Dr. Fauci is warning us that it may take more than we thought to get to herd immunity. Now that anti-science Donald Trump is on the way out and Fauci is advising President-elect Joe Biden, he’s telling us what he thinks.
A year ago, we knew next to nothing about SARS-CoV-2. Since then, experts have bootstrapped us all the way to effective vaccines. The bootstrapping started from what we know about other coronaviruses and pandemics in general. It’s a matter of informed guesses, testing them against each other and observations, modifying them, and testing again.
Because the math of epidemiology is similar to the math of chemical kinetics, I’ve been following the modeling. It is also bootstrapping, guessing parameters, testing them, and modifying them. It’s a set of multiple parameters (an unknown number of them) being fitted to data that has serious limitations. The estimates get better as we get more data. That’s what Fauci is saying. Our first guess for herd immunity was around 70%. With almost a year of data, it looks like that could be as high as 90%.
This ties in with what I’ve been thinking, but I want to let the people who are expert in epidemiology and virology lead. I can see what they are doing, but they have knowledge that they’ve acquired through experience that I don’t have. Here’s my version of what’s behind Fauci’s warning.
We don’t know R0, the inherent rate of spread of SARS-CoV-2, and we won’t know for some time. Pulling it out of the data is a statistical operation and needs a lot of data. Additionally, the data are lumpy – that’s what people are talking about in “superspreaders.” The lumpiness is measured by another parameter, k. We don’t know k either.
We can measure the rate of spread in a particular situation. I’ll call that R, but it sometimes is designated RT and other names. I have seen confusion of R and R0, even from modelers, who should know better. R0 does not vary, but R does. However, the estimate of R0 changes with time, as more data comes in. Because the level of immunization depends on R0, that changes with time too. That’s what Fauci is saying.
New Mexico has recently gone from an R of about 1.3 to an R of about 0.86. That’s R, not R0. R above 1 means the number of cases is going up; less than 1, that the number is going down. The reason R has decreased for New Mexico has very little if anything to do with the virus itself or R0. It’s because people are acting more responsibly and staying home, wearing masks, practicing hygiene. Here’s a site that estimates up to date values of R for all the states, although they call it Rt.
In order to back out R0 from that, we need to know how much of that decrease is due to staying home, how much to wearing masks, and so on. It’s hard to get at those numbers. Modelers estimate them, try them out in the models against observation, modify them, and try again.
And k. Don’t forget k. Lumpy data can help or hinder the analysis. What I see so far is that it seems to be more of a hindrance.
Fauci is probably being conservative – it’s better to predict a more difficult situation so that people can be relieved when it’s not that bad – but there are many indications that the first guesses of 70% immunization for herd immunity are too low. As percent immunization goes up, estimates of R0 and k will improve.
SARS-CoV-2 won’t be easy to control. But we control measles, and it needs 95% herd immunity. A year ago, nobody – nobody! – was immune to SARS-CoV-2. That’s why it has swept the world. For the diseases we’re familiar with, most people have some immunity, whether old folks who had the measles when they were kids or residual immunities to the flu carried over poorly every year. Better times are coming.
Cross-posted to Nuclear Diner
A couple of thoughts. First is that it is wonderful to finally have Tony Fauci unleashed, as he always should have been. He has been a national treasure of the first order for many many years.
Second, I have seen reporting that there may in fact be some natural immunity to this new disease due to T-cell cross reactivity between several of the corona viruses already in wide circulation (“common colds”) and SARS-COV2, and that may explain, in part, the prevalence of asymptomatic cases.
I don’t even pretend to understand the math, but I do trust Dr. Fauci and I’m very glad he’s advising the Biden-Harris team.
Heard on the news either late last night or early this morning that today is Dr. Anthony Fauci’s birthday — his 80th! — and that the District of Columbia has proclaimed today “Fauci Day” in his honour. Nice!
@SiubhanDuinne: Predictably, some right wingers are saying that the Mayor is trying to replace Jesus with Dr. Fauci. And of course they refuse to worship Dr. Fauci!
From what I’ve seen, this is a small effect. I know it’s tempting to grab on to intermediate research results, but I’m gonna wait for more on this. It’s one more possible factor in figuring out the parameters.
@wvng: it seems to me he is so much more relaxed when he speaks now. Not that he is downplaying the mess we are in, but that he feels free to say what he thinks and not worry about getting fired. I think he was always honest but somehow restrained before.
@Cheryl Rofer: It being a new disease and all. Yes. But hasn’t it been glorious to see the global scientific community working cooperatively at breakneck pace to solve the mysteries of this thing. In the midst of all the horror, this part has been thrilling.
It must be pure Hell trying to figure out anything about rate of spread in a country with a widespread will to hide numbers for partisan political reasons.
Like Joe has to announce who they are.
Imma channel the late, great efgoldman and say Fuckem!
@wvng: The scientific progress in this area has been amazing! It shows what we can do when we need to.
Read today that it’s looking good WRT COVID resistance 6 months after infection, something we could not have known with confidence previously. So that’s good.
But then there’s this, from Oregon’s redneck belt.
County hasn’t updated the dashboard today, but we’re only a week+ beyond the historic peak number of cases so nobody is yet claiming we’re “easing or flattening or whatevs.”
Biden and Harris totally stole the Time Person of the Year award from Fauci, in that without the election, and the convention that the newly elected Pres gets the honor, it would have been Fauci. (Or maybe “Frontline Workers”, I guess.)
Just wait until they hear about Newtonmas.
Why assume the asshole knowingly sick employee who went to work feels remorse. More likely said person is a Trumper scumbag.
This kind of thing is scarcely restricted to redder areas of the country. Struggling people throughout the country come to work when they’re sick because they’ll be docked pay or fired if they don’t. It’s one more reason we really need to mandate paid sick leave.
Ceci n est pas mon nym
How does the UK mutation affect all of this? I haven’t heard much detailed science reporting about that, except I think I heard a figure being thrown around of “70% more infectious”. That would be R0 I suppose. And the obvious question: Does immunity to the current strain (including from vaccination) carry over to the mutated strain?
Mike in NC
Last night ABC News reported that about 80 million idiot-Americans planned Christmas travel. A Trumpist couple down the street tested positive for COVID and there are four cars parked in their driveway.
My brother in Boston emailed me to report that the Christmas package he mailed us is sitting in a distribution center in San Francisco.
@Ceci n est pas mon nym: Yes, there is definitely cross immunity and the vaccines are effective against it. The reason is that the immune system makes antibodies to multiple spike proteins, just because one of them changes doesn’t really matter. So not to worry about that. But if it is more transmissible, that’s a problem in itself.
I think it’s worse than that. It’s not just partisan politics, it’s a cult of the stupid. Following shitforbrains gets the majority of his followers what, dead? That’s hardly a plus for them. It does show that racism is a strong (as well as fucking stupid) drug but really it’s that his followers seem to be incapable of basic thought, math, science and history. Not like that’s anything new.
@Parfigliano: Yeah, I’m wondering just how “remorseful” someone who knowingly infected others is really going to be.
ETA: And yeah, it’s entirely possible there were mitigating circumstances, but jeez…
@trollhattan: I’d like to know the circumstances of this person going to work symptomatic. I mean, I went to work for a couple of days because I only had the sniffles, which could have been allergies! I was “symptomatic” but didn’t know I had it. Just having the sniffles and being tired probably wouldn’t have been enough for me to even get a test. Did they have a cough and a fever and go to work anyway? Did they have a job where the employer would fire them if they didn’t show up no matter what? I mean, it’s not good, but how I feel about it depends a lot on the circumstances. It seems to me that the biggest problem is that many people are spreading it when they’re asymptomatic. Was that employer enforcing masks and distancing? Lots of questions here that don’t seem to have answers.
The Moar You Know
@Roger Moore: Was talking to a friend of my wife’s last night – safety compliance officer for a company that makes engines. They keep having to shut down plants because the workers keep showing up sick for that sweet overtime pay. Mind you, their base rate is well over 150k per year. They just want more and don’t give a shit if they kill their co-workers or not.
It’s driving her fucking insane. They catch them with the temperature checks (it’s the only reason they do them and I gotta say I’ve never considered “catching people deliberately going to work when ill” as a good reason to do them before) but as she and everyone else knows, by the time they’re running a temperature it’s way too late – they’ve been spreading for a week.
@SiubhanDuinne: ef did have a way with words.
@Ceci n est pas mon nym:
If the disease is more infectious, you increase the percent of people who need to be immunized to reach herd immunity. As a rough rule of thumb, herd immunity is reached when 1-1/R0 of the population immune. If R0 goes up, so does the fraction of the population who need to be immune to reach herd immunity.
Very importantly, though, that 1-1/R0 is the bare minimum level where the disease should go away eventually. If you just barely get to that level, it will take a really long time for the disease to die out, and it can come back if it mutates to become more infectious. The closer you get to 100% immunity the faster it will die out and the more safety margin you have against increased infectiousness.
@Roger Moore: omg! Sir Isaac thought he was Jesus!
Not clear about the statement/convention that R0 doesn’t vary.
– What about seasonality (humidity variations, seasons where there are more or fewer indoor activities involving sharing of exhaled air)?
– What about density of e.g. living arrangements?
– What about cultural differences that affect the level of sharing of exhaled air? e.g. personal space boundaries (Texas is bigger than e.g. NYC), bar and/or church cultures that involve packing loud people together, a cultural habit of not coughing in other peoples faces while sick (e.g. in Japan, where most people where a mask if they are in public and know that they are sick with a respiratory virus infection), sick leave in a society that allows sick people to stay home, etc.
Collectively, small modifications to behavior in a society might drop R a few 10ths, to below 1 if it was slightly above 1. Is it reasonable to assume that cultural changes are impossible? E.g. SARS made mask-wearing a norm in some East Asian countries when a pandemic/epidemic threatens, and this change has stuck around 15+ years.
I don’t think that we will have an accurate estimate of the K value until Trump’s toadies are no longer in control at the CDC where I have no doubt that they have been suppressing the release of the data from spread at trump rallies this past Fall.
@Cervantes: I read months ago that they thought that a certain childhood vaccine (can’t remember which one, but one that’s common nowadays) also provides some immunity. It was based on both a chemical similarity and that Germany, where this vaccine was standard from the late 60s, was doing so much better than Italy and Spain, where it became common more than a decade later.
@Miss Bianca: my daughter is an NP in a clinic and sends people every day for Covid tests. When she tells them to quarantine at least until they get their results, she usually gets a lot of attitude. And some employers won’t give an employee an excused absence without a positive test. So they are really between a rock and a hard place
Goku (aka Amerikan Baka)
@Mike in NC:
On a related note, the pet calendar I ordered December 10th supposedly shipped a few days later, but according to the tracking number with the USPS, the Postal Service still hasn’t received it; the tracking number was only created on the 16th. The ETA for the calendar was the 26th, but it seems like something has gone wrong
I vacillate between marveling at the science and speed of the vaccine development with how we have utterly failed as a nation. As Mike at comment 19 notes, how in the hell are 80 million of us traveling around to attend gatherings, etc. right now. It will break our country.
Re: Herd immunity, I saw a graphic on the news the other night about the billions around the world who won’t have access to, won’t be vaccinated, until 2022 at the earliest. Although we have declared victory on measles (yet most states have cases every year), according to the WHO, “Global measles deaths climbed nearly 50 percent since 2016, claiming an estimated 207 500 lives in 2019 alone.
On the package front, two of mine mailed Dec. 14 made it to CA and CO from Indianapolis in a week or thereabouts; but my one going 100 miles away to my dad just got delivered yesterday afternoon, taking 10 days. 240 hours/100 miles, yes, about the speed of walking…
@Goku (aka Amerikan Baka): Cafe Press phone number is (347) 916-8261.
They won’t do anything until it is past your delivery date, If it hasn’t arrived by 12/27, you can phone them.
@Eunicecycle: Yes, I get that, because that happens here, too. What we’ve got going on HERE is an unqualified Public Health Director, who got his “Masters in Public Health Administration” from an online diploma mill. That’s all fine with the Board of Health/County Commissioners (same bunch), which has hours-long hands-wringing meetings about What to Do to Get People to Comply, and then refuses to actually DO anything to Get People to Comply, like declare a mask mandate, because oh my God, what will happen to THE ECONOMY. In other words, “How do we get these shitheads that we’ve encouraged to run amok and ignore precautions to stop running amok and ignoring precautions – I know! Let’s not do ANYTHING but bleat helplessly at people to please wear masks because it’s so community-minded! Because that’s going to be a winning argument with shitheads!”
So yeah…we’ve got a real problem here similarly, and the Powers That Be are mediocre male Republican cowards, so our actual public health nurses are having a hard time getting anyone to take anything seriously.
What I’m gravely worried about is the variant virus that is overtaking the UK’s coronavirus caseload, which is considerably more contagious and affects children more readily. It does not as yet appear to be more lethal. Being more infectious, it is believed that it will rapidly become the dominant strain infecting the populace. Our experts are saying that that variant is already in the US, we likely will quickly infect our younger cohorts with it.
With the goal that has been embraced of opening up schools rapidly, and the fact that no vaccine has completed its testing in people younger than sixteen, are we seeding a larger epidemic? Is there ANY way to safely assemble kids in physical school spaces?
@Goku (aka Amerikan Baka):
USPS tracking information is usually not up to date, FWIW. My package spent two weeks being shuttled through three different facilities in Texas. The next entry was that it had departed for a “different facility.” The next day, it was delivered. I’m thinking the post office is too busy to really keep on top of all of the tracking information.
Tom Levenson’s next book.
@Cheryl Rofer: I wonder if Dr. Fauci has actually delivered a baby. I mean, he’s a medical doctor, obviously, but that doesn’t mean he has done a turn through the maternity ward, does it?
I hate having these stupid thoughts come into my head because someone who should have been “canceled” long ago was paid to make a doody in a national paper. If it wasn’t for the fuckheads at the Wall Street Journal, I wouldn’t even particularly notice “Dr.” on Jill Biden or much of anyone for that matter. It would just be “oh, that’s nice”.
Now it’s just a reminder of that idiot and the people who published him. I’m going to delude myself that 2021 is going to be better.
@Fleeting Expletive: “Are we seeding a larger epidemic?”
Yes. That’s been pretty much the “plan” since summer, and we’re doing a bang-up job of it. The malls, restaurants, and bars are filled, people are throwing parties, and our various levels of government just don’t have it in them to respond aggressively anymore. Obviously, some states are better than others, but I don’t think any of them are covering themselves in glory at this point.
Goku (aka Amerikan Baka)
I’ve had a 55-60 y/o woman try to come through my line without a mask. Company policy, in accordance with the state’s mask mandate, is to inform the customer that we cannot process their order until they put a mask on. 99% of people, including Trump supporters, have gotten with the program and wear masks in the store.
However, this woman wanted to be a PITA. “Don’t you have enough protection behind there (plexiglass barrier)?”, she asked snotily. I not only wear a mask, but safety glasses too.
I explained that it wasn’t just for my own protection but for the protection of everyone in the store.
“Well, we need some herd immunity.”
I then explained a lot of people would have to die for that to happen.
Annoyed, she said, “I’m not going to argue with you.”
I eventually got her to put up her scarf around her face. That counted as a “face covering” I guess. There are always a few people like this woman; they’ll even have masks on them while in store, just not wear them until they reach they checkout.
I’m highly tempted to tell the next person who does this, “Hey, maybe next time actually wear the mask while you’re shopping.”
@Ceci n est pas mon nym:
Not by very much, if at all. The claim that it is “more infectious” remains to be shown. Kai Kupferschmidt has two articles in Science (available to all) that go into detail.
But even if it is more infectious, the effect will be in the range of what Fauci is talking about anyway. Non-pharmaceutical interventions like masks, make more difference.
Yes. These are not really “strains” but variants, which implies a smaller difference. Here’s one of the developers of the Moderna vaccine:
I’ve heard from my boss that we’ve purchased the specialty vaccine freezer storage equipment. No other details than that; so, I hope that means they’re starting with staff soon. I imagine our elder care workers will be at front of line, followed by their patients, then the rest of clinic staff, then the rest of staff. that’s my guess.
International mail seems to be even worse. I sent packages to Canada and Germany in late November, and the tracking information suggests they still haven’t cleared customs.
Your question is precisely what I am trying to address in the OP.
There is R0, and there is R. They are different.
R0 is an idealized number, an inherent characteristic of the virus, which is why it is more difficult to determine. R is what we calculate from what we see.
Each of your factors affects R, but not R0.
@Goku (aka Amerikan Baka):
Apparently supermarkets, like traditional saloons in rough neighbourhoods, need bouncers on staff. Wonder how long this woman would be bleating about herd immunity if every grocery store in town kicked her out for mask noncompliance.
I’m starting quarantine today. My Mom in law’s new home health aide tested positive, just 2 days after I spent two hours (masked, and mostly distanced) orienting her to her chores.
So now my MIL is also quarantined, and will be without any home helper for two weeks, if she manages not to have caught the virus. I hate this timeline.
I check the Covid Act Now site for my county every day.
I don’t understand why our R number/infection rate was actually a little higher in the summer than it is now but our case numbers are much, much, much higher right now than they were back then.
But then I remember it hardly matters, my behavior remains the same, stay home and when I must leave, mask up.
@Ohio Mom: The R number has to do with the rate of spread, not the absolute number of cases. If it’s below 1, the rate is going down. If it’s above 1, the rate is increasing.
@JeanneT: Good thoughts to all involved.
@Cheryl Rofer: Can you suggest a good write-up about calculating R.
The Moar You Know
@Fleeting Expletive: No, and there never has been, claims by the Trumpists to the contrary.
@Goku (aka Amerikan Baka):
Those barriers don’t do a damn thing. Think of air like water. If you were in a fish tank with a little piece of glass in the middle, and someone pissed on one side of the fish tank, do you think it wouldn’t reach the other side?
Those things are a complete waste of money and materials. To be effective, they have to go floor to ceiling, wall to wall, and then you’d have to modify air supply and return, fire sprinklers, emergency egress, and acoustics.
I loathe those dividers. So much waste, just to make idiots feel better, and they produce worse behavior. I think they’re actually more hazardous than nothing at all.
This thread seems to be tailing off. Maybe I’ve missed it if you’ve already done it. But we have a lot of educators here and it seems time for a thread to discuss Miguel Cardona and education policy post-Trump and post-Covid.
As a teacher I have come to think that Covid is going to be as big of a 21st Century watershed event in American education as Brown v. Board of Education was in the 20th Century. Not just for K-12 but also higher education.
As a teacher I also very much like the Miguel Cardona pick. Nice to get an actual educator in there, not some academic or executive or high level administrator type for once.
@Suzanne: IDK, If someone is projectile coughing or sneezing in front of my face, I’d rather have that barrier there than not.
@Cheryl Rofer: It’s my birthday, too, and I pretended they were singing to me. Thanks to everyone in the earlier thread for all the good wishes. I fell back to sleep and feel nice and rested.
@Suzanne: Security theater is such a waste of time and money. Do we still have to take off shoes at an airport?
OT – Tom Levenson’s Money for Nothing got a nice review in the January issue of BBC History Magazine.
@Mary G: Happy Birthday, Mary G! May this upcoming year be about a 100x better than the past year. :-)
@Kent: If someone is projectile coughing and sneezing in a store, they have already been projectile coughing and sneezing for some time, and the air is already filled up with their aerosolized viral particles. And what is happening is people are thinking to themselves, “I’m behind a barrier, I don’t need a mask, too!” and then they’re removing the genuinely effective protective element.
Less than useless.
@Mary G: Yes, one still basically has to disrobe at the airport.
AND AND AND…. people take their freaking shoes off and walk on that nasty-ass floor BAREFOOT. I just cannot.
I despise people like this.
@schrodingers_cat: You have hit one of my biggest concerns about the discussions of R0. I think it is fundamentally unknowable to more than one significant figure, but I also think that doesn’t matter for three reasons.
For these reasons, I haven’t been calculating R or R0, but I have been watching what others have done.
This site gives R values (although they call them Rt) for the states. It also has a helpful FAQ at Learn More.
I did a short search and was pleased to find that some of the folks trying to calculate R0 understand just how dicey that endeavor is.
Complexity of the Basic Reproduction Number (R0)
Theory versus Data: How to Calculate R0?
What Is R0? Gauging Contagious Infections
The last is more of a general explainer and doesn’t say much about calculating R0.
@Suzanne: Oh, I agree they aren’t the solution. But honestly they still make me feel better somehow.
I expect an infectious person expels a whole spectrum of droplets from microscopic water vapor particles that persist in the air to macroscopic droplets of saliva and mucus that drop quickly. Plexiglass probably only blocks the largest liquid droplets.
But then I haven’t studied any of the science on any of this, to the extent that it exists. It seems like duration of exposure is the biggest factor, which is why I’m in and out of stores as fast as possible and would never work in close proximity to anyone right now, or dine indoors.
@Mike in NC:
I received a Christmas card from my landlord (in Florida) here in NoVA in the last few days (I check my mail only a couple of times a week)—postmarked December 7. Anecdatum. Stuff I ordered on line arrived with a quickness (both USPS and UPS). Go figure.
About the plexi dividers – I seem to recall early in the pandemic, there was a lot more talk about ‘droplets’ that were expelled and soon fell to the ground. In those circumstances, a plexiglass divider would have some utility. But in the past few months, once they realized that the virus was aerosolized and consequently hung in the air longer and circulated more thoroughly, then the dividers became less useful. But I suspect that taking them down now would be seen by too many as a sign that the pandemic is over.
On another note, over on Talking Points Memo there’s an article about “GOP Rep tears into Trump” about Trump’s dishonest complaints about the legislation he’s bashing. I was like uh-huh, sure – but then I looked into who the Rep was, and was surprised to learn that he is NOT a retiring or newly defeated Congressman! He’s just won reelection and he’s out there calling the president a liar. Yeah, you can say ‘what took you so long?’, but this is the first instance I can think of where the Republican criticizing Trump doesn’t have one foot out the door. So I’m taking that as a hopeful sign.
@Cheryl Rofer: Thanks. I too have been following rt.live. Good to know that you find it useful as well.
Have I mentioned that the NYT is garbage.
@Eunicecycle: Wife works for a fucking PHARMACY! and when she went in for testing due to a lingering sinus issue they told her to keep reporting to work until she got a positive test! I called my boss to let him know she was getting tested and he said stay home!
She tested negative.
Item I ordered to be sent to NY, according to USPS site, left Connecticut well over a week ago. By whatever twisted logic, thence traveled to Nebraska where it has been sitting “in transit” for days and days now.
@Catherine D.: Got a copy from the Seattle Library and reading it now. I like the flow.
Merry Christmas from the Russthuglican party!
Things are not only screwed up, they’re unreliably screwed up!
(I Can’t Get No) Satisfaction – The Ukulele Orchestra of Great Britain
The Fat White Duchess
@trollhattan: ‘”We can’t even imagine the tremendous remorse these people are feeling right now,” one official said…’ wtf? Somebody went to work knowing they’d tested positive and were contagious. On what basis are officials assuming that there would be remorse?
Regret, maybe…but only because they may be caught.
I don’t know that the shields are totally useless. They certainly won’t stop aerosols, but they will stop droplets, which are still an issue. It’s the same thing with sanitizing surfaces. Dirty surfaces are not the primary means of transmission, but they can be a source of spread if one gets grossly contaminated. The argument about whether they give people a false sense of security is reasonable, though. I think we’ve given people something of a false sense of security about doing things outdoors. It helps, but people should still be wearing masks and social distancing outside, and I see people who continue to do neither.
@SiubhanDuinne: I’ve seen it suggested that supermarkets should indeed hire out-of-work nightclub bouncers as their mask-enforcers.
@Baud: Am I wrong to think that this is likely to help the Dems in Georgia?
We wanted 2k, Rs said no, Trump says 2k, we say yay, let’s do it, Rs say no.
Am I being too optimistic
edit: So are the Rs basically daring Trump to veto this?
Dividers are also potentially useful as a way of enforcing physical distancing.
Not previously in this thread, no.
A timely reminder.
@WaterGirl: Dolt45 vetoes this and I guarantee you nothing will happen until the next Congress. Which means there needs to be at least the CR they should have passed in the first place by Monday. Doing this brinkmanship right before the holidays was stupid.
And yes this also means Loeffler and Perdue don’t get to run on getting a relief package done. Which should demonstrate to just enough people how useless they are. Now whether that will help is entirely a different question.
The “Variations in R0” section in the linked CDC article more clearly expresses what I was trying to articulate.
FWIW, I read the the NYTimes piece as suggesting that A. Fauci is being slightly political about it (as a rightly respected voice, he has that option); that he is carefully saying 70-90 percent but making it clear that 90 percent is a real possibility. Motive not clearly stated but probably to encourage higher vaccination rates.
An aside: this recently The Lancet piece is interesting, describing the adaptation of some early 20th C veterinary science to human populations.
A history of herd immunity (David Jones, Stefan Helmreich, September 19, 2020)
 copy of your link: Complexity of the Basic Reproduction Number (R0)
There are building scientists who are studying this. There is zero evidence that dividers are effective. There is, however, evidence in the form of CFD models that they are not effective at all in office environments. There is also evidence that they change behavior, not by enforcing distancing (which is usually already enforced by the desk/check stand/bakery case/whatever) but by giving a false sense of security, so people are removing their masks because the barrier makes them feel safer.
There is evidence that 6 air changes per hour and HEPA filtration are effective at reducing spread. Yet no one is doing this.
@Yutsano: I feel like even if people weren’t paying attention before, everything since Nov 10, at least, screams “divided government means the Rs obstruct EVERYTHING”.
I don’t see how that doesn’t help us in Georgia.
On the David Plouffe / Steve Schmidt podcast I was listening to last night, they talked about someone’s suggestion that Warnock and Ossoff travel the state, holding debates between the two of them – about whether Loeffler or Perdue is more corrupt.
I LOVE that idea; I wish they would do that.
I also have a feeling that the damn dividers (especially coupled with masks) make it harder to hear when transacting business, so people speak or shout, which expels more respiratory droplets than not speaking or speaking softly.
@Bill Arnold: That section is precisely what I find sloppy about how some epidemiologists approach R0. If R0 changes with time and environment, then what they are measuring, by my lights, is R. Which is useful, but using the terminology that way is confusing.
A zero subscript usually denotes a constant or foundational quantity. Perhaps I am quirky in demanding that it be defined as a quality of the virus itself, but if it’s not that, then it’s R, not R0.
It might make more sense just to use R and specify the conditions under which it was determined.
when I returned to work, we had been upgraded from flimsy lexan barriers, to “Fort Apache, The Bronx” level barriers.
The most significant effect they have is on distancing.
Was this idea on a recent episode?
@Aleta: Ooooh. I like it =-)
The problem is that the rate of transmission is not a property of the virus; it’s a property of the system the virus is part of. It makes some kind of sense to calculate some kind of R value for the system that assumes a naive population and no public health measures, since that’s what you need to figure out what level of immunization is necessary for herd immunity, and I assume that’s what they’re labeling as R0. Maybe they should use a different subscript to indicate that it’s a contingent property that depends on more than just the virus.
@mrmoshpotato: It was recent to me, but I listened to 3 or 4 of their episodes last night, and I don’t know which one it was on! I think it was on one of the more recent ones, definitely not the earliest.
I am finding their perspective very interesting, and they definitely have concerns about the state of our democracy
Why did you ask if it was recent or not? Have you heard that idea floated? I would be in heaven to learn that they are considering doing that.
@Baud: Vichy Times is garbage
I haven’t heard it from them (I don’t listen to their podcast), but Matthew Dowd might have come up with it first.
ETA – Professional Left link
@Cheryl Rofer: I liked the first paper, Complexity of the Basic Reproduction Number (R0).
My emphasis. I was also thinking along similar lines as Bill Arnold. In simple terms, I don’t know how there could be a universal contact rate constant; it would seem to me to vary across communities and cultures and environments. But maybe I’m missing something.
Thanks for great post, and great discussion and references to a few articles I haven’t seen before.
” The figure of merit is whether R (not R0) is greater or less than 1.”
That above is a very important point. Different ways of measuring R0 can produce different measurement scales, which cannot be compared directly, unless the structure of disease spread is intro textbook simple. Only invariant is that 1 means stable prevalence, < 1 lower prevalence, > 1 higher.
The k parameter for dispersion plays a bigger role than appreciated, and affects speed of spread before you get to the inflection point into grossly observable exponential explosion stage. One piece of evidence for the two mode theory of covid transmission (aerosol very fast super exponential spread in, say warehouses, nursing homes, and food processing plants) versus slow droplet spread is what seems to be a very slow bubbling phase of spread with a sudden explosive epidemic wave. It’s called ‘subexponential growth’ and is a little subfield of study.
@RSA: Cheryl made a very important point a while back: the simple epidemic model where you have a simple R0 that is a true structural parameter which is well defined and robust to different ways of measuring and parameterizing the disease, assumes that people act like a homogenously and randomly mixing gas.
If that ain’t true the next step of complexity is compartmentalizing the population into stable compartments that approximately meet the gas assumption, but each compartment communicates with the others at different rates. Most of the simplicity of simple model remains there, you just take weighted averages over the compartments.
When the mixing rate between the compartments change, especially due to endogenous reactions of the population to the dynamics of the disease spread, then things start getting wild. I think that is the case with covid.
Regarding shipments, I have to confess no problems with receiving packages.
Heck, last week I got an apologetic email from Chewy saying my shipment scheduled to be delivered today would be delayed for an indefinite period… and then it turned up on my doorstep about 15 minutes ago, safe and sound!
The one item I ordered to be delivered as a gift elsewhere got there right on time, too.
The issue might have more to do with the final leg of the journey. If you’re in or near a major metropolitan area, delivery is likelier to be on time simply because there’s more staff available to process and drive (whether USPS, UPS, FedEx, or Amazon). Smaller municipalities and more rural areas may not be as fortunate.
@Roger Moore: I think you and I are agreeing.
I don’t think it’s incorrect to consider an ideal rate of transmission. It makes it possible to compare viruses, which do have inherent characteristics relative to transmissibilty. It’s important to understand that that ideal rate exists within an environment that changes the actual rate, to make careful distinctions in definitions, and to recognize that we may never be able to completely pin down that ideal rate.
It’s useful to be able to partially quantitate that measles is much more transmissable than other viruses. But it’s even more useful to know what today’s actual transmission rate is in New Mexico.
@jl: Thanks. That makes good sense.
ETA: But I will add that if I were a modeler, I would drop contact rate as a factor in R0, as I would any other constant. (Not the other versions of R, of course, if it’s assumed that the contact rate varies.)
@RSA: See my response to Roger Moore (and Bill Arnold) at #99.
@Cheryl Rofer: Got it, I think. Thanks, to you and jl.
@jl: Good points and well said.
We started out knowing neither k nor R0 and have to iterate to get them. We don’t have enough information now for good values, but we are closer than we were in March, and we know that R0 has to be higher than we thought then. That’s what Fauci is saying.
@RSA: Different modelers lump different things into different parameters. One of the things that drives me crazy in trying to figure out what’s in which parameters, and what makes me angry is when modelers don’t seem to realize or care that they’re lumping things together.
NM’s Governor was the State’s Secretary of Health for a time. Her business was healthcare based before she went into politics. She declared a public health emergency when we had a handful of cases, shortly thereafter locking down the State. She handled the reopening along the CDC guidelines, mandated masks, etc. When we surged again this fall, she locked us down again for a reset. Businesses with 4 cases among their staff on a 2 week average are shutdown for 2 weeks to quarantine their employees. (Hence businesses take Covid safe practices very seriously.) Our Gov believes in testing and contact tracing. The Gov doesn’t screw around. This is necessary because we have one of the lowest bed counts per capita in the nation.
My main concern with the way the public discussion is going is that there is too much emphasis on herd immunity as a solution for our current situation. For various historical reasons, and experience with practical infectious disease control, herd immunity (as a stable no-disease steady state as opposed to the herd immunity threshold which marks the place where the effective R equals one) has usually been achieved in an environment where disease prevalence in the general population is relatively low. Where that has not been the case, the high prevalence has been limited to outbreak areas, not the general population.
In the US we are entering poorly understood territory, with a slow roll out of immunization and high prevalence pretty much all over the place. Only a handful of states have been able to keep prevalence comparable to historical experience. And even less is understood when the effect of the vaccine on transmission is unknown, which is the case now.
This can be easily fixed, as it has been in successful countries. One is short, hard and effective shutdowns with ramp up of other control measures during shutdown, but the US has failed miserably at doing those, even in places like CA and NY.
Another way is mass pulse testing with immediate quarantine/isolation, which a few countries have successfully done. That can greatly reduce prevalence in two or three weeks. That is where the accurate and mass producible $1 home test that was developed in Senegal and that a commenter mentioned here can come in.
Another is to simultaneously introduce different vaccines into the population, which will block higher number of mutations for high level of circulation of the virus, and hopefully different effectiveness on transmission rates. But we don’t know how many months away we are from more vaccines.
The neat and orderly march to a stable no-disease stable steady state is a reliable guide the future only when prevalence of the disease is low. When it’s high, the course of the disease can be messy and unpredictable, with sudden unexpected surges and waves, though their geographical extent should become smaller, or limited to smaller and smaller subpopulations as more get vaccinated.
The situation in the US only seems dire and hopeless because our public capacity to do anything for the average person seems to have completely decayed and rotted in this country.
Bottom line is the importance of getting the prevalence low is just as important now as it ever was. We can’t just sit around waiting for some unrealistic herd immunity magic.
But if you drop the contact rate, you wind up with different units from something that includes the contact rate, so they aren’t even on the same scale. At that point you aren’t dealing with R anymore; you’re dealing with some other parameter.
Anyone questioning the Post Office delivery fuck ups should know that removing the sorting machines is one of the keys. Which is why shitforbrains pick for the PO did what he did.
You drop off or purchase something to be shipped and it gets sorted and the sorting moves it into a bin(s) that are the next stop in the delivery process. This continues because each stop has to know what the next stop is, even if the item is at it’s last stop, it still has to be sorted by zones and then by route or produce a pickup notice. The post office doesn’t just send something from where ever the Amazon warehouse is to your carrier, the method and routing paid for can change that substantially.
Take out some/a lot of sorting machines and the system throws a hissy fit. And with no one trying to fix it, the problem gets much worse.
The kid put up a pic on FB and IG getting her jab, the FB post included her immunization card. She said “best Christmas present ever”.
@Cheryl Rofer: We still don’t know enough about the shape of the transmissibility curve, and not much about where it is homogenous over the population and where it varies. Not much evidence that there is extreme variation between individuals, but may be over mode of spread (aerosol versus droplet). Jargon in this field is not very standardized, but I learned it as the ‘transmission intensity function’.
Until we know more about that, I don’t think we really know much about what the estimated effective Rs are, either as estimated from time series or models, or summary statistics (there are ways of estimating using all three approaches).
They may be weighted averages from stable R0s with the weights shifting over time. Or they may be a mix of weighted average R0s and time rates of spread, which depend on both the R0s and the variation in the transmission intensity function, which is in the most commonly used models measure by the k parameter.
Good point. I wasn’t thinking about dimensional analysis.
@jl: Have you looked at the models?
I ask because I think you have a model in your head that you are working from.
The actual models out there, and there are tens of them, range from relatively simple parametrized functions through fairly complex agent models. And most of the modelers don’t talk much to each other.
There is a saying from some famous old time physicist that, if you design an experiment that requires a lot of fancy statistics, then you should have designed a better experiment. Something similar holds here for modeling and statistical analysis of covid spread. If some crucial aspects seem intractable, see if there is a way to make the control problem simpler through different control approaches that help eliminate the need to worry about so much intractable stuff.
Other countries have shown ways to do that, too bad we can’t.
IMHO, the best approach is two fold. First, get the prevalence down quickly somehow or other, There are two ways as noted above. Mass pulse testing with effective quarantine/isolation capacity is one way that has proven effective in a few countries.
The other is to try to make the disease transmission process simpler. For covid, IMHO, that means seriously trying to shutdown really big superspreader events, which the US has also been lousy at. Be serious about reporting and controlling institutional spread in nursing homes and prisons and large worksites. A huge upgrade in quality and availability of PPE, and better implementation of effective ventilation control measures would help. Some countries, Germany and Ireland are two examples, have simple guidelines for using CO2 measurements to achieve that.
The US keeps staggering from one mess to another because the country has chosen that route, not because it is necessary.
Most of Western Europe has made huge progress in beating back its resurgence. Uruguay is doing very well sandwiched in between two large countries that have been messes, Argentina and Brazil. It can be done, for various reasons, the US has chosen not to take effective measures that are both necessary, feasible, and demonstrably effective in other parts of the world.
Hell, if the Irish can do it, we can. Their reputation for wild and pugnacious behavior is on a par with ours.
@Suzanne: There do provide protection against some mask-less idiot who comes up and coughs or sneezes in ones direction.
@sdhays: Washington’s Governor Inslee has done an okay job and has bent the curve this week. Rural areas are still defying the science, and the governor. My Mike’s brother and sister are angry that Alaska Airlines (based in Seattle) has put out a catchy ad that says you can fly safely if you mask.
The resistance of these siblings drives me nuts. How do you care for them when their tribe is enraged by logic?
@Cheryl Rofer: I don’t have a model in my head. Its been so long since I worked on one, and lack of time puts me at a disadvantage. I’ve been spending most of my time on this monitoring international control efforts.
I just thing that there is ever more evidence that the 20-80 rule of spread that is driven by large superspreader events is a better picture of the structure of transmission than simpler models based on one mode of spread, and a simple or compartments with different mixing rates that can be characterized by an R0.
The 20-80 rule means that 20 percent of the transmission events produce 80 percent of the cases.
All the comprehensive and good study of outbreaks and the transmission process that I’ve seen shows something approximating the 20-80 rule. Public health officials in CA kind of admit this. They say that 90 percent of the spread in a county is due to small group spread in restaurants and small get togethers, then go on to say that the ‘real problem’ is introduction of the disease to the general community from essential workers. CA has not have, unbelievably, a system to track spread between counties and different kinds of outbreaks, even though they promised one months ago.
In CA at least, we can’t tell what things are the drivers of the epidemic, and what things act more like transmission channels of the cases from large outbreaks. You need to control both. More and more evidence is coming out in the news that CA is doing essentially nothing to control large worksite superspreader events.
@Cheryl Rofer: I do agree with you about the publicly available models. All of them have some serious omissions and/or a big black box element. One common one is only modelling confirmed cases and deaths when we know we are not capturing all of them. And most important there is cases, since I haven’t seen an estimate (really ‘guessimate’ is better) of the case ascertainment rate above 25 percent.
The big black box is the transmissibility intensity function. That is back calculated, or uses some predictive machine learning algorithm, and that approach in this situation is not guaranteed at all to ever uncover a stable structural relationship for the transmission process.
The curves for the early urban spread in western urban areas like NYC and northern Italy (e.g. Lombardy), naive/greenfield and prior to significant social distancing or lockdowns or masks, seemed consistent with a cosmopolitan urban R0 of somewhere between 5 and 10. It looked pretty scary. But tests were scarce so hospitalizations and early antibody population measurements seemed to be the best proxies available. Do you have a cite for how epidemiologists are attacking the problem?
 Niece and her now-husband (Zoom wedding!) got COVID-19 late February in NY (Brooklyn), though never tested. He lost his sense smell, which had just started to return in August, so fairly sure. Tests were literally not available, and they had lousy insurance anyway.
 What is the epidemiology term?
Another thing that is a problem in the public discussions is that some of the unknowns that we gawk at for covid may be very difficult to ever figure out. They haven’t been for many diseases that we control effectively. We don’t have good understanding of the transmission process for bacterial meningitis for example.
Better to not spend too much time worrying about things that experience has shown maybe very very difficult to understand. Figure out ways to work around the unknowns or make understanding them less important. More and more countries are showing that this approach can work for covid. The US just can’t even dream of following their examples.
I’d look at Marm Kilpatrick’s twitter.
Also, KJ Seung
They really keeps tabs on what is going on, good summaries of research, and have good BS detectors. I’d read the research they review, and links to experts following other lines of research.
My very guesstimated IMHO, is that superspreader events may have played a role. Big Chinese migrant worker industry in Italy, and slowness in shutting down mass crowds, for example pro sports events, may have played a role. Also subexponential spread might play a role. More evidence is coming in that disease introductions occurred much earlier around the world than first realized. So much more slow bubbling in the early subexponential spread phase, until it exploded than previously realized.
Edit: also huge agricultural worker outbreaks in Spain, when employers flouted regs, mining sector in Poland, may have played a big role in sparking European resurgence
Edit2: but I am biased for superspreader events. On the other side, there have been huge looking R0s and attack rates of 50 and 75 percent in rural areas of Estonia, and in Amazon forest, which are hard to explain by nursing homes. Amazon warehouses, ag processing plants, and such like.
@JeanneT: Sorry to hear about your mom’s, and your, potential exposure. The news about eighty million travelers must feel horribly different.
What will become of humanity when we have a much worse crisis, like climate?
@Bill Arnold: Also
Natalie E Dean, and Trevor Bedford, both have twitter accounts.
@Ruckus: Or, if the sorting machines we have left after the purge are overburdened and break down constantly….or if the weather at the point of delivery turns nasty and results in airline carrier delays…or if the carriers at the delivery point are all out quarantining and the subs don’t know the routes…etc. etc. There are so many nodal points in USPS delivery that delays at any one of them have incalculable knock-on effects, even not considering Orange sabotage….
@jl: I agree that we need to focus on measures that will have some practical effect. There is a role for modeling, though, because the system is complex enough that the effect of a particular intervention is not necessarily intuitive. For example, I’ve seen two modeling results now that suggest that immunizing the elderly and immunizing younger people who seem more likely to spread have similar effects on spread.
I also agree that it’s hard to see where we go from our present dreadful, and getting worse, situation, given the constraints of American expectations. I think that what is most likely is that we will muddle through much as we are doing now, while getting as many people immunized as possible as quickly as possible.
That’s going to mean a lot of people will die. I estimate a half-million dead by Inauguration, and we will be at a high point of deaths then, from the infections people are acquiring now. The downward curves in all the models are relatively steep, so, assuming that Biden can encourage better public health behavior than we’ve had, there shouldn’t be another half-million after that. Maybe 300,000, which is devastating.
@Cheryl Rofer: The issue prioritizing herd immunity or harm reduction from disease is a difficult issue. Traditional approach is to go for harm reduction first, then herd immunity. But recently on-the-ground expertise has argue experience has shown that there are situations where herd immunity should come first.
Marm Kilpatrick linked to an expert in this field over that last couple of days on his twitter.
I think if we can hold out a month, maybe Biden can get funding for a rolling regional scheme of mass testing to lower prevalence. Or we luck out and can get multiple vaccines approved and administered on the ground more quickly than anticipated.
Edit: I think history and experts with field experience in epidemic control both say that best use of models in this situation is for short term prediction closely tied to specific control efforts. Try something, get data, run a model, see if model predicts well, see if model and experience both point to what works better versus worse, then repeat.
Kind of like an OODA loop approach. Models that aren’t closely tied to data and active control efforts, tend to wander around away from most useful approaches. Turns into aimless academics.
@mrmoshpotato: As I said above :-)
@jl: And we come full circle to what I said in the OP.
@Cheryl Rofer: I was just trying to keep in the spirit of the US approach to covid control
@Dan B: I’m a fan of Gov Inslee, I think he’s done well given the circumstances. I got my first dose of Covid vaccine today, much sooner than I think would’ve happened in most other states.
J R in WV
After a MD has their degree, they spend time as “Residents” at a teaching hospital. During their Residency they rotate through most of the medical arenas, this is both to give them a little experience in a wide array of medical work, as well as to expose them to areas of medical practice so that they can make an educated choice of a specialty to spend their lives working in.
While some doctors know early on what they want to specialize in, others wait until they have rotated through several areas of practice as a Resident.
So Doctor Fauchi may very well have delivered, or helped deliver babies as a medical resident 50 odd years ago.
J R in WV
We live in southwest West Virginia, which is pretty rural, but without the huge distances involved in the rural Western states.
But our mail, especially packages, has been delivered as well as could be expected. I ordered a pair of slip-on boots from Keen Shoes, which came in way less than a week, for example. Also calendars from Balloon Juice Pets to David’s bird work have come right on schedule, or a little better than.
@Ruckus: I misunderstood the damage done to USPS operations because I thought sorting machines were more flexible than they were. Holy shit, taking out a small number of sorters doesn’t just bring down system capacity, it cripples a network. Deliveries don’t just get slower, some endpoints become inaccessible.
Even if all the sorters DeJoy ordered destroyed could come back tomorrow, it would still be a Herculean task to get them all working together again.
USPS tracking on package to Oregon from Alaska revealed it was flown first to Honolulu. 2782 miles.
Spent days in a facility there before being flown back to the mainland. 2593 miles. Total airmiles flown, 5,375 miles.
Distance from Anchorage to Portland – 1542 miles.
DeJoy needs to go to Dejail.
This is certainly true. R0 is the value at time t=0 (beginning of the outbreak – typically, before any interventions). That said, one can look up values of R0 for the more common viruses – one might expect them to vary considerably by country … or climate … but apparently there is enough similarity in global social and behavioral conditions to make it meaningful to give an R0 for the virus itself, at least to one significant digit. And it tells you a lot, so typically it’s useful to treat it as a constant.
Though in the case of the novel coronavirus, they are currently talking about significant variations in the new strains, with a higher baseline R, so that at least has to shake out.
What bothers me the most are sentences that mix R=R0 with R=Rt, which have to be read three times to work out where the transition is.
The Fat White Duchess
@Roger Moore: Thank you; that was helpful.
The Fat White Duchess
@Goku (aka Amerikan Baka): We received our calendar yesterday. Thanks again to WaterGirl and the person whose name I’m forgetting (sorry) for the great job putting it together.
The Fat White Duchess
@Goku (aka Amerikan Baka): We received our calendar yesterday. Thanks again to WaterGirl and the person whose name I’m forgetting (sorry) for the great job putting it together.
(Oh, and a Chanukah gift from my brother and sister-in-law in NH –FedExed and USPS-marked for delivery 12/10–arrived on 12/23.)