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

Hospitalizations, positivity rates and recorded infections continue in steep decline. R Number models show San Francisco in a range from .65 to 1.28, with an average still among the highest in the state.

The rise in political and social ambiguity so far in the 21st century has been driven largely by digital technology, the “war on terror,” and politicians like former Presidents Barack Obama and Donald Trump. The pandemic added a whole new personal layer and the “post-omicron” surge doesn’t suggest more certain days ahead.

Although some think “it’s over,” covid may have other ideas. Last year, the virus outwitted our slow, stumbling public health and political authorities, who relied mainly on miracles. By the end of the year, the spiky microbe had infected and killed more people in 2021 than in 2020. And there’s no indication that it has met its match. Here’s an explanation for why omicron is so contagious, and here are some possible scenarios for 2022. Instead of taking a victory lap, shouldn’t San Francisco’s Department of Public Health begin preparations for the future now?

In late 2020, a group of right-wing libertartian doctors put out “The Great Barrington Declaration,” calling for no public health interventions to control the disease, save for unspecified measures “to protect the most vulnerable.” The post-omicron call to relax or eliminate public health interventions is no longer confined to the fringe. But now there are at least specific ways proposed to protect the vulnerable. While focusing on expensive drugs that are in short supply, necessary measures, such as global vaccination, improved ventilation/filtration of indoor air, and support for isolation/recovery, are not included.

A few billionaires would be able to fund global vaccination, but so far no-one has stood up. Here’s what the global vaccination picture looks like.

The Vaccine is great, but not if people don’t get vaccinated. Vaccination uptake among the elderly, especially in the U.S., has been surprisingly low.

On its own, The Vaccine doesn’t provide lasting protection against infection. Boosters have helped, but for many, the boosters have already begun to wane.

Even in heavily masked places like Hong Kong, the virus can rage out of control.

While most commentators focus on protecting the elderly and immunocompromised, little is said about protecting low-income residents and racial minorities. It’s difficult when Google algorithms don’t approve of health equity advocates discussing “racism.”

What protections will be proposed when the Public Health Emergency lapses, which will kick 15 million off of Medicaid?

Or when jails use imprisoned minorities for drug experiments?

Or when the CDC tells you to contact your health care provider right away after testing positive, but you don’t have a “health care provider?”

Scroll down for today’s covid numbers.

As of Feb. 15, DPH reports 782,298 residents have been vaccinated, more than 89 percent of all San Francisco residents have received one dose, and over 83 percent have received two. For residents 5 and older, DPH reports the figures rise above 90 percent and above 86 percent while for those 65 and older over 90 percent have received two doses. SFDPH reports that as of Feb. 15, approximately 466,109 SF residents (65 percent of all residents, 82 percent of residents 65 and older) have received a COVID-19 booster dose.

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

On Feb. 12, DPH reports there were 159 covid hospitalizations, or about 18.1 covid hospitalizations per 100,000 residents (based on an 874,000 population). Today, the California Department of Public Health reports 167 covid patients in SF hospitals and 40 ICU patients. Unlike it’s counterparts in New York, Seattle — even Los Angeles — DPH cannot report how many covid patients are vaxxed and how many unvaxxed since September 1. This failure, both simple and spectacular, does not bode well for the future of public health in San Francisco.

The latest report from the federal Department of Health and Human Services shows Zuckerberg San Francisco General Hospital with 25 covid patients and 6 ICU beds available, while across the Mission, CPMC had 20 covid patients and 2 ICU beds available. Of 225 reported covid patients, 96 were at either SFGH or UCSF, with at least 67 ICU beds available among reporting hospitals (which does not include the Veterans Administration). The California DPH currently reports 91 ICU beds available in San Francisco. Note: The Government Accountability Office (GAO) has issued a scathing report for sustained public health crisis failures at HHS. The failures cited include “collecting and analyzing data to inform decisionmaking.”

Omicron revived SF’s standard pandemic pattern, hitting the lower socioeconomic sectors of the City the hardest. Between Dec. 13 and Feb. 11, DPH recorded 4439 new infections among Mission residents or 755 new infections per 10,000 residents. Bayview Hunters Point had the highest number of recorded new infections (4610) with a rate of 1216 new infections per 10,000 residents. Of 38 neighborhoods, 14 had rates above 700 per 10,000 residents, 13 in the east and southeast sectors of the City. Seacliff had the lowest rate with 379 new infections per 10,000 residents and Lakeshore, the only neighborhood in the City with a vaccination rate below 50 percent, had the second-lowest rate at 432 new infections per 10,000 residents.

DPH reports on Feb. 8, the 7-day average of daily new infections recorded in the City was 339 (finally lower than last winter’s peak) or approximately 38.7 new infections per day per 100,000 residents (based on an 874,000 population). According to DPH, the 7-day average infection rate among vaccinated residents was 33.2 per 100,000 “fully vaccinated” residents and  92.5 per 100,000 unvaccinated residents. It is unclear whether “fully vaccinated” includes boosters or the infection rate among those vaccinated with 2 doses.

In January, DPH reports Asians had  25.5 percent of the month’s total, up from 19.7 percent in December; Latinxs had 21.6 percent, up from 18.4 percent, Whites had 20 percent, down from 33.4 percent; Blacks 5.8 percent, up from 4.7 percent, Multi-racials had 1 percent, down from 1.2 percent, Pacific Islanders had 1 percent, the same, and Native Americans had .2 percent of January’s total, down from .3 percent in December.

In January, DPH reports San Francisco’s Latinx residents had a positivity rate of 22.4 percent, up from 10.7 percent in December; Pacific Islanders 22.1 percent, up from 12 percent; Blacks 20.2 percent, up from 9.2 percent; Multi-racials 17.9 percent, up from 9.2 percent; Native American 17.8 percent, up from 10.2 percent; Asians 14 percent, up from 6.6 percent; and White San Franciscans had a January positivity rate of 12 percent, up from 8.4 percent in December.

Six new covid-related deaths recorded in January and seven in February have raised the local covid death toll to 68 since the beginning of the year. Probably most are related to omicron. DPH won’t say how many were vaxxed and how many unvaxxed. 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 it is unknown whether or not 34.5 percent of the deaths had one or more underlying conditions. As of Feb. 9, DPH continues to report only 21 of the 761 deaths are known to have had no underlying conditions, or comorbidities.

Covid R Estimation has kept its San Francisco R Number estimate at 1.07, and its California R Number at .52. The ensemble lowered its average San Francisco R Number to .83 and raised its average California R Number to .66. Of all models, the SF R Number ranges from .65 to 1.28.

During the course of the pandemic, San Franciscans aged 0-20 had 0 covid-related deaths, or 0 percent of the total; 21-29 3 deaths, or .4 percent; 30-39 12 deaths, or 1.6 percent; 40-49 29 deaths, or 3.8 percent; 50-59 54 deaths or 7.1 percent; 60-69 113 deaths or 14.8 percent; 70-79 141 deaths or 18.5 percent; and those San Franciscans 80 and older suffered 409 deaths or 53.7 percent of all San Franciscan covid-related deaths, even though they had just 2.3 percent of the City’s recorded infections.

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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. Obama’s administration did set up a system for dealing with pandemics…that’s Trump’s administration dismantled. I don’t know if Obama can be blamed for ambiguity. Could you expand on that thought? I thought it was a millennial thing. I ignored class differences but maybe that was just a privilege that came with being born white. So I couldn’t say when the usual social significators like education and speaking clearly and not slouching became irrelevant and you can be a big ugly stupid boring slob if you’re a big spender loaded with cash- then you never run out of people to tell you have beautiful and funny and interesting. Like how David Koch is mister personality. He’s the pretty one, I’ve been told.

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    1. oops David Koch died I forgot about that. I shouldn’t talk bad about the dead.

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  2. I’m seeing lots of unsupported assertions in this article that seem irrelevant, such as: “The rise in political and social ambiguity so far in the 21st century has been driven largely by digital technology, the “war on terror” and politicians like Obama and Trump.” Makes you wonder . . .

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  3. The reason the SF and San Mateo R numbers are so high is due to a data anomaly, not a reflection of an actual increase in cases. If you look at the graphs on the source sites, you’ll see that on Feb 9, 4k new cases were reported for SF compared with a (then) 7-day daily average of 524 cases. Meanwhile, no cases were reported for Feb 10.

    This is because they follow the California DPH data feed. There was an “anomaly” for Feb 9 and 10 due to some sort of correction, likely delayed cases reported. NYTime’s tracker, which isn’t paywalled, has these dates specifically marked for this anomaly.

    Case rates on either side of Feb 9 and 10 continue to show a trend of it leveling off a little, then resuming a downward path. You can confirm these spikes independently on the CA DPH dashboard for SF and San Mateo counties, and see the NYTime’s tracker for SF and San Mateo marking the days in question as anomalies and not factoring them into their averages. Both counties’ individual case dashboard don’t show the spike, as it only existed at the state level.

    So unless the anomaly is accounted for in the R estimate model (and it clearly isn’t now), it will appear significantly higher than it actually is. Of course, all of this is without at-home tests reported, so the accuracy of the case reporting data is pretty subjective to begin with.

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    1. > There was an “anomaly” for Feb 9 and 10 due to some sort of correction, likely delayed cases reported. NYTime’s tracker, which isn’t paywalled, has these dates specifically marked for this anomaly.

      I believe the anomaly was clearing some huge backlog that then got pinned to Feb 9

      Tonight’s NYTimes number is 178 cases reported today. If I read their chart right, you have to back to December 17th to get a lower number of cases (148 were reported that day).

      Bob Wachter and others often use 10 cases/100K as their metric for easing various precautions. Tonight now we’re at about 22.5, or twice that, ah, but yesterday 36x! So if things continue like this, we really are in very good shape.

      Alas, iirc, the NYTimes data has weekly patterns and we can expect a large number tomorrow, followed by a Friday much like today’s and then the weekend blackout

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  4. “On its own, The Vaccine doesn’t provide lasting protection against infection”

    That statement is outrageous misinformation. The Covid vaccines are incredibly effective and extremely safe. And the article to which you linked (from The Atlantic, that esteemed epidemiology journal) contradicts your misinformation. Form the Article: “With widespread vaccination, many of us will still be exposed, maybe even temporarily colonized, but it won’t often be a big deal. Most of the time, we might not even notice.”

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