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

Since we seem to be at a lull between waves, Covid Tracker will publish once a week, on Wednesdays. When the next wave comes, publishing will become more frequent.

Though slowing somewhat in the last couple of days, hospitalizations, positivity rates, and recorded infections have declined over the past week, while R Number models suggest increasing community spread.

Predictably, the Russian invasion of Ukraine knocked covid off the front pages. So why did Russia choose this time to take this dangerous step? I will leave the analysis to geopolitical “experts,” only to note that Russia, like the U.S., has been unable to control the virus. And they didn’t do any better with omicron.

Although the invasion gave Biden something else to talk about during last night’s State of the Union address, he did announce some new covid programs that will now go to their covid-related deaths in Congress (except those that enrich donors).

Most of our compatriots do not think the virus is under control, but the U.S. Centers for Disease Control and Prevention seem content to tolerate high transmission. Along with lowering community risk standards, the CDC, like San Francisco’s Department of Public Health (long ago), decided to abandon contact tracing.

The changes reflect more a political reality than a public health reality, and have come under harsh criticism.

One of the pandemic’s enduring cliches is “having the tools” to fight covid. As UCSF’s Dr. Kim Rhoads noted in March, 2020, we may have the tools “but we are poorly trained in how to comply with public health interventions.” Much of the reason, she said, was that “[m]edicine divorced public health in the 1950s never looking back … “

Instead of relaxing, now would seem to be the time to prepare for the next wave and address the long-term issues that covid exposed. Even the Republican-led Congressional Budget Office agreed that Medicare for All would go a long way toward helping to fix the current mess.

Perhaps chief among those long-term issues is glaring inequality and lack of healthcare for low-income and minority residents. The pandemic has been concentrated among low-income workers, and while officials and the media tout a decline in covid deaths, this is not true across the board, especially among Black people, for whom the disease has become deadlier since The Vaccine became widely available.

Did Biden mention the pandemic’s global dimension (I fell asleep during the speech)? No matter. Behind closed doors, the U.S. and EU continue to protect private profits over public health.

Is it any wonder that some covid celebrity “experts” have already begun to cash in on their 15 minutes of fame? This is one trend I feel confident in predicting will rise.

Scroll down for today’s covid numbers.

In the past week, there has been little change in the vaccination numbers. As of March 1, DPH reports 783,551 residents have been vaccinated, more than 90 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 87 percent while for those 65 and older over 90 percent have received two doses. In addition, as of March 1, approximately 470,136 SF residents (65 percent of all residents, 83 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.

Over the past week, hospitalizations have dropped 28 percent. On Feb. 26, DPH reports there were 89 covid hospitalizations, or about 10.1 covid hospitalizations per 100,000 residents (based on an 874,000 population). ICU patients have dropped below 20 for the first time since Jan. 2. Today, the California Department of Public Health reports 87 covid patients in SF hospitals and 15 ICU patients. DPH has yet to figure out how many covid patients are vaxxed and how many unvaxxed.

The latest report from the federal Department of Health and Human Services shows Zuckerberg San Francisco General Hospital with 20 covid patients and 3 ICU beds available, while across the Mission, CPMC had 15 covid patients and 2 ICU beds available. Of 111 reported covid patients, 64 were at either SFGH or UCSF, with at least 62 ICU beds available among reporting hospitals (which does not include the Veterans Administration). The California DPH currently reports 83 ICU beds available in San Francisco.

Between Dec. 27 and Feb. 25, DPH recorded 4158 new infections among Mission residents or 708 new infections per 10,000 residents. Bayview Hunters Point had the highest number of recorded new infections (4495) with a rate of 1185 new infections per 10,000 residents. Of 38 neighborhoods, 10 had rates above 700 per 10,000 residents, all in the east and southeast sectors of the City. Seacliff had the lowest rate with 335 new infections per 10,000 residents and Lakeshore, the only neighborhood in the City with a vaccination rate below 50 percent, had a rate of 420 new infections per 10,000 residents.

DPH reports on Feb. 22, the 7-day average of daily new infections recorded in the City dropped to 141 or approximately 16.1 new infections per day per 100,000 residents (based on an 874,000 population), representing a 16 percent drop from last week. According to DPH, the 7-day average infection rate among vaccinated residents was 14.4 per 100,000 “fully vaccinated” residents and 35 per 100,000 unvaccinated residents. It is unclear whether “fully vaccinated” means 2 or 3 doses.

As of Feb. 25, DPH reports the pandemic case rate (based on the group’s population) for Pacific Islanders is 4,182 per 10,000 residents; for Latinxs 2,389, for Native Americans 1,854; for Blacks 1,736, for Asians 849; and for White San Franciscans, the pandemic case rate is 827 per 10,000 residents.

The Citywide 7-day rolling average test positivity rate has dropped below 4 percent for the first time since Dec. 17.

Seventeen new covid-related deaths have been reported, bringing the total since the beginning of the year to 95. The omicron death toll seems much higher than delta. DPH won’t say how many were vaxed and how many unvaxxed. Nor does it provide information on the race/ethnicity or socio-economic status of those who have recently died. Note: The highest monthly SF covid-related death total was 165, recorded in January 2021. 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 37 percent of the deaths had one or more underlying conditions. As of Feb. 25, DPH continues to report only 21 of the 789 deaths are known to have had no underlying conditions, or comorbidities.

Covid R Estimation, raised itscurrent estimate of the San Francisco R Number to .62 while mantaining the California R Number at .47. The ensemble, as of Feb. 28, raised its average San Francisco R Number to .73 and slightly raised its average California R Number to .71.

In nursing homes (“skilled nursing facilities”), as of Feb. 25, DPH reports 20 recorded infections for the month of February and 1 new death. In Single Room Occupancy hotels (SROs) so far in February 971 infections and 1 new death have been recorded. Nursing home and SRO deaths comprise approximately 24 percent of the City’s covid-related death toll.

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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. “while R Number models suggest increasing community spread”

    This is absolutely incorrect as the R numbers in this post (and the links) demonstrate. By definition, an R number that is less than 1 indicates a decreasing community spread. Whether it is .99 or .6 simply indicates the rate at which it is decreasing, but both indicate decreasing spread (.6 would indicate a faster decrease).

  2. > Is it any wonder that some covid celebrity “experts” have already begun to cash in on their 15 minutes of fame? This is one trend I feel confident in predicting will rise.

    ——
    from KHN

    > But three weeks after that call, on Nov. 12, Mina announced he was leaving academia to become an executive at eMed, a startup that sells some of the most expensive rapid tests.

    > In doing so, he joins the list of covid authorities who are both frequently quoted experts on national pandemic policy and working for companies profiting from that advice.

    WRT Jay Hancock in KHN’s article the implication here “But three weeks after that call” that Mina said this because he knew that in 3 weeks he would join eMed is illiterate.

    Mina has been calling for rapid testing since as early as February 2020, two years ago. (a search of his twitter for rapid) and actively working on antigen testing since at least March 17, 2020.

    His message has never changed, if Trump or later Biden had listened to him early on, we would have been in a far better situation.

    > “If Dr. Mina is acting in the capacity of a public health expert and he is financially connected to a company that could benefit from his public comments, he is in a financial conflict of interest,” said Sheldon Krimsky, a professor at Tufts University and the author of “Conflicts of Interest in Science.”

    Yes, this is true, but it’s stated as an absolute and as something unusual and with no way to measure or mitigate that COI

    Hell UC and every other school have turned their professorships into a profit centers a fast-track to CEOness as professors spin out tech startups while still working at the schools.

    I don’t know how to stop that, but I’d encourage such professors to leave academia for the duration of their tenure, freeing up academic positions to young phds.

  3. This page is a great resource, but I wonder if you could consider adding the new CDC community level measurements for SF or the entire Bay Area?

    It currently places several Bay Area counties as green (SF, San Mateo, Marin, Alameda, Sonoma, CoCo) and the rest as yellow

    I think links are discouraged here, but googling U.S. COVID-19 Community Levels by County takes me to it

    > Between Dec. 27 and Feb. 25, DPH recorded 4158 new infections among Mission residents or 708 new infections per 10,000 residents. Bayview Hunters Point had the highest number of recorded new infections (4495) with a rate of 1185 new infections per 10,000 residents. Of 38 neighborhoods, 10 had rates above 700 per 10,000 residents, all in the east and southeast sectors of the City. Seacliff had the lowest rate with 335 new infections per 10,000 residents and Lakeshore, the only neighborhood in the City with a vaccination rate below 50 percent, had a rate of 420 new infections per 10,000 residents

    I’m not sure the value of a two month summation of new cases, unless to measure the number affected by Omicron?

    1. The new CDC COVID-19 Community Level metric incorporates hospitalization rates and has received praise from health professionals. The problem is that CDC collection of case data is prone to spikes from overcounting or undercounting. It’s bad in the case of the older CDC Community Transmission Level where a county or state would jump from one level to next higher or lower level one day and return to the previous level the next day. This level jumping is NOT jitter from cases being at the borderline between levels, but is from differences of 50% or more in the case numbers.

      Example in the COVID-19 Community Levels released today – Alameda was in Low (Green) level last week but is in Medium (Yellow) level this week. This is due to CDC showing Alameda with 279 cases per 100,000 in last 7 days in today’s report. In last week’s report, Alameda was at 106 cases per 100,000 in last 7 days. If Alameda’s case rate had actually gone up by 263% in one week, people would be scrambling looking for the outbreak. Using the data from Alameda Health Department shows 77 cases per 100,000 in last 7 days ending Feb 28. I.e., CDC data for Alameda is more than 3 times higher than Alameda county data.

      These kind of up and down spikes in CDC case data have been going on from the beginning. Last year about this time, Newsom cited the CDC map for Community Transmission showing CA as only state in Yellow level when all the other states were in Red level only for the state to end back in Red level the next day. News articles would cite the good news of low case levels only for the case levels to change back the next day. These spikes also cause the occasional wild swings in the Reff numbers shown in the Mission Local Covid-19 Tracker articles. E.g., the big spike in San Mateo Reff number to 1.4 when all other Bay Area counties are going down. An Reff of 1.4 would mean San Mateo is seeing a surge in cases similar to the Omicron spike but San Mateo cases have actually been going down at similar rate as other Bay Area counties.

      I look at the CDC case data for Bay Area counties and it is wrong at least 30% of the time when compared to case data from local county health departments. Wrong here means the data is off by not just a few %, but 50% to 100% or more. I would not trust the CDC case data without comparing it to local data. Several other people have commented on these erroneous spikes in CDC data. One would think CDC would fix this problem but no one there seems to care that politicians and reporters use their bad data to incorrectly point at how well or poorly a state or county is doing.

      The two month summation of new cases is from SFDPH. I have asked why not 1 or 2 week summation of cases which would clearly show increasing or decreasing trends for neighborhoods, but never got an answer. Two month summation obscures trends in the last 1 or 2 weeks unless someone takes the time to take weekly or daily snapshots of the two month summations and run week to week change between snapshots to bring out the recent trend for neighborhoods.