Covid (@UCSF) Chronicles, Day 665
I haven’t done a SF update for a week – it’s a good time to catch up. Any impact of holiday gatherings should now be baked in, we all know scores of people with Covid, & hospitals are getting overwhelmed. So is SF’s high vax rate helping? (1/20)
Let’s look first at data @UCSFHospitals before turning to SF. 10d ago, we saw a mini-plateau & I wondered if SF's “wall of immunity” would prevent a hospital surge. Answer: no such luck.
Today, we have 75 Covid patients at UCSF Medical Center, up from 22 one month ago. (2/20)
Issue of how many of them have “incidental Covid” (testing pos. but there for another reason) has become hot; @SaraMurrayMD, @RhiannonCroci & I wrote about this @washingtonpost.… Using our method (combines diagnosis & use of antiviral Remdesivir)…(3/20) looks like ~36% (27/75) are here for "incidental Covid." The chart (thanks to our awesome data science folks for these dashboards!) shows the breakdown by floor vs. ICU – the “for” vs. “with" Covid fractions about the same (2/3 for, 1/3 with) in both settings. (4/20)
For first time I’ve seen anywhere, they’ve done crosswalk between vax status & for/with. Outside the ICU, our 2/3-1/3 ratio holds for both vaxxed & unvaxxed pts. Note that there's a fair # (23) of fully vaxxed patients here FOR Covid (23); some are likely immunosuppressed. (5/20)
But look at ICU #'s on chart: 11 ICU patients; only 1 is fully vaxxed & here FOR Covid (I don’t know the case – perhaps a Delta patient from pre-Omicron days?). So fully vaxxed can get desperately ill, but it’s quite unusual. Whereas 6/11 ICUs are unvaxxed & here FOR Covid.(6/20)
A useful reminder from ER doc @Craig_A_Spencer @nytimes that even "incidental" Covid cases take more work & time, and some patients will deteriorate in hospital. Per Craig, it’s not quite March 2020 (vax plus “milder” helps), but it’s still awful. (7/20)…
My fave piece of @UCSF data: symptomatic/asymptomatic test + rates. Symptomatic: eye-popping 46%. Asymptomatic: even more astounding 12%, ergo ~1-in-8 UCSF patients w/ NO Covid symptoms are testing +. Reasonable to extrapolate this to the population; meaning that >1-in-10…(8/20)
... folk in SF are prob. infected. (FYI, this % @UCSF was 0.4% [1-in-250] 1 mth ago.
Remember, this means that if you go into an indoor space w/ 15 people, it’s almost certain that someone is breathing out live virus. Can’t think of better argument for N95 or equivalent.(9/20)
And SF is not an outlier in this regard. Here, virologist Trevor Bedford @trvrb estimates that, in fact, ~1% of Americans are being infected each day and 5-10% of people in U.S. are currently actively infected. These are mind-blowing figures. (10/20)
Bottom line: @UCSFhospitals has lots of Covid patients, at a time that hundreds of our docs & nurses are out with Covid. The stress level is very, very high.
And keep in mind that our Covid hospital numbers are low compared with places like NYC, Miami, & Houston.(11/20)
Let’s turn to the city of SF; it mostly mirrors @UCSF trends. Big omicron question for SF was if >80% full vax rate would protect from big surge. Answer is no, at least regarding cases: now averaging 1386 cases/day in SF, up from 84 a month ago – a 16-fold increase. Crazy.(12/20)
And remember, these are reported cases; all those cases confirmed by home tests (incl. my son’s) aren't included, likely thousands more daily. It's a wild amount of virus.
In late December, it looked like cases were surging but hospitalizations were not. As with UCSF,… (13/20)
…we haven't dodged the hospitalization bullet in SF.
Hospitalizations in city aren’t overwhelming, but they’ve certainly shot up: now 155. ICU patients, though, remain relatively low (29) – undoubtedly the impact of our >80% vaccine rate. (14/20)
Note that while cases in SF are more than 3x higher than last winter’s surge, hospitalizations are ~40% lower, & ICUs >50% lower. That’s the vaunted case-hospitalization-ICU dissociation – the combined effect of Omicron's "mildness" & vaccination. (15/20)
And it's not just SF: see this piece by @DLeonhardt in @nytimes, looking at vaxxed vs unvaxxed outcomes in NYC & Seattle, the latter resembling SF in vax rates & overall approach to Covid. Even with lots of breakthru cases, vax still matters hugely.(16/20)…
The lesson from these data? Even in highly vaxxed places, Omicron’s infectiousness & partial immune escape have led to caseloads that are so jaw-dropping and expectation-defying that @CDCgov is unable to model the next few weeks reliably (below). (17/20)…
But S. Africa & London curves, & possibly-plateauing NYC curve are reassuring. In U.S., we may be 1-2 weeks from Peak Omicron. Of course, the threat doesn’t end that day; risk stays high until we descend the mountain, which’ll take several weeks. (18/20)…
Notwithstanding Omicron’s “milder” profile, Omi still causes lots of serious cases & hospitalizations, & the majority of the latter are still for Covid-related complications. By now it’s a familiar math equation: 50-70% milder x 5-10 times more cases = a lot of badness. (19/20)
But “mildness” & high vax rates DO lead to fewer ICU pts, which should translate into fewer deaths. Expect worse in less vaxxed towns.
Across U.S., there’s nothing I see in data that alters my projection that an awful January will lead to a good Feb. Till then, stay safe.(20/20)

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More from @Bob_Wachter

8 Jan
I’ve been tweeting about Covid for nearly 2 years. But this week it became personal when my 28-year-old younger son got it.
With his permission, I’ll describe his experience & how I approached his situation, given the realities of life and the rapidly changing evidence.(1/25)
My son, who lives in SF, is generally healthy but overweight, placing him in a moderately high-risk group. He’s been quite careful since March 2020, & has received 3 Modernas. He used to wear a 2-ply cloth mask; since Omi, he’s switched to an KN95 (with my “encouragement”).(2/25)
He works in downtown SF in customer service, so he has a lot of people contact. I’ve worried that he’d get it from work, or from the bus. But that’s not how it happened. Instead, one of the few friends he sometimes sees in person – another fully vaxxed young person who… (3/25)
Read 25 tweets
31 Dec 21
A brief San Francisco update. As always, SF is a key test case since it's so highly vaxxed (81% of people w/ ≥ 2 shots) & most still follow public health recs (incl. masking). Nevertheless, we see skyrocketing cases; hospitalizations more modest but starting to tick up.(1/12)
Let's look @UCSFHospitals first. Test positivity rates continue to climb, though if you squint you might see a hint of a plateau. As always, my key # is the asymptomatic test pos. rate, now 7d avg of 8.27% – implying 1 in 12 people in SF without Covid symptoms have Covid.(2/12) Image
With that prevalence, you have to assume that everybody you come in contact with might have Covid.(Cities experiencing greater surges probably have even higher asymptomatic %.)
This is why I haven't been too critical of the CDC's 5d isolation guideline – the risk of...(3/12)
Read 12 tweets
29 Dec 21
My latest tweets have mostly been bad news, which saddens me, particularly during holiday season.
Today I’ll take you to my Happy Place, with some thoughts on why we could be in good shape – and maybe even great shape – in 6-8 weeks.

A 🧵(1/24)
Let’s start by agreeing that the current state is awful, and likely to get worse. Case rates are skyrocketing (Fig L), hospitalizations are going up fast (but not nearly as fast as cases; R), it feels like everybody's infected or recently exposed, & there are shortages of…(2/24) ImageImage
…key tools, including testing (both PCR & antigen) & therapies (mostly Sotrovimab [the monoclonal Ab that works vs. Omicron] & Paxlovid, the Pfizer oral antiviral with outstanding efficacy in preventing serious illness in outpatients with Covid).(3/24)…
Read 24 tweets
28 Dec 21
Today's update on SF/@UCSF numbers. Bottom line –huge increase in cases & test positivity. Hospitalizations still pretty benign (though early signs of an uptick). Most remarkable stat is our asymptomatic test positivity rate (ATPR) @UCSFHospitals – now ~7%, or ~1-in-14.(1/16)
You'll recall that ATPR is fraction of pts getting care (hospitalization, procedure) @UCSFHospitals who we test for Covid routinely, even tho they have no symptoms. I use this as a rough approximation of the prevalence of Covid in Bay Area people who have no Covid symptoms.(2/16)
The ATPR was as low as 1/500 (0.2%) a few mths ago. Today, our 7d ATPR is 6.9%, and last 3 days it's ~8% (going up fast).
If its 8%, it means 1-in-12 people in SF who feel fine would test positive for Covid.(Not all would be in their infectious period, but most would be.)(3/16)
Read 16 tweets
28 Dec 21
There are so many Omicron #'s floating around, it’s overwhelming. In today’s 🧵,I’ll try to simplify things with a couple of rules-of-thumb that I’ve found useful. I’ll be interested in hearing if this helps or confuses more – it might hinge on whether you’re a chess fan.(1/25)
Chess? We’ll get to that in a bit. For several of the big picture Omicron issues, my go-to is not a chess board, but rather the Number 2.
Why 2? Because many of Omicron’s key variables are either just about twice, or approximately half, of what they were with Delta.(2/25)
Two key variables for which “2” is a useful rule-of-thumb:
a) How much more infectious is Omicron than Delta? About twice. (And Delta was about twice as infectious as Alpha was.)
b) How much less serious (measured by hospitalizations) is Omicron than Delta? About half. (3/25)
Read 25 tweets
24 Dec 21
Covid (@UCSF) Chronicles, Day 647 (!)
I haven’t done a San Francisco update for a while. Now seems like a good time, since SF – the most vaxxed big city in the U.S. – may offer lessons for the nation about how an Omicron surge is influenced by high vax (& masking) rates.(1/25)
Bottom line is that some normally-scary numbers (surging cases & test positivity %) haven’t led to big jumps in hospitalizations. The big question: is it still too early to tell, or is this the hoped-for case–hospitalization dissociation at play? I’m going with the latter.(2/25)
Let’s start w/ SF before focusing @UCSFHospitals. Clearly SF is seeing a big surge in cases: ~250 cases per day (7-day daily average is 161; this lags due to the steep uptick), up from avg of 45/d in late Nov. (Figure). So about a 5-fold rise in recent weeks. Concerning. (3/25)
Read 27 tweets

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