Covid-19 Tracker: The fog thickens

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

Recorded infections either took a big jump or declined, depending on whose numbers you believe. Wastewater monitoring in the Southeast sewers show a sharp and sudden rise in variants BA.4 and BA.5 from two weeks ago, but still not much of variant BA.2.75. R Number models are all over the place. Hospitalization and positivity rates are generally down.

Covid Tracker will not publish next week.

The recorded infection (case) numbers, having been down, took a big jump this week, according to San Francisco’s Department of Public Health. But wait. DPH revised its recent numbers, so what looks like up may be really down. Last week, DPH reported a daily average of 44 infections. But today, they say the average number was 106. A fairly big discrepancy.

The new numbers are completely out of line with the New York Times, U.S. Centers for Disease Control and Prevention, and the California Department of Public Health (see below). In any case, as we know, they don’t represent the true number of local infections, most of which go unrecorded.

To make matters even more inscrutable, the new jump in DPH numbers correlates with the spike in wastewater detection. Go figure.

UPDATE: SFDPH has now reported a CADPH computer glitch which affected the numbers for September. Revisions have been made and the the CADPH numbers now correlate with San Francisco. Numbers for the New York Times and CDC remain the same.

Up or down, nothing characterizes the first 30 months of the pandemic more than unreliable numbers, faulty communication and generalized uncertainty.

So, who’s to say this group of celebrity experts is wrong when they say covid is under control? As long as the hospitals don’t have to alter their business plan, apparently all is good to go. Of course, the transmission problem remains unaddressed.

Does the virus think it’s under control? Hard to know what the virus thinks, but from observed behavior, the virus is not only up to its old tricks, now it’s old tricks on steroids, or convergent evolution. What is convergent Omicron RBD evolution? As the preprint begins: “Continuous evolution of Omicron has led to numerous subvariants that exhibit growth advantage over BA.5. Such rapid and simultaneous emergence of variants with enormous advantages is unprecedented.”

An example is the emergence of the BA.2.75.2 variant, which appears to be on the move. Not only does it evade The Vaccine, it evades all but one of the currently available antibody treatments. Still in its “preliminary stage,” it has shown, like its cousin, BQ 1.1, to be capable of rapid (exponential?) growth. So far, we haven’t seen much in our sewers.

How covid manages to evolve so rapidly is only one of at least five mysteries surrounding the virus.

CDC director Rochelle Walensky has been telling anyone who will listen that it is critical that public health institutions restore and regain public trust. Good idea, Doc. But it doesn’t help when you publicly promote individual risk management for the public while you recommend decidedly public interventions to protect your children (and those of Czar Jha).

After reading that, I wondered how San Francisco public schools are doing with ventilation. I asked both DPH and the San Francisco Unified School District. To my surprise, I haven’t received a reply.

My review of DPH’s public materials yielded a general leaflet put out by California’s DPH. The school district website was more interesting. A year ago, SFUSD announced the purchase and distribution of portable air filters. Whether these devices were distributed is uncertain. As is whether they have had any effect. Or if any more permanent upgrade is planned. There is no ventilation dashboard like in Newton, Mass.

And if that isn’t enough uncertainty for you, how about playing this fall’s game of “When should I get a booster?” Spoiler alert: it depends. Seriously, you don’t want to be suboptimal.

Does the experience of the pandemic make you feel like your body is just another commodity, to be bought and sold and traded on the futures market? Good news: You’re not alone. Private equity firms agree, and are increasing their bets on the healthcare system to deliver perceived profits.

Like arms dealers, they are cashing in on death. Even so-called nonprofit chain hospitals can’t resist squeezing every last dime out of sickness, especially from those with the least resources. Here’s what handing elder care over to private equity achieved in Britain (and that was before the Marvelous Ms. Truss took over).

With that in mind, it seems appropriate to note the human body may be more than a profit center, and end with Dr. Rafael Campo’s poem “Primary Care.” Dr. Campo apparently thinks poetry has a healing effect on illness. He has no data to back up his theory, but in these days of uncertainty, who’s to say he’s wrong?

Scroll down for today’s covid numbers.

Hospitalizations are slightly down from last week. On September 24, the San Francisco Department of Public Health reported 45 covid hospitalizations, or about 5.1 covid hospitalizations per 100,000 residents (based on an 874,000 population). This represents an 8 percent drop from last week. ICU patients remained singe digits. The California Department of Public Health reports on September 22, that there were 60 covid patients in SF hospitals (a 3 percent drop) with 11 patients in ICU. For the week ending September 25, the CDC says there were 48 new covid admissions, a 25 percent increase from the previous week. According to the New York Times, on September 27, the daily average of covid hospitalizations was 67, a 13 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 6 covid patients and 7 ICU beds available, while across the Mission, CPMC had 10 covid patients and 5 ICU beds available. Of 67 reported covid patients in the City, 25 were at either SFGH or UCSF. At least 71 ICU beds are available among reporting hospitals (not including the Veterans Administration or Laguna Honda). The California DPH reports that as of September 22, SF had 67 ICU beds available. Whether those beds are actually “staffed” neither the city nor the state will say.

Between July 25 and September 23, DPH recorded 610 new infections among Mission residents (a drop of 5.2 percent from last week) or 98 new infections per 10,000 residents. During that period, Portola had the highest rate at 159 new infections per 10,000 residents. Of 38 neighborhoods, 13 had rates at or above 100 per 10,000 residents, 11 in the east and southeast sectors of the City.

DPH reports on September 20, the 7-day average of daily new infections recorded in the City rose (or dropped) to 87 or approximately 10 new infections per 100,000 residents (based on an 874,000 population). Under revised numbers (due to a CADPH computer glitch), it represents a decrease of approximately 18 percent from last week. According to DPH, the 7-day average infection rate among vaccinated residents was 9.2 per 100,000 “fully vaccinated” residents and 25.4 per 100,000 unvaccinated residents. It is unclear whether “fully vaccinated” means 2, 3 or 4 doses. The New York Times said the daily average on September 20 was 51. On September 28, the Times says the 7-day average was 31, a 54 percent decrease over the past two weeks. . The CDC says that for the week ending September 27, the daily average was 24, a 47.7 percent drop from the last week.

Wastewater monitoring shows variants BA.4 and BA.5 jumping straight up over the week to the level they were at last month (and BA.2.75 showing traces) in Southeast sewers. This report comes from the Stanford model.

As of September 23, DPH has recorded 578 infections among San Francisco’s Asian population or 26.2 percent of the recorded infections so far in September; Whites 503 infections or 22.8 percent; Latinxs 282 infections or 12.8 percent; Blacks 110 infections or 5 percent; Multi-racials 48 infections or 2.2 percent; Pacific Islanders 10 infections or .5 percent; and Native Americans have recorded 3 infections or .1 percent of the recorded infections this month.

On September 20, the 7-day rolling Citywide average positivity rate dropped 11.5 percent from last week to 5.4 percent. CADPH reports a 4.1 percent weekly average on September 22. The New York Times reports a daily average 4 percent rate on September 27.

The big jump in recorded infections over the week may have reflected increased testing. But last week, average daily testing dropped approximately 2.5 percent approaching all-time pandemic lows. Between July 25 and September 23, the Mission had a positivity rate of 7.8 percent (based on 9,047 tests) an 8.2 percent drop from last week’s report. Portola had the highest rate at 12.1 percent. As of September 23, Native Americans have a positivity rate of 9 percent so far for the month; Asians 6.2 percent; Latinxs 5.7 percent; Whites 5.2 percent; Pacific Islanders 4.3 percent; Blacks 4.1 percent and Multi-racials have a positivity rate of 3 percent so far in September. All groups show significant drops from August.

Between September 20 and September 27, DPH reports 343 San Francisco residents received their first or second shot; 175 got a booster. 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.

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 346. 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 15 estimated the San Francisco R Number at .54 while its estimate for the California R Number on September 23 was .77. The ensemble, on September 15, estimated the San Francisco R Number at .8 and on September 23 had the California R Number at .83. As of September 25, one model in the ensemble shows SF 1.03 (it is the only model reporting).

As of September 23, DPH has recorded 4 infections and 2 deaths so far this month in nursing homes (“skilled nursing facilities”).

In Single Room Occupancy hotels (SROs), 37 infections and 0 deaths have been recorded.

Among the City’s unhoused population, 27 infections have been recorded. According to DPH, only 14 homeless residents have died a covid-related death since March 2020.

So far in September, 52.6 percent of the recorded infections are female, 45.6 percent are male, .1 percent are trans female, 0 percent are trans male.