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

Infection numbers and positivity rates continue to skyrocket after the holiday reporting delays. Hospitalizations jumped, and R Number models continue to show rapidly increasing transmission.

In addition to a surge in infections, omicron has also resulted in a surge of tweets.

The U.S. Centers for Disease Control has explained its reasoning on isolation including comments on testing which will add to the general confusion. Although there’s been a lot of criticism for the CDC position, here’s one thread in support. And here’s a second opinion from The Daily Show.

One probable reason the CDC declined to advise tests is the country’s ongoing inability to provide adequate, widely available testing. Mission Local has reported on the local situation, but, predictably, it’s worse in other places, and could get much worse before it gets better.

Uncle Joe says vaxxed Americans should be concerned, but not alarmed, about omicon. He’s got a good point. Here and here are two studies which support him.

What Americans should be alarmed about is the tattered patchwork we call public health, and the failures of the Biden Administration to adequately respond to the virus at home and its on going choice to protect patents over people abroad. Fortunately, someone is actually doing something to develop a patent-free vaccine for the world.

Omicron hit theUnited Kingdom before coming to America. How are things going in London? Here’s a long, nuanced thread by the covid reporter from the Financial Times. And in New York City, where the virus has been running rampant, there are signs it may be leveling off.

Vaxxed and unvaxxed can agree we’ve experienced a pandemic of fear over the past 21 months. One doc likens our experience to post-traumatic stress disorder.

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. 4, DPH reports 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. 4, approximately 391,249 residents (55 percent of all residents) have received a COVID-19 booster dose including 76 percent of residents 65 and over, 65 percent for those 50-64, 59 percent for those 35-49 and 45 percent for those 16-34. For information on where to get vaccinated in and around the Mission, visit our Vaccination Page.

On Jan. 1, DPH reports covid hospitalizations jumped to 91, or about 10.4 per 100,000 (based on an 874,000 population), including 15 in ICU. The California Department of Public Health currently reports 114 covid patients in SF hospitals with 23 in ICU. For some perspective, during last winter’s surge, on December 1, 2020, with 185 infections, there were 93 hospitalizations and 26 in ICU. As infections rise among older residents (see below), hospitalizations are likely to keep going up. Note: SFDPH refuses to provide (or is incapable of providing) demographic information about covid patients, how many are in the hospital for covid, and how many are in the hospital for another reason and tested covid positive upon entrance, or the number of vaxxed and unvaxxed covid patients.

The latest report from the federal Department of Health and Human Services shows Zuckerberg San Francisco General Hospital with 11 covid patients and 10 ICU beds available, while across the Mission, CPMC had 3 covid patients and 6 ICU beds available. Of 52 reported covid patients, 37 were at either SFGH or UCSF, with at least 91 ICU beds available among reporting hospitals (which does not include the Veterans Administration). The California DPH currently reports 114 covid patients and  97 ICU beds available in San Francisco.

Note: DPH uses dated population figures for neighborhoods. Between Nov. 1 and Dec. 31, DPH recorded 1162 infections among Mission residents, or 198 infections per 10,000 residents. The high number (highest in the City) may be in part due to continuous testing at 24th Street. Only Sunset/Parkside has over 1000 infections. The Marina continues to have the highest rate, with 280 infections per 10,000 residents, with Mission Bay, Russian Hill, Hayes Valley, FiDi/South Beach, Poterero Hill, Pacific Heights, SOMA, Haight Ashbury, North Beach and Bayview Hunters Point also with rates exceeding 200 per 10,000. During that time frame, Chinatown had the lowest infection rate, 103 per 10,000 residents.

On Dec. 28, the 7-day average of daily new infections recorded in the City was 941 (our new graph hopefully will update soon) or approximately 107.6 new cases per day per 100,000 residents (based on an 874,000 population). The 7-day average infection rate among vaccinated residents was 106.4 per 100,000 vaccinated residents and for unvaccinated residents, 140 per 100,000 unvaccinated residents.

For the month of December, DPH reports 5,640 infections among White SF residents, 37.9 percent of the total, Latinxs, 2,891 infections, 19.4 percent, Asians 3,386 infections, 22,7 percent, Blacks 844 infections, 5.7 percent, Multi-racials 246 infections, 1.7 percent, Pacific Islanders 172 infections, 1.2 percent, and Native Americans had 50 infections, .3 percent of December totals.

Citywide recorded tests are up to a level not seen since last January while positivity rates are at a level not seen since March 2020.

So far for December, DPH reports 11 deaths.

R Number models continue to show rapidly increasing transmission. Covid R Estimation has lowered its San Francisco R Number to a still high 2.0 (no longer the highest in the state) and raised its California R Number at 2.1. The ensemble lowered its average for the  San Francisco R Number to a highly doubtful 1.01, while posting an average California R Number of 1.57. The ensemble says its figures may be off due to holiday reporting delays.

In December, DPH recorded 330 infections among those SF residents 0-4 years old, or 2.2 percent of the December totals so far, 5-11 309 infections, 5.5 percent, 12-17 540 infections, 3.6 percent, 18-20 419 infections, 2.8 percent, 21-24 1,371 infections, 9.2 percent, 25-29 2,883 infections, 19.4 percent, 30-39 4,336 infections, 29.1 percent, 40-49 2,007 infections, 13.9 percent, 50-59 1,362 infections, 9.1 percent, 60-69 691infections, 4.6 percent, 70-79 257 infections, 1.7 percent, and those 80 and above have had 119 recorded infections in December, .8 percent of the total December 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. It really is a shame that the hospitalization data can not be broken down to delineate between folks who have been hospitalized FOR Covid and those who have been infected while in the hospital for other reasons. It is completely plausible, given the transmissibility of Omicron, that entire hospitals tests positive….leading to completely unnecessary mass hysteria and public posturing by all in power. It really is a failure of the US system that these basic details can not or will not be provided for public consumption.

  2. If UCSF’s George Rutherford and Jeanne Noble are correct predicting peak omicron in the ERs and hospitalizations in the next 7 to 10 days, that R value might be closer to accurate as omicron starts running out of fuel and ER visits and hospitalizations lag

    (that’s what I’m telling myself anyway)

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