Covid-19 Tracker: A guessing game

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

Over the week, hospitalizations have been somewhat flat. Recorded infections are up (according to San Francisco’s Department of Public Health), as are positivity rates while R Number estimates continue to reflect a great deal of uncertainty.

Is it possible that we know less now about the state of the virus than we did two years ago? As public testing declines and at-home rapid tests increase, it’s increasingly difficult to get a clear sense of community spread in San Francisco. Some say the number of infections may be close to 10 times more than recorded infections.

Covid is on the rise in the Northeast states, but hospitalizations remain flat. No one knows what to expect.

Is this what it means, as some argued last spring, that we’ve entered the “endemic” phase? Hardly.

Recently, covid chronicler Ed Yong gave a talk at Yale University about the national response to the pandemic. The recording hopefully will be available soon. One point worth noting is that in the 1930s, the US spent around 3 cents on the medical expense dollar for public health. In 2019, it was 2 cents on the dollar. As Yong notes, we get what we pay for.

U.S. media and expert celebrities seem to relish kicking China for the Shanghai lockdowns. Apparently the lockdowns are not doing much to curtail the spread of the BA.2 variant, but Chinese scientists must be learning a lot. Buried in this Guardian article is the interesting fact that, at one mass testing site, only about 4 percent of those who tested positive were symptomatic.

Many have argued that hospitalizations are the best metric to use to gauge community spread. Besides the lag in hospitalizations, the lack of reporting and disagreement on standards make this metric much less reliable.

In San Francisco, it’s even worse, as the Department of Public Health withholds hospitalization demographic and vaccination data. Yes, DPH is underfunded and understaffed, but that does not explain, or excuse, its refusal to make this data public.

And, just because you’re not hospitalized doesn’t mean you aren’t seriously ill.

When public health officials withhold data, or give unsubstantiated and contradictory guidance, or view the virus mainly through individual risk assessment, is it any wonder that trust in public health is so low?

How many of us know anything about the state of our individual immune system? Relying on individual risk assessment has profound limitations for individuals, as well as the public.

Congress seems to be waking up to the travesty of private equity ownership of nursing homes. Congratulations. Maybe if Russian President Vladimir Putin owned them, there would be a quicker and more decisive response.

To end on a relatively upbeat note, here’s a thread by a vaccine researcher arguing that repeated vaccination does not lead to exhaustion of T cells.

Scroll down for today’s covid numbers.

Over the past week, hospitalizations have dropped 5 percent. On April 9, DPH reports there were 19 covid hospitalizations, or about 2.2 covid hospitalizations per 100,000 residents (based on an 874,000 population). There have been less than five ICU patients for the week, and the ICU patient population has been in single digits since March 2. On April 13, the California Department of Public Health reports 24 covid patients in SF hospitals and 4 ICU patients.

The latest report from the federal Department of Health and Human Services shows Zuckerberg San Francisco General Hospital with 2 covid patients and 7 ICU beds available, while across the Mission, CPMC had 2 covid patients and 2 ICU beds available. Of 29 reported covid patients, 16 were at either SFGH or UCSF, with at least 79 ICU beds available among reporting hospitals (which does not include the Veterans Administration). The California DPH currently reports 85 ICU beds available in San Francisco.

Between Feb. 7 and April 8, DPH recorded 490 new infections among Mission residents or 83 new infections per 10,000 residents. During that period, Mission Bay had the highest rate at 145 new infections per 10,000 residents. Of 38 neighborhoods, 9 had rates above 100 per 10,000 residents,5 in the east and southeast sectors of the City. Lakeshore, the only neighborhood in the City with fewer than 50 percent of residents vaccinated, had the lowest rate at 61 per 10,000 residents.

DPH reports on April 8, the 7-day average of daily new infections recorded in the City rose to 119 or approximately 13.6 new infections per day per 100,000 residents (based on an 874,000 population), representing a 8.2 percent rise from last week. According to DPH, the 7-day average infection rate among vaccinated residents was 13.1 per 100,000 “fully vaccinated” residents and 21.1 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 number on April 12 was 127 a 2.4 percent rise over the past week. For those interested in wastewater monitoring, see here.

We are working to improve the graph. As of April 12, DPH reports 90 percent of San Francisco’s Pacific Islander population had received “a complete vaccine series” (2 shots); Latinxs 87 percent, Asians 85 percent, Native Americans 84 percent, Blacks 75 percent; and 72 percent of the City’s White population had received two doses of The Vaccine.

Between Feb. 7 and April 8, DPH reports the Mission had a 4.1 percent positivity rate. During that period, Chinatown residents had the highest positivity rate at 5.7 percent and Treasure Island had the lowest at 2.2 percent. Of 38 neighborhoods, 20 had positivity rates in excess of 4 percent, 12 in the east and southeast sectors. Lakeshore, the least vaccinated neighborhood in the City, had a positivity rate of 2.7 percent. It also had one of the lower testing rates.

As of April 12, DPH reports 784,965 San Franciscans have received at least one vaccine dose,  90 percent of all San Francisco residents. This represents an increase of .3 percent. 83 percent have received two. For residents 5 and older, those with one dose remain above 90 percent and those with two remains at 87 percent while for those 65 and older over 90 percent have received two doses. As of April 12, approximately 476,293 SF residents (66 percent of all residents, 84 percent of residents 65 and older) have received a COVID-19 booster dose, an increase of .5 percent over the past week.

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

Three new covid-related deaths, 2 in April, have been reported, bringing the total since the beginning of the year to 157. 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. The omicron death toll seems higher than delta. During and after the delta surge, July-October, the number was 105. 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 ambiguity is heightened when currently DPH continues to report only 21 of the 851 deaths are known to have had no underlying conditions, or comorbidities.

The lack of data has made R Number estimates very uncertain. Covid R Estimation on April 5 estimated the San Francisco R Number at 1.19 while estimating the California R Number at .89 on April 9. The ensemble, as of April 11, estimates the San Francisco R Number at .7 while estimating the California R Number at .85. Two models in the ensemble have SF over 1.

For the week ending April 3, San Franciscans aged 0-4 years old recorded 24 new infections or 2.9 percent of the weekly total; 5-11 28 infections or 3.4 percent, 12-17 23 infections or 2.8 percent, and those San Franciscans 18 and older had 758 infections, or 91 percent of the week’s total.

In March, those 0-4 had 99 recorded infections or 3.4 percent of the monthly total; 5-11 116 infections or 3.9 percent;12-17 79 infections or 2.7 percent; 18-20 53 infections or 1.8 percent; 20-24 224 infections or 7.6 percent; 25-29 510 infections or 17.3 percent; 30-39 780 infections or 26.5 percent; 40-49 423 infections or 14.3 percent; 50-59 274 infections or 9.3 percent; 60-69 213 infections or 7.2 percent; 70-79 101 infections or 3.4 percent; and those San Franciscans 80 and older had 76 recorded infections or 2.6 percent of the month’s total.