If that is typical for zoonotic diseases (even if not inevitable in every case) it presents a slightly different view than what one usually conjures up. It is not the case that an animal sneezes or bleeds (or whatever) on a human, then that humna, patient zero spreads the disease to other humans. Rather, the condition of transfer from an animal reservoir becomes temporarily highly likely insead of almost impossible, and perhaps dozens of transfers happen, of which, one or two or three, perhaps, are traced to eventually by epidemiologists.

Turns out that is what probably happened with Covid-19. The transfer happened twice, over just a few weeks time. The best explanation for this is that some animal species (could be more than one) had their own epidemic of this particular coronavirus strain going on, and there happen to be a big market with this animal species (or species) on sale, and the rest is history.

There are two studies, this one and this one, seem to support this idea. When the disease experts are done being incredibly busy with Covid, maybe they can go back to Sudan/Congo and rethink the initial appearance of Ebola with this model, now no longer just some zany idea a few of us had years ago, in mind.

Have a look at this line. I call it “line going up.” Feel free to download it and use it for your own purposes.

I ask you to consider the following questions. Assume the vertical scale on the y-axis is 10:

1) What is the average value of this line?

2) What is the average value of the last 20% of the line, over to the left?

3) Assume the “line going up” is in fact upward-going indefinitely. This is the first ten units of time. What will be the average value of the second ten units of time?

4) Given the same assumption, what is the average value of all 20 units of time?

5) If you were asked to predict the total magnitude (all the areas under the curve) for all of the curve, for the next 10 units of time only, what would it be?

Answers:
1: about 5.
2: About 8
3: About 15
4: About 10
5: A lot, but it runs from about 10 to about 20, so if it is that many units per day, about 150 (the average of 10 and 20 times 10).

I know you got all those questions right. So, now that we can do baby analytical geometry and statistics, have a look at this:

This graph shows an upward trend. We know the trend is somewhat open-ended up to about 7 million a day, with new vaccines coming on line. The drop before the recent mode, which casues an average that would have been about 2.0 million per day, was caused by a preternatural natural disaster (Texas). So, the best estimate of curent production is much closer to 2.5, not 1.7, and that rate will continue to go up so in about four weeks it will be closer to 4 million a day. This is not just based on me looking at the graph and sucking my thumb. This is what the experts are saying. April through July would be 600 million doses, many of which would be one shot doses of the newest vaccines. In other words, every eligible person in the US will be vaccinated by the end of July, comfortably.

That is a very conservative estimate.

Why to people take perfectly good data combined with clear projections from the health experts and turn them into bald face lies? Oh, it is not a lie you say, just a mistake. No, I reply, it is impossible to make a mistake like this and publish it in bloomberg. This is a lie, designed to get a rise out of the readership, and that lie regardless of its intent will contribute to the gloom and doom and that has consequences.

This combination of things got me interested in both epidemiology and immunology, and I’ve been studying it (and teaching the topics) since then.

Do you remember the H1N1 pandemic of 2009? Compared to our current pandemic, it was minor. But it wasn’t nothing. There were a half million lab-confirmed cases, which is probably a fairly small percent of acutal cases, with the real number being up to 1.4 billion. The estimated death toll was well over a quarter of a million. My memories of that pandemic are sharp, because my son was born right in the middle of it. The Maternity Ward was on lock down. But, the vaccine was around and nobody in our extended family actually got sick.

Also at that time, epidemiologists and other infectious disease experts were doing a lot of talking-head work, and among them, was Michael Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota. (See for example: H1N1 could overwhelm U.S. in the next two months).

I remember at the time, or probably a year or two later, Osterholm was on a talk show with two or three other experts, including one who had written a recent definitive history of the 1918 pandemic. At one point, each of the experts had a chance to opine about the next version of such a pandemic. Interestingly, they were all fairly up beat. We have, after all, vaccines, something not really developed in 1918. And great doctors and medical ablities and stuff. There really can’t be another pandemic like 1918.

Then, Osterholm spoke. He said this: The next pandemic may be worse than 1918. It will be harder, not easier, to deal with. Yes, we will have a vaccine for the next pandemic virus, but it will take at least a year, maybe a couple of years, to get it. The virus will not wait. It will ravage our population. There will be, plain and simple, a major pandemic with no vaccine for it, for a very long time, many months at least. Meanwhile, the virus will be worse than 1918, because in 1918 we had far more hospital beds per person than we do now. Basic nursing, in a hospital, will be what will save lives, more so than fancy medical stuff.

We have transformed our medical system today to one in which people spend very little time in hospitals, and hospital stays have become something for the very sick or the very rich. Note that the first thing sane US states did (the ones run by Democratic governors, and a couple of others) when Covid-19 emerged was to figure out how to build out hospital capacity at lighting speed. That was because of Osterholm and a few of his colleagues, and their predictions of what would happen. The response plan was already in place, and has been for years. Something like this state level response was also in place at the federal level, until the Trump Crime Family dismantled it early in Trump’s term.

A bunch of smart people had studied past epidemics and pandemics. A bunch of smart people had studied epidemiology and immunology, and viruses. A bunch of smart people described what a pandemic would look like. All you had to do was to be one of the few people who happened, by chance or circumstance, to have read that literature and listened to those individuals, to remain today pretty much unsurprised by everything that has happened over the last year, and that will happen over the next year. Nobody knew the timing, but this one corner of science and public health knew this would happen, and what it would look like.

One thing none of these smart people expected was that the US would be taken over by a nefarious anti-science political party (Republicans) that would set us back decades in our ability to manage a pandemic, just when the big pandemic came along.

And, there is one other unexpected surprise, and this is surprisingly little talked about. The vaccines that are now being distributed are nothing like vaccines have ever been before. In fact, they only barely fit the definition of a vaccine. Vaccination normally involves introducing substances into the body that cause an immune reaction that doesn’t make you sick, or not too sick, but that cause the adaptive immune system to prepare for a future infection by a specific pathogen. The new RNA technology does not do that. Rather, it programs a few thousand cells in your body to produce a molecule that is the substance that causes the immune system to react. The vaccine factory is in your cells.

That is new.

From the Washington Post.

I have the impression that people who have been taken in by anti-vax thinking, but only to some degree, who are not acolytes of that cult, get the stick when push comes to shove. They think about their health, their children, and they make the right choice. Certainly, it does not go the other way. Add this to the fact that a) the most refusing population out there is the US population, and in the US the refusal (as well as the acceptance, by the way) of the vaccine is almost entirely political, and we can guess that much of the “no, no” really means “ok, whatever.”

Yet another factor is the reporting. Whenever a poll has an undecided middle, or a weak “yes” or “no” element, it is possible to report the poll in a biased matter, even if the poll itself isn’t biased. This is clearly what happens when we see “X% say nope” without mentioning that a number equal to a third or fourth of that said “I don’t know, whatever.”

Here are some data for three polls that address this topic.

An April 2020 survey in seven European countries, with 7,662 respondents showed that 81.1% of the population were indifferent or willing to be vaccinated. (73.9 were explicitly willing.)

A Pew Research Center poll in mid September of Americans compared May and September. This September poll was taken at the height of cynicism about the Trump regime’s handling of Coronavirus, just before Trump himself got the virus. In this poll, 49% of all respondents said “no” (to some degree) to the vaccine (“I don’t know” was not a choice in this survey), with 56% of Republicans preferring to not be vaccinated, and 42% of Democrats preferring not.

The May survey showed those numbers at 27% for the whole survey, and 34% and 21% for Republicans vs. Democrats, respectively.

The September poll is probably the one most cited by those who prefer to be alarmed, but it actually underscores the likelihood that people will get the the shot at much higher numbers. A waft from 27% to 49% over four months indicates that the pollsters are not sampling what the questions indicate they are sampling. There is a huge amount of elasticity in what people say. Also, the fact that this survey had no room for “I don’t really have an opinion” forced people into a category. Given the high degree of politicization of the disease, which mainly consists of many Republicans preferring to appear to be reject science (in order to make lefty big city elite academics cringe) or Democrats rejecting a vaccine they see likely to be yet another Jared Kushner scam, the best numbers, among these, in my opinion are optimistic. In May, before the politicization occurred to a great degree, 72% of Americans said yes to the disease, but only 11% felt strongly about no. That conforms with the other surveys.

A survey reported in late October and published in Nature, across 19 countries, showed that 82% were indifferent or preferred the shot (61.4% were willing, the rest indifferent). Of those who seemed not to want the shot, only 9.8% felt strongly that way.

My friend, scientist Roderiko Kampen, recently suggesting, while agreeing that resistance to the vaccine will diminish over time, to “never underestimate human stupidity. Nothing is stable or ‘normal’ now, every single day some butterfly may flap the global hurricane. Humanity has thoroughly outlived its stay and is now beginning to meet that cool adversary – i.e. my great friend – called reality.” I agree. There will be pockets of resistance that will prove troublesome, and lives will be taken and illness spread because of resistance to science. But, ultimately, most people are going to get the shot, and at some point, schools are going require Covid-19 vaccination alongside the already required vaccinations in order to attend.

Look, people endlessly complain about TSA, and they complain more about TSA and the equivilant agencies around the world, the modern security systems at airports, even more than they complained about the totally fake ineffective security that was prevalent before 9/11, especially in the US. But they still get on the plane with a some sense of security. Covid-19 is worse than terrorism, by the numbers. We are having, in the US, a 9/11 level event every single day as I write this. The vaccine is the way out of this plague. People are going to get vaccinated. I would even go one step further. Anti-vax will always be with us. It is an industry, and anti-anti-vax is also an industry. But a movement (or, really, scam) designed to hamper the fight against this pandemic will get weaker, not stronger, over the next year.

Two vaccines are racing to the finish line. We can’t say which one will arrive first, because they each have a different finish line.

The good vaccine, the one likely to be safe (though not necessarily without some side effects) and effective (though you may need two doses, which is normal for vaccines so don’t panic about that) had this deadline: When it is ready, as in, finished with Phase 3 trials. My money is still on the Oxford Jenner vaccine. If that is the first one ready, don’t expect to see it in the US because a) Jared Kushner does not have any ownership in it and b) Jared’s F-I-L is the corrupt leader of the formerly Democratic Republic of the United States. We’ll get it after Joe and Kamala, if they are not killed by Putin, are in the White House.

I’m fine with this. The fake vaccine might actually work. It will be distributed among Republicans first, and they will blindly take it because they are morons and the head of the Trump Crime Family will order them to do it. If the vaccine turns out to be dangerous, it will be they that suffer, deservedly for the adults (sorry, kids, your parents are dangerous assholes) and it will be they that later sue (if they live) Hahn and Trump over the damage done. If, on the other hand, the fake vaccine is actually a good vaccine, an emergency use authorization by Hahn will certainly speed up data collection, owing to the additional rats, er, lab rats.

See “Here’s how the U.S. could release a COVID-19 vaccine before the election—and why that scares some”

The Second Coming

Never mind what you may have heard about Covid-19’s virus not being seasonal. The assertions that it is not were falsehoods, mostly generated by the press misunderstanding what this all means, spread by people who, amazingly, are not actual epidemiologists, on Facebook. OK, admittedly, I am not actually an epidemiologist either, though back in Grad school when I discovered it exists, I almost jumped ship. And, I do play one in the classroom in the class I co-teach on immunology and epidemiology. Point is, I know a little better than the average person when I’m about to say something stupid. Usually, I then shut up. But not always, so beware.

Anyway, for all the various scientific reasons, it might be seasonal. Consider group of immunologists and epidemiologist siting around having a beer, and someone asks the question, “Is Covid-19 seasonal?” you’d get a lot of hemming and hawing. Then, the inquisitor says, “OK, fine. Each of you take this slip of paper and pencil, and write down “yes” if you think it will turn out to be seasonal, and “no” if you don’t think so. Don’t share your work. If you all turn out to say the same answer, then the beer is free for the rest of the night.”

I strongly suspect they would all write down a non-committal but educated “yes.”

The thing is, an outbreak has its own momentum. Some of the worse influenza outbreaks violated the seasonal pattern we know influenza has. All the Covid-19 outbreaks we have been having have masked any possible obvious seasonality for Covid, though one study that looked at underlying factors linked to seasonality concluded that there is a pretty good chance Covid-19 is seasonal.

On top of that, we have another (not unrelated) set of seasonal factors. No matter what you do to mitigate against spread of the disease in a school, going back to school, even in some sort of limited “hybrid” pattern, WILL result in increased spread. This is not an uncertainty. And, we are starting that now, and as you probably know, it is happening. Between back to school and climate related seasonal effects, we are looking at a long hard winter.

Related: COVID-19 rising in 26 states as US hits 6 million cases

Covid-19 is probably not mainly airborne.

But it is totally airborne as well.

I think it is funny (as in “funny, holy crap, how stupid can people be????”) that once news came out that Covid-19 is very likely airbonre, that many people actually then asserted that it was NOT spread hand to object to hand. It still is folks! KEEP WASHING YOUR DAMN HANDS PEOPLE. Jeesh.

But anyway, the evidence of airborne transmission builds and our understanding of that phenomenon deepens.

COVID-19 patients in earlier stages exhaled millions of SARS-CoV-2 per hour

Exhaled breath samples had the highest positive rate (26.9%, n=52), followed by surface swabs (5.4%, n=242), and air samples (3.8%, n=26). COVID-19 patients recruited in Beijing exhaled millions of SARS-CoV-2 RNA copies into the air per hour. Exhaled breath emission may play an important role in the COVID-19 transmission.

For refernece, this is the very rough not yet accepted article that started this whole thing: Outbreak of COVID-19 in a nursing home associated with aerosol transmission as a result of inadequate ventilation

See this for a very current summary on the airborne situation.

Or, maybe you are just on your own

The latest plan from the Trump administration, other than faking a new vaccine to make money somehow, is the do nothing and wait for herd immunity to “kick in.”

New Trump pandemic adviser pushes controversial ‘herd immunity’ strategy, worrying public health officials

One of President Trump’s top medical advisers is urging the White House to embrace a controversial “herd immunity” strategy to combat the pandemic, which would entail allowing the coronavirus to spread through most of the population to quickly build resistance to the virus, while taking steps to protect those in nursing homes and other vulnerable populations, according to five people familiar with the discussions.

The administration has already begun to implement some policies along these lines, according to current and former officials as well as experts, particularly with regard to testing.

The approach’s chief proponent is Scott Atlas, a neuroradiologist and fellow at Stanford’s conservative Hoover Institution, who joined the White House in August as a pandemic adviser. …

Irony

Yes, I am aware that the picture at the top of the post is an example of irony. That is why it is there.

One way Covid-19 spread is you shove your hand in your mouth, then you use your hand to gob onto a door knob, then the next person to come along licks the door knob. So don’t do that!

If you think I’m being silly, watch some pre-schoolers for a while.

But even adults, at a somewhat lower rate, continuously shed their sheddable viruses a little at a time onto every surface, where the viruses either die over a period of a few hours or get picked up by the next person.

So imagine a scenario in which a person is sitting in a room and a stream of people come in, one at a time, to socially distance at 6 feet away, masked, to have a conversation with that person. Further, imagine the person sitting in place is a teacher, and the visitors are little kids getting to meet their teacher before a semester of distance learning.

Sounds totally safe. Indoors, six foot distance, masks. Nothing can possibly go wrong.

OK, now lets backtrack and find the student in the parking lot. The student and her brother and two parents have just parked. They are coming from a sports event they’ve been attending weekly for a month, at which everyone is shouting and no one is wearing a mask. The are all infected but don’t know it yet. The family heads for the school, and let themselves in the front door. Four people have now touched the doorknob. They are now in the lobby and a school employee, masked and with a face shield, stops them and says, “OK, you’all stay here in the lobby but six feet away from the other families, and I’ll walk little sally to see Mr. Scary the teacher.”

While the student is away, the family gravitates over to some people they know, and start a conversation at what they think is a safe 6 foot distance, but they forget, don’t pay attention, whatever, and pretty soon they are closing in and talking around their masks at each other. Family 2 is now exposed, and has, say, a 1 in 30 chance of getting the virus. This scenario is, of course, playing out hundreds of times across the school district, so there will be some transmission at the door knobs and in the lobby. In the parking lot outside, even.

Little Sally is now being accompanied down an empty hallway by a person she does not know wearing a face shield and a mask, and she starts to cry (= major shedding) on the way down the hall and needs to have her hand held for the last few meters going into the room. While talking to her teacher she is overwrought being away from her parents in this strange place so she throws up breakfast. But that’s OK, the teacher and a para clean it up. But, remember, Little Sally is a carrier, so there is now a thin film of Covid-19 kooties from the lobby to the classroom, even where the hasty cleanup (everyone is behind schedule) happens. This is the first of a four day meet and greet, with two days this week, and two days next week. So this gives Mr. Scary and the para plenty of time to become contagious. So, on week two, one in 100 kids that come in to meet their teacher picks up Covid-19. That is’t many. But the school district has 10 elementary schools, and this scenario is happening in all of them, for a total of 3,000 kiddos. So there are now 30 sick and shedding elementary students mostly doing distance learning at home and, slowly, one by one, killing off the grandparents.

If you don’t like that scenario, make up your own. The point is, masking up and staying 6 feet apart slows, but does not eliminate, infection. As we return to schools, even with precautions, this is going to happen. Everywhere.

And now there is new research that gives us a better idea of how a 6 foot social distance is an oversimplified concept that provides a false, and in this case, deadly, sense of security. More to the point: People think that if everyone “wears” a “mask” (did you notice the scare quotes there?) and stays “six feet” away from each other, than the chance of infection is zero. It isn’t. It never was.

The following nuance inducing graphic is from “Two metres or one: what is the evidence for physical distancing in covid-19?” by Jones, Qureshi, et all, just published.

I’m not going to provide much of a summary of the article. It is very readable and clear. Just click here and find it, read it yourself.

“Instead of single, fixed physical distance rules, we propose graded recommendations that better reflect the multiple factors that combine to determine risk. This would provide greater protection in the highest risk settings but also greater freedom in lower risk settings, potentially enabling a return towards normality in some aspects of social and economic life.

Key messages:

• Current rules on safe physical distancing are based on outdated science
• Distribution of viral particles is affected by numerous factors, including air flow
• Evidence suggests SARS-CoV-2 may travel more than 2 m through activities such as coughing and shouting
• Rules on distancing should reflect the multiple factors that affect risk, including ventilation, occupancy, and exposure time

“

Never mind that the first thing bio students to know is about Hydrogen bonds, or that the first thing stats students need to know is basic probability theory. You already probably do some sort of introduction thing that gets the students oriented to your subject, with a “get to know you” component, etc.

Replace that with this. The first thing the students should encounter in your classroom is some sort of topic appropriate, level and age appropriate, encounter with pandemic reality. Many of your students are not taking this pandemic seriously. They’ve been hanging round mask-less and in close quarters with their friends all summer, maybe practicing on a team, whatever. They are not going to properly manage their own viral shed or the possibility of someone else’s pathogenic effluence. They are going to be gobbing all over each other, their desks, and you.

Now is the time to use your mad teaching skills to push at least some of your students in the direction of being more careful, and possibly, slowing the spread of the Covid-19 causing disease.

I know, I know, you are saying “we are doing distance learning, this does not matter.” But it does matter. The back to school outbreak is going to happen whether or not you, or your school, is doing distance learning, and your small part of the learning community overlaps with the rest of it. And, you never know when your college, HS administration, or school district is going to send the students back into your room. This is your chance. Take it.

Can’t think of an example of a lesson that would smart up your students, to enhance the behavioral part of their innate immune system? Don’t give me that! Of course you can, you are a great teacher! In face, once you’ve thought about it, I want to hear your ideas. Let’s get moving on this!

This is not an uncommon situations. Lots of diseases appeared out of nowhere, and were initially treated this way until other longer term solutions could be developed. But many of those diseases were rare to begin with and remained rare, so the antibody treatment was not scaled up. Just read all those books and stories about “emerging diseases” from back in the “Hot Zone” literature days and you’ll see these stories played out.

Anyway, here is what some experts say quoted in a recent Science coverage by Jon Cohen:

“If you were going to put your money down, you would bet that you get the answer with the monoclonal before you get the answer with a vaccine,” says Anthony Fauci, head of the National Institute of Allergy and Infectious Diseases (NIAID).

and

“Antibodies have the potential to be an important bridge until the vaccine is available,” says Ajay Nirula, a vice president at Eli Lilly, one of several large companies investing in them. Likely to be more effective than remdesivir and dexamethasone, the repurposed drugs shown to help against COVID-19, antibodies could protect the highest risk health care workers from becoming infected while also lessening the severity of the disease in hospitalized patients. But producing monoclonals involves using bioreactors to grow lines of B cells that make the proteins, raising concerns they could be scarce and expensive. On 15 July, Lilly, AbCellera, AstraZeneca, GlaxoSmithKline, Genentech, and Amgen jointly asked the U.S. Department of Justice (DOJ) whether they could share information about manufacturing their monoclonals without violating antitrust laws “to expand and expedite production.”

Antibody expert Amy Jenkins (Pandemic Prevention Platform (P3) program at the Defense Advanced Research Projects Agency) suggests a N ovember-December time line for seeing this technology in the field is not unrealistic.

Here’s the plan.

1) Admit there is a deadly pandemic and that we need to not feed the virus. Also recognize that a realistic estimate of when a vaccine starts to be available is during the school year after the upcoming one, and that it will take a year or so to fully deploy it in the US. The plan for starting school should not be, as it is now, “we’ll do this for the first week then… who knows?” The plan should be one that will flexible but outlined for a two or three year time range, because that is the time range over which this pandemic is going to play out.

2) Change the requirements for graduating from high school. Henceforth, students must meet the core* class requirements, and do not need to meet total credit requirements. All students who have met these requirements are graduated instantly. That would instantly reduce the number of students in the schools by a few percent.

4) Add one year to the high school plan. Call it “Covid-Extention-Year.” (Why? See below.)

3) Identify (mainly) Seniors and Juniors who have only a few core class requirements to finish. Spread those required classes over the next two years (some Seniors will thus be extending their school time into CEY). Many students in most schools will in this manner only have one class at a time, at most, with many semesters/quarters not having to attend school at all.

4) Restrict all other teaching to core requirements only. So, no electives. All teachers are switched to core requirements, all students are taking core requirements.

Suddenly, 3-4% of students would be gone. Within one semester, another 10-15% of students would be graduated, while another 20% of students would be committed to attending school for only one or two classes over about a year and a half. These first four changes simply thin out the herd gracefully and without killing anyone, as opposed to the current approach, which will thin out the herd the hard way.

5) Do as much distance learning as possible, but if classes are required…

6) Revise the one room schoolhouse model.

• Students stay in one room.
• Passing time and bathroom access is set up to minimize hallway contact.
• Teachers move from room to room (teaching core classes only) and wear hazmat
• Very few students in each room so when an infection pops up the total number of students removed from school is small. They can come back in a few weeks.
• Since teachers are suited up they do not have to be quarantined when a student in their room tests positive.

It is essential to keep the teaching staff intact. There will be more needed than usual because several will be out sick for more time than usual. Classes, both distant and in person, should have smaller class size (for most classes, some distant learning classes may not need that). The one room schoolhouse method not only reduces infection, but serves another goal: Relationship building will be easier and more solid in mostly distance learning settings.

*Many schools use the term “core” to refer to a specific subset of academics. What I mean here is different, and includes more. Think of it this way: Look at a set of class records for a sample of seniors. Consider the total number of classes, and the types of classes, that make those students viable HS graduates, and cut out everything else. In other words, pare down. Most students manage to get what we think of as a full on high school degree with a few classes extra. Some students do everything in three years, and earn a year of college. This does not mean removing art or music. It means paring down the individual student’s total work, and probably, the full range of options.

By reducing the number of students and keeping the number of teachers the same, and simplifying the offerings, it is easier to have smaller one-room learning units. While distance learning is ongoing the one-room learning units are not necessary, but they are ready to go when the students and teachers are called back into the classroom. This might be after a vaccine is available, but is still being deployed, and the virus is in smaller numbers but still a threat, which one might estimate to be some time during the 2021-2022 school year.