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

Hospitalizations, recorded infections, positivity rates and R Number models continue to rise. Wastewater covid is down from 2 weeks ago, but trending upwards.

Covid-19 Tracker will not publish next week.

Despite initial glowing reports, sales and use of the Pfizer covid treatment, Paxlovid, have been underwhelming. Last week, I linked to a controversial study which purported to show the benefits of Paxlovid in preventing “long covid”. Another new (preprint, not peer reviewed) study purports to show only a modest rebound effect from Paxlovid. Will it help sales?

This Washington Post editorial summarizes the conventional wisdom on the state of the current boosters with relation to the current variant “soup.”

What does variant soup look like?

Covid-related deaths are at near pandemic lows and trending lower. But are those deaths “of” covid or “with” covid. This has been an ongoing problem with hospitalization and death toll figures, a problem which may not go away soon.

After cutting the request for further covid spending, the Biden administration, while saying next-generation vaccines and treatments are “urgent,” has cut the ask one more time. Good luck. Biden promised bipartisanship, and we got it. The Senate voted to end the Covid-19 Emergency Declaration, with 13 Democrats joining the chorus.

Sick of the school masking debate? This new study won’t help.

The lack of money has already shown up in disappearing public health workers.

Giving up on covid has meant that hosptals have generally escaped without any meaningful change. Health costs are rising, and hospitals continue to play a driving role.

Think you can get disability benefits if you contract “long covid?” Think again.

Scroll down for today’s covid numbers.

Hospitalizations are up from last week. On November 12, the San Francisco Department of Public Health reported 53 covid hospitalizations, or about 6.1 covid hospitalizations per 100,000 residents (based on an 874,000 population). This represents an 8.1 percent increase from last week. ICU patients remain in single digits. The California Department of Public Health reports on November 10, there were 44 covid patients in SF hospitals (ten less than last week) with 3 patients in ICU. For the week ending November 13, the CDC says there were 48 new covid admissions, a 6.3 percent decrease from the previous week. In addition, the CDC says 2.9 percent of staffed ICU beds were occupied by confirmed covid patients (a .3 percent decline from the previous week). According to the New York Times, on November 15, the daily average of covid hospitalizations was 65, an 14 percent rise 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 9 covid patients and 6 ICU beds available, while across the Mission, CPMC had 8 covid patients and 5 ICU beds available. Of 64 reported covid patients in the City, 19 were at either SFGH or UCSF. At least 78 ICU beds are available among reporting hospitals (not including the Veterans Administration or Laguna Honda). The California DPH reports that as of November 10, SF had 100 ICU beds available. Whether those beds are actually “staffed” neither source will say.

Between September 12 and November 11, DPH recorded 325 new infections among Mission residents (a rise of 2.5 percent from last report) or 55 new infections per 10,000 residents. Sunset/Parkside was the only neighborhood in the City with more. During that period, Mission Bay had the highest rate at 84 new infections per 10,000 residents. Of 38 neighborhoods, 8 had rates at or above 70 per 10,000 residents, 7 in the east and southeast sectors of the City.

DPH reports on November 8 the 7-day average of daily new infections recorded in the City increased to 104 or approximately 11.6 new infections per 100,000 residents (based on an 874,000 population), a 22.4 percent rise from last week. On November 8, the Times said the 7-day average was 83. On November 15, the Times says the 7-day average 139, a 122 percent increase over the past two weeks. The CDC says that for the week ending November 9, the daily average was 110.5, a 67.4 percent rise from the previous week.

Wastewater monitoring of the City’s Southeast sewers shows variants BA.4, BA.5 and BA. 2.75 down from two weeks ago, but beginning to trend upwards. This report, from the Stanford model, does not yet include BQ.1 or any of the other omicron offspirng. If you have a source for wastewater monitoring that includes the BQ and XBB variants, please let me know.

For the month of October, DPH reports Asians recorded 669 infections or 27.7 percent of the month’s cases; Whites 609 infections or 25.2 percent; Latinxs 251 infections or 10.4 percent; Blacks 112 infections or 4.6 percent; Pacific Islanders 24 infections or 1 percent; Multi-racials 22 infections or .9 percent; and Native Americans recorded 2 infections or .1 percent of the month’s total cases.

On November 8, DPH says the 7-day rolling Citywide average positivity rate rose to 6.1 percent, a 15.1 percent rise over last week. CADPH reports a 5.6 percent weekly average on November 10. The daily average testing numbers remain below 2,000.

Between September 12 and November 11, DPH reports Mission residents had a 4.7 percent positivity rate based on 7,710 tests, the most tests in the City. Of 38 neighborhoods, 16 had positivity rates 6 percent and higher; with 10 in the east and southeast sectors.

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 while 17 percent have received two. As of November 15, 24 percent of SF residents have received the new bivalent booster.

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

Two new covid-related deaths have been reported since our last report, bringing the total since the beginning of the year to 373. 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 only 22 of all SF covid-related deaths are known to have had no underlying conditions, or comorbidities.

The lack of reliable infection numbers makes R Number estimates very uncertain. Covid R Estimation on November 3 estimated the San Francisco R Number at 1.2 while its estimate for the California R Number on November 14 was .94. The ensemble, on November 9, estimated the San Francisco R Number at 1.27 and the California R Number at 1.3.

The case (recorded infection) fatality rate in SF for this year so far is .37. The infection fatality rate should be much lower. Before The Vaccine, the SF case fatality rate was around 1.5.

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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. Mark is fine. Covid never sleeps, but Mark does need to every now and again.


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  1. gah, it seems our fav wastewater site has trimmed their data so the 26 week view is no longer available, but that view made it so much easier to figure out what short term trends were, likely noise or likely signal

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  2. Yes, please wear masks.

    B.Q.1 & B.Q.1.1 are now the dominant variants in the U.S., and they’re both resistant to all monoclonal antibody treatments (Evusheld and hospital treatments). High-risk people are screwed.

    That’s really not good news (in spite of the chipper headline):

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  3. Wear. Masks. 😷

    It goes without saying that 1 – each and every mandate should be restored, 2 – there needs to be a bigger push to get folks vaxxed & boosted, because 3 – the pandemic is not over. Don’t say it’s “just like the flu” when it kills over 3x as many people, and the flu (with RSV) have already put us in a “tripledemic” winter surge.

    Get vaxxed 💉
    Get boosted 💉
    Social distance ↔️

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