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All COVID-19 is Local, BBQ edition

Burnt Ends from LC’s BBQ in Kansas City
(photo by stu_spivak CC BY-SA 2.0)

Here in metro KC, our five county area that straddles the MO/KS border and the Missouri River did a relatively good job of shutting down, even in the face of state-level idiocy in both Topeka and Jefferson City. School buildings were closed, large gatherings were cancelled, and when the two states finally caught up and issued state-wide orders, it meant fairly little around here because metro KC had already done much of what was prescribed. It hasn’t all been easy, of course, but folks adjusted and life has gone on.

Now, though, things just got real.

From this morning’s featured story on the KC Star’s website (with emphasis added):

Arthur Bryant’s Barbecue lucked out with a hefty contract two months ago, securing 1,200 cases of brisket at a price of $2.45 per pound. As the pandemic began, meat prices actually dropped and the restaurant snagged another 400 cases at $1.75 per pound, said owner Jerry Rauschelbach.

He said those purchases mean Arthur Bryant’s will be set for the next several months. But they also show how fast the market has moved: brisket was selling for more than $6 per pound this week, he said.

At that price, menu prices would soar by the time the meat is trimmed, smoked and served.

“If I didn’t have brisket and I had to pay $6 a pound, I would take brisket and burnt ends off my menu,” he said. “There’s just no way I could consciously serve sandwiches at 20 bucks. There’s just no way.”

For the uninitiated, a brisket is a big slab of meat with two parts – the flat and the point. The point takes longer to cook properly, so the two parts are either split and cooked separately, or they are cooked together until the flat is done and then the point goes back into the pit. It has more connective tissue that needs longer time to break down, and when done right you get a dark “bark” on the surface of the meat and some of the most tender and flavorful deliciousness on the inside. They’re generally cut in cubes and served either on a plate or a sandwich and when done right, they are spectacular.

There’s a lot of folklore around BBQ and who invented different styles or cooking methods or what kind of sauce to use, and damn near every little thing about putting meat over a fire. The origin of selling burnt ends is not folklore or in doubt: they were invented at Arthur Bryant’s. The point of the brisket was seen for years as waste when you trimmed and cooked the brisket flat for sandwich slices, and the counterman at Bryant’s would cut the point in chunks and set it up on the counter for customers to nibble on while waiting to get to the front to order their food. (Note: Bryant’s has also been legendary for its lines.) Eventually they realized “Hey, we could sell this stuff!” and so they did. And then so did everyone else in town. [Time suck warning: that link goes to a 30 minute video that will introduce you not just to burnt ends, but to a good chuck of KC’s best BBQ joints as well.]

So I’ll say it again: things are getting real in KC when Arthur Bryant’s is even contemplating having to take burnt ends off the menu.

I do not want to dismiss what’s happening in hospitals and prisons and nursing homes. That’s as real as real gets. I know a lot of folks in a meatpacking town in southeast Kansas where a cluster of cases has emerged. Things got real there, really quickly, once that hit. What I am saying here is that KC takes its BBQ seriously — as seriously as the pope takes communion — and this nugget about Arthur Bryant’s BBQ is a very KC-specific cultural sign of just how deeply this pandemic is hitting. We can deal with closing our school buildings and postponing our April elections until June and even closing our church buildings, but burnt ends going off the menu of Arthur Bryant’s (even temporarily) would truly be a sign of the apocalypse.

But if BBQ is the way Kansas City identifies the the apocalypse, it’s also how KC identifies hope.

For several years, Jim White has been active in Operation BBQ Relief. which was founded in KC by a bunch of folks in the competition BBQ world. Over the last 9 years, OBR has expanded across the country, and their crews of volunteers have taken their cookers to areas hit by natural disasters, to feed both those hit by the disaster and the emergency workers who come in trying to deal with it. When I sent Jim, Marcy, Bmaz, and some others a link to the KC Star piece, Jim replied with a link to an April 8 press release about OBR and their newest project, Operation Restaurant Relief:

In addition to deploying their trademark effort of providing hot barbecue meals to those affected by natural disasters, Operation BBQ Relief launched a new program called Operation Restaurant Relief with great success last week in Kansas City.

The new initiative revives closed restaurants by utilizing their kitchens to provide free meals to those in need and those on the front lines. As part of the effort, the restaurants will rehire laid off workers to comply with the program and receive a stipend for their participation from Operation BBQ Relief.

Jim could tell you a lot more about OBR, but he’s got a very important matter to attend to at the moment* so unless/until he shows up in the comments, let me direct you to their website at the link above. He did share with me his impression that OBR is doing “pretty amazing work for a group that is populated with folks who lean to the more conservative side of things – sometimes very conservative. They are slowly learning empathy.” This sounded familiar, and sure enough, Jim wrote in more depth about this kind of empathy after he worked on a OBR mission in Wilmington, NC.

That’s another thing about BBQ. Here in KC, despite having a long and ugly history when it comes to race, BBQ is one of those things that does better when it comes to crossing racial divides, in part because some of the most respected historic BBQ joints around here are African American. Even if someone’s favorite ‘cue doesn’t come from Bryant’s or Gates or LC’s, these places get a lot of respect. Arthur Bryant’s and the original location of the Gates chain are in areas of KC that a fair number of white folk would never dream of entering — but they’ll go there happily to get their BBQ fix if that’s their favorite.  Put it this way: BBQ lovers have very firm opinions about color and argue a lot about color, but they’re usually talking about the smoke ring when you cut the meat open or the overall doneness of what you’ve prepared, not the color of the cook’s skin or anyone else’s. And when people share a disaster response cooking line with folks who don’t look like themselves, it changes the way people see each other – that’s the empathy part.

Back in the day, I waited tables and washed dishes, so I know what restaurant life is like from the worker’s point of view. If you’ve got some money and are looking for a charity out there doing great COVID-19 work on the non-medical front, you could do a lot worse than Operation BBQ Relief and their restaurant relief program.

And if you’re a praying kind of person, you might pray that burnt ends do not disappear from the menu of Arthur Bryant’s.

Ever.

______

* Marcy, knowing what happens when BBQ lovers start talking BBQ, interrupted our email discussion before it could really get going, with the observation that this subject “would be a lovely post if any one of you had access to a blog.” Since I brought up the subject, I agreed I could write it up. Jim, for his part, begged off: “The BBQ site I hang out on is having a virtual cookoff. We had two weeks to submit an entry and I forgot to load up on interesting stuff to cook and submit. But we got a spaghetti squash in our CSA basket yesterday and I have some chicken breast and sweet peppers around. Gonna roast the squash and a bunch of veggies on the grill with the chicken and then make pasta sauce to go on it with the chicken.”

Jim may hold various heretical BBQ notions, but those words above comes from the heart of a true BBQ person. When your plans go awry (or you forget to follow them), you make do with what you’ve got — and that menu sounds delicious.

Jail Couldn’t Silence The Music Of Albany In 1961 And A Voluntary Lockdown Won’t Silence Them Now

Marcy has touched on, and revisited today, the awful toll that COVID-19 is exacting on Albany, Georgia. An early in-depth look by the Atlanta Journal Constitution into how the outbreak started there showed us a very closely-knit community that has a deep history in the civil rights movement. Another very touching peek inside the community came yesterday from USA Today and really got to me, as it hit on what I saw as an echo of the complicated history of the Albany Movement.

The USA Today article goes into detail on how the Albany community refuses to “reopen” as Brian Kemp would have them do. Leaders of the community are coming together on their own to declare that they will only reopen when local health officials pronounce it safe to do so, and that point is still off in the future:

With so much loss, the idea of resuming normal life in Albany and risking a deadly second spike in cases is unthinkable. Town officials, business owners and church pastors are collectively rejecting Gov. Brian Kemp’s decision to allow certain businesses to reopen and lift a shelter-in-place order.

The people here say they will decide when their community can go out to dinner again, get a haircut at a local barbershop and worship together at church on Sunday.

And they are not ready yet.

“We are not going to listen to the federal and state people,” said Glenn Singfield Sr., who owns two restaurants in Albany. “We are going to listen to our local health community, because that’s where our trust is.”

To make the losses in Albany personal, the article opens with a focus on Elaine Williams, who lost her 38 year old son to the virus in early April. Near the end of the article, we return to Elaine Williams and her son, Kenya. They reproduced this photo she provided:

Here’s their description of how the loss has affected Ms. Williams:

Williams, meanwhile, is urging her neighbors to stay home so others are spared the pain she has endured losing her son.

Williams still doesn’t know how Kenya, who was born with Down syndrome, contracted the coronavirus. The only public place they visited in Albany was Sam’s Club on March 12.

She misses his forehead kisses, his gentle voice calling her “my dear” and the sound of him singing in his bedroom while blaring Frankie Beverly & Maze songs.

You see, singing and Albany have a deep history. You might recall that I had the opportunity back in February to join a group of people from here in Gainesville on a bus trip to important civil rights sites and museums in Montgomery and Selma, Alabama. As preparation for the trip, I started reading Hands on the Freedom Plow, which is a wonderful compilation of over 60 essays written by women who were part of the Student Non-violent Coordinating Committee (SNCC) on the roles they played as the civil rights movement unfolded in the South in the early 60’s. The essays are grouped into sections covering different aspects of the overall movement. The stories from the women on the front lines of the Albany Movement are among the most gut-wrenching in the book (which I’m still reading–it’s very long and takes time to process).

I will confess that I had not been aware of the Albany Movement and how it was one of the earliest sustained programs of mass demonstrations in the South and brought SNCC and Rev. Dr. Martin Luther King, Jr,’s Southern Christian Leadership Conference  (SCLC) together for the first time. Most “official” histories of the Albany Movement refer to it as a failure (see for example, here) since the demonstrations were halted without the local police and others instituting the reforms the demonstrators wanted. The “failure” was ascribed fairly often to infighting over power and funding between SNCC and SCLC, but my impression after reading the essays gave me more of a feeling that the people of Albany realized that the extreme physical and sexual brutality inflicted by those in power were not likely to end without structural change on a more national than local level. The Stanford history linked here does admit that the lessons learned in Albany were put to good use in the next movement in Birmingham and eventually in Selma, so the “failure” characterization isn’t really justified.

But there’s more. Although most of those who provided essays to the book only have one appear, one of the early organizers in Albany has two separate essays. Bernice Johnson Reagon played a dual role in Albany. She was a student at Albany State when demonstrations began breaking out on campuses in 1960 and she played a major role in getting demonstrations started in Albany in December of 1961. As the movement progressed, she found herself leading a key aspect of the gatherings: group songs. Her essay that focuses on the musical side of her work opens with the lyrics to “Since I Laid My Burden Down”, which she sings here in a 1986 recording:

Here is what she had to say about the song:

The Albany Movement conquered my fear of going to jail, and the songs helped to do that. They allowed us to name the people who were using jail against us, like Mayor Asa Kelley and Chief of Police Laurie Pritchett.  Not only could we call their names and say what we wanted to say, but also they could not stop our sound. Sometimes the police would say, “Stop the singing.” And we would know we were being heard, and we would just sing louder and longer. “I feel better, so much better since I laid my burden down” expressed what I felt like inside the Albany jail cell. There was a clarity about everything. I knew where I was; I knew what I was doing.  I did not like being locked up, and it was not easy. It was where I was supposed to be. My life was being used for a purpose–fighting racism–and it lifted me up to find that I could take a stand and make clear what I thought about the way we were treated in this country and in my hometown. My body was locked in jail, but I was free and centered.

The parallels between 1961 and 2020 in Albany are striking. The citizens of Albany took a stand for what is right in 1961 and were locked up for it. They realized that this suffering while locked up would help everyone in the struggle for civil rights. Today, the citizens of Albany are once again organizing and this time they’re locking themselves up. Just like before though, this round of being locked up is being undertaken with the knowledge that it is for the good of their community and their country.

But the music didn’t stop. Bernice Johnson Reagon was one of the four founders in Albany of the Freedom Singers. Even after the Albany Movement was over, the Freedom Singers went on tour raising money for SNCC. Here’s a 1963 recording that uses as a backdrop a photo of founders Bob Zellner, Bernice Johnson Reagon, Cordell Reagon, Dottie Miller (Zellner), and Avon Rollins:

And here they are singing at the March on Washington in August of 1963:

Oh, and Bernice didn’t stop there. She later founded “Sweet Honey in the Rock” and she is the performer of “Keep Your Eyes on the Prize” in the theme music for the PBS civil rights documentary series “Eyes on the Prize“.

Keyna Williams’ voice is now missing from the choir of Albany, but its rich tradition carries on and has made a lasting contribution to civil rights in our country. Now, the citizens of Albany are stepping up once again to lift their voices and dedicate their lives to making a more healthy world for us all. They are still being subjected to brutal racism from their governor and president, but they are far from new to this battle and know how to proceed.

Michigan’s Militia-Like Morons Can’t Math [UPDATE]

[Check the byline, thanks. /~Rayne]

They didn’t look very smart, the armed motley mess which staged a protest last Thursday on Michigan’s capitol steps culminating in a tantrum in the rotunda.

The protest reminded me of GOP representatives storming of a closed-door House hearing on the Ukraine quid pro quo — a staged protest meant to interfere and interrupt official governmental proceedings while providing a photo op for media and distracting the public from the underlying problem.

But last week’s armed protesters looked bad even if they were merely a distracting photo op. How does this serve their interests? They’ve undermined any credibility their right-wing ‘Blue Lives Matter’ brethren pushed since Ferguson protests in 2014.

Photo: Jeff Kowalsky, AFP-Getty Images. Shared here under Fair Use.
They’re an embarrassment to this state just as their whiny predecessors were during their Gridlock protest on April 15, violating the executive Stay Home order to rally on the capitol building’s steps, waving their Confederate flags and talking smack about the governor while puling about their lawns not getting cut and their roots not getting colored. Both protests two weeks apart violated the state’s laws related to the governor’s executive powers under a state of emergency.

But the embarrassment doesn’t end at the sight of the right-wing monkey horde barking like mad dogs at public servants who are only doing what they’re paid to do. It’s the horde’s inability to do basic math which makes them look deeply stupid.

The math:

Key:

Pink: 21 days from exposure at Easter to likely recovery.

Blue: 21 days from exposure at Gridlock protest to likely recovery.

Yellow: 21 days from exposure at Armed protest to likely recovery.

Lavender: 21 days from latest likely secondary exposure via Armed protest to likely recovery.

The period from exposure to COVID-19 carriers to average date clear of virus is about 21 days. The two protest rallies are marked off, Easter included since at least one church planned to hold service in spite of Governor Whitmer’s Stay Home order.

(Note a boo-boo on my part, should have marked April 30 as the first of 21 days ending on June 10.)

If Michiganders hadn’t had their little Gridlock tantrum on April 15, we’d have been done with Stay Home and more Michiganders would be alive today.

If all Michiganders stayed home uniformly as ordered and scrupulously obeyed the Stay Home order instead of a few hundred protesters having an armed conniption fit last Thursday, had they rigorously used masks whenever venturing into public spaces for essential business only, we’d have been done with the Stay Home order on the very day these rabid cretins protested in Lansing.

But no.

It’s bad enough that Easter observations in violation of the Stay Home order may have caused a spike in deaths 9-10 days later. But a protest which was supposed to be confined to cars?

Deaths were trending downward until the idiots’ Gridlock protest. It would be nice to know how many of the spike in deaths were people who attended the protest, or who broke the Stay Home order because they were inspired by Gridlock to do so. We may never know how many deaths were because of asymptomatic carriers exposed on that date unless researchers conduct a forensic genetic examination some time in the future.

To ignore this calculus and show up in the capitol without masks, ranting and exhaling in a confined space where law enforcement and lawmakers work is just plain moronic, risking personal health and life in a manner which also threatened others.

Or it’s something far worse — a deliberate attempt not only to interfere with the deliberative process in which all Michiganders have a stake and are represented by their democratically elected officials, but a terror attack intended to hurt and possibly kill the targets of protesters’ ire.

How many of the Michigan State Police, capitol police, lawmakers and staff will come down with COVID-19 as a direct result of this protest?

How many will represent minority majority regions of the state, disproportionately affected by COVID-19?

And how long will the rest of Michigan put up with the death cultists who threaten others, waving guns around inside our representatives’ workplace while blowing contagious viral material at others?

At this rate we’ll be under some form of quarantine all damned summer because these spoiled, stupid wretches can’t make the connection between their bad behavior and Michiganders’ deaths.

This is an open thread.

UPDATE — 05-MAY-2020 2:45 PM EST —

It doesn’t seem obvious to some people why Stay Home/shelter-in-place/lockdown is necessary in the absence of either proven pharmaceutical interventions to treat COVID-19 or a proven safe and effective vaccine targeting the underlying virus SARS-CoV-2. This tweet sums up the primary reason why Stay Home orders are necessary:

Henry Ford and Beaumont hospitals in the Detroit area experienced a month ago what happens to our health care system when people aren’t restricted from their former normal behavior. ICU beds are swamped, overflow capacity is likewise exceeded, ventilators and other respiratory aids are in short supply, painkiller and other drug inventory is decimated. Health care workers are overwhelmed and more likely to become sick themselves from a combination of stress, too many hours exposed to massive viral loads especially after personal protective gear has been depleted.

Lockdown to slow down the rate of contagion buys time for the health care system to handle the additional demand COVID-19 places on it — not to mention easing the pressure on other peripheral systems like refrigerated trucking and mortuary services.

It’s as if these armed cretins have already forgotten bodies piled up in hallways in at least on Michigan hospital.

But one additional benefit from a firm, well-enforced, and rigorously-observed lockdown: a change in citizens’ perspective. A societal reset, a reboot of our expectations.

There will be no return to what we once called normal. It’s done, gone, like poodle skirts and Brylcreem, rotary-dial phones and Betamax video, along with home parties hawking baby shit gold Tupperware.

These assholes spraying saliva as they scream at police — some of them out-of-state provocateurs — aren’t saving anything with their assault weapon intimidation. They are hanging onto a past by their fingernails while the virus has its mindless and predictable way with our population.

As contributor Peterr wrote, a virus doesn’t care. Those of us staying at home do. We don’t want to excessively burden our health care workers and system, we don’t want to hurt our friends and families by infecting them or causing them sorrow.

We want our state to get through this protracted period of discomfort and come out on the other side healthy and alive.

We’ll observe the lockdown orders long enough to break the growth of contagion. We’ll learn how to make and wear masks, and our lawmakers will learn how to ensure our law enforcement have the framework they need to maintain the break in contagion. If confirmed cases and deaths increase again, we’ll go back into another lockdown until we break it again.

This will be our new normal, our new social compact, until drug therapy and/or vaccines are ready in a year or two if we are lucky.

Lastly, we’ll observe the lockdowns because this isn’t the end of it. COVID-19 is only our here and now. Something else is out there waiting for us in the future once our new normal has been built.

These saliva-speckled jackasses screaming about their freedom while interfering with our democracy demonstrate our society isn’t ready if another pathogen like SARS-CoV-2 emerged as the climate crisis worsens.

Stay home. Wear a mask when you can’t. Keep your distance. Wash your hands.

Covid-19 and Class Structure

The Covid-19 pandemic demonstrates the class structure of the US. I’ve written several posts on the issue of class in the US, but most such analysis takes an index of some kind, wealth, education, income, and places people sequentially, then divides the line into groups which are called classes. For example, in this post I described Thomas Piketty’s classes based on wealth.

I discussed a modern Marxian class structure analysis here. Class is defined in terms of social and ownership relationships. Typically we think of three classes, the capitalists, the workers, and a small class of professionals and artisans who own their own means of production and work for themselves, but are to some extent dependent on the capitalist class. [1] This simple structure leads to difficult problems for people trying to use the analysis for social change.

1. In a large corporation, those at the bottom of the hierarchy own nothing but their labor and can only survive by selling that labor. They have little, if any, control over their working conditions. They are subject to the orders of those above them in the hierarchy. In higher levels of the hierarchy workers have limited control over the means of production, and have the power to control the actions of their subordinates. In even higher reaches, people achieve actual control over the means of production and control the actions of larger numbers of people. At the top are people who control the means of production through their power to direct their subordinates. In this more complex setting, the boundaries of class are blurred, and it is easy for people to misunderstand their position in the class structure.

It’s also difficult for people to understand that the problems they face in their jobs are common across all jobs. It isn’t just your boss who’s a jerk, your employer who has appalling policies on health care, sick leave, vacation and day-to-day irritations. Everyone faces those issues.

2. People don’t understand that capitalists exploit workers. This chart shows that the share of national income going to the labor sector has trended down since 1960. It dropped dramatically and stayed low during the last 20 years. That loss goes to the rich. I discuss the way in which capitalists justify this exploitation in this post.

3. Most people do not understand how they are exploited operationally, because everything they experience seems natural. That’s because capitalists exercise substantial control over the public understanding of issues of political economy. Their version of business history dominates. Their theory of economics, neoliberalism, is not threatened by any widespread alternative. Their concept of the role of government has controlled since the 1950s. They have an out-sized input into our choices for political office in both legacy parties. They have used that power to hold onto and increase their power.

But.

This pandemic has the potential to wake people up from their torpor. This article by Robert Reich is a good starting point. Reich identifies four classes defined in relation to the lockdown.

A. The Remotes: “…professional, managerial, and technical workers – an estimated 35% of the workforce” who are working and reasonably well-paid. They are largely unaffected by the lockdown.

B. The Essentials: the people who are required to go to their workplaces despite the lockdown, including health care workers, care-givers, farm workers, meat packers, grocery store and pharmacy employees, employees of gun stores and liquor stores.

C. The Unpaid: the non-essential workers who are now unemployed and subjected to lockdown, about 25% of the work force. Most of them lost their health insurance as well as their income, and face an unpleasant future.

D. The Forgotten: those “…for whom social distancing is nearly impossible because they’re packed tightly into places most Americans don’t see: prisons, jails for undocumented immigrants, camps for migrant farmworkers, Native American reservations, homeless shelters, and nursing homes.” The lockdown doesn’t affect them, as their lives sucked already.

Reich doesn’t mention the Fifth Class, those who are largely unaffected by the lockdown. This group has two segments. One is retirees and those near retirement, who presumably have the income and assets they need and to maintain their lifestyles. They have Medicare, stable housing, access to grocery stores and pharmacies, and generally can shelter in place with no discomfort. The second segment is people who have so much money they are not at all affected. They can just hop on their private jets and come and go as before, maybe with fewer people to serve them drinks.

The Covid-19 pandemic has sharpened the blurred lines described in Point 1. There are only two groups: the Reomoters and the Fifth Class who can can stay home and protect themselves; and the Essentials and the Unpaid. The Essentials who can’t stay home, and are at risk of serious illness and death, with whatever insurance they can cobble together. The Unnpaid are unprotected from financial ruin. The serious risks facing the Essentials and the Unpaid are the same across all jobs.

The exploitation described in Point 2 is now in the open. The rich and their politicians value capital over the lives and well-being of the Essentials and the Unpaid. First, capitalists were heavily subsidized by the Fed and Congress, Second, politicians are granting the demands of the capitalists to reopen the economy and shield them from liability if they don’t protect their workers from deadly illness. Republicans force people to choose between working for the rich or protecting their health at the cost of their unemployment benefits and their life savings.

The domination of discourse raised in Point 3 has been eroded by the rise of the political rhetoric of Sanders, Warren, and others. A large number of working people of all incomes don’t accept the assertions of the rich and their media giants as gospel. They can see the impact of Covid-19 on themselves and everyone they know. They can read about the problems faced by other workers, and see that they are in the same position.

The practical outcome? Workers at a number of giant corporations are planning a work action for May Day.

“It’s more powerful when we come together,” Chris Smalls, a lead organizer of the May 1 walkout, who was fired from Amazon’s Staten Island fulfillment center after staging a walkout on March 31, told Motherboard. “We formed an alliance between a bunch of different companies because we all have one common goal which is to save the lives of workers and communities. Right now isn’t the time to open up the economy. Amazon is a breeding ground [for this virus] which is spreading right now through multiple facilities.”

The strikers are asking consumers to boycott Amazon, Whole Foods, Instacart, Walmart, FedEx, Target, and Shipt. They say that many of the workers will walk out, call in sick, or take other action. Their demands are astonishingly minimal: personal protective gear, paid sick leave, hazard pay, and a few company specific needs.

The Essentials and the Unpaid are forced to risk their health and their finances so the Remoters and the Fifth Class can live comfortably. That’s a concrete way of showing people their position in the class structure. Where are the politicians and media people capable of articulating this so everyone gets it?

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[1] In this post, I use the term “capitalist” to mean the top .1% in wealth and the top managers of the largest businesses. It’s useful here where the basis of the analysis is more or less Marxist, but I’m ambivalent about it because I’m not particularly a Marxist. I’m just a guy who reads books. I usually use the term “filthy rich” which my mother loved, but it seems perjorative.

A Video Guide to Understanding Covid-19 without Freaking Out

It’s a complicated time, and we’re all emotionally worn out.

Here at emptywheel we’ve covered the current pandemic’s scientific side in some depth. (see Jim White’s look at the origin of the virus, Rayne has done several very good updates on the science, politics, and misinformation,
and I’ve gone into the mechanisms of the disease and how it compares to other pandemics )

But we haven’t done as much for the overtaxed, overwhelmed reader who just wants some pretty pictures and gentle talking heads to make Covid-19 make sense. Even those of you who voraciously keep up with Marcy’s intricate political  and media analyses might like to give the emotional roller coaster a break, and still feel like you have some frickin’ idea what is going on.

The Modeling

Nothing is more calming yet informative than 3Blue1Brown’s soothing and surprisingly clear explanation of epidemic models. This 3Blue1Brown explainer uses SIR, a mathematical modeling system for epidemics. While simplified, it can give you a sense for how more complicated models work, and why policies like social distancing and contact tracing are important and effective.

SIR stands for:
S = the number of susceptible individuals
I = the number of infected individuals
R = the number of removed individuals (removed here means no longer infectious, and includes both immune and deceased.)

3Blue1Brown is also one of the most pleasant-to-watch Youtubers of all time. Even when you don’t have any clue about the math he’s describing, it all comes together and you feel smarter by the end. “It’s the mental equivalent of ice-skating,” my daughter says, “You’re a little bit worried about falling over, but it’s nice.”

The smartypants at minutephysics and Aatish Bhatia teamed up to visualize the progress of Covid-19 cases around the world. They use a visualization with a logarithmic map of total cases versus new cases to clearly show both how similar the track of the disease is, and what it looks like for a geographical area to get a handle on the spread. This video explains how it works, and here is the site where you can watch the model play with current data.
But why did this happen?

The why us and why now question is lurking in the back of everyone’s mind, and SciShow comes through on it. SciShow has a long and storied history of well-researched and approachable science education, and their video tackling the zoonotic source of Covid-19 (and other viruses) in bats keeps in the tradition. Bats have evolved different approaches to having a mammalian immune system, which makes them better at handling some of the viruses and worse at handling other pathogens we can overcome easily — this is why their viruses can be so rough on us. We have a lot to learn from them, but we should probably stop disturbing their habitats if we don’t want to keep catching novel viruses from them.

The Medicine

If you’ve heard a lot of terms and you don’t know what they mean, Dr. Hope’s Sick Notes goes through 26 of them with clear and non-technical definitions. Dr. Hope is an NHS doctor who teaches and works in an English emergency department as well as a YouTuber. (His ongoing Covid-19 vlog is great, but more stress inducing than the videos featured here.) He gives easy explanations of complicated concepts with handwritten flashcards, a nice soft focus, and some comforting quiet background music. At the end he hands it over to Dr. Sonia, an anesthesiologist at the same hospital, defining some of the more hardcore technical terms we’ve been hearing in the media, but with equal calming friendliness.

Dr. Sonia appears in our next video as well, as an avid AFOL (Adult Fan of Lego). Dr. Hope and Dr. Sonia discuss how the ICU and ventilation really work, demonstrating with a detailed Lego model built by Dr. Sonia in her day off. It goes over all of the scary terms and procedures and why and how they’re used, but with Lego, so it’s fine. My daughter confirmed this too.

 

 

There’s a lot of questions about immunity, herd immunity, and the potential for re-infection, and a lot of misunderstanding about what any of those terms mean. Dr. Seema Yasmin breaks it down on a spectrum from life-long immunity to HIV (The worst). Where and how Covid-19 might fit into this is yet to be found, but she lays down the situation and puts it in context.

 

And Finally, Something of Less Value

Watching night shows, comedy news, and Youtubers adapt to filming inside their houses has been some hits and a lot of misses, but there’s a few amazing hits. These aren’t so much information about Covid-19 as a few gems life in quarantine has generated. Relax, it’s what everyone’s therapist is suggesting we do.

Stephen Colbert interviewing fellow Daily Show alumnus John Oliver is somehow both unbearable and ten minutes of comedy gold. I wish all late night interviews could be like this, but I also think that would kill me.

 

Kate McKinnon takes to a spare bedroom to reprise her role as Barbara DeDrew, trying to get you to adopt a cat, any cat, all the cats, from Whiskers R We.

 

 

 

Last but not least: what would you say to yourself, if you could travel back to January?


Please feel free to add your own calming and informative, or just funny contributions in the comments, BUT NO STRESS INDUCERS!!!11!!!!!

Um, am I doing this right?


My work for Emptywheel is supported by my wonderful patrons on Patreon. You can find out more, and support my work, at Patreon. Thanks to H.alhajji for the featured image.

Shi Zhengli Provides Proof SARS CoV-2 Was Not An Accidental Release From Wuhan Institute of Virology

On Saturday, I took a deep dive into the origin of SARS CoV-2, the virus that is the cause of the deadly COVID-19 pandemic. That post was the result of several long days of deep reading and thinking. Somehow, I missed that Scientific American had put out an update on Friday of their profile of Dr. Shi Zhengli, the scientist responsible for much of what the world knows about bat coronaviruses, including isolating the bat coronavirus from Yunnan Province that is the closest relative to SARS CoV-2 that has been seen in a laboratory. Even worse, commenter Zinsky linked to the Scientific American article in one of the earliest comments on my post.

I finally got around to reading the article today. As you might imagine, this editor’s note at the top really got my attention:

Editor’s Note (4/24/20): This article was originally published online on March 11. It has been updated for inclusion in the June 2020 issue of Scientific American and to address rumors that SARS-CoV-2 emerged from Shi Zhengli’s lab in China.

I strongly urge you to read the entire article. It provides an effective look into work that Shi had been doing prior to the outbreak and then takes us along with her as she gets the news on December 30 that a novel coronavirus had been detected in two patients in Wuhan with atypical pneumonia. On instruction from the lab director, Shi left the conference she was attending in Shanghai and rushed back to Wuhan to concentrate all of her attention on the new virus.

It is important to keep in mind that Shi’s career up to the SARS CoV-2 outbreak was aimed at just such an event. In fact, she and her team had warned us. From the Scientific American article:

With growing human populations increasingly encroaching on wildlife habitats, with unprecedented changes in land use, with wildlife and livestock transported across countries and their products around the world, and with sharp increases in both domestic and international travel, pandemics of new diseases are a mathematical near certainty. This had been keeping Shi and many other researchers awake at night long before the mysterious samples landed at the Wuhan Institute of Virology on that ominous evening last December.

More than a year ago Shi’s team published two comprehensive reviews about coronaviruses in Viruses and Nature Reviews Microbiology. Drawing evidence from her own studies—many of which were published in top academic journals—and from others, Shi and her co-authors warned of the risk of future outbreaks of bat-borne coronaviruses.

With that as background, her actions in digging into the new virus make perfect sense for how a respected scientist engaged in work with dangerous viruses would seek the source of the outbreak.

She and her team jumped into work on the train trip back to Wuhan from the conference in Shanghai:

On the train back to Wuhan on December 30 last year, Shi and her colleagues discussed ways to immediately start testing the patients’ samples. In the following weeks—the most intense and the most stressful time of her life—China’s bat woman felt she was fighting a battle in her worst nightmare, even though it was one she had been preparing for over the past 16 years. Using a technique called polymerase chain reaction, which can detect a virus by amplifying its genetic material, the team found that samples from five of seven patients had genetic sequences present in all coronaviruses.

But here’s where the character of a person who has been dedicated to science her entire career comes out:

Shi instructed her group to repeat the tests and, at the same time, sent the samples to another facility to sequence the full viral genomes. Meanwhile she frantically went through her own lab’s records from the past few years to check for any mishandling of experimental materials, especially during disposal. Shi breathed a sigh of relief when the results came back: none of the sequences matched those of the viruses her team had sampled from bat caves. “That really took a load off my mind,” she says. “I had not slept a wink for days.”

Yes, months before the rumors of an accidental release from her lab started circulating, one of Shi’s very first steps was to make sure that the sequence of the virus found in patients from the wet market did not align with the sequences of any of the viruses isolated from bats that she had in her lab. She had already warned the world of the danger posed by some coronaviruses jumping from bats to humans. [Note: even though we talk about SARS CoV-2 and the bat virus RaTG13 being “closely related”, they still differ by enough that it is clear that SARS CoV-2 came from a different source than either the virus circulating in that bat population at the time it was isolated or the virus as it exists now in the lab.]

Even more importantly, she checked lab safety records and did not sleep until she could eliminate the nightmare of her lab being responsible for the outbreak.

The article goes on to detail the steps taken to confirm SARS CoV-2 as the agent for the outbreak and the use of sequencing of multiple isolates from different patients over time to indicate that it’s very likely that there was only a single introduction of the virus into humans.

Clearly, the rumors of a leak from her lab have bothered Shi, but she will not allow them to stop her:

Despite the disturbance, Shi is determined to continue her work. “The mission must go on,” she says. “What we have uncovered is just the tip of an iceberg.” She is planning to lead a national project to systematically sample viruses in bat caves, with much wider scope and intensity than previous attempts.

/snip/

“Bat-borne coronaviruses will cause more outbreaks,” Shi says with a tone of brooding certainty. “We must find them before they find us.”

Epilogue

In my post on Saturday, I posited that if we are to believe that the outbreak was the product of an accidental release from Wuhan Institute of Virology, we would have to claim that China has removed from the record any evidence of workers from the lab, or the family or other close contacts, being infected or dying.

Now, after the details that Shi has provided, we would have to believe that a scientist with a long history of top-notch peer reviewed research would be involved in such a lie and would further fabricate the story that none of the previous isolates in her lab match the outbreak.

A scientist of this caliber would know that such a lie would eventually be uncovered. That Shi intends to continue her work unabated is very strong evidence that she is being truthful and can rightfully proceed with a clear conscience.

Those considerations prompted me to return to the “evidence” that was presented to suggest an accidental release. Recall that in my post Saturday, I was perplexed by what looked like the outlines of an information operation. First, the specificity, out of the blue, of the question from John Roberts of Fox about an intern at the lab being infected. I still haven’t heard any others make this same suggestion, so that still stands out as suspicious.

But then I went back and looked at the Josh Rogin column from the same day, where Rogin concentrated on two State Department cables from 2018 about Wuhan Institute of Virology. Here’s the setting Rogin provided for the cables:

In January 2018, the U.S. Embassy in Beijing took the unusual step of repeatedly sending U.S. science diplomats to the Wuhan Institute of Virology (WIV), which had in 2015 become China’s first laboratory to achieve the highest level of international bioresearch safety (known as BSL-4). WIV issued a news release in English about the last of these visits, which occurred on March 27, 2018. The U.S. delegation was led by Jamison Fouss, the consul general in Wuhan, and Rick Switzer, the embassy’s counselor of environment, science, technology and health. Last week, WIV erased that statement from its website, though it remains archived on the Internet.

What the U.S. officials learned during their visits concerned them so much that they dispatched two diplomatic cables categorized as Sensitive But Unclassified back to Washington. The cables warned about safety and management weaknesses at the WIV lab and proposed more attention and help. The first cable, which I obtained, also warns that the lab’s work on bat coronaviruses and their potential human transmission represented a risk of a new SARS-like pandemic.

And yet, even though Rogin says he got a copy of the first cable, this is the only money quote he chose to put into his column:

“During interactions with scientists at the WIV laboratory, they noted the new lab has a serious shortage of appropriately trained technicians and investigators needed to safely operate this high-containment laboratory,” states the Jan. 19, 2018, cable, which was drafted by two officials from the embassy’s environment, science and health sections who met with the WIV scientists. (The State Department declined to comment on this and other details of the story.)

Rogin then adds what I think is the most important part:

The Chinese researchers at WIV were receiving assistance from the Galveston National Laboratory at the University of Texas Medical Branch and other U.S. organizations, but the Chinese requested additional help. The cables argued that the United States should give the Wuhan lab further support, mainly because its research on bat coronaviruses was important but also dangerous.

Really? The scariest language that Rogin could lift from the cable warned of a “shortage of appropriately trained technicians and investigators needed to safely operate”, but then he grudgingly had to note that this was in fact tied to a request from the lab for more outside assistance in getting that training. When we couple that thought with the failure, so far, of Rogin or anyone else to have actually published the full cables, I am more convinced than ever that the whole cable story is part of a coordinated information operation where Roberts asked the specific question and then Rogin took information that had been twisted inside-out from a cable asking for help with training at the lab to try to turn it into a potential whistle-blowing event.

One more bit. I did some digging. Rick Switzer, the “embassy’s counselor of environment, science, technology and health” is not a scientist:

Rogin says the cable he saw was written by “two officials  from the embassy’s environment, science and health sections who met with the WIV scientists”. One would hope that there was at least one actual scientist among those two officials.

Research Misinfo/Disinfo: Ain’t No Sunshine Kill COVID-19 Gone

[Check the byline, thanks! /Rayne]

I thought this series would end after three posts but clearly the misinfo/disinfo related to research studies on COVID-19 continues.

This time Department of Homeland Security is one of the problem children.

By now you know about Trump’s wrong-headed comments about light and disinfectants used in and on humans’ bodies to eliminate SARS-CoV-19. You’ve also heard he gaslighted the public by claiming he was being sarcastic during Thursday’s briefing about light and disinfectants, followed by even more dog-ate-my-homework excuses.

You may have heard speculation that bleach as a COVID-19 therapy specifically may have been the result of communications with Trump by some crackpot who sells this re-labeled chlorine dioxide product as a miracle cure-all.

What you probably haven’t seen is the DHS’s “study” which may also have spurred Trump’s idiotic remarks about light or sunlight. Yahoo News reported about the “study” a week ago, sharing a link to the DHS document it received outlining DHS’s findings.

It’s not a paper. It’s a goddamned slide presentation of which stability of SARS-CoV-19 on surfaces was only a portion.

No peer-reviewed study has been published by DHS in any of the articles since Trump’s ridiculously inappropriate comments last evening.

News outlets have been all over Trump’s remarks, which as Marcy said elicited justifiable uproar. But outlets are doing a pissy job covering the sources of Trump’s practice of medicine without a license at the podium.

Newsweek offers a great example:

Fortunately, CNN got it right:

If DHS’s science and technology advisor Bill Bryan isn’t qualified to make declarative statements relying on research, who is?

Who did the research and where’s their data and output?

Why did the American public have to hear what DHS learned filtered through Trump who has proven himself to be incapable of understanding science let alone demonstrate respect for it?

We need to see the work because there are other studies which do not appear to agree with DHS’s presentation.

This widely cited piece tested the viability of SARS-CoV-2 on different surfaces after exposure to aerosolized virus. The temperature of the study was comparable to a nice spring day — 21-23 degrees Celsius or 69-73 degrees Fahrenheit — with 40% relative humidity.

Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1
van Doremalen N, Bushmaker T, Morris DH, et al.
March 17, 2020
DOI: 10.1056/NEJMc2004973
https://www.nejm.org/doi/full/10.1056/NEJMc2004973

SARS-CoV-2 is quite stable in conditions one might find in an air-conditioned indoor setting according to this study. This much agrees with what DHS presented.

This study looked at viability of the virus over time at different increasing temperatures and exposure to ultraviolet light — like solar radiation.

Stability of SARS-CoV-2 in different environmental conditions
Alex W.H. Chin, Julie T.S. Chu, Mahen R.A. Perera, Kenrie P.Y. Hui, Hui-Ling Yen, Michael C.W. Chan, Malik Peiris, Leo L.M. Poon
https://www.medrxiv.org/content/10.1101/2020.03.15.20036673v2.full.pdf

Here’s a table from the study addressing viability of SARS-CoV-2 at different temperatures:

You can see the virus is viable at 37 degrees C — that’s coincidentally 98.6F, the old average temperature for humans. The virus is stable at that temp for as long as a day. It’s not stable for long at 56C (132.8F) and not at all at 70C (158F) but then neither are humans.

Unsurprisingly, disinfectants disinfect according to the study’s results shown in the table above. Only one little burp with hand soap solution — one of three attempts showed some viability.

This study looked at the differences in number of outbreaks over time in a particular region of China, as the season changed and both temperature and amount of sunlight increased.

No Association of COVID-19 transmission with temperature or UV radiation in Chinese cities
Ye Yao, Jinhua Pan, Zhixi Liu, Xia Meng, Weidong Wang, Haidong Kan, Weibing Wang
Published online April 8, 2020.
European Respiratory Journal 2020, 2000517; DOI: 10.1183/13993003.00517-2020
https://erj.ersjournals.com/content/early/2020/04/01/13993003.00517-2020

These researchers hypothesized that COVID-19 transmission may decrease or even disappear when the temperature and UV radiation increase in the summer.

They collected the confirmed case numbers of 224 cities from China’s National Health Commission, the daily mean temperature and relative humidity collected from the China Meteorological Data Sharing Service System, and daily erythemally-weighted daily dose of UV radiation data extracted from the Dutch-Finnish Ozone Monitoring Instrument aboard NASA’s Aurora satellite. After adjustment for relative humidity and UV, they found temperature held no significant associations with cumulative incidence rate, and that UV was not significantly associated with cumulative incidence rate after adjustment for temperature and relative humidity.

These studies — though some are pre-print and in peer review — do not agree with what DHS’s Bill Bryan or the DHS presentation published a week ago said.

And none of them match what Trump said, whatsoever.

Media outlets really need to have a science reporter covering Trump’s briefings rather than the usual White House correspondents — people who are already highly versed in COVID-19 research and are able to put Trump on the spot.

Or the media needs to give up covering Trump’s briefings live if they can’t do real time pushback and demand better of the guy occupying the White House. Carrying his unfiltered bullshit will get somebody killed and damage businesses which are doing their best to operate under the strain of pandemic conditions.

~ ~ ~

We know now from the Washington Post that Trump’s unacceptable remarks on light and disinfectant therapy for treatment of COVID-19 may have been inspired by a briefing about a DHS study:

Trump’s commentary seemed to be inspired by a presentation from a Department of Homeland Security official about a promising but still inconclusive government study exploring the possibility of heat, humidity and light to kill the virus, as well as the effectiveness of disinfectants in killing it on surfaces such as tables, countertops and office workspaces.

Emphasis mine. An in-fucking-conclusive study, the same one on which Bill Bryan gave a presentation. Why was it offered at all? To provide happy talk for the daily propaganda program?

William Bryan, the department’s acting undersecretary for science and technology, first shared the study with members of the White House coronavirus task force on Wednesday and returned Thursday. He said his department had studied the virus in an air chamber and never said chemicals or UV light had been studied on humans nor suggested they be used in humans, according to several administration officials.

Why did he come back? Did some asshat on the White House coronavirus task force think Bryan could finesse this inconclusive report?

Others on the task force, including Birx, White House chief of staff Mark Meadows, as well as McEnany and others in the communications and press shops, were concerned that the Department of Homeland Security study had not been thoroughly vetted. “It was not ready at all to go to the president,” the senior official said. “There was no guideline. There was no data. There was nothing.”

Oh. Now we have sources named. At least one of these people and/or Dr. Fauci are most likely to have said this “study” was not ready to go to Trump. If these three and Dr. Fauci didn’t think it was ready, how did it end up getting in front of Trump?

Still, Vice President Pence and his team wanted Bryan to present the information to the president and to the public, eager to have something positive to share. They hoped the study would help encourage people to spend more time outdoors and to disinfect their homes, aides said.

Oh great — Mr. HIV-outbreak-of Indiana Pence with a history of ignoring public health officials’ advice to the public’s detriment, probably ignored the opinions of task force members who felt the DHS “study” was not ready for Trump’s propaganda show.

This time Pence’s bad decision-making resulted in an onslaught of calls to poison control center numbers and at least 20 people in New York alone who ingested bleach or disinfectant.

No word yet as to whether someone has fried themselves crispy outdoors in an effort to get rid of SARS-CoV-2 using ultraviolet light having relied on the misinfo/disinfo served up by the idiocracy in the White House.

Digging Through The Science—And The Noise—On What Is Known About The Origin Of SARS CoV-2

Update: In a new post we find that Shi Zhingli of Wuhan Institute of Virology has provided convincing evidence to Scientific American that SARS CoV-2 is the result of a natural jump to humans from an animal host and was not accidentally released from her lab, which had no isolates of any viruses that match closely enough to be the outbreak virus.

Although it seems that all of this has been going on forever at this point, it’s important to realize that the COVID-19 pandemic outbreak probably began less than six months ago. In the context of how we develop an understanding of a disease like this one, and the virus that causes it, SARS CoV-2, that means that we really have only just begun our analysis. Nevertheless, because of the ongoing disastrous impact on global public health as well as the global economy, it is imperative that we learn as much as we can as fast as we can.

In this post, I want to take a deep dive into what virologists and epidemiologists have pieced together on the emergence of SARS CoV-2. The problem is that what might initially appear to be straightforward scientific and public health questions eventually get muddled by accusations of disinformation, accusations of hiding data and offerings of potential leaks of intelligence that also have a chance to be disinformation. These noisy battles relate to basic facts that have a direct bearing on our understanding of the virus’ origin.

As a result, it needs to be stated from the outset that because some of the needed basic information may be hidden or some of what we think we know might be wrong. Therefore, this analysis will be unable to come to a definite conclusion. With any luck, the discussion will help us to have a framework within which we can proceed as more facts become verified.

Overview Derived From SARS CoV-2 Genetic Sequence

I want to start with the science.  The very helpful graphic below is lifted from this paper in Current Biology. It is in three sections. The section on the left illustrates what we know from the genetic sequence of the virus when that is compared to other known viruses. What it shows is that the closest overall relative to SARS CoV-2, with a sequence identity of 96%, is RaTG13, another coronovirus isolated from a bat:

Let’s move to this Nature Medicine article from March 17 and this Cell article from April 16 for the narrative on diving into the distinguishing features of SARS CoV-2 from its genetic sequence.

From the Nature Medicine article, we get a description of the features of SARS CoV-2 that distinguish it from other known viruses (these features are what the center and right panels of the graphic address):

Our comparison of alpha- and betacoronaviruses identifies two notable genomic features of SARS-CoV-2: (i) on the basis of structural studies and biochemical experiments, SARS-CoV-2 appears to be optimized for binding to the human receptor ACE2; and (ii) the spike protein of SARS-CoV-2 has a functional polybasic (furin) cleavage site at the S1–S2 boundary through the insertion of 12 nucleotides, which additionally led to the predicted acquisition of three O-linked glycans around the site.

To translate some of the terms and clarify a bit, there are four genera of coronaviruses, with alpha and beta infecting mammals and delta and gamma infecting birds. The genome is the genetic sequence of the virus. I would usually say the DNA sequence, but coronaviruses are RNA viruses. There has been much discussion of ACE2 on this blog in the comments, so for now let’s just say ACE stands for angiotensin converting enzyme and ACE2 is present on the surface of many cell types found in many different tissues within the body. So what stands out here is that the structure of the virus spike protein, as determined from its genetic sequence and tests in the lab, allows it to bind exceptionally well to ACE2 when compared to other coronaviruses.

The middle panel of the graphic shows us that although the overall sequence of SARS CoV-2 is very closely aligned to the bat virus, when we narrow it down to only compare the region where the spike protein binds to ACE2, it is a perfect match of that part of a pangolin virus, while it is very different from the bat virus. For the important stretch of the spike protein (these amino acids are not next to each other when the gene sequence is read from start to finish, but once the protein is assembled from amino acids, the amino acids are close to each other from the way the protein assumes its three dimensional structure), the gene encodes a string of five amino acids in the protein that matches exactly with the pangolin virus sequence but in only the first of the five positions on the bat virus sequence.

But that final panel and the second half of the Nature Medicine snippet goes further in what is different about this virus. The gene for the spike protein encodes two subunits, S1 and S2. Remarkably, SARS CoV-2 has acquired a site where the two subunits can be separated using a enzyme called furin that is found in mammalian cells. The right panel shows us that neither the bat sequence nor the pangolin sequence has a furin cleavage site.

The Cell paper tells us that a furin cleavage site has not been seen in the betacoronaviruses closely related to SARS CoV-2. It has been seen in other human coronaviruses, though. Of further significance is that a furin cleavage site also appears in the more pathogenic bird flu viruses.

Not A Lab Construct

From the Nature Medicine article, we get one of the most convincing arguments I’ve seen against the virus being created in a lab:

While the analyses above suggest that SARS-CoV-2 may bind human ACE2 with high affinity, computational analyses predict that the interaction is not ideal and that the RBD sequence is different from those shown in SARS-CoV to be optimal for receptor binding. Thus, the high-affinity binding of the SARS-CoV-2 spike protein to human ACE2 is most likely the result of natural selection on a human or human-like ACE2 that permits another optimal binding solution to arise. This is strong evidence that SARS-CoV-2 is not the product of purposeful manipulation.

So, in other words, if someone in the lab wanted to set out to make a virus with the best possible ACE2 binding site, this is not the sequence the computer or the literature would have given them. That suggests that this very good binding sequence is a product of natural evolution instead. The Nature Medicine article also further noted that the genetic sequence of SARS CoV-2 differs too much from that of any other known coronavirus sequence for one of the known viruses to have been used as a starting point in engineering this stronger pathogen.

The Species Jump

Perhaps the most important step in the emergence of SARS CoV-2 is the jump from its initial host species to humans. This could have happened directly, or as in the case of MERS CoV, which went from bats to camels to humans, with an intermediate host. Note that MERS still has not adapted to efficient human to human transmission, and so when we see it, it’s usually from multiple camel to human events.

The problem here is that we don’t have proof of the host from which humans were first infected with SARS CoV-2. In other words, no virus isolated from an animal so far is related closely enough at the sequence level to SARS CoV-2 that we can say this is where humans were first infected, as we can tell from the MERS jumps from camels to humans. As we will discuss below, and as you are well aware, early suspicion on the origin of human infection centered on the wet market in Wuhan. Remarkably, authors of the Cell paper visited the market and took these pictures in October 2014 because they were concerned that wet markets in general, and this one in particular, represent a particularly large risk for bringing humans into contact with less commonly encountered hosts of potentially deadly viruses:

The caption properly notes that many early cases are linked to the market, but we don’t yet have proof of where and how the first human infection(s) took place. In discussing the jump and subsequent outbreak, the Cell authors continue:

The emergence and rapid spread of COVID-19 signifies a perfect epidemiological storm. A respiratory pathogen of relatively high virulence from a virus family that has an unusual knack of jumping species boundaries, that emerged in a major population center and travel hub shortly before the biggest travel period of the year: the Chinese Spring Festival.

/snip/

While our past experience with coronaviruses suggests that evolution in animal hosts, both reservoirs and intermediates, is needed to explain the emergence of SARS-CoV-2 in humans, it cannot be excluded that the virus acquired some of its key mutations during a period of “cryptic” spread in humans prior to its first detection in December 2019. Specifically, it is possible that the virus emerged earlier in human populations than envisaged (perhaps not even in Wuhan) but was not detected because asymptomatic infections, those with mild respiratory symptoms, and even sporadic cases of pneumonia were not visible to the standard systems used for surveillance and pathogen identification. During this period of cryptic transmission, the virus could have gradually acquired the key mutations, perhaps including the RBD and furin cleavage site insertions, that enabled it to adapt fully to humans. It wasn’t until a cluster of pneumonia cases occurred that we were able to detect COVID-19 via the routine surveillance system. Obviously, retrospective serological or metagenomic studies of respiratory infection will go a long way to determining whether this scenario is correct, although such early cases may never be detected.

So, the sequence information comes to a dead end here until the details of the epidemiology are reconstructed. As the authors note, it likely will prove impossible to sample many of the most important animals and humans that would clarify the route and timing. It is further worth noting that the bat from which the RaTG13 sequence is derived was found in Yunnan province, a very long way from Wuhan.

Epidemiology

It appears that as of this writing, the earliest known infection may have been a shrimp seller in the wet market who first developed symptoms on November 17. Also, this Lancet article provides further details on some of the early studies showing a high concentration of cases affiliated with the market in December. The Lancet graphic suggests a case on December 1 not affiliated with the market and the start of the market cluster on the tenth, with 27 of the 41 early patients considered here being associated with the wet market. If that were indeed the earliest case, we might think we’ve seen the index case. But if the South China Post article is to be believed, the shrimp seller fell ill on November 17 and, according to the article, one to five people a day from that day forward had the disease. If we believe that information, then the virus appears to have already been circulating before the middle of November.

It is when we start getting into this information that accusations of hiding information are thrown about. Were there earlier cases that China suppressed or that simply went undetected? We have no way of knowing at this point.

A further point that comes from the Cell paper is that SARS CoV-2 has been circulating long enough that minor variations in the gene sequence are arising that don’t affect pathogenicity but allow for tracing of various lineages of the virus in its spread around the globe. They also note that the lineages allow them to go back in time over the evolution of those sequences and the diversity diminishes a lot as they get back to the early isolates from Wuhan. This is further confirmation for Wuhan being essential in the earliest part of the outbreak.

Accidental Release

It is here that the noise gets really loud. If we accept the really strong evidence that SARS CoV-2 was not deliberately made in a laboratory, there remains the possibility that the virus could have escaped from a laboratory that studies potential pandemic agents.

As long ago as 2004, Rutgers scientist Richard Ebright spoke out against the massive amount of funding that was funneled into research on bioweapons after the 2001 anthrax attacks. From the New York Times:

Dr. Ebright disagrees with much of the security community about how best to protect the nation from attacks with biological weapons.

The government and many security experts say one crucial step is to build more high-security laboratories, where scientists can explore the threats posed not only by deadly natural germs, but also by designer pathogens — genetically modified superbugs that could outdo natural viruses and bacteria in their killing power. To this end, the Bush administration has earmarked hundreds of millions of dollars to erect such laboratories in Boston; Galveston, Tex.; and Frederick, Md., among other places, increasing eightfold the overall space devoted to the high-technology buildings.

Dr. Ebright, on the other hand, views the plans as a recipe for catastrophe. The laboratories, called biosafety level 4, or BSL-4, are costly, unnecessary and dangerous, he says.

”I’m concerned about them from the standpoint of science, safety, security, public health and economics,” he added in an interview. ”They lose on all counts.”

Ebright continues:

The labs, Dr. Ebright says, are a perilous overreaction to an inflated threat and will do more harm than good.

Although the threat of biological warfare is real, the weapons used by terrorists are unlikely to be the next-generation agents that the high-security labs are intended to study, he says. Yet by increasing the availability of such pathogens, Dr. Ebright argues, the labs will ”bring that threat to fruition.”

”It’s arming our opponents,” he said.

In addition, he says, the laboratories could leak. They could put deadly pathogens into irresponsible hands and they will divert money from other worthy endeavors like public health and the frontiers of biology. Moreover, their many hundreds of new employees would become a pool of deadly expertise that could turn malevolent, unleashing lethal germs on an unsuspecting public.

Note the “leak” bit. The article goes on:

But Dr. Ebright noted that the deadly SARS virus recently escaped from BSL-4 and BSL-3 labs in Taiwan, Singapore and Beijing, in each case setting off minor epidemics that killed or sickened people.

This 2014 paper from the Center for Arms Control goes into detail on two separate escapes of SARS from the same laboratory in Beijing,  along with four other documented cases of releases of possibly pandemic pathogens if you care to read further. Suffice it to say that Ebright was right that with the proliferation of these new labs, there would be leaks. So far, they’ve all been accidental instead of the type feared by Ebright where someone from inside a laboratory deliberately releases a pathogen.

With regard to the SARS CoV-2 outbreak, rumors from nearly the very beginning swirled about a lab in Wuhan. There is in fact a level 4 containment lab in Wuhan and there is also a level 2 lab as well, that I believe is very close to the wet market.

Should there have been an accidental release from either of these labs, at this point we would have to postulate that China has specifically quashed all information relating to this event and kept the laboratory personnel and any close family or other contacts who may have been infected out of the databases of patients.

But that hasn’t stopped the noise. Some aspects of the noise even begin to look to me like an information operation of sorts. Of course, since we don’t know the originator of the operation, we don’t know if it is actual intelligence being leaked or if it is disinformation being sown to add to the chaos.

At any rate, this April 2 column from David Ignatius put the idea of an accidental leak from a Wuhan lab into the Washington Post. Those who follow intelligence community news know that Ignatius is often thought of as a mouthpiece for information the CIA wants disseminated. Are they his source here? Was some other information operative his source?

Then things really heated up on April 15. Here is John Roberts of Fox News asking Trump a question during the April 15 “press conference”:

Wow. That’s an incredibly specific question. It assumes a female intern at the lab who infected a boyfriend and then she (or did he, not clear to me from Roberts’ phrasing) went to the market. Even though this was April 15, I’ve seen no further pushing of this specific version of the story.

But Trump’s response is a bit concerning. Note that he says they’re “hearing that story a lot”, but then makes a really big deal of the word “sources”. Given Trump’s history of spilling classified intelligence, and the constant warnings to him about such leaks compromising “sources and methods”, I almost wonder if that’s a genuine response of his lizard brain to all those warnings. We simply have no way of knowing that or knowing if perhaps those “sources” happen to lie outside the intelligence community and among circle of wingnuts who have the ears of Trump and Fox News and he’s really proud of them but doesn’t want to divulge them.

That same day, Josh Rogin put out a Washington Post column pushing the leak from a lab story, this time tying it directly to the State Department cables in 2018 about lax biosecurity protocols at the level 4 containment lab in Wuhan that Roberts mentioned. But Rogin didn’t include the specifics about the intern.

I’ve heard nothing further on the intern question, but the general idea of an escape from a Wuhan lab still gets tossed around. Ignatius returned to the idea of an accidental release on April 23. He even talked to Ebright:

“Science is not going to shift this from a ‘could have been’ to a ‘probably was,’ ” messaged Richard H. Ebright, a leading biosafety expert at Rutgers. “The question whether the outbreak virus entered humans through an accidental infection of a lab worker . . . can be answered only through a forensic investigation, not through scientific speculation.” Ebright told me the Chinese government should launch a forensic investigation by reviewing “facilities, samples, records, and personnel.”

Given Ebright’s history of predicting just such an accidental release, I find it very reassuring that he isn’t ready to say that’s what happened. As he rightfully points out, we can only know what happened when detailed information is assembled on the epidemiology of the earliest cases. Only Chinese medical investigators can know whether any laboratory personnel, and especially whether any family or other close contacts of them appear on the timeline of the early infections. It is also crucial to know where any such infections, if they exist, fall on the timeline in relation to cases affiliated with the wet market.

My gut feeling is that the evidence still very strongly points to the virus originating through the wet market, but I also think the index case there likely goes back even earlier than the November 17 case discussed above, since there are suggestions there were other cases appearing daily by then. Also, it’s hard to imagine that if the official intelligence community had a story as specific as the intern story and had evidence to back it up, that Trump wouldn’t be trumpeting it on a daily basis to deflect the criticism being heaped on his response to the outbreak.

Stay tuned. I suspect the story will take several more turns before we ever reach any level of certainty.

On Mountains, Mountain Climbing, and COVID-19

Memorial to climbers who have died on Mount Everest at the Pheriche Aid Post (h/t akunamatata via flikr; CC BY-ND 2.0)

The language of mountains and mountain climbing is all over the COVID-19 coverage, from the talk of “reaching the peak” of infections to the euphoria of those who proclaim that in various areas, we are “hitting the plateau.” But as a mountain-climbing friend once told me “Climbing the mountain is the easy part — it’s the descent that’ll kill you.”

This is not just a cliche, or a (non-)urban legend, but backed up by the experience of those who know the mountains best:

Kami Rita Sherpa knows Mount Everest better than anyone else: He’s summited the world’s tallest peak 24 times, more than any person in history. . . .

Sherpa said problems arise not from those lines [of climbers waiting at altitude to pass along single-file sections of the climb], but when people accidentally push past what their body can support. Some research suggests that Everest climbers can develop a kind of “summit fever,” racing to the top to prove they can, even when their bodies are showing signs of giving out.

“At that altitude, it takes everything to put one foot in front of the other,” Everest climber and exercise psychologist Shaunna Burke recently told Business Insider. “If you haven’t judged how much gas you have left in the tank, then you can’t make it down. That’s why some climbers sit down and don’t get back up.”

Sherpa echoed this.

“When returning, their body is out of energy, and many people die due to this cause,” he said.

It’s not just one or two climbers’ opinion, either. In 2006, Paul Firth and his colleagues published “Mortality on Mount Everest, 1921-2006: descriptive study” in the British Medical Journal, which looked at every documented death on Mount Everest and sought to understand what commonalities might be found among the fatalities. They first distinguished between deaths below 8000 meters as climbers and their guides traversed areas prone to avalanches, crevasses, and other features of the mountain, and the deaths that took place above 8000 meters, where the mountain is generally more stable but fatigue and altitude sickness are the greatest dangers. On the lower part of the mountain, guides were more likely to be the ones who died, which the authors surmise is because the guides make multiple trips up and down the climbing route, setting ropes and bringing supplies up to the higher camp, before they guide the climbers along the route they found and made more safe. When it came to the deaths above 8000 meters, however, things reversed, and they noticed some shocking numbers:

Table 3 presents data on the mountaineers who died after reaching 8000 m. Fifty three (56%) died during the descent, 16 (17%) after turning back below the summit, and nine (10%) during the ascent. The stage of the summit bid was unknown for 12 mountaineers (13%), and four (5%) died before leaving the final camp.

Look at those top three figures again: 10% died while making the push for the summit, and 73% died while descending. For every death going up, there were 7 going down.

Maybe these climbers who died on the way back down pushed too hard going up, and had nothing left for the descent. Maybe they became disoriented because of lack of oxygen and quit thinking clearly. Maybe they were so excited at having made it to the top that they got sloppy as they turned around and headed down the mountain.

Whatever the cause, the study was clear: descending from the peak is more deadly that making the climb up. As our veteran climber cited above put it:

Burke said that although all climbers want to reach the summit, that objective alone can be a problematic.

“The summit is only halfway,” she said. “Your ultimate goal should be to make it back to camp alive.”

I look at the images of the folks protesting the “stay-at-home” orders issued to fight the COVID-19 epidemic, and their cheers of things like “We made it! We stopped the disease! Now let’s open things up again and get back to work!” I read the tweets to “liberate” this or that state, cheering on those who think the task is done. Then I think of the mountain climbers cheering at having reached the top of the mountain, who don’t realize how dangerous things can be on the way back down. That’s what worries me about all the talk of opening back up right now.

Yes, some places may have reached the peak of new infections, the peak of ICU bed usage, and the peak number of intubated patients. But here’s the thing: we are still on the mountain. Getting to the top is great, but the goal is to make it back to camp alive.

I don’t want to minimize the accomplishment of the climb, whether speaking of those who scale mountains or those who have been struggling to keep ahead of the increasing numbers of those hit by COVID-19. But relatively speaking, climbing the mountain is the easy part. It’s the descent that’s much more likely to kill. Face it, people: This journey has a long way to go, with plenty of opportunities for negligence and for misplaced cheering which will give life to a virus that deals out death.

This is no time for getting complacent or sloppy. Stay home, stay safe, save lives.

COVID-19 Tick-Tock Redux — Gridlocked Edition

[Check the byline, thanks! /~Rayne]

On March 25 I published a post in which I counted out the anticipated time required from a surge of new COVID-19 exposures to the date when the exposed persons would likely be recovered, dead, or free of SARS-CoV-2 virus.

At that time the last big public event at which people would have gathered closely and ignored social distancing was St. Patrick’s Day on March 17. Several states issued shelter-in-place/Stay Home orders after the last of the green beer was served, among them Michigan on March 23.

See Marcy’s post for a list of other states’ lockdown orders.

Of course Trump’s malignant narcissism, megalomania, and oppositional defiant disorder kicked in several times during his near-daily coronavirus briefing cum re-election campaign rally. He has champed at restraints on business, in part because Trump organization businesses have been shut down and cut into whatever their revenue streams may be, and in part because his good-old-boy network has been prodding him about the market and their businesses’ lack of revenue.

Which in turn has been used by the right-wing and white nationalists to foment unease and dissension among the Tea Party-ish types.

Like these embarrassments to my state.

Photo: Jeff Kowalsky/AFP via Getty Images

While the DeVos family denies having any ties to the Michigan Freedom Fund and the Michigan Conservative Coalition which organized the “Operation Gridlock” protest for this Wednesday in Lansing, somebody surely funded the groups behind these racist feckwits.

And somebody organized these mouthbreathing zombies in Ohio so they would protest in Ohio’s capital city Columbus at the same time.

Photo: Joshua A. Bickel/Columbus Dispatch

And somebody organized these sheep-dip-for-brains in Kentucky as well, also protesting in Kentucky’s capital city.

Sure feels like Tea Party 2.0, just missing the tea bags.

But it’s possible there’s some other entity behind this neatly coordinated multi-state tantrum. Let’s not forget that in 2016 a foreign influence operation persuaded Floridians to hold rally-like pro-Trump events via Facebook.

Somebody knows exactly who the easily motivated Trumpists are who would jump in their car on relatively short notice. It’s just not clear yet whether this was homegrown or if there was help from abroad. Such effort could explain the number of Trump flags and other pro-Trump paraphernalia present at these protests. It would also explain the presence of the far right Proud Boys.

Whatever the case, these whiny morons protesting the lockdowns in their respective states as incursions against their freedoms have likely spread COVID-19 amongst themselves due to their lack of adequate social distancing.

That photo of the mouthbreathers in Columbus fogging up the glass is a perfect example of the aerosolized exhalation humans give off and other humans breath in when there is poor air circulation and a lack of distance between humans. It’s highly possible this photo captured the moment of exposure between individuals. I do hope some well-masked journalist asked these people their names so they could follow up with them:

— in 5 days time when infection has likely set in and earliest symptoms begin;
— in 10-14 days when mild cases will have symptoms and severe to critical cases will seek medical treatment or hospitalization; and again
— in 21-28 days when the exposed have been hospitalized, treated, begun to recover, or died leaving their loved ones behind to answer questions.

We’ll be watching the calendar for the wave of new cases which will likely start this weekend.

Calendar: days until primary and secondary exposures post-Gridlock have cleared

Thanks to these thoughtless morons demanding their freedom to buy lawn fertilizer and visit their hair colorist right the fuck now, the rest of us could be looking at lockdown extended to Memorial Day.

Yes, it will be nearly the end of May until the secondary exposures and infections die out after the primary wave of new exposures recover or fade.

It was bad enough that we will likely have a small wave of new cases because of resistance from evangelical and fundamentalist Christian churches which insisted on holding services for Easter. Those exposures would result in new cases from a primary exposure requiring recovery through the first week of May.

Freedom for the rest of us is sadly dependent on waiting out the illness and death of the persuadable and stupid.

This is an open thread.