Covid-19 Tracker: The unpredictable virus

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

Hospitalizations fluctuate but have fallen well off their spring peak. Recorded infections and positivity rates are both down. R Number models show local transmission below 1, and current wastewater monitoring remains somewhat flat, just below where it was two weeks ago, also well off this spring’s peak.

Sorry for the delay. Unexpected traveling (airports, planes and a packed funeral — quite the covid challenge). There will be no Covid Tracker next week.

The U.S. Centers for Disease Control and Prevention have loosened their covid guidelines, particularly with respect to schools and contact quarantine. Is the CDC “following the science”? Not everyone thinks so.

It’s far from clear how long the virus remains infectious.

According to the CDC, the positivity rate of self-administered rapid antigen tests tracked well with PCR tests throughout the omicron and subvariant waves.

Although numbers are falling, the virus has been rapidly circulating around San Francisco for months. Is this what “endemic” means? Who knows? How about persistent?

Unlike public officials and most media, the virus is not suffering from “pandemic fatigue.” It continues to evolve, and evolve fast.

To date, Congress has not approved new funding for vaccines or treatments. Nonetheless, the Biden administration plans to roll out a new booster this fall. No vaccine has been authorized and, other than targeting variants now in the rearview mirror, many questions remain: When will it be ready, for what population groups, how much protection will be provided, and for how long?

Though new variants will probably be more transmissible and more adept at escaping the vaccine protections, the extent of viral shedding is unknown, and there is no reason to expect the fall variants to be any less severe.

Researchers at the Massachusetts Institute of Technology have created new tests to help determine antibody levels. Hoping to cash in, they have filed for a patent and are looking for business deals before applying for approval.

There seems to be more movement on the Long Covid front, with more than 20 drug trials now ongoing, though “many are too small or lack the necessary control groups to give clear results.”

A new study looks at the impact of brain infections of covid patients. Cognitive rehab may help elders dealing with covid-related brain fog.

Have you heard of the new “novel virus, the “langya henipavrirus” (whatever happened to simple Greek?)? It may, or may not, be the next global pandemic. No one knows.

Scroll down for today’s covid numbers.

On August 8, the San Francisco Department of Health reports there were 117 covid hospitalizations, exactly where it was last week, or about 13.5 covid hospitalizations per 100,000 residents (based on an 874,000 population). ICU patients remained stable, below 20. The California Department of Public Health reports as of August 9, there were 121 covid patients in SF hospitals with 14 patients in ICU. For the week ending August 9, the CDC says there were 99 new admissions, an increase of 1.1 percent decrease from the previous week. The CDC won’t say (like state and local officials) which hospitals are included in their survey. DPH does not report on admissions, nor does it report on covid positive patients who were hospitalized “for” covid, and those hospitalized “with” covid.

The latest report from the U.S. Department of Health and Human Services shows Zuckerberg San Francisco General Hospital with 17 covid patients and 9 ICU beds available, while across the Mission, CPMC had 12 covid patients and 6 ICU beds available. Of 133 reported covid patients in the City, 54 were at either SFGH or UCSF. Usually, the two hospitals generally account for 50 percent or more of the covid patients. This has not held during the recent wave. At least 87 ICU beds are available among reporting hospitals (which do not include the Veterans Administration or Laguna Honda). The California DPH reports that as of August 9, SF had 93 ICU beds available. Whether those beds are actually “staffed” neither the city nor the state will say.

Between June 7 and August 6, DPH recorded 1,588 new infections among Mission residents (a decrease of 15 percent from last week) or 224 new infections per 10,000 residents. During that period, Bayview Hunters Point had the highest rate at 391 new infections per 10,000 residents. Of 38 neighborhoods, 4 had rates above 300 per 10,000 residents, all in the east and southeast sectors of the City. Lakeshore had a rate of 168 per 100,000 residents

DPH reports on August 4, the 7-day average of daily new infections recorded in the City dropped to 244 or approximately 27.9 new infections per 100,000 residents (based on an 874,000 population), a decrease of approximately 21 percent from last week. According to DPH, the 7-day average infection rate among vaccinated residents was 25.9 per 100,000 “fully vaccinated” residents and 69.6 per 100,000 unvaccinated residents. It is unclear whether “fully vaccinated” means 2, 3 or 4 doses. The latest report from the New York Times says the 7-day average on August 11 was 233, a 37 percent decrease over the past two weeks. Wastewater monitoring shows covid in the City’s southeast sewers slightly falling from two weeks ago. This report comes from the Stanford model. Apparently, California residents are still suffering from constipation as the state says its reports are delayed due to “supply chain” issues.

For the month of July, Asians recorded 3,132 infections or 29.4 percent of the month’s total; Whites 2,248 infections or 21.1 percent; Latinxs 1,541 or 14.4 percent, Blacks 540 infections or 5.1 percent; Pacific Islanders 60 infections or .6 percent, Multi-racials 59 infections or .6 percent and Native Americans 16 infections or .2 percent of July’s recorded infections.

On August 4, the 7-day rolling Citywide average positivity rate dropped 15 percent during the past week to 11 percent, while average daily testing dropped approximately 6.3 percent. Between June 7 and August 6, the Mission had a positivity rate of 13 percent, the same as our last report.

Between August 1 and August 11, 1523 San Francisco residents received their first or second shot. Vaccination rates in SF show virtually no change for the past two or three 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 August 9, DPH estimates 63 percent of Mission residents have received at least one booster. Note: Over 90 percent of residents in Bayview Hunters Point have been vaccinated and 66 percent have at least one booster. Less than 50 percent of Lakeshore residents have been vaccinated and 34 percent have received at least one booster.

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

Fourteen new covid-related deaths have been reported over the past week, bringing the total since the beginning of the year to 266. So far, 28 have been recorded in July and 0 in August. Between March and the end of July there have been 114 covid-related deaths. During the same period in 2020, there were 70. DPH won’t say 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 make R Number estimates very uncertain. Covid R Estimation on August 5 estimated the San Francisco R Number at .84 while its estimate for the California R Number on August 9 was .91. The ensemble, as of August 8, estimated the San Francisco R Number at .91 and the California R Number at .93. Note: All models in the ensemble show SF below 1.

For the month of July San Franciscans aged 0-4 recorded 467 infections or 4.4 percent of the month’s total; 5-11 419 infections or 3.9 percent; 12-17 319 infections or 3 percent; 18-20 219 infections or 2.1 percent; 21-24 506 infections or 4.7 percent; 25-29 1,050 infections or 9.8 percent; 30-39 2,201 infections or 20.6 percent; 40-49 1,601 infections or 15 percent; 50-59 1,538 infections or 14.4 percent; 60-69 1,217 infections or 11.4 percent; 70-79 692 infections or 6.5 percent; and those San Franciscans aged 80 and above recorded 430 infections or 4 percent. During the month of July the proportion of older infected residents (60+) was higher than it has been during most of the pandemic.