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

Omicron continues out of control in the city as infections, hospitalizations and positivity rates remain sky high. R Number models show no decrease in transmission rates.

Pooper-good news: Wastewater and sewage samples in Boston and Santa Clara show omicron decreasing in those areas. In San Francisco, it might not be necessary to descend into the sewers. Imagine what we might learn if we could bribe DPW to clean our sidewalks and streets.

This morning, there are other signs of an omicron retreat in U.S. cities where it appeared early on.

Whereas The Vaccine has been shown to help prevent serious illness among individuals, it has proved to be less effective in preventing infection. The standard two-dose regimen apparently does little to stop the spread, and there’s no data on the effectiveness of the booster. Nonetheless, both Pfizer and Moderna have begun manufacturing the fourth shot, which is now being tried out in the Pfizer lab, also known as Israel. Without data, the FDA has already approved a fourth shot for elderly and immunocompromised individuals. Once the companies have hit their production quotas, will a fourth shot for all become standard protocol?

The World Health Organization called for more research on whether The Vaccine should get updated to protect against infection, a point which was made during yesterday’s UCSF Grand Rounds. Will a fourth shot provide more than temporary protection against infection? Will it improve the response of the immune system (the B cells and the T cells)? The European Union’s head of Vaccine Strategy says, “While use of additional boosters can be part of contingency plans, repeated vaccinations within short intervals would not represent a sustainable long-term strategy,” adding his concern that that a strategy of giving boosters every four months hypothetically poses the risk of overloading people’s immune systems and leading to fatigue in the population.

No sooner than I went off on San Francisco’s Department of Public Health for having disappeared during the omicron crisis, officials showed up. They wrung their hands, reiterated some wishful thinking, and offered very little in terms of action. Vaccination requirements for mega events at Chase Center have been in effect for months, and Chase has previously announced boosters (third shots) would be required starting in February. If The Vaccine doesn’t work against infection, what will it do to stop the spread among thousands of cheering, screaming (many maskless) fans?

With respect to the isolation guidance offered, I am consulting with a panel of Talmudic scholars to interpret all the contradictory and confusing guidance on isolation we’ve gotten recently. It may take a while. In any case, I believe DPH did not address the real problem for many.

Congrats to the San Francisco Unified School District, which promised teachers to provide masks, tests and to otherwise improve safety at schools.

Omicron, even if mild for individuals, is already having a major impact on hospitals, and especially healthcare workers. Requiring nurses to work if they test positive but are asymptomatic, or use their own sick days and vacation time if they’re too sick to work, seems incredibly stupid, cynical and dangerous. Is it any wonder that nurses around the country are striking?

In addition to providing as safe a workplace as possible, there is one obvious solution to staff shortages at hospitals.

Scroll down for today’s covid numbers.

The U.S. Centers for Disease Control data used for the chart lags behind the data supplied from the San Francisco Department of Public Health. As of Jan. 13, DPH reports 773,212 residents, more than 88 percent of all San Francisco residents have received one dose, and over 81 percent have received two. For residents 5 and older, DPH reports the figures rise above 90 percent and above 85 percent and over 90 percent of those 65 and older have received two doses. SFDPH reports that as of Jan. 13, approximately 426,715 residents (60 percent of all residents) have received a COVID-19 booster dose.

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

Hospitalizations took another big jump since the last report and ICU patients have begun to increase. On Jan. 10, DPH reports there were 203 covid hospitalizations, or about 23.2 hospitalizations per 100,000 residents (based on an 874,000 population). The California Department of Public Health currently reports 228 covid patients in SF hospitals with 41 in ICU. We’ve heard a lot about hospitals potentially getting overwhelmed, but nothing about a Plan B if this happens.

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 15 covid patients and 4 ICU beds available. Of 112 reported covid patients, 65 were at either SFGH or UCSF, with at least 76 ICU beds available among reporting hospitals (which does not include the Veterans Administration). The California DPH currently reports 67 ICU beds available in San Francisco.

Note: DPH uses dated population figures for neighborhoods. Between Nov. 10 and Jan. 9, DPH recorded 1941 infections among Mission residents or 330 infections per 10,000 residents. The high number (highest in the City) may be in part due to continuous testing at 24th Street (thanks to LTF and UCSF). Sunset/Parkside,Bayview Hunters Point, Excelsior, West of Twin Peaks and Outer Richmond also report over 1000 infections. Bayview Hunters Point has the highest rate, with 467 infections per 10,000 residents. Of 38 neighborhoods, 17 have rates over 300 per 10,000 residents.

DPH says “the California Department of Public Health (CDPH) is experiencing issues with their disease reporting system. As a result locally reported daily and total COVID case counts are currently an underestimate.” On Jan. 6, the 7-day average of daily new infections recorded in the City was 1630 or approximately 186.3 new infections per day per 100,000 residents (based on an 874,000 population). The 7-day average infection rate among vaccinated residents was 170.6 per 100,000 vaccinated residents and for unvaccinated residents, 329.8 per 100,000 unvaccinated residents. Remember, there are about 9 times as many vaccinated as unvaccinated SF residents. Note: Don’t get too excited about the little hook at the end of the graph as it reflects even “less reliable” numbers.

Infection rates among racial and ethnic groups (based on the group’s population) as of Jan. 9, show Pacific Islanders with a rate of 3,425 per 10,000 Pacific Islander residents, Latinxs 1,848, Native American 1,554, Blacks 1,368, Whites 670, and Asians 559 infections per 10,000 Asian residents.

Between Nov. 10 and Jan 9, the Mission posted a positivity rate of 10.5 percent. Treasure Island had the highest, posting 13.8 percent. Of 38 neighborhoods, 14 had rates at or in excess of 10.5 percent. Seacliff had a rate of 5.6 percent, lowest in the City.

Covid R Estimation slightly raised its San Francisco R Number to 1.90 the same as its California R Number. The ensemble raised its average for the  San Francisco R Number to 1.17 (although still heavily influenced by one model estimating SF at .89, other models are showing small drops) and posting an average California R Number of 1.34.

Despite very big changes in infection numbers reported among population groups since Delta, this chart oddly remains mostly static. These are the only demographic numbers DPH reports on covid-related deaths.

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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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