outbreak! (ebola, sars, coronavirus, etc)

I've resumed the cautious dining indoors again, always at lunch at a place I know with open doors and windows and whose staff is masked.

Speaking of Chicago, I could have sworn I saw, at least in passing, that despite a supposed vaccine mandate the mayor is letting the unvaxxed school employees slide, at least for now. I mean, you want labor shortage? The Chicago schools can't even afford to lose 1% of their employees. Apparently it's been a mess at the relatively stable local middle schools where I am, with kids just wilding out, lots of fights, pushing back against teachers, all often overseen by old folks brought out of retirement to help but unable to intervene. There was a big fight a couple of weeks ago, and one of these retired teachers supposedly looked to a student and implored, feebly, "do something." So the kid got involved, got punched in the face, and then got suspended for fighting.

And re: violence in Chicago, I never thought shootouts on the highway were a thing, but ... they're sure a thing now.

never thought shootouts on the highway were a thing, but ... they're sure a thing now.

One of the NRA's stupidest and most loathsome pieces of propaganda was their pushing the idea that arming everyone would ensure a more polite society, because everyone would realize that if they made anyone else angry, they'd get shot, and therefore everyone would go out of their way never to anger anyone else. I used to hear this one a lot when I was around gun nuts. It's the kind of 'logical conclusion' that also spawns libertarians who believe the cure for all our social ills is pure, unfettered laissez faire capitalism.

xpost - Yeah, Lightfoot is doing a tremendous job at buckling every time a union pushes back about a mandate. Fwiw, I don't think she's changed anything about the school employees, but pushed back the deadline six weeks (which still sucks, but it's not really changing - they always could opt out by testing 2x per week (which is also still dumb, but hardly unique to Chicago at this point)).

This is what I saw in the Trib

Chicago Public Schools employees who are not fully vaccinated against COVID-19 by Friday’s deadline will still be able to work Monday, but they will have to undergo weekly testing at their schools, the district’s CEO said Wednesday.

“Employees will not be barred from coming (to) work (the) Monday after the Oct. 15 deadline. What we’re going to be doing is just working with them. They will have to get tested, and we’ll have COVID testing at their schools, so that will be convenient for them,” new CPS CEO Pedro Martinez said at a news conference.

“And then we’re going to just work with them to see where they’re at in the vaccination process, what hesitation they might have, what information we can give them. I feel fairly confident, just based on how high our (vaccination) percentage is, that it’s not going to be a big issue in our district.”

Martinez said more than 85% of CPS staff are vaccinated, and employees are submitting proof of vaccination every day.

The similar thing with city workers, I guess, who now have until the end of the year to get vaxxed. Same test-out option, I think, but at their own expense.

j/v/c, yes, it was all jokes.

trust me when i say that i find the dirtbike and quad crew in Philly to be fucking rad, but also terribly noisome and occasionally dangerous. luckily it's most just lots of group rides that move at a rapid clip, no taking over intersections for hours...at least in my neighborhood.

I knew you were joking, hence my E-40 post.

it's kind of striking to look at the graphs of new cases by individual state. Most of the southern states had massive spikes and now have some of the lowest daily rates. Did delta just burn through the population to the point where it's run out of places to go? Is this what herd immunity looks like? I don't expect this will last, but I wasn't expecting such a dramatic turnaround.

it's sort of what it's been doing in most places.

Florida right now has 3.8% test positivity rate and less than 20,000 cases this week. we didn't get there by actually giving a shit or anything.

- Fewer people left to infect

- However small the daily numbers, people get vaccinated every day; the totals rise

- Masks and social distancing observed in major cities

- Some kind of low level herd immunity

I'm fairly skeptical about #2 and #3 being a factor here

It is in Florida's cities, overwhelmingly blue.

https://covidactnow.org/us/florida-fl/?s=24301344

fully vaccinated was 49% august 1 and it's 59% now. fraction with one dose also up by 10% in the same period.

this is a pretty handy chart to see how vaccinations have progressed by state

https://ourworldindata.org/us-states-vaccinations

looks like a uniform 10% climb across southern states during that same period of time, although Florida has been way out ahead overall during that time

See, we'll all put up different charts.

I use the CDC's. Even given Miami-Dade County's propensity to count visiting Latin Americans who give phony addresses, our rates, if you discount them, are above 60-65%

https://covid.cdc.gov/covid-data-tracker/#vaccinations-county-view|Florida|12086|Vaccinations|Administered_Dose1_Pop_Pct

also didn't realize until just now that nearly half the world's population, 3.73 billion people, has had at least one shot. I imagined it was hundreds of millions but not yet billions. That's pretty impressive!

especially given the time frame. got to be some sort of first in human history.

this suggests that human behavior doesn't have too much to do with it.

Worldwide, cases have also dropped more than 30 percent since late August. “This is as good as the world has looked in many months,” Dr. Eric Topol of Scripps Research wrote last week.

These declines are consistent with a pattern that regular readers of this newsletter will recognize: Covid’s mysterious two-month cycle. Since the Covid virus began spreading in late 2019, cases have often surged for about two months — sometimes because of a variant, like Delta — and then declined for about two months.

Epidemiologists do not understand why. Many popular explanations, like seasonality or the ebbs and flows of social distancing, are clearly insufficient, if not wrong. The two-month cycle has occurred during different seasons of the year and occurred even when human behavior was not changing in obvious ways.

The most plausible explanations involve some combination of virus biology and social networks. Perhaps each virus variant is especially likely to infect some people but not others — and once many of the most vulnerable have been exposed, the virus recedes. And perhaps a variant needs about two months to circulate through an average-sized community.

Human behavior does play a role, with people often becoming more careful once caseloads begin to rise. But social distancing is not as important as public discussion of the virus often imagines. “We’ve ascribed far too much human authority over the virus,” as Michael Osterholm, an infectious-disease expert at the University of Minnesota, has told me.

The recent declines, for example, have occurred even as millions of American children have again crowded into school buildings.

https://www.nytimes.com/2021/10/04/briefing/covid-caseload-retreat-us-cases.html

But social distancing is not as important as public discussion of the virus often imagines. “We’ve ascribed far too much human authority over the virus,” as Michael Osterholm, an infectious-disease expert at the University of Minnesota, has told me.

^ what bothers me about that quote is that, although the journalist is basing their article upon information and opinions gathered during interviews with experts, the journalist then summarizes on their own authority as if their statements were absolutely conclusive and incontrovertible facts, rather than simply quoting their expert sources.

there are so many qualifiers in that statement ("not as important," "often imagines") that it doesn't really mean anything.

Osterholm also a controversial source (though a lot of times it's based on warping of his actual words)

it is an interesting notion of the virus as some kind of damped sinusoid, oscillating at a months-long frequency.

So I haven't been paying a shit ton of attention to these gain of function claims and obviously dismiss anything rand paul says immediately, but it sounds like more stuff came out this week about the NIH and research in Wuhan that seems to indicate that perhaps Paul was correct and the NIH was funding this research? does anyone have a reasonable news source on this stuff?

I havent followed it closely but zeynep is good and has a thread

Oops missing screenshot. Left, baseless certainty from Vox based on a single commentary from March 2020. Right, perhaps the world's foremost coronavirologist, honestly, on the limits to certainty. Also, much new info since March 2020. What's wrong with "we don't know for sure"? pic.twitter.com/HGWN8Kwyc9

— zeynep tufekci (@zeynep) October 24, 2021

the people who out of one side of their mouths insist COVID was engineered in a lab speak out the other side talking about how "viruses tend to do this or that so we're ignoring the usual path of viruses and being overcautious" ,but if it was an engineered virus, it wouldn't necessarily behave like virii that emerged in the wild so pick your poison!

there are so many qualifiers in that statement ("not as important," "often imagines") that it doesn't really mean anything.

― Thus Sang Freud, Sunday, October 24, 2021 3:13 PM (one hour ago) bookmarkflaglink

This. There are many people who spend days and nights posting pictures of beach parties and college football games with comments like "enjoy your surge superspreaders!" The fact that events of this kind don't reliably produce outbreaks doesn't mean human behavior is irrelevant to the disease cycle (how could it be?) or that the relationship between behavior and disease is completely unknowable, just that it's not deterministic and transparently legible the way some people want to think it is.

this is the best, most objective assessment of the possible virus origins that I've read, not conclusive but yes there are parts of the virus that are specifically tailored to humans. whether that came from a lab or some kind of research/bat accident or the live market is ultimately irrelevant.

what I like about this article is that they don't care about the specific origin so much as having proper analysis leading to better solutions

https://thebulletin.org/2021/05/the-origin-of-covid-did-people-or-nature-open-pandoras-box-at-wuhan/

Thanks for that article. Halfway through and it is, uh, alarming.

the people who out of one side of their mouths insist COVID was engineered in a lab speak out the other side talking about

who?

whom, ok

Not sure if this was posted before:

https://theintercept.com/2021/09/23/coronavirus-research-grant-darpa/

Perhaps the most troubling question about the proposal is why, within the small group of scientists who have been searching for information that could shed light on the origins of the pandemic, there has apparently been so little awareness of the planned work until now. Peter Daszak and Linfa Wang, two of the researchers who submitted the proposal, did not previously acknowledge it. Daszak, the EcoHealth Alliance president, has actively sought to quash interest in the idea that the novel coronavirus originated in a lab.

The bulletin article is an interesting read. As a layperson it's hard to know if there's any serious rebuttal?

the people who are unsure whether 'who' or 'whom' is correct are legion

this is the best, most objective assessment of the possible virus origins that I've read, not conclusive but yes there are parts of the virus that are specifically tailored to humans. whether that came from a lab or some kind of research/bat accident or the live market is ultimately irrelevant.

I don't understand why you think the origin of the virus outbreak is irrelevant, surely it matters in terms of trying to prevent something like this from happening again?

I think the smartest thing we can do right now is reverse engineer the virus and see if we can make it better, more transmissible and easier to weaponize. That would prove that humans were behind it, since nature is nowhere near as ruthless as science, at least when we really put our minds to it.

the issue is - most of the people who are really championing the lab leak theory don't just want it investigated further, they want it adopted as the de facto answer, now. and probably for xenophobic or political reasons.

Obviously if this WAS the actual answer, I don't think any scientist worth their salt would be expending lots of energy denying it's the fact, but what *will* make them skeptical of the lab leak theory is the motivation of the people pushing the theory, which is unambiguously bad faith.

scientists are actively trying to find the answer, which is why it's ridiculous that some (not here, mind you) are accusing scientists of trying to obfuscate the origins are complete shitfucks. there are tons of committees staffed by scientists literally trying to answer this question now, but it's not an answer we're going to get in five minutes.

-are complete shitfucks, apparently I didn't remember how I started the sentence

Bat accident

Not my theory, I just like the phrase.

Does the NTSB study bat accidents?

Bat accident is for females, they call it a bar accident for males

As a layperson it's hard to know if there's any serious rebuttal?

I don't feel equipped to judge the competing claims but this article was good imo:

https://foreignpolicy.com/2021/06/15/lab-leak-theory-doesnt-hold-up-covid-china/

A report from the field. Nothing new, you could say, but that's the problem.

https://www.zanesvilletimesrecorder.com/story/news/local/2021/10/24/zanesville-genesis-covid-19-ccu/8538656002/

The patients get to talk to their families one last time before intubation, when their communication is cut off, and they enter some level of sedation to help them cope with the tubes in their throats. Often, that conversation is the last interaction they have with their families.

A sad truth that's been repeated now hundreds of thousands of times in the past 20 months. The main difference between the early months and now is that the hospitals have had a lot of time to regularize the process, because 'practice makes perfect' and they've had way too much practice.

well, it happened

https://www.nature.com/articles/s41423-021-00779-5

In summary, A.30 exhibits a cell line preference not observed for other viral variants and efficiently evades neutralization by antibodies elicited by ChAdOx1 nCoV-19 or BNT162b2 vaccination. SARS-CoV-2 entry into cell lines depends on S protein activation by the cellular proteases cathepsin L or TMPRSS2 [8], and activation by the latter is thought to support viral spread in the lung. Therefore, it is noteworthy that enhanced A.30 entry was observed for cell lines with cathepsin L (Vero, 293 T, Huh-7, A549 cells)—but not TMPRSS2 (Calu-3, Caco-2)-dependent entry [8]. Thus, one could speculate that A.30 might use cathepsin L with increased efficiency and slight (but not statistically significant) resistance of A.30 against the cathepsin L inhibitor MDL 28170 supports this possibility (Supplemental information, Fig. S1c). Notably, robust entry into cell lines was combined with high resistance against antibodies induced upon ChAdOx1 nCoV-19 or BNT162b2 vaccination. Neutralization resistance exceeded that of the Beta (B.1.351) variant, which is markedly neutralization resistant in cell culture and, in comparison with the Alpha (B.1.1.7) variant, is less well inhibited by the ChAdOx1 nCoV-19 vaccine [9]. Nevertheless, heterologous ChAdOx1 nCoV-19/BNT162b2 vaccination, which was previously shown to augment neutralizing antibody responses against VOCs compared to corresponding homologous vaccinations [7, 10], might offer robust protection against the A.30 variant. Collectively, our results suggest that the SARS-CoV-2 variant A.30 can evade control by vaccine-induced antibodies and might show an increased capacity to enter cells in a cathepsin L-dependent manner, which might particularly aid in the extrapulmonary spread. As a consequence, the potential spread of the A.30 variant warrants close monitoring and rapid installment of countermeasures.

you still get some protection from mRNA vaccines/BNT/Pfizer, though, just not as much

i'm hoping people who haven't gotten vaccinated but have had covid are also equally "protected", otherwise 2022 is going to be another fun year

ok but, evasion of antibodies is only one part of the equation. there are variants that are much better than Delta than evading antibody protection, but they never gained a foothold because they weren't as transmissible as Delta.

way too soon to be sounding the alarm here.

we were hearing air raid sirens when Mu came out, for instance

that's a good point

i dunno what i’m hearing about cathepsin L inhibitor MDL 28170 response is bananas

someone is going to have to translate that