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

Hospitalizations, recorded infections and positivity rates are up, while R Number models are mixed and wastewater monitoring is down.

Does “endemicity” mean out of control? Are we now faced with multiple covids, more unpredictable and less subject to the clinical “tools’ that have been developed so far? The variants are coming fast and furious, and the time between waves has considerably shortened. The new omicron variants have taken over in California, and have been shown to be not only more contagious but also capable of causing reinfection.

Although some estimate that about 40 percent of covid infections are asymptomatic, and most result in minor cold or flu symptoms, covid is not the common cold. Nor are the worst outcomes limited to elders. In 2021, covid was the leading cause of death in Americans ages 45 to 54. No one can guess what’s coming down the road from repeated infection.

And how much do we really know about the virus? Here’s a thread on research suggesting covid is a vascular rather than a lung disease, which can explain some symptoms and long covid. It is interesting, and indicative that not everyone has thrown up their hands and gone to the beach. Disclaimer: I cannot vouch for the doctor who posted this thread, nor can I comment on the validity of the argument. I found the thread on the Twitter feed of University of California, San Francisco doc Kim Rhoads, which I regularly consult.

Covid has been an unmitigated disaster for most of us. But for a precious few, it’s a bonanza. If you wonder who won (and keeps winning) the “fight” against covid, go no further. Not only did Pfizer double its profits last year, but it has also raised the price of boosters, which we pay for (via taxes). No, this inflation is not a function of anything as exotically complex as a “supply chain issue,” or the Shanghai lockdown, but just simple greed.

YouTube video

As the article suggests, high transmission of a quickly and endlessly evolving virus means ever-changing vaccines. Remember when it took three to five years to create a vaccine? A lot of that time was taken up with various levels of clinical trials to assure effectiveness and safety. The first round of the vaccine was achieved mainly through speeding up trials, and some of the early claims (remember 95 percent protection against infection?) have now been proven “misleading”. Where is that famous “wall” of “herd immunity?”

Now the company wants to do away with trials altogether. Why bother? Will the fall vaccine actually work against the dominant variants now, or then? Who knows?

Here’s the latest on vaccine efficacy with respect to hospitalization.

The increasing transmission also helps sell what appear to be solutions. Unfortunately, Paxlovid, has run into trouble, with more variants capable of dodging the drug. Although little is known of the value Paxlovid adds to vaccination, Pfizer earlier this month halted a large trial of the drug in standard-risk covid patients because it was failing to show statistically significant protection against death or hospitalization.

Without mandates and lockdowns, Japan has done fairly well in limiting the virus spread. Why? This article from the New York Times suggests that the Japanese are mindless conformists (much like they portray the Chinese). Really? Maybe ordinary Japanese people understand that avoiding crowded spaces, close contact, closed rooms, getting vaccinated and wearing a good mask might be the simplest and common sense protection, for the individual and society.

The story of masks in America has been an endless source of friction and fascination. Instead of producing and distributing high-quality, comfortable and reusable masks, the federal government, hospitals and nursing homes continue to prefer cheap disposable imports. Why? The environmental and economic idiocy of this approach gets more painful when considering elastomeric respirators.

Scroll down for today’s covid numbers.

Over the past week, hospitalizations rose 9 percent (representing 10 more patients). On July 2, DPH reports there were 118 covid hospitalizations, or about 13.5 covid hospitalizations per 100,000 residents (based on an 874,000 population). ICU patients had climbed to 22, but have fallen back to 14. The California Department of Public Health currently reports 117 covid patients in SF hospitals with 19 patients in ICU.

The latest report from the federal Department of Health and Human Services shows Zuckerberg San Francisco General Hospital with 14 covid patients and 10 ICU beds available, while across the Mission, CPMC had 13 covid patients and 5 ICU beds available. Of 125 reported covid patients in the City, 53 were at either SFGH or UCSF, with at least 71 ICU beds available among reporting hospitals (which does not include the Veterans Administration or Laguna Honda). The California DPH reports that as of July 5, SF had 109 ICU beds available. Whether those beds are actually “staffed” neither the City nor the State will say.

Between April 30 and June 29, DPH recorded 1,455 new infections among Mission residents (an increase of 4.8 percent from last week) or 248 new infections per 10,000 residents. During that period, Mission Bay continued with the highest rate at 426 new infections per 10,000 residents. Although Mission Bay was the only neighborhood with a rate above 400, 14 others had rates above 300 per 10,000 residents, with 11 in the east and southeast sectors of the City. In a surprise, Glen Park posted a rate of 303 per 100,000 residents (perhaps the City will pay more attention to transmission now).

DPH reports on June 28, the 7-day average of daily new infections recorded in the City rose to 439 or approximately 50.2 new infections per 100,000 residents (based on an 874,000 population), an increase of approximately 4.5 percent. According to DPH, the 7-day average infection rate among vaccinated residents was 47.1 per 100,000 “fully vaccinated” residents and 103.7 per 100,000 unvaccinated residents. It is unclear whether “fully vaccinated” means 2, 3 or 4 doses. According to the New York Times, the 7-day average number on June 28 was 492. The latest report from the Times says the 7-day average on July 5 was 501, an 8 percent increase over the past two weeks. As noted above, wastewater monitoring shows a decrease in the southeast sewers. This report comes from the Stanford model. The state is still reporting “staffing problems.”

In June, Asians recorded 3,935 new infections or 31.3 percent of the month’s cases; Whites 2,821 infections or 22.4 percent; Latinxs 1,596 infections or 12.7 percent; Blacks 603 infections or 4.8 percent; Multi-racials 88 infections or 0.7 percent; Pacific Islanders 63 infections or 0.5 percent; and Native Americans had 27 recorded infections in June or 0.2 percent of the June totals.

On June 28, the 7-day rolling Citywide average positivity rate rose 7.7 percent during the past week to 15.4 percent, while average daily testing dropped approximately 1.6 percent. Over the past two months, the Mission has had a positivity rate of 11.6 percent. In June, Native Americans had a positivity rate of 16.7 percent, Asians 15.1 percent, Latinxs 14.1 percent, Multi-racials 13.6 percent, Blacks 12.6 percent, Pacific Islanders 12.6 percent, and Whites had a positivity rate of 11.4 percent.

Vaccination rates in SF show virtually no change from last week. 90 percent of all San Franciscans have received one shot, 84 percent two shots and 74 percent have received at least one 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, bringing the total since the beginning of the year to 220. DPH won’t say how many were vaccinated. Nor does it provide information on the race, ethnicity or socio-economic status of those who have recently died. 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, incredibly 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 number data makes R Number estimates very uncertain. Covid R Estimation on June 28 estimated the San Francisco R Number at .85 while its estimate for the California R Number on July 4 was .89. The ensemble, as of July 3, estimated the San Francisco R Number at 1.13 and its California R Number at .97. Note: Models are mixed on SF.

For the month of June, DPH reports those San Franciscans aged 0-4 recorded 573 infections or 4.3 percent of the month’s total; 5-11 479 infections or 3.6 percent; 12-17 379 infections or 2.9 percent; 18-20 265 infections or 2 percent; 21-24 713 infections or 5.4 percent; 25-29 1,458 infections or 11 percent; 30-39 3,111 infections or 23.4 percent; 40-49 2,038 infections or 15.4 percent; 50-59 1,830 infections or 13.8 percent; 60-69 1,325 infections or 10 percent; 70-79 656 infections or 4.9 percent; and those San Franciscans 80 and above recorded 438 infections or 3.3 percent of all infections for the month of June.

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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. You neglected to mention that in 2021 Covid was the 2nd leading cause of death for people aged 35-44. This is an important fact in the face of Covid denialism in that age group
    (For people aged from 1-24 the leading cause of death was guns; it used to be car accidents).

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  2. Not a COVID denier or anti-vaxxer. But, is the death, hospitalization data distinguishing between “for COVID” vs. “With COVID” anywhere? I know everyone who enters the hospital gets a COVID test; is that always considered a hospitalization due to COVID even it it’s not the reason they went to the hospital? If that person then dies, is that a COVID death? I am not interested in minimizing or maximizing the problem with this dangerous pathogen. Just want the right data to make the right risk assessment. Thanks, Mark.

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    1. You are quite right Kid. The issue of “for’ or “with” covid is one of the many things DPH can’t or won’t tell us about hospitalization. Other jurisdictions, bigger ones like New York, do it with no problem. They also are able to report demographic information and vax information. Not a good look for SF. Suggests that DPH is out of touch with hospitals (and as hospitalizations became more of a key indicator, less information has been provided), or a shocking level of incompetence. You and anyone interested may want write to Alison Hawkes at DPH She’s their PR go to person. After raising this issue a couple times, I have not heard back from her for months (which is not unusual for DPH).

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