Prevalence

I think we’re going to see a lot more reports like this:

BOSTON — The Centers for Disease Control and Prevention is now “actively looking into” results from universal COVID-19 testing at Pine Street Inn homeless shelter.

The broad-scale testing took place at the shelter in Boston’s South End a week and a half ago because of a small cluster of cases there.

Of the 397 people tested, 146 people tested positive. Not a single one had any symptoms.

“It was like a double knockout punch. The number of positives was shocking, but the fact that 100 percent of the positives had no symptoms was equally shocking,” said Dr. Jim O’Connell, president of Boston Health Care for the Homeless Program, which provides medical care at the city’s shelters.

particularly over time. The article goes on to discuss the implications of those results for testing in Boston’s homeless shelters but I think there’s a lot more to it than that. The assumptions behind much of present policy include that, for example, it’s possible to avoid exposure to SARS-CoV-2. What if it’s sufficiently widespread that you can’t?

Another possible issue is that whatever test they’re using is giving lots of false positives. As I’ve pointed out before a test that produces lots of false positives and lots of false positives is pretty dubious. I wouldn’t want to use its results as a guide for policy.

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Modeling COVID-19

I found this article at STAT by Sharon Begley interesting:

A widely followed model for projecting Covid-19 deaths in the U.S. is producing results that have been bouncing up and down like an unpredictable fever, and now epidemiologists are criticizing it as flawed and misleading for both the public and policy makers. In particular, they warn against relying on it as the basis for government decision-making, including on “re-opening America.”

“It’s not a model that most of us in the infectious disease epidemiology field think is well suited” to projecting Covid-19 deaths, epidemiologist Marc Lipsitch of the Harvard T.H. Chan School of Public Health told reporters this week, referring to projections by the Institute for Health Metrics and Evaluation at the University of Washington.

and

The chief reason the IHME projections worry some experts, Etzioni said, is that “the fact that they overshot” — initially projecting up to 240,000 U.S. deaths, compared with fewer than 70,000 now — “will be used to suggest that the government response prevented an even greater catastrophe, when in fact the predictions were shaky in the first place.”

That could produce misplaced confidence in the effectiveness of the social distancing policies, which in turn could produce complacency about what might be needed to keep the epidemic from blowing up again.

If you’re not already aware of it you may find this informative:

There are two tried-and-true ways to model an epidemic. The most established, dating back a century, calculates how many people are susceptible to a virus (in the case of the new coronavirus, everyone), how many become exposed, how many of those become infected, and how many recover and therefore have immunity (at least for a while). Such “SEIR” models then use what researchers know about a virus’s behavior, such as how easily it spreads and how long it takes for symptoms of infection to appear, to calculate how long it takes for people to move from susceptible to infected to recovered (or dead).

“The fundamental concept of infectious disease epidemiology is that infections spread when there are two things: infected people and susceptible people,” Lipsitch said.

Newer, “agent-based models” are like the video game SimCity, but with a rampaging pathogen: using computing power unimagined even a decade ago, they simulate the interactions of millions of individuals as they work, play, travel, and otherwise go about their lives. Both of these approaches have often nailed projections of, for instance, U.S. cases of seasonal flu.

The IHME model doesn’t use either approach.

If I were made of money and had nothing but time, I would try feeding every shred of information we have on people who’ve contracted and people who’ve died of COVID-19 on a day by day basis into a neural net. What you’d get from the exercise would probably not be actionable but it would be interesting if it were better able to predict incidence and outcomes than the “tried and true” approaches.

I suspect that none of the models are actually much use as a guide to policy-makers because they depend so greatly on their assumptions. A reality of model creation is that what a model produces for you depends on what you put into it, particularly on the model’s assumptions. For example:

how many people are susceptible to a virus (in the case of the new coronavirus, everyone)

is something we don’t necessarily know is true or false. It’s an assumption. It may be that some previous pathogen is enough like SARS-CoV-2 that those who contracted that previous pathogen and survived have some level of immunity to the virus we’re facing now.

Additionally, “susceptibility” has more than one component. The component referred to above is those who have immunity because they’ve already had the disease and that’s given them some level of immunity over some period of time. That, too, is an assumption. It may be true or false.

Some people are immune to some pathogens by virtue of hereditary or congenital immunity. For example, some are immune to HIV. There are some forms of cancer which strike people who have certain genes. We simply don’t know enough to claim with any confidence that everybody is susceptible to SARS-CoV-2. We don’t know that everybody is susceptible to the flu.

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Just a Cigar?

I have been running across a bumper crop of conspiracy theories about SARS-CoV-2. Pat Lang, whose opinion I generally regard highly, is convinced that the virus did not just originate in China but is a Chinese plot. Maybe he’s right or maybe he’s just lost in the “wilderness of mirrors”.

This article at Forbes, mostly devoted to the gamesmanship of Gilead’s announcements, expresses a different notion but a conspiracy theory all the same:

Bizarrely, China has just suspended one trial of the drug Remdesivir in Jin Yin-tan hospital in the outbreak capital of Wuhan and terminated another in Bin Cao Beijing, and the government report says, “The epidemic of COVID-19 has been controlled well at present, no eligible patients can be recruited.”

It is possible the Chinese government are worried Remdesivir is too effective and have moved to shut down the trials over fears the US drug could corner the global market. However, further tests are underway on the US west coast, including hundreds of hospitals and care homes.

Studies are currently being conducted at universities like University of Alabama at Birmingham School of Medicine – Infectious Disease, University of California, San Diego Health Jacobs Medical Center, and University of California Los Angeles Medical Center – Westwood Clinic.

Worldwide testing has begun in France, including studies in Paris, Nantes and Lille, there is testing underway in Oslo, Norway, and also in The Democratic Republic of the Congo in Africa.

I suspect that Remdesivir’s being covered on the news this morning won’t hurt Gilead’s share value, either.

My view is that sometimes a cigar is just a cigar, as Freud observed about images in dreams. Maybe China is ending its trials of the drug because they have just run out of patients. That seems incredible to me but maybe it’s true. The truth will emerge in time.

However great our sense of urgency, the real world is not a movie and not everything will be revealed in 110 minutes.

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The Most Important Questions in the World

Despite our daily briefing from mayor, governor, and president and the focus of our major media outlets notwithstanding, the most important questions in the world are not about the United States and SARS-CoV-2 but about India and the virus.

India has not tested very many people at this point—about 1% as many relative to its population as the United States which many people contend is too few. It has been claimed with some reason that were India to test 10 times as many people it would identify 10 times as many cases of COVID-19.

Neither South Korea nor Japan nor Germany nor the United States is the model for the many poor, populous countries in the world. India is. If India cannot control COVID-19, it will be a global disaster however the U. S. fares.

India has some handicaps. Not only is it poor, populous, and its cities densely populated it has terrible air quality and diabetes is believed to be quite common among its population. It has a fraction of the physicians, hospital beds, and ventilators relative to its population as the U. S. and the countries of Europe do. But it has advantages, too. Its health care system can be of higher quality than in many other poor, populous countries. It is the world’s largest producer of hydroxychloroquine. The entire country has been on lockdown for weeks. And it is hoped, at least, that India’s climate will stymie the virus, especially during the summer.

The history of SARS-CoV-2 will be written in India. If the worst case scenario is realized, millions will die there. And in Nigeria, Indonesia, Bangladesh, Malaysia, and other poor, populous countries.

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Things To Come

At Politico John F. Harris muses over a “backlash” that may emerge over the “stay at home” directives. Much of the piece consists of chortling about supposed discomfiture of Rand Paul in contracting the virus but he then turns to more substantive observations:

Now that Paul has recovered—he says he felt fine and symptom-free the whole time—it is a good time to ask: Are we sure that the pandemic joke will ultimately be on him?

What if the opposite is true? Far from rendering Paul’s brand of politics irrelevant, it seems possible, even probable, that the wake of the coronavirus will be a powerful boost to the animating spirt of libertarianism: Leave me alone.

Among the questions looming over American politics is about the nature of what promise to be multiple backlashes over different dimensions of the coronavirus crisis. Most obvious is what price Trump pays for his administration’s tardiness in responding to the contagion in its early stages. Less obvious is what price supporters of activist government pay for the most astounding and disruptive intervention in the everyday life of the nation since World War II.

The imminent libertarian surge is not a sure thing but it more than a hunch. In informal conversations, one hears the sentiment even from people I know to be fundamentally progressive and inclined to defer to whatever health officials say is responsible and necessary to mitigate the worst effects of coronavirus. It is possible both to support the shutdown and powerfully resent it — the draconian nature of the response, and the widespread perception that to voice skepticism of any aspect of its necessity is outside respectable bounds.

The absolutist nature of the country’s shutdown and the economic rescue package have democratic consent—enacted by a bipartisan roster of governors and overwhelming votes in Congress—but it was the kind of consent achieved by warning would-be dissenters, Are you serious? There is no choice!

Many people concluded that for now there is nothing to do but suck it up. It won’t be surprising if some of those people eventually have an intense desire to spit out.

If so, this would be entirely consistent with the history of crises, both recent ones and more distant. Very often, after some cataclysmic external event, politics responds in ways that scramble normal divisions and create the impression—as in that recent 96-0 vote—that familiar ideological dynamics have been suspended.

Almost always, this is an illusion. Ideology hasn’t been suspended. It has been forcibly suppressed—in ways that inevitably will come roaring back, sometimes in highly toxic ways.

He then turns to a comparison I think is completely specious:

The most vivid example in American history likely was around World War II. As the world was aflame, but the United States not yet engaged in hostilities, the country was bitterly and intensely divided over the all-consuming question of that era: intervention or isolation. Then came Pearl Harbor, and the debate ended in an instant. Isolationism looked to be a defunct ideological force. Except it wasn’t really. The movement’s essential spirit—fear of corrupt and scheming interests beyond American borders—found new and malicious expression in McCarthyism in the late 1940s and early 1950s.

That’s basically nonsense or else he’s using an eccentric definition of “isolationism” to mean, presumably, “beliefs held by people I don’t like”. The attack on Pearl Harbor killed isolationism as a political force in the U. S. There was more than one kind of isolationism (basically Jacksonian and Jeffersonian) and all varieties have largely been silenced as a consequence of the attack. The U. S. could no longer shut itself off from the rest of the world and there was a fear that the Atlantic and Pacific could no longer protect the U. S. mainland. That and the American Civil War are the sources of our present trigger-happiness. We do not want to fight a war within our borders and have decided that the best way to prevent that is to ensure that wars that start elsewhere end elsewhere as well.

It is not isolationist to think that when a foreign power has infiltrated not just your government but many other of your institutions as well that something should be done about it. But Joe McCarthy was no libertarian and conflating him with libertarians as this article does is not constructive.

IMO the longer, the stricter, and the more hypocritical “shelter in place” directives are, the greater the chafing against them will become. The scene yesterday in Lansing, Michigan was a mild preview of what is to come.

What do I mean by “hypocritical”? Chicago Mayor Lori Lightfoot was called out, embarrassingly, on having her hair done. She blurted out a feeble explanation of being the “face of Chicago” which I guess was better than “Suck it up, peasants” but everybody knew that’s what she meant. Police officers not following “social distancing” guidelines or facemask directives are other examples. You can’t make one set of rules for politicians and public employees and another for everybody else.

Arbitrary determinations of what are or are not essential businesses are problematic as well. Here lawn services are on the list of “essential businesses”. ‘Splain me, Lucy. Are clothing stores that sell candy bars at their sales counters essential while those that do not aren’t?

I continue to hear claims about “bending the curve” but still see that as mostly wishful thinking. Consider this graph from the Illinois Department of Public Health:

Each succeeding bar of that columnar bar chart is taller by a few than the preceding. That is not “bending the curve” and the state has had a “stay at home” directive in place for nearly a month now.

If “stay at home” directives remain in place long enough, they will inevitably disrupt the food supply chain and elected officials will have much, much more to worry about than not overloading the health care system.

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Legislate In Haste

Repent at leisure. Forbes reports that there is, surprise!, a provision in the CARES “stimulus” act that we might want to be corrected:

While wealthy Americans are not eligible for the comparatively measly $1,200 stimulus checks that are now being disbursed to many Americans, they are on pace to do even better. 43,000 taxpayers, who earn more than $1 million annually, are each set to receive a $1.7 million windfall, on average, thanks to a provision buried in the Coronavirus Aid, Relief, and Economic Security (CARES) Act.

You may or may not be surprised that some of the language conveniently inserted into the $2.2 trillion-dollar Coronavirus Aid, Relief, and Economic Security Act (CARES) skews heavily in favor of the wealthy. The provision doling out literally millions of dollars is aimed at a limitation that was created in 2017 when Republicans overhauled the tax code. It “temporarily suspends a limitation on how much owners of businesses formed as “pass-through” entities can deduct against their non-business income, such as capital gains, to reduce their tax liability,” according to The Washington Post.

and

“For those earning $1 million annually, a tax break buried in the recent coronavirus relief legislation is so generous that its total cost is more than total new funding for all hospitals in America and more than the total provided to all state and local governments,” said Doggett. “Someone wrongly seized on this health emergency to reward ultrarich beneficiaries, likely including the Trump family, with a tax loophole not available to middle class families. This net operating loss loophole is a loser that should be repealed.”

Policy is hard and it’s a lot easier to enact flawed legislation in a panic than it will be to amend that legislation once enacted into law.

IMO there are serious constitutional questions about the legality of the CARES act, e.g. the pesky Origination Clause in the Constitution. That there was an emergency and how could you possibly expect our legislators to know what was in the law for which they voted are not good excuses.

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China’s Coronavirus Cover-Up

At Newsweek Jason Lemon reports that a group of “international policy experts and politicians” have penned an open letter criticizing China’s response to the COVID-19 pandemic:

A group of international policy experts and politicians strongly criticized China’s government in an open letter about its coverup and mishandling of the coronavirus pandemic, referring to the botched response as a “Chernobyl moment.”

The letter was published Tuesday on the website of Canada’s Macdonald-Laurier Institute, a national public policy think tank based in Ottawa. It was signed by more than 100 policy experts, lawmakers and academics who hail largely from North America, Europe and Oceania.

“While the exact source and spread of the virus are not clear yet the question of origin is highly important, for the people of China and for all humankind: only by understanding how this global disaster could emerge we can prevent it from happening again,” the letter argued.

It went on to say that the origins of the global pandemic “are in a cover-up by CCP [Chinese Communist Party] authorities in Wuhan, Hubei province.”

To my eye there were few if any Americans among the signatories but they did appear to be notable neoconservatives. I do not believe this will be the last such declaration. It may well turn out that SARS-CoV-2 will be the least of China’s problems. As one commentator noted, the CCP has taken an axe to their own business model.

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Not Exactly a Roadmap

It’s not exactly a roadmap but it’s a start. California Gov. Gavin Newsom outlined six criteria for reopening the Golden State:

California’s six indicators for modifying the stay-at-home order are:

  • The ability to monitor and protect our communities through testing, contact tracing, isolating, and supporting those who are positive or exposed;
  • The ability to prevent infection in people who are at risk for more severe COVID-19;
  • The ability of the hospital and health systems to handle surges;
  • The ability to develop therapeutics to meet the demand;
  • The ability for businesses, schools, and child care facilities to support physical distancing; and
  • The ability to determine when to reinstitute certain measures, such as the stay-at-home orders, if necessary.

Since I have been calling for just such criteria to be promulgated, I found this an encouraging first step. I was disappointed, however, because none of the criteria were quantified. Without that you cannot determine whether progress is being made. That’s the sort of commitment that I think is needed rather than simple aspirational goals. Does anyone actually disagree with any of them? The devil is in the details.

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Seasonality, Susceptibility, and Transmission of SARS-CoV-2

If you’re following the scholarship relating to the present pandemic at all closely, you should find this paper from Science very illuminating. Be aware that it’s pretty technical. In the paper they explore the effects of seasonality (the tendency of a virus to return on a seasonal basis) and susceptibility (which includes but is not limited to acquired immunity) on prevalence. Here’s a snippet from the conclusion:

In summary, the total incidence of COVID-19 illness over the next five years will depend critically upon whether or not it enters into regular circulation after the initial pandemic wave, which in turn depends primarily upon the duration of immunity that SARS-CoV-2 infection imparts. The intensity and timing of pandemic and post-pandemic outbreaks will depend on the time of year when widespread SARS-CoV-2 infection becomes established and, to a lesser degree, upon the magnitude of seasonal variation in transmissibility and the level of cross-immunity that exists between the betacoronaviruses. Social distancing strategies could reduce the extent to which SARS-CoV-2 infections strain health care systems. Highly-effective distancing could reduce SARS-CoV-2 incidence enough to make a strategy based on contact tracing and quarantine feasible, as in South Korea and Singapore. Less effective one-time distancing efforts may result in a prolonged single-peak epidemic, with the extent of strain on the healthcare system and the required duration of distancing depending on the effectiveness. Intermittent distancing may be required into 2022 unless critical care capacity is increased substantially or a treatment or vaccine becomes available. The authors are aware that prolonged distancing, even if intermittent, is likely to have profoundly negative economic, social, and educational consequences.

or, as others have put it more succinctly, we need to ensure that the cure is not worse than the disease.

There is an enormous number of things we simply don’t know. In the past I have suggested that the closest analogy we have to SARS-CoV-2 is the seasonal flu and that’s the assumption on which this paper is predicated but we just don’t know. The paper is silent, as it should be, on whether “highly-effective distancing) or contact tracing are practical in the United States. I incline towards believing that neither can be due to our physical and population size, the structure of our society, and our low degree of social cohesion.

I strongly believe that investigations of this sort should inform policy which is not to say that experts should be making the policies. Relying on science and putting policy decisions in the hands of scientists are not identical. Indeed, effective policy cannot be left to the experts.

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Update on Abbott’s Rapid COVID-19 Test

Abbott has updated its information on its rapid COVID-19 test:

  • Through Saturday, April 11, we have shipped 566,000 of our rapid ID NOW tests to all 50 states, Washington DC, Puerto Rico and the Pacific Islands. The majority of these tests have been sent to outbreak hotspots and we’ve asked that customers prioritize frontline health care workers and first responders.
  • We’re currently manufacturing 50,000 tests per day, plan to increase ID NOW manufacturing capacity to 2 million tests a month by June and are working to expand beyond that.
  • We have shipped more than 1 million tests to customers across the U.S. We’re also shipping these tests to customers throughout the world.
  • There are approximately 200 m2000 instruments in hospital, academic center and reference labs throughout the U.S.

I’m having a bit of trouble reconciling the numbers I’m seeing not just here but in other things I’ve read. In particular I had previously read that there were 18,000 ID Now devices installed in the U. S. There’s a big difference between 200 and 18,000. Is there more than one model? I researched that and couldn’t identify one. Is there a predecessor model with a larger user base? Capability and compatibility may be issues.

Whatever the case scaling up to 2 million tests per month by June sounds like a lot but isn’t particularly hopeful if your objective is testing everyone in the U. S. let alone everyone in the world and the thought of scaling up other, less automated testing approaches is even more discouraging.

That doesn’t even start to address the issue of false negatives and positives which originally led me to stumble across Abbott’s update. I’ve read that the number of false negatives is 30% which is being interpreted as multiple tests per individual are needed.

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