Links 5/22/20

Links for you. Science:

Strong Social Distancing Measures In The United States Reduced The COVID-19 Growth Rate
Thirty-six Thousand Feet Under the Sea
‘Weird as hell’: the Covid-19 patients who have symptoms for months (about five percent of cases–I’ve been saying this is a problem)
Where’s the data? In a pandemic, now is no time to sit on Covid-19 trial results
Antibody study shows just 5% of Spaniards have contracted the coronavirus


OK But What If This Story Dropped in 2016? The FBI has found a Saudi military trainee who orchestrated a terrorist attack on a U.S. military base in Pensacola, Florida had ties to al Qaeda.
‘We’ve been muzzled’: CDC sources say White House putting politics ahead of science
Arkansas coronavirus outbreak linked to church services (38% contracted COVID-19, three percent died)
This Is the Last Hurrah for All the Fake Conspiracies Trump Has Fed the Rubes Since 2015
26 people run the Metrorail system, and their office has major safety issues
Some Restaurant Owners Want to Close. The Problem Is, It’s Not That Simple.
Just Put The Cash On The Table
DC Students Could Be in Classrooms Just 1 or 2 Days Per Week This Fall
Health leaders: We stuck together to #StayHome, now we can start together to #OpenSafely
Trump just said the corrupt part out loud
We Should Help Workers, Not Kill Them
EPA staff warned that mileage rollbacks had flaws. Trump officials ignored them.
China updates its ‘Art of (Hybrid) War’
Joe Biden Is Pivoting to the Left. What? Why?
Why a battle between tech visionaries, privacy advocates, Uber, and transportation officials is about much more than scooter data
Asian American doctors and nurses are fighting racism and the coronavirus
On Race and Masculinity in the Age of Face Masks
How France Lost the Weapons to Fight a Pandemic
Republicans are serious about voter suppression. Here’s how to stop them.

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Some Thoughts on the Mid-Term Future of COVID-19

I’m reluctant to engage in any kind of COVID-19 prognostication because figuring out how the human side of the equation will react is, as always, very challenging (and that’s an understatement). That said, I want to follow up on a post I wrote earlier this week, and tie it to an excellent article by Kai Kupferschmidt–and I wish I had seen his article before writing my post. Anyway, to revisit my post about chuckleheads who want to return to the gym*:

First, the reality is that everyone who uses that gym will be fine…until they’re not. As Yogi Berra would have put it had he been an epidemiologist, the best way to avoid getting an infectious disease is to avoid people who are infected. That is, right now, the odds of a suburban area off the beaten path (tourist season hasn’t started yet in Wildwood, NJ) having very many COVID-19 positive people is low. Additionally, a fair number of the infected will be at home (though not the presymptomatic people) and some of the infections will be within a household, so the number of contacts with an infected person will be limited.

That gym will be fine, until someone who is sick decides to use it, at which point there is a non-negligible chance of a local outbreak (like the Provisional IRA used to say, it only has to get lucky once).

At a larger scale, over the next few months, as various locations in the U.S. loose restrictions, what I think we’ll see is a patchwork of local outbreaks, that have a high degree of randomness. Luck will definitely be a player in all of this, as an infected individual happens into an ‘open’ community–and if things break wrong (for the humans, not the virus), then there’s an outbreak. In other words, the frequency is so low and patchily distributed that many people haven’t been exposed to it at all, and won’t be for some random length of time.

What I didn’t add is that this will be like sparks that set off fires: some will self-extinguish immediately, others might burn a small bit and then go out (e.g., one or two people), and some might turn into serious fires (lots of people). But even a massive sweep is really lots of little outbreaks. The reason I thought this–rather inchoately–is because the spread of SARS-CoV2 is itself patchily distributed as Kupferschmidt notes (boldface mine):

But SARS-CoV-2, like two of its cousins, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), seems especially prone to attacking groups of tightly connected people while sparing others. It’s an encouraging finding, scientists say, because it suggests that restricting gatherings where superspreading is likely to occur will have a major impact on transmission, and that other restrictions—on outdoor activity, for example—might be eased…

Most of the discussion around the spread of SARS-CoV-2 has concentrated on the average number of new infections caused by each patient. Without social distancing, this reproduction number (R) is about three. But in real life, some people infect many others and others don’t spread the disease at all. In fact, the latter is the norm, Lloyd-Smith says: “The consistent pattern is that the most common number is zero. Most people do not transmit.”

…Estimates of k for SARS-CoV-2 vary. In January, Julien Riou and Christian Althaus at the University of Bern simulated the epidemic in China for different combinations of R and k and compared the outcomes with what had actually taken place. They concluded that k for COVID-19 is somewhat higher than for SARS and MERS. That seems about right, says Gabriel Leung, a modeler at the University of Hong Kong. “I don’t think this is quite like SARS or MERS, where we observed very large superspreading clusters,” Leung says. “But we are certainly seeing a lot of concentrated clusters where a small proportion of people are responsible for a large proportion of infections.” But in a recent preprint, Adam Kucharski of LSHTM estimated that k for COVID-19 is as low as 0.1. “Probably about 10% of cases lead to 80% of the spread,” Kucharski says.

That could explain some puzzling aspects of this pandemic, including why the virus did not take off around the world sooner after it emerged in China, and why some very early cases elsewhere—such as one in France in late December 2019, reported on 3 May—apparently failed to ignite a wider outbreak. If k is really 0.1, then most chains of infection die out by themselves and SARS-CoV-2 needs to be introduced undetected into a new country at least four times to have an even chance of establishing itself, Kucharski says. If the Chinese epidemic was a big fire that sent sparks flying around the world, most of the sparks simply fizzled out.

To tie this back to predictions, I think the U.S. will be alright, even with loosened restrictions, over the summer. There will be some localized flare ups, but no massive spread. A gym’s patrons might be hit hard (eventually), but it eventually burn itself out. But when September rolls around and schools and universities are back in session, Memorial Day weekend is over, people get increasingly lax, state to state travel picks up, and workers start returning to offices, all of that mixing among different groups means that one unlucky event can be spread through multiple social circles (e.g., your workplace, your kids’ school, etc.). There will be more sparks and more flammable terrain, and the number of cases will surge.

If we’re not careful, and I haven’t seen much evidence we will be (and the lengthy presymptomatic period of the virus makes it really challenging), then September and October could be really bad, even though the summer won’t be. Though I hope I’m wrong about the fall, obviously.

*Yes, they’re chuckleheads.

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Links 5/21/20

Links for you. Science:

Gilead should ditch remdesivir and focus on its simpler and safer ancestor
Coronavirus Test Shortages Trigger a New Strategy: Group Screening
Iowa Disease Experts Say Face Shields Could Help Country Reopen Safely
JetBlue’s Founder Helped Fund A Stanford Study That Said The Coronavirus Wasn’t That Deadly. A Stanford whistleblower complaint alleges that the controversial John Ioannidis study failed to disclose important financial ties and ignored scientists’ concerns that their antibody test was inaccurate.
Experiment shows human speech generates droplets that linger in the air for more than 8 minutes


The Post-Pandemic Workweek Should Be Reduced by 10 Hours
F.D.A. Halts Coronavirus Testing Program Backed by Bill Gates (ignore the FDA until arrested)
He thought the coronavirus was ‘a fake crisis.’ Then he contracted it and changed his mind. (I keep telling people this thing is nasty)
West Wing nervous breakdown — and media still won’t demand Trump resign
How We Got to Sesame Street
Nobody belonged to the salt marshes of coastal Georgia more than Ahmaud Arbery. His family’s roots there run more than 200 years deep. A native of those same marshes writes about who Ahmaud was, how well he was loved, and what his community must reckon with in the wake of his murder.
Two Coasts. One Virus. How New York Suffered Nearly 10 Times the Number of Deaths as California.
Racism, Rather Than Facts, Drove U.S. Coronavirus Travel Bans
DC Public Library Board of Trustees Votes to Eliminate All Overdue Fines
Fed shipment of Q-tip-style coronavirus swabs puzzles Washington state officials, latest wrinkle in supply woes (heckuva job, Kushie!)
What It’s Like To Care For A Loved One With Dementia In The Midst Of A Pandemic
Anti-vaccine movement could undermine efforts to end coronavirus pandemic, researchers warn
The tyranny of the Congressional Budget Office
Alaska legislator compares pandemic safety measures at Capitol to Nazi treatment of Jews
There’s No Coronavirus Plan. There’s Just Donald and Jared. (there is a plan, but the observations about Kushner are very good)
Puerto Rico to hold statehood referendum amid disillusion
Coronavirus infected apres-ski in the Austrian Alps; criminal probe and litigation now follow
Peter Brancazio, Who Explored the Physics of Sports, Dies at 81
The New New Deal
COVID-19 impacts every corner of the Navajo Nation

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Secondary Effects of COVID-19: Bathing the World in a Dilute Solution of Quaternary Ammonium Compounds

Because you need one more fucking thing to worry about.

One of the consequences of a global pandemic is that we are forced to do things that will have harmful consequences to combat the pandemic. Using less mass transit exacerbates global warming, but probably lessens the spread of COVID-19, especially when it is not under control (as is the case in most of the U.S.). One thing that hasn’t been considered in terms of its harmful effects–but still needs to be done–is the use of disinfectants. Obviously, they need to be used in hospitals and other high-risk settings, such as nursing homes, even in the absence of a pandemic. And keeping your home and workplace clean is good!

But we’re also seeing the use of disinfectants in places where they’re typically not used (or used in such amounts) such as subways and outdoor areas (the latter is just general spraying disinfectants). One commonly used disinfectant, and which is effective against many viruses, is the class of compounds known as quaternary ammonium compounds (‘QACs’). When you hear about cleaning compounds that have a ‘lemon scent’, they’re usually QACs–not because QACs have a lemon scent, but because QACs smell…not good, and the lemon scent masks the smell (imagine a hybrid of mothballs and worn socks. Not good). If you’ve ever used a cleaner than has things in it named ‘benzalkonium chloride’, such as 409 cleaner*, then you’ve used QACs.

To be clear, QACs are very good at killing enveloped viruses, fungi, and bacteria. So you know what that means: bacteria evolved resistance to QACs. There are a bunch of genes that confer resistance to QACs, which biologists have cleverly called qac. One of the most common qac genes is qacEdelta1, which is found in E. coli and relatives, and co-occurs with a particular set of sulfonamide, trimethoprim, and streptomycin resistance genes. Often, tetracycline resistance genes and erythromycin resistance genes travel along with qacEdelta1 (mercury resistance genes too. It’s a real party). While none of these genes are ‘last line’ antibiotics, they are still used, and we would like to keep those older antibiotics working for as long as we can.

It gets worse (you didn’t think I was finished, did you?). Looking at some genomic data, I estimate that about seventy percent of isolates that have a KPC carbapenemase–a gene that confers resistance to virtually of the penicillin derivatives including the last line carbapenemases–also have qacEdelta1. It’s typically not physically linked to KPC carbapenemases; it’s usually on a different plasmid–a mobile ‘mini-chromosome. But they are found in the same cell, so exposure to QACs provides these isolates a selective advantage, meaning it will be that much harder to reduce the frequency of KPC carbapenemases (and other antibiotic resistance genes) solely through less use of those drugs.

All that said, we do need to use disinfectants, including QACs, especially in the face of a massive viral outbreak for which we have no vaccine or proven therapies. But maybe spraying them on city streets isn’t the best idea ever.

*Not that you can find 409 or other QAC-based cleaners in most stores in the U.S. Got Non-medical PPE?

Posted in Antibiotics, COVID-19 | 2 Comments

Links 5/20/20

Links for you. Science:

Moving Personal Protective Equipment Into the Community: Face Shields and Containment of COVID-19
The airborne lifetime of small speech droplets and their potential importance in SARS-CoV-2 transmission
Snakes have friends too
Without A Vaccine, Herd Immunity Won’t Save Us
Georgia officials warn of 4-foot-long invasive lizards that eat ‘anything they want’


You Don’t Need Invasive Tech for Successful Contact Tracing. Here’s How It Works. (must-read)
Planning the Post-Pandemic City: During crises when residents flee to cars and suburbs, metropolises have panicked. This time can be different.
How are COVID-19 deaths counted?
Tumlin Talks Post-COVID Muni: Everything has changed with the pandemic. But with crisis comes opportunity
As Florida re-opens, COVID-19 data chief gets sidelined and researchers cry foul
The Lockdown Protestors Are Not Working Class (no, they’re mostly middle to upper-middle)
The Phony Coronavirus Class War: Defiance of public health directives has become a mark of right-wing identity.
Copper masks are the latest craze. Should you buy one?
James Weaver, who helped bring music to the Smithsonian museums, died after contracting covid-19
How D.C.’s Workspaces Will Fundamentally Change After COVID-19
We Asked for Your Quarantine Gripes. You DELIVERED. Jerky animals. Mysterious yardwork. And what is UP with that person playing recorder?
The Coronavirus Class War
HEALTH DEPARTMENTS: Interim Guidance on Developing a COVID-19 Case Investigation & Contact Tracing Plan
Trump’s purge just got much more corrupt. Here’s what’s coming next.
A Deeper Dive into Understanding Neighbor Covid-19 Numbers (D.C. data)
Busted: Pentagon Contractors’ Report on ‘Wuhan Lab’ Origins of Virus Is Bogus
Trump and his Republican allies have given up on COVID-19 — and now are only offering incoherent rhetoric about ‘choice’
Do not let Denmark make this mistake
It’s time to talk (and maybe just talk) about reopening (I feel this way about the mask paper: I think people should be wearing masks, but I think that modeling paper & some very credulous pundits are overstating the case–but I don’t want to be used by anti-mask assholes)

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Public Health Big Data: The Wages of Privatization

I spent a significant part of my career in and around these kinds of data, and I think the article below, while very good in terms of description of the failures of COVID-19 data collection, misses the larger picture: this is a result of massive underfunding of public data collection, and also the failures of privatized data collection. We excel at using ‘big data’ to determine what needless crap you will be more likely to buy–and by “excel”, I mean dump tons of money and personnel into that (this is a substantial part of the tech economy, which is to say, advertising). At the same time, we have massively underfunded public data collection, to the point, where most of these systems are run on shoestring budgets with too few personnel. Those personnel are almost always tasked with simultaneously keeping existing systems from collapsing, while somehow also developing new systems, while underpaid and given too few resources for the amount of work they’re expected to do (retention is an issue).

Anyway, onto the article (boldface mine):

Yet when it comes to evaluating NPI use in this pandemic, we seem unable or unwilling to muster the testing data that could inform statistical models and guide our actions. Forecasters and planners desperately need timely testing data. Yet as the absence of comprehensive public data on race and ethnicity revealed, the United States has underfunded and undermined its disease surveillance programs and done a poor job of organizing its 50 state systems for collecting and reporting testing data. The pandemic affects all states, yet states’ data are incomplete and uneven at best… The shortcomings are even more puzzling in the light of two decades of bipartisan federal efforts to build measurement and public reporting systems for health care and implement electronic health records.

The best database on testing for Covid-19 in the United States, created through valiant efforts by news media organizations to fill the gap left by the CDC, contains testing data limited to aggregated counts of the tests done each day, the states where tests were performed, and the number of positive results. The validity and reliability of the data are not fully known. Inspection of the data suggests a patchwork of inconsistent reporting from state and commercial labs. The database lacks basic information about tests such as the characteristics of the people tested, where they were tested, how they were selected for testing, and what factors led to the decision to test them. Yet these data are the best we have.

That the United States is failing such a simple test of its capacity to protect public health is shocking. Collecting and reporting public health data are not rocket science. Other countries, notably Canada and Belgium, are already reporting nationwide data on testing at the individual level, including individual demographic data (using ranges for each person to protect privacy) and other key attributes for each test. The United States was once a leader in collecting systematic federal data on population health. Now our national disease-tracking effort seems stuck with well-meaning but scattershot efforts by tech companies using cellular phone signals, social media surveys, online searches, and smart thermometers as we try to guess where Covid-19 outbreaks may be lurking. Small one-off studies using convenience samples have popped up to try to fill the vacuum with basics such as percentages of cases that are asymptomatic and of symptomatic people who seek care. Because of sampling bias, these studies are producing wildly different and nearly uninterpretable results. Estimates are so wide ranging that modelers have little choice but to default back to imprecise assumptions.

In the information age, the United States seems to be swimming in big data. This country has generated many of the world’s largest, most innovative, most profitable data companies. Yet when it comes to forecasting the spread of a major pandemic that is killing Americans and wreaking havoc on our economy, we seem oddly lost. With more than 80,000 dead and no end in sight, our national efforts seem feebler and more halting than the 19th-century work of Florence Nightingale in the Crimean War and William Farr in England, where they used systematically collected epidemiologic data and rigorous analysis to save countless lives. Would that our statistical models had such standardized, systematically collected, and readily reported data to inform them. Reopening state economies without the precision provided by analysis of rigorously reported testing data seems a peculiarly American form of madness.

Let’s talk about a couple of the specifics.

First, electronic health records aren’t about public reporting, they’re about billing. Anyone who has ever tried to get antibiotic susceptibility testing data–these are the lab tests that determine which antibiotics will be effective against bacterial infections–from private institutions knows that all of the hospital laboratory information management systems (LIMS) are variable and different, even when supposedly using the same software vendors. These systems were never designed for public health information extraction, but for billing. To the extent these LIMS inform patient care, they are designed to provide the minimal amount of information needed for a physician to treat: anything more, such as making data extraction easy for public health agencies, costs more, so it’s not a priority (to say the least). One reason why public health agencies have built sentinel surveillance systems is because it is so difficult to get this information from the existing healthcare system*.

Second, as I noted at the beginning, our ‘big data’ is not harnessed for the public good. When it is, in my experience, the companies doing the work do not have the experience, though they do have the resources–often an excess of resources–to do what needs to be done. These companies are in an excellent position to poach the expertise that exists in public health and other science agencies. Why work for a lower salary doing the same thing in government that one could do in the private sector?** This, in turn, leads to an increased dependency on these companies, and can often leave public health agencies in a very dependent position–and often with inferior systems.

If you want good public health systems, then you have to pay for them. You have to keep these expertise in the government. While that might not be possible with salaries, a good working environment and benefits helps. Part of that good working environment involves adequate resources and personnel, so workers aren’t robbing Peter to pay Paul. You have to build the expertise in house, because, if you don’t, then you’ll pay more to an external company, and often fail to get what you need. When we contrast the small size of public health budgets, much of which have little to do with electronic data collection, to the massive amounts we spend in private ‘tech’ data collection, it becomes obvious how underfunded these systems are.

You get what you pay for, and we didn’t pay for it.

*This is one more reason why we need a universal healthcare system, regardless of how BERNIE WILL PAY FOR IT? and other concerns.

**The only advantage the public sector can have is job security, though agencies are using contractors more and more, especially in the information tech areas, so that even isn’t the advantage it once was. While this patterns has accelerated under Republican rule, this first began under Al Gore’s ‘reinventing government’ initiative.

Posted in Bioinformatics, COVID-19, Funding, Public Health, We're Really Fucked | Leave a comment

Links 5/19/20

Links for you. Science:

How Coronavirus Spreads through the Air: What We Know So Far
Coronavirus shut-downs pose huge threat to Australian research jobs
High SARS-CoV-2 Attack Rate Following Exposure at a Choir Practice — Skagit County, Washington, March 2020
Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission
New Worm Species with Jewel-Like Scales Discovered in Deep Ocean Darkness: A mysterious video shows worms fighting and dancing the “jitterbug.”


Why the Neoliberals Won’t Let This Crisis Go to Waste (very interesting, even with the bad title. Should be “why the left, construed somewhat broadly, constantly loses”)
Jared Kushner Is a National Disaster: The popular perception of Trump’s son-in-law is that he’s a foppish nepotism hire, but he has a plan to enrich himself at your expense.
How Florida slowed coronavirus: Everyone stayed home before they were told to. A Tampa Bay Times data analysis and interviews with 15 experts help answer the question: Why not Florida? (and it came later, and dumb luck, and…)
Coronavirus has been devastating to the Navajo Nation, and help for a complex fight has been slow
How Not to Listen to Donald Trump. Until the president comes up with actual evidence for his allegations, we’re under no obligation to pay attention.
Major nursing home chain violated federal standards meant to stop spread of disease even after start of covid-19, records show
Phyllis George, female sportscasting pioneer, dies at 70
Covid testing is about saving lives. Trump thinks it’s just about numbers.
The U.S. Is Building A Contact-Tracer Army: As many as 180,000 contact tracers are needed, but many states face challenges in rapidly scaling up this new workforce. (not the feds though, which means the data are going to be all over the place)
Wondering what’s safe as states start to reopen? Here’s what some public health experts say.
No Vaccine in Sight. The U.S. was once at the cutting edge of pandemic prevention. Then Big Pharma took over.
The unsurpassed 125-year-old network that feeds Mumbai
Almost 90,000 dead, and no hint of national mourning. If this is a war, are these not our fallen?
The Deficit Hawks Are Circling Their Old Roosts (“The problem for Democrats, whose brand relies upon helping the wage-earning masses, is that the entire country is depending upon them to avoid a depression for the second time in a dozen years and that, once again, to meet the moment, they will have to beat back harmful yet effective rhetoric on deficits that their own party leaders, backed by many of their cocktail party peers in the elite press, help to legitimize.”)
Trump admission and covid-19 response cast light on politics and limits of D.C. statehood.
Even the Pandemic Can’t Kill the Open-Plan Office
Wisconsin’s economy is reopening and it’s a hot coronavirus mess. Don’t do what we did.
In A Pandemic, Transportation Ushers In A New Age Of Agile Experimentation
The Economics and Politics of Social Democracy: A Reconsideration
Reopen the Economy; or Charge of the Right Brigade

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