizations was 61, an 8 percent drop from two weeks ago. Neither the CDC, NYT or the CaDPH say which hospitals are included in their survey. Should the brain fog ever lift at SFDPH, we may find out 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 4 covid patients and 11 ICU beds available, while across the Mission, CPMC had 5 covid patients and 5 ICU beds available. Of 61 reported covid patients in the City, 27 were at either SFGH or UCSF. At least 76 ICU beds are available among reporting hospitals (not including the Veterans Administration or Laguna Honda). The California DPH reports that as of October 9, SF had 77 ICU beds available. Whether those beds are actually “staffed” neither the city nor the state will say.

Between August 8 and October 7, DPH recorded 419 new infections among Mission residents (a drop of 37 percent from last report) or 71 new infections per 10,000 residents. During that period, Mission Bay had the highest rate at 95 new infections per 10,000 residents. Of 38 neighborhoods, 17 had rates at or above 70 per 10,000 residents, 10 in the east and southeast sectors of the City.

DPH reports on October 4 the 7-day average of daily new infections recorded in the City rose to 94 or approximately 10.8 new infections per 100,000 residents (based on an 874,000 population). Since September 17, recorded infection numbers have fluctuated in the high 80s and low 90s. On October 11, the New York Times says the 7-day average was 35, a 14 percent increase over the past two weeks. The CDC says that for the week ending October10, the daily average was 57, a 69 percent drop from the last week.

Wastewater monitoring of the City’s Southeast sewers shows variants BA.4 and BA.5 slightly above where they were two weeks ago, and BA.2.75 still showing only traces. This report comes from the Stanford model.

During the month of September, DPH has recorded 752 infections among San Francisco’s Asian population or 26.1 percent of the recorded infections in September; Whites 675 infections or 23.4 percent; Latinxs 361 infections or 12.5 percent; Blacks 129infections or 4.5 percent; Multi-racials 58 infections or 2 percent; Pacific Islanders 12 infections or .4 percent; and Native Americans recorded 3 infections or .1 percent of the recorded infections in September.

On October 4, the 7-day rolling Citywide average positivity rate rose 7.4 percent from the last report to 5.8 percent. CADPH reports a 5.3 percent weekly average on October 9. The New York Times reports a daily average 5.3 percent rate on October 11.

Between August 8 and October 7, DPH reports Mission residents had a 6.1 percent positivity rate based on 8,509 tests.

Between October 4 and October 11, DPH reports 225 San Francisco residents received their first or second shot. Vaccination rates in SF show little change since January: 90 percent of all San Franciscans have received one shot, 86 percent two shots and 64 percent have received at least one booster. Only 17 percent of the City’s population has received a second booster. DPH has no information on who has received the new booster.

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

Five new covid-related deaths have been reported since our last report, bringing the total since the beginning of the year to 351. In August 50 covid-related deaths were reported. To those who like to say covid-related deaths are no longer an issue, please note August had the 6th highest monthly figure for the entire pandemic. 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. It gets worse as DPH reports (you guessed it) only 21 of the deaths are known to have had no underlying conditions, or comorbidities. Note: the demographics of covid-related deaths in California have changed significantly this year.

The lack of reliable infection numbers makes R Number estimates very uncertain. Covid R Estimation on September 29 estimated the San Francisco R Number at 1.15 while its estimate for the California R Number on October 7 was .75. The ensemble, on October 9, estimated the San Francisco R Number at 1.27 and the California R Number at 1.07. Three of nine estimates in the ensemble show SF over 1.

For the month of September, DPH reports those San Franciscans 0-4 recorded 90 infections, or 3.1 percent of the month’s total; 5-11 71 infections or 2.5 percent; 12-17 54 infections or 1.9 percent; 18-20 54 infections or 1.9 percent; 21-24 117 infections or 4.1 percent; 25-29 254 infections or 8.8 percent; 30-39 586 infections or 20.3 percent; 40-49 426 infections or 14.8 percent; 50-59 416 infections or 14.4 percent; 60-69 411 infections or 14.3 percent; 70-79 240 infections or 8.3 percent, and those San Franciscans aged 80 and above recorded 159 infections or 5.5 percent of recorded infections in September. Since April, during he current surge, the proportion of recorded infecions among those residents 60 and older has gone from 13.3 percent to 28.1 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. > What changes have been made on a local level so we don’t have to shut down the City for a year when the next pandemic comes?

    Well, we have parklets now

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    1. Or, we could just not “shut down” the city. Even if SAn Franciscans and Angelinos might still have the appetite for that, almost nowhere else will folks sign on for shutdowns. To put it mildly, lockdowns are not viewed by the vast majority of folks in this country as having been a smashing success. The well-to-do laptoppers might be up for another round but no one else is.

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      1. I think you’re right, but there are other things that could be done before ever thinking of a lockdown, and that would be ensuring plenty of ventilation, especially in smaller stores and restaurants.

        The city could be helping businesses, either through speedy permitting or subsidies or both to do the remodeling necessary to improve ventilation throughout

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  2. These data are not accurate AND I don’t see how they inform any real-world decisions of any significance. The hospitalization numbers are forever compromised by not differentiating between folks who are so sick with COVID they have to go to the hospital and folks who go to the hospital for some other reason, take a routine COVID test as they must do when they enter, and test positive. If you test everyone, of course you will find many positives for a virus as infectious as this one.

    This coronavirus is now among the other 4 or 5 that circulate among humans and will circulate for millennia, infecting us all multiple times. I don’t like it any more than anyone else but it’s a fact and we must make decisions/ plans accordingly.

    Mark, why don’t you show the age and comorbidity breakdown for COVID as you do for race, ethnicity etc.? Here it is: and

    I find that info reassuring as a parent, knowing that our kids are very unlikely to suffer harms from the virus. Yet, they suffer the most harm from restrictions like masking and, most catastrophically of all, the denial of in person schooling.
    For those advocating restrictions, can you please say when those restrictions should end? It’s one thing to say “Oh no, people are getting sick and dying! Look at the wastewater! Burning Man is going to cause a huge spike in 2 weeks, etc.!” Quite another to identify what the end game is for any particular course of action, much less way the harms of an intervention against the benefits.

    As usual, I will stipulate that pointing out these facts and proposing to use them to craft a reasonable and effective public health strategy means that I (and the other 99% of us) are unvirtuous, murdering idiots who want everyone to die. No need for any replies to point that out again. Please just articulate your plan, please.

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