Covid-19 Tracker: Not over yet

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

After a week of reporting record lows, R Number models today show a new increase in transmission rates, as positivity rates, hospitalizations and recorded infections continue a downward trend.

As one wave wanes, and before another takes hold, most of the talk has been about what individuals can do to lessen their risk of severe disease. Even mild disease can become severe over time.

Yet, if we’ve learned anything at all over the past two years, it’s that without a credible and functional public health system, what individuals can or can’t do will depend to a large extent on profoundly unequal socio-economic circumstances.

Instead of premature celebrations, agencies like San Francisco’s Department of Public Health, might begin to rebuild an infratructure which has been decimated for over four decades. Here’s a to-do list out of the UK, beginning with indoor ventilation, which can and should be taken up immediately.

Given that all of the waves have been accompanied by hysterical cries of failing hospitals, it would seem imperative to improve the pay and working conditions for hospital and healthcare workers.

It is also critical to improve data and surveillance systems. The UK, even under brain-dead Tories, take public health more seriously than the U.S. and have data and surveillance systems that can provide useful data in real time.

With better systems in place, the next omicron may not come as much of a surprise.

Perhaps the rise in the R Number reflects the appearance of omicron 2.0, aka BA.2 said to be more contagious than the original. South Africa, which first reported the presence of the original omicron, has now been taken over by BA 2. Here is what they are learning.

Omicron BA 2 has begun to gain traction in the U.S.

Not only does the U.S. lag behind the UK when it comes to public health, it’s even further behind Denmark.

In the debates and theories concerning the origins of the virus, Wuhan lab virologist Shi Zhengli has come under scrutiny and criticism. Here is a deeper, more nuanced, report on the woman, focusing on the process and context of her work.

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 Feb. 10, DPH reports 781,293 residents have been vaccinated, more than 89 percent of all San Francisco residents have received one dose, and over 82 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. 10, approximately 463,963 SF residents (64 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.

On Feb. 7, DPH reports there were 197 covid hospitalizations, or about 22.5 hospitalizations per 100,000 residents (based on an 874,000 population). Today, the California Department of Public Health reports 203 covid patients in SF hospitals and 37 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 41 covid patients and 6 ICU beds available, while across the Mission, CPMC had 24 covid patients and 2 ICU beds available. Of 262 reported covid patients, 122 were at either SFGH or UCSF, with at least 54 ICU beds available among reporting hospitals (which does not include the Veterans Administration). The California DPH currently reports 64 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. 8 and Feb. 6, DPH recorded 4355 new infections among Mission residents or 741 new infections per 10,000 residents. Bayview Hunters Point had the highest number of recorded new infections (4531) with a rate of 1195 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 363 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 422 new infections per 10,000 residents.

DPH reports on Feb. 3, the 7-day average of daily new infections recorded in the City was 441 (down from a peak of 2238 on Jan. 9) or approximately 50.4 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 42.2 per 100,000 “fully vaccinated” residents and  124.3 per 100,000 unvaccinated residents. It is unclear whether “fully vaccinated” includes boosters or the infection rate among those vaccinated with 2 doses. The New York Times reports that on Feb. 8, the daily average was 524.

For the month of January, Asians had 11,255 recorded infections or 27.5 percent of the month’s total; Latinxs had 9,669 or 23.7 percent, Whites had 9,301 or 22.8 percent, Blacks 2,797 or 6.8 percent, Multi-racials 574 or 1.4 percent, Pacific Islanders 445 or 1.1 percent, and Native Americans had 106 recorded infections or .3 percent of the month’s total.

The Citywide average positivity rate has taken a big dip, dropping below 10 percent for the first time since December 25.

DPH today reports that of Feb. 6, there have been at least 54 covid-related deaths in the City so far in January and 1 so far recorded in Februrary. 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. 6, DPH continues to report only 21 deaths are known to have had no underlying conditions, or comorbidities.

Having lowered its R Number estimation in San Francisco to all-time pandemic lows, Covid R Estimation has revised its numbers and raised its San Francisco R Number estimate again above 1 to 1.07, and raising its California R Number to .70. The ensemble also raised its average San Francisco R Number to .75 and its average California R Number to .66. All ensemble models, but one, report the SF R Number today below 1.

For the month of January, DPH recorded 106 infections in nursing homes (“skilled nursing facilities”) and 7 covid-related deaths. There have been 3 additional deaths in Februrary so far. In single room occupancy hotels (SROs) DPH reports 976 January infections and 3 covid-related deaths with 0 new deaths yet reported in February. Among those unhoused, DPH reports 524 January infections and 1 new covid-related death. According to DPH, there have only been 1,792 recorded infections and 8 covid-related deaths among the unhoused since the pandemic began.