Day 300: Zombie Mink

The world is at 61 million coronavirus cases, with the #1 US at 13 million, #2 India at 9 million, #3 Brazil at 6 million, #4 Russia at 2 million, and #5 France at their heels, also with 2 million.

Mink are rising again from their hastily-dug, shallow graves in Denmark. The graves must therefore be guarded against intrusion from other wildlife. (American mink themselves are not native to Europe.)

In other mink news, the Netherlands have culled their 70th infected mink farm. France has also joined the growing list of European countries with infected mink farms.

Day 291: The 0.1 Percent

Today's big news is 0.1% of North Dakotans dying "with" COVID-19. Recently there have also been more mink, more vaccines, and more immunity.

Massachusetts cases are up one and a third percent today.

Day 290: The Cassandra Who Cried COVID

A "Northeastern University computational social scientist" predicts 10,000 cases a day in Massachusetts in December unless we repent "take steps now." The steps were unspecified in the news story.

Both yesterday and today, Massachusetts cases were up one and one-seventh percentage points.

Day 288: The War on Thanksgiving

The world is at 54 million cases, with the US accounting for 11 million of them. Mexico is moments away from the million case mark. Moldova, a nation of only 4 million people (barely an accounting error in China's census) recently surpassed China to take 60th place in international total case counts.

In the US, the latest target of hand-wringing is the approaching Thanksgiving holiday. Vermont has preemptively cancelled it. Massachusetts is reopening a field hospital (sadly still not on Corey Hill, but back at the DCU Center in Worcester) to handle the anticipated tryptophan COVID casualties. New Yorkers are already announcing their intent to flout Governor Cuomo's Thanksgiving dinner limit, and a recent survey indicates that 40% of Americans plan to join them at celebrations with more than 10 people.

Massachusetts cases are up 1.7% today.

Day 287: The Long Haul

MedPage Today calls for more clarity and less credulousness over presumed COVID "long haul" cases:

First, we need clear definitions. What counts as impaired memory? Can we measure it with available scales? And, what is needed to diagnose someone with prior COVID? Some people report long COVID symptoms with negative PCR and Ab tests to SARS-CoV-2. Of course, there can be false negatives, but there can also be true negatives. How can we separate the two to better understand this problem?

A paper in Nature analyzes the sample bias in "numerous observational studies" of COVID risk factors:

Numerous studies have reported risk factors associated with COVID-19 infection and subsequent disease severity, such as age, sex, occupation, smoking and ACE-inhibitor use1,2,3,4,5,6,7,8,9,10. But to make reliable inference about the causes of infection and disease severity, it is important that the biases which induce spurious associations in observational data are understood and assessed. Bias due to confounding remains well-understood and attempts to address it are typically made (bar rare exceptions e.g. ref. 11). But the problem of collider bias (sometimes referred to as selection bias, sampling bias, ascertainment bias, Berkson’s paradox) has major implications for many published studies of COVID-19 and is seldom addressed.

A collider is most simply defined as a variable that is influenced by two other variables, for example when a risk factor and an outcome both affect the likelihood of being sampled (they “collide” in a Directed Acyclic Graph, Fig. 1a). Colliders become an issue when they are conditioned upon in analysis, as this can distort the association between the two variables influencing the collider. [...]

As illustration, consider the hypothesis that being a health worker is a risk factor for severe COVID-19 disease. Under the assumption of a higher viral load due to their occupational exposure, healthcare workers will on average experience more severe COVID-19 symptoms compared to the general population. The target population within which we wish to test this hypothesis is adults in any occupation (or unemployed); the exposure is being a health worker the outcome is COVID-19 symptom severity. The only way we can reliably estimate COVID-19 status and severity is by considering individuals who have a confirmed positive polymerase chain reaction (PCR) test for COVID-19. However, restrictions on the availability of testing especially in the early stages of the pandemic mean that the available study sample is necessarily restricted to those individuals who have been tested for active COVID-19 infection. If we take the UK as an example (until late April 2020), let us assume a simplified scenario where all tests were performed either on frontline health workers (as critical vectors for disease among high-risk individuals), or members of the general public who had symptoms severe enough to require hospitalisation (as high-risk individuals). In this testing framework, our sample of participants will have been selected for both the hypothesised risk factor (being a healthcare worker) and the outcome of interest (severe symptoms). Our sample will therefore contain all health workers who are tested regardless of their symptom severity, while only non-health workers with severe symptoms will be included. In this section of the population, health workers will therefore generally appear to have relatively low severity compared to others tested, inducing a negative association in our sample, which does not reflect the true relationship in the target population (Fig. 2b). It is clear that naive analysis using this selected sample will generate unreliable causal inference, and unreliable predictors to be applied to the general population.

The cities and towns data came out yesterday. The map colors are toned down a bit (things were getting fairly dark), and bear even less of a relationship to the grey/green/yellow/red color scheme the state has been using to declare some of us "red" since that, too, has changed. Instead of continuing to use simple case rates for the colors and just increasing the case rate cutoffs so the entire state is not red, the MDPH now does a complicated calculation involving population size, absolute case numbers, case rates, and positivity (the most nonsensical, dependent variable of all) that takes an entire page of the report to explain.

There's nothing particularly notable this week, unless it's the relatively low case rates in a couple of the Stop the Spread cities: Taunton, Randolph, and Marlborough are currently below the state average in daily case counts.

(Pop out.)

P.S. Massachusetts cases were up 1.6% today.

Day 286: Big Bad Data

The autumn wave has brought new countries into the million case club, most recently #10 Italy. In the US, curfews and lockdowns are spreading: Starting tomorrow, New York City will sleep at 10pm along with the rest of the state, and indoor dining is off the table in San Francisco. Forbes is tracking them all.

In pre-2020 epidemiology, locking down was always the wrong decision. In late 2020, lockdowns are often excused with bad logic or bad data; the Wall Street Journal has gone into some depth over the bad mask compliance data coming out of the IMHE and ending up in journals like Nature:

More than 100 news outlets trumpeted the study’s findings in the days following its publication—“The Price for Not Wearing Masks: Perhaps 130,000 Lives” was the New York Times’s headline—and a few hundred more articles have been written since. Reporting was often paired with calls for a national mask mandate, echoing President-elect Biden and now Anthony Fauci, the top U.S. infectious-disease official. The study was also invoked by Francis Collins, head of the National Institutes of Health, to push for stricter masking requirements. Recognizing the potential importance, Nature Medicine rushed the study into print after an expedited peer-review process that took only seven days to complete.

Unfortunately, the IHME modelers’ findings contained an error that even minimal scrutiny should have caught. The projected number of lives saved, and the implied case for a mask mandate, are based on a faulty statistic. Using a months-old survey, IHME modelers assumed erroneously that the U.S. mask-adoption rate stood at only 49% as of late September, and therefore had plenty of room to increase to “universal adoption,” defined as 95%, or to a more plausible 85%. According to more recent survey findings, however, America’s mask-adoption rate has hovered around 80% since the summer.

P.S. Massachusetts cases were up 1.5% again today.

Day 285: Virtual Veterans' Day

In honor of Veterans' Day, some Holyoke Soldiers' Home news: the culprits former officials accused of wrongdoing pled not guilty last Thursday to the resulting criminal charges. The Commonwealth is seeking a new superintendant and contemplating renovations. Their COVID victims were honored in the city of Holyoke's virtual Veterans' Day celebration.

In other local news, Massachusetts cases are up 1.5% today.

Day 284: Mink Reprieve

Opposition leader Jakob Ellemann-Jensen has put a wrench in the gears of Danish Prime Minister Mette Frederiksen's neovisicide plans for the country. The illegal and inhumane culling of all mink in the country has been called off. Some old US mink news has come out of the reporting frenzy about the mink mutation:

The American Veterinary Medical Association said at least 8,000 minks have died of infection with Sars-CoV-2 on farms in Utah. And nearly 3,400 mink are reported to have died from the coronavirus at a mink farm in Wisconsin. It added that the infection seems to be deadlier among older minks.

AlJazeera has more on our mink.

Massachusetts human cases are up one and a quarter percent today.

Day 283: Pfizer Pats Pback

The world is at 51 million coronavirus cases, with one and a quarter million deaths. In the US, Texas is well in the lead with more than a million cases. Despite our ongoing second wave, Massachusetts recently fell to #22 in case counts, having been displaced by the rapid rise of Minnesota.

The big news of the day is Pfizer's press release praising their vaccine candidate for being "more than 90% effective in preventing COVID-19 in participants without evidence of prior SARS-CoV-2 infection in the first interim efficacy analysis".

On the COVID only comes out at night front, more places are joining the curfew craze. Denver is explicitly restricting residents' movement after 10pm. (In Massachusetts the restrictions are mainly on businesses, not people.) New Jersey is closing restaurant dining at 10pm as well as indoor food and drink service at "bars, clubs and lounges". PlagueBlog is jealous that they have bars, clubs and lounges.

P.S. Massachusetts cases were up three quarters of a percentage point today.

Day 282: Man Walks Dog

We are not alone in our nonsensical nocturnal COVID curfew. In Czechia, a man was caught walking a stuffed dog as a way around their 9pm curfew. Upon being caught, he claimed to be joking and was let off with a warning.

Massachusetts cases are up one percent today.

Some locals are annoyed that, for this week's cities and towns report, the Commonwealth has defined "red" down to the point that not every town in the state is red, so the map is still marginally useful for detecting hot spots. Out of respect for these incensed innumerates, PlagueBlog has used the same color scale this week as last week for easier comparison. As our color scale was finer than red-yellow-green, our map is still marginally useful in its darkened state.

(Pop out.)

Day 281: Curfew Smurfew

The world has exceeded 50 million coronavirus cases, with the US pulling its weight at 10 million cases, with a recent rate of over 100,000 a day. India's 8.5 million cases are nothing to cough at, either.

The PlagueBlog mobile SUV was out tonight after 10pm, and our news team noticed very little curfew compliance.

Massachusetts cases were up one and three-eighths of a percentage point today.

Day 280: Pandemic Theater

The Boston Herald reports that Harvard epidemiologist Julia Marcus called Governor Baker's new unscientific 24/7 outdoor masking rule "pandemic theater" on Twitter. She also wrote about the dangers of quarantine fatigue in the Atlantic back when it was a new thing.

Despite the MDPH having moved their weekly reporting time from Wednesdays at 4pm to Thursdays at 5pm, the Massachusetts cities and towns data for this week is still not available today (Friday at noonish), so maps will be delayed.

P.S. Massachusetts cases were up one and a quarter percentage points today, partly due to delayed reporting of October cases from "a national laboratory".

Day 279: More Mink

The election isn't the only thing that's dragging on. In mink news, there is much panic and a bit less reasonable skepticism about their SARS-CoV-2 mutation. North Jutland has been locked down to prevent its spread.

A COVID Mary has been found—an asymptomatic immunocompromised cancer patient who shed virus for 70 days. She tested positive fourteen separate times

Massachusetts cases were up one and one seventh of a percentage point today. It was also our last day to breathe free here, and the state seems to have switched from abusing the SMS emergency alert system to merely sending out annoying texts and phone calls about the coming curfew and post-scientific masking policy.

Day 278: Mink Mutation

The world is at 48 million coronavirus cases. France has exceeded 1.5 million cases and at their current rate may take over Russia's #4 spot. In the US, Texas took over the top spot from California a few days ago, depending on who's counting. Florida remains a distant third.

On the animal front, a symptomatic Knoxville, TN tiger tested positive last week, and two other tigers are presumed positive. There are no plans to kill the tigers.

The minks are not so lucky; neovisicide rages on in northern Europe where Denmark now plans to cull their entire mink population over an unspecified mutant SARS-CoV-2 strain that has already infected humans. It may differ enough from the common strains to be an issue.

P.S. Massachusetts cases are up one percent today.

Day 277: Welcome to Efrafra

PSA: The CDC says the infected can vote in person today.

Greg Cochran blogs briefly at West Hunter; the meat is in the comments. On his COVID-19 post yesterday, Free Parameter, he made a passing reference to the rabbit disease myxomatosis, a.k.a. white blindness, which inspired a commenter to compare our SARS reactions to the rabbit military dictatorship of Efrafra in Watership Down:

Woundwort thinks that the white blindness is a disease used by humans to harm rabbits (shades of how some think COVID-19 is a Chinese-made weapon), so he tries to stop it by keeping his rabbits underground, out of human sight.

Although his theory’s off, his measures would limit Efrafra’s exposure to natural reservoirs of myxomatosis. [...]

[But] he’s too strict, too cruel. No Efrafran rabbit will report feeling sick, because they’ll be punished. And if they did, their Owsla officer would likely try to keep it a secret, for the same reason. White blindness will become deeply entrenched at Efrara before Woundwort even knows it’s there.

That’s the irony of being a totalitarian dictator: you want obedient underlings, but instead you get skilled liars. To fight disease you need clear information about where it began and how far it’s spread, and Woundwort has set up an incentive structure that ensures he’ll never get it.

A real-life parallel happened in 2002, when SARS broke out in Guangdong in China. The province had a 12% economic growth target to hit, come hell or high water, and “negative news” was suppressed by the state. As a result, the disease snowballed and became far more devastating than it had to be.

It is left to the reader to draw the obvious parallels to SARS-CoV-2.

Like the weekly data, Massachusetts' daily numbers are now coming out later, in perpetuity. While we wait, here's last week's long-awaited map, with a notable increase in the orangeness of the percent change panel (showing the area of increasing case counts):

(Pop out.)

P.S. Massachusetts cases were up two thirds of a percentage point today.

Day 276: Massachusetts Overreacts to Autumn

It's a sad day for both science and civil liberties in Massachusetts, where the innocent populace are about to be subjected to both a curfew and an outdoor mask requirement—regardless of whether anyone else is around. The overreaction is in response to a relatively minor and inevitable uptick in cases (up just half a percentage point today) due to the onset of autumn and the fact that you cannot hide forever from a communicable disease.

PlagueBlog hopes that neither measure will survive the inevitable legal challenges, but notes that the innocent victims of our satanic panic four decades ago have never been exonerated, so recommends against holding your breath (especially in a mask). Now is also not the time to read the latest research on just how scientifically baseless and potentially dangerous casual and ersatz mask use is.

Day 275 Retrospective: England Locks Down

Prime Minister Boris Johnson is planning a new lockdown starting Thursday and allegedly ending December 2nd, though there's still a chance that fellow Conservatives will vote it down on Wednesday. Pubs and restaurant dining rooms in England will be closed.

Massachusetts cases were up seven tenths of a percentage point today, and Massachusetts deaths exceeded 10,000 in total.