Interesting and/or Informative Coronavirus Link Dump

I see a fair amount of speculation that COVID-19 is a deliberate attempt at some kind of biological warfare. I haven’t seen any evidence presented for that theory. This article reports on actual scientists who have examined the question and found it wanting.

Andersen assembled a team of evolutionary biologists and virologists, including Garry, from several countries to analyze the virus for clues that it could have been human-made, or grown in and accidentally released from a lab.

“We said, ‘Let’s take this theory — of which there are multiple different versions — that the virus has a non-natural origin … as a serious potential hypothesis,’ ” Andersen says.

Meeting via Slack and other virtual portals, the researchers analyzed the virus’s genetic makeup, or RNA sequence, for clues about its origin.

It was clear “almost overnight” that the virus wasn’t human-made, Andersen says. Anyone hoping to create a virus would need to work with already known viruses and engineer them to have desired properties.

A nice presentation of a model that attempts to project the capacity of the health care system to handle the case load over the next few months.

You can see that Washington state is doing pretty well

Thanks to @gdyckmd for the link.

This Nature article summarizes research conducted on the passengers of the Diamond Princess cruise ship that was quarantined on February 3 in Japanese waters. Since the population was isolated and everyone received testing, often multiple times, it makes a good controlled study of the characteristics of the virus and possibly measure the effectiveness of quarantine efforts.

The DP-3T protocol stands for Decentralized Privacy Preserving Proximity Tracing. It’s a clever way to establish contact tracing in a way that doesn’t compromise privacy. The idea is that you would implement this protocol using a standard cell phone and it could keep track of contacts.

There is a useful comic that explains it


Read the whole thing

This is a pretty good explainer about why the COVID-19 outbreak is not like the flu. It’s all about the trends. There is a good graph which shows pretty well

One thing I did not know is that the flu deaths are normally combined with pneumonia since it exhibits “flu-like symptoms”.

This is a fantastic set of interactive graphs with COVID-19 data

I might even be able to embed one here

[Nope, I can’t embed it but I can one-box it.]

Everything is sourced and the data is downloadable.

Found another good perspective on data and recommendations — http://www.jasgeorgia.org/resources/Programs-Events/Events/COVID%20Shock%202.pdf

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I will look up more on “Our World In Data” … and … would be grateful for anyone else’s insight on its validity, reputation, sources, etc. If it shows a high enough level of quality and objectivity, I can see promoting it more.

Thanks for any insight on “Our World In Data”.

This article makes me feel pretty good about my City/State, but it also is exasperating to see how little of this is going on elsewhere and at the national level.

Get the politicians out and put the experts front and center. Why do we have so much trouble doing that here?

I love these genetic tracing stories. This kind of stuff feels a lot more like programming (and especially debugging) software.

It’s common to hear that it’ll take 18 months to get a coronavirus vaccine. I’m afraid that sounds a bit like magical thinking. It’d be great and the smart people are saying it’s possible but this article lays out what needs to happen.

I really like these interactive explainer things. This is the future of on-line curriculum, or at least it should be. Imaging teaching kids physics thing this kind of thing. It is still pretty difficult to pull off but the tools for creating these things are getting more and more powerful.

This kinda aligns with my thinking lately so of course I’m going to link to it.

“I’m quite certain that this is going to go in waves,” she added. “It won’t be a tsunami that comes across America all at once and then retreats all at once. It will be micro-waves that shoot up in Des Moines and then in New Orleans and then in Houston and so on, and it’s going to affect how people think about all kinds of things.”

I’ve been thinking a bit lately about the concept of the Natural Experiment and how the pandemic (specifically the reduction in human activity related to the pandemic) presents new opportunities for research. So I was glad to listen to this 99% invisible podcast that presents a few examples.

I expect a lot of PhD dissertations in a broad variety of fields will be written as a direct result of what we are experiencing now. A small silver lining I suppose.

This looks into risk assessment. The formula is

Exposure X Time 

Outdoor environments are much safer. Church services are singled out as particularly risky based on the amount of singing. Makes sense. Singing requires deeper breathing and takes multiple minutes of a whole group exhaling.

Stay-at-home orders were necessary but ruinous, economically and emotionally. Their purpose was to buy time for the country to catch its breath, steel its hospitals, and roll out a public-health plan capable of quashing the virus. Many such plans exist. Umpteen think tanks and academics have produced their own road maps for dialing society back up. These vary in their details, but are united in at least having some. By contrast, the Trump administration’s guidelines for “opening up America again” are so bereft of operational specifics that they’re like a cake recipe that simply reads, “Make cake.”

We are tragically unprepared for the future and there is no real plan, I think, beyond getting rid of our useless President in November.

This one is of particular interest to me since I do a lot of baking. The King Arthur Flour company has seen the demand for its products go through the roof. If memory serves, one of the CEOs has a PhD from Kansas State. According to the article they appear to be managing the very difficult situation pretty well.

The team briefly looked at the one part of its production capacity that was going largely untapped: the group of facilities dedicated to producing the 50-pound bags that shipped, usually in quantity, to bakeries and other food-service businesses. While home baking was taking off, bakeries were being closed down, sharply reducing demand for the big bags of flour. (To help keep some of them afloat, the company has spent $30,000 so far during the pandemic paying some of its bakery customers around the country — including Empire Baking — to bake bread and donate it to local good causes. Its own bakers have been doing the same for essential workers and those in need in Norwich.) But, frustratingly, there was no good way to convert those production lines and the associated shipping logistics to fill and deliver the five- and 10-pound bags that made sense to consumers.

I would hope that those bakeries continue to buy the 50-pound bags and then turn around and sell their surplus directly to consumers. I see that happening at our local bakeries Preserve & Gather and Coyle’s Bakeshop.

Most people don’t appreciate how much of the US Heathcare system (such as it is) still relies on the fax machine. Just another barrier we have to contend with because we refuse to consider smart reform efforts.

Ed Yong is a science writer for The Atlantic. This article is a wide-ranging indictment of the US response to the coronavirus pandemic. There are too many good quotes but here are a few:

How it exaggerates our existing inequities…

The coronavirus found, exploited, and widened every inequity that the U.S. had to offer. Elderly people, already pushed to the fringes of society, were treated as acceptable losses. Women were more likely to lose jobs than men, and also shouldered extra burdens of child care and domestic work, while facing rising rates of domestic violence. In half of the states, people with dementia and intellectual disabilities faced policies that threatened to deny them access to lifesaving ventilators. Thousands of people endured months of COVID‑19 symptoms that resembled those of chronic postviral illnesses, only to be told that their devastating symptoms were in their head. Latinos were three times as likely to be infected as white people. Asian Americans faced racist abuse. Far from being a “great equalizer,” the pandemic fell unevenly upon the U.S., taking advantage of injustices that had been brewing throughout the nation’s history.

How our leadership and its enablers have failed (and continue to fail)…

Trump never rallied the country. Despite declaring himself a “wartime president,” he merely presided over a culture war, turning public health into yet another politicized cage match. Abetted by supporters in the conservative media, he framed measures that protect against the virus, from masks to social distancing, as liberal and anti-American. Armed anti-lockdown protesters demonstrated at government buildings while Trump egged them on, urging them to “LIBERATE” Minnesota, Michigan, and Virginia. Several public-health officials left their jobs over harassment and threats.

How our science illiteracy fails us…

Science famously self-corrects. But during the pandemic, the same urgent pace that has produced valuable knowledge at record speed has also sent sloppy claims around the world before anyone could even raise a skeptical eyebrow. The ensuing confusion, and the many genuine unknowns about the virus, has created a vortex of fear and uncertainty, which grifters have sought to exploit. Snake-oil merchants have peddled ineffectual silver bullets (including actual silver). Armchair experts with scant or absent qualifications have found regular slots on the nightly news. And at the center of that confusion is Donald Trump.

Yong’s prescription, I think is spot on…

COVID‑19 is an assault on America’s body, and a referendum on the ideas that animate its culture. Recovery is possible, but it demands radical introspection. America would be wise to help reverse the ruination of the natural world, a process that continues to shunt animal diseases into human bodies. It should strive to prevent sickness instead of profiting from it. It should build a health-care system that prizes resilience over brittle efficiency, and an information system that favors light over heat. It should rebuild its international alliances, its social safety net, and its trust in empiricism. It should address the health inequities that flow from its history. Not least, it should elect leaders with sound judgment, high character, and respect for science, logic, and reason.

It’s a damn good article.

I didn’t realize how difficult it is to take viral samples from aerosols without killing them.

The research was exacting. Aerosols are minute by definition, measuring only up to five micrometers across; evaporation can make them even smaller. Attempts to capture these delicate droplets usually damage the virus they contain.

“It’s very hard to sample biological material from the air and have it be viable,” said Shelly Miller, an environmental engineer at the University of Colorado Boulder who studies air quality and airborne diseases.

Controlling for the variables is also difficult.

…the team collected air samples from a room in a ward dedicated to Covid-19 patients at the University of Florida Health Shands Hospital. Neither patient in the room was subject to medical procedures known to generate aerosols, which the W.H.O. and others have contended are the primary source of airborne virus in a hospital setting.

The team used two samplers, one about seven feet from the patients and the other about 16 feet from them. The scientists were able to collect virus at both distances and then to show that the virus they had plucked from the air could infect cells in a lab dish.

The genome sequence of the isolated virus was identical to that from a swab of a newly admitted symptomatic patient in the room.

The room had six air changes per hour and was fitted with efficient filters, ultraviolet irradiation and other safety measures to inactivate the virus before the air was reintroduced into the room.

That sounds like how real science it conducted.